A new genus for a rare African vespertilionid bat: insights from South Sudan

A new genus is proposed for the strikingly patterned African vespertilionid "Glauconycteris" superba Hayman, 1939 on the basis of cranial and external morphological comparisons. A review of the attributes of a newly collected specimen from South Sudan (a new country record) and other museum specimens of "Glauconycteris" superba suggests that "Glauconycteris" superba is markedly distinct ecomorphologically from other species classified in Glauconycteris and is likely the sister taxon to Glauconycteris sensu stricto. The recent capture of this rarely collected but widespread bat highlights the need for continued research in tropical sub-Saharan Africa and in particular, for more work in western South Sudan, which has received very little scientific attention. New country records for Glauconycteris cf. poensis (South Sudan) and Glauconycteris curryae (Gabon) are also reported.DeeAnn M. Reeder, Kristofer M. Helgen, Megan E. Vodzak, Darrin P. Lunde, Imran Ejotr

Historically low mitochondrial DNA diversity in koalas (Phascolarctos cinereus)

Maria C Avila-ArcosBACKGROUND: The koala (Phascolarctos cinereus) is an arboreal marsupial that was historically widespread across eastern Australia until the end of the 19th century when it suffered a steep population decline. Hunting for the fur trade, habitat conversion, and disease contributed to a precipitous reduction in koala population size during the late 1800s and early 1900s. To examine the effects of these reductions in population size on koala genetic diversity, we sequenced part of the hypervariable region of mitochondrial DNA (mtDNA) in koala museum specimens collected in the 19th and 20th centuries, hypothesizing that the historical samples would exhibit greater genetic diversity. RESULTS: The mtDNA haplotypes present in historical museum samples were identical to haplotypes found in modern koala populations, and no novel haplotypes were detected. Rarefaction analyses suggested that the mtDNA genetic diversity present in the museum samples was similar to that of modern koalas. CONCLUSIONS: Low mtDNA diversity may have been present in koala populations prior to recent population declines. When considering management strategies, low genetic diversity of the mtDNA hypervariable region may not indicate recent inbreeding or founder events but may reflect an older historical pattern for koalas.Kyriakos Tsangaras, María C Ávila-Arcos, Yasuko Ishida, Kristofer M Helgen, Alfred L Roca and Alex D Greenwoo

Two new species of Pteropus from Samoa, probably extinct.

37 p. : ill., maps ; 26 cm. "June 25, 2009." Includes bibliographical references (p. 30-37).Two new species of flying foxes (genus Pteropus) from the Samoan archipelago are described on the basis of modern museum specimens collected in the mid-19th century. A medium-sized species (P. allenorum, n. sp.) is introduced from the island of Upolu (Independent Samoa), based on a specimen collected in 1856 and deposited in the Academy of Natural Sciences of Philadelphia. It has not been collected again, and we regard it as almost certainly extinct. This species is smaller bodied and has much smaller teeth than both extant congeners recorded in the contemporary fauna of Samoa (Pteropus samoensis and P. tonganus). The closest relative of this new species may be Pteropus fundatus of northern Vanuatu. The disjunct historical distribution of these two small-toothed flying foxes (in Vanuatu and Samoa) suggests that similar species may have been more extensively distributed in the remote Pacific in the recent past. Another species, a very large flying fox with large teeth (P. coxi, n. sp.), is described from two skulls collected in Samoa in 1839-1841 during the U.S. Exploring Expedition; it too has not been collected since. This robust species resembles Pteropus samoensis and Pteropus anetianus of Vanuatu in craniodental conformation but is larger than other Polynesian Pteropus, and in some features it is ecomorphologically convergent on the Pacific monkey-faced bats (the pteropodid genera Pteralopex and Mirimiri). On the basis of eyewitness reports from the early 1980s, it is possible that this species survived until recent decades, or is still extant. These two new Samoan species join Pteropus tokudae of Guam, P. pilosus of Palau, P. subniger of the Mascarenes, and P. brunneus of coastal north-eastern Australia as flying foxes with limited insular distributions that survived at least until the 19th century but are now most likely extinct.American Museum of Natural History

Biogeography and taxonomy of extinct and endangered monk seals illuminated by ancient DNA and skull morphology

