Welcome to Evol.Fri! This is meant to be an informal reading group to accomplish the goal of staying current with the literature in evolutionary biology. It is hosted by the EckertTurbeville, and Verrelli labs in the Department of Biology located at Virginia Commonwealth University.

I would like participants to nominate papers that are interesting. The only guideline is that it must fall broadly within the field of evolutionary biology. If you find papers of interest, please e-mail them to me (aeckert2@vcu.edu) and I will post them.

There will be no formal structure to this group. The person who nominates the paper will make a single statement about why the paper was chosen and that is it. The rest of the time will be open for discussion.

Every Friday at 4:00 pm

Where: We will wander off to a nice place with refreshments for the actual discussion after meeting at LSC 340/342.

Note the readings are in reverse order (future to past) and that additional posts can be located by clicking on the link "Older Posts" in the bottom right corner.
May 18, 2018

Fig. 1: Zhang (2018)
This week we will discuss a pair of papers addressing the role of the Neutral Theory in our understanding of molecular variation. Unlike last week these papers are a tad more friendly to the Neutral Theory as explanatory, or at least useful, for understanding biological patterns. Hope to see you there. 
Fig. 1: Yoder et al. (2018)

Fig. 1: Kern & Hahn (2018)
May 11, 2018

This week we will discuss a pair of papers addressing the role of the Neutral Theory in our understanding of molecular variation. Both papers provide excellent resources and citation lists for knowledge, as well as strongly argued opinions. Thanks to Brandon for picking these papers! Hope to see you there, as this will be one of the last opportunities to debate with the newly minted Dr. Lind!

Fig. 1: Josephs (2018)
April 13, 2018

This week we will discuss genotype-by-environment interactions and the evolutionary forces that shape them. Thanks to Mitra for picking this one.

Fig. 3: Schell (2018)
April 06, 2018

This week we will visit the realm of urban evolutionary ecology. Schell (2018) reviews the standing body of literature about adaptation and plasticity in urban areas and discusses the role of genome level data to aid in testing hypotheses about the relative roles of adaptation and plasticity in urban evolution. Thanks to Lindsay for picking this one.

Schell, C. J. (2018). Urban evolutionary ecology and the potential benefits of implementing genomics. Journal of Heredity 109: 138-151
Fig. 1: Peischl et al. (2017)
March 30, 2018

This week we discuss relaxed selection during range expansions using humans as an example. Thanks to Brandon and Mitra for picking this one! 

March 23, 2018
Fig. 1: Exposito-Alonso et al. (2017)

This week we discuss adaptation to extreme drought in Arabidopsis. The authors identified variants conferring increased survival under extreme drought conditions and then examined frequencies of these variants in natural populations. Thanks to Brandon for picking this one. 

Exposito-Alonso, M. et al. (2017). Genomic basis and evolutionary potential for extreme drought adaptation in Arabidopsis thaliana. Nature Ecology & Evolution 2: 352-358
Lamichhaney et al. (2018): Fig. 1
March 2, 2018

This week we are reading about rapid hybrid speciation in Darwin's finches. The new hybrid lineage also has the wonderful title of the Big Bird lineage. Ah, Sesame Street lives on in all of us. What could be better to discuss than that over snacks and drinks?

February 23, 2018

Seabra et al. (2018): Fig. 2
This week we are reading about the role of genomic background on affecting evolutionary outcomes in new environments.  Very cool stuff about convergence that leverages naturally occurring clines in Drosophila in an experimental evolution setup. Thanks to Trevor for picking this one!

February 16, 2018

Moreno-Mayar et al. (2018): Fig. 1a.
This week we will explore the topic of the peopling of North America. Specifically, new genomic evidence was used by the authors to infer several attributes about the timing of divergence and continued connectivity among populations of humans that crossed the Beringian land bridge to people North America. Thanks to Brandon for picking this one!

