Messing about on the river: the role of geographic barriers in shaping the genetic structure of Bornean small mammals in a fragmented landscape

Genetic Characterization of the Co-Invasive Rodent Parasite Heterakis spumosa (Nematoda, Heterakidae)

Heterakis spumosa, a parasitic worm infecting rodents, is globally prevalent in black rats, brown rats, and house mice. It is hypothesized to originate from Asia due to its widespread presence in Southeast Asia in various Murinae. Previous molecular studies focused on European, African, and Japanese specimens, but none included samples from the putative native range. Rodents were collected between 2008 and 2015 across various localities in Southeast Asia and Europe, identified by morphology or genetic barcoding. Viscera were examined or preserved for later inspection. DNA was extracted from H. spumosa. PCR amplification targeting the mtCOI gene and ITS1 region was conducted in this study using newly designed primers (based on Heterakis reference sequences). PCR amplicons were subsequently sequenced and analyzed. In this study, the phylogenetic analysis using ITS1 sequences revealed that Heterakis samples from Thai and Laotian rodents belong to the species H. spumosa, exhibiting low genetic variation compared to samples from other regions. Genetic distance calculations using mtCOI sequences confirmed the marked distinction of H. spumosa from other Heterakis species. Our phylogenetic analyses using partial mtCOI and ITS1 sequences have significantly enhanced our comprehension of the genetic diversity and evolutionary history of the nematode H. spumosa.

Barriers and corridors: Assessment of gene flow and movement among red panda populations in eastern Himalayas

Landscape features can impede dispersal, gene flow, and population demography, resulting in the formation of several meta-populations within a continuous landscape. Understanding a species' ability to overcome these barriers is critical for predicting genetic connectivity and population persistence, and implementing effective conservation strategies. In the present study, we conducted a fine-scale spatial genetic analysis to understand the contemporary gene flow within red panda populations in the Eastern Himalayas. Employing geometric aspects of reserve design, we delineated the critical core habitats for red pandas, which comprise 14.5 % of the landscape (12,189.75 Km2), with only a mere 443 Km2 falling within the protected areas. We identified corridors among the core habitats, which may be vital for the species' long-term genetic viability. Furthermore, we identified substantial landscape barriers, including Sela Pass in the western region, Siang river in the central region, and the Dibang river, Lohit river, along with Dihang, Dipher, and Kumjawng passes in the eastern region, which hinder gene flow. We suggest managing red panda populations through the creation of Community Conservation Reserves in the identified core habitats, following landscape-level management planning based on the core principles of geometric reserve design. This includes a specific emphasis on identified core habitats of red panda (CH-RP 5 and CH-RP 8) to facilitate corridors and implement meta-population dynamics. We propose the development of a comprehensive, long-term conservation and management plan for red pandas in the transboundary landscape, covering China, Nepal, and Bhutan.

Using citizen science data to assess the population genetic structure of the common yellowjacket wasp, Vespula vulgaris

Monitoring insect genetic diversity and population structure has never been more important to manage the biodiversity crisis. Citizen science has become an increasingly popular tool to gather ecological data affordably across a wide range of spatial and temporal scales. To date, most insect-related citizen science initiatives have focused on occurrence and abundance data. Here, we show that poorly preserved insect samples collected by citizen scientists can yield population genetic information, providing new insights into population connectivity, genetic diversity and dispersal behaviour of little-studied insects. We analysed social wasps collected by participants of the Big Wasp Survey, a citizen science project that aims to map the diversity and distributions of vespine wasps in the UK. Although Vespula vulgaris is a notorious invasive species around the world, it remains poorly studied in its native range. We used these data to assess the population genetic structure of the common yellowjacket V. vulgaris at different spatial scales. We found a single, panmictic population across the UK with little evidence of population genetic structuring; the only possible limit to gene flow is the Irish sea, resulting in significant differentiation between the Northern Ireland and mainland UK populations. Our results suggest that queens disperse considerable distances from their natal nests to found new nests, resulting in high rates of gene flow and thus little differentiation across the landscape. Citizen science data has made it feasible to perform this study, and we hope that it will encourage future projects to adopt similar practices in insect population monitoring.

