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Anthropogenic disturbances involving land use change, climate disruption, pollution and invasive species have been shown to impact immune function of wild animals. These immune changes have direct impacts on the fitness of impacted animals and, also, potentially indirect effects on other species and on ecological processes, notably involving the spread of infectious disease. Here, we investigate whether the selective loss of large wildlife can also drive changes in immune function of other consumer species. Using a long-standing large-scale exclosure experiment in East Africa, we investigated the effects of selective removal of large wildlife on multiple measures of immune function in the dominant small rodent in the system, the East African pouched mouse, Saccostomus mearnsi. We find support for a general increase in immune function in landscapes where large wildlife has been removed, but with some variation across immune parameters. These changes may be mediated in part by increased pathogen pressure in plots where large wildlife has been removed due to major increases in rodent density in such plots, but other factors such as changes in food resources are also likely involved. Overall, our research reveals that the elimination of large-bodied wildlife - now recognized as another major form of global anthropogenic change - may have cascading effects on immune health, with the potential for these effects to also impact disease dynamics in ecological communities. Lay Summary Functional Ecology

The golden jackal of Africa (Canis aureus) has long been considered a conspecific of jackals distributed throughout Eurasia, with the nearest source populations in the Middle East. However, two recent reports found that mitochondrial haplotypes of some African golden jackals aligned more closely to gray wolves (Canis lupus) [1, 2], which is surprising given the absence of gray wolves in Africa and the phenotypic divergence between the two species. Moreover, these results imply the existence of a previously unrecognized phylogenetically distinct species despite a long history of taxonomic work on African canids. To test the distinct-species hypothesis and understand the evolutionary history that would account for this puzzling result, we analyzed extensive genomic data including mitochondrial genome sequences, sequences from 20 autosomal loci (17 introns and 3 exon segments), microsatellite loci, X- and Y-linked zinc-finger protein gene (ZFX and ZFY) sequences, and whole-genome nuclear sequences in African and Eurasian golden jackals and gray wolves. Our results provide consistent and robust evidence that populations of golden jackals from Africa and Eurasia represent distinct monophyletic lineages separated for more than one million years, sufficient to merit formal recognition as different species: C. anthus (African golden wolf) and C. aureus (Eurasian golden jackal). Using morphologic data, we demonstrate a striking morphologic similarity between East African and Eurasian golden jackals, suggesting parallelism, which may have misled taxonomists and likely reflects uniquely intense interspecific competition in the East African carnivore guild. Our study shows how ecology can confound taxonomy if interspecific competition constrains size diversification.

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 largewildlife 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 smallmammal 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.

Ninu (greater bilby, Macrotis lagotis) are desert-dwelling, culturally and ecologically important marsupials. In collaboration with Indigenous rangers and conservation managers, we generated the Ninu chromosome-level genome assembly (3.66 Gbp) and genome sequences for the extinct Yallara (lesser bilby, Macrotis leucura). We developed and tested a scat single-nucleotide polymorphism panel to inform current and future conservation actions, undertake ecological assessments and improve our understanding of Ninu genetic diversity in managed and wild populations. We also assessed the beneficial impact of translocations in the metapopulation (N = 363 Ninu). Resequenced genomes (temperate Ninu, 6; semi-arid Ninu, 6; and Yallara, 4) revealed two major population crashes during global cooling events for both species and differences in Ninu genes involved in anatomical and metabolic pathways. Despite their 45-year captive history, Ninu have fewer long runs of homozygosity than other larger mammals, which may be attributable to their boom-bust life history. Here we investigated the unique Ninu biology using 12 tissue transcriptomes revealing expression of all 115 conserved eutherian chorioallantoic placentation genes in the uterus, an XY 1 Y 2 sex chromosome system and olfactory receptor gene expansions. Together, we demonstrate the holistic value of genomics in improving key conservation actions, understanding unique biological traits and developing tools for Indigenous rangers to monitor remote wild populations., (© 2024. The Author(s).)

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., (© 2024 The Authors. Conservation Biology published by Wiley Periodicals LLC on behalf of Society for Conservation Biology.)

