Phylogeography and subspecies revision of the hispid pocket mouse,Chaetodipus hispidus(Rodentia: Heteromyidae)

Cryptic diversity begets challenges and opportunities in biodiversity research

How many species of life are there on Earth? This is a question that we want to know but cannot yet answer. Some scholars speculate that the number of species may reach 2.2 billion when considering cryptic diversity and that each morphology-based insect species may contain an average of 3.1 cryptic species. With nearly two million described species, such high estimates of cryptic diversity would suggest that cryptic species are widespread. The development of molecular species delimitation has led to the discovery of a large number of cryptic species, and cryptic biodiversity has gradually entered our field of vision and attracted more attention. This paper introduces the concept of cryptic species, how they evolve, and methods by which they may be discovered and confirmed, and provides theoretical and methodological guidance for the study of hidden species. A workflow of how to confirm cryptic species is provided. In addition, the importance and reliability of multi-evidence-based integrated taxonomy are reaffirmed as a way to better standardize decision-making processes. Special focus on cryptic diversity and increased funding for taxonomy is needed to ensure that cryptic species in hyperdiverse groups are discoverable and described. An increased focus on cryptic species in the future will naturally arise as more difficult groups are studied, and thereby, we may finally better understand the rules governing the evolution and maintenance of cryptic biodiversity.

Biogeographic consequences of shifting climate for the western massasauga ( Sistrurus tergeminus )

The western massasauga (Sistrurus tergeminus) is a small pit viper with an extensive geographic range, yet observations of this species are relatively rare. They persist in patchy and isolated populations, threatened by habitat destruction and fragmentation, mortality from vehicle collisions, and deliberate extermination. Changing climates may pose an additional stressor on the survival of isolated populations. Here, we evaluate historic, modern, and future geographic projections of suitable climate for S. tergeminus to outline shifts in their potential geographic distribution and inform current and future management. We used maximum entropy modeling to build multiple models of the potential geographic distribution of S. tergeminus. We evaluated the influence of five key decisions made during the modeling process on the resulting geographic projections of the potential distribution, allowing us to identify areas of model robustness and uncertainty. We evaluated models with the area under the receiver operating curve and true skill statistic. We retained 16 models to project both in the past and future multiple general circulation models. At the last glacial maximum, the potential geographic distribution associated with S. tergeminus occurrences had a stronghold in the southern part of its current range and extended further south into Mexico, but by the mid‐Holocene, its modeled potential distribution was similar to its present‐day potential distribution. Under future model projections, the potential distribution of S. tergeminus moves north, with the strongest northward trends predicted under a climate scenario increase of 8.5 W/m². Some southern populations of S. tergeminus have likely already been extirpated and will continue to be threatened by shifting availability of suitable climate, as they are already under threat from desertification of grasslands. Land use and habitat loss at the northern edge of the species range are likely to make it challenging for this species to track suitable climates northward over time.

Sexual dimorphism in cranial shape and size in geomyoid rodents: multivariate and evolutionary perspectives

Geomyoid rodents provide a great study system for the analysis of sexual dimorphism. They are polygynic and many inhabit harsh arid environments thought to promote sexual dimorphism. In fact, there has been extensive work published on the sexual size dimorphism of individual populations and species within this rodent clade. However, little work has been undertaken to assess the evolutionary patterns and processes associated with this sexual dimorphism. We use multivariate analyses of cranial measurements in a phylogenetic framework to determine the distribution of size and shape dimorphism among geomyoids and test for Rensch’s rule. Our results suggest that sexual dimorphism is more common in geomyids than heteromyids, but it is not in fact universal. There is evidence for variation in sexual dimorphism across populations. Additionally, in many taxa, geographic variation appears to overwhelm existing sexual dimorphism. We find support for the repeated independent evolution of shape and size dimorphism across geomyoid taxa, but we do not find support for an association between size and shape dimorphism. There is no evidence for Rensch’s rule in geomyoids, whether at the superfamily or family level. Together, our findings suggest that there is no single explanation for the evolution of sexual dimorphism in geomyoids and that, instead, it is the product of numerous evolutionary events. Future studies incorporating phylogenetic relationships will be necessary to paint a more complete picture of the evolution of sexual dimorphism in geomyoids.

