1. Toxin resistance in all taxa is important for their survival. Resistance to bufadienolide toxin is mediated by molecular changes to the sodium-potassium-pump. As for toads themselves, the parotid is consisted of extremely high concentration of bufadienolide toxin, it indicates toads need stronger resistance for self-protection than any other species involved in toad predation. Thus, besides the widespread convergence of Na+/K+-ATPase, toads may develop a unique self-resistance way for their accumulated bufadienolide toxin. 2. Our studies on invasive cane toads from Australia and common asiatic toads from China showed that toads store defensive venom in parotid as a combinatorial library composed of low-toxic protoxin (conjugated bufadienolides), which is characterized by two building blocks, i.e. high-toxic toxin (free bufadienolide) and the argininyl side chain contributed to toxin absorption promotion. This protoxin could be hydrolyzed to high-toxic toxin for defense immediately as it is discharged from parotid at the time when toad is attacked or stimulated by predators. 3. Our results revealed that toads indeed develop a unique protoxin self-resistance way to their own extremely high concentration of bufadienolide toxin for self-protection besides the widespread convergence of Na+/K+-ATPase. The revelation of this protoxin self-resistance way highlights the importance and ecological multifunctionality of the sophisticated combinatorial chemistry of nature and may partly account for the strong adaptability of toad as infamous ailing invaders. It completes the picture of self-resistance mechanism to their own bufadienolide toxin for toad or may even for many other venomous animals.

A document by Nasrin Amini Tehrani, written on Authorea.

The niches of species that are geographically separated can either be conserved or diverge. This dynamic has been studied over time through Species Distribution Modeling and quantification of niche metrics. Here I have conducted this study for South Asian Dolphins. The Ganges River Dolphin and the Indus Dolphins are considered sub-species but there has been debate on this classification. The niche overlap was found to be very low meaning Indus Dolphin which most likely separated through the process of drainage capture has diverged from its original niche. The niche equivalency test also showed that there is a niche divergence is statistically significant. These dolphins could well be two separate species given their difference in niches but further study especially genetic studies are needed to affirm this. But the study highlights deviations from niche conservatism for the taxa due to significant niche shifts.

The evolutionary origins and hybridization patterns of Canis species in North America has been hotly debated for the past 30 years. Disentangling ancestry and timing of hybridization in Great Lakes wolves, eastern Canadian wolves, red wolves, and eastern coyotes is most often partitioned into a 2-species model that assigns all ancestry to grey wolves and/or coyotes, and a 3-species model that includes a third, North American evolved eastern wolf genome. The proposed models address recent or sometimes late Holocene hybridization events but have largely ignored Pleistocene era opportunities for hybridization that may have impacted the current mixed genomes in eastern Canada and the United States. Here, we re-analyze contemporary and ancient mitochondrial DNA genomes with Bayesian phylogenetic analyses to more accurately estimate divergence dates among lineages. We combine that with a review of the literature on Late Pleistocene Canis distributions to illuminate opportunities for ancient hybridization events between extinct Beringian grey wolves (C. lupus) and extinct large wolf-like coyotes (C. latrans orcutti) that we propose as a potentially unrecognized source of introgressed genomic variation within contemporary Canis genomes. These events speak to the potential origins of contemporary genomes and provide a new perspective on Canis ancestry, but do not influence/negate current conservation priorities of dwindling wolf populations with unique genomic signatures and key ecologically critical roles.

1. Landscape change is a key driver of biodiversity declines due to habitat loss and fragmentation, but spatially shifting resources can also facilitate range expansion and invasion. Invasive populations are reproductively successful, and landscape change may buoy this success. 2. We show how modelling the spatial structure of reproductive success can elucidate the mechanisms of range shifts and sustained invasions for mammalian species with attendant young. We use an example of white-tailed deer (deer; Odocoileus virginianus) expansion in the Nearctic boreal forest, a North American phenomenon implicated in severe declines of threatened woodland caribou (Rangifer tarandus). 3. We hypothesized that deer reproductive success is linked to forage subsidies provided by extensive landscape change via resource extraction. We measured deer occurrence using data from 62 camera-traps in northern Alberta, Canada, over three years. We weighed support for multiple competing hypotheses about deer reproductive success using multi-state occupancy models and generalized linear models in an AIC-based model selection framework. 4. Spatial patterns of reproductive success were best explained by features associated with petroleum exploration and extraction, which offer early seral vegetation resource subsidies. Effect sizes of anthropogenic features eclipsed natural heterogeneity by two orders of magnitude. We conclude that deer populations are likely buffered from overwinter mortality by landscape change, wherein early seral forage subsidies support high springtime reproductive success to offset or exceed winter losses. 5. Synthesis and Applications. Modelling spatial structuring in reproductive success can become a key goal of remote camera-based global networks, yielding ecological insights into mechanisms of invasion and range shifts to inform effective decision-making for global biodiversity conservation.

