Clonal conundrum, part deux

© smh.com.au

© smh.com.au

In the second installment of the clonal conundrum, one hallmark of clonality is one that surprisingly hasn’t been validated that many times using species that have both sexually and asexually reproducing populations. Theoretically, clonal reproduction should generate massive …

Heterozygote excess

Mutations accumulate in clonal lineages as the two alleles at each locus irreversibly diverge within individuals (Balloux et al. 2003). This should generate largely negative Fis values. As clonality increases, Fis decreases:

Figure 1 from Balloux et al. 2003: Fis as a function of the rate of clonal reproduction. The line represents analytical results and the solid circles simulation results.

Figure 1 from Balloux et al. (2003): Fis as a function of the rate of clonal reproduction. The line represents analytical results and the solid circles simulation results.

Balloux et al. (2003) suggest that strict clonality can, thus, be easily detected in populations due to the excess of heterozygotes. But, the occurrence of sex, even infrequently, what they term cryptic sex, might also be detected. Fis values will be variable among loci:

Figure 2 from Balloux et al. (2003). Standard errors of Fis as a function of the rate of clonal reproduction.

Figure 2 from Balloux et al. (2003). Standard errors of Fis as a function of the rate of clonal reproduction.

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Procrustes Analyses in R

Procrustes transformations (i.e. a form of multidimensional scaling that allows the comparison of two data sets) have been used extensively in recent literature to assess the similarity of geographical and genetic distributions of species, following the lead of Wang et al. (2010). See Jeremy’s post describing the method and its application to genomic data. I’ve scoured the internet but can’t seem to find a way to make these plots using R (or any software for that matter). Here’s a simple tutorial on how to do this in R using principal components (PC1, and PC2) already computed from a PCA on SNP data (using your favorite tool – eg. EIGENSOFT, or even in R, and geographical coordinates for each individual. This tutorial uses the package “MCMCpack” to compute Procrustes transformations. As an example, I am using a chunk of the European data-set published in Novembre et al. (2008), which I downloaded from here. Note that this file already contains geographical information (latitude and longitude), and PC’s 1 and 2 computed using EIGENSOFT.

nov

Procrustes analyses of genetic and geographic coordinates in Europe, sensu Wang et al. (2010).

 install.packages(“MCMCpack”)
library(MCMCpack)
library(maps)
nov<-read.table("PCA.txt",header=TRUE,sep="\t")
X<-as.matrix(cbind(nov$longitude,nov$latitude))
Xstar<-as.matrix(cbind(nov$PC1,nov$PC2))
p<-procrustes(Xstar,X,translation=TRUE,dilation=TRUE)
map(database="world",regions=c('belgium','netherlands',
'austria','denmark','portugal','italy','spain','uk','germany',
'france','sweden','norway','finland','luxemburg',
'greece','monaco','ireland'),xlim=c(-10,20),ylim=c(35,60))
map.axes()
text(p$X.new,col=c(nov$alabels),labels=nov$alabels,cex=0.45)
text(nov$longitude,nov$latitude,col=c(nov$alabels),
labels=nov$alabels)

And voila! My best reproduction of Figure 1 of Wang et al. (2010) – please note that I only used a portion of the data-set in this tutorial. Feel free to play around with other data-sets, and let me know how it goes!

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Interview: The landscape of Ian Wang’s reading list

Relationships between pairwise genetic distance (dots) and both geographic and environmental distances. Linked from supplemental material of Wang and Bradburd (2014)

To follow up on some recent posts on The Molecular Ecologist about landscape genetics and isolation by environment, I brought in an expert.

Dr. Ian Wang is an assistant professor in the Department of Environment Science, Policy, and Management at UC Berkeley and has spent the bulk of his career asking questions and developing techniques that further the general field of landscape genetics. Dr. Wang was a visiting seminar speaker here at Ohio State a couple of weeks ago, and he graciously volunteered to answer some questions based on our conversations during his visit:

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Adaptive divergence in the monkey flower

soething

The yellow monkey flower, Mimulus guttatus. Photo from wikimedia.org

Theory suggests adaptive divergence can proceed in the face of gene flow when adaptive alleles occur in areas of the genome, such as chromosomal inversions, that are protected from recombination, which can break up beneficial allele pairings. In their recent Evolution paper, Twyford and Friedman determine phylogeographic structure and the role of an inversion in the adaptive divergence of life history strategies in the yellow monkey flower, Mimulus guttatus, across northwest North America.

