Geography and elevation as drivers of cloacal microbiome assemblages of a passerine bird distributed across Sulawesi, Indonesia

BACKGROUND

Empirical field studies allow us to view how ecological and environmental processes shape the biodiversity of our planet, but collecting samples in situ creates inherent challenges. The majority of empirical vertebrate gut microbiome research compares multiple host species against abiotic and biotic factors, increasing the potential for confounding environmental variables. To minimize these confounding factors, we focus on a single species of passerine bird found throughout the geologically complex island of Sulawesi, Indonesia. We assessed the effects of two environmental factors, geographic Areas of Endemism (AOEs) and elevation, as well as host sex on the gut microbiota assemblages of the Sulawesi Babbler, Pellorneum celebense, from three different mountains across the island. Using cloacal swabs, high-throughput-amplicon sequencing, and multiple statistical models, we identified the core microbiome and determined the signal of these three factors on microbial composition.

RESULTS

The five most prevalent bacterial phyla within the gut microbiome of P. celebense were Proteobacteria (32.6%), Actinobacteria (25.2%), Firmicutes (22.1%), Bacteroidetes (8.7%), and Plantomycetes (2.6%). These results are similar to those identified in prior studies of passeriform microbiomes. Overall, microbiota diversity decreased as elevation increased, irrespective of sex or AOE. A single ASV of Clostridium was enriched in higher elevation samples, while lower elevation samples were enriched with the genera Perlucidibaca (Family Moraxellaceae), Lachnoclostridium (Family Lachnospiraceae), and an unidentified species in the Family Pseudonocardiaceae.

CONCLUSIONS

While the core microbiota families recovered here are consistent with other passerine studies, the decreases in diversity as elevation increases has only been seen in non-avian hosts. Additionally, the increased abundance of Clostridium at high elevations suggests a potential microbial response to lower oxygen levels. This study emphasizes the importance of incorporating multiple statistical models and abiotic factors such as elevation in empirical microbiome research, and is the first to describe an avian gut microbiome from the island of Sulawesi.

Native and Introduced Trypanosome Parasites in Endemic and Introduced Murine Rodents of Sulawesi

The Indonesian island of Sulawesi is a globally significant biodiversity hotspot with substantial undescribed biota, particularly blood-borne parasites of endemic wildlife. Documenting the blood parasites of Sulawesi's murine rodents is the first fundamental step towards the discovery of pathogens likely to be of concern for the health and conservation of Sulawesi's endemic murines. We screened liver samples from 441 specimens belonging to 20 different species of murine rodents from 2 mountain ranges on Sulawesi, using polymerase chin reaction (PCR) primers targeting the conserved 18S rDNA region across the protozoan class Kinetoplastea. We detected infections in 156 specimens (10 host species) with a mean prevalence of 35.4% (95% confidence interval [CI] = 30.9-39.8%). Sequences from these samples identified 4 infections to the genus Parabodo, 1 to Blechomonas, and the remaining 151 to the genus Trypanosoma. Within Trypanosoma, we recovered 17 haplotypes nested within the Trypanosoma theileri clade infecting 117 specimens (8 host species) and 4 haplotypes nested within the Trypanosoma lewisi clade infecting 34 specimens (6 host species). Haplotypes within the T. theileri clade were related to regional Indo-Australian endemic trypanosomes, displayed geographic structuring but with evidence of long-term connectivity between mountains, and had substantial phylogenetic diversity. These results suggest T. theileri clade parasites are native to Sulawesi. Conversely, T. lewisi clade haplotypes were recovered from both endemic and introduced rodents, demonstrated complete geographic separation between clades, and had low genetic diversity. These results suggest that the T. lewisi clade parasites invaded Sulawesi recently and likely in 2 separate invasion events. Our results provide the first records of metakinetoplastids in Sulawesi's rodents and highlight the need for more extensive sampling for pathogens in this biodiversity hotspot.

Cetacean biodiversity, spatial and temporal trends based on stranding records (1920-2016), Victoria, Australia

Cetacean stranding records can provide vital information on species richness and diversity through space and time. Here we collate stranding records from Victoria, Australia and assess them for temporal, spatial and demographic trends. Between 1920 and 2016, 424 stranding events involving 907 individuals were recorded across 31 Cetacea species from seven families, including five new species records for the state. Seven of these events were mass strandings, and six mother and calf strandings were recorded. Importantly, 48% of the species recorded are recognised as data deficient on the IUCN Red List. The most commonly recorded taxa were Tursiops spp. (n = 146) and Delphinus delphis (common dolphins, n = 81), with the greatest taxonomic richness (n = 24) and highest incidence of stranding events documented within the Otways mesoscale bioregion. We found no seasonal stranding patterns anywhere in the state. While our findings improve understanding of the spatial and temporal patterns of cetacean diversity within Victoria, we suggest greater effort to collect demographic data at stranding events in order to better study state-wide patterns through time. We conclude with guidelines for minimum data collection standards for future strandings to maximise information capture from each event.

