Genetic diversity and structure related to expansion history and habitat isolation: stone marten populating rural-urban habitats

Unique among high passes: Phylogenetic inferences from DNA barcoding of the butterfly fauna of Ladakh Trans-Himalaya, India

The butterfly assemblage of Ladakh Trans-Himalaya demands a thorough analysis of their population genetic structure owing to their typical biogeographic affinity and their adaptability to extreme cold-desert climates. No such effort has been taken till date, and in this backdrop, we created a barcode reference library of 60 specimens representing 23 species. Barcodes were generated from freshly collected leg samples using the Sanger sequencing method, followed by phylogenetic clade analyses and divergence calculation. Our data represents 22% of Ladakh's Rhopaloceran fauna with the novel barcode submission for six species, including one Schedule II species, Paralasa mani . Contrary to the 3% threshold rule, the interspecific divergence between two species pairs of typical mountain genus Hyponephele and Karanasa was found to be 2.3% and 2.2%, respectively. The addition of conspecific global barcodes revealed that most species showed little increase in divergence value, while a two-fold increase was noted in a few species. Bayesian clade clustering outcomes largely aligned with current morphological classifications, forming monophyletic clades of conspecific barcodes, with only minor exceptions observed for the taxonomically complicated genus Polyommatus and misidentified records of Aulocera in the database. We also observed variations within the same phylogenetic clades forming nested lineages, which may be attributed to the taxonomic intricacies present at the subspecies level globally, mostly among Eurasian species. Overall, our effort not only substantiated the effectiveness of DNA Barcoding for the identification and conservation of this climatically vulnerable assemblage but also highlighted the significance of deciphering the unique genetic composition among this geographically isolated population of Ladakh butterflies.

An anthropogenic landscape reduces the influence of climate conditions and moonlight on carnivore activity

Abstract

Abiotic factors are limitations that can affect animal activity and distribution, whether directly or indirectly. The objective of this study was to evaluate how abiotic factors influence the activity of two mustelid species inhabiting the same region but different habitats in NE Poland-pine marten inhabits forests and stone marten occupy built-up areas. From 1991 to 2016, we obtained 23,639 year-round observations of 15 pine martens and 8524 observations of 47 stone martens. We explore the influence of ambient temperature, snow cover depth and moonlight reaching the ground and interactions between these variables on the probability of martens' activity. The activity of pine martens living in natural habitats is more affected by climate conditions and moonlight than that of stone martens living in anthropogenic areas. Pine martens inhabiting forests increased activity when the ambient temperature was above 0 °C and snow cover was absent, as well as when the ambient temperature dropped to - 15 °C and snow cover depth was about 10 cm. Stone marten occupying anthropogenic areas did not reduce their activity if the temperature dropped. Variation of activity in relation to ambient conditions is probably related to pine martens' behavioural thermoregulation. The pine marten was active more frequently on bright nights, while moonlight intensity did not affect the activity of the stone marten. Our study concludes that complex interactions among abiotic factors concerning different habitats play a synergetic role in shaping carnivore activity and suggest that climate warming may affect the behaviour of both martens.

Significance statement

The survival and reproduction of animals depends on their activity, which is subject to various constraints. We studied the influence of climate conditions and moonlight intensity on the ground on the activity of pine and stone marten. We found that pine martens in natural habitat were greatly impacted by ambient conditions, whereas stone martens in built-up areas were less so. Natural habitats involve limitations related to harsh winters but may mitigate the effects of high temperatures. In contrast, animals living in built-up areas are exposed to higher temperatures in summer, which is of particular importance in the face of climate change. Our results show that the combination of several environmental factors affects animal behaviour and these factors have varying effects in various habitats.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00265-023-03331-9.

African wild dogs (Lycaon pictus) from the Kruger National Park, South Africa are currently not inbred but have low genomic diversity

African wild dogs (Lycaon pictus) have undergone severe population reductions and are listed as endangered on the International Union for Conservation of Nature Red List. Small, isolated populations have the potential to suffer from threats to their genetic diversity that may impact species viability and future survival. This study provides the first set of population-wide genomic data to address conservation concerns for this endangered species. Whole genome sequencing data were generated for 71 free-ranging African wild dogs from the Kruger National Park (KNP), South Africa, and used to estimate important population genomic parameters. Genomic diversity metrics revealed that variation levels were low; however, this African wild dog population showed low levels of inbreeding. Very few first- and second-order relationships were observed in this cohort, with most relationships falling into the third-order or distant category. Patterns of homozygosity could have resulted from historical inbreeding or a loss in genome variation due to a population bottleneck. Although the results suggest that this stronghold African wild dog population maintains low levels of inbreeding, likely due to their cooperative breeding system, it may lead to a continuous population decline when a reduced number of suitable mates are available. Consequently, the low genomic variation may influence species viability over time. This study highlights the importance of assessing population genomic parameters to set conservation priorities. Future studies should include the investigation of the potential of this endangered species to adapt to environmental changes considering the low genomic diversity in this population.

