The ability to select for copious fruit selection (maximize female flowers) implies genetic underpinning.

pollen (containing sperm) or carpels (containing eggs/ovules)

This presentation of alternative hypotheses often happens after a manuscript has been peer reviewed and sent back to the authors to change.

Ericales!

Important to be prepared for this.

Important to acknowledge this!

It's helpful for any project design to acknowledge experimental elements, complete with plans for assessment.

Does anyone have thoughts on this?

in other words, differences between the high and low density categories are not due to high density plots being in one area and low density in another. There was no spatial autocorrelation detected. that's a good thing.

I think of many hunters as conservationists.

This is too common. When resources are locally abundant, local communities may not know their global value/rarity and permit over-harvesting/over-exploitation.

This may also be a way to preserve/protect traditional knowledge in the long-term as well.

Sound familiar? Doing some of this in our course!

Can see this paper here. For those who are curious about how papers are now written on species natural histories, this is a good example complete with maps, photographs of the plants, phylogeny, PCA's, pen-and-ink drawings, tables with previous species concepts, etc.

Here again an application to conservation biology and ecology.

Does this make sense to everyone? Taxonomy is needed for these reasons. Ecologists can't do their work without knowing who's who.

May be a good one for the Silene dream team, Autumn and Cam?

Basically, do you want more data for few samples? Or less data for more samples? Trade-off here.

This is what Hannah is using for her MS research on Potentilla robbinsiana on the White Mountains. She will squeeze about 300 samples onto a single NGS lane to get good population-level data.

This whole genome sequencing is one of the methods we explored during 'drug week' -- transcriptomics would also involve sampling the entire transcriptome as opposed to the subsampling (i.e., "reduced representation") methods used in this paper.

This refers to diversification RIGHT at the species/population boundary. A couple of interesting terms:

• incipient species = a group of individuals in the process of becoming reproductively isolated, on its way to becoming a distinct species.
• species complex = a group of closely related organisms that are genetically divergent, but so similar in appearance that boundaries between them are often unclear.
• cryptic species = a species that is genetically distinct from closely related species, but genetics are hidden by similar morphology that makes species difficult to distinguish from others.

This graph shows "How different are families within these supergroups?" As you can see, as you move to the right, overall morphological differences become fewer and fewer... again, think about why floral canalization occurs. Also think about why we might see such a range of morphologies among early-diverging lineages of flowering plants.

How might this also relate to 'fading borders'?

Note this! It's the combination of traits represented by the largest number of flowering plant families. Fused carpels, few seeds, with parietal placentation.

Thoughts on this?

This is a good and interesting expectation for reducing competition!

If you are interested in bee vision and want to learn more about it, check out papers by this person. They are the go-to resource!

You can check out this paper with figures here: https://bmcecolevol.biomedcentral.com/articles/10.1186/1471-2148-8-94

Morphological canalization occurs because of one or more evolutionary constraints. The example of shells is famous-- certain forms that should be possible in theory are not present among extant taxa because they are not streamlined enough, or make the shell more vulnerable to predation, etc etc.

Looking at where forms are missing form a morphospace can tell us a lot about the selection pressures influencing the evolution of form!

Just as in Figure 1 above, where there are no species occupying the section of morphospace where plants with long, narrow, free petals are (top back left quadrant).

Just for fun, here is a flowering plant with long, narrow, free petals obviously not used in their example.

means the order of genes is preserved

Genetic orthologs are related by common descent. They may differ from each other in sequence and they may code for proteins with different functions, but they have a common ancestor.

Goals of the study!!

Chinese herbal medicine variety of P. somniferum

In other words, there are plant species that are easy to take through the genetic engineering and propagation, but some of the native species are tough!

I have seen this only one other time, but it is really thoughtful...

