Adam W. Ferguson

Microbiome analysis among bats describes influences of host phylogeny, life history, physiology and geography

Metagenomic methods provide an experimental approach to inform the relationships between hosts and their microbial inhabitants. Previous studies have provided the conceptual realization that microbiomes are dynamic among hosts and the intimacy of relation between micro‐ and macroorganisms. Here, we present an intestinal microflora community analysis for members of the order Chiroptera and investigate the relative influence of variables in shaping observed microbiome relationships. The variables ranged from those considered to have ancient and long‐term influences (host phylogeny and life history) to the relatively transient variable of host reproductive condition. In addition, collection locality data, representing the geographic variable, were included in analyses. Results indicate a complex influence of variables in shaping sample relationships in which signal for host phylogeny is recovered at broad taxonomic levels (family), whereas intrafamilial analyses disclosed various degrees of resolution for the remaining variables. Although cumulative probabilities of assignment indicated both reproductive condition and geography influenced relationships, comparison of ecological measures among groups revealed statistical differences between most variable classifications. For example, ranked ecological diversity was associated with host phylogeny (deeper coalescences among families were associated with more microfloral diversity), dietary strategy (herbivory generally retained higher diversity than carnivory) and reproductive condition (reproductively active females displayed more diverse microflora than nonreproductive conditions). Overall, the results of this study describe a complex process shaping microflora communities of wildlife species as well as provide avenues for future research that will further inform the nature of symbiosis between microflora communities and hosts.

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.

Multilocus phylogeography of a widespread savanna‐woodland adapted rodent reveals the influence of Pleistocene geomorphology and climate change in Africa's Zambezi region

Understanding historical influences of climate and physiographic barriers in shaping patterns of biodiversity remains limited for many regions of the world. For mammals of continental Africa, phylogeographic studies, particularly for West African lineages, implicate both geographic barriers and climate oscillations in shaping small mammal diversity. In contrast, studies for southern African species have revealed conflicting phylogenetic patterns for how mammalian lineages respond to both climate change and geologic events such as river formation, especially during the Pleistocene. However, these studies were often biased by limited geographic sampling or exclusively focused on large‐bodied taxa. We exploited the broad southern African distribution of a savanna–woodland‐adapted African rodent, Gerbilliscus leucogaster (bushveld gerbil) and generated mitochondrial, autosomal and sex chromosome data to quantify regional signatures of climatic and vicariant biogeographic phenomena. Results indicate the most recent common ancestor for all G. leucogaster lineages occurred during the early Pleistocene. We documented six divergent mitochondrial lineages that diverged ~0.270–0.100 mya, each of which was geographically isolated during periods characterized by alterations to the course of the Zambezi River and its tributaries as well as regional ‘megadroughts’. Results demonstrate the presence of a widespread lineage exhibiting demographic expansion ~0.065–0.035 mya, a time that coincides with savanna–woodland expansion across southern Africa. A multilocus autosomal perspective revealed the influence of the Kafue River as a current barrier to gene flow and regions of secondary contact among divergent mitochondrial lineages. Our results demonstrate the importance of both climatic fluctuations and physiographic vicariance in shaping the distribution of southern African biodiversity.

Mitochondrial DNA and karyotypic data confirm the presence of Mus indutus and Mus minutoides (Mammalia, Rodentia, Muridae, Nannomys) in Botswana

Abstract We use a combination of cytochrome b sequence data and karyological evidence to confirm the presence of Mus indutus and Mus minutoides in Botswana. Our data include sampling from five localities from across the country, including one site in northwestern Botswana where both species were captured in syntopy. Additionally, we find evidence for two mitochondrial lineages of M. minutoides in northwestern Botswana that differ by 5% in sequence variation. Also, we report that M. minutoides in Botswana have the 2n=34 karyotype with the presence of a (X.1) sex-autosome translocation.

Phylogeography of a widespread small carnivore, the western spotted skunk (Spilogale gracilis) reveals temporally variable signatures of isolation across western North America

Abstract We analyzed phylogeographic patterns in the western spotted skunk, Spilogale gracilis Merriam, 1890 (Carnivora: Mephitidae) in relation to historical events associated with Pre‐Pleistocene Divergence (PPD) and Quaternary climate change (QCC) using mitochondrial DNA from 97 individuals distributed across Western North America. Divergence times were generated using BEAST to estimate when isolation in putative refugia occurred. Patterns and timing of demographic expansion was performed using Bayesian skyline plot. Putative climatic refugia resulting from Quaternary climate change were identified using paleoecological niche modeling and divergence dates compared to major vicariant events associated with Pre‐Pleistocene conditions. We recovered three major mitochondrial clades corresponding to western North America (California, Baja, and across the Great Basin), east‐central North America (Texas, central Mexico, New Mexico), and southwestern Arizona/northwestern Mexico. Time to most recent common ancestor for S. gracilis occurred ~1.36 Ma. Divergence times for each major clade occurred between 0.25 and 0.12 Ma, with signature of population expansion occurring 0.15 and 0.10 Ma. Ecological niche models identified three potential climatic refugia during the Last Interglacial, (1) west coast of California and Oregon, (2) northwestern Mexico, and (3) southern Texas/northeastern Mexico as well as two refugia during the Last Glacial Maximum, (1) western USA and (2) southern Texas/northeastern Mexico. This study supports PPD in shaping species‐level diversity compared to QCC‐driven changes at the intraspecific level for Spilogale, similar to the patterns reported for other small mammals (e.g., rodents and bats). Phylogeographic patterns also appear to have been shaped by both habitat and river vicariance, especially across the desert southwest. Further, continuing climate change during the Holocene coupled with anthropogenic modifications during the Anthropocene appears to be removing both of these barriers to current dispersal of western spotted skunks.

