Testing Species Boundaries in an Ancient Species Complex with Deep Phylogeographic History: GenusXantusia(Squamata: Xantusiidae)

Parsing variance by marker type: Testing biogeographic hypotheses and differential contribution of historical processes to population structure in a desert lizard

A fundamental goal of population genetic studies is to identify historical biogeographic patterns and understand the processes that generate them. However, localized demographic events can skew population genetic inference. Assessing populations with multiple types of genetic markers, each with unique mutation rates and responses to changes in population size, can help to identify potentially confounding population-specific demographic processes. Here, we compared population structure and connectivity inferred from microsatellites and restriction site-associated DNA loci among 17 populations of an arid-specialist lizard, the desert night lizard, Xantusia vigilis, in central California to test among historical processes structuring population genetic diversity. We found that both marker types yielded generally concordant insights into population genetic structure including a major phylogenetic break maintained between two populations separated by less than 10 km, suggesting that either marker type could be used to understand generalized demographic patterns across the region for management purposes. However, we also found that the effects of demography on marker discordance could be used to elucidate population histories and distinguish among competing biogeographic hypotheses. Our results suggest that comparisons of within-population diversity across marker types provide powerful opportunities for leveraging marker discordance, particularly for understanding the creation and maintenance of contact zones among clades.

Thermoregulatory strategies of three reclusive lizards (genus Xantusia) from the Baja California peninsula, Mexico, under current and future microenvironmental temperatures

The thermal quality of the habitat is key for the regulation of body temperature in terrestrial ectotherms and, therefore, permits them to carry out their fundamental biological activities. In thermally heterogeneous environments, ectotherms might follow different behavioral or physiological strategies to maintain their body temperature within biologically adequate boundaries, for which they depend on microhabitat selection. These aspects are, thus, relevant in the context of habitat degradation and land-use change. In this study, we characterized the thermal ecology of three lizard species (genus Xantusia) that differ in microhabitat use along the Baja California peninsula, Mexico. We made three predictions: (1) the three species will follow different thermoregulatory strategies according to habitat thermal quality; (2) the thermal requirements and tolerances of these species will match the environmental or microenvironmental thermal conditions; and (3) due to their habitat and range restriction, the species studied will be highly vulnerable to climate change. Our results indicate the existence of thermoregulatory mechanisms in Xantusia to face thermal heterogeneity, including behavioral thermoregulation by choosing different microhabitats, shifts in activity periods, and adaptation to particular high thermal quality microhabitats. Furthermore, despite their association to specific microhabitats and specialized physiology, the studied species will not be adversely affected by climate change, as the increased microenvironmental temperatures will lead to a higher habitat thermal quality and lower costs of thermoregulation. However, we do not discard other indirect adverse effects of climate change not considered in this study.

Mixed-sex offspring produced via cryptic parthenogenesis in a lizard

Facultative parthenogenesis in vertebrates is believed to be exceptional, and wherever documented, it always led to single-sex progeny with genome-wide homozygosity. We report the first challenge to this paradigm: frequent facultative parthenogenesis in the previously assumed sexually reproducing tropical night lizard Lepidophyma smithii results in offspring of both sexes and preserves heterozygosity in many loci polymorphic in their mothers. Moreover, we documented a mixture of sexually and parthenogenetically produced progeny in a single clutch, which documents how cryptic a facultative parthenogenesis can be. Next, we show that in the studied species, 1) parthenogenetically produced females can further reproduce parthenogenetically, 2) a sexually produced female can reproduce parthenogenetically, 3) a parthenogenetically produced female can reproduce sexually, and 4) a parthenogenetically produced male is fully fertile. We suggest that facultative parthenogenesis should be considered even in vertebrates with frequent males and genetically variable, heterozygous offspring.

