Data from: Predator-induced phenotypic plasticity within- and across-generations: a challenge for theory?Matthew R. Walsh, Kelsey Biles, Frank Cooley & Stephan B. Munch
Much work has shown that the environment can induce non-genetic changes in phenotype that span multiple generations. Theory predicts that predictable environmental variation selects for both increased within- and across-generation responses. Yet, to the best of our knowledge, there are no empirical tests of this prediction. We explored the relationship between within- versus across-generation plasticity by evaluating the influence of predator cues on the life-history traits of Daphnia ambigua. We measured the duration of predator-induced...
Data from: Does variation in the intensity and duration of predation drive evolutionary changes in senescence?Matthew R. Walsh, Deirdre Whittington & Melissa J. Walsh
1. The evolutionary theory of senescence predicts that increased rates of extrinsic mortality select for faster declines in fertility and survival with age. One predicted mechanism is that increased mortality favors alleles that enhance fitness early in life at the expense of survival or reproduction later in life (antagonistic pleiotropy). 2. We tested these predictions in natural populations of Daphnia ambigua from lakes that vary in the severity and duration of fish predation. Daphnia are...
Data from: Diversification and asymmetrical gene flow across time and space: lineage sorting and hybridization in polytypic barking frogsJeffrey W. Streicher, Thomas J. Devitt, Caren S. Goldberg, John H. Malone, Heath Blackmon & Matthew K. Fujita
Young species complexes that are widespread across ecologically disparate regions offer important insights into the process of speciation because of their relevance to how local adaptation and gene flow influence diversification. We used mitochondrial DNA and up to 28,152 genome-wide SNPs from polytypic barking frogs (Craugastor augusti complex) to infer phylogenetic relationships and test for the signature of introgressive hybridization among diverging lineages. Our phylogenetic reconstructions suggest (1) a rapid Pliocene-Pleistocene radiation that produced at...
Data from: Two low coverage bird genomes and a comparison of reference-guided versus de novo genome assembliesDaren C. Card, Drew R. Schield, Jacobo Reyes-Velasco, Matthew K. Fujita, Audra L. Andrew, Sara J. Oyler-McCance, Jennifer A. Fike, Diana F. Tomback, Robert P. Ruggiero & Todd A. Castoe
As a greater number and diversity of high-quality vertebrate reference genomes become available, it is increasingly feasible to use these references to guide new draft assemblies for related species. Reference-guided assembly approaches may substantially increase the contiguity and completeness of a new genome using only low levels of genome coverage that might otherwise be insufficient for de novo genome assembly. We used low-coverage (~3.5–5.5x) Illumina paired-end sequencing to assemble draft genomes of two bird species...
Data from: Genetic consequences of post-glacial range expansion in two codistributed rodents (genus Dipodomys) depend on ecology and genetic locusTereza Jezkova, Brett R. Riddle, Daren C. Card, Drew R. Schield, Mallory E. Eckstut & Todd A. Castoe
How does range expansion affect genetic diversity in species with different ecologies, and do different types of genetic markers lead to different conclusions? We addressed these questions by assessing the genetic consequences of post-glacial range expansion using mitochondrial DNA (mtDNA) and nuclear restriction site associated DNA (RAD) sequencing in two congeneric and co-distributed rodents with different ecological characteristics: the desert kangaroo rat (Dipodomys deserti), a sand specialist, and the Merriam's kangaroo rat (D. merriami), a...
Data from: Species delimitation using genome-wide SNP dataAdam D. Leaché, Vladimir N. Minin, Remco R. Bouckaert & Matthew K. Fujita
The multispecies coalescent has provided important progress for evolutionary inferences, including increasing the statistical rigor and objectivity of comparisons among competing species delimitation models. However, Bayesian species delimitation methods typically require brute force integration over gene trees via Markov chain Monte Carlo (MCMC), which introduces a large computation burden and precludes their application to genomic-scale data. Here we combine a recently introduced dynamic programming algorithm for estimating species trees that bypasses MCMC integration over gene...
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National Marine Fisheries Service1
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University of Nevada, Las Vegas1