Assessing models of speciation under different biogeographic scenarios; an empirical study using multi-locus and RNA-seq analyses

Divergence in Regulatory Regions and Gene Duplications May Underlie Chronobiological Adaptation in Desert Tortoises

Many cellular processes and organismal behaviours are time-dependent, and asynchrony of these phenomena can facilitate speciation through reinforcement mechanisms. The Mojave and Sonoran desert tortoises (Gopherus agassizii and G. morafkai respectively) reside in adjoining deserts with distinct seasonal rainfall patterns and they exhibit asynchronous winter brumation and reproductive behaviours. We used whole genome sequencing of 21 individuals from the two tortoise species and an outgroup to understand genes potentially underlying these characteristics. Genes within the most diverged 1% of the genome (FST ≥ 0.63) with putatively functional variation showed extensive divergence in regulatory elements, particularly promoter regions. Such genes related to UV nucleotide excision repair, mitonuclear and homeostasis functions. Genes mediating chronobiological (cell cycle, circadian and circannual) processes were also among the most highly diverged regions (e.g., XPA and ZFHX3). Putative promoter variants had significant enrichment of genes related to regulatory machinery (ARC-Mediator complex), suggesting that transcriptional cascades driven by regulatory divergence may underlie the behavioural differences between these species, leading to asynchrony-based prezygotic isolation. Further investigation revealed extensive expansion of respiratory and intestinal mucins (MUC5B and MUC5AC) within Gopherus, particularly G. morafkai. This expansion could be a xeric-adaptation to water retention and/or contribute to differential Mycoplasma agassizii infection rates between the two species, as mucins help clear inhaled dust and bacterial. Overall, results highlight the diverse array of genetic changes underlying divergence, adaptation and reinforcement during speciation.

Aposematic color polymorphism is a poor indicator of species boundaries in North American Paranthrene (Lepidoptera: Sesiidae) as evidenced by a multi-gene phylogeny

Color polymorphism among animal species can influence speciation. Factors such as natural and sexual selection, genetic drift and gene flow contribute to the maintenance of color polymorphism within the species or spur speciation. The evolutionary and ecological mechanisms for color polymorphism are taxon specific and only a few species have been studied. A phylogeny provides an evolutionary framework to understanding the association between color polymorphism and species. Paranthrene species are day flying aposematic moths that mimic wasps in both appearance and behavior. The genus has several polymorphic species and some color forms were originally described as species. Paranthrene presents the opportunity to test for an association between color polymorphism and species boundaries. We reconstructed a phylogeny using DNA sequence from COI, EF-1alpha, and Wingless genes from 67 specimens representing all North American Paranthrene species, nine color variants, and two outgroups. Parsimony and Bayesian analyses generally agreed in topology and support values. Paranthrene simulans (Grote, 1881) was polyphyletic, and monophyly of P. pellucida Greenfield and Karandinos, 1979 was not recovered. Paranthrene robiniae Hy. Edwards, 1880 was polyphyletic and genitalic and genetic differences among the three clades supported the recognition of two new pseudocryptic species, Paranthrene oasis Smith, Taft and, Cognato, new species and Paranthrene gilaensis Smith, Taft and, Cognato, new species. Paranthrene color variants did not overwhelming associate with species boundaries. Of the nine color forms we examined, only two were monophyletic, had DNA sequence divergence comparable to other species, and associated with species diagnostic morphology. It is likely that genetic drift and allopatric isolation explains the fixation of color variants with species. The mechanisms maintaining color polymorphisms within Paranthrene species will remain unknown until experimentation concerning the degree of aposematic protection in reference to wasp models is conducted.

