1,180 Matching Annotations
  1. Apr 2018
    1. we were surprised to see that several consanguineous pedigrees showed large, rare, inherited homozygous deletions within linked regions, some of which are very likely causative mutations

      Although the authors did not sequence all linked regions (because of the time and cost associated with sequencing such large amounts of genetic material), they were surprised to find that several of the consanguineous families had rare inherited deletions.

      The authors suggest that these large deletions may contribute to autism.

    2. two families shared linkage to an overlapping region of chromosome 2q (AU-4500, lod = 2.41, and AU-4200, lod = 1.81) that has been previously implicated in other autism linkage studies

      Only two families showed the same abnormality, in chromosome 2q. This abnormality has been previously found to contribute to autism.

    3. Potentially linked loci were generally nonoverlapping between families, consistent with genetic heterogeneity

      The results of the authors' homozygosity mapping showed that there is considerable diversity between different consanguineous autism families. They also found that the abnormalities in the chromosomes of patients with autism were not shared between families.

      Taken together, these results suggest multiple genetic origins for autism.

    4. The relatively reduced M/F ratio of affected children and the reduced rate of linked de novo CNVs in the consanguineous sample (not significantly different from rates in control) both suggest that consanguineous pedigrees with autism are enriched for autosomal recessive causes similar to other congenital neurological disorders in consanguineous populations

      The higher proportion of affected women and the reduced rate of de novo CNVs in the consanguineous sample from this study both suggest a higher frequency of autosomal recessive causes for autism (and other neurological disorders) in consanguineous families.

    5. overall rates of de novo CNVs that segregated with ASD were 0% in consanguineous multiplex (0 of 42 patients) and 1.9% in consanguineous simplex families (1 of 52 patients), which were considerably lower than reported for nonconsanguineous families

      The data showed that de novo CNVs were much less frequent in consanguineous families (both simplex and multiplex) and the amount of inherited CNVs was high.

      As stated above, the low rate of de novo CNVs that segregate with disease suggests that inherited factors have a larger role.

    6. the M/F ratio was 2.6:1 (34 males: 13 females) (fig. S1), compared to 7.4:1 (81 males: 11 females) for the other categories of families (i.e., nonconsanguineous and consanguineous simplex) (chi-square = 5.37, df = 1, P = 0.02)

      The authors observed that the proportion of affected women from consanguineous multiplex families was double that of the HMCA as a whole, and triple that of simplex families.

      This finding suggests an increased role of inherited autosomal mutations (as opposed to de novo mutations).

    7. An increased role for inherited factors in autism families with shared ancestry was also suggested by a low rate of de novo CNVs that segregated with disease

      The low rate of de novo CNVs suggests that abnormalities in autistic patients' genomes came from mutations that were already present in the parents, rather than new mutations.

    1. Most of the chemicals found by our analysis are well known to confer direct and indirect anti-herbivore protection to plants

      The Piper species that were sampled were found to contain secondary chemicals that likely function to protect the plant from herbivores.

    2. Our results suggest that Piper species that are chemically dissimilar from those already present in a patch would be more likely to colonize and persist within the patch.

      Species with different chemical properties are less likely to compete with one another, therefore tend to coexist with each other.

    3. Nonetheless, phylogenetic underdispersion was significant for both -NRI and -NTI, a result that supports the idea that the effect of phylogeny on community assembly is associated with strongly conserved traits not measured in this study.

      Species that are closely related tend to coevolve, which allows them to coexist together more easily than non-related species.

  2. Mar 2018
    1. Linkage disequilibrium values were of 20% for the population from Haiti and 6% for that from the Dominican Republic. The Gonaïves locality showed clear evidence of inbreeding with a large Fis positive value of 0.232 (Table 2).

      The values of the Haitian population of palms were higher which means that there were more alleles that were associated non-randomly.

    2. Therefore we recommend not translocating material between these two populations for genetic conservation or ecological restoration programs until the taxonomy of this species within Coccothrinax is further studied.

      Genetic conservation of this population is important due to the few individuals left in Haiti and the Dominican Republic.

      Upon meeting with the author, the difficulty of finding the purebred species was discussed as were the methods.

    3. The taxonomic uncertainties between the two populations of C. jimenezii have important implications for reintroduction programs. These two sites of C. jimenezii represent two clear management units for conservation, and the population genetic data suggest that we cannot rule out that they are two distinct taxa.

      The authors concluded based off of the molecular data, that the two species of C. jimenezii could not be identified as two different taxa.

    4. We have not been able to find data regarding the environmental history in these two populations since the 15th century. However, there is agreement among conservation biologists that since the arrival of the Europeans to this island there has been habitat fragmentation and deforestation linked to rapid expansion of urban and rural activities (Sambrook et al., 1999; Alscher, 2011; Foxx, 2012). Palms have long-life cycles; therefore, the detrimental consequences of genetic drift on genetic diversity can take a long period of time to manifest because of their long generation time and the presence of overlapping cohorts (Duminil et al., 2009).

      Since the extinction of C. jimenezii is of primary concern, the authors use resources from other works to help solidify this concept. It is clear that the conservation of this species is vital to this study.

    5. The Dominican Republic population had a very low Fis value of 0.092 showing only a small degree of inbreeding. The Fst value was 0.497 and Nm between the two sites was 0.253. Over 50% of the molecular variation (AMOVA test) was between populations.

      Statistically the DR populations of the palms were more interbred than the ones that were in Haiti

    6. However, the high proportion of homozygotes detected in these two loci could also be the result of stochastic processes associated to genetic drift and inbreeding.

      Higher proportions of homozygotes have been found to be a result of a random occurrence in the process.

    1. a finding of hyperpolarization mediated by r-opsin would be unprecedented.

      The studies done to date suggest that any given type of opsin is involved in only one phototransduction pathway.

      This means that if the r-opsin present in E. scolopes is able to initiate both rhabdomeric and ciliary cascades, this would be the first instance of an opsin functioning in more than one pathway.

    2. Genes associated with hyperpolarizing ciliary phototransduction also are present in the light organ, and their sequence characteristics predict that they could be capable of driving the associated activities in ciliary phototransduction, but no ciliary opsin was detected.

      In addition to the presence of genes involved in ciliary phototransduction, both rhabdomeric and ciliary opsin are present in diverse invertebrates.

      Consequently, it is possible that c-opsin could be present in E. scolopes, even though it was not detected.

    3. Whereas the opsin expressed in the light organ is of the rhabdomeric type, and all key components of the rhabdomeric cascade are present in the light organ, the ERG spectra demonstrate hyperpolarization of the photoreceptor cell membranes.

      The molecular and immunochemistry data provide strong evidence that rhabdomeric phototransduction is present in the light organ. However, the electroretinogram data suggest that both rhabdomeric and ciliary pathways are present, even though no ciliary opsin was found.

    4. arrestin message could be detected only in the eye and light organ, rhodopsin and rhodopsin kinase messages were present also in the optic lobe of the brain, and rhodopsin kinase was detectable at low levels in other tissues.

      Arrestin and rhodopsin were found only in tissues responsible for modulation of light, i.e., the eye and light organ. Rhodopsin kinase was found in these tissues and at low levels in other tissues.

    5. the provision of the proteins of phototransduction cascades is constitutive, i.e., that it is independent of the presence of symbiont luminescence.

      The authors tested the light organ tissues from animals without Vibrio (hatchlings) and from those with Vibrio (juveniles) to determine if the Vibrio are necessary to trigger the phototransduction cascades.

      The authors found phototransduction proteins in the hatchlings, suggesting that the presence of Vibrio is not necessary for phototransduction to occur.

    6. characteristic rhabdomeric depolarization was observed in the electroretinographic spectra of the eyes, whereas the light-organ tissue responded with hyperpolarization

      The rhabdomeric form of opsin (r-opsin) is involved in the visual systems of invertebrates. When r-opsin is excited (a stimulus is applied), the expected response in an electroretinogram is depolarization.

      Only r-opsin was found in the light organ of E. scolopes. Because of this, the authors were surprised when they excited tissue in the light organ and it hyperpolarized. Hyperpolarization is usually associated with c-opsin, the form of opsin found in vertebrates.

    7. Also present were genes with similarities to those encoding proteins typically associated with ciliary photoreceptor cells,

      Ciliary photoreception is generally associated with vision in vertebrates and is characterized by different phototransduction proteins than those involved in rhabdomeric phototransduction.

      This finding suggests that the light organs have several pathways that may allow for sensing light.

    8. In 5 instances (i.e., in the case of rhodopsin, arrestin, rhodopsin kinase, G alpha i, and G protein beta subunit 1), the same isoform seems to occur in both eye and light organ tissues.

      Five key proteins that are required for the perception of light in the eyes of Euprymna were also found in the light organ. This suggests that the light organ also contains the biochemical pathways necessary to sense light.

    9. predicted proteins are highly similar to the phototransduction constituents that are associated with rhabdomeric photoreception

      Rhabdomeric photoreception is generally associated with vision in insects and molluscs and is characterized by specific phototransduction proteins. The authors identified the proteins they expected to find in E. scolopes.

    10. To ensure that these cDNAs were host derived, we also examined the symbiont genome for similar sequences,

      If proteins associated with the visual transduction cascade were found in both Euprymna (host) and Vibrio (symbiont), the results would be very challenging to interpret. Because of this, the authors made sure the sequences were only from Euprymna.

    1. We found that rates of latitudinal and elevational shifts are substantially greater than reported in a previous meta-analysis, and increase with the level of warming.

      This paragraph is the authors' summary of the results and conclusions of the paper.

    2. we found that species have exhibited a high diversity of range shifts in recent decades

      Among individual species, there is much variation in range shift response to climate change. Therefore, the average range shift rates do not provide enough information to predict how an individual species will react to climate change.

