British fineSTRUCTURE

Posted on 20 Mar, 2015 by Stacy Krueger-Hadfield

Leslie et al. (2015) provide an analysis of genome-wide SNP data from over 2,000 individuals in the United Kingdom in a paper out this week in Nature.

© artpause.com

© artpause.com


The population structure in the UK was limited with FST estimates averaged 0.0007, with a maximum of 0.003. But, unlike earlier studies, they used a new method for detecting fine-scale population structure called fineSTRUCTURE (Lawson et al. 2012).

In contrast to commonly used approaches, fineSTRUCTURE explicitly models the correlation between nearby SNPs and uses extended multi-marker haplotypes throughout the genome. This substantially increases its power to detect subtle levels of genetic differentiation.

They found a pattern of genetic differentiation that was concordant with geography. Their genetic clustering did not take into account geographic location of the samples, thus providing confidence that they had detected real population differentiation occurring at fine scales. For example, in the southwest of England, they were able to distinguish Cornwall from Devon.
Then, they compared genetic structure to a European data set in order to further describe genetic differences due to different patterns of migration and admixture from other populations outside the UK.
There has been a long debate about the Saxon replacement of the existing populations in the present day UK. Using their ancestry profiles and another analytical tool called GLOBETROTTER (Hellenthal et al. 2014), they provide evidence for the Saxon migration, but exclude the possibility of long-term replacement by the Saxons.
Interestingly, they did not find clear genetic evidence of a vast Danish Viking occupation of a large swathe of England, nor a generalized Celtic population in the non-Saxon parts of the UK. For example, one might expect Cornwall to resemble the other Celctic corners of the UK, but it was more similar to Devon and Central and Southern England.
References
Hellenthal et al. (2014) A genetic atlas of human admixture history. Science 343, 747–751.
Lawson et al. (2012) Inference of population structure using dense haplotype data. PLoS Genet. 8, e1002453.
Leslie et al. (2015) The fine-scale genetic structure of the British population. Nature, 519, 309–314.

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dN(eutralist) = dS(electionist) Part 3

Posted on 19 Mar, 2015 by Arun Sethuraman

In a previous post, I discussed the phenomenon of background selection, which results in rapid expungement of neutral alleles linked to loci under purifying or negative selection, and conversely, the rapid fixation of neutral variants that are linked to loci of high fitness (hitchhiking during a selective sweep, positive selection). Both processes lead to an overall reduction in genomic diversity at neutral sites (eg. Charlesworth et al. 1993).
In highly inbred populations, theory predicts the efficacy of selection to be lower, due to a fall in the effective population size. This fits well into the theory of sexual system evolution – particularly the transition from cross- to self-fertilization, which is often seen as an “evolutionary dead-end” (accumulation of deleterious mutations, small population sizes, limited ability to adapt to changing environments). Evolutionary persistence of selfers is thus hypothesized due to the phenomenon of “purging”, or strong negative selection against deleterious mutations. This seems contradictory – we expect lower efficacy of selection in smaller selfing populations, and expect greater efficacy of selection to purge recessive deleterious mutations to persist nonetheless.

Eichornia paniculata; Panel C (Top) shows an outcrossing flower, versus (Bottom), a selfer. Image courtesy: The Barrett Lab, http://labs.eeb.utoronto.ca/BarrettLab/Research.html


In a recent publication, Arunkumar et al. (2015) analyze the distribution of fitness effects (DFE’s) across different selective classes of new mutations in outcrossing and selfing populations of the aquatic flowering plant, Eichhornia paniculata. In short, they (1) simulate genomic datasets under varying outcrossing rates, population sizes, recombination rates, dominance, and compare the DFE’s of outcrossing versus selfing populations, and (2) sequence E. paniculata transcriptomes from selfing and outcrossing populations, identify variants, and compare strengths of selection at each variant site.
Results from their study (a) show more power to detect purging in selfing populations with increasingly recessive mutations (lower dominance), (b) with increasing dominance, greater proportion of nearly neutral mutations, compared to outcrossing populations, and (c) with variability in both dominance, and selection coefficients, they detect the presence of both strongly deleterious (purging) variants, and variants under relaxed purifying selection (weakly deleterious). Also, the sequencing, and the simulation studies found an overall decline in fitness of selfers, and that selfers accumulated more non-synonymous mutations, than outcrossers.
In conclusion, both simulated and the empirical data show evidence of purging (due to purifying selection against recessive deleterious mutations), reduced efficacy of selection (due to reduced effective population sizes) in selfing populations, and that these patterns are distributed across a variety of dominance and selection coefficients across selfing E. paniculata genomes. In yet another standstill, the neutralist-selectionist debate continues.
References:
Arunkumar, Ramesh, et al. “The Evolution of Selfing Is Accompanied by Reduced Efficacy of Selection and Purging of Deleterious Mutations.” Genetics(2014): genetics-114. DOI: http://dx.doi.org/10.1534/genetics.114.172809
Charlesworth, Brian, M. T. Morgan, and D. Charlesworth. “The effect of deleterious mutations on neutral molecular variation.” Genetics 134.4 (1993): 1289-1303.