February 09, 2018
Willi et al. (2018): Fig. 2

This week we will read about the interactions between demography and the accumulation of mutational load in Arabidopsis lyrata. Specifically, the authors noted that intergenic diversity decreased towards range margins, but that signatures of mutational load within exons did the opposite (e.g. Pn/(Pn + Ps) increased). Lots of other cool stuff, too!

February 02, 2018

This week we will explore two opinion/review pieces about evolution caused by extreme events and conservation strategies in the face of climate change that explicitly recognize the role of evolutionary and ecological forces in selecting the winners (rather than humans via assisted migration, etc.). Thanks to Bonnie for picking these!

Bunnefeld et al. (2017): Fig. 1
January 26, 2018

Welcome to the first week of Evolution Fridays for the Spring 2018 semester! We will kick the semester off with a reading about the role of genomics in testing hypotheses about the assembly of ecological communities. Thanks to Justin for picking this one! 

Fig. 1: Keith et al. (2107)
October 06, 2017

This week we will enter the realm of community genetics. Keith et al. (2017) test the hypothesis that genetically based interactions between two foundational species, one tree and one insect species, affect arthropod community structure, function, and interaction networks. They demonstrate that genetically based interactions between the foundational species do affect arthropod communities composed of 139 species. They extend these results to Darwin's 'entangled bank' metaphor by showing that genetics can directly and indirectly underlie ecological complexity. Thanks to Justin for suggesting this paper. 

September 22, 2017
Fig. 1: Huber et al. (2017)

This week we will examine a new paper about the evolution of dominance. Huber et al. (2017) use naturally occurring mating system variation in Arabidopsis thaliana to jointly estimate the distribution of fitness effects and dominance coefficients for newly arising amino acid mutations.  They discovered a relationship between the magnitude of deleterious effects of new mutations and whether or not they were recessive (i.e. more deleterious mutations were more likely to be recessive). They also illustrated that this relationship is context dependent, with the relevant context being expression levels and connectivity within gene expression networks. They conclude that dominance evolved as an outcome of complex interactions within these networks. There is no one to blame other than me for this paper. 

Fig. 1: Bay et al. (2017)
September 15, 2017

This week we will examine a review about rapid adaptation to environmental change. Bay et al. (2017) examine the theory and empirical trends currently available in the literature about rapidity of adaptation. They use this review to then highlight where genomic data can be used to help increase knowledge about the role of architecture and its evolution to rapid adaptation. Thanks to Brandon for picking this one! 

September 8, 2017

There will be no reading group this week. Many of us are traveling or attending other important events. See you next week.  
Fig. 1a: Gompert et al. (2017)
September 1, 2017

Welcome back to for fall! This week we will examine a review about the use of genomics and clines to study the processes associated with speciation. Gompert et al. (2017) review concepts, methods, and outstanding questions related to the outcomes of clinal analyses and studies of introgression across hybrid zones. 

May 04, 2017

Fig. 1A: Hodgins et al. (2016)

This week we will examine a paper studying the links among gene expression, divergence, and positive selection. Hodgins et al. (2016) take a genomics approach to study the links between gene expression divergence between pines and spruces. Overall, they find relationships among sequence divergence, gene expression divergence, gene expression levels, and several measures of sequence polymorphism. They conclude that negative selection has driven much of these patterns, including relaxation of negative selection as potentially influencing gene expression divergence between these species. Thanks to Mitra for choosing this paper. 

April 20, 2017
Fig. 2: Kooyers et al. (2017)

This week we will touch on the subjects of ecological sorting and character displacement as they affect niche evolution.  Kooyers et al. (2017) use two species of monkeyflowers to examine the role of character displacement in niche evolution. They show that the dichotomy between ecological sorting and character displacement as mechanisms of niche evolution is likely naive (as most dichotomies are in biology) because both mechanisms are determined by (multivariate) trait evolution. Thanks to Connie for inspiring the choice of this paper.

Fig. 1: Zhan et al. (2014)
April 13, 2017

This week we are off an running with a paper about monarch butterflies. Zhan et al. (2014) take a population genomics approach to dissect multiple phenotypes within monarch butterflies into their genetic components. Along the way, they also provide information about the evolutionary and demographic history of these species. Thanks to Justin for picking this paper. 

