Fish play vital roles in river ecosystems; however, traditional investigations of fish usually cause certain ecological damage. Extracting DNA from aquatic environments and identifying DNA sequences offers an alternative, non-invasive approach for detecting fish species. In this study, environmental DNA (eDNA), coupled with PCR and next-generation sequencing, and electrofishing were used to compare their effects in identifying fish community characteristics. In three subtropical rivers of southern China, fish specimens and eDNA in water were collected from headwaters to estuaries. Both eDNA OTU richness and individual abundance (including number and biomass) could group 38 sampling sites into eight spatial zones with significant differences in local fish community composition. Compared with the order-/family-level grouping, the genus-/species-level grouping could more accurately recognize the differences between upstream zones I − III, midstream zones IV − V, and downstream zones VI – VIII. From headwaters to estuary, two environmental gradients significantly influenced the longitudinal distribution of fish species, including the first gradient composed of habitat and physical water parameters and the second gradient composed of chemical water parameters. The high regression coefficient of alpha diversity between eDNA and electrofishing methods as well as the accurate recognition of dominant, alien, and biomarker species at each spatial zone indicated that eDNA could characterize fish community attributes at a similar level of traditional approach. Generally, our results demonstrated that eDNA metabarcoding can be used as an effective tool in revealing fish composition and diversity, which is important for using the eDNA technique in aquatic field monitoring.

Understanding the adaptive evolution of species has long interested evolutionary biologists. Adaptive phenotypes can result from changes in protein-coding sequences that affect protein structure and function. The Rhinolophus macrotis group as a specific group has low echolocation frequency relative to body size compared with other rhinolophids, suggesting a special evolutionary process of this group. Transcription bridges genetic information and phenotypes. Here, we sequenced transcriptomes of the brain, liver, and cochlea for five species of the macrotis group and its closely related species, R. pusillus, to explore the molecular basis of the adaptation in the macrotis group at the sequence level. Strong and significant positive selection signals for species within the macrotis group was detected in seven genes (CRYM, FOXM1, MAP6, PYCARD, SLC35A2, WRB and SPRY2) linked to hearing. Unexpectedly, we also detected five PSGs (ARRDC3, LZTFL1, RAB8A, IGFBPL1 and TRNT1) linked to vision in species with relatively low frequencies. These results suggested that natural selection has led to the positive selection of some sensory-related genes. Furthermore, PSGs identified in the macrotis group significantly enriched in GO categories related to metabolism (e.g. catalytic activity and oxidoreductase activity), which provided evidence to parse the genetic adaptations of the species with low frequencies within the macrotis group. This is the first attempt to detect genome-wide sequence evolution across the macrotis group and our study provided valuable resources for studying the genetic mechanisms of rhinolophids adaptation.

Climate change is likely to drive widespread species range shifts and extirpations, mostly on the warm distribution edges, where habitat tends to be fragmented, of lower quality, support lower population density, and at greater risk from extreme weather events. In the Intermountain West, future climate will likely be warmer and drier, driving a reduction in sagebrush (Artemesia sp.) and other shrubland cover. Among the species threatened by more xeric climate is the Greater sage-grouse (Centrocercus urophasianus), which depends on sagebrush for forage and shelter, though their response to temperature is not well studied. We deployed 75 data loggers across two valleys in southern Utah and Nevada, near the southern edge of sage-grouse distribution, and collected temperature data for 27 months. We used random forest models to test the impacts of temperature, land cover, and topography on sage-grouse habitat selection and found that temperature influenced selection in all seasons and both sites. In Utah, the warmer site, sage-grouse selected areas near trees during the extremes of both winter and summer. In autumn and spring those extremes were rarer and sage-grouse avoided habitat near trees. Conversely, sage-grouse in the cooler Nevada site selected contiguous patches of sagebrush in extremes periods but only selected habitat near trees during winter cold, avoiding trees during summer. Our findings show that extreme temperatures drive sage-grouse to select habitat near trees despite the risk likely posed by avian predators. The difference between the Utah and Nevada sites suggests that sage-grouse prefer sagebrush as thermal shelter but that it may be inadequate during the hottest times, forcing riskier selection. These models point toward a more mechanistic understanding of how sage-grouse distribution may retract at its warm edges. This will refine our understanding of seasonal habitat requirements and inform management decisions to prioritize thermal refugia for an imperiled species.