Effects of insularity on genetic diversity within and among natural populations

We conducted a quantitative literature review of genetic diversity (GD) within and among populations in relation to categorical population size and isolation (together referred to as "insularity"). Using populations from within the same studies, we were able to control for between-study variation in methodology, as well as demographic and life histories of focal species. Contrary to typical expectations, insularity had relatively minor effects on GD within and among populations, which points to the more important role of other factors in shaping evolutionary processes. Such effects of insularity were sometimes seen-particularly in study systems where GD was already high overall. That is, insularity influenced GD in a study system when GD was high even in non-insular populations of the same study system-suggesting an important role for the "scope" of influences on GD. These conclusions were more robust for within population GD versus among population GD, although several biases might underlie this difference. Overall, our findings indicate that population-level genetic assumptions need to be tested rather than assumed in nature, particularly for topics underlying current conservation management practices.

Different increase rate in body mass of two marten species due to climate warming potentially reinforces interspecific competition

Many species show spatial variation in body size, often associated with climatic patterns. Studying species with contrasting geographical patterns related to climate might help elucidate the role of different drivers. We analysed changes in the body mass of two sympatric medium-sized carnivores—pine marten (Martes martes) and stone marten (Martes foina)—across Europe over 59 years. The body mass of pine marten increased with decreasing latitude, whereas stone marten body mass varied in a more complex pattern across its geographic range. Over time, the average body mass of pine martens increased by 255 g (24%), while stone marten by 86 g (6%). The greatest increase of body mass along both martens’ geographic range was observed in central and southern Europe, where both species occur in sympatry. The body mass increase slowed down over time, especially in allopatric regions. The average pine/stone marten body mass ratio increased from 0.87 in 1960 to 0.99 in 2019, potentially strengthening the competition between them. Thus, a differential response in body size to several drivers over time might have led to an adaptive advantage for pine martens. This highlights the importance of considering different responses among interacting species when studying animal adaptation to climate change.

Origin and dispersion pathways of guava in the Galapagos Islands inferred through genetics and historical records

Guava (Psidium guajava) is an aggressive invasive plant in the Galapagos Islands. Determining its provenance and genetic diversity could explain its adaptability and spread, and how this relates to past human activities. With this purpose, we analyzed 11 SSR markers in guava individuals from Isabela, Santa Cruz, San Cristobal, and Floreana islands in the Galapagos, as well as from mainland Ecuador. The mainland guava population appeared genetically differentiated from the Galapagos populations, with higher genetic diversity levels found in the former. We consistently found that the Central Highlands region of mainland Ecuador is one of the most likely origins of the Galapagos populations. Moreover, the guavas from Isabela and Floreana show a potential genetic input from southern mainland Ecuador, while the population from San Cristobal would be linked to the coastal mainland regions. Interestingly, the proposed origins for the Galapagos guava coincide with the first human settlings of the archipelago. Through approximate Bayesian computation, we propose a model where San Cristobal was the first island to be colonized by guava from the mainland, and then, it would have spread to Floreana and finally to Santa Cruz; Isabela would have been seeded from Floreana. An independent trajectory could also have contributed to the invasion of Floreana and Isabela. The pathway shown in our model agrees with the human colonization history of the different islands in the Galapagos. Our model, in conjunction with the clustering patterns of the individuals (based on genetic distances), suggests that guava introduction history in the Galapagos archipelago was driven by either a single event or a series of introduction events in rapid succession. We thus show that genetic analyses supported by historical sources can be used to track the arrival and spread of invasive species in novel habitats and the potential role of human activities in such processes.