April 6, 2017

Fig. 1: Yang et al. (2017)

After a hiatus due to personal travel, we will pick up our meetings this week with a paper about isolation-with-migration (IM) models. These models are routinely used to differentiate between models of speciation with and without gene flow. Yang et al. (2017) argue that genomic data, no matter how large in dimension, will not be able to differentiate between divergence models that incorporate anything beyond no gene flow or continuous gene flow since divergence. This ought to be a fun conversation. See you all at our new meeting time - Thursdays at 3:30 PM.

March 17, 2017

Fig. 1: Barker et al. (2017)
This week we will examine rapid evolution in yellow starthistles, an invasive plant species of western North America (and Souther America, as well). Barker et al. use ddRADSeq generated SNPs to examine population structure and to fit demographic models using Approximate Bayesian Computation. In brief, they found pronounced genetic structure across the native range of this species, with the source population for invasion into western North America resulting from admixture between two divergent lineages (eastern European and Asian) in western Europe. Thanks to Trevor and Lindsay for selecting the same paper. Whether it is convergence or parallelism is up for debate. 

March 10, 2017

Fig. 1: De La Torre (2017)
This week we will examine a new study about rates of molecular evolution in plants. De La Torre et al. (2017) generate a comparative data set across land plants with which they compare rates of molecular evolution and the frequency at which those patterns are generated by non-neutral evolution. In general, they found that rates of molecular evolution for gymnosperm lineages are about 7 times slower than angiosperm lineages, but that gymnosperms have greater levels of purifying and diversifying selection. There is no one to blame other than me for picking this cool, new paper. 

March 03, 2017

Fig. 1: Christe et al. (2017)

This week we will examine divergence among genomes of two tree species undergoing a history of divergence with gene flow. Christe et al. (2017) examine patterns of diversity and divergence between Populus tremula and P. alba to address historical demography and selection during the divergence of these species. The authors use these results to describe the roles of adaptive divergence and segregating deleterious variation on the development, as well as breakdown, of reproductive isolation. This ought to be a complex yet fun discussion over snacks. Thanks to Brandon for picking this one. 

February 10, 2017

Fig. 1: Kueppers et al. (2016)

This week we are heavy on the ecology side, with a look at a stellar experiment addressing the effects of climate warming on seedling establishment in subalpine environments. In general, these experiments demonstrate that climate warming will likely affect Engelmann spruce more so than limber pine in subalpine forests of the Rocky Mountains. The consequence is an enrichment of limber pine in subalpine forests currently dominated by spruce. One does not have to think too hard or quickly to speculate about the ecological ramifications of this transition. 

February 03, 2017

Fig. 1: Puzey et al. (2016)

This week we are heavy on the evolutionary biology side, with a look at a good old population genomic survey and what it can (and cannot) tell us about patterns of genetic diversity and local adaptation. In addition, Mimulus is a pretty cool system, even from my tree-centric point of view.

January 27, 2017

Fig. 1: Kuester et al. (2017)

We will continue with the theme of  ecologists and evolutionary biologists needing to come together as one big and happy family. Kuester et al. (2017) illustrate this point in their recent paper where they illustrate that human-mediated selective pressures have resulted in shifts of mating systems in Ipomoea purpurea. Shifts in mating systems have direct short-term and long-term consequences for ecological interactions and continued evolutionary responses. 

January 20, 2017
Fig. 4: Kokko et al. (2017)

Analogies are great tools with which to explain difficult concepts. This week we will read a paper using the supply-demand concept to explain the link between research paradigms in ecology and evolution. Kokko et al. (2017) outline the standard argument that ecological context provides demands on the evolutionary supply of fitness related variation to call for more synthesis across the disciplines of ecology and evolution. As known by many ecologists, fitness landscapes are in constant flux due to changing environments and ecological contexts. As known by evolutionary biologists, these changing fitness landscapes by themselves do not preclude rapid (even on ecological timescales) adaptation by populations with sufficient segregating variation. Now, if we could only get these types of folks together over a beverage to communicate more clearly. Oh wait, that is what we are doing. Hope to see you there. 

