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 Eckert, Rivera,  Turbeville, 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 3:30 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.
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! 
April 15, 2016
Fig. 1: Harrison and Larson (2016)

This week we will read an opinion paper/review about genomic patterns of diversity and divergence in hybridization zones. The authors spend some time on carefully thinking about the often observed pattern of "islands of divergence" and what evolutionary processes contribute to the formation and maintenance of these islands. I think this will be a nice conceptual paper to focus discussion on concepts and not necessarily data types, analysis types or statistical models. There is no one to blame for this choice other than me this week. 
April 8, 2016
Fig. 1: Marques et al. (2016)

This week we will read a paper about genomic patterns of diversity and divergence across sympatric and parapatric ecotypes of stickleback fish. The authors document islands of divergence that are apparent in both sympatric and parapatric ecotypes, which suggests they harbor variants experiencing divergent (i.e. habitat-induced) selection. Moreover, these islands of divergence are concentrated in QTLs documented as affecting trait divergence between ecotypes. Even though adult beverages are involved, let us please try to avoid fleshing out the nomenclature of linked sites (i.e. no debate about islands, archipelagos, or continents of divergence, please). Thanks to Brandon for picking this paper. 

April 1, 2016
Fig. 2: McCormack et al. (2010)

This week we will read a paper about niche divergence and speciation. The authors use a set of methods to test whether or not divergence of climate niches was correlated with speciation in Mexican jays. They found that this was not the case, so that a model of ecological speciation for these birds can be rejected. Thanks to Mitra and Connie for inspiring this choice. 

McCormack, J. E. et al. (2010). Does niche divergence accompany allopatric divergence in Aphelocoma jays as predicted under ecological speciation?: Insights from tests with niche models. Evolution 64: 1231-1244.
Fig. 1: Cannon et al. (2016)
March 25, 2016

This week we will read a pair of papers addressing the placement of Xenacoelomorpha within the the tree of life. As clearly argued by the authors this issue once resolved sheds light on the evolution of bilaterian features. With quite a large genomic dataset the authors argue for a sister relationship between Xenacoelomorpha and Nephrozoa, which allowed for inferences about the body plan and morphology of the last common ancestor of all bilaterians. Thanks to Clint for picking these papers. 

March 18, 2016

Fig. 1: Holliday et al. (2016)

This week we will return from the land of the dinosaurs and take up the issue of parallel evolution in Populus. Holliday et al. (2016) use genome-wide to show that clines emerge along similar gradients, but that the architecture of these clines is not necessarily the same and that clustering of adaptive alleles in genomes emerges at short spatial scales. Thanks to Mitra for picking this paper. 

March 4, 2016
Fig. 1: Brusatte & Carr (2016)

What could be better to discuss than the evolutionary history of tyrannosauroid dinosaurs? The authors compile a large dataset and infer a phylogenetic tree for this iconic group of dinosaurs using parsimony and Bayesian methods. They use this phylogeny to clarify recent discrepancies in taxonomy, argue that the evolution of the tyrannosauroid body plan occurred piecemeal, and that the ancestral T. rex may have evolved in Asia (potentially among the ancestral members of the genus Pinus also thought to have evolved there). Maybe we should all watch Jurassic Park prior to this meeting to get in the mood. Thanks to Brandon for picking this paper. 

Fig. 1: Sedghifar et al. (2016)
February 26, 2016

This week we will discuss population structure and what it can reveal about evolutionary processes. Here, the authors  use data sampled from multiple clines, although the data only come from the end points of each cline, to study how the magnitude of genetic differentiation is distributed across the genome of Drosophila simulans. The use of replicated clines allowed the authors to look for genomic regions differentiated in the same way along each cline, thus suggesting that these regions may be evolving non-neutrally. Thanks to Brian for suggesting this paper. 
Fig. 1: Fraisse et al. (2015)
February 19, 2016

This week we will discuss the role of geography in structuring introgression among species and how this influences genome scans for selection. Fraisse et al. (2015) use target enrichment sequencing to study patterns of introgression in species of mussels (think tasty, aquatic conifers that live in shells) with overlapping ranges. They show that localized introgression can create genomic signatures indicative of local selection, so that naive genome scans may be misleading. Oh the complexity of scanning genomes! Time to drown our sorrows. Thanks to Mitra for suggesting this one. 
Fig. 1: Stankowski et al. (2015)
February 12, 2016

This week we will discuss the role of geography in divergence with gene flow and how it affects multitrait adaptation. To do so, however, we will have examine a paper about plants with flowers (orange bush monkey-flower), as opposed to our normal majestic conifers. Barring that issue, Stankowski et al. (2015) use a multidisciplinary approach to show that a sharp cline in floral traits is maintained in the face of gene flow as the result of spatially variable selection. They use this conclusion to discuss how geography influences the evolution of pre-mating isolation. Hold on to your drinks, this floral. 
Fig. 1: Hornoy et al. (2016)
February 5, 2016

