72 Matching Annotations
  1. Apr 2020
    1. S. Lamichhaney, F. Han, J. Berglund, C. Wang, M. S. Almen, M. T. Webster, B. R. Grant, P. R. Grant, L. Andersson, Science 352, 470-474 (2016).

      This paper reports the identification of the importance of the HMGA2 gene in affecting beak shape in Darwin's finches, especially during natural selection that occurred during a drought in 2004-05.

    2. all Big Birds were homozygous

      The constant frequency of L alleles for HMGA2 and B alleles for ALX1 indicate that at these loci, the allele frequencies have reached an equilibrium.

    3. HMGA2 and ALX1, two closely linked loci (7 Mb apart) previously shown to be associated with variation in bill morphology in Darwin’s finches (15, 26)

      Lamichhaney and colleagues (2015) searched genomes of closely related species that had different beak sizes and identified ALX1, a homeobox gene that controls development in the face and neck, and correlates well with differences in beak shape.

      Lamichhaney and colleagues (2016) analyzed finches whose beak sizes changed during a drought and identified HMGA2, a nearby gene locus also related to beak size.

    4. P. R. Grant, B. R. Grant, Evolution 48, 297-316 (1994).

      In this summary of genes and traits of hybridizing finches on Daphne Major, the authors established general patterns found in hybridization of the finches on this island: that hybrids are generally intermediate between parental species and often go on to mate with members of the parental species.

      They discuss hybridization as a source of genetic variation within existing species and suggest that it can happen through new combinations of genes (additive genetic variance) as well as new patterns of dominance or co-dominance among known genes, or even the establishment of new combinations of genes on chromosomes.

      They also note how rare it would be to see hybridization produce birds much larger than parent species, and how unusual occurrences might be necessary to provide the conditions for this to happen.

    5. L. H. Rieseberg, M. A. Archer, R. K Wayne, Heredity 83, 363-372 (1999)

      In this discussion of transgressive segregation, Riesenberg et al. review many studies and conclude that the genetic basis of transgressive segregation is through complementary alleles: new combinations of alleles that provide novel combinations of genotypes.

      They find that transgressive segregation occurs most frequently in crosses between closely related species and that niche separation is the most important factor in favoring the establishment of hybrids.

    6. H. S. Swarth, Occas. Pap. Calif. Acad. Sci. 18, 1-299 (1931)

      Swarth's paper reorganized the classification of Darwin's finches slightly, particularly with regard to the Geospiza genus.

    7. D. L. Lack, Darwin's Finches (Cambridge Univ. Press, 1947)

      Lack's book recounts what he learned about Darwin's finches from a visit to the Galapagos in late 1938-39, one of the first visits to the island focused on the finches since Darwin's time. The work includes the classification of the finches as well as notes on speciation, adaptive radiation, and evolution.

    8. P. R. Grant, B. R. Grant, Philos. Trans. R. Soc. Lond. B Biol Sci. 365, 1065-1076 (2010)

      Grant and Grant use genetic information to quantify the effects of the gene exchange between populations of birds. They explore two situations: genes that enter a population through mating with a bird of the same species (conspecific) but from a different population on another island; and genes that enter a population from a member of a different species (heterospecific). They conclude that while both types of gene flow are rare, they do occur and have measurable effects on the populations that are complex and change through time rather than being steady.

    9. S. Lamichhaney, J. Berglund, M. S. Almen, K. Maqbool, M. Grabherr, A. Martinez-Barrio, M. Promerova, C. -J. Rubin, C. Wang, N. Zamani, B. R. Grant, P. R. Grant, M. T. Webster, L. Andersson, Nature 518, 371-375 (2015).

      This paper presents the results of a whole genome study of 120 of Darwin's finches and identifies the ALX1 gene as important in determining beak shape. The study also helps revise the phylogenetic tree of the finches and provides evidence for hybridization as the finches evolved.

    10. P. R. Grant, B. R. Grant, How and Why Species Multiply (Princeton Univ. Press, 2008)

      This book gives a complete evolutionary history of Darwin's finches. Grant and Grant explain the speciation that occurred and the mechanisms that underpin the formation of different species of finches in the Galapagos Islands.

    11. M. Schumer, G. G. Rosenthal, P. Andolfatto, Evolution 68, 1553-1560 (2014)

      In the article "How Common is Homoploid Hybrid Speciation?" Schumer et al. indicate that in the study of this topic future research needs to clarify the mechanisms of this type of event. They also propose criteria by which to judge the strength of evidence for this event, arguing that evidence for hybridization's role in speciation is somewhat limited.

