Incomplete lineage sorting and phenotypic evolution in marsupials.

Incomplete lineage sorting (ILS) makes ancestral genetic polymorphisms persist during rapid speciation events, inducing incongruences between gene trees and species trees. ILS has complicated phylogenetic inference in many lineages, including hominids. However, we lack empirical evidence that ILS leads to incongruent phenotypic variation. Here, we performed phylogenomic analyses to show that the South American monito del monte is the sister lineage of all Australian marsupials, although over 31% of its genome is closer to the Diprotodontia than to other Australian groups due to ILS during ancient radiation. Pervasive conflicting phylogenetic signals across the whole genome are consistent with some of the morphological variation among extant marsupials. We detected hundreds of genes that experienced stochastic fixation during ILS, encoding the same amino acids in non-sister species. Using functional experiments, we confirm how ILS may have directly contributed to hemiplasy in morphological traits that were established during rapid marsupial speciation ca. 60 mya.

Dire wolves were the last of an ancient New World canid lineage.

Dire wolves are considered to be one of the most common and widespread large carnivores in Pleistocene America1, yet relatively little is known about their evolution or extinction. Here, to reconstruct the evolutionary history of dire wolves, we sequenced five genomes from sub-fossil remains dating from 13,000 to more than 50,000 years ago. Our results indicate that although they were similar morphologically to the extant grey wolf, dire wolves were a highly divergent lineage that split from living canids around 5.7 million years ago. In contrast to numerous examples of hybridization across Canidae2,3, there is no evidence for gene flow between dire wolves and either North American grey wolves or coyotes. This suggests that dire wolves evolved in isolation from the Pleistocene ancestors of these species. Our results also support an early New World origin of dire wolves, while the ancestors of grey wolves, coyotes and dholes evolved in Eurasia and colonized North America only relatively recently.

Combining camera trap surveys and IUCN range maps to improve knowledge of species distributions.

Reliable maps of species distributions are fundamental for biodiversity research and conservation. The International Union for Conservation of Nature (IUCN) range maps are widely recognized as authoritative representations of species' geographic limits, yet they might not always align with actual occurrence data. In recent area of habitat (AOH) maps, areas that are not habitat have been removed from IUCN ranges to reduce commission errors, but their concordance with actual species occurrence also remains untested. We tested concordance between occurrences recorded in camera trap surveys and predicted occurrences from the IUCN and AOH maps for 510 medium- to large-bodied mammalian species in 80 camera trap sampling areas. Across all areas, cameras detected only 39% of species expected to occur based on IUCN ranges and AOH maps; 85% of the IUCN only mismatches occurred within 200 km of range edges. Only 4% of species occurrences were detected by cameras outside IUCN ranges. The probability of mismatches between cameras and the IUCN range was significantly higher for smaller-bodied mammals and habitat specialists in the Neotropics and Indomalaya and in areas with shorter canopy forests. Our findings suggest that range and AOH maps rarely underrepresent areas where species occur, but they may more often overrepresent ranges by including areas where a species may be absent, particularly at range edges. We suggest that combining range maps with data from ground-based biodiversity sensors, such as camera traps, provides a richer knowledge base for conservation mapping and planning.