Posted in adaptation, evolution, genomics, natural history, plants, population genetics, selection | Tagged , | Leave a comment

Reviewing the reviews: Twelve years of Landscape Genetics

Posted on 18 Mar, 2015 by Rob Denton


Landscape genetics has grown feverishly since its first formal definition in 2003 (Manel et al). The beauty of combining genetic, environmental, and spatial variation to answer biological questions sure is alluring, and the quest for improving the methodology of landscape genetics has been a reoccurring theme.
Entire issues are devoted to the subject in Evolution, Molecular Ecology, and Landscape Ecology. It is a broad field with a lot to talk about, and that comes with quite a few reviews over the years. Almost every review paper includes summaries of the topic and a dedicated section of future issues. Tracking the disparities between the “past” and “future” between review articles can give you an informative trajectory of a field: what problems are solved, what problems linger on, and what might not get solved any time soon.
Data return from SCOPUS using the search terms (landscape AND genetics). You can go play with the data yourself here.

Data return from SCOPUS using the search terms (landscape AND genetics). You can go play with the data yourself here.


In a (perhaps foolish) effort to distill some of the major issues down to a coffee break read, I’ve chosen some of the most influential reviews on landscape genetics (or landscape genomics) and broke down the evolution of the following components: the questions, the data, and the analyses.
Continue reading →

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Socially structured gut microbiomes in wild baboons

Posted on 17 Mar, 2015 by Noah Snyder-Mackler

Male yellow baboon grooming a female baboon (photo by Noah Snyder-Mackler)

Male yellow baboon grooming a female baboon (photo by Noah Snyder-Mackler)


“You can pick your friends and you can pick your nose, but you can’t pick your friend’s nose.”
Well, that old adage may still be true, but baboons certainly pick (up) their friends’ gut microbes. A new study by Jenny Tung and colleagues tested how baboon social structure, which includes both group membership and social relationships, predicted variation in gut microbiota.
Continue reading →

Posted in community ecology, genomics, metagenomics, natural history, primates | Tagged , , | 5 Comments

To sequence a genome or not to sequence a genome, that is the question

Posted on 16 Mar, 2015 by Stacy Krueger-Hadfield

In a paper out last month in the Journal of Phycology, Bhattacharya et al. (2015) provide a perspective on the need for more algal genomes.

[A] relevant question on the minds of many phycologists might be: do we really need more algal genomes or, should we stop and focus on the hard job of developing genetic tools and other resources for already sequenced taxa?

Chondrus crispus, one of the first macroalgal genomes (Collén et al. 2013) © SA Krueger-Hadfield

Chondrus crispus, one of the first macroalgal genomes (Collén et al. 2013) © SA Krueger-Hadfield


Algal molecular work has historically lagged a bit behind similar work in other taxonomic groups even though algae are important primary producers in marine environments.
Continue reading →

Posted in bioinformatics, evolution, genomics, horizontal gene transfer, mutation, next generation sequencing, selection | Tagged , , , , | Leave a comment

Just in time for spring break- the phylogenetic and medicinal history of Aloe vera

Posted on 16 Mar, 2015 by Melissa DeBiasse
Aloe vera plant. Photo from www.aloeverahq.com
Aloe vera plant. Photo from www.aloeverahq.com

It’s spring break season across the United States, which means many undergraduates are shedding their winter layers and flocking to warm, tropical destinations. After a week of fun in the sun, I’m sure many of them will rely on  Aloe vera to soothe their sunburns.