The re-introduction of native species that have been extirpated or in low abundance in the Great Lakes has been a binational initiative between the United States and Canadian governments. Recently, new management programs have been unway that use current hatchery facilities for the restoration of native forage fishes in Lake Ontario. These species include Bloater ( Coregonus hoyi), which has been extirpated from Lake Ontario for approximately four decades, and Cisco ( C. artedi), which exists at a fraction of its former abundance. We assessed morphometrics, length-weight relationships, and condition factors during early life development for eight cohorts of Cisco and Bloater reared during 2012-2019. Weekly samples for Cisco and Bloater were measured from hatch until release (29-45 weeks, 133-1,002 samples annually). Head width, gape, mandible length, and mouth height metrics were all larger for Cisco than Bloater at any given size but increased at similar rates for both species. Average condition factors for Cisco and Bloater were 0.54317 and 0.55892, respectively. his information may also improve field identification of these species, helping managers evaluate the relative success of different release strategies for rehabilitation of populations of these native species.

As an island endemic with a decreasing population, the Critically Endangered Grenada Dove Leptotila wellsi is threatened by accelerated loss of genetic diversity resulting from ongoing habitat fragmentation. Small, threatened populations are difficult to sample directly but advances in molecular methods mean that non-invasive samples can be used. We performed the first assessment of genetic diversity of populations of Grenada Dove by a) assessing mtDNA genetic diversity in the only two areas of occupancy on Grenada, b) defining the number of haplotypes present at each site and c) evaluating evidence of isolation between sites. We used non-invasively collected samples from two locations: Mt Hartman (n=18) and Perseverance (n=12). DNA extraction and PCR were used to amplify 1,751 bps of mtDNA from two mitochondrial markers: NADH dehydrogenase 2 (ND2) and Cytochrome b (Cyt b). Haplotype diversity (h) of 0.4, a nucleotide diversity (π) of 0.4 and two unique haplotypes were identified within the ND2 sequences; one haplotype was identified within the Cyt b sequences. Of the two haplotypes identified; the most common haplotype (haplotype A = 73.9%) was observed at both sites and the other (haplotype B = 26.1%) was unique to Perseverance. Our results show low mitochondrial genetic diversity, a non-expanding population and clear evidence for genetically isolated populations. The Grenada Dove needs urgent conservation action, including habitat protection and potentially augmentation of gene flow by translocation in order to increase genetic resilience and diversity with the ultimate aim of securing the long-term survival of this Critically Endangered species.

Aposematic coloration plays an important role for species, as it serves as a clear signal of danger to visually-oriented predators regarding the potential toxicity of individuals displaying this condition. However, considerable gaps remain on this subject, and, primarily, empirical data are lacking to support robust discussions on the topic. The harlequin frog Atelopus hoogmoedi exhibits a range of aposematic colors across different populations, yet we still do not know how this characteristic was selected throughout evolution nor what the impacts of this characteristic are on the species' biology, ecology, and behavior. Considering that this topic deserves further in-depth studies, particularly due to being one of the most threatened groups of vertebrates and still lacking research, we present possible insights to guide future investigations on this subject.

Ectotherms are expected to be particularly vulnerable to climate change driven increases in temperature. Understanding how populations adapt to novel thermal environments will be key for informing mitigation plans. We took advantage of threespine stickleback (Gasterosteus aculeatus) populations inhabiting adjacent geothermal (warm) and ambient (cold) habitats to test whether their evolutionary divergence was adaptive using field reciprocal transplant experiment. We found evidence for adaptive morphological divergence, as growth (length change) in the non-native habitat was found to relate to head, posterior and total body shape. Higher growth in fish transplanted to a non-native habitat was found to be associated with shape profiles closer to that of the native fish. The consequences of transplantation were asymmetric with cold sourced fish transplanted to the warm habitat suffering from lower survival rates and greater parasite prevalence than warm sourced fish transplanted to the cold habitat. We also found evidence for divergent shape allometries that related to growth. Our findings suggest that wild populations can adapt quickly to thermal conditions. However, immediate transitions to warmer conditions may be particularly difficult.