Combinación de censos con fototrampas y mapas de extensión de la UICN para incrementar el conocimiento sobre la distribución de las especies Resumen Los mapas confiables de la distribución de las especies son fundamentales para la investigación y conservación de la biodiversidad. Los mapas de distribución de la Unión Internacional para la Conservación de la Naturaleza (UICN) están reconocidos como representaciones de autoridad de los límites geográficos de las especies, aunque no siempre se alinean con los datos actuales de su presencia. En los mapas recientes de área de hábitat (ADH), las áreas que no son hábitat han sido eliminadas de la distribución de la UICN para reducir los errores de comisión, pero su concordancia con la presencia actual de las especies tampoco ha sido analizada. Analizamos la concordancia entre la presencia registrada por los censos de fototrampas y pronosticamos la presencia a partir de los mapas de la UICN y de ADH de 510 especies de mamíferos de talla mediana a grande en 80 áreas de muestreo de fototrampas. Las cámaras detectaron sólo el 39% de las especies esperadas con base en la distribución de la UICN y los mapas de ADH en todas las áreas; el 85% de las disparidades con la UICN ocurrieron dentro de los 200 km a partir del borde de la distribución. Sólo el 4% de la presencia de las especies fue detectada por las cámaras ubicadas fuera de la distribución de la UICN. La probabilidad de disparidad entre las cámaras y la UICN fue significativamente mayor para los mamíferos de talla pequeña y para los especialistas de hábitat en las regiones Neotropical e Indomalaya y en áreas con doseles forestales más bajos. Nuestros hallazgos sugieren que los mapas de distribución y ADH pocas veces subrepresentan las áreas con presencia de las especies, pero con frecuencia pueden sobrerrepresentar la distribución al incluir áreas en donde las especies pueden estar ausentes, en particular los bordes de la distribución. Sugerimos que la combinación de los mapas de distribución con los sensores de biodiversidad en tierra, como las fototrampas, proporciona una base más rica de conocimiento para el mapeo y la planeación de la conservación.

Widespread male sex bias in mammal fossil and museum collections.

A recent study of mammoth subfossil remains has demonstrated the potential of using relatively low-coverage high-throughput DNA sequencing to genetically sex specimens, revealing a strong male-biased sex ratio [P. Pecnerová et al., Curr. Biol. 27, 3505-3510.e3 (2017)]. Similar patterns were predicted for steppe bison, based on their analogous female herd-based structure. We genetically sexed subfossil remains of 186 Holarctic bison (Bison spp.), and also 91 brown bears (Ursus arctos), which are not female herd-based, and found that ∼75% of both groups were male, very close to the ratio observed in mammoths (72%). This large deviation from a 1:1 ratio was unexpected, but we found no evidence for sex differences with respect to DNA preservation, sample age, material type, or overall spatial distribution. We further examined ratios of male and female specimens from 4 large museum mammal collections and found a strong male bias, observable in almost all mammalian orders. We suggest that, in mammals at least, 1) wider male geographic ranges can lead to considerably increased chances of detection in fossil studies, and 2) sexual dimorphic behavior or appearance can facilitate a considerable sex bias in fossil and modern collections, on a previously unacknowledged scale. This finding has major implications for a wide range of studies of fossil and museum material.

Impacts of Inference Method and Data set Filtering on Phylogenomic Resolution in a Rapid Radiation of Ground Squirrels (Xerinae: Marmotini).

Phylogenomic data sets are illuminating many areas of the Tree of Life. However, the large size of these data sets alone may be insufficient to resolve problematic nodes in the most rapid evolutionary radiations, because inferences in zones of extraordinarily low phylogenetic signal can be sensitive to the model and method of inference, as well as the information content of loci employed. We used a data set of $>$3950 ultraconserved element (UCE) loci from a classic mammalian radiation, ground-dwelling squirrels of the tribe Marmotini (Sciuridae: Xerinae), to assess sensitivity of phylogenetic estimates to varying per-locus information content across four different inference methods (RAxML, ASTRAL, NJst, and SVDquartets). Persistent discordance was found in topology and bootstrap support between concatenation- and coalescent-based inferences; among methods within the coalescent framework; and within all methods in response to different filtering scenarios. Contrary to some recent empirical UCE-based studies, filtering by information content did not promote complete among-method concordance. Nevertheless, filtering did improve concordance relative to randomly selected locus sets, largely via improved consistency of two-step summary methods (particularly NJst) under conditions of higher average per-locus variation (and thus increasing gene tree precision). The benefits of phylogenomic data set filtering are variable among classes of inference methods and across different evolutionary scenarios, reiterating the complexities of resolving rapid radiations, even with robust taxon and character sampling.

Sex biases in bird and mammal natural history collections.