In a recent BMC Evolutionary Biology paper, Grace et al. (2015) examined the phylogenetic history of Aloe vera and its relatives, tracing the medicinal use of plants in the genus. The authors collected sequence data from nuclear and plastid loci for 239 taxa in the family Xanthorrhoeaceae, including 197 species in the Aloe, Aloidendron, Aloiampelos, Aristaloe, Gonialoe and Kumara genera. They constructed phylogenetic trees, estimated divergence dates, and obtained information from a dataset of 1400+ records from the literature to test for phylogenetic signal in the use of aloes.

Continue reading →
Posted in medicine, phylogenetics, plants, Uncategorized | Leave a comment

Mating systems

Posted on 13 Mar, 2015 by Stacy Krueger-Hadfield

In a new paper, published online in Molecular Ecology, Pannell (2015) reviews the literature on the evolution of mating systems and dispersal in colonizing species as component of a special issue called Invasion Genetics: The Baker and Stebbins Legacy. 
This issue is also the product of a special symposium at Asilomar in August 2014. I couldn’t resist a painting of that beautiful coastline where I spent my days as a budding molecular ecologist as well as writing about mating systems!

Asilomar Beach © karenwinters.com

Asilomar Beach © karenwinters.com


Self-compatibility should be a common feature among colonizing species (aka Baker’s Law). Colonization of oceanic islands, range expansions, biological invasions and metapopulation dynamics have all  been discussed within the context of Baker’s Law. But as with any law, there has been a lot of debate about its generality.
Models invoking the evolution of mating systems and dispersal seem to be at odds with models invoking Baker’s Law. Indeed, the

overwhelming feeling one gets from the literature on the evolution of reproductive and dispersal traits in colonizing species is one of cryptic complexity. Terms such as colonization, self-fertilization and dispersal roll easily off the tongue (or pen), but each of these terms encompasses a hazardously broad range of possible meanings.

Pannell argues for a more “nuanced consideration of dispersal” and the necessity of outcrossing and selfing rates as opposed to the ability to undergo self-fertilization.
Plants, in particular, are known for the plasticity of plant sexuality. Yet, we have a

poor understanding of the distribution of reproductive and dispersal traits in colonizing species.

Certainly, more empirical and theoretical work is necessary, but this work should also go beyond plants and animals that a diploid-dominant.
Pannell, JR (2015) Evolution of the mating system in colonizing plants. Molecular Ecology DOI: 10.1111/mec.13087

Posted in adaptation, Coevolution, conferences, evolution, Molecular Ecology, the journal, selection | Tagged , , , , , | 2 Comments

Exploring color palettes in R

Posted on 12 Mar, 2015 by Arun Sethuraman

How often have you had to squint at figures with unpleasant color palettes in a manuscript online or in print, and ultimately given up on distinguishing between fifty (or maybe just around 30) shades of gray?
I found the RColorBrewer package extremely helpful when it comes to picking colors for figures – instead of the standard way of letting R decide your palette (using say ‘rainbow’, or ‘topo.colors’ – see this link).
Here I describe some uses of RColorBrewer to make neat admixture bar-plots in R. You should be able to use the same color palettes for use in other kinds of plots as well (see my previous posts).
Say you have a Q (admixture proportion) matrix obtained from your favorite program (STRUCTURE/ADMIXTURE/FASTRUCT/etc) – named q.txt. Here, I ran multinomial clustering with K = 3 subpopulations, requiring a three color palette from RColorBrewer. The data set that I used was mined from the Tishkoff lab as part of the supplementary material of a paper on microsatellite variation in African populations. Eg: “q.txt” –

0	1	0
0.312204	0.687796	0
0	1	0
0	1	0
0	0.88985	0.11015
0.457319	0.542681	0
0.149153	0.850847	0
0.451845	0.477733	0.070422
0.405077	0.350571	0.244352
0	1	0
0	1	0
0.131876	0.707725	0.1604
...

To read the data file, install libraries:

install.packages(“RColorBrewer”)
library(RColorBrewer)
q<-read.table(“q.txt”)
barplot(t(as.matrix(q)),col=rainbow(3),xlab="Individual #", ylab="Ancestry",border=NA)

This should produce a bar plot with generic colors, picked using the ‘rainbow’ function.
rainbow
To use ColorBrewer, I recommend playing around with different accent colors (you should be able to display them all using the display.brewer.pal(n, name) function. Alternately, you should be able to visualize a variety of schemes on the ColorBrewer2 website here.
For example:

display.brewer.pal(3, “Greys”)
display.brewer.pal(6, “Accent”)

Thereon, create your own color palette using:

mypal<-brewer.pal(3, “Accent”)

You could also let ColorBrewer decide red-green colorblind friendly palettes, using:

mypal<-display.brewer.all(3, “Accent”, colorblindFriendly=TRUE)

Now you should be able to plot this directly by plugging your customized palette into the barplot function as:

barplot(t(as.matrix(q)),col=mypal,xlab="Individual #", ylab="Ancestry",border=NA)

Here are two examples – one in grayscale, one using a spectral color scheme.
spectral gray
Speaking of colors, here are some spectacular images from Holi celebrations across the world! Happy Spring, everyone!