Diversity and transmission of Aleutian mink disease virus in feral and farmed American mink and native mustelids

Aleutian mink disease virus (AMDV), which causes Aleutian disease, is widely spread both in farmed mink and wild mustelids. However, only limited data are available on the role of wild animals in AMDV transmission and spread. Our aim was to shed light on AMDV transmission among wild mustelids and estimate the effect of intense farming practices on the virus circulation by studying AMDV prevalence and genetic diversity among wild mustelids in Poland. We compared AMDV seroprevalence and proportion of PCR-positive individuals in American mink, polecats, otters, stone martens, and pine martens and used the phylogenetic analysis of the NS1 region to study transmission. In addition, we used a metagenomic approach to sequence complete AMDV genomes from tissue samples. In eastern Poland, AMDV seroprevalence in wild mustelids varied from 22 per cent in otters to 62 per cent and 64 per cent in stone martens and feral mink, respectively. All studied antibody-positive mink were also PCR positive, whereas only 10, 15, and 18 per cent of antibody-positive polecats, pine martens, and stone martens, respectively, were PCR positive, suggesting lower virus persistence among these animal species as compared to feral mink. In phylogenetic analysis, most sequences from feral mink formed region-specific clusters that have most likely emerged through multiple introductions of AMDV to feral mink population over decades. However, virus spread between regions was also observed. Virus sequences derived from farmed and wild animals formed separate subclusters in the phylogenetic tree, and no signs of recent virus transmission between farmed and wild animals were observed despite the frequent inflow of farmed mink escapees to wild populations. These results provide new information about the role of different mustelid species in AMDV transmission and about virus circulation among the wild mustelids. In addition, we pinpoint gaps of knowledge, where more studies are needed to achieve a comprehensive picture of AMDV transmission.

Aleutian mink disease: Spatio-temporal variation of prevalence and influence on the feral American mink

Pathogens are one of the factors driving wildlife population dynamics. The spread of pathogens in wildlife is currently highly related to the transmission of pathogens from farmed animals, which has increased with the constant development of farming. Here, we analysed the spatio-temporal variation in the prevalence of Aleutian mink disease virus (AMDV) antibodies in feral American mink (Neovison vison) populations in Poland (1,153 individuals from nine sites) in relation to mink farming intensity. AMDV was detected in feral mink at all study sites and the prevalence ranged from 0.461 in the northern region to 0.826 in the western region. Mink males and adults were infected more often than females and subadults; the infection was also more frequent during the mink breeding season than during non-breeding. The prevalence of AMDV changed non-linearly in consecutive years and the peak of prevalence was every 3-4 years. The predicted AMDV prevalence was low at sites where the number of farmed mink was also low and increased linearly with the increase in the number of mink kept on farms. The predicted AMDV prevalence at sites with low mink farming intensity strongly varied between years, whereas at sites with high mink farming intensity, the predicted prevalence did not change significantly. AMDV infection affected the mink's body condition and caused an increase in the size of the spleen, liver and kidneys. This study shows that Aleutian mink disease strongly affects feral mink but the spatio-temporal variation of its prevalence is complex and partly related to the transmission of the virus from farmed mink to feral populations. The study highlights the complexity of AMDV circulation in feral mink populations and implicates a potential spillover of the virus to native species.

Spatial ecology of the stone marten in an Alpine area: combining camera-trapping and genetic surveys

A species’ potential distribution can be modelled adequately only if no factor other than habitat availability affects its occurrences. Space use by stone marten Martes foina is likely to be affected by interspecific competition with the strictly related pine marten Martes martes, the latter being able to outcompete the first species in forested habitats. Hence, to point out the environmental factors which determine the distribution and density of the stone marten, a relatively understudied mesocarnivore, we applied two non-invasive survey methods, camera-trapping and faecal-DNA based genetic analysis, in an Alpine area where the pine marten was deemed to be absent (Val Grande National Park N Italy). Camera trapping was conducted from October 2014 to November 2015, using up to 27 cameras. Marten scats were searched for between July and November 2015 and, to assess density, in spring 2017. Species identification was accomplished by a PCR-RFLP method, while 17 autosomal microsatellites were used for individual identification. The stone marten occurred in all available habitats (83% of trapping sites and 73.2% of scats); nonetheless, habitat suitability, as assessed using MaxEnt, depended on four major land cover variables—rocky grasslands, rocks and debris, beech forests and chestnut forests—, martens selecting forests and avoiding open rocky areas. Sixteen individuals were identified, of which 14 related to each other, possibly forming six different groups. Using capwire estimators, density was assessed as 0.95 (0.7–1.3) ind/km2. In the study area, the widespread stone marten selected forested areas, attaining density values like those reported for the pine marten in northern Europe and suggesting that patterns of habitat selection may depend on the relative abundance of the two competing martens.