Genome Evolution and the Future of Phylogenomics of Non-Avian Reptiles

Non-avian reptiles comprise a large proportion of amniote vertebrate diversity, with squamate reptiles-lizards and snakes-recently overtaking birds as the most species-rich tetrapod radiation. Despite displaying an extraordinary diversity of phenotypic and genomic traits, genomic resources in non-avian reptiles have accumulated more slowly than they have in mammals and birds, the remaining amniotes. Here we review the remarkable natural history of non-avian reptiles, with a focus on the physical traits, genomic characteristics, and sequence compositional patterns that comprise key axes of variation across amniotes. We argue that the high evolutionary diversity of non-avian reptiles can fuel a new generation of whole-genome phylogenomic analyses. A survey of phylogenetic investigations in non-avian reptiles shows that sequence capture-based approaches are the most commonly used, with studies of markers known as ultraconserved elements (UCEs) especially well represented. However, many other types of markers exist and are increasingly being mined from genome assemblies in silico, including some with greater information potential than UCEs for certain investigations. We discuss the importance of high-quality genomic resources and methods for bioinformatically extracting a range of marker sets from genome assemblies. Finally, we encourage herpetologists working in genomics, genetics, evolutionary biology, and other fields to work collectively towards building genomic resources for non-avian reptiles, especially squamates, that rival those already in place for mammals and birds. Overall, the development of this cross-amniote phylogenomic tree of life will contribute to illuminate interesting dimensions of biodiversity across non-avian reptiles and broader amniotes.

Using Genomic Data to Infer Historic Population Dynamics of Nonmodel Organisms

Genome sequence data are now being routinely obtained from many nonmodel organisms. These data contain a wealth of information about the demographic history of the populations from which they originate. Many sophisticated statistical inference procedures have been developed to infer the demographic history of populations from this type of genomic data. In this review, we discuss the different statistical methods available for inference of demography, providing an overview of the underlying theory and logic behind each approach. We also discuss the types of data required and the pros and cons of each method. We then discuss how these methods have been applied to a variety of nonmodel organisms. We conclude by presenting some recommendations for researchers looking to use genomic data to infer demographic history.

The Agassiz's desert tortoise genome provides a resource for the conservation of a threatened species

Agassiz's desert tortoise (Gopherus agassizii) is a long-lived species native to the Mojave Desert and is listed as threatened under the US Endangered Species Act. To aid conservation efforts for preserving the genetic diversity of this species, we generated a whole genome reference sequence with an annotation based on deep transcriptome sequences of adult skeletal muscle, lung, brain, and blood. The draft genome assembly for G. agassizii has a scaffold N50 length of 252 kbp and a total length of 2.4 Gbp. Genome annotation reveals 20,172 protein-coding genes in the G. agassizii assembly, and that gene structure is more similar to chicken than other turtles. We provide a series of comparative analyses demonstrating (1) that turtles are among the slowest-evolving genome-enabled reptiles, (2) amino acid changes in genes controlling desert tortoise traits such as shell development, longevity and osmoregulation, and (3) fixed variants across the Gopherus species complex in genes related to desert adaptations, including circadian rhythm and innate immune response. This G. agassizii genome reference and annotation is the first such resource for any tortoise, and will serve as a foundation for future analysis of the genetic basis of adaptations to the desert environment, allow for investigation into genomic factors affecting tortoise health, disease and longevity, and serve as a valuable resource for additional studies in this species complex.

The desert tortoise trichotomy: Mexico hosts a third, new sister-species of tortoise in the Gopherus morafkai-G. agassizii group

Desert tortoises (Testudines; Testudinidae; Gopherusagassizii group) have an extensive distribution throughout the Mojave, Colorado, and Sonoran desert regions. Not surprisingly, they exhibit a tremendous amount of ecological, behavioral, morphological and genetic variation. Gopherusagassizii was considered a single species for almost 150 years but recently the species was split into the nominate form and Morafka’s desert tortoise, Gopherusmorafkai, the latter occurring south and east of the Colorado River. Whereas a large body of literature focuses on tortoises in the United States, a dearth of investigations exists for Mexican animals. Notwithstanding, Mexican populations of desert tortoises in the southern part of the range of Gopherusmorafkai are distinct, particularly where the tortoises occur in tropical thornscrub and tropical deciduous forest. Recent studies have shed light on the ecology, morphology and genetics of these southern ‘desert’ tortoises. All evidence warrants recognition of this clade as a distinctive taxon and herein we describe it as Gopherusevgoodeisp. n. The description of the new species significantly reduces and limits the distribution of Gopherusmorafkai to desertscrub habitat only. By contrast, Gopherusevgoodeisp. n. occurs in thornscrub and tropical deciduous forests only and this leaves it with the smallest range of the three sister species. We present conservation implications for the newly described Gopherusevgoodei, which already faces impending threats.