The following glossary excerpt (from NCBI) may help with understanding the column headers here:

Assembly level - the highest level of assembly for any object in the assembly:

• Complete genome - all chromosomes are gapless and have no runs of 10 or more ambiguous bases (Ns), there are no unplaced or unlocalized scaffolds, and all the expected chromosomes are present (i.e. the assembly is not noted as having partial genome representation). Plasmids and organelles may or may not be included in the assembly but if present then the sequences are gapless.
• Chromosome - there is sequence for one or more chromosomes. This could be a completely sequenced chromosome without gaps or a chromosome containing scaffolds or contigs with gaps between them. There may also be unplaced or unlocalized scaffolds.
• Scaffold - some sequence contigs have been connected across gaps to create scaffolds, but the scaffolds are all unplaced or unlocalized
• Contig - nothing is assembled beyond the level of sequence contigs

Again, this is possible with new sequencing techniques that can provide us with LOTS of data on DNA sequence, RNA transcripts present, or even proteins synthesized-- and the data can be gathered very quickly.

This is the balance we all maintain in our cells to stay alive-- balanced pH, pressure, ions, etc all critical for staying alive and well.

This is why this research is happening now, and hasn't been possible in the past.

These approaches are more accessible now than they have been in the past because of high throughput, 'next generation' sequencing technologies.

Anyone remember operons in bacteria? The OG gene cluster.

Ideas about why natural selection would favor the production of 'medicine'?

EMPHASIS HERE. This probably should not be the focus of our discussion today, but these traditional practices were developed over long periods of time by specific groups of people. These kinds of traditional knowledge do not belong to everyone, nor are they understood by most people who consume medicinal plants regularly.

This is developing an understanding of biosynthetic pathways: what are the reactants and products, including intermediate molecules, what types of proteins are needed, how are genes regulated, etc.

The way these pathways are discovered is through examining mutants, so creating mutants is a big part of the process.

Looking for an explanation of how mutagenesis relates to understanding biosynthetic pathways? I enjoyed this: https://www.ncbi.nlm.nih.gov/books/NBK22044/

Just a few ideas here: This will circumvent the need for people to develop plant identification skills. It also means that even if a medicinal plants becomes extinct (or locally extirpated) due to overexploitation or natural causes, people will still have access to the medicinal compounds that were produced by those plants. It also means that medicinal plants need not be harvested from the wild or grown in monocultures.

A "bioactive" product is simply one that has an effect on the organism it's in!

And within those countries, in wealthy state counties.

What are some other biological or experimental reasons why isolation-by-distance was not found among New England populations?

Might this happen if this plant were also rhizomatous, producing clones and increasing population size that way?

How likely is long-distance dispersal in this species?

So there's seed dispersal, but even if a seed were to disperse, it needs to land on a mycorrhizal fungus to germinate, then grow to seedling, juvenile, adult stages... if any one of these doesn't happen then the trace of migration is lost.

This is the number of time CT is repeated in the sequence. I.e., CTCTCTCTCTCTCTCTCT etc.

This is a good solution to low sample sizes, a common problem with rare species. Combine populations into metapopulation groups or by some other criterion.

This procedure is standard (nothing special here) but is detailed here to permit others to follow/modify the same protocol. For example, I might study a related species and want to use these PCR cocktail and thermocycler settings.

This is what is meant by 'sampling'-- they are sampling genetic diversity by collecting a small amount of leaf tissue (1-2 square cm) from individual plants. They dry the tissue quickly to preserve the DNA intact, then isolate the DNA in a lab. Many of you have done DNA isolations before in one or more of your courses.

When scientists are not permitted to sample a bit of leaf tissue for these studies, it's because managers are concerned about affecting the health of the plant. Removing a leaf could be stressful or impact photosynthetic ability. I don't usually agree with their assessments, but 'better safe than sorry' right?

hmm.

Greater geographic range, but still a core in Appalachia. Honestly, looking at the shape of this flower I can def imagine how sclosely related species could have smaller flowers that remain 'closed' for longer (like I. medeoloides).

This involves collecting a tiny bit of leaf from each plant included in the study and isolating DNA from it.

Selfing should be pretty evident from the appearance of the flower.

orchid capsules (a dry fruit!) contain thousands of these tiny seeds which have no endosperm, just an embryo. The seed coat forms a little 'wing' to disperse the seed some distance, but most land pretty close to the parent plant.

This go-to paper describing all the different processes and expectations of population genetics under different circumstances is kind of dense but may be a good resource for pop gen enthusiasts!

oh, what kins of processes could they be talking about here?

We've mentioned glacial refugia that occur as islands within glaciated areas, but I didn't mention that southern areas of North America and Eurasia not covered by ice during the last glacial maximum are commonly referred to as glacial refugia as well.

