Biology subjects

Myers, E. A.

Publications and source records attributed to Myers, E. A..

5 recordsLinked to original sources

bioRxiv2024

The first complete assembly for a lungless urodelan with a "miniaturized" genome, the Northern Dusky Salamander (Plethodontidae: Desmognathus fuscus)

Salamanders have some of the largest genomes among animals. However, there is a great disparity in total size, ranging from [~]8-120GB depending on the lineage. Species in the lungless genus Desmognathus (Plethodontidae) are among the smallest, with estimated genome sizes of 13-15GB. Salamander genomes have exceptional interest in numerous topics ranging from genome-size evolution, the genetic basis of evolutionary differences in life history, and the physiological basis of regeneration, vision, and immunity. However, their large genomes have limited previous attempts at sequencing and assembly, particularly given the difficulties of mapping extensive repeat regions with short-read data. Here we assemble a draft genome of Desmognathus fuscus using PacBio HiFi reads and generate transcriptomic data from two specimens. The combined assembly resulted in a 16.1GB genome in 19,640 contigs and an N/L50 of 2,455/1.75MB, with the longest contig at 27.9MB. The assembly and transcriptome are nearly complete with 93% of the 5,310 BUSCO tetrapod orthologs identified. Attempts to scaffold these data to the existing Ambystoma genome resulted in only 5.8GB of the D. fuscus genome mapping to this reference. This low success suggests substantial syntenic and sequence divergence across salamanders, which may be the result of significant miniaturization in the Desmognathus genome. Identification and annotation of transposable elements reveals that only 26% of the genome is single copy with 74% corresponding to TEs. The most common class of TE in the genome are LTRs (35% of the total genome) and LINEs ([~]15% of the genome). The relative divergence landscape of these TEs shows an early expansion and slow contraction of LINEs, followed by a quick recent expansion of both LTRs and DNA transposons. This assembly will serve as an important reference for amphibian genomics.

genomics↗

bioRxiv2022

Predictors of genomic diversity within North American squamates

Comparisons of intraspecific genetic diversity across species can reveal the roles of geography, ecology, and life history in shaping biodiversity. The wide availability of mitochondrial DNA (mtDNA) sequences in open-access databases makes this marker practical for conducting analyses across several species in a common framework, but patterns may not be representative of overall species diversity. Here, we gather new and existing mtDNA sequences and genome-wide nuclear data (genotyping-by-sequencing; GBS) for 30 North American squamate species sampled in the Southeastern and Southwestern United States. We estimated mtDNA nucleotide diversity for two mtDNA genes, COI (22 species alignments; average 16 sequences) and cytb (22 species; average 58 sequences), as well as nuclear heterozygosity and nucleotide diversity from GBS data for 118 individuals (30 species; four individuals and 6,820-44,309 loci per species). We showed that nuclear genomic diversity estimates were highly consistent across individuals for some species, while other species showed large differences depending on the locality sampled. Range size was positively correlated with both cytb diversity (Phylogenetically Independent Contrasts: R2 = 0.31, p = 0.007) and GBS diversity (R2 = 0.21; p = 0.006), while other predictors differed across the top models for each dataset. Mitochondrial and nuclear diversity estimates were not correlated within species, although sampling differences in the data available made these datasets difficult to compare. Further study of mtDNA and nuclear diversity sampled across species ranges is needed to evaluate the roles of geography and life history in structuring diversity across a variety of taxonomic groups.

genomics↗

bioRxiv2021

Complex genetic patterns and distribution limits mediated by native congeners of the worldwide invasive red-eared slider turtle