Conservation areas encompassing elevation gradients are biodiversity hotspots because they contain a wide range of habitat types in a relatively small space. Studies of biodiversity patterns along elevation gradients, mostly on small mammal or bird species, have documented a peak in diversity at mid elevations. Here, we report on a field study of medium and large mammals to examine the impact of elevation, habitat type, and gross primary productivity on community structure. Species richness was observed using a camera trap transect with 219 sites situated across different habitat types from 2329 to 4657 m above the sea level on the western slope of Mt Kenya, the second highest mountain in Africa. We found that the lowest elevation natural habitats had the highest species richness and relative abundance and that both metrics decreased steadily as elevation increased, paralleling changes in gross primary productivity, and supporting the energy richness hypothesis. We found no evidence for the mid-domain effect on species diversity. The lowest elevation degraded Agro-Forestry lands adjacent to the National Park had high activity of domestic animals and reduced diversity and abundance of native species. The biggest difference in community structure was between protected and unprotected areas, followed by more subtle stepwise differences between habitats at different elevations. Large carnivore species remained relatively consistent but dominant herbivore species shifted along the elevation gradient. There was some habitat specialization and turnover in species, such that the elevation gradient predicts a high diversity of species, demonstrating the high conservation return for protecting mountain ecosystems for biodiversity conservation., Competing Interests: No conflicts of interest are known between any co‐author and outside entities regarding fiscal, board membership, consultancy, or any other overlap., (© 2024 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)

Photoluminescence in the pelage of mammals, a topic that has gained considerable recent research interest, was first documented in the 1700s and reported sporadically in the literature over the last century. The first detailed species accounts were of rabbits and humans, published 111 years ago in 1911. Recent studies have largely overlooked this earlier research into photoluminescent mammalian taxa and their luminophores. Here we provide a comprehensive update on existing research on photoluminescence in mammal fur, with the intention of drawing attention to earlier pioneering research in this field. We provide an overview on appropriate terminology, explain the physics of photoluminescence, and explore pigmentation and the ubiquitous photoluminescence of animal tissues, before touching on the emerging debate regarding visual function. We then provide a chronological account of research into mammalian fur photoluminescence, from the earliest discoveries and identification of luminophores to the most recent studies. While all mammal fur is likely to have a general low-level photoluminescence due to the presence of the protein keratin, fur glows luminously under ultraviolet light if it contains significant concentrations of tryptophan metabolites or porphyrins. Finally, we briefly discuss issues associated with preserved museum specimens in studies of photoluminescence. The study of mammal fur photoluminescence has a substantial history, which provides a broad foundation on which future studies can be grounded., (© The Author(s) 2023. Published by Oxford University Press on behalf of the American Society of Mammalogists.)

Gut microbiota studies often rely on a single sample taken per individual, representing a snapshot in time. However, we know that gut microbiota composition in many animals exhibits intra-individual variation over the course of days to months. Such temporal variations can be a confounding factor in studies seeking to compare the gut microbiota of different wild populations, or to assess the impact of medical/veterinary interventions. To date, little is known about the variability of the koala ( Phascolarctos cinereus ) gut microbiota through time. Here, we characterise the gut microbiota from faecal samples collected at eight timepoints over a month for a captive population of South Australian koalas ( n individuals = 7), and monthly over 7 months for a wild population of New South Wales koalas ( n individuals = 5). Using 16S rRNA gene sequencing, we found that microbial diversity was stable over the course of days to months. Each koala had a distinct faecal microbiota composition which in the captive koalas was stable across days. The wild koalas showed more variation across months, although each individual still maintained a distinct microbial composition. Per koala, an average of 57 (±16) amplicon sequence variants (ASVs) were detected across all time points; these ASVs accounted for an average of 97% (±1.9%) of the faecal microbial community per koala. The koala faecal microbiota exhibits stability over the course of days to months. Such knowledge will be useful for future studies comparing koala populations and developing microbiota interventions for this regionally endangered marsupial., Competing Interests: Kellie Leigh is employed by Science for Wildlife Ltd., (© 2023 Eisenhofer et al.)

Leptospirosis is the most common bacterial zoonosis globally. The pathogen, Leptospira spp., is primarily associated with rodent reservoirs. However, a wide range of other species has been implicated as reservoirs or dead-end hosts. We conducted a survey for Leptospira spp. in bats and rodents from Papua New Guinea. Kidney samples were collected from 97 pteropodid bats (five species), 37 insectivorous bats from four different families (six species) and 188 rodents (two species). Leptospires were detected in a high proportion of pteropodid bats, including Nyctimene cf. albiventer (35%), Macroglossus minimus (34%) and Rousettus amplexicaudatus (36%). Partial sequencing of the secY gene from rodent and bat leptospires showed host species clustering, with Leptospira interrogans and L. weilii detected in rodents and L. kirschneri and a potential novel species of Leptospira detected in bats. Further research is needed in Papua New Guinea and other locales in the Pacific region to gain a better understanding of the circulation dynamics of leptospires in reservoir species and the risks to public and veterinary health., (© 2022 The Authors. Transboundary and Emerging Diseases published by Wiley-VCH GmbH.)