Noteworthy record of the Ethiopian genet, Genetta abyssinica, (Carnivora, Viverridae) from Djibouti informs its phylogenetic position within Genetta

Abstract The molecular phylogeny of extant genets (Carnivora, Viverridae, Genetta) was generated using all species with the exception of the Ethiopian genet Genetta abyssinica. Herein, we provide the first molecular phylogenetic assessment of G. abyssinica using molecular sequence data from multiple mitochondrial genes generated from a recent record of this species from the Forêt du Day (the Day Forest) in Djibouti. This record represents the first verified museum specimen of G. abyssinica collected in over 60 years and the first specimen with a specific locality for the country of Djibouti. Multiple phylogenetic analyses revealed conflicting results as to the exact relationship of G. abyssinica to other Genetta species, providing statistical support for a sister relationship to all other extant genets for only a subset of mitochondrial analyses. Despite the inclusion of this species for the first time, phylogenetic relationships among Genetta species remain unclear, with limited nodal support for many species. In addition to providing an alternative hypothesis of the phylogenetic relationships among extant genets, this recent record provides the first complete skeleton of this species to our knowledge and helps to shed light on the distribution and habitat use of this understudied African small carnivore.

Conservation Status of the Plains Spotted Skunk, Spilogale putorius interrupta, in Texas, with an Assessment of Genetic Variability in the Species

Robert C. Dowler, Department of Biology at Angelo State University is the corresponding author, robert dot dowler at angelo dot edu

Spatial Organization and Home Range Patterns of the American Hog-nosed Skunk (Conepatus leuconotus)

Abstract The American hog-nosed skunk (Conepatus leuconotus) is an understudied mesocarnivore for which no extensive ecological studies have been conducted. We radio-collared 29 skunks (15 male, 14 female) at a site in west-central Texas, U.S.A. and used data from 14 (5 male, 9 female) to determine patterns of home range and spatial organization. Home range (95% fixed kernel) of males averaged three times that of females (1.9 km2 vs. 0.64 km2) and extensive intrasexual and intersexual overlap in home ranges was documented. Female home ranges and core areas differed significantly in their topography (changes with which were associated with habitat difference) from those of males. Home range sizes were correlated with body size and gender, but intersexual differences between home range sizes and their topography indicate space-use patterns between male and female American hog-nosed skunks are influenced by factors beyond metabolic requirements alone. Specifically, we believe male home ranges are large to maximize encounters with females whereas females selectively choose areas to ensure availability of resources such as foraging and den sites.

Mammals of Africa (Vol. I-VI.)

Kingdon, J., D. Happold, T. Butynski, M. Hoffmann, M. Happold, and J. Kalina (eds.). 2013. Mammals of Africa (6 volumes). Bloomsbury Publishing, London, United Kingdom, 3,720 pp. Price (hardbound),

Mammalia, Chiroptera, Emballonuridae, Peropteryx leucoptera Peters, 1867 and Peropteryx pallidoptera Lim, Engstrom, Reid, Simmons, Voss and Fleck, 2010: Distributional range extensions in Ecuador

940.00. Kingdon, J., D. Happold, M. Hoffmann, T. Butynski, M. Happold, and J. Kalina (eds.). 2013. Mammals of Africa. Volume I: Introductory Chapters and Afrotheria. Bloomsbury Publishing, London United Kingdom, 351 pp. ISBN-978-1-4081-2251-8 (print); ISBN-978-1-4081-8990-1 (epdf). Butynski, T. M., J. Kingdon, and J. Kalina (eds.). 2013. Mammals of Africa. Volume II: Primates. Bloomsbury Publishing, London, United Kingdom, 556 pp. ISBN-978-1-4081-2252-5 (print); ISBN-978-1-4081-8991-7 (epdf). Happold, D. C. D. (ed.). 2013. Mammals of Africa. Volume III: Rodents, Hares and Rabbits. Bloomsbury Publishing, London, United Kingdom, 789 pp. ISBN-978-1-4081-2253-2 (print); ISBN-978-1-4081-8992-4 (epdf). Happold, M., and D. C. D. Happold (eds.). 2013. Mammals of Africa. Volume IV: Hedgehogs, Shrews and Bats. Bloomsbury Publishing, London, United Kingdom, 800 pp. ISBN-978-1-4081-2254-9 (print); ISBN-978-1-4081-8993-1(epdf). Kingdon, J., and M. Hoffmann (eds.). 2013. Mammals of Africa. Volume V: Carnivores, Pangolins, Equids and Rhinoceroses. Bloomsbury Publishing, London, United Kingdom, 544 pp. ISBN-978-1-4081-2255-6 (print); ISBN-978-1-4081-8994-8 (epdf). Kingdon, J., and M. Hoffmann (eds.). 2013. Mammals of Africa. Volume VI: Pigs, Hippopotamuses, Chevrotain, Giraffes, Deer and Bovids. Bloomsbury Publishing, London, United Kingdom, 680 pp. ISBN-978-1-4081-2256-3 (print); ISBN-978-1-4081-8995-5 (epdf).