Whenever you see this 'oides' at the end of a specific epithet it means "resembles"... in this case it is named for the similarity of its whorled leaves to Medeola virginiana, wild cucumber root. For those of you who have not excavated and crunched into a wild cucumber root, you are in for a treat!

ah ha!

Just checked out the distribution on iNaturalist. This species is NOT photographed very much!

Nine plant species reviewed in this Science paper, with a pretty great figure on page 2! "The ability of species to track their ecological niche after climate change is a major source of uncertainty in predicting their future distribution."

Mostly animals of all kinds but one plant, Saxifraga oppisitifolia. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1693318/pdf/15101575.pdf

This goes along with the idea that areas of endemism contain the highest genetic diversity.

Does this make sense to everyone? Aside from glacial refugia, it would have been nearly impossible for plant populations to have survived glaciation.

Anyone in our course stood next to a big glacier?

Resembles a Juniper! https://upload.wikimedia.org/wikipedia/commons/f/fb/Callitris_glaucophylla_DSC_2465.jpg

King Billy pine, Athrotaxis sellaginoides, is a really interesting Tasmanian species!

Lots of prescribed burning projects aim for this-- moderate frequency of low intensity burns,

What an insight here!

What is ENSO? Read about it here: https://www.climate.gov/enso

This phrase reminds me of the Alaskan Pacific Maritime ecosystem; as the climate changes, this cool, wet "non-fire" ecosystem is experiencing more drought conditions. These conditions are expected to lead to very intense and widespread wildfires.

Like grassy hills of invasive Avena along the California coast, so many examples in the west.

This meeting summary can be viewed here.

The meeting itself centered on The evolution of Australia over the last 25 million years: the consequences of aridification and ice-age cycles.

So... one of the fire-adaptations proposed is flammability, how easily a plant species can catch on fire and spread that fire, promoting fire in an ecosystem and enhancing fitness of serotinous plants. The paper cited here argues that adaptation to fire can be more abstract: highly flammable plants provide canopy openings (in death) where progeny can get a foot-hold. Pretty cool, huh?

Here is a recent, comprehensive paper covering the evolution of serotiny; prob more than you want to know but even a look at the Abstract is pretty interesting! When thinking fire-prone habitats, be thinking Mediterranean ecotype (though not exclusive, this is one of the big ones!).

Something to consider: a characteristic may evolve for one function (defense against frugivores) but take on a secondary function later (protection against fire or use of fire as chemical cue that conditions are good for germination and growth). Lots of examples of secondary adaptations; one biologist termed this exaptation.

This repeated phrase is making me grumpy. Biological organisms have evolved in the presence of (and in response to) fire. Are the authors implying that fire has also evolved?? Hmmm :(

"club moss" not moss... :(

Ha ha I have never thought of combustion as anti-photosynthesis. I hope this makes intuitive sense to some of you but if it doesn't, don't overthink it!

This is true! I worked on one of the prescribed burn studies in the early 2000's that helped establish basic knowledge about fire ecology in the US. Out in the Pacific Northwest (dry side).

Does anyone have this personal experience of feeling upset viewing an area 'devastated' by fire? It can be a powerful feeling!

ooh la la

insects!

Free data sets here. Cool!

You can find this paper here: https://www.pnas.org/content/pnas/104/50/19891.full.pdf

How might a graph like this be used? How might this be useful to someone hoping to encourage , protect, or conseve native habitat?

It may be that these bees mostly use water lilies, but utilize other species as secondary food sources. The expectation for most pollination syndromes (and plant-pollinator specializations reflecting coevolution) is that the majority of foraging occurs on a specific host or host type, but there will always be some drift onto other hosts. Best to think of as a bell curve.

Anyone thinking about competition for these special bee species?

Does anyone know what producing a bee fauna requires? How would someone go about doing this?

Here's part of the larger evolutionary picture, right??

In an autoregulatory feedback loop, a transcription factor (a protein that binds to a very specific sequence of DNA to initiate transcription) regulates its own transcription. These feedback loops are typically highly conserved. Any ideas why?

Thoughts?