Invasive rat drives complete collapse of native small mammal communities in insular forest fragments

As tropical forests are becoming increasingly fragmented, understanding the magnitude and time frame of biodiversity declines is vital for 21^st century sustainability goals. Over three decades, we monitored post-isolation changes in small mammal species richness and abundance within a forest landscape fragmented by the construction of a dam in Thailand.^1,2 We observed the near-complete collapse of species richness within 33 years, with no evidence of a recolonization effect across repeatedly sampled islands. Our results further revealed a decline in species richness as island size decreased and isolation time increased, accelerated by the increasing dominance of the ubiquitous Malayan field rat, Rattus tiomanicus. This species was already hyper-abundant on smaller islands in the initial surveys (1992-1994, 66% of individuals) but became monodominant on all islands, regardless of island size, by the most recent survey (2020, 97%). Our results suggest that insular forest fragments are highly susceptible to rapid species loss, particularly due to the competitive nature of Rattus accelerating the rate at which extinction debts are paid. To mitigate these impacts, reducing the extent of habitat degradation, as triggered by fragmentation and exacerbated by isolation time, can help to sustain native biodiversity while averting Rattus hyper-abundance.

Population dynamics and genetic connectivity in recent chimpanzee history

Knowledge on the population history of endangered species is critical for conservation, but whole-genome data on chimpanzees (Pan troglodytes) is geographically sparse. Here, we produced the first non-invasive geolocalized catalog of genomic diversity by capturing chromosome 21 from 828 non-invasive samples collected at 48 sampling sites across Africa. The four recognized subspecies show clear genetic differentiation correlating with known barriers, while previously undescribed genetic exchange suggests that these have been permeable on a local scale. We obtained a detailed reconstruction of population stratification and fine-scale patterns of isolation, migration, and connectivity, including a comprehensive picture of admixture with bonobos (Pan paniscus). Unlike humans, chimpanzees did not experience extended episodes of long-distance migrations, which might have limited cultural transmission. Finally, based on local rare variation, we implement a fine-grained geolocalization approach demonstrating improved precision in determining the origin of confiscated chimpanzees.

A genetic analysis of grey squirrel (Sciurus carolinensis) populations in Ireland

The grey squirrel (Sciurus carolinensis) is an invasive rodent in Ireland that has had detrimental impacts on the native Irish red squirrel (S. vulgaris) as well as on silviculture. This invasive species spread rapidly throughout Ireland, but in recent years appears to be declining in certain areas of the country. This study analysed the genetic profile of grey squirrel populations in Ireland to gain insight into their introduction, evolutionary history in Ireland, and vulnerability to management strategies. The genetic diversity and population structure of eight grey squirrel populations in Ireland was assessed using 11 species-specific microsatellite loci, and was compared to a small population from Tennessee, U.S.A., part of the native range of the grey squirrel. This is the first time these microsatellite markers developed specifically for grey squirrels have been used to study the species in Ireland. We found low to moderate genetic diversity overall across Irish populations as well as the presence of inbreeding. One population in particular, (in Co. Kildare), was differentiated from all other populations, which could indicate genetic isolation between Irish populations or a secondary introduction of S. carolinensis to Ireland.

The critical role of natural forest as refugium for generalist species in oil palm-dominated landscapes

In Borneo, oil palm plantations have replaced much of natural resources, where generalist species tend to be the principal beneficiaries, due to the abundant food provided by oil palm plantations. Here, we analyse the distribution of the Asian water monitor lizard (Varanus salvator) population within an oil palm-dominated landscape in the Kinabatangan floodplain, Malaysian Borneo. By using mark-recapture methods we estimated its population size, survival, and growth in forest and plantation habitats. We compared body measurements (i.e. body weight and body length) of individuals living in forest and oil palm habitats as proxy for the population's health status, and used general least squares estimation models to evaluate its response to highly fragmented landscapes in the absence of intensive hunting pressures. Contrary to previous studies, the abundance of lizards was higher in the forest than in oil palm plantations. Recruitment rates were also higher in the forest, suggesting that these areas may function as a source of new individuals into the landscape. While there were no morphometric differences among plantation sites, we found significant differences among forested areas, where larger lizards were found inhabiting forest adjacent to oil palm plantations. Although abundant in food resources, the limited availability of refugia in oil palm plantations may intensify intra-specific encounters and competition, altering the body size distribution in plantation populations, contrary to what happens in the forest. We conclude that large patches of forest, around and within oil palm plantations, are essential for the dynamics of the monitor lizard population in the Kinabatangan floodplain, as well as a potential source of individuals to the landscape. We recommend assessing this effect in other generalist species, as well as the impact on the prey communities, especially to reinforce the establishment of buffer zones and corridors as a conservation strategy within plantations.

