Signatures of landscape and captivity in the gut microbiota of Southern Hairy-nosed Wombats (Lasiorhinus latifrons)

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.Raphael Eisenhofer, Kristofer M. Helgen, and David Taggar

Host reproductive cycle influences the pouch microbiota of wild southern hairy-nosed wombats (Lasiorhinus latifrons)

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.Sesilje Weiss, David Taggart, Ian Smith, Kristofer M. Helgen and Raphael Eisenhofe

Individuality and stability of the koala (Phascolarctos cinereus) faecal microbiota through time

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.Raphael Eisenhofer, Kylie L. Brice, Michaela DJ Blyton, Scott E. Bevins, Kellie Leigh, Brajesh K. Singh, Kristofer M. Helgen, Ian Hough, Christopher B. Daniels, Natasha Speight and Ben D. Moor

First record of Rattus rattus in Botswana

K. M. Helge

Additional material of the enigmatic golden mole Cryptochloris zyli, with notes on the genus Cryptochloris (Mammalia: Chrysochloridae)

Van Zyl’s golden mole (Cryptochloris zyli) is a distinctive but little-known species from  the northwestern Cape Province of South Africa. Many authors have mentioned that it is known only by the holotype. Two other specimens are now known to exist; one was discovered in the Museum of Comparative Zoology at Harvard University, and the other, which has been mentioned in publication but overlooked, is in the Natural History Museum in London. Differentiation of C. zyli from sympatric chrysochlorids, and from itscongener C. wintoni, are discussed.Keywords:Chrysochloridae, systematics, SouthAfrica

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.Victor C. Mason, Kristofer M. Helgen, and William J. Murph

Caribbean Myotis (Chiroptera, Vespertilionidae), with description of a new species from Trinidad and Tobago

We describe a new species of Myotis (Vespertilionidae, Myotinae) from the Republic of Trinidad and Tobago, Tobago Island. The new species (Myotis attenboroughi sp. nov.) can be distinguished from all other Neotropical congeners by cranial features and cytochrome-b gene sequences. Myotis attenboroughi sp. nov. is allied morphologically with species in the albescens group (like M. nigricans), and is sister to a clade including M. cf. handleyi, M. nesopolus, and 3 possibly undescribed species from Central and South America. A review of Myotis collections from the Caribbean confirms M. nyctor for Barbados and Grenada; M. dominicensis for Dominica and Guadeloupe; M. martiniquensis for Martinique; M. pilosatibialis and M. riparius for Trinidad; and M. attenboroughi for Tobago. The occurrence of M. attenboroughi on Trinidad is still an open question. Describimos una nueva especie de Myotis (Vespertilionidae, Myotinae) de la República de Trinidad y Tobago, isla de Tobago. La nueva especie (Myotis attenboroughi sp. nov.) se distingue de otros congéneres Neotropicales en sus rasgos craneanos y secuencias del gen citocromo b. Myotis attenboroughi sp. nov. es morfológicamente similar a especies del grupo albescens (tal como M. nigricans) y es hermana de un clado que incluye a M. cf. handleyi, M. nesopolus, y tres especies, posiblemente no descritas, de Centro y Sud América. Una revisión de las series de Myotis del Caribe confirma a M. nyctor para Barbados y Granada; M. dominicensis para Dominica y Guadalupe; M. martiniquensis para Martinica; M. pilosatibialis y M. riparius para Trinidad; y M. attenboroughi para Tobago. La presencia de M. attenboroughi en Trinidad sigue siendo hoy un enigma.Ricardo Moratelli, Don E Wilson, Roberto L M Novaes, Kristofer M Helgen, Eliécer E Gutiérre

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. 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.Graham Gower, Lindsey E. Fenderson, Alexander T. Salis, Kristofer M. Helgen, Ayla L. van Loenen, Holly Heiniger, Emilia Hofman-Kamińska, Rafał Kowalczyk, Kieren J. Mitchell, Bastien Llamas, and Alan Coope

Biodiversity in Sri Lanka and the Western Ghats [1] (multiple letters)

Science3085719199-SCIE

Leben in der Frauenkirche: Das Magazin der Stiftung Frauenkirche Dresden

The genus Equus is richly represented in the fossil record, yet our understanding of taxonomic relationships within this genus remains limited. To estimate the phylogenetic relationships among modern horses, zebras, asses and donkeys, we generated the first data set including complete mitochondrial sequences from all seven extant lineages within the genus Equus. Bayesian and Maximum Likelihood phylogenetic inference confirms that zebras are monophyletic within the genus, and the Plains and Grevy’s zebras form a well-supported monophyletic group. Using ancient DNA techniques, we further characterize the complete mitochondrial genomes of three extinct equid lineages (the New World stilt-legged horses, NWSLH; the subgenus Sussemionus; and the Quagga, Equus quagga quagga). Comparisons with extant taxa confirm the NWSLH as being part of the caballines, and the Quagga and Plains zebras as being conspecific. However, the evolutionary relationships among the non-caballine lineages, including the now-extinct subgenus Sussemionus, remain unresolved, most likely due to extremely rapid radiation within this group. The closest living outgroups (rhinos and tapirs) were found to be too phylogenetically distant to calibrate reliable molecular clocks. Additional mitochondrial genome sequence data, including radiocarbon dated ancient equids, will be required before revisiting the exact timing of the lineage radiation leading up to modern equids, which for now were found to have possibly shared a common ancestor as far as up to 4 Million years ago (Mya)