Extinctions and declines of large marine vertebrates have major ecological impacts and are of critical concern in marine environments. The Caribbean monk seal, Monachus tropicalis, last definitively reported in 1952, was one of the few marine mammal species to become extinct in historical times. Despite its importance for understanding the evolutionary biogeography of southern phocids, the relationships of M. tropicalis to the two living species of critically endangered monk seals have not been resolved. In this study we present the first molecular data for M. tropicalis, derived from museum skins. Phylogenetic analysis of cytochrome b sequences indicates that M. tropicalis was more closely related to the Hawaiian rather than the Mediterranean monk seal. Divergence time estimation implicates the formation of the Panamanian Isthmus in the speciation of Caribbean and Hawaiian monk seals. Molecular, morphological and temporal divergence between the Mediterranean and "New World monk seals" (Hawaiian and Caribbean) is profound, equivalent to or greater than between sister genera of phocids. As a result, we classify the Caribbean and Hawaiian monk seals together in a newly erected genus, Neomonachus. The two genera of extant monk seals (Monachus and Neomonachus) represent old evolutionary lineages each represented by a single critically endangered species, both warranting continuing and concerted conservation attention and investment if they are to avoid the fate of their Caribbean relative.Dirk-Martin Scheel, Graham J. Slater, Sergios-Orestis Kolokotronis, Charles W. Potter, David S. Rotstein, Kyriakos Tsangaras, Alex D. Greenwood, Kristofer M. Helge

Hybridization capture reveals evolution and conservation across the entire koala retrovirus genome

The koala retrovirus (KoRV) is the only retrovirus known to be in the midst of invading the germ line of its host species. Hybridization capture and next generation sequencing were used on modern and museum DNA samples of koala (Phascolarctos cinereus) to examine ca. 130 years of evolution across the full KoRV genome. Overall, the entire proviral genome appeared to be conserved across time in sequence, protein structure and transcriptional binding sites. A total of 138 polymorphisms were detected, of which 72 were found in more than one individual. At every polymorphic site in the museum koalas, one of the character states matched that of modern KoRV. Among non-synonymous polymorphisms, radical substitutions involving large physiochemical differences between amino acids were elevated in env, potentially reflecting anti-viral immune pressure or avoidance of receptor interference. Polymorphisms were not detected within two functional regions believed to affect infectivity. Host sequences flanking proviral integration sites were also captured; with few proviral loci shared among koalas. Recently described variants of KoRV, designated KoRV-B and KoRV-J, were not detected in museum samples, suggesting that these variants may be of recent origin.Kyriakos Tsangaras, Matthew C. Siracusa, Nikolas Nikolaidis, Yasuko Ishida, Pin Cui, Hanna Vielgrader, Kristofer M. Helgen, Alfred L. Roca, Alex D. Greenwoo

Taxonomic revision of the olingos (Bassaricyon), with description of a new species, the Olinguito

Published 15 August 2013We present the first comprehensive taxonomic revision and review the biology of the olingos, the endemic Neotropical procyonid genus Bassaricyon, based on most specimens available in museums, and with data derived from anatomy, morphometrics, mitochondrial and nuclear DNA, field observations, and geographic range modeling. Species of Bassaricyon are primarily forest-living, arboreal, nocturnal, frugivorous, and solitary, and have one young at a time. We demonstrate that four olingo species can be recognized, including a Central American species (Bassaricyon gabbii), lowland species with eastern, cis-Andean (Bassaricyon alleni) and western, trans-Andean (Bassaricyon medius) distributions, and a species endemic to cloud forests in the Andes. The oldest evolutionary divergence in the genus is between this last species, endemic to the Andes of Colombia and Ecuador, and all other species, which occur in lower elevation habitats. Surprisingly, this Andean endemic species, which we call the Olinguito, has never been previously described; it represents a new species in the order Carnivora and is the smallest living member of the family Procyonidae. We report on the biology of this new species based on information from museum specimens, niche modeling, and fieldwork in western Ecuador, and describe four Olinguito subspecies based on morphological distinctions across different regions of the Northern Andes.Kristofer M. Helgen, C. Miguel Pinto, Roland Kays, Lauren E. Helgen, Mirian T. N. Tsuchiya, Aleta Quinn, Don E. Wilson, Jesús E. Maldonad

A gene-tree test of the traditional taxonomy of American deer: the importance of voucher specimens, geographic data, and dense sampling