Introgression obscures lineage boundaries and phylogeographic history in the western banded gecko, Coleonyx variegatus (Squamata: Eublepharidae)

The geomorphological formation of the Baja California peninsula and the Gulf of California is a principal driver of diversification for the reptiles of North America’s warm deserts. The western banded gecko, Coleonyx variegatus, is distributed throughout the Mojave, Sonoran and Peninsular deserts. In this study we use multilocus sequence data to address deep phylogeographic structure within C. variegatus. Analyses of mtDNA data recover six divergent clades throughout the range of C. variegatus. Topology of the mtDNA gene tree suggests separate origins of peninsular populations with an older lineage in the south and a younger one in the north. In contrast, analyses of multilocus nuclear data provide support for four lineages, corresponding to the subspecies C. v. abbotti, C. v. peninsularis, C. v. sonoriensis and C. v. variegatus. Phylogenetic analyses of the nuclear data recover C. v. abbotti and C. v. peninsularis as a clade, indicating a single origin of the peninsular populations. Discordance between the nuclear and mtDNA data is largely the result of repeated episodes of mtDNA introgression that have obscured both lineage boundaries and biogeographic history. Dating analyses of the combined nuclear and mtDNA data suggest that the peninsular clade diverged from the continental group in the Late Miocene.

Geographical features are the predominant driver of molecular diversification in widely distributed North American whipsnakes

Allopatric divergence following the formation of geographical features has been implicated as a major driver of evolutionary diversification. Widespread species complexes provide opportunities to examine allopatric divergence across varying degrees of isolation in both time and space. In North America, several geographical features may play such a role in diversification, including the Mississippi River, Pecos River, Rocky Mountains, Cochise Filter Barrier, Gulf of California and Isthmus of Tehuantepec. We used thousands of nuclear single nucleotide polymorphisms (SNPs) and mitochondrial DNA from several species of whipsnakes (genera Masticophis and Coluber) distributed across North and Central America to investigate the role that these geographical features have played on lineage divergence. We hypothesize that these features restrict gene flow and separate whipsnakes into diagnosable genomic clusters. We performed genomic clustering and phylogenetic reconstructions at the species and population levels using Bayesian and likelihood analyses and quantified migration levels across geographical features to assess the degree of genetic isolation due to allopatry. Our analyses suggest that (i) major genetic divisions are often consistent with isolation by geographical features, (ii) migration rates between clusters are asymmetrical across major geographical features, and (iii) areas that receive proportionally more migrants possess higher levels of genetic diversity. Collectively, our findings suggest that multiple features of the North American landscape contributed to allopatric divergence in this widely distributed snake group.

Historical Environment Is Reflected in Modern Population Genetics and Biogeography of an Island Endemic Lizard (Xantusia riversiana reticulata)

The restricted distribution and isolation of island endemics often produces unique genetic and phenotypic diversity of conservation interest to management agencies. However, these isolated species, especially those with sensitive life history traits, are at high risk for the adverse effects of genetic drift and habitat degradation by non-native wildlife. Here, we study the population genetic diversity, structure, and stability of a classic “island giant” (Xantusia riversiana, the Island Night Lizard) on San Clemente Island, California following the removal of feral goats. Using DNA microsatellites, we found that this population is reasonably genetically robust despite historical grazing, with similar effective population sizes and genetic diversity metrics across all sampling locations irrespective of habitat type and degree of degradation. However, we also found strong site-specific patterns of genetic variation and low genetic diversity compared to mainland congeners, warranting continued special management as an island endemic. We identify both high and low elevation areas that remain valuable repositories of genetic diversity and provide a case study for other low-dispersal coastal organisms in the face of future climate change.

Convergent evolution of kin-based sociality in a lizard

Studies of social birds and mammals have produced extensive theory regarding the formation and dynamics of kin-based social groups in vertebrates. However, comparing kin dynamics in birds and mammals to social reptiles provides the opportunity to identify selective factors that promote independent origins of kin sociality across vertebrates. We combined a 5-year mark-recapture study with a DNA microsatellite analysis of relatedness in a social lizard (Xantusia vigilis) to examine the formation and stability of kin groups. We found that these lizards are highly sedentary and that groups often form through the delayed dispersal of offspring. Groups containing juveniles had higher relatedness than adult-only groups, as juveniles were commonly found in aggregations with at least one parent and/or sibling. Groups containing nuclear family members were more stable than groups of less-related lizards, as predicted by social theory. We conclude that X. vigilis aggregations conform to patterns of kin sociality observed in avian and mammalian systems and represent an example of convergent evolution in social systems. We suggest that kin-based sociality in this and other lizards may be a by-product of viviparity, which can promote delayed juvenile dispersal by allowing prolonged interaction between a neonate and its mother.