    3. For latitudinal studies, on average 22% (average of N = 23 species groups × regions) of the species actually shifted in the opposite direction to that expected. Similarly, 25% of species shifted downhill rather than to higher elevations (average of N = 29 species groups × regions)

      On average, 22% to 25% of the species in each taxonomic group moved in a direction opposite to that expected based on the temperature change.

    4. lag in elevation response (Fig. 1B; 2 points above the 1:1 line, 28 below; χ2 = 22.53, 1 df, P < 0.001) is equally surprising

      The observed elevation shifts are mostly smaller than the expected shifts. Elevation responses appear to lag behind climate change.

      The authors express surprise at this result, and discuss possible reasons for it in the rest of the paragraph.

    5. mean latitudinal shifts are not consistently lagging behind the climate

      The observed latitudinal shifts match the expected shifts. The authors conclude that the average latitude responses are sufficient to track climate change.

    6. We found that both observed latitudinal and elevation range shifts were correlated with predicted distances (Fig. 1A, N = 20 species groups × regions, r = 0.65, P = 0.002 for latitude; Fig. 1B, N = 30 groups × regions, r = 0.39, P = 0.035 for elevation), so our analyses directly link terrestrial range shifts to regional and study differences in the warming experienced.

      Observed latitudinal range shifts had a positive, significant correlation with expected range shifts. The correlation of elevational range shifts was also positive, though less significant.

      With these results, the authors demonstrated the direct statistical link between range shifts and levels of climate warming that was not demonstrated by previous studies.

    7. We found that observed latitudinal and elevational shifts (the latter more weakly) have been significantly greater in studies with higher levels of warming

      Taxonomic groups in locations with larger temperature increases made larger range shifts.

    8. Our estimated mean rates are approximately three and two times higher than those in (14), for latitude and elevation respectively, implying much greater responses of species to climate warming than previously reported

      The observed rates of range shift are significantly higher than those reported in Reference 14.

      This analysis is an important update using the results of studies that were not yet available when the previous meta-analysis was done.

    9. The latitudinal analysis revealed that species have moved away from the Equator at a median rate of 16.9 km decade−1

      For each group in Table S1, the authors calculated a rate of range shift by dividing the observed range shift by the duration.

      They found statistically significant rates of range shift both in latitude (median 16.9 kilometers poleward per decade) and elevation (median 11.0 meters uphill per decade).

    10. The latitudinal analysis revealed that species have moved away from the Equator

      For each group in Table S1, the authors calculated a rate of range shift by dividing the observed range shift by the duration.

    1. Figure 1.

      The stationary partition (a) yielded the results of 96%-100% bootstrap proportions whereas the nonstationary partition (b) gave results of 100% bootstrap proportions throughout.

    1. One limitation of HRM analysis is that genotyping is restricted to the collection of available reference genotypes. The more Symbiodinium strains genotyped by the scientific community, the more power HRM will gain. Another limitation of HRM is that it is constrained to the detection of monotypic Symbiodinium populations. In our case, this limitation was proven when performing the pairwise combinations of Symbiodinium strains. Therefore, in cases where genotypes cannot be identified, these could be the result of either a lack of an appropriate reference genotype at the time of the analysis and ⁄ or the presence of a mixture of strains.

      There are two restrictions to HRM analysis; it only refers to the available genotype collections and can only detect monotypic Symbiodinium populations.

    2. In this study, we showed that high-resolution DNA melting analysis (HRM) allows precise genotyping of Symbiodinium strains. There are several advantages of HRM, making it an attractive technique. HRM is a closedtube technique that reduces cross-contamination and does not require the handling of hazardous materials, such as acrylamide, formamide and ethidium bromide. It is time-effective, requiring <2 h per run, which facilitates rapid turnover. This technique is sensitive, simple, nondestructive and of low cost.

      HRM analysis was shown to be just as effective in detecting the genetic make-up of Symbodium strains as DGGE analysis. Some examples include less time to run the procedure, cross-contamination prevention, and inexpensive runs.

    3. For (b–d), the difference of the fluorescence between a chosen melting curve set as standard and each melting profile was plotted against temperature resulting in a ‘fluorescence difference’ plot.

      The mixed strains had a different melting point than that of the pure strains.

    4. The melting profiles of each clade were clearly distinctive. Moreover, different melting profiles were obtained within Symbiodinium clades (Fig. 1b). These differences were attributed to variation in the nucleotide composition. For example, Symbiodinium types A3 and A4 have 50 bp different when comparing their sequences from DGGE bands, while the difference between types D1a and D1 was only 2 bp. This distinction was clearly seen in their melting profiles (Fig. 1a).

      Keep in mind that even a single base change in the DNA sequence can cause differences in the High-Resolution Melting curve. In this experiment, forms of the same Symbiodinium clade, A3 and A4, have 50 different base pair changes whereas the clade, D1a and D1 have a smaller base pair (bp) difference of 2 bp.

    5. HRM consisted of a temperature ramp between 78 and 90 "C, rising by 0.1 "C⁄ 2 s. Samples with the best amplification were used as reference controls for each genotype

      HRM analysis began after the PCR procedure. The amplicon DNA was gradually heated from 78°C to 90°C. As the temperature increased, the melting point temperature of the amplicon was reached. The sample DNA denatured and the double stranded DNA separated. As a result, the fluorescence faded away.

    6. HRM assays were performed using the Rotor-Gene 6000 (Qiagen) with the provided Rotor-Gene Q Series Software v1.7 (Qiagen). PCR was carried out using the Type-It HRM PCR kit (Qiagen), with 1 lL of 1 ng ⁄ lL template, 1· HRM PCR Master Mix (2· HRM PCR Master Mix containing HotStartTaq Plus DNA polymerase, Type-it HRM PCR buffer (with EvaGreen dye), Q-solution, dNTPs; Qiagen), 0.7 lM of each primer (ITSintfor2 and ITS2rev), and adjusted with RNase-free water to a final volume of 10 lL.

      Within the DNA sequence, the region of interest was first amplified (known as an amplicon) using the polymerase chain reaction (PCR) method. During PCR, a special saturation dye called, EVAGreen, was added to the reaction. This allowed the amplicon product to fluoresce in the presence of double stranded DNA. Moreover, as the amplicon concentration increased in the reaction tube, the more light was emitted.

    7. Results showed that twenty cultures were correctly genotyped in <2 h using HRM analysis with a percentage of confidence >90%

      By using the HRM technique, the genetic make-up (genotype) of twenty Symbiodinium cultures were identified in less than 2 hours with a confidence percentage of greater than 90%. A >90% confidence interval means that more than 90% of the population distribution is contained in the confidence interval. In other words, there is only a 10% chance that the cultures were incorrectly genotyped.

    1. First, many electric fish scan and swim with rigid control of the spine and body posture, which should maintain the relative orientation of field generator to field receptors and so reduce undesirable reafferent modulations. Our video and simulation results strongly support this conclusion.

      Based on the movement of the electric fish around the "ping-pong ball apparatus" created by the authors, electric fish preserve the positions of their electric field generator and receptors and thus reduce changes to their sensory stimulation by maintaining a rigid body posture and control of their spine while swimming. These important physiological characteristics of electric fish are supported by their precise tail-first cartwheels while interacting with the "ping-pong apparatus".

    2. electrophysiological studies at higher levels of the nervous system, for example, by predicting specific emergent features in the midbrain and cerebellum.

      This sentence highlights another example where the products of this research can be used in future experiments. In this example, the authors are stating it can be used in future neurological oriented studies of the midbrain and cerebellum; areas of the brain that are primarily oriented with executive functions.

    3. These ascending patterns should help to elucidate both the descending input and the neural computations within the ELL.

      The author describes here that with the data he has discovered and portrayed in the graph above the understanding of how neural computations and descending input for these fish occur will become clearer to understand and even reproduced if there is a need to help validate the findings of his experiment. Also the visual components of his findings allow the readers, both from the science community and from the general population, to more conceptually understand the travel of the high-frequency electrolocation travels.

    4. The models proposed here may therefore stimulate renewed experimental interest in the neural basis of electrolocation.

      In this statement, the authors concluded that the quantitative models and methods they employed throughout their experiment will attract interest to the neural components of electrolocation by providing visual representations of their results, which ultimately make these complex concepts and relationships between different sets of data easier to understand. In other words, simply just sharing data and results without any visuals using with complicated scientific jargon is ineffective in conveying the author's messages.

    5. Video and simulation results from a scanning behavior of Apteronotus albifrons.

      Data from the videos and the scans (which produced dipolar distortions) provided results showing how certain kinetic movement patterns exhibited by the fish are use to maneuver in their environment.

    6. These results are summarized in Fig. 4

      Overall, multiple features of an EOD map contribute to one physical characteristic of an electric fish, rather than each feature affecting one specific characteristic exclusively.

    1. First, the focal populations were effectively asexual, meaning that trait variation was not continuous and traits were perfectly linked. Nonetheless, it is not clear how more continuous variation or less linkage between traits would influence the effect of evolutionary change on spread velocity.

      When comparing this study to results that might be found in the wild, a few things must be taken into consideration. First, the plants used in the study were asexual. This means that evolving traits were the same traits in every population, and the variation developed by evolution would be directly passed on to offspring. The second consideration is that the while the changes to genes were intentional, there's a chance that some of the changes could have been due to unintentional maternal or epigenetic effects. And lastly, the conclusions were made assuming that all genes were carried through the dispersal and none were left behind. This point is important because if genes that favored dispersal were the only genes being carried by dispersing populations, the response of the population would be more due to a genetic drift or narrowing of potential traits than to evolution.

    2. Height and the average distance of the farthest dispersed seed, traits correlated with one another (Spearman rank correlation coefficient rs = 0.55, P = 0.046), increased with landscape patchiness (backward and rightward shift of the replicates with increasing patchiness in Fig. 3; P = 0.008 and 0.060, respectively, Table 1).