December 02, 2016
Fig. 1: Gompert et al. (2016)

This week we will examine a paper about measurement of selection on correlated genetic loci. Gompert et al. (2016) investigate the use of Bayesian sparse linear mixed models (BSLMMs) to estimate selection on individual loci. As noted by the authors, this is a special case of genome-wide association mapping (GWAS), thus allowing methodologies used in GWAS to be utilized for this purpose. The authors use a mixture of simulations and real data to show that BSLMMs can indeed be useful for the estimation of selection at individual loci, but that the power of this method is related to the underlying architecture of the traits determining fitness. In the end, this method is likely to be most powerful in highly heritable traits with concentrated architectures. Thanks to Trevor for picking this paper. 

November 18, 2016
Fig. 1: Seehausen et al. (2016)

This week we will examine a review paper about the role of genomics in addressing questions related to speciation biology. Seehausen et al. (2016) provide a synthesis in which they propose how to better incorporate genomics in speciation research, derive hypotheses that are testable using genomic data, and formally coin the field of speciation genomics. There should be lots of conversation about the biology, as well as the proliferation of <_fill in an adjective _> genomics terms in the literature (e.g. ecological genomics, population genomics, landscape genomics, conservation genomics, community genomics).

Fig. 1: Harvey et al. (2016)
November 11, 2016

This week we will examine a paper about the relationship between population structure within species and the rate of speciation. Harvey et al. (2016) use an enormous dataset to show that there is a positive relationship between the rate of speciation, as inferred using a phylogeny of 176 New World birds, and the magnitude of population structure, based on 17,746 individual birds across those 176 species. As the authors rightly point out, this relationship has long been assumed, but rarely ever tested. Again, there is no one to blame other than me for this choice. Hope to see you there.

Fig. 1: Chaves et al. (2016)
November 4, 2016

This week we will examine a paper about the genomic landscape of divergence among species of Darwin's finches. The authors use a combination of empirical population genetic and genome-wide association (GWAS) approaches to characterize the genetic architecture of beak morphology among three different species. Overall, the authors find a mixture of shared and unique architectures across species. There is no one to blame for this choice other than me.

Fig. 1: Fitzpatrick & Keller (2015)
October 28, 2016

This week we will examine a paper about modelling adaptation and its genomic architecture across landscapes. Fitzpatrick and Keller (2015) take a novel approach to the statistical analysis of environmental and genetic data to discover, model, and predict future gene-environment associations (GEA). Thanks to Mitra for suggesting this one. 

Fig. 1: Li et al. (2016)
October 14, 2016

This week we will veer off track to discuss population structure in brown bandicoots. Yes, you read that correctly - bandicoots! Li et al. (2016) use SSRs and a landscape genetic analysis framework to describe patterns of population structure and the effect of habitat fragmentation on those patterns. After applying a suite of traditional landscape genetic analyses, the authors conclude that habitat fragmentation can lead to profound differences in genetic connectivity. Thanks to Lindsay for selecting this paper. 

October 7, 2016
Fig. 1: Yeaman et al. (2016)

This week we are remain on track with another paper about trees. This week we will take a look at the case for convergent evolution in the genetic architecture of climate adaptation for two conifers separated by approximately 140 million years of evolution. This should be a fun read. Hope to see everyone there!

September 30, 2016

Fig. 2: Mayol et al. (2015)
This week we are back on track with a paper about trees. Mayol et al. (2015) tackle the problem of how the range of English yew (Taxus baccata) established its range since the last glacial maximum. They framed the problem as one of isolation-by-distance and isolation-by-environment. In the latter, genetic structure among populations, even at neutral markers, should be correlated with environment. Using a combination of genetic markers and climate data (past and present), the authors argue that the range of English yew was established not only by geographical isolation but by environmental isolation. Thanks to Mitra for suggesting this paper. 