Multispecies reservoir of Spirometra erinaceieuropaei (Cestoda: Diphyllobothridae) in carnivore communities in north-eastern Poland

Background

Spirometra erinaceieuropaei is a diphylobothriid tapeworm with a complex life-cycle including definitive, intermediate and paratenic (transport) hosts. Multiple routes of parasite transmission often make it impossible to determine what type of host a specific infected animal is considered to be. Spargana larvae cause sparganosis, a severe food- and water-borne disease mainly found in Asia. In Poland, Spirometra sp. was reported in large carnivores in Białowieża Primeval Forest for the first time in the 1940s and was recently confirmed as S. erinaceieuropaei in several mammals and snakes using molecular methods.

Methods

In total, 583 carcasses of 9 carnivore species were necropsied between 2013 and 2019 in north-eastern (NE) Poland. The larvae of S. erinaceieuropaei (spargana) were isolated from subcutaneous tissue, counted, and preserved for genetic analyses. We calculated the prevalence and intensity of infection. To assess spatial variation in S. erinaceieuropaei infection probability in NE Poland, we applied a generalized additive model (GAM) with binomial error distribution. To confirm the species affiliation of isolated larvae, we amplified a partial fragment of the 18S rRNA gene (240 bp in length).

Results

Spirometra larvae were found in the subcutaneous tissue of 172 animals of 7 species and confirmed genetically as S. erinaceieuropaei. The overall prevalence in all studied hosts was 29.5% with a mean infection intensity of 14.1 ± 33.8 larvae per individual. Native European badgers and invasive raccoon dogs were characterized by the highest prevalence. An analysis of parasite spread showed a spatially diversified probability of infection with the highest values occurring in the biodiversity hot spot, Białowieża Primeval Forest.

Conclusions

Our study revealed that various mammal species (both native and non-native) can serve as S. erinaceieuropaei reservoirs. The frequency and level of infection may differ between selected hosts and likely depend on host diversity and habitat structure in a given area. Further studies are needed to assess the distribution of the parasite throughout Europe and the environmental and biological factors influencing infection severity in wild mammals.

Wildlife-transmitted Taenia and Versteria cysticercosis and coenurosis in humans and other primates

Wild mustelids and canids are definitive hosts of Taenia and Versteria spp. while rodents act as natural intermediate hosts. Rarely, larval stages of these parasites can cause serious zoonoses. In Europe, four cases of Taenia martis cysticercosis have been diagnosed in immunocompetent women, and two cases in zoo primates since 2013. In North America, a zoonotic genotype related but distinct from Versteria mustelae has been identified in 2014, which had caused a fatal infection in an orangutan and liver- and disseminated cysticercoses in two severely immune deficient human patients in 2018, respectively. Additionally, we could attribute a historic human case from the USA to this Versteria sp. by reanalysing a published nucleotide sequence. In the last decades, sporadic zoonotic infections by cysticerci of the canid tapeworm Taenia crassiceps have been described (4 in North America, 8 in Europe). Besides, 3 ocular cases from North America and one neural infection from Europe, all in immunocompetent patients, 6 cutaneous infections were described in severely immunocompromised European patients. Correspondingly, besides oral infections with taeniid eggs, accidental subcutaneous oncosphere establishment after egg-contamination of open wounds was suggested, especially in cases with a history of cutaneous injuries at the infection site. Taenia multiceps is mainly transmitted in a domestic cycle. Only five human coenurosis cases are published since 2000. In contrast, T. serialis coenurosis (1 human case since 2000) is primarily transmitted by wild canids. The etiological diagnosis of exotic cysticercoses is challenging. Usually, clinical material does not allow for a morphological identification, and serological tests are not available. These limitations have partly been overcome by molecular tools. Without claiming any dramatic emergence of cysticercoses and coenuroses transmitted by wild carnivores, further sporadic cases of such ‘exotic’ infections have to be expected.

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Wild canids and mustelids transmit rare but potentially fatal cysticercoses and coenuroses.

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Martens and weasels can rarely transmit dangerous parasitic infections.

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Tapeworm eggs may contaminate wounds and develop locally.

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In North America, the mustelid tapeworm Versteria causes severe human infections.

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Molecular analyses from minute clinical material allows for a specific diagnosis.