Dispersal ability predicts spatial genetic structure in native mammals persisting across an urbanization gradient

As the rate of urbanization continues to increase globally, a growing body of research is emerging that investigates how urbanization shapes the movement-and consequent gene flow-of species in cities. Of particular interest are native species that persist in cities, either as small relict populations or as larger populations of synanthropic species that thrive alongside humans in new urban environments. In this study, we used genomic sequence data (SNPs) and spatially explicit individual-based analyses to directly compare the genetic structure and patterns of gene flow in two small mammals with different dispersal abilities that occupy the same urbanized landscape to evaluate how mobility impacts genetic connectivity. We collected 215 white-footed mice (Peromyscus leucopus) and 380 big brown bats (Eptesicus fuscus) across an urban-to-rural gradient within the Providence, Rhode Island (U.S.A.) metropolitan area (population =1,600,000 people). We found that mice and bats exhibit clear differences in their spatial genetic structure that are consistent with their dispersal abilities, with urbanization having a stronger effect on Peromyscus mice. There were sharp breaks in the genetic structure of mice within the Providence urban core, as well as reduced rates of migration and an increase in inbreeding with more urbanization. In contrast, bats showed very weak genetic structuring across the entire study area, suggesting a near-panmictic gene pool likely due to the ability to disperse by flight. Genetic diversity remained stable for both species across the study region. Mice also exhibited a stronger reduction in gene flow between island and mainland populations than bats. This study represents one of the first to directly compare multiple species within the same urban-to-rural landscape gradient, an important gap to fill for urban ecology and evolution. Moreover, here we document the impacts of dispersal capacity on connectivity for native species that have persisted as the urban landscape matrix expands.

Molecular identification and phylogenetic analysis of a Callosciurus notatus complete mitogenome from Peninsular Malaysia

The mitogenome of a plantain squirrel, Callosciurus notatus, collected from Bukit Tarek Forest Reserve (Extension), Selangor, Malaysia was sequenced using BGISEQ-500RS technology. The 16,582 bp mitogenome consists of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 control region. A phylogenetic and BLASTn analysis against other available datasets showed that the mitogenome matched with 99.49% similarity to a previously published C. notatus mitogenome from Peninsular Malaysia. However, it also diverged by nearly 8% (92.24% match) from a second previously published mitogenome for the same species, sampled in East Kalimantan, Indonesia. This suggests a difference in landscape features between both localities might affect its genetic connectivity.

Molecular phylogeny and morphological diversity of the Niviventer fulvescens species complex with emphasis on species from China

The Niviventer fulvescens species complex (NFSC), a group of abundant and taxonomically ambiguous rodent taxa, is distributed from Southeast Asia to south-eastern China. We combined molecular and morphological datasets to clarify the species composition and variation of the NFSC. Our phylogenetic analyses, using molecular data, recovered eight genetic lineages in the NFSC, including a novel, distinct lineage from Jilong, Tibet, China, which is described as a new species, N. fengi sp. nov. The species status of N. fengi is supported by a species delimitation analysis, and it is morphologically distinguished from other members of the NFSC by its greyish dorsal fur, soft hairs covering the whole body and a hairy tail. NFSC species bearing well-developed spines are found at lower elevations. A comprehensive taxonomic revision of the NFSC within China is provided, represented by five species: N. cremoriventer, N. fulvescens, N. huang, N. mekongis comb. nov. and N. fengi. A further study of this species complex, including samples from Southeast Asia, is needed.

Dispersal and genetic structure in a tropical small mammal, the Bornean tree shrew (Tupaia longipes), in a fragmented landscape along the Kinabatangan River, Sabah, Malaysia

Background

Constraints in migratory capabilities, such as the disruption of gene flow and genetic connectivity caused by habitat fragmentation, are known to affect genetic diversity and the long-term persistence of populations. Although negative population trends due to ongoing forest loss are widespread, the consequence of habitat fragmentation on genetic diversity, gene flow and genetic structure has rarely been investigated in Bornean small mammals. To fill this gap in knowledge, we used nuclear and mitochondrial DNA markers to assess genetic diversity, gene flow and the genetic structure in the Bornean tree shrew, Tupaia longipes, that inhabits forest fragments of the Lower Kinabatangan Wildlife Sanctuary, Sabah. Furthermore, we used these markers to assess dispersal regimes in male and female T. longipes.

Results

In addition to the Kinabatangan River, a known barrier for dispersal in tree shrews, the heterogeneous landscape along the riverbanks affected the genetic structure in this species. Specifically, while in larger connected forest fragments along the northern riverbank genetic connectivity was relatively undisturbed, patterns of genetic differentiation and the distribution of mitochondrial haplotypes in a local scale indicated reduced migration on the strongly fragmented southern riverside. Especially, oil palm plantations seem to negatively affect dispersal in T. longipes. Clear sex-biased dispersal was not detected based on relatedness, assignment tests, and haplotype diversity.

Conclusion

This study revealed the importance of landscape connectivity to maintain migration and gene flow between fragmented populations, and to ensure the long-term persistence of species in anthropogenically disturbed landscapes.