Robert W. Bryson

ELUCIDATION OF CRYPTIC DIVERSITY IN A WIDESPREAD NEARCTIC TREEFROG REVEALS EPISODES OF MITOCHONDRIAL GENE CAPTURE AS FROGS DIVERSIFIED ACROSS A DYNAMIC LANDSCAPE

We investigate the evolutionary history of the wide‐ranging Nearctic treefrog Hyla arenicolor through the integration of extensive range‐wide sampling, phylogenetic analyses of multilocus genetic data, and divergence dating. Previous phylogeographic studies of this frog documented a potential signature of introgressive hybridization from an ecologically and morphologically divergent sister species. Based on our Bayesian phylogenetic analyses of mitochondrial DNA, we inferred strong phylogeographic structure in H. arenicolor as indicated by seven well‐supported clades, five of which correspond to well‐defined biogeographic regions. Clades from the Balsas Basin and southwestern Central Mexican Plateau in Mexico, and the Grand Canyon of Arizona, group with the morphologically, behaviorally, and ecologically divergent mountain treefrogs in the H. eximia group, rendering H. arenicolor as paraphyletic. The phylogenetic position of at least two of these three H. arenicolor clades within the H. eximia group, however, is most likely the result of several episodes of introgressive hybridization and subsequent mitochondrial gene capture separated in time and space, as supported by evidence from the nuclear genes. Hyla arenicolor from the Balsas Basin appear to be deeply divergent from other H. arenicolor and represent a distinctly different species. Results suggests that introgressive hybridization events, both ancient and contemporary, coupled with late Neogene vicariance and Pleistocene climate‐driven range shifts, have all played a role in the historical diversification of H. arenicolor.

Relative roles of Neogene vicariance and Quaternary climate change on the historical diversification of bunchgrass lizards (Sceloporus scalaris group) in Mexico.

Neogene vicariance during the Miocene and Pliocene and Quaternary climate change have synergistically driven diversification in Mexican highland taxa. We investigated the impacts of these processes on genetic diversification in the widely distributed bunchgrass lizards in the Sceloporus scalaris group. We searched for correlations between timing in diversification and timing of (1) a period of marked volcanism across the Trans-Mexican Volcanic Belt in central Mexico 3-7.5million years ago (Ma) and (2) a transition to larger glacial-interglacial cycles during the mid-Pleistocene. From our phylogenetic analyses of mitochondrial DNA we identified two major clades that contained 13 strongly supported lineages. One clade contained lineages from the two northern sierras of Mexico, and the other clade included lineages associated with the Trans-Mexican Volcanic Belt and Central Mexican Plateau. Results provided support for Neogene divergences within the S. scalaris group in response to uplift of the Trans-Mexican Volcanic Belt, a pattern observed in several co-distributed taxa, and suggested that Quaternary climate change likely had little effect on diversification between lineages. Uplift of the Trans-Mexican Volcanic Belt during specific time periods appears to have strongly impacted diversification in Mexican highland taxa.

An asymmetry in niche conservatism contributes to the latitudinal species diversity gradient in New World vertebrates

The Tropical Niche Conservatism hypothesis is a leading explanation for why biodiversity increases towards the equator. The model suggests that most lineages have tropical origins, with few dispersing into temperate regions. However, biotas are comprised of lineages with differing geographical origins, thus it is unclear whether lineages that originated on different continents will exhibit similar patterns of niche conservatism. Here, we summarised biogeographical patterns of New World vertebrates and compared species diversity patterns between families that originated in North and South America. Overall, families with southern origins exhibit niche conservatism with many lineages restricted to the Neotropics, whereas many northern-origin families are distributed across the Neotropics and the Nearctic. Consequently, northern lineages have contributed to high tropical biodiversity, but southern lineages have contributed relatively little to temperate biodiversity in North America. The asymmetry in niche conservatism between northern and southern lineages is an important contributor to the biodiversity gradient.