    12. rare and extreme events

      Other hybridization events are likely to be caused by climate change and therefore are of concern to conservationists.

      Read more in Aububon News: https://www.audubon.org/magazine/climate-change-causing-some-mixed-wildlife

      Watch more at ibiology.org: https://www.ibiology.org/ecology/loss-biodiversity-human-dominated-world/#part-1

    13. the chance occurrence of strong selection against large bill size in a competitor species, G. fortis, in 2004-05 (12, 26)

      In 2004-05, a severe drought caused competition between two species of finch on the island of Daphne Major. The medium ground finch (G. fortis) and large ground finch were in competition for decreased food sources. Because medium ground finches with large beaks were at a disadvantage, the size of beaks for these finches decreased as a result of this selection pressure.

      This natural experiment was studied by Lamichhaney and colleagues (2016) and by Grant and colleagues (2014).

    14. it can be established in only three generations

      The authors summarize all their evidence that homoploid hybrid speciation has occurred in the Big Bird lineage. They note how unusual this example is because it occurs faster than expected.

    15. hybrid species

      Hybrids are problematic for conservation policy. Hybrids that do not form new species can be seen as decreasing the "purity" of a species, or as threatening to eliminate one species if it is absorbed into another. Hybrids may be seen as not worthy of conservation, even if they are rare. Conservation guidelines need to be updated.

      Read more in the Related Resources tab or at Current Zoology (will start a PDF download).

    16. it is likely that the founder population has already become reproductively isolated from G. conirostris

      The authors suggest in this paragraph that the Big Bird lineage is likely to be reproductively isolated from both parental species, providing further support that the lineage is on its way to becoming a new species.

    17. reproductive isolation

      Means that the species cannot breed to produce fertile offspring because of some barrier. That barrier could be geographic, behavioral, or some other type. A well-known animal that is reproductively isolated is the mule.

    18. transgressive segregation produced genotype combinations

      Because the bill depth trait changed without changes in body size or bill length, the authors suggest that the unique combinations produced by transgressive segregation were an adaptation that allowed these birds to survive and reproduce.

    19. more indicative of selection than of drift.

      The authors combine the knowledge of genotype frequencies with the changes in bill shape and conclude that the likely reason for this is natural selection, further support for their argument that speciation is occurring.

    20. allelic series

      The alleles for a certain locus listed according to their dominance, that is, their effect on the phenotype they affect.

    21. they are consistent with the hypothesis

      The different effects of the B alleles, and the fact that they segregate, support the idea that at the ALX1 gene locus, there are more than two alleles, all of which affect bill size differently. However, more data are needed to further support this hypothesis.

    22. in laboratory populations of animals (21)

      Bolsted and colleagues describe how they changed the allometric relationship of wing size to body size in fruit flies, Drosophila melanogaster, through artificial selection.

      This shows that selection can change allometric relationships and supports the authors' suggestion that natural selection is the cause of the changes in allometric relationship between bill size and body size in the Big Bird population.

    23. possibly caused by natural selection

      Based on their detailed analysis of the body size and bill shape of these Big Birds, the authors conclude that a change in the characteristics of the population is occurring such that it is becoming different than the parent populations. They suggest that it is possible that natural selection is the method by which this change is occurring, which supports their argument that a new species is forming.

    24. due to large bill and body size, and a distinctive song (12)

      In "40 Years of Evolution" (reference 12), Grant and Grant devote an entire chapter to the analysis of this possible new hybrid species that supports these conclusions about bill and body size, as well as song. 

      Their analysis includes extensive pedigrees and data on beak depth and width, heterozygosity, and song analysis.

      The current paper explores the beak morphology and genetic data more closely to contribute to the understanding of the hybrid lineage success and reproductive isolation.

    25. low quantitative variation

      The authors used descriptive statistics, calculating the mean and the standard error of the mean to quantify the variation in the populations. n=42 means that 42 measurements were included in the calculations.

    26. linkage disequilibrium

      This term means that the association of certain alleles at different loci is not random. Essentially, certain alleles of certain genes are often linked together and found in these combinations in the Big Birds.

    27. genetic drift

      Occurs when the frequency of alleles in an organism changes due to chance. Genetic drift (sometimes referred to as drift) is strongest in small populations such as the one studied here, because chance (random sampling) strongly affects the alleles present in the population.