      The correlation between between height and average dispersal distance is significant. It is very likely that the relationship between height and the dispersal is not caused by random chance. The correlation between landscape patchiness and dispersal distance is significant and It is difficult to dispute the influence of patchiness on the distance a seed is dispersed.

    3. We also found that evolving populations showed significantly less among-replicate variation in spread than nonevolving populations (fig. S1).

      Evolving populations showed less variation in velocity in replicate trials than did non-evolving populations. This means that the amount of spreading from evolving populations was fairly consistent in replicate trials, and population numbers increased at approximately the same rate, making expansion more predictable. Likewise, non-evolving populations did not have consistent spreading rates and varied between replicates in population increases. This made them less predictable for estimating expansion.

    4. The effects of evolutionary change were so strong in patchy landscapes that evolving populations showed no significant reduction in velocity as the size of gaps increased from 4 to 8 to 12 times the mean dispersal distance (generation-six location of dark green line in Fig. 2, B to D) (F1,25 = 0.014, P = 0.908), even as velocity slowed in the nonevolving populations (F1,28 = 8.52, P = 0.007).

      Velocity of spreading kept increasing regardless of distance in evolving populations in variable environments, even as the distance doubled and tripled. Non-evolving populations, however, slowed in population growth.

    5. We found that after six generations of spread in continuous landscapes, evolving populations spread a modest 11% farther than nonevolving populations (Fig. 2A), a difference that was only marginally significant (t13.5 = –2.05, P = 0.060). By contrast, in experimental landscapes with gaps 12 times the mean dispersal distance, evolving populations spread three times as far as their nonevolving counterparts (Fig. 2D) (t10.4 = –3.36, P = 0.007), leading to a significant gap size by evolution interaction (F1,72 = 10.77, P = 0.002).

      Populations which evolved spread slightly faster than populations which did not evolve in continuous landscapes. However, the effect of evolution was much stronger when the landscape had large gaps between soil. This indicates that evolution is very important to promoting biological invasions in fragmented landscapes.

    1. (ii) We observed “mood-dependent” alteration of activity in the trunk somatosensory cortex, specifically an activity increase after tickling phases (Fig. 2, B and C), anxiogenic suppression of responses (Fig. 3, D and E), and a reduction of microstimulation thresholds for evoking calls after tickling. Such “mood-dependent” modulation of the somatosensory cortex is unexpected, as it is nontactile and there is little evidence to date for mood effects in other cortical areas.

      Ticklishness is mood dependent: It is increased by a playful state and suppressed by an anxious state.

      This result is surprising, because the somatosensory cortex has previously been shown to a have a role in detecting touch, but not in incorporating the emotional value of that touch.

    2. Microstimulation in the deep layers, but not in the superficial layers, evoked USVs (Fig. 4I).

      USVs are triggered by stimulation of neurons in the deep layers of the somatosensory cortex, but not by stimulation of neurons in the surface layers of the somatosensory cortex.

    3. Tickling-evoked USVs were significantly suppressed in the anxiogenic condition and recovered in control conditions (Fig. 3, B and C). Similarly, anxiogenic conditions suppressed neuronal response to tickling (Fig. 3D) and inverted the sign of response index to tickling (Fig. 3E).

      When rats were anxious, tickling no longer caused an increase in USV production or the neuron firing rate.

    4. As in the cells shown in fig. S2B, responses to tickling predicted play responses (chasing hand) across the population (Fig. 2E), which suggests a neural link between tickling and play behavior.

      The data suggest a possible connection between hand chasing and tickling as both response indices are similar.

    5. Most cells increased their firing rate during trunk tickling, trunk gentle touch, and chasing hand (~77%, ~67%, and ~80% of the cells showed higher firing rates during interaction than during break, respectively; fig. S2B, top, and C to E), whereas a minority of cells were suppressed during interaction phases (fig. S2B, bottom, and C to E).

      Most of the neurons showed an increased rate of firing during tickling, gentle touch, and hand-chasing. However, there were some neurons that had a decreased rate of firing during these behaviors.

      The rate of firing during breaks was greater than it was during pretickling, but lower than during tickling.

    6. Similar to USVs, activity in the trunk cortex was lower before initial tickling (Fig. 2, B and C, Pre) than during the short breaks between interactions (Fig. 2, B and C, Break).

      The rate of neural activity showed a pattern similar to the rate of USV production: Activity increased during tickling and remained elevated (relative to pretickling) during breaks.

    7. Rats seemed to warm up to tickling and vocalized less before the initial interaction than during breaks between interaction episodes (Pre versus Break; Fig. 1, C and D).

      Rats produced more USVs during the breaks between tickling than they did in the time before being tickled.

    1. Using a simple model adapted from (26), we tested whether reduced flowering in other ecosystems could drive the evolution of pollinator foraging traits as indicated for alpine bumble bees (15). The model predicts changes in the energetic advantage of generalization with floral density. Long-tongued bumble bees exhibit greater specialization than that of short-tongued bees (16, 30). Across a range of flight speed and plant community composition (15), the advantage of generalizing increases as flower density declines (Fig. 4).

      The data suggest that the decrease in floral density seen in alpine regions leads to the favoring of short-tongued bumble bees over long-tongued bumble bees across a wide range of plant communities.

    2. Alternatively, shifts in bumble bee tongue length may reflect competition from subalpine congeners moving upward with climate change. Comparisons of past (1960s and 1970s)

      Bumble bee communities in the Pennsylvania Mountain and in the Front Range have increased in species diversity and short tongued bees. These short tongue bees come from subalpine climates and could be replacing the long tongue bees, explaining their 24.1% decrease in the community.

  3. Feb 2018
    1. Optimal foraging theory predicts that foragers will expand their niche in response to such resource scarcity (25, 26). When bumble bees (B. balteatus) encounter low densities of preferred host plants, they incorporate shallower flowers into their diet (F1,194 = 29.39, P < 0.0001) (table S4) (15).

      According to optimal foraging theory, organisms will attempt to find the most efficient food source with respect to time and energy used to obtain it. As food becomes more scarce, the organism will increase the range of food sources it will forage. Bumble bees will select to feed from the flower who’s corolla length is closest to the length of their tongue. However, in desperate times, they will feed on shallower flowers, competing with the flower’s original bees for resources.

    2. Temporal changes in bumble bee tongue length are not explained by plasticity in body size. When phenotypic variance in tongue length is partitioned among underlying sources, size accounts for less than 20% of variation (table S1) (15). Size has declined in some populations (B. balteatus: F2,96= 8.61, P = 0.0004; B. sylvicola: F1,76 = 29.01, P < 0.0001) (fig. S1 and table S1) and is phenotypically correlated with tongue length [correlation coefficient (r) = 0.50 to 0.60, P < 0.005] (fig. S1) but contributes little to its reduction over time. After removing variance explained by body size, analysis of covariance shows significant temporal changes in tongue length (B. balteatus: F1,23 = 17.02, P = 0.0004; B. sylvicola: F1,67 = 46.14, P < 0.0001) (Fig. 1 and table S1).

      The variation in the size of the bumble bees only accounts for less than 20% of variation in bee tongue length, and is therefore not a valid explanation for changes in tongue length over time. There is some correlation between decrease in bee size in some populations and their tongue length, however this does not contribute to the reduction in tongue length observed over time.

    1. Table 1. Marginal values of carbon stored by additional species to a grassland ecosystem for three carbon prices capturing the range summarized by the Interagency Working Group on the Social Cost of Carbon (25). Values are means and 95% confidence intervals in $ sp−1 ha−1 for ecosystem carbon (soil and plants) averaged across the BigBIO and BioCon grassland experiments. Values are in 2010 U.S. dollar (USD).

      An increased number of species in an environment decreases estimated social cost.

      The values are averaged between BioCon and BigBIO experiments, so this suggests that both of these experiments lead to the conclusion of a lower social cost being associated with increased species richness.

    2. ig. 3. Marginal present discounted economic value over 50 years from adding one species as a function of final species richness, using three estimates of the social cost of carbon: low (green), medium (blue), and high (purple) estimates described by the U.S. government (25) and in Materials and Methods. Marginal values were estimated from the two grassland experiments shown in Fig. 1 and are expressed here as USD (2010) per species per hectare, integrated over 50 years. (A) The marginal values for BigBio. (B) The marginal values for BioCON. Lines indicate means for each of the three estimates for the social cost of carbon. Shaded regions indicate 95% confidence intervals. For ease of visualization of values for BioCON, the confidence interval for the high estimate of the social cost of carbon is truncated at species richness of 15, and the confidence interval for the low estimate of the social cost of carbon begins at species richness of 3. For orientation, the position on the y axis (ordinate) corresponding to the x axis (abscissa) value of 5 shows the marginal value of adding the fifth species to a grassland initially containing four species.

      Marginal value changes in BigBio and BioCON with increasing species richness.

      For both instances, the amount of marginal value added per species decreases as species richness increases.

      This is likely due to competition between species. As the species have to compete with each other, they are not able to contribute as much to the ecosystem.

    3. Although the values declined with increasing diversity, at no point did the 95% confidence limit overlap zero: There was always a positive economic value for carbon storage to increasing species richness up to 16 species.

      Though the results show that carbon accumulation decreases at higher levels, at no point did carbon accumulation drop below what was accumulated in the control fields and this was thanks to the plant diversity.

    4. Fig. 1. Marginal carbon storage, which is the incremental change in cumulative carbon storage over 50 years caused by adding one additional species, as a function of final species richness, estimated from two grassland experiments (BioCON shown in gray; BigBio in blue). Means are shown in solid lines, with shaded regions indicating 95% confidence intervals estimated from bootstrapping for plant carbon (top), soil carbon (middle), and total ecosystem carbon (bottom).

      Marginal carbon storage changes in plants, soil, and entire ecosystems as species richness increases.