Natural history specimens are widely used across ecology, evolutionary biology and conservation. Although biological sex may influence all of these areas, it is often overlooked in large-scale studies using museum specimens. If collections are biased towards one sex, studies may not be representative of the species. Here, we investigate sex ratios in over two million bird and mammal specimen records from five large international museums. We found a slight bias towards males in birds (40% females) and mammals (48% females), but this varied among orders. The proportion of female specimens has not significantly changed in 130 years, but has decreased in species with showy male traits like colourful plumage and horns. Body size had little effect. Male bias was strongest in name-bearing types; only 27% of bird and 39% of mammal types were female. These results imply that previous studies may be impacted by undetected male bias, and vigilance is required when using specimen data, collecting new specimens and designating types.

Temporal shifts in the distribution of murine rodent body size classes at Liang Bua (Flores, Indonesia) reveal new insights into the paleoecology of Homo floresiensis and associated fauna.

Liang Bua, the type locality of Homo floresiensis, is a limestone cave located in the western part of the Indonesian island of Flores. The relatively continuous stratigraphic sequence of the site spans the past ∼190 kyr and contains ∼275,000 taxonomically identifiable vertebrate skeletal elements, ∼80% of which belong to murine rodent taxa (i.e., rats). Six described genera are present at Liang Bua (Papagomys, Spelaeomys, Hooijeromys, Komodomys, Paulamys, and Rattus), one of which, Hooijeromys, is newly recorded in the site deposits, being previously known only from Early to Middle Pleistocene sites in central Flores. Measurements of the proximal femur (n = 10,212) and distal humerus (n = 1186) indicate five murine body size classes ranging from small (mouse-sized) to giant (common rabbit-sized) are present. The proportions of these five classes across successive stratigraphic units reveal two major changes in murine body size distribution due to significant shifts in the abundances of more open habitat-adapted medium-sized murines versus more closed habitat-adapted smaller-sized ones. One of these changes suggests a modest increase in available open habitats occurred ∼3 ka, likely the result of anthropogenic changes to the landscape related to farming by modern human populations. The other and more significant change occurred ∼60 ka suggesting a rapid shift from more open habitats to more closed conditions at this time. The abrupt reduction of medium-sized murines, along with the disappearance of H. floresiensis, Stegodon florensis insularis (an extinct proboscidean), Varanus komodoensis (Komodo dragon), Leptoptilos robustus (giant marabou stork), and Trigonoceps sp. (vulture) at Liang Bua ∼60-50 ka, is likely the consequence of these animals preferring and tracking more open habitats to elsewhere on the island. If correct, then the precise timing and nature of the extinction of H. floresiensis and its contemporaries must await new discoveries at Liang Bua or other as yet unexcavated sites on Flores.

Comparative Phylogeography of Forest-Dependent Mammals Reveals Paleo-Forest Corridors throughout Sundaland.

The evolutionary history of the colugo, a gliding arboreal mammal distributed throughout Sundaland, was influenced by the location of and connections between forest habitats. By comparing colugo phylogenetic patterns, species ecology, sample distributions, and times of divergence to those of other Sundaic taxa with different life-history traits and dispersal capabilities, we inferred the probable distribution of paleo-forest corridors and their influence on observed biogeographic patterns. We identified a consistent pattern of early diversification between east and west Bornean lineages in colugos, lesser mouse deer, and Sunda pangolins, but not in greater mouse deer. This deep east-west split within Borneo has not been commonly described in mammals. Colugos on West Borneo diverged from colugos in Peninsular Malaysia and Sumatra in the late Pliocene, however most other mammalian populations distributed across these same geographic regions diverged from a common ancestor more recently in the Pleistocene. Low genetic divergence between colugos on large landmasses and their neighboring satellite islands indicated that past forest distributions were recently much larger than present refugial distributions. Our analysis of colugo evolutionary history reconstructs Borneo as the most likely ancestral area of origin for Sunda colugos, and suggests that forests present during the middle Pliocene within the Sunda Shelf were more evergreen and contiguous, while forests were more fragmented, transient, seasonal, or with lower density canopies in the Pleistocene.

Talpid Mole Phylogeny Unites Shrew Moles and Illuminates Overlooked Cryptic Species Diversity.