Mimulus gattatus plants employ perennial or annual life history strategies. Perennial plants tend to occur in wetter sites, invest heavily in vegetative growth, and flower later in the season while annual plants occur in drier, drought prone areas and reproduce early in the season. The two ecotypes differ in flowering and senescence time, flower size, and potential to spread clonally, but have overlapping ranges and are fully interfertile. Previous studies found adaptive traits that differ between the perennial and adaptive ecotypes map to a chromosomal inversion that contains hundreds of genes. Continue reading

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Clonal conundrum, part un

Molecular ecologists are faced with a clonal conundrum when we wish to investigate the evolutionary ecology of clonal organisms. An attack of the clones is not something that should frighten one away …

© wirdou.com

Attack or herding of the clones? © wirdou.com

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Posted in Coevolution, community ecology, conservation, domestication, evolution, haploid-diploid, natural history, population genetics | Tagged , , | 1 Comment

The brave new world of environmental genomics

A new special issue of Heredity reflects on the recent advances in environmental genomics (see other posts about eDNA here and here) and highlights the ways NGS can aid in characterizing complex biological systems.

© usatoday.com

© usatoday.com

The cryptic, as well as the rare but active fraction of biodiversity are now accessible to study in all environments. (Joly and Faure 2015)

One of the highlights was the review of E&R (evolve and resequence) by Schlotterer et al. (2015). The authors discuss the use whole genome sequencing of pools of individuals (Pool-Seq).

[The selection for a well-defined trait in a controlled experiment], assures that both the phenotypic and the underlying genomic response are triggered either directly or indirectly by the selection regime applied during the experiment.

The cool thing about this approach is what can be done beyond the characterization of different allele frequencies between two selection regimes (i.e., selected and control populations). It is possible to sample evolving populations at different time points and, thus,

to study the trajectories of the selected alleles and thus elucidate their evolutionary dynamics.

Schlotterer et al. continue with the potential challenges E&R studies face, including experimental design and validation of candidate loci, but conclude that the reliability of E&R interpretation will continue to improve. In time, the method will be extended to a broader range of taxa and species.

References

Joly D and Faure D (2015) Next-generation sequencing propels environmental genomics to the front line of research. Heredity 114 429-430. doi:10.1038/hdy.2015.23

Schlötterer C, Kofler R, Versace E, Tobler R and Franssen SU (2015) Combining experimental evolution with next-generation sequencing: a powerful tool to study adaptation from standing genetic variation. Heredity 114, 431-440. doi:10.1038/hdy.2014.86

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dN(eutralist) < dS(electionist) Part 5

The neutral theory predicts that species with small census (and effective) population sizes are subject to greater drift (or allele frequency fluctuations), and vice versa. In other words, species with larger population sizes are expected to maintain more neutral diversity (polymorphisms). Intuitively then, the efficacy of selection in larger populations could constrain neutral genomic diversity, and vice versa. Little evidence exists however, of the maintenance of levels of neutral diversity due to population size (or drift) alone – “an old riddle” (Leffler et al. 2012), also termed Lewontin’s Paradox (Lewontin 1974). Today’s discussion of the neutralist-selectionist debate borrows thus from several concepts that I have written about over a series of posts – background selection (or negative selection at sites), and hitchhiking (or positive selection, and selective sweeps at sites), both leading to an overall reduction in genomic diversity at linked neutral sites. Diversity reduction is also correlated with site-specific recombination rates (as discussed here).

Species with large census sizes (eg. watermelon, silkmoths), versus small census sizes (orange, olive baboon). Image courtesy: http://dx.doi.org/10.1371/journal.pbio.1002113.g001

Species with large census sizes (eg. watermelon, silkmoth), versus small census sizes (orange, olive baboon). Image courtesy: http://dx.doi.org/10.1371/journal.pbio.1002113.g001

Positive correlation between the impact of natural selection and the geographic range of a species (A) - Figure 2 from Corbett-Detig et al. (2015)

Positive correlation between the impact of natural selection and the geographic range of a species (A) – Figure 2 from Corbett-Detig et al. (2015)

In a recent publication, Corbett-Detig et al. (2015) in quite possibly the largest study of its kind, report strong evidence for the effects of natural selection in maintaining neutral diversity across multiple species. In analyzing variation across windows using genomes from 40 species of plants and animals, of varying census population sizes, the authors (a) call variants (against reference genomes), (b) estimate recombination rates, (c) fit and estimate likelihood under models of background selection, hitchhiking, and neutrality to determine genome-wide reduction in polymorphism, and (d) correlate recombination rates, and impact of selection with proxies for census population sizes (geographic range, and body size). Their analyses indicate strong evidence for the impact of natural selection on reduction of linked neutral diversity in species with large census sizes (eg. invertebrates, herbaceous plants). Conversely, species with small population sizes (eg. vertebrates, woody plants) show greater evidence of genetic drift influencing neutral genomic diversity. Significance of these findings remains when accounting for genome assembly quality, variations in genome size, recombination rates, sampling variance across chromosomes, and polymorphism levels affected by domestication. Their model also predicts that hitchhiking removes more linked neutral diversity in species with greater census population sizes, than background selection, although background selection is more prevalent among all species analyzed.

This study, while concretizing evidence for explanations to Lewontin’s paradox, also discusses violations of the neutral theory for several species (particularly those with large census population sizes).

It is therefore essential to consider selective processes when studying the distribution of genetic diversity within and between species. Incorporating selection into standard population genetic models of evolution will be a central and important challenge for evolutionary geneticists going forward.