Phylogeography of supralittoral rocky intertidal Ligia isopods in the pacific region from central California to central Mexico

Background

Ligia isopods are widely distributed in the Pacific rocky intertidal shores from central California to central Mexico, including the Gulf of California. Yet, their biological characteristics restrict them to complete their life cycles in a very narrow range of the rocky intertidal supralittoral. Herein, we examine phylogeographic patterns of Ligia isopods from 122 localities between central California and central Mexico. We expect to find high levels of allopatric diversity. In addition, we expect the phylogeographic patterns to show signatures of past vicariant events that occurred in this geologically dynamic region.

Methodology/Principal Findings

We sequenced two mitochondrial genes (Cytochrome Oxidase I and 16S ribosomal DNA). We conducted Maximum Likelihood and Bayesian phylogenetic analyses. We found many divergent clades that, in general, group according to geography. Some of the most striking features of the Ligia phylogeographic pattern include: (1) deep mid-peninsular phylogeographic breaks on the Pacific and Gulf sides of Baja peninsula; (2) within the Gulf lineages, the northern peninsula is most closely related to the northern mainland, while the southern peninsula is most closely related to the central-southern mainland; and, (3) the southernmost portion of the peninsula (Cape Region) is most closely related to the southernmost portion of mainland.

Conclusions/Significance

Our results shed light on the phylogenetic relationships of Ligia populations in the study area. This study probably represents the finest-scale phylogeographic examination for any organism to date in this region. Presence of highly divergent lineages suggests multiple Ligia species exist in this region. The phylogeographic patterns of Ligia in the Gulf of California and Baja peninsula are incongruent with a widely accepted vicariant scenario among phylogeographers, but consistent with aspects of alternative geological hypotheses and phylo- and biogeographic patterns of several other taxa. Our findings contribute to the ongoing debate regarding the geological origin of this important biogeographic region.

Phylogeny, divergence times and species limits of spiny lizards (Sceloporus magister species group) in western North American deserts and Baja California

The broad distribution of the Sceloporus magister species group (squamata: phrynosomatidae) throughout western North America provides an appropriate model for testing biogeographical hypotheses explaining the timing and origins of diversity across mainland deserts and the Baja California Peninsula. We inferred concordant phylogenetic trees describing the higher-level relationships within the magister group using 1.6 kb of mitochondrial DNA (mtDNA) and 1.7 kb of nuclear DNA data. These data provide strong support for the parallel divergence of lineages endemic to the Baja California Peninsula (S. zosteromus and the orcutti complex) in the form of two sequential divergence events at the base of the magister group phylogeny. A relaxed phylogenetic analysis of the mtDNA data using one fossil and one biogeographical constraint provides a chronology of these divergence events and evidence that further diversification within the Baja California clades occurred simultaneously, although patterns of geographical variation and speciation between clades differ. We resolved four major phylogeographical clades within S. magister that (i) provide a novel phylogenetic placement of the Chihuahuan Desert populations sister to the Mojave Desert; (ii) illustrate a mixed history for the Colorado Plateau that includes Mojave and Sonoran Desert components; and (iii) identify an area of overlap between the Mojave and Sonoran Desert clades near Yuma, Arizona. Estimates of bidirectional migration rates among populations of S. magister using four nuclear loci support strong asymmetries in gene flow among the major mtDNA clades. Based on the nonexclusivity of mtDNA haplotypes, nuclear gene flow among populations and wide zones of phenotypic intergradation, S. magister appears to represent a single geographically variable and widespread species.