      For plants, soil, and ecosystems, the amount of carbon storage added per species decreases as species richness increases.

    5. Fig. 2. Marginal carbon accumulation over time at different levels of species richness. Each line shows the additional carbon accumulated over time caused by increasing species richness by one species. Numeric labels on each curve indicate the specific increment in species richness, with “2” indicating the marginal carbon accumulation caused by increasing S from 1 to 2, “3” indicating the marginal carbon accumulation caused by increasing S from 2 to 3, etc., up to 16.

      Carbon uptake increases significantly less per species at high levels of species richness than it does at low levels of species richness.

      It also shows that cumulative marginal carbon uptake rate declines over time.

    6. Carbon accumulation slowed during the 50-year simulation (Fig. 2). Annual marginal carbon accumulation and annual marginal value were highest early in the 50-year simulation and declined over time.

      The results state that the carbon intake decreased over a 50-year period as suggested in Figure 2. The annual marginal carbon uptake was higher earlier in the 50-year stimulation and declined as time went on. These results conclude that the highest amount of carbon accumulation occurs in more primitive environments.

    7. As a result, the largest marginal values of cumulative carbon storage occurred at low levels of species richness, and the smaller marginal values occurred at the high richness levels.

      The results show that the largest marginal values, of carbon accumulation, occurred at lower levels of plant diversity and marginal values decrease at higher levels of species richness.

      This occurred because of increased competition between plant species as species richness increased. This indicates that lower levels of plant diversity are the best situation for accumulating the most carbon, in plants and the soil, in an environment.

    8. Adding species increased cumulative carbon storage in plant, soil, and ecosystem carbon pools (Fig. 1):

      The results of the experiment show that an increase in plant diversity, in the American grassland fields, increased the amount of carbon accumulated in the plants and soil as shown in Figure 1. By increasing the amount of different plant species, in an environment, this increased the total amount of plant growth and also increased the amount of carbon stored in the soil.

    9. twice the economic value of increasing species richness from 1 to 2.

      Each additional degree of species richness is worth less than the previous degree of richness in terms of economic value. Therefore, the economic value does not increase in direct proportion with the species richness, although they are correlated.

    1. To dissect the transcriptional regulatory circuitry of the insulin signaling cascade in the CA in response to starvation, transcript levels for 4 key genes were analyzed in the CA of 4 days old adult females fed sugar or water (Fig. 3).Transcript levels for the insulin receptor (INSr), the Forkhead-box-binding protein (FOXO) and the translation initiation inhibitor eIF4E-binding protein (4EBP) were significantly increased in the CA of starved females. Transcripts for the target of rapamycin (TOR) protein were significantly decreased in the CA of starved females.

      Transcript levels are the rate that transcription is occurring, this can be important to determine what is affecting the starving females within the 4 key genes that were tested.

    2. FOXO knockdown in starved cockroaches elicited an increase of JH biosynthesis; implying that FOXO plays an inhibitory role on JH biosynthesis during starvation

      Since FOXO is a protein that regulates gene expression and is not nutritionally regulated. When the mosquitoes are given water with no sucrose the FOXO stops the role of the JH biosynthesis. This happens because the FOXO is not being transcriptionally regulated when the mosquito is being deprived of nutrients.

    1. From an evolutionary perspective, it is tempting to suggest that fish may not have evolved a muscular system capable of minimum contraction times such that they would be able to swim at speeds exceeding 10-15 m s−1(depending on fish size), given that it would result in costly damage to the fins.

      This statement explains why fish most likely cannot swim faster. Their muscular systems do not evolve because swimming any faster than the current rate would result in damage to their fins.

    2. Based on the estimated absolute speeds, sailfish appear to be the fastest of the four species investigated here, however, they were also 50-80 cm longer than the other three species and maximum speed is known to increase with fish length (Wardle, 1975). Using a length-speed relationship based on burst swimming performance of various species (Videler, 1993), we found that the size-corrected speed performance is highest in little tunny and barracuda, followed by dorado and sailfish (Fig. 2D).

      The goal of this study was to determine whether earlier studies were correct in their determination of maximum swimming speeds in sailfish as well as comparing sailfish speeds to other large marine predators. Here the author explains that compared to the other predators, the speed performance in sailfish based on size was the lowest. This is supported with Figure 2D

    3. i.e. fish are taken out of the water and do not consider additional effects of drag.

      Their estimated swimming speeds are slightly higher than what is observed during predator-prey interactions because taking the fish out of the water and measuring its muscle would have not been limited by the real-life environment the fish normally swim in when chasing their prey, especially as they swim back and forth. So, their estimates can only give the theoretical maximum speed the fish can swim at without cavitation occurring, even if the fish don't actually swim at that speed.

    4. full curves represent an estimate of maximum swimming speed caused by the cavitation limit at shallow depth

      Full curves in the graph represent the estimated maximum swimming speed which is limited by cavitation occuring in a shallow depth. It is important to mention "at shallow depth" because that would imply the fish are near the surface in warmer water, which would allow them to reach higher speeds before cavitation occurs than if they were in colder water.

    5. The calculated maximum attainable swimming speeds for the four species expressed in m s−1 (A) and in Lf s−1

      From graph A it can be seen that the sailfish had the highest maximum swimming speed. Next was the Barracuda, then the Little tunny. The Dorado had the lowest maximum swimming speed.

    6. Sailfish had significantly higher maximum swimming speeds (m s−1) than the other species (post hoc Tukey test, P<0.05); however, when considering size-corrected performance (i.e. residuals), sailfish had the lowest values

      Using certain statistical tests, the authors were able to find the differences they could properly analyze between the maximum swimming speed of the sailfish and the other 3 marine species. From here, they found that sailfish could reach higher swimming speeds than the other fish (shown in graph A). However, (in graph C) the maximum swimming speeds they OBSERVED in the barracudas, little tunny, and dorados were closer to the corresponding swimming speed they PREDICTED than for the sailfish (residuals = observed - predicted).

    1. We used Non-negative Matrix Factorization to perform our Skills andSelf-ID clusterings. NMF attempts to find a matrix factorization whereall elements of the basis vectors are constrained to be non-negative.This is natural in data sets such as our skills rankings, which rangefrom 0 (lowest or missing) to 21 (highest).The R NMF package that we used is not currently available via CRAN,but can be downloaded from the archives.We used the standard Brunet et al. (2004) method, which attempts tominimize KL-divergence. Note that NMF attempts to globally opti‐mize a non-smooth function from a random initial state, and so weused 200 random runs to find a relatively reliable factorization. (Seemain text for several skills/self-ID terms that sometimes fell into othergroups when different random seeds were chosen. These small dif‐ferences did not appreciably affect our overall results.) The ranks of 5and 4 (for Skills and Self-ID, respectively) were chosen to maximizethe informativeness and interpretability (evaluated subjectively) of theresulting basis vectors. Lower ranks yielded vague factors, while higherranks yielded less informative results compared to the raw ranks/ratings.
    1. An additional model for DEET repellency was based purely on its molecular structure.

      The hypothesis that DEET repellency is due to its non-polar molecular structure is rejected as studies of the insect sensilla show that DEET does not have any long term effect on the membrane or disrupt the odor detection.

    1. dietary desiccation tests showed reduction of oocyte Wolbachia titer rather than an increase, suggesting that sugar-based titer responses are unrelated to hydration.

      What was hypothesized to be a player in the mechanism of Wolbachia colonization of the germ line cells ended up being a dead end. The processes of hydrating the cell were not related to concentration of Wolbachia.

    2. Thus, ovary volume reduction associated with sweet tastants parallels that induced by sugar-enriched diets. However, as sugar-enriched diets elevate oocyte Wolbachia titer and sweet tastants do not, this indicates that oocyte Wolbachia titer is not specified exclusively by ovary size.

      In order to test taste perception as a mechanism, sweet tastants were used as well. What was found was that although these tastants did impact ovary size similarly to sugar, there was no significant difference with Wolbachia concentration.

    3. Through apparent impacts on systemic insulin signaling, sucrose-rich diets have been shown to reduce ovary size, whereas yeast-rich diets increase it (Fig. 3A) (Geminard et al., 2009; LaFever and Drummond-Barbosa, 2005; Morris et al., 2012). Direct measurement of ovary volume in response to these diets confirms that the size changes are substantial (Fig. 3B).

      Referencing the control, there was significant difference when comparing this group to the substance-enriched environments when observing ovary size. For yeast-fed cells, the ovary size would size would increase while sucrose-fed cells would decrease in ovary size.

    4. According to this analysis, no significant differences in oocyte area were identified between control and sucrose-enriched conditions [χ2(2)=12.2, P=0.085], nor control and yeast-enriched conditions [χ2(2)=6.6, P=0.811] (Fig. 2G). Significance was detected when comparing oocyte area values between sucrose- and yeast-enriched conditions [χ2(2)=18.7, P=0.004].

      Comparing yeast-enriched to sucrose-enriched, there was a significant difference in oocyte size, but not any significance when comparing either to the control. Therefore, oocyte size was not necessarily responsive either to control or substance-enriched regions.

    5. According to these criteria, oocyte Wolbachia titer in the yeast-enriched condition was significantly lower than the control [χ2(2)=27.3, P<0.001] (Fig. 2D). Though higher oocyte Wolbachia titers were detected in the sucrose-enriched condition, the values did not differ significantly from the control [χ2(2)=15.6, P=0.056]. Significant oocyte titer differences were detected between the yeast and sucrose conditions

      Although the presence of sucrose was not significantly increasing the concentration of bacteria compared to the control cells, it definitely was significantly higher than that of the yeast-fed cells.

    1. Our reanalysis of Rokas et al.'s data indicates that their estimate of the number of genes required to infer a phylogeny confidently was inflated by signal heterogeneity caused by their inclusion of nonstationary genes. In addition, the conclusion that there are no useful predictors of phylogenetic performance does not hold.