Geological events and historical environmental change can strongly affect the genetic structures and differentiation of fish populations. Although the central region of the Yunnan-Guizhou Plateau contains the highest concentration of rift-subsidence lakes in China, the effects of key geological events on the distributions and genetic structures of the regional fauna remain poorly understood. Fishes of the genus Sinocyclocheilus are endemic to the Yunnan-Guizhou Plateau, where they are found in karst landforms. As a result of environmental pollution and other human activities, Sinocyclocheilus populations have decreased sharply, and the genus is currently listed under Class II of the nationally protected animals classification in China. Examining the phylogeographic patterns of Sinocyclocheilus fishes can be useful for elucidating the spatio-temporal dynamics of their population size, dispersal history and extent of geographical isolation, thereby providing a theoretical basis for their protection. Here, we used Restriction Site Associated DNA Sequencing (RAD-seq) to investigate the evolution of Sinocyclocheilus fishes. Our analysis supports the endemicity of Sinocyclocheilus, and identifies the formation of Dianchi Lake and Fuxian Lake as key geological events shaping Sinocyclocheilus population structure. We estimate that the most recent common ancestor (MRCA) of Sinocyclocheilus fish occurred in the Central Yunnan Basin 3.75~3.11 Ma. It is the first time to prove that the altitude change has a great influence on the genetic variation among the populations of Sinocyclocheilus. We discuss the implications of our results for the protection and management of Sinocyclocheilus grahami and other cave fishes.

Sigmodontines (Rodentia: Cricetidae), the largest living radiation of Neotropical rodents (90 genera, 489 species), show about 10% having specializations related to a semiaquatic habitat. In addition, this mode of life is unequally distributed among the several clades which compose the subfamily, concentrated in the Ichthyomyini and in a few large-bodied Oryzomyini. The observed taxonomical and geographical pattern is here discussed in a biogeographical historical context. As working hypothesis is advanced that the risk of predation (exerted by animalivorous fresh-water vertebrates) shaped and limited since the late Miocene the semiaquatic performance of the subfamily. Moreover, by exploring the fossil record can also be argued that during the Pleistocene is registered an important number of amphibious sigmodontines extinctions. Therefore, the scarcity of living semiaquatic sigmodontine rodents can be attributed to a combination of an undervalued habitat (mostly by risk of predation) plus a recent pauperization (by a sum of biological extinctions) of the members of that guild. A shallow comparison of the sigmodontine case against murids suggests that continental waterbodies resulted partially refractory to muroid colonizations.

Rampant environmental change and forest destruction push elephants, both Asian and African, to explore human spaces to fulfil their dietary and ecological requirements. Many ‘novel’ elephant behaviour in sharing spaces come to the limelight. Elephant calf burial is reported in African literature but remains absent from the Asian context. We concretely report calf burials by Asian elephants in the eastern Himalayan floodplains of the north Bengal landscape. The study area consists of fragmented forests, tea gardens, agricultural lands, and defence establishments, among others. Tea gardens form the majority of elephant corridors, and we explain the burial strategy of elephants in the trenches of tea gardens. We present four case reports of calf burials by elephants. We aimed to understand the perimortem strategy and postmortem behaviour of Asian elephants. The major findings reflect that the carcasses were carried through trunks and legs for a distance before burying in a ‘legs-upright-position’. We further investigated the underlying reason for calf deaths through postmortem examinations. Direct human intervention was not recorded in any of the four deaths. Through opportunistic observation, digital photography and fieldnotes, and postmortem examination report, we suggest that the carcasses were buried in an abnormal recumbent style irrespective of the reason for calf deaths. Through long-term observation, we further report that the elephants in this region clearly avoid the paths where carcasses were buried, attributing to “bad milestones” and “bad omens”. We discuss and connect the literature of two distinct elephant species and also compared thanatological studies of other sentient nonhuman species. Keywords: Thanatology, animal behaviour, Asian elephant, calf burial, eastern Himalayas, tea gardens

Mitochondrial DNA analyses were carried out in order to determine the haplogroups of 6 individuals recovered from the cemetery of Resuloğlu and dated to the Early Bronze Age (EBA III). Using bioinformatics tools, it was determined that two of the individuals belonged to the T2+150 haplogroup and four belonged to the H2a2a1, H32, T2+16189, and J1b7 haplogroups. These results support a link between the origins of the present-day European population and the farmers of the Anatolian Neolithic period. Furthermore, a detailed analysis of single nucleotide polymorphisms revealed T16189C and C150T mutations in four of the six individuals, which are associated with the risk of melanoma and cervical cancer - HPV infection. These molecular findings are consistent with the health profiles of the excavated skeletons, which indicate that the community struggled with infectious and metabolic diseases. This is the first case of cancer detected in human skeletons from the remains of ancient cities in Türkiye and the first case of carcinoma detected at the mitochondrial genome level in Europe.