There are no figures in Charlesworth et al. (1982).
As Darwin might have said, it is one long argument.
September 23, 2016

This week we will read an oldie but goodie addressing a neo-Darwinian response to the microevolution-macroevolution distinction derived from the punctuated equilibrium crowd. The punctuated equilibrium crowd, driven by notable evolutionary biologists such as Stephen J. Gould, argued that the fossil record displays trends in phenotypic evolution that are at odds with the neo-Darwinian perspective. Specifically, this crowd argued that the apparent pattern of phenotypic stasis followed by rapid phenotypic evolution (i.e. punctuated equilibrium type evolution) is not explainable by the neo-Darwinist perspective, which they characterize as requiring constant and gradual change to occur. Charlesworth et al. take the punctuated equilibrium folks to task in this response. They argue that the fossil record pattern is not indicative of any new type of evolution. Regardless of the age of this paper, the topics here continually creep into evolutionary biology, so this is a good introduction to their origin and debate. Thanks to Mitra for suggesting this one.

September 16, 2016
Fig. 1: Ament-Velasquez et al. (2016)

This week we will read about the population genomics of sexual and asexual lineages in ribbon worms. The authors describe patterns of nucleotide diversity within lineage of worms with different forms of reproduction. They show that the asexual lineage, which reproduces via fissiparity, has extremely high heterozygosity as well as an elevated Ka/Ks ratio. They explain this observation through hybridization of changes in ploidy. The Meselson effect, a new term for me, was also discussed. This should be a fun discussion. Thanks to Clint for suggesting this one. 

September 9, 2016
Fig. 1: Ikeda et al. (2016)

This week we will examine a paper about the role of genetics in species distribution modeling. Basic species distribution models treat all individuals within a species as exchangeable (i.e. they are all independent realizations of a species drawn from a common population of individuals that define the species of interest). We have known for over a century, however, that this convenient statistical assumption is wrong. Individuals within species are related (i.e. they are not independent) and display differences throughout geographic  ranges (e.g. subspecies, ecotypes, locally adapted populations, etc.). The paper this week examines how much better methods are that take these violations of the usual assumptions into account. The authors show that genetically informed models far exceed the power of those ignoring genetics. You have no one to blame for this choice other than me. Hope to see everyone there. 

August 26, 2016
Fig. 2: Hoban et al. (2016)

Welcome back to the fall semester! We will be starting off with a newly published synthesis about local adaptation and the ability to study its genomic basis. The authors review the standing literature and provide suggestions for best practices. This ought to get us off to nice start to the semester. Remember, we have moved the time up to 3:30 PM and now meet either at the Eckert lab (Room 342 in Life Sciences) or at Postbellum. Thanks to Brandon for suggesting this paper. 

Fig. 1: Csillery et al. (2014)
May 13, 2016

This week we will examine patterns of local adaptation at fine spatial scales in European beech. The authors use a candidate gene approach in combination with a multilocus perspective to demonstrate patterns consistent with local adaptation. We are expecting a small group due to a conflict with another VCU event, so bring lots of discussion points. 
Fig. 1: Wu et al. (2016)
April 29, 2016

This week we will tackle the issue of invasion genetics and read a paper about population genetic patterns in gypsy moth (Lymantria dispar). Despite their obvious similarities to conifers that fly, these little buggers are an ideal system with which to test hypotheses about the role of genetic and adaptation in invasion. Thanks to Trevor for suggesting this one. 
April 22, 2016
Fig. 1: Kierepka & Latch (2016)

Go Wisconsin badgers! Not the basketball team, but actual furry, little animals will be our subject this week. Kierepka and Latch (2016) use a landscape genetic approach to assess the influence of landscape heterogeneity on population structure. Although the question is standard fare for landscape "geneticists", the approach by the authors is more rigorous than usual (except for the oh so popular use of "individual-based studies", which implies that I have totally missed out on those real life population blobs living out on landscapes). Thanks to Jane for suggesting this one!