Cranial variation in species and subspecies of kangaroo rats (Dipodomys, Dipodomyinae, Rodentia) according to geometric morphometrics

Traditional Dipodomys (sub)species identification uses geography, phenotype, and external/skull measurements. Such measurements are correlated with size and thus redundant. I assessed the value of scaled cranial shape, based on two-dimensional landmarks (analyzed using geometric morphometric methods) in distinguishing Dipodomys taxa, and in summarizing their variation. My dataset includes 601 adult specimens from 20 species (49 operational taxonomic units - OTUs) across 190 localities. Cranial shape was highly useful in classifying Dipodomys taxa without considering geography. The auditory bulla was the most variable region-taxa differed in its hypertrophy, accompanied by different degrees of nearby structure crowding. Cranial shape was weakly allometric, with no significant sexual dimorphism. Weak size dimorphism was detected. (Sub)specific taxonomy is not reflective of shape variation, as the number of subspecies per species is not associated with disparity. Shape had significant phylogenetic signal, but subspecies did not always cluster with conspecifics and species did not always cluster according to phylogenetic relationship/taxonomy. Shape variation was correlated with climate, and species differed in morphological disparity and degree of specialization, which may contribute to divergence in shape variation patterns from phylogeny. D. deserti was the most specialized species, diverging greatly from the genus mean; D. heermanni was the least specialized. This study provides new insights into morphological variation of North American keystone species, several of conservation interest, for example, D. heermanni berkeleyensis, D. h. dixoni, D. nitratoides brevinasus, and D. n. nitratoides.

The taxonomic basis of subspecies listed as threatened and endangered under the endangered species act

More than 170 subspecies are listed as threatened or endangered under the US Endangered Species Act. Most of these subspecies were described decades ago on the basis of geographical variation in morphology using relatively primitive taxonomic methods. The US Fish and Wildlife Service defaults to subspecies descriptions by taxonomists working with specific groups of organisms, but there is no single definition of subspecies across plants and animals. Valid tests today usually entail molecular analyses of variation within and among populations, although there is no reason that behavioral, ecological or molecular characters could not be used, and include tests for significant differences between samples of the putative endangered subspecies and its nearest geographic relatives. We evaluated data gathered since subspecies listed under the ESA were described finding about one-third are valid (distinct evolutionary taxa), one-third are not, and one-third have not been tested. Therefore, it should not be assumed that because a subspecies occurs in a checklist, it is taxonomically valid. If the US Fish and Wildlife Service intends to continue listing subspecies, we suggest that they convene taxonomic experts representing various groups of organisms to provide a minimal set of criteria for a subspecies to be listed under the ESA.

Lost in a sagebrush sea: comparative genetic assessment of an isolated montane population of Tamias amoenus

The montane sky islands of the Great Basin are characterized by unique, isolated habitats and communities that likely are vulnerable to extirpation with environmental change. A subspecies of yellow pine chipmunk, the Humboldt yellow pine chipmunk (Tamias amoenus celeris), is associated with the whitebark and limber pine forests of the Pine Forest Range (PFR) in Nevada. We sampled T. amoenus and least chipmunks (T. minimus) from the isolated PFR and compared genetic diversity between these populations and more “mainland” populations, including other subspecies of chipmunks. Given the high frequency of hybridization in Tamias, we tested for hybridization between T. amoenus and T. minimus in the PFR. We examined phylogenetic relationships, population divergence and diversity, and screened populations for a common pathogen, Borrelia hermsii, to gain insight into population health. We found T. amoenus of the PFR are closely related to T. amoenus in the Warner Mountains and Sierra Nevada, but maintain substantively lower genetic variation. Microsatellite analyses show PFR T. amoenus are highly genetically differentiated from other populations. In contrast, PFR T. minimus had higher genetic diversity that was comparable to the other T. minimus population we sampled. Pathogen screening revealed that T. amoenus carried higher pathogen loads than T. minimus in the PFR, although the prevalence of infection was similar to other Tamias populations. Our assessment of habitat associations suggests that the Humboldt yellow pine chipmunk almost entirely is restricted to the conifer systems of the PFR, while least chipmunks are prevalent in the other forests. Our work highlights the need for continued conservation and research efforts to identify how response to environmental change can be facilitated in isolated species and habitats.

Survey for Morro Bay Kangaroo Rat: A Rare Mammal of Uncertain Status

The Morro Bay kangaroo rat Dipodomys heermanni morroensis is a small, nocturnal, burrowing rodent endemic to the vicinity of Morro Bay in San Luis Obispo County, California. It was listed as endangered pursuant to the U.S. Endangered Species Act in 1973. Despite many searches over three decades, the Morro Bay kangaroo rat has not been captured or sighted in the wild since 1986. While recognizing that the Morro Bay kangaroo rat may be extinct, two of us in a previous paper also speculated it may be persisting at extremely low density in isolated colonies and recommended surveying with wildlife scent-detection dogs and baited camera traps. We searched with a wildlife scent-detection dog and baited camera traps in four historically occupied areas and detected no Morro Bay kangaroo rats. Unfortunately, our data combined with all other existing data do not allow us to conclude whether the Morro Bay kangaroo rat is extinct or extant. Essentially, the International Union for the Conservation of Nature international standard has not been met to make a definitive determination of extinction. That is, a species should be considered extinct only when there is no reasonable doubt that the last individual has died. We acknowledge that because of resource limitation we surveyed only a small sample of the numerous patches of habitat in the expansive landscape. Further, we now consider the Morro Bay sand spit (total area 4.35 km2, foredunes 3.75 km2), a peripheral area, as potentially part of the geographic range with suitable habitat, and it has never been searched. Therefore, considering all available information, we conclude that the Morro Bay kangaroo rat must be considered as possibly extant. We recommend that search efforts continue in several specific areas, including the Morro Bay sand spit. If the Morro Bay kangaroo rat still exists, it will be challenging and difficult to rediscover because of its likely low density and patchy distribution in the expansive landscape, combined with its small size, nocturnal nature, and secretive lifestyle.