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., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2022 Elsevier Inc. All rights reserved.)

Aim: Comprehensive, global information on species' occurrences is an essential biodiversity variable and central to a range of applications in ecology, evolution, biogeography and conservation. Expert range maps often represent a species' only available distributional information and play an increasing role in conservation assessments and macroecology. We provide global range maps for the native ranges of all extant mammal species harmonised to the taxonomy of the Mammal Diversity Database (MDD) mobilised from two sources, the Handbook of the Mammals of the World (HMW) and the Illustrated Checklist of the Mammals of the World (CMW)., Location: Global., Taxon: All extant mammal species., Methods: Range maps were digitally interpreted, georeferenced, error-checked and subsequently taxonomically aligned between the HMW (6253 species), the CMW (6431 species) and the MDD taxonomies (6362 species)., Results: Range maps can be evaluated and visualised in an online map browser at Map of Life (mol.org) and accessed for individual or batch download for non-commercial use., Main Conclusion: Expert maps of species' global distributions are limited in their spatial detail and temporal specificity, but form a useful basis for broad-scale characterizations and model-based integration with other data. We provide georeferenced range maps for the native ranges of all extant mammal species as shapefiles, with species-level metadata and source information packaged together in geodatabase format. Across the three taxonomic sources our maps entail, there are 1784 taxonomic name differences compared to the maps currently available on the IUCN Red List website. The expert maps provided here are harmonised to the MDD taxonomic authority and linked to a community of online tools that will enable transparent future updates and version control., Competing Interests: CONFLICT OF INTEREST The authors declare no competing interests.

Bone responds to elevated mechanical loading by increasing in mass and density. Therefore, wild animals should exhibit greater skeletal mass and density than captive conspecifics. This expectation is pertinent to testing bone functional adaptation theories and to comparative studies, which commonly use skeletal remains that combine zoo and wild-caught specimens. Conservationists are also interested in the effects of captivity on bone morphology as it may influence rewilding success. We compared trabecular bone volume fraction (BVF) between wild and captive mountain lions, cheetahs, leopards and jaguars. We found significantly greater BVF in wild than in captive felids. Effects of captivity were more marked in the humerus than in the femur. A ratio of humeral/femoral BVF was also lower in captive animals and showed a positive relationship to home range size in wild animals. Results are consistent with greater forelimb than hindlimb loading during terrestrial travel, and possibly reduced loading of the forelimb associated with lack of predatory behaviour in captive animals. Thus, captivity among felids has general effects on BVF in the postcranial skeleton and location-specific effects related to limb use. Caution should be exercised when identifying skeletal specimens for use in comparative studies and when rearing animals for conservation purposes., Competing Interests: We declare we have no competing interests., (© 2022 The Authors.)

Competing Interests: The authors declare no competing interest.

Cooper et al . (Research Articles, 19 February 2021, p. 811) propose that the Laschamps geomagnetic inversion ~42,000 years ago drove global climatic shifts, causing major behavioral changes within prehistoric groups, as well as events of human and megafaunal extinction. Other scientific studies indicate that this proposition is unproven from the current archaeological, paleoanthropological, and genetic records.

The flying squirrels (Pteromyini, Rodentia) are the most diverse and widely distributed group of gliding mammals. Taxonomic boundaries and relationships within flying squirrels remain an area of active research in mammalogy. The discovery of new specimens of Pteromys ( Hylopetes ) leonardi Thomas, 1921 previously considered a synonym of Hylopetes alboniger , in Yunnan Province, China allowed a morphological and genetic reassessment of the status of this taxon. Phylogenetic reconstruction was implemented using sequences of two mitochondrial (12S ribosomal DNA and 16S ribosomal DNA) and one nuclear (interphotoreceptor retinoid-binding protein) gene fragments. Morphological assessments involved examinations of features preserved on skins, skulls, and penises of museum specimens, supplemented with principal component analysis of craniometric data. Together these assessments revealed that this taxon should be recognized not only as a distinct species, and should also be placed within a new genus, described here as Priapomys .