The nests of ground-nesting birds rely heavily on camouflage for their survival, and predation pressures, often linked to human activity, are a major source of mortality. Numerous ground-nesting bird populations are in decline, so understanding the effects of camouflage on their nesting behaviour is of relevance to their conservation concern. Habitat three-dimensional (3D) geometry together with predator visual abilities, viewing distance, and viewing angle determine whether a nest is either visible, occluded or too far away to detect. While this link is intuitive, few studies have investigated how fine-scale geometry is likely to help defend nests from different predator guilds. We quantified nest visibility based on 3D occlusion, camouflage, and predator visual modelling in northern lapwing, Vanellus Vanellus, on different land management regimes. Lapwings selected local backgrounds that had a higher 3D complexity at a spatial scale greater than their entire clutches compared to nearby control sites. Importantly, our findings show that habitat geometry – rather than predator visual acuity restricts nest visibility to terrestrial predators, and that an open field would actually be perceived as a closed habitat to a terrestrial predator searching for nests on the ground. Taken together with lapwings’ careful nest site selection, our findings highlight the importance of considering habitat geometry for understanding the evolutionary ecology and management of conservation sites for ground-nesting birds.

Climate change is altering the distribution and abundance of marine species, especially in Arctic and sub-Arctic regions. In the eastern Bering Sea, home of the world’s largest run of sockeye salmon (Oncorhynchus nerka), juvenile sockeye salmon abundance has increased and their migration path shifted north with warming, 2002-2018. For these sockeye salmon, we quantify environmental and biological covariate effects within spatio-temporal species distribution models. Spatio-temporally, with respect to juvenile sockeye salmon densities: 1) sea surface temperature had a nonlinear effect, 2) Calanus, a minor prey item, and age-0 pollock (Gadus chalcogrammus), a major prey item during warm years, had no significant effect, and 3) juvenile pink salmon (Oncorhynchus gorbuscha) had a positive linear effect on juvenile sockeye salmon densities. Temporally, juvenile sockeye salmon abundance was positively correlated with sea surface temperature, age-0 pollock abundances, and juvenile pink salmon abundance. Changes in population dynamics of sockeye salmon in response to environmental have potential implications for projecting specific future food securities and management of fisheries in Arctic waters.

The existence of adult sexual dimorphism is typically explained as a consequence of sexual selection, yet coevolutionary drivers of sexual dimorphism frequently remain untested. Here, I investigate the role of sexual dimorphism in host-parasite interactions of the brood parasitic diederik cuckoo, Chrysococcyx caprius. Female diederik cuckoos are more cryptic in appearance and pose a threat to the clutch, while male diederik cuckoos are conspicuous and not a direct threat. Specifically, I examine whether sexual dimorphism in diederik cuckoos provokes threat-level sensitive responses in Southern red bishop, Euplectes orix, hosts. I use experimentally simulated nest intrusions to test whether hosts have the capacity to differentially (i) detect, and/or (ii) discriminate between, male and female diederik cuckoos, relative to controls. Overall, I found no evidence that diederik cuckoos differ in detectability, since both sexes are comparable to controls in the probability and speed of host detection. Furthermore, neither male nor female hosts discriminate between sexually dimorphic diederik cuckoos when engaging in frontline nest defences. However, hosts that witnessed a male diederik cuckoo during the trial were more than twice as likely to reject odd eggs compared to those that saw a control. Moreover, hosts were more likely to reject experimental eggs when exposed to a male compared to a female diederik cuckoo: the reverse of a beneficial threat-level sensitive response. While the cryptic appearance of female diederik cuckoos does not differentially avoid detection by hosts, it does appear to provide the benefit of anonymity given the egg rejection costs of male-like appearance in the nest vicinity. These findings have implications for the evolution and maintenance of sexual dimorphism across the Cuculidae, and highlight the value of testing assumptions about the ecological drivers of sexual dimorphism.