Food habits are important factors for wild nonhuman primates’ environment adaptation. White-headed langurs (Trachypithecus leucocephalus) are endemic to the limestone forest and face to the habitat fragmentation, which have to adjust the food habits to adapt the special environment. In this study, we compared the dietary data for white-headed langurs living in Chongzuo White-headed Langur National Nature Reserve over two separate study periods to evaluate interannual variations in diet. Our results indicated that young leaves were the preferred major food for the langur. The plant parts consumption pattern was similar between the two separate study periods. The consumption of young leaves was varied with the availability of young leaves, whereas the consumption of mature leaves was negative correlated with the young leaf’s availability. The consumption of plant species and diet diversity varied in the two separate study periods, which were higher in 2013 than 2016. In both 2013 and 2016, the diet diversity varied with the consumption of mature leaves, but negative correlated with the consumption and availability of young leaves. Dietary interannual variation probably linked to the phenology variations, or probably mean that the white-headed langurs has a flexible ecological adaptation coping with habitat fragmentation.

1. 1. Thermal imaging technology is a developing field in wildlife management. Most thermal imaging work in wildlife science has been limited to larger ungulates and surface-dwelling mammals. Little work has been undertaken on the use of thermal imagers to detect fossorial animals and/or their burrows. Survey methods such as white-light spotlighting can fail to detect the presence of burrows (and therefore the animals within), particularly in areas where vegetation obscures burrows. Thermal imagers offer opportunity to detect the radiant heat from these burrows, and therefore the presence of the animal, particularly in vegetated areas. Thermal imaging technology has become increasingly available through the provision of smaller, more cost-effective units. Their integration with drone technology provides opportunities for researchers and land managers to utilise this technology in their research/management practices. 2. We investigated the ability of both consumer (AUD$65,000) mounted on drones to detect rabbit burrows (warrens) and entrances in the landscape as compared to visual assessment. 3. Both types of imager and visual inspection detected active rabbit warrens when vegetation was scarce. The presence of vegetation was a significant factor in detecting entrances (P<0.001, α=0.05). The consumer imager did not detect as many warren entrances as either the professional imager or visual inspection (P=0.009, α=0.05). Active warren entrances obscured by vegetation could not be accurately identified on exported imagery from the consumer imager and several false-positive detections occurred when reviewing this footage. 4. We suggest that the exportable Hz rate was the key factor in image quality and subsequent false positive detections. This feature should be considered when selecting imagers. Thermal imagers are a useful additional tool to aid in identification of entrances for active warrens and professional imagers detected more warrens and entrances than either consumer imagers or visual inspection.

The structure of Apteryx’s eggshell has generated much debate over the decades because it does not fit well with most allometric predictions. Apteryx eggshells are unusually thin and have been reported to be 60% less porous than expected. It has been suggested that these adaptations are compensations for a very long incubation period. Most studies so far have been carried out in what has been reported as Apteryx australis, and using infertile eggs or eggs laid in captivity. However, A. australis once comprised all kiwi with brown plumage, now separated into three distinct species: Brown Kiwi (A.mantelli), Rowi (A.rowi), and Tokoeka (A.australis). These three species use different habitats and live at different latitudes and altitudes. In addition, captive eggs are much smaller than wild laid eggs. These confounding factors make necessary to revise the assumptions made for Apteryx in the past. In this study, we analysed the physical characteristics of the Apteryx eggshells making a comparison between the three species of brown coloured kiwi and for some of the analysis we included some specimens of Roroa (A. haastii, Great Spotted Kiwi). We found that shell characteristics are different between the different species studied. The pore area of Apteryx eggshells was higher than previously suggested, and the water vapour conductance was much closer to what is expected for an egg that size. We found several new features such as triangular mineral particles composing the cuticle, only reported for a cretaceous Theropod, and the presence of plugs and caps on the eggshell pores. We suggest that the characteristics of the eggshells of the different species relate to the mating system of each species in addition to environmental variables, particularly pluviosity. We also suggest that the erosion of the cuticle during incubation is an adaptation to a long incubation period in a burrow.

