Link E. Olson

Guidelines of the American Society of Mammalogists for the Use of Wild Mammals in Research

Abstract General guidelines for use of wild mammal species are updated from the 1998 version approved by the American Society of Mammalogists (ASM) and expanded to include additional resources. Included are details on marking, housing, trapping, and collecting mammals. These guidelines cover current professional techniques and regulations involving mammals used in research. Institutional animal care and use committees, regulatory agencies, and investigators should review and approve procedures concerning use of vertebrates at any particular institution. These guidelines were prepared and approved by the ASM, whose collective expertise provides a broad and comprehensive understanding of the biology of nondomesticated mammals in their natural environments.

A New Genus of African Monkey, Rungwecebus: Morphology, Ecology, and Molecular Phylogenetics

A new species of African monkey, Lophocebus kipunji, was described in 2005 based on observations from two sites in Tanzania. We have since obtained a specimen killed by a farmer on Mount Rungwe, the type locality. Detailed molecular phylogenetic analyses of this specimen demonstrate that the genus Lophocebus is diphyletic. We provide a description of a new genus of African monkey and of the only preserved specimen of this primate. We also present information on the animals ecology and conservation.

Inferring divergence times within pikas (Ochotona spp.) using mtDNA and relaxed molecular dating techniques.

Although several studies have recently addressed phylogenetic relationships among Asian pikas (Ochotona spp.), the North American species have been relatively neglected and their monophyly generally unquestioned or assumed. Given the high degree of intraspecific diversity in pelage and call structure, the recent identification of previously unrecognized species of pika in Asia, and the increasing evidence for multiple trans-Beringian dispersals in several small mammal lineages, the monophyly of North American pikas warrants reexamination. In addition, previous studies have applied an externally calibrated rate to examine the timing of diversification within the genus. This method has been increasingly shown to return results that, at the very least, are overly narrow in their confidence intervals, and at the worst can be entirely spurious. For this study we combined GenBank sequences from the mitochondrial genes cyt b and ND4 with newly generated sequence data from O. hyperborea and O. collaris to investigate the origin of the North American lineages and the timing of phylogenetic diversification within the genus Ochotona. Specifically, we address three goals (1) summarize and reanalyze the molecular evidence for relationships within the genus using statistically supported models of evolution; (2) add additional sequences from O. collaris and O. hyperborea to rigorously test the monophyly of North American pikas; (3) examine the timing of the diversification within the genus using relaxed molecular clock methods. We found no evidence of multiple trans-Beringian dispersals into North America, thereby supporting the traditional hypothesis of a single invasion of North America. We also provide evidence that the major splits within the genus occurred in the Miocene, and the Nearctic pikas diverged sometime before the Pleistocene.

Phylogeny, phylogeography, and geographic variation of Sylvisorex howelli (Soricidae), an endemic shrew of the Eastern Arc Mountains, Tanzania

The Eastern Arc Mountains of eastern Africa are notable for the high levels of endemism exhibited by various forest-dwelling organisms of this ancient montane archipelago. There has been virtually no assessment of the variation among populations of small mammal species living on these unique mountains, but recent faunal surveys have produced sufficient material to initiate such studies. Cranial morphometric and DNA sequence data were examined from six populations of Sylvisorex howelli Jenkins, 1984, an endemic shrew found in several different massifs of the Eastern Arc Mountains, to assess variation across the archipelago in the context of various hypotheses of historical biogeography. Twenty-two cranial measurements were analysed using principal components analysis. Age classes (based on tooth wear) and sex had little effect on the variation exhibited by the variables studied. Overall, specimens of S. howelli from the East Usambara Mountains are smaller than specimens from other known populations. The mitochondrial ND2 and 12S rRNA genes from representatives of each montane population of S. howelli in addition to several crocidurine taxa from eastern Africa and three soricine outgroup species were sequenced to assess phylogenetic relationships among these taxa. Neither maximum likelihood, maximum parsimony, nor Bayesian analyses support monophyly of the genus Sylvisorex, but S. howelli populations were consistently recovered as a well-supported clade. Over 40 individuals of S. howelli from six disjunct montane ranges, comprising the entire known distribution of the species, were sequenced for 504 base pairs of ND2 to investigate phylogeographic patterns. Phylogenetic analysis recovered six reciprocally monophyletic haplotype clades grouped by locality. Branch lengths are consistent with relatively long periods of isolation among populations from the Uluguru, Ukaguru, Nguru, Nguu, East Usambara and West Usambara Mountains, with low levels of diversity observed within each population. These results are interpreted within the historical context of the Eastern Arc Mountains.

