Top 10 Biorxiv Papers Today in Evolutionary Biology


2.016 Mikeys
#1. Increased genetic marker density reveals high levels of admixture between red deer and introduced sika in Kintyre, Scotland
S. Eryn McFarlane, Darren C Hunter, Helen V Senn, Stephanie L Smith, Rebecca Holland, Jisca Huisman, Josephine M Pemberton
Hybridization is a natural process at species range boundaries, but increasing numbers of species are experiencing it due to human intervention. In such cases of anthropogenic hybridization, subsequent introgression can threaten the survival of native species. To date many such systems have been studied with too few genetic markers to assess the level of threat resulting from advanced backcrossing. Here we use 44,999 single nucleotide polymorphisms and the ADMIXTURE program to study two areas of Scotland where a panel of 22 diagnostic microsatellites previously identified introgression between native red deer (Cervus elaphus) and introduced Japanese sika (Cervus nippon). In Kintyre we reclassify 26% deer from the pure species categories to the hybrid category whereas in the NW Highlands we only reclassify 2%. As expected, the reclassified individuals are mostly advanced backcrosses. We also investigate the ability of marker panels selected on different posterior allele frequency criteria to find hybrids assigned by the full marker...
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biorxivpreprint: Increased genetic marker density reveals high levels of admixture between red deer and introduced sika in Kintyre, Scotland https://t.co/6dPOY4OOWh #bioRxiv
biorxiv_evobio: Increased genetic marker density reveals high levels of admixture between red deer and introduced sika in Kintyre, Scotland https://t.co/lroWMrxTdo #biorxiv_evobio
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Sample Sizes : None.
Authors: 7
Total Words: 7786
Unqiue Words: 2279

2.008 Mikeys
#2. Genetic structure of prey populations underlies the geographic mosaic of arms race coevolution
Michael Hague, Amber Stokes, Chris Feldman, Edmund Brodie, Edmund Brodie
Reciprocal adaptation is the hallmark of arms race coevolution, but the symmetry of evolutionary change in each species is often untested even in the best-studied battles between natural enemies. We tested whether prey and predator exhibit a symmetrical pattern of local co-adaptation in the classic example of a geographic mosaic of coevolution between toxic newts ( Taricha granulosa ) and resistant garter snakes ( Thamnophis sirtalis ). Contrary to conventional wisdom, landscape variation in the newt toxin TTX is best predicted by neutral population divergence and not predator resistance, whereas snake resistance is clearly explained by prey toxin levels. Prey populations structure variation in levels of TTX, which in turn structures selection on predators—implying that neutral processes including gene flow, rather than reciprocal adaptation, are the primary source of variation across the coevolutionary mosaic.
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biorxivpreprint: Genetic structure of prey populations underlies the geographic mosaic of arms race coevolution https://t.co/aVZydXYwYi #bioRxiv
biorxiv_evobio: Genetic structure of prey populations underlies the geographic mosaic of arms race coevolution https://t.co/RmGzZoogBz #biorxiv_evobio
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Sample Sizes : [138, 169]
Authors: 5
Total Words: 6325
Unqiue Words: 2388

2.008 Mikeys
#3. The role of genetic constraints and social environment in explaining female extra-pair mating
Daiping Wang, Wolfgang Forstmeier, Katrin Martin, Alastair Wilson, Bart Kempenaers
Why females of socially monogamous species copulate with males other than their partner has been a long-standing, unresolved puzzle. We previously reported that female promiscuity appears to be a genetic corollary of male promiscuity (intersexual pleiotropy hypothesis). Here we put this earlier finding to a critical test using the same population of zebra finches Taeniopygia guttata . After three generations of artificial selection on male courtship rate, a correlate of extra-pair mating, we assess whether female promiscuity changed by indirect selection and we re-examine the crucial genetic correlations. Our new analyses with substantially increased statistical power clearly reject the hypothesis that male and female promiscuity are genetically homologous traits. Our study highlights that individual females show low repeatability in extra-pair mating behavior across different social environments. This emphasizes the potential importance of pair bond strength and the availability of favored extra-pair males as factors explaining...
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razibkhan: The role of genetic constraints and social environment in explaining female extra-pair mating https://t.co/X85Ih7JBOf #genetics #evolution
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Sample Sizes : None.
Authors: 5
Total Words: 11407
Unqiue Words: 3329