The mammalian family Talpidae (moles, shrew moles, desmans) is characterized by diverse ecomorphologies associated with terrestrial, semi-aquatic, semi-fossorial, fossorial, and aquatic-fossorial lifestyles. Prominent specializations involved with these different lifestyles, and the transitions between them, pose outstanding questions regarding the evolutionary history within the family, not only for living but also for fossil taxa. Here, we investigate the phylogenetic relationships, divergence times, and biogeographic history of the family using 19 nuclear and 2 mitochondrial genes (∼16 kb) from ∼60% of described species representing all 17 genera. Our phylogenetic analyses help settle classical questions in the evolution of moles, identify an ancient (mid-Miocene) split within the monotypic genus Scaptonyx, and indicate that talpid species richness may be nearly 30% higher than previously recognized. Our results also uniformly support the monophyly of long-tailed moles with the two shrew mole tribes and confirm that the Gansu mole is the sole living Asian member of an otherwise North American radiation. Finally, we provide evidence that aquatic specializations within the tribes Condylurini and Desmanini evolved along different morphological trajectories, though we were unable to statistically reject monophyly of the strictly fossorial tribes Talpini and Scalopini.

Phylogenetic analysis of the tree-kangaroos (Dendrolagus) reveals multiple divergent lineages within New Guinea.

Amongst the Australasian kangaroos and wallabies (Macropodidae) one anomalous genus, the tree-kangaroos, Dendrolagus, has secondarily returned to arboreality. Modern tree-kangaroos are confined to the wet tropical forests of north Queensland, Australia (2 species) and New Guinea (8 species). Due to their behavior, distribution and habitat most species are poorly known and our understanding of the evolutionary history and systematics of the genus is limited and controversial. We obtained tissue samples from 36 individual Dendrolagus including representatives from 14 of the 17 currently recognised or proposed subspecies and generated DNA sequence data from three mitochondrial (3116 bp) and five nuclear (4097 bp) loci. Phylogenetic analysis of these multi-locus data resolved long-standing questions regarding inter-relationships within Dendrolagus. The presence of a paraphyletic ancestral long-footed and derived monophyletic short-footed group was confirmed. Six major lineages were identified: one in Australia (D. lumholtzi, D. bennettianus) and five in New Guinea (D. inustus, D. ursinus, a Goodfellow's group, D. mbaiso and a Doria's group). Two major episodes of diversification within Dendrolagus were identified: the first during the late Miocene/early Pliocene associated with orogenic processes in New Guinea and the second mostly during the early Pleistocene associated with the intensification of climatic cycling. All sampled subspecies showed high levels of genetic divergence and currently recognized species within both the Doria's and Goodfellow's groups were paraphyletic indicating that adjustments to current taxonomy are warranted.

Genetic Structure and Diversity Among Historic and Modern Populations of the Sumatran Rhinoceros (Dicerorhinus sumatrensis).

The Sumatran rhinoceros (Dicerorhinus sumatrensis), once widespread across Southeast Asia, now consists of as few as 30 individuals within Sumatra and Borneo. To aid in conservation planning, we sequenced 218 bp of control region mitochondrial (mt) DNA, identifying 17 distinct mitochondrial haplotypes across modern (N = 13) and museum (N = 26) samples. Museum specimens from Laos and Myanmar had divergent mtDNA, consistent with the placement of western mainland rhinos into the distinct subspecies D. s. lasiotis (presumed extinct). Haplotypes from Bornean rhinos were highly diverse, but dissimilar from those of other regions, supporting the distinctiveness of the subspecies D. s. harrissoni. Rhinos from Sumatra and Peninsular Malaysia shared mtDNA haplotypes, consistent with their traditional placement into a single subspecies D. s sumatrensis. Modern samples of D. s. sumatrensis were genotyped at 18 microsatellite loci. Rhinos within Sumatra formed 2 sub-populations, likely separated by the Barisan Mountains, though with only modest genetic differentiation between them. There are so few remaining Sumatran rhinoceros that separate management strategies for subspecies or subpopulations may not be viable, while each surviving rhino pedigree is likely to retain alleles found in no other individuals. Given the low population size and low reproductive potential of Sumatran rhinos, rapid genetic erosion is inevitable, though an under-appreciated concern is the potential for fixation of harmful genetic variants. Both concerns underscore 2 overriding priorities for the species: 1) translocation of wild rhinos to ex situ facilities, and 2) collection and storage of gametes and cell lines from every surviving captive and wild individual.