      The data provided by Rokas showed that there needed to be a high number of genes to obtain good and confident results on a phylogenic tree. The reason why this was inferred was because nonstationary genes were used. In this paper it was proven that not many genes need to be used since stationary genes provide more accurate results with fewer genes, proving that there are good indicators to obtain phylogenetic trees

    2. When the randomly sampled orthologous nucleotides are bootstrapped in the same manner as the contiguous gene sequences, much greater variances are apparent (Fig. 6, open circles), although these variances are not directly comparable to the contiguous gene bootstrap variances because they do not include a variance component related to variation in gene size.

      It was concluded that when the randomly sampled orthologous nucleotides are bootstrapped utilizing the same process as the contiguous gene sequences the amount of variances probable increased. However, the variances are not proportional to the contiguous gene bootstrap variances since there is no link to variation in gene size.

    3. Figure 5

      Both these graphs gave the results that stationary genes (triangles) produce higher bootstrap values with fewer genes compared to nonstationary genes. For Branch 2, only 7 stationary genes were needed to achieve a BP of 95% whereas 18 nonstationary were needed to achieve that same value. For Branch 3, 23 nonstationary genes were needed to achieve the same BP as 10 stationary genes did.

    4. A similar pattern was found with maximum likelihood.

      The data shown in Figure 4 represents the maximum likelihood that nonstationary genes (squares) are more susceptible to an “off” phylogenetic signal when compared to stationary genes (triangles).

    5. A concatenated gene analysis across all codon positions demonstrates that the stationary partition recovers the S. kluyveri–basal branch 5 with significantly fewer sampled genes

      The stationary Condon position demonstrated that it was slightly easier and faster to reach branch 5 of a phylogenetic tree with fewer genes.This exemplifies what this paper is trying to prove in regards of using fewer genes in order to build an accurate phylogenetic tree.

    6. When analyzed this way, 61% of the stationary genes were found to yield trees that were identical to or fully compatible with the species tree. By contrast, only 38% of the nonstationary genes yielded identical or fully compatible topologies.

      The comparison of topological incongruence went to exemplify how the tested "nonstationary" genes resulted in significantly lower ratios of identical or "fully compatible" trees in comparison to those in stationary conditions. The author does point out, however, this examination was altered form previous works, done by others, because of their belief of treating polytomies as soft instead of treating them all as hard.

    7. Randomly sampled orthologous nucleotides have significant variance in bootstrap values using a standard nonparametric bootstrap. Each data point represents the mean and minus one 95% confidence interval of 100 branch-and-bound parsimony bootstrap replicates. Randomly sampled orthologous nucleotides from the complete data set (circles) have significant variance. Randomly sampled nucleotides from the stationary partition (triangles) recover the correct S. kluyveri–basal branch 5 with fewer nucleotides for a given level of support than randomly sampled nucleotides from the nonstationary partition (squares).

      Random sampling extracted from stationary partitions yielded above nonstationary samples, in addition to also resulting superiorly in comparison to the complete data set. Graph six clearly illustrates such observations through its "triangles" and "squares" symbolizing stationary and nonstationary, respectively.

    8. We compared the performance of the stationary and nonstationary partitions for these two branches, finding once again that the stationary partition performed significantly better for both branches (Fig. 5)

      Using the data acquired from Figure 5, the conclusion was made that stationary genes are again much more efficient at producing phylogenetic trees in comparison to nonstationary genes.

    9. Figure 4

      In figure 4a, the graph depicts how the third codon position stationary partition outperforms the non stationary partition as the number of genes increase and the bootstrap value rises. In figure 4b, the performance of the all-codon stationary partition was notably better. The amount of genes required to obtain higher than 95 percent of bootstrap value was 8 stationary genes to 21 nonstationary genes.

    10. When third positions alone were analyzed, the stationary half yielded the species tree with 96% to 100% support at all nodes (Fig. 1a), whereas the nonstationary half of the data set yielded the incorrect S. castellii–basal tree with 100% support at all nodes (Fig. 1b). The incongruence between stationary and nonstationary third-position partitions was significant (P = 0.002, ILD test in PAUP*, 500 replicates).

      Using the results from Figure 1, the conclusion was made that nonstationary genes provided a less accurate phylogenetic tree compared to the stationary genes because it incorrectly provided a 100% bootstrap value to S. castelli (SCAS).

  4. Jan 2018
    1. Therefore, current evidence argues that repellency by DEET does not involve the global inhibition of olfactory receptors.

      Orco mutants are unaffected by the presence of DEET, leading to the conclusion that olfactory receptors are not the sole reason for repellency against DEET.

    2. Although the mechanism is not yet clear, DEET likely alters the activity of olfactory receptors either in the context of odors or on its own.

      When speaking with the author of this paper, he explained the importance of understanding the molecular pathways of DEET.

      By having a greater understanding of this repellant, it will be possible to create a new insect repellent with better functionality and protection against disease carrying mosquitoes.

    3. Electrophysiology recordings in Aedes aegypti have also shown that DEET activates bitter taste neurons in the labellum that respond to many other bitter compounds

      The results of this experiment testing the effect of DEET on bitter tasting gustatory receptors conclude that insects are repelled by the taste of DEET which is perceived to be bitter.

    1. generates a new splice donor site (gt) 42 bases upstream of the wild-type donor site, thus generating a 14–amino acid deletion in the corresponding transcript (Fig. 3D).

      The authors found that the scaleless mutation is caused by the deletion of 14 amino acids in the EDF protein.

      Their analysis indicates that the deletion is caused by the insertion of a 688-base-pair fragment which changes the way the gene is spliced (a process by which noncoding sequences are removed from mRNA before a protein is transcribed).

    2. These results reveal a new evolutionary scenario where hairs, feathers, and scales of extant species are homologous structures inherited, with modification, from their shared reptilian ancestor’s skin appendages already characterized by an anatomical placode and associated signaling molecules.

      The authors found that the placode and the placode's signaling molecules are highly conserved—meaning they are found across many species. This study shows that the placode is responsible for the formation of many different structures such as feathers, scales, and hair.

    3. These results indicate that all three characteristics (epidermal thickening, expression of epidermal placode markers, and expression of dermal Bmp4), that is, the presence of an anatomical placode, are required for proper development of scales in reptiles.

      Epidermal thickening, patterning of markers, and expression of dermal Bmp4, all characteristics of an anatomical placode, are necessary for reptiles to properly develop scales.

    4. It has been previously hypothesized (47) that reptilian scales are more similar to avian reticulate scales (covering the foot pad) than to both avian scutate scales (covering the anterior metatarsal region) and feathers

      It was previously thought that reptilian scales are more similar to some types of avian scales (such as those covering the foot pad) than others. However, the current study suggests that this is not the case.

      All avian scales develop from an anatomical placode similar to reptile scales.

    5. The squamate anatomical placode, whose existence had remained undetected because of its transitory developmental dynamic, exhibits all the major features characterizing avian and mammalian placodes: local epidermal thickening with columnar cells and reduced proliferation rate, shared early spatially restricted expression of epidermal molecular markers, and localized conserved signaling in the underlying dermis

      The major finding of this paper is that reptile scales develop from an anatomical placode, similar to mammalian hair and avian feathers.

      Scientists were previously unsure if this was the case because the reptilian anatomical placode is very short-lived during development (and thus hard to detect).

    6. The data presented here put this debate to rest by demonstrating that most skin appendages in amniotes, including snake and lizard overlapping scales, not only share signaling pathways during morphogenesis but also truly develop from anatomical placodes.

      The results here support the idea that most skin appendages in reptiles, mammals, and birds are homologous because they share signaling pathways and arise from an anatomical placode.

    7. The fossil record lacks any evidence of intermediate forms (hence, of homology) between scales and hairs.

      One of the major challenges of tracing an organism's evolutionary history is an incomplete fossil record. Where there is no intermediate between two forms, scientists have to use the available evidence to make predictions about what this intermediate would have looked like.

    8. Similarly, Ctnnb1 andEdar, two other placode markers, also show marked differences in expression between wild-type and scaleless dragons. In both phenotypes, expression of these two genes is first ubiquitous across the whole epidermis before becoming restricted to the placodes in wild-type individuals only (Fig. 4B). These results indicate that expression of each of these three placode markers in reptiles is similar to the expression dynamic of the corresponding genes in mammals (27) and birds (20, 28,39). On the other hand, the absence of an anatomical placode in scaleless dragons coincides with the inability of signaling pathways to pattern the skin, similar to what is observed in mice deficient in Eda/Edar(40).

      The authors demonstrate that Shh, Ctnnb1, and Edar expression is similar in reptiles, mammals, and birds. They also conclude that the absence of an anatomical placode in scaleless lizards disrupts these pathways' ability to pattern the skin, which has also been observed in mice (a mammal) with similar mutations.

    1. Sources of uncertainty in our estimates result from the relatively few measurements of waste generation, characterization, collection, and disposal, especially outside of urban centers. Even where data were available, methodologies were not always consistent, and some activities were not accounted for, such as illegal dumping (even in high-income countries) and ad hoc recycling or other informal waste collection (especially in low-income countries). In addition, we did not address international import and export of waste, which would affect national estimates but not global totals.

      Another important part of science is recognizing sources of uncertainty in the data that lead to uncertainty in the results.

    2. Because no global estimates exist for other sources of plastic into the ocean (e.g., losses from fishing activities or at-sea vessels, or input from natural disasters), we do not know what fraction of total plastic input our land-based waste estimate represents

      An important part of science is recognizing the limits of the conclusions that can be drawn from a given data set.

    3. Our estimate of plastic waste entering the ocean is one to three orders of magnitude greater than the reported mass of floating plastic debris in high-concentration ocean gyres and also globally

      The authors' estimate of plastic waste entering the ocean is between 10 and 1000 times greater than the previously reported amount of waste floating in the ocean.