Non-native (invasive) species offer a unique opportunity to study the geographic distribution and range limits of species, wherein the evolutionary change driven by interspecific interactions between native and non-native closely related species is a key component. The red-eared slider turtle, Trachemys scripta elegans (TSE), has been introduced and successfully established worldwide. It can coexist with its native congeners T. cataspila, T. venusta and T. taylori in Mexico. We performed comprehensive fieldwork, executed a battery of genetic analyses and applied a novel species distribution modeling approach to evaluate their historical lineage relationships and contemporary population genetic patterns. Our findings support the historical common ancestry between native TSE and non-native (TSEalien), while also highlighting the genetic differentiation of the exotic lineage. Genetic patterns are associated with their range size/endemism gradient, the microendemic T. taylori showed significant reduced genetic diversity and high differentiation, whereas TSEalien showed the highest diversity and signals of population size expansion. Counter to our expectations, lower naturally occurring distribution overlap and little admixture patterns were found between and its congeners, exhibiting reduced gene flow and clear genetic separation across neighboring species despite having zones of contact. We demonstrate that these native Trachemys species have distinct climatic niche suitability, likely preventing establishment of and displacement by the non-native TSE. Additionally, we found major niche overlap between TSEalien and native species worldwide, supporting our prediction that sites with closer ecological optima to the invasive species have higher establishment risk than those that are closer to the niche-center of the native species.

evolutionary biology↗

bioRxiv2020

Comparative phylogeography reveals how a barrier filters and structures taxa in North American warm deserts

The study of biogeographic barriers have been instrumental in understanding the evolution and distribution of taxa. Now with the increased availability of empirical datasets, it is possible to infer emergent patterns from communities by synthesizing how barriers filter and structure populations across species. We assemble phylogeographic data for a barrier and perform spatially-explicit simulations to quantify temporal and spatial patterns of divergence, the influence of species traits on these patterns, and understand the statistical power of differentiating alternative diversification modes. We incorporate published datasets to examine taxa around the Cochise Filter Barrier, separating the Sonoran and Chihuahuan deserts of North America, to synthesize phylogeographic structuring across the community with respect to organismal functional traits. We then use a simulation and machine learning pipeline to assess the power of phylogeographic model selection. Taxa distributed across the Cochise Filter Barrier show heterogeneous responses to the barrier in levels of gene flow, phylogeographic structure, divergence timing, barrier width, and divergence mechanism. These responses vary concordantly with locomotor and thermoregulatory traits. Many taxa show a Pleistocene population genetic break, often with introgression after divergence. Allopatric isolation and isolation-by-environment are the primary mechanisms purported to structure taxa. Simulations reveal that in spatially-explicit isolation-with-migration models across the barrier, age of divergence, presence of gene flow, and presence of isolation-by-distance can confound the interpretation of evolutionary history and model selection by producing easily-confusable results. By synthesizing phylogeographic data for the Cochise Filter Barrier we show a pattern where barriers interact with species traits to differentiate taxa in communities over millions of years. Identifying the modes of differentiation across the barriers for these taxa remains challenging because commonly invoked demographic models may not be identifiable across a range of likely parameter space.

evolutionary biology↗

bioRxiv2020

Resolving spatial complexities of hybridization in the context of the gray zone of speciation in North American ratsnakes (Pantherophis obsoletus complex)

Inferring the history of divergence between species in a framework that permits the presence of gene flow has been crucial for characterizing the gray zone of speciation, which is the period of time where lineages have diverged but have not yet achieved strict reproductive isolation. However, estimates of both divergence times and rates gene flow often ignore spatial information, for example the formation and shape of hybrid zones. Using population genomic data from the eastern ratsnake complex (Pantherophis obsoletus), we infer phylogeographic groups, gene flow, changes in demography, the timing of divergence, and hybrid zone widths. We examine the spatial context of diversification by linking migration and timing of divergence to the location and widths of hybrid zones. Artificial neural network approaches are applied to understand how landscape features and past climate have influenced population genetic structure among these lineages prior to hybridization. Rates of migration between lineages are associated with the width and shape of hybrid zones. Timing of divergence is not related to migration rate across species pairs and is therefore a poor proxy for inferring position in the gray zone. However, timing of divergence is related to the number of loci weakly introgressing through hybrid zones.

evolutionary biology↗