Understanding trade-offs in wild populations is difficult, but important if we are to understand the evolution of life histories and the impact of ecological variables upon them. Markers that reflect physiological state and predict future survival would be of considerable benefit to unravelling such trade-offs and could provide insight into individual variation in senescence. However, currently used markers often yield inconsistent results. One underutilised measure is haematocrit, the proportional of blood comprising of erythrocytes, which relates to the blood’s oxygen-carrying capacity and viscosity, and to individual endurance. Haematocrit has been shown to decline with age in cross-sectional studies (which may be confounded by selective appearance/disappearance). However, few studies have tested whether haematocrit declines within-individuals or whether low haematocrit impacts survival in wild taxa. Using longitudinal data from the Seychelles warbler (Acrocephalus sechellensis), we demonstrated that haematocrit increases with age in young individuals (<1.5 years) but decreases with age in older individuals (1.5–13 years). In breeders, haematocrit was higher in males than females and varied relative to breeding stage. High haematocrit was associated with lower survival in young individuals, but not older individuals. Thus, while we did not find support for haematocrit as a marker of senescence, high haematocrit is indicative of poor condition in younger individuals. Possible explanations are that these individuals were experiencing dehydration and/or high endurance demands prior to capture, which warrants further investigation. Our study demonstrates that haematocrit can be an informative metric for life-history studies investigating trade-offs between survival, longevity and reproduction.

Accurate determination of animal diets is difficult. Methods such as molecular barcoding or metagenomics offer a promising approach, allowing quantitative and sensitive detection of different taxa. Here we show that rapid and inexpensive diet quantification is possible through metagenomic sequencing with the portable Oxford Nanopore Technologies (ONT) MinION. Using an amplification-free approach, we profiled the stomach contents from 24 wild-caught rats. We conservatively identified diet items from over 50 taxonomic orders, ranging across nine phyla, including plants, vertebrates, invertebrates, and fungi. This highlights the wide range of taxa that can be identified using this simple approach. We calibrated the accuracy of this method by comparing the characteristics of reads matching the ground-truth host genome (rat) to those matching diet items, and show that at the family-level, taxon assignments are approximately 97.5% accurate. Some inaccuracies may arise from database biases; we suggest a way to mitigate for database biases when using metagenomic approaches. Finally, we implemented a constrained ordination analysis and show that we can identify the sampling location of an individual rat within tens of kilometres based on diet content alone. This work establishes proof-of-principle for long-read metagenomic methods in quantitative diet analysis. We show that diet content can be quantified even with limited expertise, using a simple, amplification free workflow and a relatively inexpensive and accessible next generation sequencing method. Continued increases in the accuracy and throughput of ONT sequencing, along with improved genomic databases, suggests that a metagenomic approach for quantification of animal diets will become an important method in the future.

Understanding the processes that enable species coexistence has important implications for assessing how ecological systems will respond to global change. Morphology and functional similarity increase the potential for competition, and therefore, co-occurring morphologically similar but genetically unique species are a good model system for testing coexistence mechanisms. We used DNA metabarcoding and High Throughput Sequencing to characterise for first time the trophic ecology of two recently-described cryptic bat species with parapatric ranges, Myotis escalerai and Myotis crypticus. We collected faecal samples from allopatric and sympatric regions and locations to describe the diet both taxonomically and functionally and compare prey consumption with prey availability. The two bat species had similar diets characterised by high arthropod diversity, particularly Lepidoptera, Diptera and Araneae, and a high proportion of prey that is not volant at night, which points to extensive use of gleaning. Diet overlap at the prey-item level was lower in locally sympatric than allopatric locations, supporting trophic shift under fine-scale sympatry. Furthermore, locally sympatric samples of M. escalerai had a marginally lower proportion of not nocturnally volant prey, suggesting that the shift in diet may be driven by a change in foraging mode. Our findings suggest that fine-scale coexistence mechanisms can have implications for maintaining broad-scale diversity patterns. This study highlights the importance of including both allopatric and sympatric populations and choosing meaningful spatial scales for detecting ecological patterns. We conclude that a combination of high taxonomic resolution with a functional approach helps identify patterns of niche shift.