Delimiting cohesion species: extreme population structuring and the role of ecological interchangeability

Species exhibiting morphological homogeneity and strong population structuring present challenging taxonomic problems: morphology-based approaches infer few species, whereas genetic approaches often indicate more. Morphologically cryptic, yet genetically divergent species groups require alternative approaches to delimiting species that assess adaptive divergence and ecological interchangeability of lineages. We apply such an approach to Promyrmekiaphila, a small genus (three nominal taxa) of trapdoor spiders endemic to northern California to define cohesion species (lineages that are genetically exchangeable and ecologically interchangeable). Genetic exchangeability is evaluated using standard phylogeographical techniques (e.g. nested clade analysis); ecological interchangeability is assessed using two GIS-based approaches. First, climatic values are extracted from layer data for each locality point and utilized in a principal components analysis followed by MANOVA. Second, niche-based distribution models of genetically divergent lineages are created using a maximum-entropy modelling approach; the amount of overlap among lineages is calculated and evaluated against a probability distribution of null overlap. Lineages that have significant amounts of predicted overlap are considered ecologically interchangeable. Based on a synthetic evaluation of ecological interchangeability, geographical concordance, and morphological differentiation, we conclude that Promyrmekiaphila comprises six cohesion species, five of which are cryptic (i.e. undetectable by conventional means).

Multi-locus DNA sequence data reveal a history of deep cryptic vicariance and habitat-driven convergence in the desert night lizardXantusia vigilisspecies complex (Squamata: Xantusiidae)

The lizard genus Xantusia of southwestern North America has received recent attention in relation to delimiting species. Using more than 500 lizards from 156 localities, we further test hypothesized species boundaries and clarify phylogeographical patterns, particularly in regions of potential secondary contact. We sequenced the entire mitochondrial cytochrome b gene for every lizard in the study, plus a second mitochondrial DNA (mtDNA) region and two nuclear introns for subsets of the total sample. Phylogenetic analyses of the mtDNA recover a well-resolved, novel hypothesis for species in the Xantusia vigilis complex. The nuclear DNA (nDNA) data provide independent support for the recognition of X. arizonae, X. bezyi and X. wigginsi. Differences between the respective mtDNA and nDNA topologies result from either the effects of lineage sorting or ancient introgression. Nuclear data confirm the inference that some populations of X. vigilis in northwestern Arizona converged on rock-crevice-dwelling morphology and are not X. arizonae with an introgressed X. vigilis mtDNA genome. The historical independence of ancient cryptic lineages of Xantusia in southern California is also corroborated, though limited introgression is detected. Our proposed biogeographical scenario indicates that diversification of this group was driven by vicariance beginning in the late Miocene. Additionally, Pleistocene climatical changes influenced Xantusia distribution, and the now inhospitable Colorado Desert previously supported night lizard presence. The current taxonomy of the group likely underestimates species diversity within the group, and our results collectively show that while convergence on the rock-crevice-dwelling morphology is one hallmark of Xantusia evolution, morphological stasis is paradoxically another.

Unraveling evolutionary lineages in the limbless fossorial skink genus Acontias (Sauria: Scincidae): are subspecies equivalent systematic units?

Subspecies in the limbless, endemic African fossorial skink genus Acontias constitute ill-defined operational taxonomic units, consequently considerable systematic debate has lingered on the systematic diversity within Acontias. In the present study, the systematic affinities among acontine taxa are explored with the utility of partial sequence data from two mitochondrial gene loci (16S rRNA and cytochrome oxidase subunit 1 (COI)) for all taxa, while two additional loci (12S rRNA, cytochrome b) were used to investigate relationships within the Acontias meleagris complex. Phylogenetic results, derived from the combined analysis, revealed two monophyletic clades. Clade 1 is comprised of small-bodied skinks while clade 2 comprised the medium bodied skinks. Within clade 2 none of the traditionally recognized subspecies formed reciprocally monophyletic groups. Furthermore, constraining the topology and enforcing sister taxa relationships between the assumed subspecies, consistently recovered a topology that was statistically significant worse, indicating that the traditionally designated subspecies groupings probably represent invalid taxonomic units, thus clearly reflecting considerable discord with current taxonomy. The burrowing life style of these lizards has probably led to marked convergent evolution and constrained the development of diagnostic morphological characters among these species. Morphological similarities in color as well as scale architecture within Acontias are labile and highly homoplaseous and do not reflect the evolutionary history of the group. Taxonomic implications of these results are discussed.