The taxonomy of American deer has been established almost entirely on the basis of morphological data and without the use of explicit phylogenetic methods; hence, phylogenetic analyses including data for all of the currently recognized species, even if based on a single gene, might improve current understanding of their taxonomy. We tested the monophyly of the morphology-defined genera and species of New World deer (Odocoileini) with phylogenetic analyses of mitochondrial DNA sequences. This is the first such test conducted using extensive geographic and taxonomic sampling. Our results do not support the monophyly of Mazama, Odocoileus, Pudu, M. americana, M. nemorivaga, Od. hemionus, and Od. virginianus. Mazama contains species that belong to other genera. We found a novel sister-taxon relationship between “Mazama” pandora and a clade formed by Od. hemionus columbianus and Od. h. sitkensis, and transfer pandora to Odocoileus. The clade formed by Od. h. columbianus and Od. h. sitkensis may represent a valid species, whereas the remaining subspecies of Od. hemionus appear closer to Od. virginianus. Pudu (Pudu) puda was not found sister to Pudu (Pudella) mephistophiles. If confirmed, this result will prompt the recognition of the monotypic Pudella as a distinct genus. We provide evidence for the existence of an undescribed species now confused with Mazama americana, and identify other instances of cryptic, taxonomically unrecognized species-level diversity among populations here regarded as Mazama temama, “Mazama” nemorivaga, and Hippocamelus antisensis. Noteworthy records that substantially extend the known distributions of M. temama and “M.” gouazoubira are provided, and we unveil a surprising ambiguity regarding the distribution of “M.” nemorivaga, as it is described in the literature. The study of deer of the tribe Odocoileini has been hampered by the paucity of information regarding voucher specimens and the provenance of sequences deposited in GenBank. We pinpoint priorities for future systematic research on the tribe Odocoileini.Eliécer E. Gutiérrez, Kristofer M. Helgen, Molly M. McDonough, Franziska Bauer, Melissa T.R. Hawkins, Luis A. Escobedo-Morales, Bruce D. Patterson, Jesus E. Maldonad

New material of Coryphomys buehleri Schaub, 1937, and description of a second species of the genus.

80 p. : ill. (some col.), maps ; 26 cm. Issued July 21, 2010.Large collections of fragmentary animal bones excavated from archaeological contexts in East Timor between 1968 and 2002 provide new material referable to the recently extinct, gigantic murine genus Coryphomys. We document the upper and lower dentition and palatal anatomy of C. buehleri Schaub, 1937, and identify and name a second species of Coryphomys, based on differences in molar size and morphology and skeletal robusticity. Alternative interpretations of the observed morphological and metric variability (sexual dimorphism, resource-based polymorphism, sample heterochroneity) are each carefully assessed and rejected, and we conclude that the genus comprised two species of approximately similar body size. Preserved cranial elements of both species of Coryphomys feature a high degree of anatomical specialization, including an unusual elaboration of the maxillary sinus complex. Though the specialized anatomy of Coryphomys invites consideration of its phylogenetic relationships, this exercise is hindered by a demonstrable high level of homoplasy (i.e., multiple, independent evolutionary losses and gains) in many of the key craniodental features traditionally surveyed within Murinae, while other features are insufficiently well surveyed for broad-scale analysis. Nevertheless, our comparisons highlight two potentially related lineages among the geographically proximate Murinae - the Philippine Phloeomyini and the Australo-Papuan Hydromyini. The remains of Coryphomys are relatively scarce in all the archaeological samples, but distributional evidence suggests that both species of Coryphomys were found primarily in upland habitats. Late Pleistocene samples document their former presence at lower elevations, possibly reflecting cooler climatic conditions at that time

Review of Leptomys

60 p. : ill. (some col.), maps ; 26 cm.Includes bibliographical references (p. 56-60).Two new species of the endemic New Guinea rodent genus Leptomys Thomas, 1897, are described: L. paulus, indigenous to the montane forests in the Owen Stanley Range in eastern New Guinea, and L. arfakensis, known only from the Arfak Mountains on the Vogelkop Peninsula in western New Guinea. These descriptions are presented within a taxonomic review of Leptomys based on all known specimens in collections of the world's museums. In addition to the new species, the morphological attributes and geographic distributions of three others are documented. Leptomys elegans occurs in southcentral and southeastern New Guinea both north and south of the Central Cordillera, ranging from the Kikori River Basin in the west to the southern slopes of the Owen Stanley Range, then extending round to the north side of the Cordillera in the Maneau Range, and in the outlying highland block of Mount Victory. Leptomys signatus is recorded only from the Fly and Kikori River drainages south of the Central Cordillera. Leptomys ernstmayri is found in montane forests of the eastern Central Cordillera (Aroa River to Mt. Karimui), reaches to the outlying mountains on the Huon Peninsula and the Adelbert Range, and also occurs in the isolated Foja Mountains of far western New Guinea. Judged by variation in qualitative and morphometric external, cranial, and dental traits associated with available samples, L. arfakensis, n. sp., is likely more closely related to L. elegans and L. signatus, all with large bodies and relatively short tails, than to L. ernstmayri and L. paulus, n. sp., that are characterized, among other features, by smaller body size and relatively longer tails. There is significant phenetic divergence among the geographic samples identified here as L. ernstmayri, and additional inquiry, especially utilizing data from molecular sources, is required to determine whether this intersample variation reflects the presence of separate species, each endemic to the Huon Peninsula, Adelbert Range, Central Cordillera, and possibly the Foja Mountains, or instead represents montane variation within a single morphologically variable species