    4. 31.9 million MT were classified as mismanaged and an estimated 4.8 to 12.7 million MT entered the ocean in 2010, equivalent to 1.7 to 4.6% of the total plastic waste generated in those countries

      The authors predicted the amount of plastic waste that entered the ocean from coastal regions in 2010.

    5. we estimate that 99.5 million MT of plastic waste was generated in coastal regions in 2010

      The authors calculated the mass of plastic waste that came from coastal regions in 2010.

    6. We estimate that 2.5 billion MT of municipal solid waste was generated in 2010 by 6.4 billion people living in 192 coastal countries (93% of the global population).

      Using population density data and waste generation rates, the authors estimated the total amount of solid waste generated in 2010 by people living in coastal countries.

  5. Dec 2017
    1. similar phenotypes in other vertebrates because of impairments of the EDA receptor (EDAR; a member of the TNF family) (18) or its ligand EDA, indicating a conserved role of this pathway in reptiles as well

      Similar phenotypes are observed in other vertebrates (including mammals and birds) when the same pathway is interrupted. This suggests the pathway is conserved in reptiles, too.

    2. argued homologous to those characterized in chicken

      The authors found that the patterns between patterning of the tracts that give rise to chicken feathers and those that give rise to reptile scales could be homologous.

    3. spatiotemporal development is highly similar between the two species

      In Nile crocodiles and bearded dragons, scales developed from a similar anatomical placode and patterned similarly both spatially and temporally.

    4. Bmp4 is also shown for lizard. Red double-headed arrows indicate the body region processed for sectioning.

      The expression of Bmp4 in lizards strongly suggests a developmental evolutionary link among all reptiles, as well as birds and mammals.

    5. This set of new results coherently and conclusively indicates that most skin appendages in amniotes are homologous

      The authors' results suggest that, because the anatomical placode is crucial to the development of skin appendages in mammals, birds, and reptiles, these appendages are homologous.

    1. Table 1

      mtDNA CO1 is a gene found within the mitochondria, it is used to measure the genetic difference between organisms. A higher mean indicates a larger difference between two organisms, which is indicative of being a different species. (JP)

    2. Fig. 2

      In general, this graph illustrates that as genetic distance between species increases (this is measured by Nei's D) then mtDNA divergence increases as well. Overall, compatibility between two different organisms will be less if they have high mtDNA divergence and a high Nei's D value. (JP)

    3. All the shrimps we studied are shallow water, fully marine forms with planktonic larvae.

      Main subjects studied. Planktonic larva is significant in this study because larva shrimp would migrate to different regions of the Isthmus of Panama which may be a significant contributor to speciation events ~J.D.A. (+ JP)

    4. Even the least divergent pairs show substantial reproductive isolation

      Species so closely related showed two differ clutches. Isolation could've been geographical, though nothing that could completely cut them off from each other since they are similar. If anything, this could infer that they could've been selective in mating, or aggressive in behavior to even mate, thus preventing creation of offspring between them. ~J.D.A

    5. The null hypothesis, that isolation was simultaneous but rates of divergence are highly variable, is incompatible with the observed pattern because metabolic enzymes, mtDNA, and mate recognition share no mechanistic basis that would cause their divergence rates to be automatically associated.

      Basically, the null is rejected because it contradicts the observed data. The null states that isolation occurred around at the same time, but the observed data shows divergence indicators such as metabolic enzymes, mtDNA, and mate recognition, all of which are not associated at a single mechanistic basis required for concurrent divergence. ~S.Z.

    6. However, they do show some distributional differences that could affect sensitivity to changing conditions associated with gradual rise of the isthmus.

      The physical location of the shrimp could effect the divergence associated with the gradual rise of isthmus. ~S.Z

    7. Pacific members of the most divergent pairs are found deeper in the intertidal or are rare in habitats with heavy sedimentation (25) (Fig. 2). Thus, larval avoidance (26) of shoaling waters over the rising isthmus (6, 7) may have accelerated genetic isolation of these pairs.

      The shrimp located closer to the sea floor had a slimmer chance of being pushed over the isthmus; therefore had a higher chance of isolation and divergence. ~S.Z.

    8. Our data can also be used to estimate rates of divergence in reproductive compatibility. Even the least divergent pairs show substantial reproductive isolation

      The less compatible they are the more they have diverged. ~S.Z.

    9. Geographic isolation is thought to permit divergence and speciation by disruption of gene flow

      The physical barrier created by the Isthmus of Panama prevented the exchange of genes; therefore, allowing the organism to develop differently on wither side of the barrier or diverge. (SZ)

    1. This work suggests that high MSI1 expression levels in neural precursors could be a key contributor to the fetal neurotropism exhibited by ZIKV (2, 10, 37) (fig. S13). Intriguingly, MSI1 is also highly expressed in the retina and testis, other tissues deemed vulnerable to ZIKV infection

      A contributor to the infection of nerve cells in fetuses caused by ZIKV is the expression of MSI1. The ZIKV infection can affect other areas of the body also, such as the retina and the testis, because MSI1 is highly expressed in these regions.

    2. These findings also imply that MSI1 expression increases susceptibility of HEK293T cells to ZIKV infection (35). Furthermore, we noted an apparent dose-dependent effect of MSI1 on viral replication; those U-251 and HEK293T clones that express higher levels of MSI1 displayed greater viral RNA levels and increased cell death (Fig. 4, B and D to G, and figs. S11 and S12).

      Cells that contain A148V mutations in MSI1 cannot support Zika virus replication. Musashi 1 wild types cells had an increase in Zika virus RNA levels and cell death while the cells containing the mutant Musashi 1 gene did not replicate the Zika virus. Thus, HEK293 cells, cells that normally lack Musashi 1 expression, are better able to replicate Zika virus infection when the Musashi 1 gene is expressed.

    3. In summary, we identify MSI1 as an important factor for ZIKV replication, both in primary and transformed neural cell lines.

      MSI1 and the genome of the ZIKV RNA directly interact to cause ZIKV to replicate. The replication can be seen in the replication assays conducted after MSI1 was introduced into cells.

    4. These data confirm an interaction between MSI1 and ZIKV RNA, which is, at least in part, mediated by the 3′UTR of the virus.

      Authors found that MSI1 binds to the 3’ untranslated region (UTR) of PE243 by analyzing RNA pulldowns. Results were confirmed by mutating the MSI1 sites in the 3’UTR. The weakened interactions demonstrate an interaction between MSI1 and PE243 ZIKV RNA mediated by 3’UTR, revealing where the protein binds to the RNA.

    1. a phosphorylation-mimicking Thr205→Glu205 (T205E) tau variant coprecipitated significantly less with PSD-95 as compared with nonmutant and T205A (A, Ala) tau (Fig. 4C and fig. S21)

      Phosphorylation at T205 inhibits complex formation.

    2. T205 phosphorylation of tau is part of an Aβ toxicity–inhibiting response.

      Phosphorylation at T205 on tau limits Amyloid beta toxicity.

    3. p38γ regulated PSD-95/tau/Fyn complexes, likely at the level of PSD-95/tau interaction

      From Fig. 3 the authors conclude that p38y reduces PSD-95/tau/Fyn complex formation by affecting PSD-95/Fyn interactions.

    4. PTZ transiently increased PSD-95/tau/Fyn complex formation in p38γ+/+ animals; this effect was even more noticeable in p38γ−/− mice

      p38y was shown to inhibit the formation of complexes, but the addition of PTZ lowers the protective function of p38y.

    5. PSD-95/tau/Fyn interaction was reduced in transgenic mice with neuronal expression of p38γCA

      The interactions that are required to form the complexes are reduced in mice with an active form of p38y, demonstrating that p38y may prevent complex formation.

    6. PSD-95 copurified more tau and Fyn from p38γ−/− versus p38γ+/+ brains, and even more from APP23.p38γ−/− compared with APP23.p38γ+/+ and p38γ−/− brains

      An immunoprecipitation for PSD-95 was ran. The proteins that were associated with PSD-95 complexes also precipitated due being in a complex with PSD-95. The results show that tau and Fyn were contributing more to the PSD-95 complexes when p38y was not present.

    7. PSD-95/tau/Fyn interaction was enhanced in Alz17.p38γ−/− animals versus Alz17.p38γ+/+ mice

      Results show that more PSD-95/tau/Fyn complexes were in the brains of p38𝛾-/- vs. p38𝛾+/+. This shows that PSD-95/tau/Fyn complexes are associated Amyloid-beta induced excitotoxicity

    8. when compared to tau−/−.p38γ+/+mice, tau−/−.p38γ−/− animals showed similar protection from PTZ-induced seizures

      p38y only protects agianst PTZ-induce siezures only when tau is present. A difference between p38y being present and p38 being absent is only seen in mice that have tau.

    9. These data also showed that, compared with APP23 mice, APP23.p38γ−/− animals had aggravated memory deficits that persisted with aging

      APP23.p38y+/+ mice survived longer and had performed better in water maze than APP23.p38y-/- mice. Also shown in the results is that APP23.p38y+/+.tau-/- vs. APP23.p38y-/-tau-/- mice, are statistically the same, suggesting that the protective effect of p38 comes from phosphorylating tau.

    10. The exacerbating effects of p38γ loss on reduced survival, memory deficits, and neuronal network dysfunction of APP23 mice were virtually abolished in APP23.p38γ−/−.tau−/− mice

      The APP23 deficits improved when tau was not present in mice.

    11.  p38γ−/− mice showed no deficits and had normal motor function

      The lack of p38y kinase did not negatively affect the movement and motor function of the mice.

    12. Aβ pathology was comparable in the brains of APP23.p38γ−/− and APP23.p38γ+/+ mice (fig. S6), but p38γ deletion aggravated premature mortality and memory deficits of APP23 mice

      APP23 mice that had p38y and did not have p38y displayed similar traits, but the deficits in mice that did not possess p38y kinase were worse.