The hominin fossil record of Island Southeast Asia (ISEA) indicates that at least two endemic 'super-archaic' species-Homo luzonensis and H. floresiensis-were present around the time anatomically modern humans arrived in the region >50,000 years ago. Intriguingly, contemporary human populations across ISEA carry distinct genomic traces of ancient interbreeding events with Denisovans-a separate hominin lineage that currently lacks a fossil record in ISEA. To query this apparent disparity between fossil and genetic evidence, we performed a comprehensive search for super-archaic introgression in >400 modern human genomes, including >200 from ISEA. Our results corroborate widespread Denisovan ancestry in ISEA populations, but fail to detect any substantial super-archaic admixture signals compatible with the endemic fossil record of ISEA. We discuss the implications of our findings for the understanding of hominin history in ISEA, including future research directions that might help to unlock more details about the prehistory of the enigmatic Denisovans.

Dire wolves are considered to be one of the most common and widespread large carnivores in Pleistocene America 1 , 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 Canidae 2,3 , 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.

Background: Marsupials are born much earlier than placental mammals, with most crawling from the birth canal to the protective marsupium (pouch) to further their development. However, little is known about the microbiology of the pouch and how it changes throughout a marsupial's reproductive cycle. Here, using stringent controls, we characterized the microbial composition of multiple body sites from 26 wild Southern Hairy-nosed Wombats (SHNWs), including pouch samples from animals at different reproductive stages., Results: Using qPCR of the 16S rRNA gene we detected a microbial community in the SHNW pouch. We observed significant differences in microbial composition and diversity between the body sites tested, as well as between pouch samples from different reproductive stages. The pouches of reproductively active females had drastically lower microbial diversity (mean ASV richness 19 ± 8) compared to reproductively inactive females (mean ASV richness 941 ± 393) and were dominated by gram positive bacteria from the Actinobacteriota phylum (81.7-90.6%), with the dominant families classified as Brevibacteriaceae, Corynebacteriaceae, Microbacteriaceae, and Dietziaceae. Three of the five most abundant sequences identified in reproductively active pouches had closest matches to microbes previously isolated from tammar wallaby pouches., Conclusions: This study represents the first contamination-controlled investigation into the marsupial pouch microbiota, and sets a rigorous framework for future pouch microbiota studies. Our results indicate that SHNW pouches contain communities of microorganisms that are substantially altered by the host reproductive cycle. We recommend further investigation into the roles that pouch microorganisms may play in marsupial reproductive health and joey survival.

Background: Herbivorous mammals co-opt microbes to derive energy and nutrients from diets that are recalcitrant to host enzymes. Recent research has found that captive management-an important conservation tool for many species-can alter the gut microbiota of mammals. Such changes could negatively impact the ability of herbivorous mammals to derive energy from their native diets, and ultimately reduce host fitness. To date, nothing is known of how captivity influences the gut microbiota of the Southern Hairy-nosed Wombat (SHNW), a large herbivorous marsupial that inhabits South Australia. Here, using 16S rRNA gene sequencing, we characterized the faecal microbiota of SHNWs in captivity and from three wild populations, two from degraded habitats and one from an intact native grass habitat., Results: We found that captive SHNWs had gut microbiota that were compositionally different and less diverse compared to wild SHNWs. There were major differences in gut microbiota community membership between captive and wild animals, both in statistically significant changes in relative abundance of microbes, and in the presence/absence of microbes. We also observed differences in microbial composition between wild populations, with the largest difference associated with native vs. degraded habitat., Conclusions: These results suggest that captivity has a major impact on the gut microbiota of SHNWs, and that different wild populations harbour distinct microbial compositions. Such findings warrant further work to determine what impacts these changes have on the fitness of SHNWs, and whether they could be manipulated to improve future management of the species.