White-Nose Syndrome Fungus in a 1918 Bat Specimen from France.

White-nose syndrome, first diagnosed in North America in 2006, causes mass deaths among bats in North America. We found the causative fungus, Pseudogymnoascus destructans, in a 1918 sample collected in Europe, where bats have now adapted to the fungus. These results are consistent with a Eurasian origin of the pathogen.

Endogenous Gibbon Ape Leukemia Virus Identified in a Rodent (Melomys burtoni subsp.) from Wallacea (Indonesia).

UNLABELLED: Gibbon ape leukemia virus (GALV) and koala retrovirus (KoRV) most likely originated from a cross-species transmission of an ancestral retrovirus into koalas and gibbons via one or more intermediate as-yet-unknown hosts. A virus highly similar to GALV has been identified in an Australian native rodent (Melomys burtoni) after extensive screening of Australian wildlife. GALV-like viruses have also been discovered in several Southeast Asian species, although screening has not been extensive and viruses discovered to date are only distantly related to GALV. We therefore screened 26 Southeast Asian rodent species for KoRV- and GALV-like sequences, using hybridization capture and high-throughput sequencing, in the attempt to identify potential GALV and KoRV hosts. Only the individuals belonging to a newly discovered subspecies of Melomys burtoni from Indonesia were positive, yielding an endogenous provirus very closely related to a strain of GALV. The sequence of the critical receptor domain for GALV infection in the Indonesian M. burtoni subsp. was consistent with the susceptibility of the species to GALV infection. The second record of a GALV in M. burtoni provides further evidence that M. burtoni, and potentially other lineages within the widespread subfamily Murinae, may play a role in the spread of GALV-like viruses. The discovery of a GALV in the most western part of the Australo-Papuan distribution of M. burtoni, specifically in a transitional zone between Asia and Australia (Wallacea), may be relevant to the cross-species transmission to gibbons in Southeast Asia and broadens the known distribution of GALVs in wild rodents. IMPORTANCE: Gibbon ape leukemia virus (GALV) and the koala retrovirus (KoRV) are very closely related, yet their hosts neither are closely related nor overlap geographically. Direct cross-species infection between koalas and gibbons is unlikely. Therefore, GALV and KoRV may have arisen via a cross-species transfer from an intermediate host whose range overlaps those of both gibbons and koalas. Using hybridization capture and high-throughput sequencing, we have screened a wide range of rodent candidate hosts from Southeast Asia for KoRV- and GALV-like sequences. Only a Melomys burtoni subspecies from Wallacea (Indonesia) was positive for GALV. We report the genome sequence of this newly identified GALV, the critical domain for infection of its potential cellular receptor, and its phylogenetic relationships with the other previously characterized GALVs. We hypothesize that Melomys burtoni, and potentially related lineages with an Australo-Papuan distribution, may have played a key role in cross-species transmission to other taxa.

Description of a new species of Hoolock gibbon (Primates: Hylobatidae) based on integrative taxonomy.

We describe a species of Hoolock gibbon (Primates: Hylobatidae) that is new to science from eastern Myanmar and southwestern China. The genus of hoolock gibbons comprises two previously described living species, the western (Hoolock hoolock) and eastern hoolock (H. leuconedys) gibbons, geographically isolated by the Chindwin River. We assessed the morphological and genetic characteristics of wild animals and museum specimens, and conducted multi-disciplinary analyses using mitochondrial genomic sequences, external morphology, and craniodental characters to evaluate the taxonomic status of the hoolock population in China. The results suggest that hoolocks distributed to the east of the Irrawaddy-Nmai Hka Rivers, which were previously assigned to H. leuconedys, are morphologically and genetically distinct from those to the west of the river, and should be recognized as a new species, the Gaoligong hoolock gibbon or skywalker hoolock gibbon (H. tianxing sp. nov.). We consider that the new species should be categorized as Endangered under IUCN criteria. The discovery of the new species focuses attention on the need for improved conservation of small apes, many of which are in danger of extinction in southern China and Southeast Asia.