Diversification in the Mexican horned lizard Phrynosoma orbiculare across a dynamic landscape

The widespread montane Mexican horned lizard Phrynosoma orbiculare (Squamata: Phrynosomatidae) represents an ideal species to investigate the relative impacts of Neogene vicariance and Quaternary climate change on lineage diversification across the Mexican highlands. We used mitochondrial DNA to examine the maternal history of P. orbiculare and estimate the timing and tempo of lineage diversification. Based on our results, we inferred 11 geographically structured, well supported mitochondrial lineages within this species, suggesting P. orbiculare represents a species complex. Six divergences between lineages likely occurred during the Late Miocene and Pliocene, and four splits probably happened during the Pleistocene. Diversification rate appeared relatively constant through time. Spatial and temporal divergences between lineages of P. orbiculare and co-distributed taxa suggest that a distinct period of uplifting of the Transvolcanic Belt around 7.5-3 million years ago broadly impacted diversification in taxa associated with this mountain range. To the north, several river drainages acting as filter barriers differentially subdivided co-distributed highland taxa through time. Diversification patterns observed in P. orbiculare provide additional insight into the mechanisms that impacted differentiation of highland taxa across the complex Mexican highlands.

High Phylogenetic Utility of an Ultraconserved Element Probe Set Designed for Arachnida

Arachnida is an ancient, diverse and ecologically important animal group that contains a number of species of interest for medical, agricultural and engineering applications. Despite their importance, many aspects of the arachnid tree of life remain unresolved, hindering comparative approaches to arachnid biology. Biologists have made considerable efforts to resolve the arachnid phylogeny; yet, limited and challenging morphological characters, as well as a dearth of genetic resources, have hindered progress. Here, we present a genomic toolkit for arachnids featuring hundreds of conserved DNA regions (ultraconserved elements or UCEs) that allow targeted sequencing of any species in the arachnid tree of life. We used recently developed capture probes designed from conserved regions of available arachnid genomes to enrich a sample of loci from 32 diverse arachnids. Sequence capture returned an average of 487 UCE loci for all species, with a range from 170 to 722. Phylogenetic analysis of these UCEs produced a highly resolved arachnid tree with relationships largely consistent with recent transcriptome‐based phylogenies. We also tested the phylogenetic informativeness of UCE probes within the spider, scorpion and harvestman orders, demonstrating the utility of these markers at shallower taxonomic scales and suggesting that these loci will be useful for species‐level differences. This probe set will open the door to phylogenomic and population genomic studies across the arachnid tree of life, enabling systematics, species delimitation, species discovery and conservation of these diverse arthropods.

Vaejovis montanus (Scorpiones: Vaejovidae), a new species from the Sierra Madre Occidental of Mexico

Abstract A new species of montane scorpion is described from the Sierra Madre Occidental of Mexico. The species is morphologically similar to scorpions distributed throughout the “sky island” region of the southwestern United States and northwestern Mexico and is a member of the “vorhiesi” subgroup of the Vaejovis “mexicanus” group. The morphology of the new species is compared to that of “vorhiesi” subgroup taxa, and biogeographic hypotheses about the diversification of this group are provided.

Phylogenetic Position of Porthidium Hespere (Viperidae: Crotalinae) and Phylogeography of Arid-Adapted Hognosed Pitvipers Based on Mitochondrial DNA