This week we will discuss the less exciting topic of white spruce and adaptation to climate. I mean it is difficult to be more exciting than wild sex in zebrafish. Again on a more serious note, Hornoy et al. (2016) use an environmental association approach to study adaptation to climate in white spruce. They claim to have results supporting theoretical predictions about recent adaptation in the face of gene flow. Thanks to Brandon for suggesting this one. 
Fig. 1: Wilson et al. (2014)
January 29, 2016

This week we will discuss the very exciting topic of wild sex in zebra fish. What a nice and wholesome way to start our semester. On a serious note, Wilson et al. (2014) used a RAD approach to study sex-linked polymorphisms in natural strains of zebrafish. Interestingly, sex-specific genotypes often developed into the opposite than predicted sex in natural strains. It is nice to see model organism folks out in nature, but I really wish they would stop it with the use of "strain" to label lineages. I think we should drown our concerns in cheesy tots and beverages. Thanks to Lindsay for picking this one. 
Spring 2016
Twilight on the Baltic Sea in Finland.

Welcome back! We will start meeting for Evolution Friday on January 22, 2016. We hope you all had a wonderful break and are now ready to discuss some science. 

Fig. 2: Li et al. (2015)
December 4, 2015

This week we will discuss genome duplication and conifer genomes. New research suggests that genome duplication, thought not to be present in conifers, actually played an important role in the early evolution of this group of awesome plants. Thanks to Brandon for suggesting this one. 

Li, Z. et al. (2015). Early genome duplications in conifers and other seed plants. Science Advances 1: e1501084.

Fig. 1: Slotte (2014)
November 20, 2015

This week we will discuss linked selection and the patterns it creates in plant genomes. The motivation behind this paper is the observation that genome-wide patterns of polymorphism and divergence for plant species do not often follow patterns expected from the theory of linked selection or those observed in animal species (e.g. Drosophila). Slotte (2014) reviews the evidence for this pattern and then discusses why this pattern may exist, including the idea that rejection of recurrent hitchhiking as prevalent in plant genomes does not translate into a lack of evidence of natural selection affecting genomic variation.

Fig. 1: Dale et al. (2015)
November 13, 2015

This week we will discuss colorful birds and sexual selection in relation to plumage coloration. What could be better to discuss on a Friday afternoon? These little critters even live in trees, which makes them much cooler. In all seriousness, though, the authors of this paper use a suite of analyses to address the question of whether or not plumage decorations in female birds is the outcome of genetic linkage with male plumage or is the outcome of direct selection on the signalling needs of females. Thanks to Abbie for picking this paper. 

Fig. 2: Platt et al. (2015)
November 6, 2015

This week our topic is the role of epigenetics in local adaptation. Platt et al. address this issue using valley oak (Quercus lobata) and show that certain methylation-based markers are consistent with being the targets or linked to the targets undergoing spatially divergent selection. Thanks to Mitra for suggesting this paper. 

Fig. 1: Sanders et al. (2015)
October 30, 2015

This week our topic is the genetic dissection of human male sexual orientation. The authors used standard linkage analyses to discover genetic regions correlating to human male sexual orientation.  The authors discovered two chromosomal regions significantly correlated with male sexual orientation. Thanks to Trevor for suggesting this one.

Fig. 1: Haasl et al. (2015)
October 23, 2015

In celebration of my wonderful wife's birthday, we will read a synthesis paper about genome-wide scans for natural selection. This paper makes the case that genome-wide scans are needed outside of human genetics, but also that such scans need to incorporate genomic context into their analyses. Maybe a few beverages will hep us figure out how that can happen in non-model organisms. 

Fig. 1: Gerke et al. (2015)
October 09, 2015

This week we will read yet another maize paper. In this paper, Gerke et al. address the genomic impacts of genetic drift and natural selection on the performance of hybrids created two highly inbred lines. The authors document strong effects of genetic drift in explaining the reduction in heterozygosity within lines, as well as differentiation between lines. In addition, they document many instances of non-neutral evolution within each lines, most of which are unique. They use this to argue that hybrid performance in maize, at least for these lines, is most consistent with the dominance model of heterosis. 

September 11, 2015
Fig. 1: O'Neil et al. (2014)

Welcome to a new semester! This week we will examine a paper addressing local adaptation and gene expression. We should definitely be able to have a lively discussion about this one. Thanks to Lindsay for suggesting this paper. 

