Jerry W. Dragoo

Pattern and timing of diversification of the mammalian order Carnivora inferred from multiple nuclear gene sequences.

The mammalian order Carnivora has attracted the attention of scientists of various disciplines for decades, leading to intense interest in defining its supra-familial relationships. In the last few years, major changes to the topological structure of the carnivoran tree have been proposed and supported by various molecular data sets, radically changing the traditional view of family composition in this order. Although a sequence of molecular studies have established a growing consensus with respect to most inter-familial relationships, no analysis so far has included all carnivoran lineages (both feliform and caniform) in an integrated data set, so as to determine comparative patterns of diversification. Moreover, no study conducted thus far has estimated divergence dates among all carnivoran families, which is an important requirement in the attempt to understand the patterns and tempo of diversification in this group. In this study, we have investigated the phylogenetic relationships among carnivoran families, and performed molecular dating analyses of the inferred nodes. We assembled a molecular supermatrix containing 14 genes (7765 bp), most of which have not been previously used in supra-familial carnivoran phylogenetics, for 50 different genera representing all carnivoran families. Analysis of this data set led to consistent and robust resolution of all supra-familial nodes in the carnivoran tree, and allowed the construction of a molecular timescale for the evolution of this mammalian order.

A Comparison of Population Survey Techniques for Swift Foxes (Vulpes velox) in New Mexico

Abstract We compared survey techniques for estimating relative and absolute abundances of swift foxes (Vulpes velox) in New Mexico. For relative abundance surveys, the most efficient technique is collection of scats followed by verification of species depositing scats with DNA analysis. By collecting scats, the proportions of individual locations where swift foxes were detected were 61.9% and 67.7% during surveys in 2000 and 2001, which were greater than the proportions using scent stations (31.4%, 47.1%) or trapping (11.5%, 8.4%). By collecting scats, we detected swift foxes in 100% of the fox home ranges within the study area. If scent-station surveys are used instead, scent-station transects consisting of stations spaced at 1.6 km (1.0 mile) intervals and operated for three nights are the most practical. Searching for tracks, spotlighting and calling are much less efficient techniques. For absolute abundance surveys, trapping and resighting with cameras at bait stations was more accurate than counting unique microsatellite DNA genotypes from collected scats. Using trapping/resighting, we estimated the 95% confidence intervals for the swift fox population within the study area to be 17.8–30.0, 11.9–25.3 and 15.2–17.3 in the periods November 1999–January 2000, February 2000 and January–March 2001, respectively. We counted 63 and 27 unique genotypes in early 2000 and 2001, respectively. The numbers of unique genotypes, which were much greater than population estimates obtained from trapping and resighting, were overestimated because of the presence of transient swift foxes and poor quality DNA from scats leading to allelic drop-out and/or false alleles.

Volatile Components in Defensive Spray of the Hooded Skunk, Mephitis macroura

GC-MS analysis of the anal sac secretion from the hooded skunk, Mephitis macroura, showed the following seven major components comprised 99% of the volatiles in this secretion: (E)-2-butene-1-thiol, 3-methyl-1-butanethiol, S-(E)-2-butenyl thioacetate, S-3-methylbutenyl thioacetate, 2-phenylethanethiol, 2-methylquinoline, and 2-quinolinemethanethiol. Minor volatile components identified in this secretion are phenylmethanethiol, S-phenylmethyl thioacetate, S-2-phenylethyl thioacetate, bis[(E)-2-butenyl] disulfide, (E)-2-butenyl 3-methylbutyl disulfide, bis(3-methylbutyl) disulfide, and S-2-quinolinemethyl thioacetate. This secretion is similar to that of the striped skunk, Mephitis mephitis, differing only in that it contains four compounds not reported from the striped skunk: phenylmethanethiol, S-phenylmethyl thioacetate, 2-phenylethanethiol, and S-2-phenylethyl thioacetate.

TAXONOMIC STATUS OF WHITE-BACKED HOG-NOSED SKUNKS, GENUS CONEPATUS (CARNIVORA: MEPHITIDAE)

Abstract The taxonomic status of white-backed hog-nosed skunks (genus Conepatus, subgenus Oryctogale) was examined using external and cranial morphology as well as mitochondrial deoxyribonucleic acid sequence. Two species, Conepatus leuconotus and C. mesoleucus, and their subspecies were determined to represent only a single species, C. leuconotus. Within this species there are 3 management units, or subspecies, recognized conservatively. These subspecies are C. l. leuconotus (including C. l. texensis, C. m. mearnsi, C. m. mesoleucus, C. m. nelsoni, C. m. venaticus, C. m. nicaraguae, C. m. sonoriensis, and C. m. filipensis); C. l. figginsi (=C. m. figginsi and including C. m. fremonti); and C. l. telmalestes (=C. m. telmalestes). In the case of C. l. figginsi and C. l. telmalestes, further genetic research may indicate that these taxa are not valid, but the populations that they represent (if not extinct) will require different management strategies from the wide-ranging C. l. leuconotus.

Relationships within the Calomys callosus species group based on amplified fragment length polymorphisms

Calomys callosus was identified almost 40 years ago as the rodent reservoir of Machupo virus (MACV, Arenaviridae), which causes Bolivian hemorrhagic fever (BHF), a disease endemic to northeastern Bolivia. However, the range of C. callosus s. l. far exceeds the known distribution of MACV and BHF. Four sampling regions representing different mitochondrial lineages within the C. callosus species group and an outgroup were evaluated for their genetic relationships using amplified fragment length polymorphisms (AFLP). Four AFLP primer combinations generated 596 bands, which were used for phylogenetic and population analyses. We show, using nuclear genetic markers, that the populations of rodents responsible for the maintenance and transmission of MACV are an independent monophyletic lineage, different from other lineages in other areas of Bolivia and South America. These data support the conclusions reached using mitochondrial DNA sequence from the cytochrome b and control region (D-loop) genes.