    28. ADMIXTURE (19) analysis

      ADMIXTURE is a program that can quantify inbreeding by estimating allele frequencies and ancestry proportions. It helps scientists to understand how much of a genome is derived from inbreeding with other populations in the past.

      This analysis and the inbreeding coefficient analysis helped to confirm the founder's species as G. conirostris.

    29. inbreeding coefficient (F)

      A statistical calculation that estimates the probability that an individual inherited two identical genes from one ancestor that occurs on both sides of the pedigree. The higher it is, the more inbred the organism is.

      It was used to both help assign the founder bird to a species and to quantify the genetic diversity of the Big Bird population as it bred amongst itself.

    30. until recently

      In 2010, Grant and Grant analyzed genetic data to search for the effect of breeding with immigrant birds (reference 16). They used genetic studies to quantify the effect of genes from the same species (from populations on other islands) compared to those of different species.

    31. confirmed pedigree assignments

      A computer program was used to create many possible pedigrees based on the genetic data and to analyze the likelihood of each relationship in the pedigree using the genomic data. The most likely pedigree inferred from the data was mostly in agreement with the pedigree based on observations, with only a few changes.

    32. finch species imprint on features of their parents early in life

      Rosemary and Peter Grant developed this idea based on observations of mating pairs, as well as experiments. In some experiments, they played recorded birdsongs from either the same or a different species and recorded the birds' responses. Other experiments involved presenting birds with a stuffed specimen of either the same or a different species and recording their responses.

    33. An immature male finch immigrated to the small Galápagos Island of Daphne Major (0.34 km2) in 1981 (11–13).

      Rosemary and Peter Grant have led the study of the bird species of the Galapagos Islands since the 1970s. Individual birds on the island have been banded and described, so migrants such as the one described can be identified when they arrive.

    34. stringent criteria

      Schumer and colleagues present three criteria: 1) demonstration of a mechanism of reproductive isolation, 2) evidence of hybridization (preferably genetic and based on whole genome evidence), and 3) hybridization-derived isolation (establishing that the hybridization led to the reproductive isolation and not some other factor).

    35. new species

      Understanding the mechanisms by which new species form is a central issue in the study of biology.

      Read more at Scientific American: https://blogs.scientificamerican.com/science-sushi/evolution-watching-speciation-occur-observations/

    36. transgressive segregation

      When hybrid offspring show traits that are more extreme than those of the parents. For example, when a hybrid plant offspring is much taller than, or much shorter than, either of the parent plants.

    37. lineage

      Here, a genetic group of individuals that are all descended from one initial ancestor.

    38. hybrid speciation

      Referring to the formation of a new species when two different species mate to produce a new species.

  2. Mar 2019
    1. R. J. Abbott, N. H. Barton, J. M. Good, Mol. Ecol. 25, 2325-2332 (2016).

      Abbott et al. summarize why studying hybridization is important to evolutionary biologists, and how the genomic data now available can help scientists better understand the mechanisms of speciation and the particular genes responsible for maintaining hybrids as separate populations.

      The authors indicate that homoploid hybrid speciation, while theoretically possible, has few strongly supported examples and there is little detail known about how it works. This helps us understand why this research paper is so important and interesting.

    2. incipient

      Something that is in the initial, or beginning, stages.

    3. interspecific mating

      Breeding between members of two different species.

    4. imprinting

      A learning process that young animals go through soon after birth. The nearby adults serve as models for their identification of members of their own species.

    5. sympatric

      Living within the same geographical area.

    6. ecological segregation

      Because of their unique beak shape, the Big Birds can occupy an ecological niche that is not already occupied by any of the species already living on the island.

    7. segregating

      The separation of two alleles during meiosis when sex cells (sperm and eggs) are formed.

    8. loci

      Plural of locus. A locus is a particular location in the genome where a certain gene is found. All alleles for one gene are found at the same locus. Each gene has its own, unchanging locus.

    9. alleles

      Different versions of a particular gene. When we refer to homozygous, we are describing alleles for a particular gene that are the same as each other.

    10. epistasis

      Describes a situation where two different genes interact to affect a single phenotype. It often refers to a case where one set of genes might be modified or suppressed by a different set of genes.

    11. phenotypes

      The physical appearance and traits of an organism.

    12. static allometries

      Allometries are relationships between measurable traits, such as bill length and body size.