Trachypithecus , which currently contains 20 species divided into four groups, is the most speciose and geographically dispersed genus among Asian colobines. Despite several morphological and molecular studies, however, its evolutionary history and phylogeography remain poorly understood. Phayre's langur ( Trachypithecus phayrei ) is one of the most widespread members of the genus, but details on its actual distribution and intraspecific taxonomy are limited and controversial. Thus, to elucidate the evolutionary history of Trachypithecus and to clarify the intraspecific taxonomy and distribution of T. phayrei , we sequenced 41 mitochondrial genomes from georeferenced fecal samples and museum specimens, including two holotypes. Phylogenetic analyses revealed a robustly supported phylogeny of Trachypithecus , suggesting that the T. pileatus group branched first, followed by the T. francoisi group, and the T. cristatus and T. obscurus groups most recently. The four species groups diverged from each other 4.5-3.1 million years ago (Ma), while speciation events within these groups occurred much more recently (1.6-0.3 Ma). Within T. phayrei , we found three clades that diverged 1.0-0.9 Ma, indicating the existence of three rather than two taxa. Following the phylogenetic species concept and based on genetic, morphological, and ecological differences, we elevate the T. phayrei subspecies to species level, describe a new species from central Myanmar, and refine the distribution of the three taxa. Overall, our study highlights the importance of museum specimens and provides new insights not only into the evolutionary history of T. phayrei but the entire Trachypithecus genus as well.

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.

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. Pečnerová 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., Competing Interests: The authors declare no conflict of interest.

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., (Copyright © 2019 The Authors. Published by Elsevier Ltd.. All rights reserved.)

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., (© The American Genetic Association 2018. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Adopting the name Canis dingo for the Dingo to explicitly denote a species-level taxon separate from other canids was suggested by Crowther et al.  (2014) as a means to eliminate taxonomic instability and contention. However, Jackson et al.  (2017), using standard taxonomic and nomenclatural approaches and principles, called instead for continued use of the nomen C. familiaris for all domestic dogs and their derivatives, including the Dingo. (This name, C. familiaris, is applied to all dogs that derive from the domesticated version of the Gray Wolf, Canis lupus, based on nomenclatural convention.) The primary reasons for this call by Jackson et al.  (2017) were: (1) a lack of evidence to show that recognizing multiple species amongst the dog, including the Dingo and New Guinea Singing Dog, was necessary taxonomically, and (2) the principle of nomenclatural priority (the name familiaris Linnaeus, 1758, antedates dingo Meyer, 1793). Overwhelming current evidence from archaeology and genomics indicates that the Dingo is of recent origin in Australia and shares immediate ancestry with other domestic dogs as evidenced by patterns of genetic and morphological variation. Accordingly, for Smith et al.  (2019) to recognise Canis dingo as a distinct species, the onus was on them to overturn current interpretations of available archaeological, genomic, and morphological datasets and instead show that Dingoes have a deeply divergent evolutionary history that distinguishes them from other named forms of Canis (including C. lupus and its domesticated version, C. familiaris). A recent paper by Koepfli et al.  (2015) demonstrates exactly how this can be done in a compelling way within the genus Canis-by demonstrating deep evolutionary divergence between taxa, on the order of hundreds of thousands of years, using data from multiple genetic systems. Smith et al.  (2019) have not done this; instead they have misrepresented the content and conclusions of Jackson et al.  (2017), and contributed extraneous arguments that are not relevant to taxonomic decisions. Here we dissect Smith et al.  (2019), identifying misrepresentations, to show that ecological, behavioural and morphological evidence is insufficient to recognise Dingoes as a separate species from other domestic dogs. We reiterate: the correct binomial name for the taxon derived from Gray Wolves (C. lupus) by passive and active domestication, including Dingoes and other domestic dogs, is Canis familiaris. We are strongly sympathetic to arguments about the historical, ecological, cultural, or other significance of the Dingo, but these are issues that will have to be considered outside of the more narrow scope of taxonomy and nomenclature.

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.

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., (Copyright © 2018 Elsevier Inc. All rights reserved.)

The koala, the only extant species of the marsupial family Phascolarctidae, is classified as 'vulnerable' due to habitat loss and widespread disease. We sequenced the koala genome, producing a complete and contiguous marsupial reference genome, including centromeres. We reveal that the koala's ability to detoxify eucalypt foliage may be due to expansions within a cytochrome P450 gene family, and its ability to smell, taste and moderate ingestion of plant secondary metabolites may be due to expansions in the vomeronasal and taste receptors. We characterized novel lactation proteins that protect young in the pouch and annotated immune genes important for response to chlamydial disease. Historical demography showed a substantial population crash coincident with the decline of Australian megafauna, while contemporary populations had biogeographic boundaries and increased inbreeding in populations affected by historic translocations. We identified genetically diverse populations that require habitat corridors and instituting of translocation programs to aid the koala's survival in the wild.

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.