Confirmation of Choclo virus as the cause of hantavirus cardiopulmonary syndrome and high serum antibody prevalence in Panama

Choclo virus (CHOV) was described in sigmodontine rodents, Oligoryzomys fulvescens, and humans during an outbreak of hantavirus cardiopulmonary syndrome (HCPS) in 1999–2000 in western Panama. Although HCPS is rare, hantavirus‐specific serum antibody prevalence among the general population is high suggesting that CHOV may cause many mild or asymptomatic infections. The goals of this study were to confirm the role of CHOV in HCPS and in the frequently detected serum antibody and to establish the phylogenetic relationship with other New World hantaviruses. CHOV was cultured to facilitate the sequencing of the small (S) and medium (M) segments and to perform CHOV‐specific serum neutralization antibody assays. Sequences of the S and M segments found a close relationship to other Oligoryzomys‐borne hantaviruses in the Americas, highly conserved terminal nucleotides, and no evidence for recombination events. The maximum likelihood and maximum parsimony analyses of complete M segment nucleotide sequences indicate a close relationship to Maporal and Laguna Negra viruses, found at the base of the South American clade. In a focus neutralization assay acute and convalescent sera from six Panamanian HCPS patients neutralized CHOV in dilutions from 1:200 to 1:6,400. In a sample of antibody‐positive adults without a history of HCPS, 9 of 10 sera neutralized CHOV in dilutions ranging from 1:100 to 1:6,400. Although cross‐neutralization with other sympatric hantaviruses not yet associated with human disease is possible, CHOV appears to be the causal agent for most of the mild or asymptomatic hantavirus infections, as well as HCPS, in Panama. J. Med. Virol. 82:1586–1593, 2010.

Conepatus leuconotus (Carnivora: Mephitidae)

Abstract Conepatus leuconotus (Lichtenstein, 1832) is a mephitid commonly called the white-backed or American hog-nosed skunk. It is a sexually dimorphic species with a single white stripe along the back, and is 1 of 4 species in the genus Conepatus. It has been reported as far north as Colorado and throughout the southwestern United States including southern Arizona, New Mexico, and Texas. The species occurs throughout Mexico and as far south as northern Costa Rica. It has been reported in a variety of habitats from canyons, stream sides, rocky terrain, various grasslands, tropical areas, mountains, and coastal plains. Several populations have been extirpated and others may be declining throughout the range.

Rabies in Hooded and Striped Skunks in Arizona

Arizona is home to four species of skunks, and rabies is enzootic in the region in which their ranges overlap. Examination of state health data from 1985 to 2004 revealed an irregular 4–10 yr periodicity in the number of cases annually, which may be related to past precipitation patterns. The number of rabid skunks peaked during springtime. Locations of rabies epizootics changed over time, but there was no evidence of a large-scale geographic spread. Skunks live-trapped during 1996–2002 had a low prevalence of rabies-virus neutralizing antibodies. This study was the first to document rabies in hooded skunks (Mephitis macroura).

Identification of Skunk Species Submitted for Rabies Testing in the Desert Southwest

Skunks usually are identified by their common name (skunk) when submitted for rabies testing. In the desert southwest (Arizona, New Mexico, Texas, USA; and northern Mexico), there are five species of skunks; four of which can occur in sympatry. To better understand the ecology of skunk rabies in these areas, it is imperative that species be properly identified. We used the displacement loop (d-loop) of the mitochondrial genome to identify to species 24 skunk brain samples submitted for rabies testing in New Mexico from 2001 to 2002. Most were identified as striped skunks (Mephitis mephitis), but hooded (Mephitis macroura) and hog-nosed (Conepatus leuconotus) skunks were also found.

Genetic differentiation of island spotted skunks, Spilogale gracilis amphiala

Abstract The island spotted skunk (Spilogale gracilis amphiala) is endemic to the 2 largest California Channel Islands, Santa Cruz and Santa Rosa. Unlike the island fox (Urocyon littoralis) and island subspecies of the deer mouse (Peromyscus maniculatus), the island spotted skunk shows no morphological differentiation between islands and is differentiated only weakly from mainland subspecies, suggesting recent colonization. However, the islands have been isolated from each other and the mainland throughout the Quaternary Period. We used 8 microsatellite loci to investigate the distribution of genetic variation within and among populations of spotted skunks from 8 localities (the 2 islands and 6 mainland localities), representing 4 subspecies. Tissue samples were obtained from 66 fresh specimens collected from 2000 to 2002 and 142 museum specimens collected from 1906 to 1994. Allelic richness and heterozygosity in island spotted skunk populations was approximately 30% lower than that found in mainland localities or subspecies. All localities or subspecies were significantly differentiated (mean FST was 0.17 and 0.13 for localities and subspecies, respectively). Contrary to comparisons based on morphological data, genetic differentiation was especially strong between islands and between island and mainland localities or subspecies. Patterns of differentiation suggest that skunks colonized the Channel Islands shortly before rising sea levels separated Santa Cruz and Santa Rosa islands (11,500 years ago). Our results indicate that the taxonomic status of the island spotted skunk should be reconsidered and that both island populations might constitute evolutionarily significant units worthy of conservation.