Declines in large wildlife increase landscape-level prevalence of rodent-borne disease in Africa.

Populations of large wildlife are declining on local and global scales. The impacts of this pulse of size-selective defaunation include cascading changes to smaller animals, particularly rodents, and alteration of many ecosystem processes and services, potentially involving changes to prevalence and transmission of zoonotic disease. Understanding linkages between biodiversity loss and zoonotic disease is important for both public health and nature conservation programs, and has been a source of much recent scientific debate. In the case of rodent-borne zoonoses, there is strong conceptual support, but limited empirical evidence, for the hypothesis that defaunation, the loss of large wildlife, increases zoonotic disease risk by directly or indirectly releasing controls on rodent density. We tested this hypothesis by experimentally excluding large wildlife from a savanna ecosystem in East Africa, and examining changes in prevalence and abundance of Bartonella spp. infection in rodents and their flea vectors. We found no effect of wildlife removal on per capita prevalence of Bartonella infection in either rodents or fleas. However, because rodent and, consequently, flea abundance doubled following experimental defaunation, the density of infected hosts and infected fleas was roughly twofold higher in sites where large wildlife was absent. Thus, defaunation represents an elevated risk in Bartonella transmission to humans (bartonellosis). Our results (i) provide experimental evidence of large wildlife defaunation increasing landscape-level disease prevalence, (ii) highlight the importance of susceptible host regulation pathways and host/vector density responses in biodiversity-disease relationships, and (iii) suggest that rodent-borne disease responses to large wildlife loss may represent an important context where this relationship is largely negative.

Evolutionary history of endemic Sulawesi squirrels constructed from UCEs and mitogenomes sequenced from museum specimens.

BACKGROUND: The Indonesian island of Sulawesi has a complex geological history. It is composed of several landmasses that have arrived at a near modern configuration only in the past few million years. It is the largest island in the biodiversity hotspot of Wallacea-an area demarcated by the biogeographic breaks between Wallace's and Lydekker's lines. The mammal fauna of Sulawesi is transitional between Asian and Australian faunas. Sulawesi's three genera of squirrels, all endemic (subfamily Nannosciurinae: Hyosciurus, Rubrisciurus and Prosciurillus), are of Asian origin and have evolved a variety of phenotypes that allow a range of ecological niche specializations. Here we present a molecular phylogeny of this radiation using data from museum specimens. High throughput sequencing technology was used to generate whole mitochondrial genomes and a panel of nuclear ultraconserved elements providing a large genome-wide dataset for inferring phylogenetic relationships. RESULTS: Our analysis confirmed monophyly of the Sulawesi taxa with deep divergences between the three endemic genera, which predate the amalgamation of the current island of Sulawesi. This suggests lineages may have evolved in allopatry after crossing Wallace's line. Nuclear and mitochondrial analyses were largely congruent and well supported, except for the placement of Prosciurillus murinus. Mitochondrial analysis revealed paraphyly for Prosciurillus, with P. murinus between or outside of Hyosciurus and Rubrisciurus, separate from other species of Prosciurillus. A deep but monophyletic history for the four included species of Prosciurillus was recovered with the nuclear data. CONCLUSIONS: The divergence of the Sulawesi squirrels from their closest relatives dated to ~9.7-12.5 million years ago (MYA), pushing back the age estimate of this ancient adaptive radiation prior to the formation of the current conformation of Sulawesi. Generic level diversification took place around 9.7 MYA, opening the possibility that the genera represent allopatric lineages that evolved in isolation in an ancient proto-Sulawesian archipelago. We propose that incongruence between phylogenies based on nuclear and mitochondrial sequences may have resulted from biogeographic discordance, when two allopatric lineages come into secondary contact, with complete replacement of the mitochondria in one species.

Genome sequence, population history, and pelage genetics of the endangered African wild dog (Lycaon pictus).