Deep mitochondrial DNA phylogeographic divergence in the threatened aoudad Ammotragus lervia (Bovidae, Caprini)

The aoudad or Barbary sheep (Ammotragus lervia) is a threatened ungulate emblematic of North Africa, whose population structure and subspecific taxonomy have not been examined genetically. This knowledge is essential and urgently needed to inform ongoing conservation and management efforts. We analysed the mitochondrial cytochrome b gene and four nuclear genes (casein kappa, spectrin beta nonerythrocytic 1, thyroglobulin, thyrotropin subunit beta) for the first phylogeographic survey of the aoudad, and uncovered a deep Mediterranean-Saharan mitochondrial split separating two highly distinct evolutionary lineages. Their level of divergence is greater than or comparable to those observed between several pairs of congeneric species of different caprine genera. The split was estimated to have occurred in the Early Pleistocene, about 1.3 million years ago. None of the four nuclear genes surveyed, chosen because they have been used in phylogeographic and species-level phylogenetic studies of bovids, allowed us to detect, likely due to their slow evolutionary rate, the substantial and geographically coherent subdivision revealed by mitochondrial DNA. This study is evidence and testament to the ability of mitochondrial DNA, probably unrivalled by any other single-locus marker, as an exploratory tool for investigating population genealogy and history and identifying potential evolutionarily significant units for conservation in animals.

Phylogeography and taxonomic revision of Nelson’s pocket mouse (Chaetodipus nelsoni)

Chaetodipus nelsoni occurs on rocky substrates across the Mexican Altiplano. We investigated phylogeographic diversity within the species using morphologic, karyotypic, and molecular data. Data from nuclear (AFLP) and mitochondrial DNA support three distinct genetic groups with minimal substructuring coincident with biogeographic barriers previously identified in the Chihuahuan Desert and drainage basins of the Altiplano. We examined the morphological and karyotypic data in light of the molecular data. The results support recognition of three species within the currently accepted widespread C. nelsoni: 1) C. nelsoni restricted to a distribution centered on the El Salado River Basin; 2) elevation of C. n. collis to species, with two subspecies: one centered on Trans-Pecos Texas, the other on the Mapimí Basin (new subspecies); and 3) recognition of a new species, C. durangae, centered on the Nazas Basin and upper Río Mezquital drainage.

Population genetic structure of Texas horned lizards: implications for reintroduction and captive breeding

The Texas horned lizard (Phrynosoma cornutum) inhabits much of the southern Great Plains of North America. Since the 1950s, this species has been extirpated from much of its eastern range and has suffered declines and local extinctions elsewhere, primarily due to habitat loss. Plans are underway to use captive breeding to produce large numbers of Texas horned lizards for reintroduction into areas that were historically occupied by this species and that currently have suitable habitat. We used mitochondrial markers and nuclear microsatellite markers to determine levels of genetic diversity and population structure in 542 Texas horned lizards sampled from across Texas and some neighboring states to help inform these efforts. Texas horned lizards still retain high genetic diversity in many parts of their current range. We found two highly divergent mitochondrial clades (eastern and western) and three major genetic groupings at nuclear microsatellite loci: a west group corresponding to the western mitochondrial clade and north and south groups within the eastern mitochondrial clade. We also found some evidence for human-mediated movement between these genetic clusters that is probably related to the historical importance of this species in the pet trade and as an iconic symbol of the southwestern United States. We do not know, however, if there are fitness costs associated with admixture (especially for the western and eastern clades) or if there are fitness costs to moving these lizards into habitats that are distinctly different from their ancestral areas. If present, either one or both of these fitness costs would decrease the effectiveness of reintroduction efforts. We therefore recommend that reintroduction efforts should maintain current genetic structure by restricting breeding to be between individuals within their respective genetic clusters, and by reintroducing individuals only into those areas that encompass their respective genetic clusters. This cautionary approach is based on the strong divergence between genetic groupings and their correspondence to different ecoregions.