2.004 Mikeys
#4. Population divergence time estimation using individual lineage label switching
Peter Beerli, Haleh Ashki, Somayeh Mashayekhi, Michael Palczewski
Divergence time estimation from multilocus genetic data has become common in population genetics and phylogenetics. We present a new Bayes inference method that treats the divergence time as a random variable. The divergence time is calculated from an assembly of splitting events on individual lineages in a genealogy. The waiting time for such a splitting event is drawn from a hazard function of the truncated normal distribution. This allows easy integration into the standard coalescence framework used in programs such as MIGRATE. We explore the accuracy of the new inference method with simulated population splittings over a wide range of divergence time values and with a dataset of the Zika virus; the geographic analyses of the expansion of the pathogen follows a trajectory from Africa to Asia to America, corroborating analyses based only on the dates of incidences. Evaluations of simple divergence models show high accuracy, whereas the accuracy of the results of isolation with migration (IM) models depend on the magnitude of the...
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razoralign: Population divergence time estimation using individual lineage label switching https://t.co/H0Oyqw7B6X
Github

Repository for python converter that takes a MIGRATE data file and converts it to other data-formats

Repository: dataconverters
User: pbeerli
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Subscribers: 1
Forks: 0
Open Issues: 0
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Sample Sizes : [1000]
Authors: 4
Total Words: 10288
Unqiue Words: 2301

2.003 Mikeys
#5. Estimating Diversity Through Time using Molecular Phylogenies: Old and Species-Poor Frog Families are the Remnants of a Diverse Past
Olivier Billaud, Daniel Moen, Todd Parsons, Hélène Morlon
Estimating how the number of species in a given group varied in the deep past is of key interest to evolutionary biologists. However, current phylogenetic approaches forobtaining such estimates have limitations, such as providing unrealistic diversity estimates at the origin of the group. Here we develop a robust probabilistic approach for estimating Diversity-Through-Time (DTT) curves and uncertainty around these estimates from phylogenetic data. We show with simulations that under various realistic scenarios of diversifcation, this approach performs better than previously proposed approaches. We also characterize the effect of tree size and undersampling on the performance of the approach. We apply our method to understand patterns of species diversity in anurans (frogs and toads). We found that Archaeobatrachia - a species-poor group of old frog clades often found in temperate regions - formerly had much higher diversity and net diversification rate, but the group declined in diversity as younger, nested clades diversified....
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razibkhan: Estimating Diversity Through Time using Molecular Phylogenies: Old and Species-Poor Frog Families are the Remnants of a Diverse Past https://t.co/0SmcU6dzkk #evolution
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Authors: 4
Total Words: 10502
Unqiue Words: 2629

2.002 Mikeys
#6. A Divide-and-Conquer Method for Scalable Phylogenetic Network Inference from Multi-locus Data
Jiafan Zhu, Xinhao Liu, Huw Ogilvie, Luay Nakhleh
Reticulate evolutionary histories, such as those arising in the presence of hybridization, are best modeled as phylogenetic networks. Recently developed methods allow for statistical inference of phylogenetic networks while also accounting for other processes, such as incomplete lineage sorting (ILS). However, these methods can only handle a small number of loci from a handful of genomes. In this paper, we introduce a novel two-step method for scalable inference of phylogenetic networks from the sequence alignments of multiple, unlinked loci. The method infers networks on subproblems and then merges them into a network on the full set of taxa. To reduce the number of trinets to infer, we formulate a Hitting Set version of the problem of finding a small number of subsets, and implement a simple heuristic to solve it. We studied their performance, in terms of both running time and accuracy, on simulated as well as on biological data sets. The two-step method accurately infers phylogenetic networks at a scale that is infeasible with...
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razoralign: A Divide-and-Conquer Method for Scalable Phylogenetic Network Inference from Multi-locus Data https://t.co/pTbrYYOzOx
anacatarinaas: RT @biorxivpreprint: A Divide-and-Conquer Method for Scalable Phylogenetic Network Inference from Multi-locus Data https://t.co/Ke6hdyW3kF…
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Authors: 4
Total Words: 8971
Unqiue Words: 2018

2.002 Mikeys
#7. Estimating and accounting for genotyping errors in RAD-seq experiments
Luisa Bresadola, Vivian Link, Alex Buerkle, Christian Lexer, Daniel Wegmann
In non-model organisms, evolutionary questions are frequently addressed using reduced representation sequencing techniques due to their relatively low cost, ease of use, and because they do not require genomic resources such as a reference genome. However, evidence is accumulating that many such techniques may be affected by specific biases, questioning the accuracy of obtained genotypes, and as a consequence, their usefulness in evolutionary studies. Here we introduce three strategies to assess genotyping error rates in such data: through the comparison with high quality genotypes obtained with a different technique, from independent replicates of some samples, or from a population sample when assuming Hardy-Weinberg equilibrium. Applying these strategies to data obtained with Restriction site Associated DNA sequencing (RAD-seq), arguably the most popular reduced representation sequencing technique, revealed per-allele genotyping error rates that were much higher than sequencing error rates, particularly at heterozygous sites...
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Dr_Stoat: RT @biorxivpreprint: Estimating and accounting for genotyping errors in RAD-seq experiments https://t.co/UdB2god8OZ #bioRxiv
fuffyfoster: RT @biorxivpreprint: Estimating and accounting for genotyping errors in RAD-seq experiments https://t.co/UdB2god8OZ #bioRxiv
QuentinREvo: RT @biorxiv_evobio: Estimating and accounting for genotyping errors in RAD-seq experiments https://t.co/0CaWUYWPDu #biorxiv_evobio
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Sample Sizes : None.
Authors: 5
Total Words: 9047
Unqiue Words: 2610