The biogeography of introgression in the critically endangered African monkey Rungwecebus kipunji

In the four years since its original description, the taxonomy of the kipunji (Rungwecebus kipunji), a geographically restricted and critically endangered African monkey, has been the subject of much debate, and recent research suggesting that the first voucher specimen of Rungwecebus has baboon mitochondrial DNA has intensified the controversy. We show that Rungwecebus from a second region of Tanzania has a distinct mitochondrial haplotype that is basal to a clade containing all Papio species and the original Rungwecebus voucher, supporting the placement of Rungwecebus as the sister taxon of Papio and its status as a separate genus. We suggest that the Rungwecebus population in the Southern Highlands has experienced geographically localized mitochondrial DNA introgression from Papio, while the Ndundulu population retains the true Rungwecebus mitochondrial genome.

Additional molecular evidence strongly supports the distinction between the recently described African primate Rungwecebus kipunji (Cercopithecidae, Papionini) and Lophocebus

Department of Mammalogy, University of Alaska Museum, 907 Yukon Drive, Fairbanks, AK 99775, USA b Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK 99775, USA Department of Anthropology, Yale University, P.O. Box 208277, New Haven, CT 06520-8277, USA Division of Vertebrate Zoology, Peabody Museum of Natural History, Yale University, New Haven, CT 06520-8118, USA Department of Zoology, Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL 60605, USA Wildlife Conservation Society, Tanzania Program, P.O. Box 1475, Mbeya, Tanzania

Colonization from divergent ancestors: glaciation signatures on contemporary patterns of genomic variation in Collared Pikas (Ochotona collaris)

Identifying the genetic structure of a species and the factors that drive it is an important first step in modern population management, in part because populations evolving from separate ancestral sources may possess potentially different characteristics. This is especially true for climate‐sensitive species such as pikas, where the delimitation of distinct genetic units and the characterization of population responses to contemporary and historical environmental pressures are of particular interest. We combined a restriction site‐associated DNA sequencing (RADSeq) data set containing 4156 single nucleotide polymorphisms with ecological niche models (ENMs) of present and past habitat suitability to characterize population composition and evaluate the effects of historical range shifts, contemporary climates and landscape factors on gene flow in Collared Pikas, which are found in Alaska and adjacent regions of northwestern Canada and are the lesser‐studied of North Americas two pika species. The results suggest that contemporary environmental factors contribute little to current population connectivity. Instead, genetic diversity is strongly shaped by the presence of three ancestral lineages isolated during the Pleistocene (~148 and 52 kya). Based on ENMs and genetic data, populations originating from a northern refugium experienced longer‐term stability, whereas both southern lineages underwent population expansion – contradicting the southern stability and northern expansion patterns seen in many other taxa. Current populations are comparable with respect to generally low diversity within populations and little‐to‐no recent admixture. The predominance of divergent histories structuring populations implies that if we are to understand and manage pika populations, we must specifically assess and accurately account for the forces underlying genetic similarity.

Phylogenetic Relationships among Treeshrews (Scandentia): A Review and Critique of the Morphological Evidence

Although the supraordinal relationships of Scandentia (treeshrews) have been studied in great detail from both morphological and molecular perspectives, the phylogenetic relationships among treeshrews have been largely ignored. Here we review several published studies of qualitative morphological variation among living treeshrews and their contribution to our understanding of intraordinal phylogenetic relationships. Reanalysis of the data from each of these studies demonstrates that none of the trees in the original publications represents the most parsimonious interpretation. In addition to performing new analyses, we argue that all such studies to date suffer from one or more fundamental shortcomings, notably the failure to include reference to nonscandentian outgroups and the a priori assumption of generic monophyly of the relatively speciose genus Tupaia. Parsimony analyses of these data sets fail to resolve either intergeneric or interspecific relationships. Finally, several inconsistencies and conflicts with respect to character coding both within and between published studies are discussed. We conclude that a more rigorous investigation of morphological character state variation is sorely needed, one that explicitly identifies voucher specimens and does not make any assumptions of generic monophyly. This is necessary not only for the purpose of resolving phylogenetic relationships, but also for inference of ancestral states in a group that continues to figure prominently in studies of placental mammal diversification.

Contamination and chimerism are perpetuating the legend of the snake-eating cow with twisted horns (Pseudonovibos spiralis). A case study of the pitfalls of ancient DNA.