Subspecific Differentiation Events of Montane Stag Beetles (Coleoptera, Lucanidae) Endemic to Formosa Island

Taxonomic debates have been carrying on for decades over Formosan stag beetles, which consist of a high proportion of endemic species and subspecies featuring morphological variations associated with local adaptation. With the influence of periodical Pleistocene glaciations and the presence of several mountain ranges, the genetic differentiation and taxonomic recognition, within this medium-size island, of two endemic subspecies for each of four montane stag beetles, i.e. Lucanus ogakii, L. kanoi, Prismognathus davidis, and Neolucanus doro, has been an appealing issue. Based on monophyletic lineages and population structure, possible divergent scenarios have been proposed to clarify the subspecific status for each of the above mentioned stag beetles. Phylogenetic inferences based on COI+16S rDNA+28S rDNA of 240 Formosan lucanids have confirmed most species are monophyletic groups; and the intraspecific (<2%) and interspecific (>2%) genetic distances of the two mitochondrial genes could be applied concordantly for taxonomic identification. On account of Bayesian-based species delimitation, geographic distribution, population structure, and sequence divergences, the subspecific status for L. ogakii, L. kanoi, and Pri. davidis are congruent with their geographic distribution in this island; and the calibration time based on the mitochondrial genes shows the subspecific split events occurred 0.7–1 million years ago. In addition, a more complicated scenario, i.e. genetic differentiation including introgression/hybridization events, might have occurred among L. ogakii, L. kanoi, and L. maculifemoratus. The geological effects of mountain hindrance accompanied by periodical glaciations could have been vital in leading to the geographical subspecific differentiation of these montane stag beetles.

Phylogeographic assessment of the northern pygmy mouse, Baiomys taylori

The northern pygmy mouse, Baiomys taylori, occurs throughout the Trans-Mexican Volcanic Belt and southern Altiplano of central Mexico and extends northward in 3 projections into northern Mexico and the United States. We used mitochondrial DNA (from the cytochrome-b and NADH dehydrogenase 2 genes) and morphological data to assess diversity within B. taylori across its geographic range in relation to recognized subspecies and putative physiographic filter-barriers. Our results indicate 5 distinct mitochondrial clades despite little morphological variation across the species’ geographic range. The Sierra Madre Oriental and Sierra Madre Occidental separate clades representing the eastern (Gulf coastal lowlands), central (Altiplano), and Pacific coastal lowlands, which appear to be divided into 3 major mitochondrial clades. Based on a preliminary analysis of cranial morphology, we are able to reject the Balcones Escarpment of Texas as an impediment to the well-documented recent northern expansion of the species, while we are unable to reject a causal role of filter-barriers elsewhere in subspecific differentiation. Revision of subspecific taxonomy must await further genetic sampling, particularly along the western and southeastern portions of the species’ distribution.

El ratón pigmeo norteño, Baiomys taylori, se distribuye a través del Eje Volcánico Transmexicano y la parte sur del Altiplano del centro de México y se extiende hacia el norte de México y los Estados Unidos en tres direcciones. Utilizamos ADN mitocondrial (del citocromo-b y del gen NADH deshidrogenasa) y datos morfológicos para evaluar la diversidad dentro de B. taylori a través de su rango geográfico en relación con las subespecies reconocidas y las supuestas barreras-filtro fisiográficas. Nuestros resultados indican 5 clados mitocondriales distintos a pesar de la escasa variación morfológica a lo largo de su rango geográfico. La Sierra Madre Oriental y la Sierra Madre Occidental separan los clados representantes de las tierras bajas del este (tierras bajas del Golfo), del centro (Altiplano), y las tierras bajas del Pacífico, que parecen estar divididas en 3 clados mitocondriales principales. Basados en un análisis preliminar de la morfología craneal, pudimos rechazar el Escarpe de Balcones de Texas como un impedimento a la bien documentada expansión norteña de la especie, mientras que no fue posible rechazar el rol causal de las otras barreras-filtro en la diferenciación subespecífica. La revisión de la taxonomía subespecífica deberá esperar un mayor muestreo genético, en particular a lo largo de las porciones oeste y sureste de la distribución de la especie.