Also see the commentary on this paper by Roland Roberts here.

References:

Corbett-Detig RB, Hartl DL, Sackton TB (2015) Natural Selection Constrains Neutral Diversity across A Wide Range of Species. PLoS Biol 13(4):e1002112. doi:10.1371/journal.pbio.1002112

Leffler EM, Bullaughey K, Matute DR, Meyer WK, Ségurel L, et al. (2012) Revisiting an Old Riddle: What Determines Genetic Diversity Levels within Species? PLoS Biol 10(9): e1001388. doi:10.1371/journal.pbio.1001388

Lewontin RC (1974) The genetic basis of evolutionary change. New York: Columbia University Press. xiii, 346 p.

Roberts RG (2015) Lewontin’s Paradox Resolved? In Larger Populations, Stronger Selection Erases More Diversity. PLoS Biol 13(4): e1002113. doi:10.1371/journal.pbio.1002113

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Migration on the brain

Salmon

If you’ve watched any number of nature shows in your lifetime, you’ve seen the astounding migrations made by salmonid fishes. You can count on seeing a shot of salmon darting against the current and catapulting themselves over turbulent falls (like this!). These migrations between freshwater streams and the ocean are spectacular for both their magnitude and difficulty, but the changes that happen within each fish to get them to migrate in the first place might be just as interesting.

Salmon comparison

The two forms of Oncorhynchus mykiss: the anadromous steelhead (top) and the resident rainbow trout (bottom)

This month’s issue of Molecular Ecology includes a new study from Garrett McKinney and colleagues that compares the gene expression patterns within brains of rainbow trout that are resident or migrant forms. The rainbow trout form that completes long migration events to the ocean and back, called Steelhead or anadromous, undergo striking changes in phenotype to make these journeys. This includes a different body shape, different coloration, and various physiological changes to deal with saltwater. These developmental changes have been previously associated with genetic differences, but little is known about how and when those genetic differences manifest themselves.

Currently, studies of transcriptome-wide patterns of gene expression in salmonids have largely ignored ontogenetic changes during early development and little is known about the timing of activation of molecular pathways that regulate phenotypic differentiation.

McKinney and colleagues generated transcriptomes from the brain tissue of trout that were migratory or resident types. This sampling happened at multiple points over a year, and the authors showed that major differences in gene expression happen at around eight months, especially in males.

The majority of differentially expressed genes between migrants and residents were unique not only to a single time point but also to a single sex, indicating possible temporal differences in gene expression during development and significant sex differences. This raises the possibility that males and females may be developing at different rates or utilizing different molecular pathways during development.

At eight months old, these fish are still a year away from the big phenotypic differences that aid in migration, but their expression pathways are already cranking up proteins that are specific to those physiological differences. In addition, the authors map these expression differences to previously-documented QTLs and chromosomes that are associated with migration phenotypes.

As with other transcriptome-based research on non-model organisms, the authors are limited in what genes that can actually annotate, so who knows how many undescribed genes are also determining what fish “just keep swimming”.

 

McKinney G.J., Hale M.C., Goetz G., Gribskov M., Thrower F.P. & Nichols K.M. (2015). Ontogenetic changes in embryonic and brain gene expression in progeny produced from migratory and resident Oncorhynchus mykiss , Molecular Ecology, 24 (8) 1792-1809. DOI: http://dx.doi.org/10.1111/mec.13143

Posted in Molecular Ecology, the journal, natural history, RNAseq, transcriptomics | Tagged , | 2 Comments

The gopher tortoise gut microbiome

A gopher. Not a gopher tortoise. From the movie Caddyshack.

A few weeks ago I wrote about a study on socially structured gut microbiomes in wild baboons. Well, now I’m here to tell you about a new study that examined the population structure of tortoise gut microbiomes. Continue reading

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Plastic and evolved responses to host fruit in apple maggot flies

Phil Huntley-Franck bugguide.net

The apple maggot fly, Rhagoletis pomonella, which is so much prettier than its name implies! Photo by Phil Huntley-Franck, bugguide.net

The apple maggot fly, Rhagoletis pomonella, is a prominent system for the study of sympatric speciation. Sister taxa in the R. pomonella species complex, the apple-infesting race of R. pomonella and the snowberry-infesting R. zephyria, have sympatric distributions and the fruiting time of their preferred hosts widely overlaps. However, apple trees and snowberry fruits contain distinct secondary metabolites that have toxic effects on herbivorous insects and may facilitate adaptive divergence in Rhagoletis.

In their new Molecular Ecology paper, Ragland et al. performed reciprocal transplants and measured variation in performance (larval survivorship, larval development time, and pupal mass) and gene expression in fly larvae of the apple-infesting R. pomonella and R. zephyria raised on different host fruit. The aim of the study was to examine the plastic and evolved performance differences between R. pomonella and R. zephyria, which hybridize with low frequency in the field but remain genetically and morphologically distinct.  Continue reading

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