      Static allometries are measured in several individuals within one population who are all at the same developmental stage.

    13. polygenic inheritance

      Occurs when one trait (such as height in humans) is influenced by many genes.

    14. phylogenetic tree

      A diagram that represents the evolutionary relationships between organisms. Each group is descended from a common ancestor and so are related genetically. Phylogenetic trees can be based on morphology and on genetic information.

    15. inbreeding

      When families or closely related groups breed together to produce offspring.

    16. Interbreeding of two species

      Though interbreeding can be a source of genetic diversity for populations, it also can be a challenge when deciding which populations of a species are eligible for protection when conservation decisions are made.

      Read more in Science: http://science.sciencemag.org/content/362/6416/789.3

    17. morphology

      The study of the form of an organism: Its size, shape, structure, and the relationships between those parts.

    18. endogamously

      Means breeding that is confined to a specific group; in this case, the newly established species.

    19. Homoploid

      Meaning maintaining the same chromosome number: For example, staying diploid (two copies of each chromosome) rather than going from diploid to tetraploid (four copies of each chromosome).

    20. larger mean bill size than five adults that died

      These data further support that natural selection is acting on bill size, as birds with smaller bills did not survive.

    21. the allele frequency

      The authors measure allele frequencies to see if they are changing, which is an indication of continuing natural selection.

    22. allometric

      Allometry is the study of how body structures or processes scale compared to body size. In this case, the authors are comparing bill size to body size. An allometric shift means that the bill size compared to body size has a different numerical value in the hybrid species than in either of the parental species.

    23. more detailed morphological analysis

      The authors analyzed body size and several components of bill size to give a more complete comparison of the Big Bird lineage to both of its parental species. Results of these analyses are found in Figure 3.

    24. average nucleotide diversity

      This measure of genetic diversity is based on DNA sequence. It tells us the average proportion of nucleotides that are different between any two randomly selected sequences in an organism's DNA. Lower values indicate lower diversity.

    25. Hybrid speciation without chromosomal doubling

      Hybrid speciation in plants that includes increasing the chromosome number is known to occur.

  3. Feb 2019
    1. morphological measurements and whole genome sequencing

      The authors used bill size and body mass (morphological measurements) and genetic data.

      The genetic data used was the entire DNA sequence for each bird (whole genome sequencing) for sections to analyze, not just particular sections of DNA, as had been done in the past.

    2. P. R. Grant, B. R. Grant, Proc. Natl. Acad. Sci. U.S.A. 106, 20131-20148 (2009)

      In this paper, Grant and Grant report the establishment of the Big Bird lineage and discuss the mechanisms of reproductive isolation that exist for its population.

    3. B. R. Grant, P. R. Grant, 40 Years of Evolution: Darwin's Finches on Daphne Major Island (Princeton Univ. Press, 2014)

      This book summarizes the evidence for evolution gathered over the entire research project on Daphne Major that the Grants led. It concludes that natural selection occurred repeatedly during that time, and that competition for food in times of drought drove that evolution.

    4. A. W. Nolte, D. Tautz, Trends Genet. 26, 54-58 (2010).

      Nolte and Tautz discuss homoploid hybrid speciation and indicate that there is a need to understand the mechanisms involved in this type of speciation. They argue that the best way to examine these mechanisms is through observing hybrid populations that may or may not be on their way to forming new species, either in natural situations or in experiments.

    5. analysis

      The phylogenetic tree analysis consists of scanning the genomes of all 46 members of the Big Bird lineage and comparing them to the genomes of 180 other finches from Daphne Major for which there are genome data.

      A computer program is used to generate many phylogenetic trees, and mathematical parameters are used to ensure that the data are properly interpreted in the program. Then, a statistical test is used to evaluate the reliability of each split in the tree.

    6. evolutionary importance of rare and chance events

      The authors conclude that chance events were important in this speciation event: these include the founder male's unusual song, unusual migration, his immature age, and the selection event mentioned in the next sentence.

    7. imperfect copying of a Daphne finch by the founder after it had first learned its father’s song on Española (or Gardner) (13)

      This phenomenon has been observed on Daphne Major in several cases. It is a possible factor in causing hybridization events.

  4. Jan 2019
    1. progeny

      Another word for progeny is offspring.

    2. homozygosity

      An organism that is homozygous for a particular allele has two identical alleles at that locus. High homozygosity means the organism is homozygous for many genes. It is likely to be found in inbred organisms.