"homology"-- is everyone clear on what this concept means? Similarity based on shared common ancestry. It is different from other types of similarity, like "analogy".

Here's the giant database you can query if you're looking for the identity of a piece of DNA: https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=tblastx&PAGE_TYPE=BlastSearch&BLAST_SPEC=&LINK_LOC=blasttab

Here's where you can search for these accessions and analyze the data yourself if you wanted: https://www.ncbi.nlm.nih.gov/geo/

Relative Abundance

Microarrays are used for a lot of applications! Here's a description: https://www.news-medical.net/life-sciences/How-Do-Microarrays-Work.aspx

This is the goal of this paper?

If you want to see where these are in the phylogeny of flowering plants, here's a reference! Look for Nymphaeales, Laurales, Ranunculales, Brassicales...

"comparative analyses" were an improvement over previous experiments. Why?

What might be some examples of these "fundamental changes in floral organization"?

Spermatophytes

Anyone remember what the B functions are?

By "derived eudicot model systems" the authors mean Arabidopsis thaliana. Many lineages of flowering plants are earlier-diverging in the Angiosperm phylogeny, so there's some question about whether Arabadopsis is a good model for ALL of flowering plants.

What kind of "genetic manipulations" could give us information about how floral development is regulated?

What does this phrase mean, "regulation of floral development"?

This plant again, Arabadopsis thaliana! Why doe sthis plant come up in so many papers?

What is meant by this 'diverse assemblage of floral forms'?

Early Cretaceous origin of flowering plants.

This is when the transcription/translation of one gene (that makes a protein!) triggers the transcription/translation/etc. of other genes.

Something to figure out: what makes these species 'phylogenetically pivotal'?

Not sure what Darwin's "Abominable Mystery" is? Check out this extensive paper on the subject!

35ish million years ago.

Look: the authors here use ~352 published DNA sequences and generate ~312 of their own to double the Allen et al. data set!

Always good to highlight the goals of the paper: (1) determine the genetic structure of Sibbaldia circumboreally-- i.e. how many lineages and where do they come from and disperse to? (2) what aspects of climate may have affected this plant's dispersal path?

Definition for OVEREXPLOITATION here :)

The authors point to superior technology as facilitating destruction, but a finer point here is the wholesale movement of cultural practices from the place they originated (western Europe) to a new continent, North America, where those practices may not be sustainable. Many immigrants bring cultural elements (sometimes including exotic plants and animals!) with them, which is culturally interesting/important, but ecologically risky.

And this. An appropriate model for resource management (species conservation) needs to account for the needs of as many species as possible. Interesting!

important! (2/2)

this section and the next important (1/2)....

convection is the loss of heat from a leaf to the surrounding air-- heat is carried off by air turbulence.

A bit more description here with some thoughts/comments in last paragraph about Lycopsid ecology and evolution... including the suggestion that speciation in Lycopsids may have occurred outside of a swampy environment.

How quickly can these plants convert atmospheric CO2 to glucose? And by what means?

portend!

Please consider this consumer pressure.

Formal definition here and link to original paper, which includes the biodiversity hotspot map I showed in a previous lecture, along with some important tables. Kind of old now, but check it out!

Note that this is measurable, but must have before/after data.

Invasive plants.

Tylerzb12, this citation. They compared diversity in forest fragments with diversity in contiguous forests. In another study they studied recruitment the same way-- how fast can forest trees recolonize after logging, forest regrowth?

This! Photosynthetic bacteria in water and lichens on land!

Thoughts on this anyone?

Here we go with clean water... extremely important!

In lecture (2/4) I talked about the use of DDT in areas of the world where mosquitoes transmit malaria and zika; it is problematic for the US to disparage the use of DDT when we do not face these challenges.

Eddie commented: "What are your thoughts on genetically modifying certain mosquitos to minimize the breeding of certain types of mosquitos?" https://www.bbc.com/news/world-us-canada-53856776

This statement resonates with me.

Not monoculture!

In our first class I think I heard indirect and direct references to this in our chat.

I'm very excited to explore this with all of you.

Here we go: biology, philosophy, and history...conservation involves many disciplines!

Important to note that mission-driven will be more prone to bias. Conservation biologists WANT a certain outcome, to preserve ecosystems health and function. Thoughts?

does this work?