Our understanding of mechanisms operating over deep timescales to shape phenotypic diversity often hinges on linking variation in one or few trait(s) to specific evolutionary processes. When distinct processes are capable of similar phenotypic signatures, however, identifying these drivers is difficult. We explored ecomorphological evolution across a radiation of ground-dwelling squirrels whose history includes convergence and constraint, two processes that can yield similar signatures of standing phenotypic diversity. Using four ecologically relevant trait datasets (body size, cranial, mandibular, and molariform tooth shape), we compared and contrasted variation, covariation, and disparity patterns in a new phylogenetic framework. Strong correlations existed between body size and two skull traits (allometry) and among skull traits themselves (integration). Inferred evolutionary modes were also concordant across traits (Ornstein-Uhlenbeck with two adaptive regimes). However, despite these broad similarities, we found divergent dynamics on the macroevolutionary landscape, with phenotypic disparity being differentially shaped by convergence and conservatism. Such among-trait heterogeneity in process (but not always pattern) reiterates the mosaic nature of morphological evolution, and suggests ground squirrel evolution is poorly captured by single process descriptors. Our results also highlight how use of single traits can bias macroevolutionary inference, affirming the importance of broader trait-bases in understanding phenotypic evolutionary dynamics., (© 2018 The Author(s). Evolution © 2018 The Society for the Study of Evolution.)

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.

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.

Understanding the effects of anthropogenic disturbance on zoonotic disease risk is both a critical conservation objective and a public health priority. Here, we evaluate the effects of multiple forms of anthropogenic disturbance across a precipitation gradient on the abundance of pathogen-infected small mammal hosts in a multi-host, multi-pathogen system in central Kenya. Our results suggest that conversion to cropland and wildlife loss alone drive systematic increases in rodent-borne pathogen prevalence, but that pastoral conversion has no such systematic effects. The effects are most likely explained both by changes in total small mammal abundance, and by changes in relative abundance of a few high-competence species, although changes in vector assemblages may also be involved. Several pathogens responded to interactions between disturbance type and climatic conditions, suggesting the potential for synergistic effects of anthropogenic disturbance and climate change on the distribution of disease risk. Overall, these results indicate that conservation can be an effective tool for reducing abundance of rodent-borne pathogens in some contexts (e.g. wildlife loss alone); however, given the strong variation in effects across disturbance types, pathogen taxa and environmental conditions, the use of conservation as public health interventions will need to be carefully tailored to specific pathogens and human contexts.This article is part of the themed issue 'Conservation, biodiversity and infectious disease: scientific evidence and policy implications'., (© 2017 The Authors.)

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., (© 2017 Wiley Periodicals, Inc.)

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., (© The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

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.

The Australian continent exhibits complex biogeographic patterns but studies of the impacts of Pleistocene climatic oscillation on the mesic environments of the Southern Hemisphere are limited. The koala (Phascolarctos cinereus), one of Australia's most iconic species, was historically widely distributed throughout much of eastern Australia but currently represents a complex conservation challenge. To better understand the challenges to koala genetic health, we assessed the phylogeographic history of the koala. Variation in the maternally inherited mitochondrial DNA (mtDNA) Control Region (CR) was examined in 662 koalas sampled throughout their distribution. In addition, koala CR haplotypes accessioned to Genbank were evaluated and consolidated. A total of 53 unique CR haplotypes have been isolated from koalas to date (including 15 haplotypes novel to this study). The relationships among koala CR haplotypes were indicative of a single Evolutionary Significant Unit and do not support the recognition of subspecies, but were separated into four weakly differentiated lineages which correspond to three geographic clusters: a central lineage, a southern lineage and two northern lineages co-occurring north of Brisbane. The three geographic clusters were separated by known Pleistocene biogeographic barriers: the Brisbane River Valley and Clarence River Valley, although there was evidence of mixing amongst clusters. While there is evidence for historical connectivity, current koala populations exhibit greater structure, suggesting habitat fragmentation may have restricted female-mediated gene flow. Since mtDNA data informs conservation planning, we provide a summary of existing CR haplotypes, standardise nomenclature and make recommendations for future studies to harmonise existing datasets. This holistic approach is critical to ensuring management is effective and small scale local population studies can be integrated into a wider species context., Competing Interests: EH is employed by Ecoplan Australia Pty Ltd. This does not alter the authors' adherence to PLOS ONE policies on sharing data and materials.