In 1994, several unusual horns collected from markets in Vietnam and Cambodia were described as a new genus and species of wild bovid, Pseudonovibos spiralis (Peter and Feiler, 1994a,b). The horn sheaths possessed a unique and distinct lyriform twist, as well as annulations throughout their entire length. This animal, named ‘‘linh duong’’ in Vietnam or ‘‘kting voar’’ in Cambodia (but see Brandt et al., 2001), was known only from detached horn sheaths or frontlets (partial frontal bones with bony horn cores) with horn sheaths. This lack of anatomical information was largely responsible for the confusion regarding the taxonomic status of this species, with morphologists debating whether it was a close relative of the tribe Antilopini (gazelles) (Peter and Feiler, 1994a), Caprini sensu lato (goats, sheep, and allies) (Nadler, 1997), or Bovini (oxen, bison, and buffaloes) (Dioli, 1997; Timm and Brandt, 2001). Given both the paucity and variable taxonomic interpretation of the morphological data, hopes were initially high that DNA sequence would resolve the issue of Pseudonovibos taxonomic status and phylogenetic position. However, three ensuing DNA sequencing studies using different putative P. spiralis specimens gave rise to mutually incompatible hypotheses: (1) Hammer et al. (1999), using a 415-bp DNA fragment of the mitochondrial cytochrome b gene, proposed affinities with the Caprini sensu lato. However, Hassanin and Douzery (2000) challenged the authenticity of the Hammer et al. (1999) sequence and interpreted it as the result of DNA contamination from chamois (Rupicapra) in the laboratory. (2) Hassanin et al. (2001) revealed that some horns assigned to P. spiralis are simply cow horns that had been artificially carved and twisted. Two DNA markers were sequenced from four trophies of P. spiralis collected in Indochina during 1925: a 243-bp fragment of the mitochondrial cytochrome b and a 327-bp fragment of the nuclear lactoferrin gene. The phylogenetic results showed that the enigmatic horns of the linh duong belonged to domestic cattle (Bos taurus) (Hassanin et al., 2001). Morphological inspection indicated that horn sheaths, originally smooth, were carved to create the annulations, while the twist in the upper part of the horns was made by artificial torsion (Thomas et al., 2001). This raised the question of whether all horns of the linh duong are fraudulent or not. In other words, did the species P. spiralis ever really exist (see review in Brandt et al., 2001)? (3) Most recently, Kuznetsov et al. (2001) suggested that P. spiralis was a new species of buffalo based on a 962-bp fragment of the mitochondrial 12S rRNA gene. However, one of us (Hassanin, 2002) demonstrated that the putative sequence of P. spiralis was a chimera obtained from three different species: B. taurus, Bubalus bubalus (domesticated Asian water buffalo), and Saiga tatarica (saiga antelope). In addition, several factors indicated that their specimen was artificially made using horns and a frontlet from domestic cattle, B. taurus. The ongoing and increasingly heated controversy surrounding P. spiralis has been covered in Science (Malakoff, 2001), Nature (Whitfield, 2002), and the New York Times (Mydans, 2002), with emphasis on both the folkloric portrayals of a snake-eating cow-like creature Molecular Phylogenetics and Evolution 27 (2003) 545–548

Networks, trees, and treeshrews: assessing support and identifying conflict with multiple loci and a problematic root.

Multiple unlinked genetic loci often provide a more comprehensive picture of evolutionary history than any single gene can, but analyzing multigene data presents particular challenges. Differing rates and patterns of nucleotide substitution, combined with the limited information available in any data set, can make it difficult to specify a model of evolution. In addition, conflict among loci can be the result of real differences in evolutionary process or of stochastic variance and errors in reconstruction. We used 6 presumably unlinked nuclear loci to investigate relationships within the mammalian family Tupaiidae (Scandentia), containing all but one of the extant tupaiid genera. We used a phylogenetic mixture model to analyze the concatenated data and compared this with results using partitioned models. We found that more complex models were not necessarily preferred under tests using Bayes factors and that model complexity affected both tree length and parameter variance. We also compared the results of single-gene and multigene analyses and used splits networks to analyze the source and degree of conflict among genes. Networks can show specific relationships that are inconsistent with each other; these conflicting and minority relationships, which are implicitly ignored or collapsed by traditional consensus methods, can be useful in identifying the underlying causes of topological uncertainty. In our data, conflict is concentrated around particular relationships, not widespread throughout the tree. This pattern is further clarified by considering conflict surrounding the root separately from conflict within the ingroup. Uncertainty in rooting may be because of the apparent evolutionary distance separating these genera and our outgroup, the tupaiid genus Dendrogale. Unlike a previous mitochondrial study, these nuclear data strongly suggest that the genus Tupaia is not monophyletic with respect to the monotypic Urogale, even when uncertainty about rooting is taken into account. These data concur with mitochondrial DNA on other relationships, including the close affinity of Tupaia tana with the enigmatic Tupaia splendidula and of Tupaia belangeri with Tupaia glis. We also discuss the taxonomic and biogeographic implications of these results.