Baleen whales (Mysticeti) possess the necessary anatomical structures and genetic elements for olfaction. Nevertheless, the olfactory receptor gene (OR) repertoire has undergone substantial degeneration in the cetacean lineage following the divergence of Artiodactyla and Cetacea. The functionality of the highly degenerated mysticete ORs within their olfactory epithelium remains unknown. In this study, we extracted total RNA from the nasal mucosa of common minke whales (Balaenoptera acutorostrata) to investigate the localized expression of ORs. All three sections of the mucosae examined in the nasal chamber displayed comparable histological structure, whereas the posterior portion of the frontoturbinal region exhibit notably high expression of ORs and another gene specific to the olfactory mucosa. Neither the olfactory bulb nor the external skin exhibited expression of these genes. Although this species possesses four intact class-1 ORs, all the ORs expressed in the nasal mucosa belong to class-2, implying the loss of aversion to specific odorants. These anatomical and genomic analyses suggest that ORs are still responsible for olfaction within the nasal region of baleen whales, enabling them to detect desirable scents such as prey and potential mating partners.

1. Temperature is essential for the survival and development of eggs. Some anurans have evolved and developed foam nesting traits, with thermal insulation considered to be among their functions. Foam nesting frogs tend to exhibit reproductive plasticity. For example, they oviposit on both trees and the ground. How such plasticity affects foam nest function is of major relevance and is likely related to the adaptation of foam nesting frogs. However, this has not been well studied. 2. In this study, we studied the interaction between foam nest site, foam nest function, and egg fate using the Japanese green tree frog, Zhangixalus arboreus, and analysed how nest site differences (arboreal or terrestrial) affect the thermal function of foam nests. 3. We compared the thermal functions of foam nests between arboreal and terrestrial oviposition sites of Z. arboreus. We artificially replaced half of the arboreal nests to terrestrial environments and recorded temperature in and outside of the experimental terrestrial nest and original arboreal nests. We also examined egg survival and hatching rate for all the nests. 4. The results indicated superior heat insulation in terrestrial nests, with warmer temperatures inside than outside the nests, especially at night, which led to a high egg survival rate. Therefore, terrestrial ovipositing should be valid under cold weather conditions. This may be related to the evolutionary history of oviposition site plasticity of this genus, which originally had an arboreal oviposition trait but evolved into terrestrial site use owing to global cooling. 5. Our novel insights into the evolution and adaptivity of foam nesting and oviposition site use in Z. arboreus make a significant contribution to animal ecology.

Aim Identification of taxonomically cryptic species is essential for the effective conservation of biodiversity. Freshwater-limited organisms tend to be genetically isolated by drainage boundaries, and thus may be expected to show substantial cryptic phylogenetic and taxonomic diversity. By comparison, populations of diadromous taxa, that migrate between freshwater and marine environments, are expected to show less genetic differentiation. Here we test for cryptic diversity in Australasian populations (both diadromous and non-diadromous) of two widespread Southern Hemisphere fish species. Location Throughout both their Australian ranges (including Lord Howe Island) and localities in New Zealand (including the Subantarctic Islands and Chatham Island). Taxon Galaxias brevipinnis and Galaxias maculatus. Methods mtDNA and nuclear markers were used to assess the presence of cryptic species and to determine if differences in species ecology could influence the degree of cryptic diversity. Results Both mtDNA and nuclear markers reveal putative cryptic species within these taxa. The substantial diversity detected within G. brevipinnis may be explained by its strong climbing ability which allows it to form isolated inland populations. In island populations, G. brevipinnis similarly show deeper genetic divergence than those of G. maculatus, which may be explained by the greater abundance of G. maculatus larvae in the sea allowing more ongoing dispersal. Main conclusions Our study highlights that even widespread, ‘high-dispersal’ species can harbour substantial cryptic diversity and therefore warrant increased taxonomic and conservation attention.