May 15, 2015
Fig. 2: Vallejo-Marin et al. (2015)

This week we will examine the role of polyploidization in speciation. Vallejo-Marin et al. (2015) examine the role of polyploidization in a recent speciation event (i.e. 140 years ago) within Mimulus. They also quantify the genomic effects of such events using next-generation sequencing. Thanks to Chris for the suggestion. 

Fig. 1: Parker et al. (2013)
May 01, 2015

This week we will examine a pair of papers addressing the issue of adaptive convergence at the level of DNA sequences (i.e. adaptive molecular convergence). The pair of papers addresses the question of whether or not genomic data support the adaptive molecular convergence of DNA sequences in echolocating mammals. The debate between the two papers is the choice of an appropriate null model. Good old statistics never seem to go away. 

Fig. 1: Farby and Svenning (2015)
April 17, 2015

Estimation of species dense phylogenetic trees is a difficult process. As the authors of this week's reading highlight, this difficulty is really twofold: (1) too many taxa for efficient computation and (2) too many taxa with little or no data. The authors propose a "novel" method with which to address these concerns and use the estimation of the mammalian phylogeny as a test case. Thanks to Kelsey for choosing this paper. 

April 10, 2015

Fig. 1: Willoughby et al. (2015)
This week we will examine the genetic effects of captive breeding on levels of genetic diversity. The authors use a mixture of empirical data analysis and simulations to address this question for three methods of captive breeding: mean kinship, random mating, and selection for docility. The authors argue that genetic diversity is lost less quickly (for microsatellites and mtDNA at least) for captive breeding programs based on mean kinship. Thanks to Lindsay for suggesting this paper.

Fig. 1: Lamichhaney et al. (2015)
April 03, 2015

This week we will examine evolutionary patterns in Darwin's finches. Lamichhaney et al. (2015) use genome sequencing to describe nucleotide diversity and divergence within these finches, as well as associate this diversity to beak morphology, a major component of fitness for these birds. Thanks to Brandon for picking this paper.

Fig. 1: Levy et al. (2015)
March 27, 2015

This week we will examine how the spectrum of beneficial mutations affects the evolutionary dynamics of populations. The authors use an experimental evolution approach based on Saccharomyces to address this issue. They show that evolution via adaptation can be predictable early on and that stochasticity becomes more important as time progresses. Thanks to Abbie for suggesting this paper. 

Fig. 1: Invergo et al. (2013)
March 20, 2015

This week we will examine patterns of molecular evolution within the phototransduction system. The authors relate patterns of natural selection to network attributes, so that position of a protein within a network of interacting proteins (e.g. Fig. 1) affects the type and strength of natural selection acting on it. Thanks to Kristen for suggesting this paper. 

Fig. 2: Kistler et al. (2015)
March 6, 2015

This week we investigate the use of mitogenomic data to resolve relationships within extant and recently extinct lemurs, as well as to search for genetic correlates of extinction. Thanks to Kelsey for suggesting this paper.

Fig. 1: Cropley et al. (2012)
February 27, 2015

This week we will look at epigenetics and the role of natural selection in affecting epigenetic variability. The authors used isogenic lines of mice to demonstrate that an environmentally induced epigenetic state was heritable and able to be increased in frequency through artificial selection. Relaxation of  selection, moreover, resulted in the rapid loss of this state. According to the authors, this is the first demonstration in mammals of natural selection acting on purely epigenetic variation resulting in cumulative germline effects. Thanks to Lindsay for choosing this paper.

February 20, 2015

Fig. 1: Sousa and Hey (2013)
This week we will look at a review paper addressing the process of speciation when it is accompanied by gene flow. Thanks to Brandon for suggesting this paper. 

February 13, 2015
Fig. 1: Lanier and Knowles (2015)

Inference of species level phylogenies is much benefited from the use of statistical methods addressing evolutionary processes producing discordance between gene and species trees. This week we will read a paper addressing the use of these methods in deeper time. The novelty here is that much of the discordance between gene and species trees is expected to be on timescales around 4Ne, where Ne is the effective population size, generations, whereas the relationships here likely exceed this expectation by quite a lot in some cases. 

Fig. 1: Gibson and Fuentes (2014).
February 06, 2015

Parasitism and sex is a great topic for a Friday afternoon discussion. Specifically, we will read a paper addressing the relationship between the rate of outcrossing and parasitism using the phylum Nematoda as a model. The authors take a phylogenetic approach to demonstrate that selfing and asexuality are significantly less likely to evolve in parasitic lineages relative to free living lineages. 

Fig. 1: Renaut et al. (2013).
January 30, 2015

Genomic islands of divergence among species is a mouthful of a phrase to process both verbally and mentally. This week we will read an investigation illustrating that these islands are related primarily to reduced levels of recombination suggesting that genomic architecture plays an important role in structuring adaptive divergence.