BACKGROUND: The African wild dog (Lycaon pictus) is an endangered African canid threatened by severe habitat fragmentation, human-wildlife conflict, and infectious disease. A highly specialized carnivore, it is distinguished by its social structure, dental morphology, absence of dewclaws, and colorful pelage. RESULTS: We sequenced the genomes of two individuals from populations representing two distinct ecological histories (Laikipia County, Kenya and KwaZulu-Natal Province, South Africa). We reconstructed population demographic histories for the two individuals and scanned the genomes for evidence of selection. CONCLUSIONS: We show that the African wild dog has undergone at least two effective population size reductions in the last 1,000,000 years. We found evidence of Lycaon individual-specific regions of low diversity, suggestive of inbreeding or population-specific selection. Further research is needed to clarify whether these population reductions and low diversity regions are characteristic of the species as a whole. We documented positive selection on the Lycaon mitochondrial genome. Finally, we identified several candidate genes (ASIP, MITF, MLPH, PMEL) that may play a role in the characteristic Lycaon pelage.

Phylogeny, biogeography and systematic revision of plain long-nosed squirrels (genus Dremomys, Nannosciurinae).

The plain long-nosed squirrels, genus Dremomys, are high elevation species in East and Southeast Asia. Here we present a complete molecular phylogeny for the genus based on nuclear and mitochondrial DNA sequences. Concatenated mitochondrial and nuclear gene trees were constructed to determine the tree topology, and date the tree. All speciation events within the plain-long nosed squirrels (genus Dremomys) were ancient (dated to the Pliocene or Miocene), and averaged older than many speciation events in the related Sunda squirrels, genus Sundasciurus. Within the plain long-nosed squirrels, the most recent interspecific split occurred 2.9 million years ago, older than some splits within Sunda squirrels, which dated to the Pleistocene. Our results demonstrate that the plain long-nosed squirrels are not monophyletic. The single species with a distinct distribution, the Bornean mountain ground squirrel (Dremomys everetti), which is endemic to the high mountains of Borneo, is nested within the Sunda squirrels with high support. This species diverged from its sister taxa in the Sunda squirrels 6.62 million years ago, and other plain long-nosed squirrels over 11 million years ago. Our analyses of morphological traits in these related genera support the re-classification of the Bornean mountain ground squirrel, Dremomys everetti, to the genus Sundasciurus, which changes its name to Sundasciurus everetti. Past inclusion in the plain long-nosed squirrels (Dremomys) reflects convergent evolution between these high elevation species.

Context-dependent effects of large-wildlife declines on small-mammal communities in central Kenya.

Many species of large wildlife have declined drastically worldwide. These reductions often lead to profound shifts in the ecology of entire communities and ecosystems. However, the effects of these large-wildlife declines on other taxa likely hinge upon both underlying abiotic properties of these systems and on the types of secondary anthropogenic changes associated with wildlife loss, making impacts difficult to predict. To better understand how these important contextual factors determine the consequences of large-wildlife declines on other animals in a community, we examined the effects of three common forms of large-wildlife loss (removal without replacement [using fences], removal followed by replacement with domestic stock, and removal accompanied by crop agricultural use) on small-mammal abundance, diversity, and community composition, in landscapes that varied in several abiotic attributes (rainfall, soil fertility, land-use intensity) in central Kenya. We found that small-mammal communities were indeed heavily impacted by all forms of large-wildlife decline, showing, on average: (1) higher densities, (2) lower species richness per site, and (3) different species assemblages in sites from which large wildlife were removed. However, the nature and magnitude of these effects were strongly context dependent. Rainfall, type of land-use change, and the interaction of these two factors were key predictors of both the magnitude and type of responses of small mammals. The strongest effects, particularly abundance responses, tended to be observed in low-rainfall areas. Whereas isolated wildlife removal primarily led to increased small-mammal abundance, wildlife removal associated with secondary uses (agriculture, domestic stock) had much more variable effects on abundance and stronger impacts on diversity and composition. Collectively, these results (1) highlight the importance of context in determining the impacts of large-wildlife decline on small-mammal communities, (2) emphasize the challenges in extrapolating results from controlled experimental studies to predict the effects of wildlife declines that are accompanied by secondary land-uses, and (3) suggest that, because of the context-dependent nature of the responses to large-wildlife decline, large-wildlife status alone cannot be reliably used to predict small-mammal community changes.