1.998 Mikeys
#8. A phenotypically plastic magic trait promoting reproductive isolation in sticklebacks?
Monica Garduno-Paz, Felicity Huntingford, Colin Adams
This study identifies one possible mechanism whereby gene flow is interrupted in populations undergoing evolutionary divergence in sympatry; this is an important issue in evolutionary biology that remains poorly understood. Variation in trophic morphology was induced in three-spined stickleback by exposing them from an early age either to large benthic or to small pelagic prey. At sexual maturity, females given a choice between two breeding males, showed positive assortative mate choice for males raised on the same diet as themselves. The data indicate that this was mediated through a preference for males with trophic morphology similar to that of fish with which the females were familiar (from their pre-testing holding tanks). This study has shown for the first time that expression of a plastic trait induced at an early age not only results in specialisation for local foraging regimes but can also play a significant role in mate choice. This is equivalent to an environmentally induced, plastic version of the magic traits that...
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salazarbiol: RT @biorxiv_evobio: A phenotypically plastic magic trait promoting reproductive isolation in sticklebacks? https://t.co/f5CeaB7nua #biorxi…
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Sample Sizes : [7]
Authors: 3
Total Words: 5351
Unqiue Words: 1851

1.997 Mikeys
#9. Morphological variation in Blommersia pelvic shape coincides with muscular architecture and parallels genus phylogenetic evolution
Javier H. Santos-Santos, Mireia Guinovart-Castan, David Vieites
Mantellids are a hyperdiverse group of frogs endemic to Madagascar, showing a large variation in morphology and ecological specialization that parallels their phylogenetic diversification. Among them, the genus Blommersia comprises several small species of small to miniature frogs, two of which occur in syntopy on the Comorian archipelago, which was colonized by their ancestor several millions of years ago in an event of transoceanic dispersal from Madagascar. They have evolved in isolation, which has supposed an evolutionary experiment of morphological and genetic divergence without competition. In mantellids, as well as in other amphibians, body size is correlated with dispersal capabilities and these may have allowed the colonization of new habitats in parallel to morphological divergence. Consequently, we hypothesized that variation in the Blommersia musculoskeletal anatomy implicated in locomotor performance would reflect potential differences between species in accordance to their diversification into different ecological...
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Authors: 3
Total Words: 9737
Unqiue Words: 2746

1.996 Mikeys
#10. Genomic landscape of the global oak phylogeny
Andrew L Hipp, Paul S Manos, Marlene Hahn, Michael Avishai, Cathérine Bodénès, Jeannine Cavender-Bares, Andrew Crowl, Min Deng, Thomas Denk, Sorel Fitz-Gibbon, Oliver Gailing, M. Socorro González-Elizondo, Antonio González-RodrÍguez, Guido W Grimm, Xiaolong Jiang, Antoine Kremer, Isabelle Lesur, John D McVay, Christophe Plomion, Hernando RodrÍguez-Correa, Ernst-Detlef Schulze, Marco C Simeone, Victoria L. Sork, Susana Valencia-Avalos
The tree of life is highly reticulate, with the history of population divergence buried amongst phylogenies deriving from introgression and lineage sorting. In this study, we test the hypothesis that there are regions of the oak ( Quercus , Fagaceae) genome that are broadly informative about phylogeny and investigate global patterns of oak diversity. We utilize fossil data and restriction-site associated DNA sequencing (RAD-seq) for 632 individuals representing ca. 250 oak species to infer a time-calibrated phylogeny of the world's oaks. We use reversible-jump MCMC to reconstruct shifts in lineage diversification rates, accounting for among-clade sampling biases. We then map the > 20,000 RAD-seq loci back to a recently published oak genome and investigate genomic distribution of introgression and phylogenetic support across the phylogeny. Oak lineages have diversified among geographic regions, followed by ecological divergence within regions, in the Americas and Eurasia. Roughly 60% of oak diversity traces back to four clades that...
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Authors: 24
Total Words: 18170
Unqiue Words: 5163

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