    13. Surprisingly, only p38γ depletion (p38γ−/−), but not systemic p38β, p38δ, or neuronal p38α (p38αΔneu) knockout, changed PTZ-induced seizures

      The only knockout mouse that displayed a change associated with PTZ-seizures was p38y. Because p38y was the only one that influenced the results, it is the focus of all the experiments.

    14. Finally, we found that tau-dependent Aβ toxicity was modulated by site-specific tau phosphorylation, which inhibited postsynaptic PSD-95/tau/Fyn complexes, revealing an Aβ toxicity–limiting role of p38γ in AD that is distinct and opposite to the effects of p38α and p38β (11, 13, 14).

      The authors state, contrary to popular belief, that tau can play a protective role in limiting amyloid beta toxicity by interacting with p38γ. By phosphorylating specific sites tau can increase neuron survival and improve memory loss.

    15. PTZ-induced seizures are reduced in tau−/− mice (8, 9). Adeno-associated virus (AAV)–mediated expression of WT and T205A neurons, but not T205E tau or green fluorescent protein (GFP), in the forebrains of tau−/− mice enhanced PTZ-induced seizures (Fig. 4D and fig. S25).

      The data shows that the tau-/-.AAV tauWT and tau-/-.AAV tauT205A were the most susceptible to seizures and had the most severe seizures out of the four genotypes.

    16. Hence, phosphorylation of tau at T205 should similarly mitigate neurotoxicity. Aβ caused cell death in WT and T205A neurons but significantly less in T205E tau-expressing neurons (fig. S23). Similarly, neurons expressing p38γ and, more so, p38γCA were significantly more resistant to Aβ-induced cell death than controls (fig. S24).

      The results from previous experiments showed that neurons survived at higher rates when they had T205E and p38γ.

    17. Pan-p38 inhibition stopped p38γ/p38γCA-induced disruption of PSD-95/tau/Fyn complexes

      If p38y is completely inhibited, the complexes are stable.

    18. Hence, p38γ regulated PSD-95/tau/Fyn complexes via phosphorylating tau at T205.

      The results of this experiment showed that p38γ helped to disrupt the PSD-95/tau/Fyn complexes through phosphorylation of T205.

    19. Increasing p38γ levels compromised PSD-95/tau/Fyn interaction in cells, and expression of a constitutively active p38γ variant (p38γCA) completely abolished this interaction

      p38y was shown to prevent the interactions required to form the complexes associated.

    20. Similarly, pT205 was markedly reduced in APP23.p38γ−/− animals compared with APP23.p38γ+/+ mice (Fig. 4B)

      The results of the previous experiment showed that APP23p38𝛾-/- mice had decreased T205 phosphorylation compared to the APP23p38𝛾+/+, which had T205 phosphorylation.

    21. no PSD-95/tau/Fyn complexes were isolated from tau−/− and tau−/−.p38γ−/− brains

      Demonstrates that the complexes will not form if unless tau is present.

    22. In summary, the levels of active p38γ kinase and tau phosphorylation at T205 determined susceptibility to excitotoxicity and Aβ toxicity.
    23. the effects of p38γ on excitotoxicity and Aβ toxicity were tau-dependent.

      The protective qualities of p38y are dependent on tau being present. If tau is not present, amyloid-beta toxicity effects the cells the same, even if p38y is present.

    24. increasing tau levels in p38γ−/− mice [brought about by crossing with nonmutant tau-expressing Alz17 mice (23)] significantly enhanced PTZ-induced seizures in Alz17.p38γ−/− mice

      Mice that had higher levels of tau were more susceptible to seizures.

    25. In summary, p38γ depletion exacerbated excitotoxicity, neuronal circuit synchronicity, mortality, and memory deficits in APP23 mice, without changes in Aβ pathology.

      Overall, every deficit associated with APP23 was made worse when p38y was not present.

    26. Electroencephalography showed enhanced spontaneous epileptiform activity and interictal hypersynchronous discharges in APP23.p38γ−/− compared with APP23.p38γ+/+ mice

      From the results, the researchers can infer that the presence of p38𝛾 kinase has a protective ability that lessens the amount of seizure trains that occur due to Aβ density bodies

    27. Compared with APP23.p38γ+/+ mice, APP23.p38γ−/− animals had increased sensitivity to PTZ-induced seizures

      From the results conducted in the experiment, specifically the Fig. 1 G-J, mice that did not possess p38y were more sensitive to seizures

    28. only p38γ localized to postsynapses and limited excitotoxicity.

      The only knockout mouse that was shown to cause a change in PTZ-induced seizures was p38𝛾. p38𝛾 was also the only kinase that was shown to localize in postsynapses between neurons.

    1. GeCKO can identify essential genes and that enrichment analysis of depleted sgRNAs can pinpoint key functional gene categories in negative selection screens.

      The significant decrease in the diversity of sgRNAs present at the end of the 14-day screen suggested that the GeCKO library was an effective way to identify survival genes.

      Because of this, the authors concluded that they could use this method to identify genes essential for cell function.

    1. Our results reveal that starvation decreased JH synthesis via a decrease in insulin signaling in the CA. Starvation-induced up regulation of the insulin receptor increased CA insulin sensitivity and might “prime” the gland to respond rapidly to increases in insulin levels after feeding resumption. During this response to starvation the synthetic potential of the CA remained unaffected, and the gland rapidly and efficiently responded to insulin stimulation by increasing JH synthesis to rates similar to those of CA from non-starved females.

      When insulin signaling and JH synthesis are low this causes starvation in mosquitoes. When these mosquitoes were fed again the gland was "primed"; which means it responds faster to insulin levels. Now that the gland has been primed it responds faster that way insulin signaling and JH synthesis return to their normal rates. -Emma

  6. Nov 2017
    1. Finally, it is important to recognize that our sampling was limited to juvenile plants and lasted only 12 months. Insect herbivore populations can strongly vary in different years, and thus, it is possible that our sampling missed important herbivores that are associated with P. subserratum.

      This is a very important limitation to put the results and conclusions of the experiment in perspective. If the sampling may have been done differently the experiment may have revealed different or additional understandings of defense allocation and speciation.

      • Carolina Jimenez-Pinilla
    2. The existence of this trade-off has been well supported by many different temperate and tropical studies looking at allocation to growth and defense in plants adapted to different light and nutrient availabilities, both within species

      The difference in nutrient resources can affect the size of plants and their maturity which correlates with the previously cited growth-defense-trade-off because the study claims a correlation between the size of the leaf and defense strategies. This may be due to the unique collection of herbivorous insects that prey on the plants.

      • Carolina Jimenez-Pinilla
    3. unlike most members of the family Burseraceae, P. subserratum does not yield measureable amounts of monoterpenes and only trace amounts of sesquiterpenes

      Those two plants did not produce enough amounts of monoterpenes, a class of organic compounds, produced by plants, to be taken into account; and very small amounts of sesquiterpenes. The important part of this result was that it was not expected in the scientists' hypothesis and was unusual in comparison to the other members of the plant family.

      • Carolina Jimenez-Pinilla
    4. We found that insect herbivores collected from Protium subserratum showed strong patterns of dissimilarity across different habitat types (Fig. 3). Moreover, we found significantly more insects feeding on terra firme plants than on white-sand plants, correlating with the large differences in resource availability between the habitat types. Taken together, these results suggest that there exists substantial variation in diversity and abundance of insect herbivores associated with P. subserratumacross white-sand and terra firme habitats.

      The results showed that there was a strong variation between insect species, habitat types, and abundance. As mentioned before, the terra firme lineage had different growth strategies than the white sand lineage and the terre firme plants were also found to have more herbivores feeding on them. This correlated since the terra firme seemed to provide more resources. The herbivores that were found also showed that they there was a variation across habitats.

      -Angela Mujica

    5. Terra firme populations exhibited significantly greater height and leaf growth and allocated more to chlorophyll production than white-sand populations in both soil types, demonstrating that different growth strategies have a genetic basis

      The reciprocal transplant experiment that was done with the different soil types showed that the terra firme lineage had greater height, greater leaf growth, and higher chlorophyll production in both soil types, while the white sand lineage did not. This worked to show that the growth strategies between each lineage was significantly different.

      Figure four illustrates these results.

      -Angela Mujica

    6. differences among the dominant herbivores, the species composition of the entire P. subserratum herbivore fauna exhibited high turnover among sites and habitats

      The data that was collected from the herbivores and their abundance and variation between the plant species showed that most of the insects preferred terra firme plants instead of the white sand plants. It was also seen that, out of the species that were collected, the majority of them were chrysomelid beetles. Since the plants tested were in different locations, it was found that a small percentage of that correlated with the amount herbivore variation.

      -Angela Mujica

    1. mimicking site-specific tau phosphorylation alleviated Aβ-induced neuronal death and offered protection from excitotoxicity.

      The site that is phosphorylated by p38y was found to be important for reducing effects of AD. Demonstrates that the function of p38y is important, and the mere presence of p38y in the cell is not protective, it has to be functional.

    2. depletion of p38γ exacerbated neuronal circuit aberrations, cognitive deficits, and premature lethality in a mouse model of AD, whereas increasing the activity of p38γ abolished these deficits

      The research found that the presence of p38y reduced the effects of AD in the mouse model.

    1. Caribbean reef shark populations can benefit from the local respite from fishing pressure provided by marine reserves.

      The authors results supports their hypothesis, showing that there is a positive correlation between marine reserves and the abundance of reef sharks. - Emily

    2. Because the vast majority of BRUV deployments in the non-reserve sites resulted in zero reef sharks being observed it was not possible to evaluate the impact of environmental variables and reserve versus non-reserve effects in the same model

      In the study, the majority of the BRUV deployed sharks developed no observable reef sharks . Because of this, environmental factors were not able to be considered.