Urbanization processes are taking place at a very high rate, especially in Africa, these. At the same time, a number of small mammal species, be they native of invasive, take advantage of these human-induced habitat modifications. They represent commensal communities of organisms that cause a number of inconveniences to humans, including as potential reservoirs of zoonotic diseases. We studied via live trapping and habitat characterization such commensal small mammal communities in small villages to large cities of Senegal, to try understand how the species share this particular space. Seven major species were recorded, with exotic invasive house mice (Mus musculus) and black rats (Rattus rattus) dominating in numbers. The shrew Crocidura olivieri appeared as the main and more widespread native species, while native rodent species (Mastomys natalensis, M. erythroleucus, Arvicanthis niloticus and Praomys daltoni) were less abundant and/or more localized. Habitat preferences, compared between species in terms of room types and characteristics, showed differences between house mice, black rats and M. natalensis especially. Niche (habitat component) breadth and overlap were measured. Among invasive species, the house mouse showed a larger niche breadth than the black rat, and overall, all species displayed high overlap values. Co-occurrence patterns were studied at the locality and local scales. The latter show cases of aggregation (between the black rat and native species, for instance) and of segregation (as between the house mouse and the black rat in Tambacounda, or between the black rat and M. natalensis in Kédougou). While updating information on commensal small mammal distribution in Senegal, a country submitted to a dynamic process of invasion by the black rat and the house mouse, we bring original information on how species occupy and share the commensal space, and make predictions on the evolution of these communities in a period of ever-accelerating global changes.

A study of bird frugivory in Desamparaditos de Puriscal in Costa Rica in 2021 showed the importance of two tropical trees, Gumbo Limbo (Bursera simaruba) and Huevos de Caballo (the common Spanish name of Tabernaemontana donnell-smithii) within habited areas. The study also focused on which species fed on lipid-rich fruits and which fed on lipid-poor fruits — Gumbo Limbo fruits are lipid-poor, whereas Huevos de Caballo “fruits” are lipid-rich — and whether the feeding choices of various birds in this community would reflect the distinction in lipid content. The study was done during the beginning of the rainy season, and compared with a recent analysis of bird frugivory studies. Results showed numerous similarities regarding the birds feeding on Gumbo Limbo, but more differences were found for the birds feeding on Huevos de Caballo. Most significant was that a number of species were observed feeding on both of these fruits that had not been observed in the other studies. Additionally, the study indicated that both trees might be important nutritional sources for young birds. A follow-up study was conducted in 2022. That study showed more feeding by some species on Gumbo Limbo fruits, and demonstrated the importance of Gumbo Limbo for these species during the late dry season. The 2022 study began on 26 January and ended on 7 March, the date when the 2021 study began. Data from 2022 (summarized in Appendices 3 and 3A) will not be fully analyzed, but may be referred to in the discussion.

With global climates changing rapidly, animals must adapt to new environmental conditions with altered weather and phenology. Key to adapting to these new conditions is adjusting the timing of reproduction to maximize fitness. Using a long-term dataset on a wild population of yellow-bellied marmots (Marmota flaviventer) at the Rocky Mountain Biological Laboratory (RMBL), we investigated how the timing of reproduction changed with changing spring conditions over the past 50 years. Marmots are hibernators with a four-month active season. It is thus crucial to reproduce early enough in the season to have time to prepare for hibernation, but not too early so as snow cover prevents access to food. Importantly, climate change in this area has increased spring temperatures by 5 oC and decreased spring snowpack by 50 cm over the past 50 years. We evaluated how female marmots adjust the timing of their reproduction in response to the changing conditions and estimated the importance of both genetic variance and plasticity in the variation in this timing. We showed that, within a year, the timing of reproduction is not as tightly linked to the date a female emerges from hibernation as previously thought. We reported a positive effect of spring snowpack but not of spring temperature on the timing of reproduction. We found inter-individual variation in the timing of reproduction, including low heritability, but not in its response to changing spring conditions. There was directional selection for earlier pup emergence date since it increased the number and proportion of pups surviving their first winter. Taken together, the timing of marmot reproduction might evolve via natural selection, however, plastic changes will also be extremely important as long as plasticity is not limited. Further, future studies on the marmots should not operate under the assumption that females reproduce immediately following their emergence.

The subgenus Aschizomys belongs to the genus Alticola (Central Asian mountain vole) and consists of two species: Alticola macrotis and Alticola lemminus. Phylogenetic relationships within the subgenus Aschizomys remain obscure due to limited sampling, an insufficient number of molecular markers used in phylogenetic studies, and paraphyly observed on mitochondrial trees. In this work, to infer reliable phylogenetic relationships and evaluate putative scenarios of ancient hybridization within the subgenus, we applied double-digest restriction site–associated DNA paired-end (quaddRAD) sequencing to 20 DNA samples (20 individuals), including five species of the genus Alticola, and dated the divergence of cytochrome b (cytb) lineages within Aschizomys using a “second calibration” approach. We showed monophyly of the two species on the basis of thousands of nuclear loci and demonstrated traces of introgression also in the nuclear genome. Observed paraphyly in cytb could be explained by an introgression event rather than incomplete lineage sorting. This explanation was confirmed by an analysis of the cytb divergence time. Overall, our results support the hypothesis of extensive migration of the Aschizomys species during the Late Pleistocene, with this migration leading to population divergence and introgression. We expect our article to become a starting point for a series of rigorous studies on the population history of the genus Alticola as a whole.

