Publications by EEOB faculty July 1 - July 31

July 27, 2018
eeob 2016

Genome-specific histories of divergence and introgression between an allopolyploid unisexual salamander lineage and two ancestral sexual species

Robert D. Denton  Ariadna E. Morales  H. Lisle Gibbs. 2018. Evolution 72(8):1689-1700. DOI: 10.1111/evo.13528  

Abstract
Quantifying introgression between sexual species and polyploid lineages traditionally thought to be asexual is an important step in understanding what drives the longevity of putatively asexual groups. Here, we capitalize on three recent innovations—ultraconserved element (UCE) sequencing, bioinformatic techniques for identifying genome‐specific variation in polyploids, and model‐based methods for evaluating historical gene flow—to measure the extent and tempo of introgression over the evolutionary history of an allopolyploid lineage of all‐female salamanders and two ancestral sexual species. Our analyses support a scenario in which the genomes sampled in unisexual salamanders last shared a common ancestor with genomes in their parental species ∼3.4 million years ago, followed by a period of divergence between homologous genomes. Recently, secondary introgression has occurred at different times with each sexual species during the last 500,000 years. Sustained introgression of sexual genomes into the unisexual lineage is the defining characteristic of their reproductive mode, but this study provides the first evidence that unisexual genomes have undergone long periods of divergence without introgression. Unlike other sperm‐dependent taxa in which introgression is rare, the alternating periods of divergence and introgression between unisexual salamanders and their sexual relatives could explain why these salamanders are among the oldest described unisexual animals.

Local prey community composition and genetic distance predict venom divergence among populations of the northern Pacific rattlesnake (Crotalus oreganus)

Matthew L. Holding  Mark J. Margres  Darin R. Rokyta  H. Lisle Gibbs. 2018. Evolutionary Biology. doi: 10.1111/jeb.13347

Abstract

Identifying the environmental correlates of divergence in functional traits between populations can provide insights into the evolutionary mechanisms that generate local adaptation. Here, we assess patterns of population differentiation in expressed venom proteins in Northern Pacific rattlesnakes (Crotalus oreganus) from 13 locations across California. We evaluate the relative importance of major biotic (prey species community composition), abiotic (temperature, precipitation and elevation) and genetic factors (genetic distance based on RAD‐seq loci) as correlates of population divergence in venom phenotypes. We found that over half of the variation in venom composition is associated with among‐population differentiation for genetic and environmental variables and that this variation occurred along axes defining previously observed functional trade‐offs between venom proteins that have neurotoxic, myotoxic and hemorrhagic effects. Surprisingly, genetic differentiation among populations was the best predictor of venom divergence, accounting for 46% of overall variation, whereas differences in prey community composition and abiotic factors explained smaller amounts of variation (23% and 19%, respectively). The association between genetic differentiation and venom composition could be due to an isolation‐by‐distance effect or, more likely, an isolation‐by‐environment effect where selection against recent migrants is strong, producing a correlation between neutral genetic differentiation and venom differentiation. Our findings suggest that even coarse estimates of prey community composition can be useful in understanding the selection pressures acting on patterns of venom protein expression. Additionally, our results suggest that factors other than adaptation to spatial variation in prey need to be considered when explaining population divergence in venom.


A global analysis of bats using automated comparative phylogeography uncovers a surprising impact of Pleistocene glaciation

Bryan C. Carstens, Ariadna E. Morales, Kathryn Field, Tara A. Pelletier. 2018. Journal of Biogeography. https://doi.org/10.1111/jbi.13382

Abstract
Aim: Our work seeks to understand the global demographical response of bat spe-cies to the climate change that occurred at the Last Glacial Maximum (LGM).
Location: All continents except Antarctica.
Methods: Mitochondrial DNA sequences were sampled from bat species through-out the planet where we could associate a georeferenced sample with a given DNAsequence. Our investigation estimates the historical demographical response usingover 12,000 samples from >300 nominal species of bats. Custom PYTHON and Rscripts were written to aggregate sequence data from GenBank, locality informationfrom GBIF, and to associate these records to individual samples. We conductedapproximate Bayesian computation to calculate the posterior probability of demo-graphical bottleneck and expansion responses to the end of the Pleistocene, andthen collected organismal trait data to identify traits that were associated witheither demographical response. We also used R to estimate current and end-Pleisto-cene species distribution models (SDM) for species where >10 georeferenced sam-ples were available.
Results: Analysis of the genetic data indicate that some temperate insectivoresresponded to the end of the Pleistocene by undergoing a demographical expansion.However, the neotropical family Phyllostomidae experienced the most dramaticresponse, with many of its species undergoing demographical bottlenecks. Largerbats, and those with shorter forewings, were more likely to undergo a demographi-cal bottleneck. In contrast with the results of the genetic data analysis, the auto-mated SDMs all predicted range expansion since the LGM.
Main conclusions: Historical populations of Neotropical bats that rely on Angios-perms for resources (i.e., pollen, nectar, fruit) were negatively influenced by the cli-mate change that occurred at the end of the Pleistocene. Our work highlights theutility of incorporating exploratory trait-based analyses in phylogeography. It servesas an example of automated big data phylogeography, and suggests that repurposed data can lead to new insights about global biodiversity.


High Levels of Glyphosate Resistance in Conyza canadensis from Agricultural and Non-Agricultural Sites in Ohio and Iowa

Zachery T. Beres, Emily E. Ernst, Bruce A. Ackley, Mark M. Loux, Micheal D. K. Owen & Allison A. Snow. 2018.Scientific Reports volume 8, Article number: 10483.

Abstract
Glyphosate is an important herbicide worldwide, but its efficacy has been compromised where weed species have evolved glyphosate resistance. To better understand evolutionary outcomes of continued and strong selection from glyphosate exposure, we characterized variation in resistance in self-pollinating Conyza canadensis (horseweed) in Ohio and Iowa, where glyphosate resistance was first reported in 2002 and 2011, respectively. In 2015, we collected seeds from a total of 74 maternal plants (biotypes) from no-till soybean fields vs. non-agricultural sites in each state, using one representative plant per site. Young plants from each biotype were sprayed with glyphosate rates of 0x, 1x (840 g ae ha−1), 8x, 20x, or 40x. Resistant biotypes with at least 80% survival at each dosage were designated as R1 (1x), R2 (8x), R3 (20x), or R4 (40x). Nearly all Ohio agricultural biotypes were R4, as were 62% of biotypes from the non-agricultural sites. In Iowa, R4 biotypes were clustered in the southeastern soybean fields, where no-till agriculture is more common, and 45% of non-agricultural biotypes were R1–R4. Our results show that resistance levels to glyphosate can be very high (at least 40x) in both states, and that non-agricultural sites likely serve as a refuge for glyphosate-resistant biotypes.