Understanding how wildlife interacts with human activities across non-protected areas are critical for conservation. This is especially true for ungulates that inhabit human-dominated landscapes outside the protected area system in Nepal, where wildlife often coexist with livestock. Here we investigated how elevation, agricultural land, distance from roads, and the relative abundance of livestock influenced wild ungulate (chital (Axis axis), nilgai, barking deer (Muntiacus muntjak), wild boar (Sus scrofa) and sambar (Rusa unicolor)) abundance and occurrence. We counted all individuals of wild ungulates and livestock along 35 transects conducted between November 2017 and March 2018 in Bara and Rautahat forests in the lowlands of Nepal. We assessed abundance and occurrence relation to covariates using Generalized Linear Models. We found that livestock outnumbered wild ungulates 6 to 1. Wild boar was the most abundant wild ungulate, followed by nilgai, chital, barking deer and sambar. We found that elevation and livestock abundance were the most important covariates affecting the overall abundance of wild ungulates and the distribution of each individual ungulate species. Our results suggest spatial segregation between wild ungulates, which occur mainly on highlands, and livestock that concentrate across lowland habitats. Our results provide critical information to improve conservation in community forest areas of Nepal, where wildlife interacts with people and their livestock. Finding better strategies to allow the coexistence of ungulates with people and their livestock is imperative if they are to persist into the future.

The Himalayan red panda (Ailurus fulgens) is of special interest in evolutionary studies due to its taxonomic uniqueness. Globally, Nepal represents the Westernmost edge of the red panda distribution. Fewer studies of red panda have been carried out which hinders the implementation of effective conservation actions of the species. We aim to determine important habitat features influencing the distribution of red panda and recommend possible habitat corridors. We conducted an extensive field survey and analyzed red panda presence data, key food resources (bamboo), and bioclimatic variables to build a Maxent habitat model and determine habitat requirements of the red panda. Himalayan red pandas were confined between the range of 2600 m - 3,600 m, with most records between 3250 m - 3400 m on the north and west-facing slopes. The potentially suitable habitat of the red panda in Western Nepal is estimated to be about 3,222 km2 with a relative abundance of 3.34 signs/km. Important habitat attributes for red panda occurrence include aspects, canopy cover, bamboo cover, and distance to water. Combining species habitat requirements and disturbance factors (human footprint), we suggested five potential biological corridors in Western Nepal. Western Nepal has suitable habitat attributes for the red panda distributions. Ecological variables such as canopy cover, bamboo cover, distance to the water, and aspects are important attributes for red panda occurrence in Western Nepal alike Central Nepal. We suggested five potential corridors in Western Nepal; however, due to a lack of detailed knowledge on corridors and connectivity, a comprehensive field-based assessment is required to validate it scientifically. Keywords: Biological Corridor; Distribution; Habitat requirements; Red panda

This is the first study to document the genetic diversity of the white-tailed deer population on St. John, US Virgin Islands. The island population was founded by a small number of animals, has very limited hunting or predation, and recently experienced a reduction in size following an extended drought in 2015. DNA samples were collected from hair from 23 anesthetized adult deer (13 males, 10 females) ranging in age from 1-8 years (3.36+ 1.9 yr) and also from fecal DNA samples, for a total of 42 individuals analyzed for genetic diversity. The St. John deer data set averaged 4.19 alleles per marker and demonstrates the second lowest number of alleles (A) when compared to other populations of Odocoileus virginianus (4.19). Heterozygosity was similar to the other studies (0.54) with little evidence of inbreeding. To explain the level of heterogygosity and lack of inbreeding within the St. John population, three hypotheses are proposed, including the effect of intrinsic biological traits within the population, a recent infusion of highly heterogeneous loci from North American populations, and a consistent level of immigration from a nearby island. Additional work is needed to further understand the genetic history of the St. John and regional deer populations.