Posted in howto, population genetics, R, software, STRUCTURE | Tagged , , | 8 Comments

Phylogenetic dispersion aversion

Posted on 11 Mar, 2015 by Rob Denton

image source
How biological communities form and are maintained is a complex and fascinating area of molecular ecology. Gerhold et al. offer up an interesting take on community phylogenetics in a recent Functional Ecology paper that argues against the use of phylogenetic dispersion as a proxy for the mechanisms behind community assembly.
The authors take the time to work through some of the assumptions made in these proxy analyses and weigh their real support in the literature. This list of assumptions includes:

  •  (i) phylogenetic dispersion reflects trait dispersion
  • (ii) a given ecological function can be performed only by a single trait state or combination of trait states
  • (iii) trait similarity causes enhanced competition;
  • (iv) competition causes species exclusion
  • (v) communities are at equilibrium with processes of assembly having been completed
  • (vi) assembly through habitat filtering decreases in importance if assembly through competition increases, such that the relative balance of the two can be thus quantified by a single parameter
  • (vii) observed phylogenetic dispersion is driven predominantly by local and present-day processes.

The lack of support for some of these isn’t that surprising (such as ii and vii), but I was surprised to find some of the concepts that I consider well-supported (such as iv) might not be so accepted after all.
Gerhold et al. suggest the way forward is to incorporate more evolution into the first steps of forming questions:

Despite an increasing number of pictures of Charles Darwin in conference presentations of community ecologists, the questions asked in many of these studies do not concern any evolutionary processes.

It turns out that these same assumptions that the authors criticize make for fantastic hypotheses to test using the same types of data. This context shift in how community assembly questions are asked is the true purpose of this paper, and makes it well worth the read:

Phylogenetic dispersion of communities is of limited value for understanding ecological assembly processes, but of high value to address other questions in eco-evolutionary research. The links between ecological assembly processes and trait patterns, and between trait patterns and phylogenetic dispersion of communities, might be too complex and weak. Instead, information on phylogenetic community structure is a potentially valuable tool to answer evolutionary questions, where community ecology can be seen as macroevolution in action.

 
Gerhold P., Cahill J.F., Winter M., Bartish I.V. & Prinzing A. (2015). Phylogenetic patterns are not proxies of community assembly mechanisms (they are far better), Functional Ecology, n/a-n/a. DOI: http://dx.doi.org/10.1111/1365-2435.12425

Posted in community ecology, phylogenetics | Tagged | Leave a comment

Speciation by selection (and drift) in the sea

Posted on 9 Mar, 2015 by Melissa DeBiasse

The orangeband surgeonfish, Acanthurus olivaceus. Photo from reefguide.org

The Orangeband Surgeonfish, Acanthurus olivaceus. Photo from reefguide.org


Marine systems challenge the view that speciation is the result of geographic isolation. Many marine taxa have large effective population sizes, which slows lineage sorting, larval dispersal phases that may extend for days, weeks, and sometimes months, potentially connecting far flung populations, and they exist in an environment that lacks obvious physical isolating barriers. All of these characteristics should theoretically lead to panmictic populations with little chance of divergence and yet marine ecosystems, particularly coral reefs, are among the most species-rich on the planet.
In their recent Molecular Ecology paper, Gaither et al. (2015) used mitochondrial and nuclear intron sequences and 3,700+ genome-wide SNPs to test the mechanism of speciation in two members of the Orangeband Surgeonfish species complex, Acanthurus olivaceus  and  A. reversus. The authors focused on peripheral populations that split from the main central-west Pacific lineage at approximately the same time (~0.5 million years ago; see figure below). The Hawaiian population is morphologically indistinguishable from the main central-west Pacific lineage but the Marquesas population differs morphologically and in its ecological niche.   Continue reading →

Posted in genomics, next generation sequencing, selection, speciation | 1 Comment