Early life adversity predicts shorter adult lifespan in several animal taxa. Yet, work on long-lived primate populations suggests the evolution of mechanisms that contribute to resiliency and long lives despite early life insults. Here, we tested associations between individual and cumulative early life adversity and lifespan on rhesus macaques at the Cayo Santiago Biological Field Station using 50 years of demographic data. We performed sex-specific survival analyses at different life stages to contrast short-term effects of adversity (i.e., infant survival) with long-term effects (i.e., adult survival). Rhesus macaques exposed to adversity at birth suffered a significant increase in mortality risk during infancy with both individual and cumulative adversities having the highest impact among affected females. However, when considering adult lifespan, affected males showed higher vulnerability to both individual and cumulative adversities early in life. Our study shows profound immediate effects of insults at birth on female infant cohorts and suggests that affected female adults are more robust (i.e., viability selection). In contrast, adult males who experienced harsh conditions early in life showed an increased mortality risk at older ages as expected from hypotheses of long-term effects of individual, as well as cumulative, adversity early in life. Our study reveals that mortality risk during infancy is mainly driven by the type of adversity, rather than their accumulation at birth. However, cumulative adversity seems to play a major role in adult survival. Our analysis suggests sex-specific selection pressures on life histories and highlights the need for studies addressing the effects of early life adversity across multiple life stages. This information is critical for planning life stage-specific strategies of conservation interventions.

Animal dietary choices help understand a species’ feeding niche and are particularly relevant in conservation management. In this study, we aimed to gather knowledge on food niche and the foraging ecology of the Grizzled Giant Squirrel (Ratufa macroura) in Chinnar Wildlife Sanctuary, Southern Western Ghats, Kerala, India. Specifically, the objectives were to identify food composition, the seasonal variation in food choice and feeding technique. Through focal animal sampling, the Grizzled Giant Squirrel in Chinnar Wildlife Sanctuary was found to feed on 30 plant species belonging to 18 families. The most utilized plant family was Fabaceae, with eight species, followed by Moraceae (four species) and Anacardiaceae (two species). The feeding species included 22 trees, four climbers, one liana, one paraphyte, one shrub and one succulent species. The maximum duration of feeding was observed on Bauhinia racemosa (19.79%), followed by Tamarindus indica (14.08%) and Nothopegia beddomei (9.89%). The squirrel’s choice of diet was primarily affected by the availability of food tree species and food items rather than the season and non-tree species also have been reported from the diet of Grizzled Giant Squirrel. Even though the Grizzled Giant Squirrel shows plasticity in the food niche, the availability of mature trees and plants appears important for its conservation in the fragmented riparian forest in the Western Ghats, southern India.

1. The fixation index, FIS has been a staple measure to detect selection or departures from random mating in populations. However, current Next Generation Sequencing (NGS) cannot easily estimate Fis, in multi-locus gene families, which contain multiple loci having similar or identical arrays of variant sequences of ≥1 kilobase, which differ at multiple positions. In these families, high-quality short-read NGS data typically identify variants, but not the genomic location, which is required to calculate Fis (based on locus-specific observed and expected heterozygosity). Thus, to assess assortative mating, or selection on heterozygotes, from NGS of multi-locus gene families, we need a method that does not require knowledge of which variants are allelic at which locus in the genome. 2. We developed such a method. Like Fis, our novel measure, 1His, is based on the principle that positive assortative mating, or selection against heterozygotes, reduces within-individual variability relative to the population. 3. We demonstrate high accuracy of 1His on a wide-range of simulated scenarios, and two datasets from natural populations of penguins and dolphins. 4. 1His is important because multi-locus gene families are often involved in assortative mating, or selection on heterozygotes. 1His is particularly useful for multi-locus gene families such as toll-like receptors, the major-histocompatibility-complex in animals, homeobox genes in fungi and self-incompatibility genes in plants.