1. Dietary specialization is common in animals and has important implications for individual fitness, inter- and intraspecific competition, and the adaptive potential of a species. Differences in diet composition have been well-studied in shorebirds and their allies (Charadriiformes) and can be influenced by an individual’s morphology, social status, and acquired skills. In particular, sexual size dimorphism is thought to facilitate resource partitioning in some shorebird species. 2. We assessed the role of age- and sex-related dietary specialization in facilitating resource partitioning between seasons and among demographic groups in the sexually dimorphic western sandpiper (Calidris mauri). Using stable isotope mixing models, we quantified the contribution of biofilm, microphytobenthos, and benthic invertebrates to the diets of western sandpipers during mid-winter (January/February) and at the onset of the breeding migration (April). 3. Diet composition differed between seasons, among demographic groups, and among demographic groups within each season. In winter, prey consumption was similar among demographic groups, but, in spring, diet composition differed among demographic groups with bill length and body mass explaining 31% of the total variation in diet composition. Epifaunal invertebrates made up a greater proportion of the diet in males which had lesser mass and shorter bills than females. Consumption of Polychaeta increased with increasing bill length and was greatest in adult females. In contrast, consumption of microphytobenthos, thought to supply nutrition for migrating sandpipers, increased with decreasing bill length and was greatest in juvenile males. 4. Our results provide evidence that age- and sex-related dietary specialization in western sandpipers facilitate seasonal resource partitioning that would reduce competition during spring at the onset of the breeding migration. 5. Understanding resource partitioning throughout the annual cycle and among different demographic groups is critical because dietary specialization has important implications for the ecology, evolution, and conservation of a species.

Habitat connectivity is indispensable for the survival of species that occupy a small habitat area and have isolated habitat patches from each other. At present, the development of human economy not only squeezes the living space of wild animals, but also strongly interferes and hinders the migration of species. Therefore, we need to enhance the habitat connectivity of species in broken habitats, which would facilitate the proliferation of species, enhance gene exchange between populations and improve the ability of species to respond to environmental changes. Przewalski's gazelle, as one of the world's most endangered ungulate mammals, has historically experienced a significant reduction in population and severe habitat shrinkage. At present, even though the population of this species has recovered to a certain extent, humans Infrastructure severely hindered the gene flow between several patches of this species. Therefore, we used habitat suitability index model combined with Przewalski's gazelle movement characteristics to establish 11 habitat patches, and used the least cost path and circuit theory based on resistance model to jointly simulate the landscape network pattern of this species. In addition, we also analyzed and selected important patches and key migration paths as important references for establishing corridors. Overall, our research aims to provide habitat networks and maintain landscape connectivity to achieve the fundamental goal of protecting and revitalizing Przewalski's gazelle populations.

1. In many social species, reproductive success varies between individuals within a population, resulting in socially structured populations. Social network analyses of familial relationships may provide insights on how fitness influences population-level demographic patterns. These methods have however rarely been applied to genetically-derived pedigree data from wild populations. 2. Here we use social networks to reconstruct parent-offspring relationships and create a familial network from polygamous boreal woodland caribou (Rangifer tarandus caribou) in Saskatchewan, Canada, to inform recovery efforts. We collected samples from 933 individuals at 15 variable microsatellite loci along with caribou-specific primers for sex identification. Using social network metrics, we assess the contribution of individual caribou to the population with several centrality metrics and then determine which metrics are best suited to inform on the population demographic structure. We look at the centrality of individuals from eighteen different local areas, along with the entire population. 3. We found substantial differences in centrality of individuals in different local areas, that in turn contributed differently to the full network, highlighting the importance of analyzing social networks at different scales. The full network revealed that boreal caribou in Saskatchewan form a complex, interconnected social network with strong familial ties, as the removal of edges with high betweenness did not result in distinct subgroups. Alpha, betweenness, and eccentricity centrality were the most informative metrics to characterize the population demographic structure and for spatially identifying areas of highest fitness levels and social cohesion across the range. 4. Synthesis and applications: Our results demonstrate the value of different network metrics in assessing genetically-derived familial networks. The spatial application of the familial networks identified areas of higher fitness levels and social cohesion across the range in support of population monitoring and recovery efforts.