Abstract Gaps in recent studies of hognosed pit vipers in the genus Porthidium have left researchers with an incomplete estimate of the evolutionary history of this group. Mitochondrial DNA sequence data from the poorly known P. hespere and additional Porthidium sequences obtained from GenBank were used to re-analyze the phylogenetic relationships of Porthidium. Using sequence data from the South American Porthidium, we also updated a previous molecular clock calibration based on the uplift of the Isthmus of Panamá, and utilized this updated calibration to evaluate the phylogeography of arid-adapted Porthidium. Results from Bayesian Markov chain Monte Carlo phylogenetic methods underscore the historical pattern of bi-directional dispersal into and out of South America within Porthidium, and place P. hespere as the sister species to P. dunni. The three species of arid-adapted Porthidium distributed across the Pacific coast of southern Mexico and northern Central America may have diverged in the late Miocene after the enlargement of the Río Balsas drainage following the formation of the Mexican Transvolcanic Belt and the volcanic uplifting across the Chiapan–Guatemalan highlands. Debido a la ausencia de algunas especies en los estudios recientes de las nauyacas nariz de cerdo del género Porthidium, los investigadores no tienen una estimación completa de la historia evolutiva de este grupo. Se utilizaron nuevas secuencias de ADN mitocondrial de la poco conocida P. hespere y otras secuencias obtenidas de GenBank para reanalizar las relaciones filogenéticas de Porthidium. Usando secuencias de Porthidium sudamericanas, también se actualizó una calibración previa del reloj molecular basada en la elevación del Istmo de Panamá, y esta calibración actualizada se utilizó para evaluar la filogeografía de las especies de Porthidium adaptadas a la aridez. Los resultados de los métodos filogenéticos Bayesianos Markov chain Monte Carlo enfatizan el patrón histórico de dispersión bidireccional hacia y desde Sudamérica en Porthidium, y ubican a P. hespere como especie hermana de P. dunni. Las tres especies de Porthidium adaptadas a la aridez de la costa Pacífica del sur de México y norte de Centroamérica podrían haber divergido en el Mioceno tardío después del ensanchamiento del drenaje del Río Balsas que siguió a la formación del Eje Neovolcánico y la elevación volcánica de las tierras altas de Chiapas y Guatemala.

Multivariate methods support the distinction of a new highland Vaejovis (Scorpiones: Vaejovidae) from the Sierra de los Ajos, Mexico

Abstract Multivariate analyses of morphological characters provide strong evidence that a highland Vaejovis from the Sierra de los Ajos, a Madrean ‘sky island’ in northern Sonora, Mexico, represents a distinct new species of the V. vorhiesi group. This new species is described and compared to other geographically adjacent species of the V. vorhiesi group, named V. bandido, and brief notes on ecology are provided. Results from this study provide evidence that multivariate analysis of morphological characters is a powerful tool to delimit small and otherwise cryptic scorpion species.

A multilocus perspective on the speciation history of a North American aridland toad (Anaxyrus punctatus).

Interpretations of phylogeographic patterns can change when analyses shift from single gene-tree to multilocus coalescent analyses. Using multilocus coalescent approaches, a species tree and divergence times can be estimated from a set of gene trees while accounting for gene-tree stochasticity. We utilized the conceptual strengths of a multilocus coalescent approach coupled with complete range-wide sampling to examine the speciation history of a broadly distributed, North American warm-desert toad, Anaxyrus punctatus. Phylogenetic analyses provided strong support for three major lineages within A. punctatus. Each lineage broadly corresponded to one of three desert regions. Early speciation in A. punctatus appeared linked to late Miocene-Pliocene development of the Baja California peninsula. This event was likely followed by a Pleistocene divergence associated with the separation of the Chihuahuan and Sonoran Deserts. Our multilocus coalescent-based reconstruction provides an informative contrast to previous single gene-tree estimates of the evolutionary history of A. punctatus.

Hidden histories of gene flow in highland birds revealed with genomic markers.

Genomic studies are revealing that divergence and speciation are marked by gene flow, but it is not clear whether gene flow has played a prominent role during the generation of biodiversity in species‐rich regions of the world where vicariance is assumed to be the principal mode by which new species form. We revisit a well‐studied organismal system in the Mexican Highlands, Aphelocoma jays, to test for gene flow among Mexican sierras. Prior results from mitochondrial DNA (mtDNA) largely conformed to the standard model of allopatric divergence, although there was also evidence for more obscure histories of gene flow in a small sample of nuclear markers. We tested for these ‘hidden histories’ using genomic markers known as ultraconserved elements (UCEs) in concert with phylogenies, clustering algorithms and newer introgression tests specifically designed to detect ancient gene flow (e.g. ABBA/BABA tests). Results based on 4303 UCE loci and 2500 informative SNPs are consistent with varying degrees of gene flow among highland areas. In some cases, gene flow has been extensive and recent (although perhaps not ongoing today), whereas in other cases there is only a trace signature of ancient gene flow among species that diverged as long as 5 million years ago. These results show how a species complex thought to be a model for vicariance can reveal a more reticulate history when a broader portion of the genome is queried. As more organisms are studied with genomic data, we predict that speciation‐with‐bouts‐of‐gene‐flow will turn out to be a common mode of speciation.