Spatially heterogeneous impact of climate change on small mammals of montane California

Resurveys of historical collecting localities have revealed range shifts, primarily leading edge expansions, which have been attributed to global warming. However, there have been few spatially replicated community-scale resurveys testing whether species' responses are spatially consistent. Here we repeated early twentieth century surveys of small mammals along elevational gradients in northern, central and southern regions of montane California. Of the 34 species we analysed, 25 shifted their ranges upslope or downslope in at least one region. However, two-thirds of ranges in the three regions remained stable at one or both elevational limits and none of the 22 species found in all three regions shifted both their upper and lower limits in the same direction in all regions. When shifts occurred, high-elevation species typically contracted their lower limits upslope, whereas low-elevation species had heterogeneous responses. For high-elevation species, site-specific change in temperature better predicted the direction of shifts than change in precipitation, whereas the direction of shifts by low-elevation species was unpredictable by temperature or precipitation. While our results support previous findings of primarily upslope shifts in montane species, they also highlight the degree to which the responses of individual species vary across geographically replicated landscapes.

Historical resurveys reveal persistence of smoky mouse (Pseudomys fumeus) populations over the long-term and through the short-term impacts of fire

Context Range contractions are often the first indicator that a species is in decline. However, natural population fluctuations, characteristic of many Australian rodents, make differentiating between natural lows and unsustainable declines challenging. The endangered smoky mouse (Pseudomys fumeus) is a prime example. Surveys have failed to detect the species across much of its range over the past decade, but P. fumeus is known to experience fluctuations in abundance and periods of low detectability. Aims We compared past and current distributions of P. fumeus in the Victoria Range, Grampians–Gariwerd National Park (Victoria, Australia), to assess long-term population persistence over 40 years and short-term population persistence following a high-severity fire. Methods To evaluate the efficacy of surveys in detecting P. fumeus, we conducted analyses to explicitly model detectability using historical (1974, 2002) and modern (2013) survey data. We also tested the short-term impacts of fire on the presence of P. fumeus by surveying burned and unburned sites 3 months prior to, and 7 to 21 months following, a severe wildfire. Key results Our surveys detected P. fumeus at five new sites, confirmed presence at one historical site, and absence from two historical sites. The species persisted in situ through fire, and for at least 21 months following. We detected resident populations in burned and unburned wet drainage systems. Conclusions Despite periods of low density in which the species was undetected, P. fumeus persisted in an 8 km radius area of the eastern escarpment of Victoria Range of the Grampians–Gariwerd National Park for at least four decades through droughts, the presence of invasive predators, and the short-term impacts of wildfire. Implications Although P. fumeus persisted through a severe fire, factors influencing survival must be assessed before generalisations are made about the impacts of wildfire on the species. Management of P. fumeus should recognise that the species survives and breeds in wet drainage systems. Regular resurveys incorporating statistical estimates of detectability are necessary to identify and track distributional changes of threatened species, like P. fumeus, particularly in the context of natural, sustainable fluctuations.

Iridescent colour production in hairs of blind golden moles (Chrysochloridae)

Relative to other metazoans, the mammalian integument is thought to be limited in colour. In particular, while iridescence is widespread among birds and arthropods, it has only rarely been reported in mammals. Here, we examine the colour, morphology and optical mechanisms in hairs from four species of golden mole (Mammalia: Chrysochloridae) that are characterized by sheens ranging from purple to green. Microspectrophotometry reveals that this colour is weak and variable. Iridescent hairs are flattened and have highly reduced cuticular scales, providing a broad and smooth surface for light reflection. These scales form multiple layers of light and dark materials of consistent thickness, strikingly similar to those in the elytra of iridescent beetles. Optical modelling suggests that the multi-layers produce colour through thin-film interference, and that the sensitivity of this mechanism to slight changes in layer thickness and number explains colour variability. While coloured integumentary structures are typically thought to evolve as sexual ornaments, the blindness of golden moles suggests that the colour may be an epiphenomenon resulting from evolution via other selective factors, including the ability to move and keep clean in dirt and sand.

Population structure, timing of divergence and contact between lineages in the endangered Hastings River mouse (Pseudomys oralis)

Management of threatened species requires understanding their genetic structure, particularly when the potential for cryptic lineages exists for species with a broad geographic range. The Hastings River mouse (Pseudomys oralis) is an endangered species found along the eastern coast of Australia. Previous genetic investigation revealed two mitochondrial lineages, separated by an unsampled gap in northern New South Wales. Using new samples from within this gap and from throughout the species’ range, we recovered two evolutionary lineages in agreement with previous studies. Importantly, we identified Washpool National Park as the area of lineage overlap, located at the northern limit of the Macleay–McPherson Overlap Zone. We confirmed limited haplotype sharing between localities, suggesting low levels of gene flow. Historical demography suggested recent population expansion and decline for Lineages I and II, respectively. Our dating estimates placed lineage divergence at 300 000–900 000 years ago, at the lower limit of percentage divergence between other sister species in Pseudomys. While these results support separate management consideration for each lineage, nuclear markers are needed to evaluate whether these lineages represent separate species. In addition, comparative phylogeographic analyses of divergence times among lineages of other species distributed across the Macleay–McPherson Overlap Zone are needed to determine the significance of this biogeographic contact zone for ecological communities in the region generally.