    3. For example, sharks may move between proximate reefs; they may migrate at higher latitude reefs in response to seasonal temperature changes and they may be more likely to emigrate from a reef as competitor density increases or prey availability decreases. Caribbean reef sharks could be acoustically monitored at reefs of different levels of isolation, latitude and prey abundance to further test these hypotheses.

      This passage indicated that while the results obtained were conclusive in terms of the hypothesis promoted by the author, it was inconclusive in terms of the greater picture because there were many sources of error or outcomes that could not have been taken into account due to the settings of the reserves. The author mentioned that the results could have been bettered if accounted for prey-predator relationships in the reserves. This is because it could have provided more data as to why sharks were only being pinged the certain amount of times that they were as opposed to more or less times.<br> -Sindy

    4. We purposefully put the larger tags in larger sharks because of concerns that small sharks might be adversely affected by the V16 transmitters. As a result, the 14 V9 tagged sharks were smaller than the 20 V16 tagged sharks

      Tag size was an important consideration when it came to the assigning of a tag size and type to a specific shark. Smaller sharks were placed with smaller tags because the size and density of the tag could have affected the health of the overall infantile or smaller shark that it was paced in. This measure ensured that results and data for the experiment were viable and the the loves of the sharks were also accounted for and their safety ensured in that area of the study. -Sindy

    1. electrophysiological studies at higher levels of the nervous system, for example, by predicting specific emergent features in the midbrain and cerebellum.

      This sentence highlights another example where the products of this research can be used in future experiments. In this example, the authors are stating it can be used in future neurological oriented studies of the midbrain and cerebellum; areas of the brain that are primarily oriented with executive functions.

      -Kierra Hobdy

    1. first, the sex-determining proteins studied in the present work evolve at constant rates, as suggested by global molecular clock tests (Table 1).

      From Table 1, the following sex-determining proteins display InL, InL(clock), and the p-value. These factors display the final calculations. From what the author first concluded, the InL(clock) values show that there is in fact a constant rate with which the proteins evolve. It is tested by the likelihood ratio tests based off the models of evolution defined. -Melanie

    2. Combined with local molecular clock analyses (Fig. 3b), these results indicate that episodic adaptive selection was probably responsible for the nonclock-like behavior of Sxl during its recruitment into sex-specific functions in drosophilids (Mullon et al. 2012).

      Episodic selection can be defined as a form of selection that sporadically selects organisms with varying differences per generation, otherwise known as short-term fitness. In this sense, it can be concluded that SXL works alongside episodic selection rather than the molecular clock hypothesis in order to develop sex-specific functions within drosophilids. Learn about episodic selection here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2666517/ -Eri-Ray

    1. The high levels of genetic differentiation detected within C. jimenezii raise questions whether these two populations can be treated as different varieties/subspecies within this taxon or if indeed they may represent two different species.

      In this study, the researchers found some questions as to whether the two species of C. jimenezii could be grouped with the same taxa.

      Upon meeting with the author, it was stated that the molecular tools used, found a large amount of differentiation. This was not what the authors hoped and in turn was concluded that they were to remain in separate taxa.


    2. Therefore we recommend not translocating material between these two populations for genetic conservation or ecological restoration programs until the taxonomy of this species within Coccothrinax is further studied.

      Genetic conservation of this population is important due to the few individuals left in Haiti and the Dominican Republic.

      Upon meeting with the author, the difficulty of finding the purebred species was discussed as were the methods.


    3. The taxonomic uncertainties between the two populations of C. jimenezii have important implications for reintroduction programs. These two sites of C. jimenezii represent two clear management units for conservation, and the population genetic data suggest that we cannot rule out that they are two distinct taxa.

      The authors concluded based off of the molecular data, that the two species of C. jimenezii could not be identified as two different taxa.


    4. We have not been able to find data regarding the environmental history in these two populations since the 15th century. However, there is agreement among conservation biologists that since the arrival of the Europeans to this island there has been habitat fragmentation and deforestation linked to rapid expansion of urban and rural activities (Sambrook et al., 1999; Alscher, 2011; Foxx, 2012). Palms have long-life cycles; therefore, the detrimental consequences of genetic drift on genetic diversity can take a long period of time to manifest because of their long generation time and the presence of overlapping cohorts (Duminil et al., 2009).

      Since the extinction of C. jimenezii is of primary concern, the authors grab resources from other works to help solidify this concept. It is clear that the conservation of this species is vital to this study.


    1. Funding the sequencing of thousands of invertebrate genomes will require creative and collaborative approaches that go beyond the traditional funding mechanisms of individual principal investigator grants (Oleksyk et al. 2012). While the GIGA team has started exploring possible funding opportunities, we invite feedback and participation from the scientific community for joint fund-seeking strategies and ideas.

      Funding for the sequencing research will require collaboration among researchers as well as creative approaches beyond traditional funding. GIGA is open to funding ideas and opportunities.

    2. Future efforts will concentrate on expanding the GIGA community, refining its goals, developing hypotheses, and establishing genomics research and educational resources. GIGA welcomes all members of the scientific community who wish to contribute to comparative approaches for understanding the genomic diversity of the large number of still underexplored animal phyla. We also invite new members with expertise in rare taxa and with the collection experience to ensure proper identification and preservation standards for successful genome sequencing and interpretations. The link to join can be found at http://giga.nova.edu. This is an opportunity for those who have devoted their lives to the study of particular taxa to merge their deeper insights of the evolutionary history of their organisms into a genomics context. A second, larger GIGA workshop is currently planned for late 2014

      GIGA plans to continuously expand and improve and welcomes all members of the scientific community to contribute to their cause by helping understand the under-explored phyla. M.G.

    3. The long-range impact of GIGA will go beyond understanding phylogenetic relationships among invertebrate taxa, leading to new avenues of research in comparative developmental biology, environmental genomics, biodiversity, and climate change research, as is routinely done in many recent ecological studies focusing on gene expression data under stress conditions

      GIGA will go beyond just invertebrate genome studies by opening pathways t new research in many other related fields.

    4. The answers to fundamental questions about the origins of animal life and the evolution of their diverse phenotypes may be held in the genomes of distinct invertebrate phyla.

      The conclusion explains why they investigated what standards an invertebrate must reach to be tested for a successful genome sequencing. The researchers also add that geneticists could choose another option than searching an organism that meets their criteria. This option is sequencing organisms and modeling them for another organism. This would allow the geneticist to understand the other organism by having an idea of how the genome functions.

      The researchers also state a challenge faced by the science community is understanding the data they collect from the genome sequence, apart from also gathering the sequences. They state the research they do will help advance knowledge about invertebrate genomes by providing the necessary tools to investigate the sequences. (NAJ)

    1. most likely overestimations.

      Fishermen most likely overestimated the speeds of the fish they caught out of excitement and pride that they caught "such a fast fish" so they over-exaggerated how fast these fish really swam, contributing to the entrancing myth of the swimming speed of billfishes, what this paper addresses.

    2. broken curves represent the power limitation

      Broken curves in the graph represent limits on speed by the environment of the fish such as the strength of water current.

    3. Shaded areas represent contraction times corresponding to 5, 15, and 35 ms respectively

      The shaded graph shows the contraction times at each location of a fish defined in actual length in meters rather than just as percentage of the fish's body length.

    4. The only significant post hoc comparisons were those between sailfish and little tunny (P=0.009), and between sailfish and barracuda (P=0.028).

      The only places they found significant differences in swimming speeds between fishes were between sailfish and little tunny and between sailfish and barracuda.

    5. a general increase in contraction time from head to tail

      In little tunny, the muscles near the head contracted faster than those by the tail, which was different from the other fish that relied more on their tails to propel through water, and hence had lower contraction times near their tails than their heads.

    6. although size-corrected performance was highest in little tunny and lowest in sailfish.

      Though sailfish swam the fastest, some of that speed is attributed to the fact that sailfish were the longest fish and larger size increases a fish speed. After considering this and correcting the swimming speeds by the fishes' sizes, it was found that sailfish had the lowest size-corrected speed and little tunny were actually the fastest considering their size.

    1. Likewise, there is no evidence for differences among the pairs in historical effective population sizes or generation times that can be related to divergence (20).

      The generation types (ex. F1, F2, etc.) and population size were taken into account for each shrimp pair. These factors were found to not support the phenomenon of divergence among shrimp pairs because no differences were found. ~J.D.A.

    2. Our data can also be used to estimate rates of divergence in reproductive compatibility.

      The less compatible they are the more they have diverged. ~S.Z.

    3. Pacific members of the most divergent pairs are found deeper in the intertidal or are rare in habitats with heavy sedimentation (25) (Fig. 2). Thus, larval avoidance (26) of shoaling waters over the rising isthmus (6, 7) may have accelerated genetic isolation of these pairs.

      The shrimp located closer to the sea floor had a slimmer chance of being pushed over the isthmus; therefore had a higher chance of isolation and divergence. ~S.Z.

    4. However, they do show some distributional differences that could affect sensitivity to changing conditions associated with gradual rise of the isthmus.

      The physical location of the shrimp could effect the divergence associated with the gradual rise of isthmus. ~S.Z

    5. The null hypothesis, that isolation was simultaneous but rates of divergence are highly variable, is incompatible with the observed pattern because metabolic enzymes, mtDNA, and mate recognition share no mechanistic basis that would cause their divergence rates to be automatically associated.

      Basically, the null is rejected because it contradicts the observed data. The null states that isolation occurred around at the same time, but the observed data shows divergence indicators such as metabolic enzymes, mtDNA, and mate recognition, all of which are not associated at a single mechanistic basis required for concurrent divergence. ~S.Z.

    6. Geographic isolation is thought to permit divergence and speciation by disruption of gene flow

      The physical barrier created by the Isthmus of Panama prevented the exchange of genes; therefore, allowing the organism to develop differently on wither side of the barrier or diverge. (SZ)