Evolutionary theory predicts that infection by a parasite that reduces future host survival or fecundity should select for increased investment in current reproduction. In this study we use the cestode Ligula intestinalis and its intermediate fish host Engraulicypris sardella in Wissman Bay, Lake Nyasa (Tanzania) as a model system. Using data about infection of E. sardella fish hosts by L. intestinalis collected for a period of 10 years, we explored whether parasite infection affects the fecundity of the fish host E. sardella, and whether host reproductive investment has increased at the expense of somatic growth. We found that L. intestinalis had a strong negative effect on the fecundity of its intermediate fish host. For the non-infected fish we observed an increase in relative gonadal weight at maturity over the study period, while size at maturity decreased. These findings suggest that the life history of E. sardella has been shifting towards earlier reproduction. Further studies are warranted to assess whether these changes reflect plastic or evolutionary responses. We also discuss the interaction between parasite and fishery-mediated selection as a possible explanation for the decline of E. sardella stock in the lake. KEYWORDS Life history evolution; African Great Lakes; Lake Nyasa; Usipa; Lake Malawi sardine; Parasite invasion; Environmental change.

The scientific literature includes a plethora of terms to denote within-species phenotypic diversity (e.g., morphotypes; ecotypes; ecomorphotypes; ecophenotypes; polymorphisms; and life histories). Here we discuss a particular situation in which different terms (ecotypes and life histories) have been used to describe the same within-species diversity of adult Pacific lamprey Entosphenus tridentatus, note an important challenge in using “ecotypes”, and conclude with a recommendation to use “life histories” to describe the ocean- and stream-maturing forms of Pacific lamprey.

1. Microsatellite genotyping is an important genetic method for a number of research questions in biology. Given that the traditional fragment length analysis using polyacrylamide gel or capillary electrophoresis has several drawbacks, microsatellite genotyping-by-sequencing (GBS) has arisen as a promising alternative. Although GBS mitigates many of the problems of fragment length analysis, issues with allelic dropout and null alleles often remain due to mismatches in primer binding sites and unnecessarily long PCR products. This is also true for GBS in catarrhine primates where cross-species amplification of loci (often human derived) is common. 2. We therefore redesigned primers for 45 microsatellite loci based on 17 available catarrhine reference genomes. Next, we tested them in singleplex and different multiplex settings in a panel of species representing all major lineages of Catarrhini and further validated them in wild Guinea baboons (Papio papio) using faecal samples. 3. The final panel of 42 microsatellite loci can efficiently be amplified with primers distributed into three amplification pools. 4. With our microsatellite panel, we provide a tool to universally genotype catarrhine primates via GBS from different sample sources in a cost- and time-efficient way, with higher resolution, and comparability among laboratories and species.

The capacity and extent to which prey species forage is often dependent on the temporal and/or spatial distribution of predators. Predation risk within a given habitat may differ according to the structure of the landscape and ecological community. Predators may frequent selected habitat patches and it is these areas prey are expected to avoid. Aside from the direct removal of prey individuals through predation, the density of prey populations may be altered as a result of a perceived predator presence and the energetically expensive responses initiated. A predator presence may be perceived upon the detection of sensory environmental cues, including a predator’s pheromones. The Landscape of Fear (LOF) concept proposes the exposure to a real or perceived predation threat may disrupt prey distribution and activity. Such an environment may be referred to as a ‘landscape of fear’, though the interspecies complexes and abiotic factors affecting a predator-prey relationship should not be omitted when quantifying the effects of predation. Here, we summarise the initial and more recent publications addressing the LOF theory, identifying known aspects and potential for future research.

Multi-level societies are complex social systems where basic core units associate in a hierarchical manner, allowing animals to adjust group size in response to local conditions. Each tier of multi-level societies may have evolved under different selective pressures and understanding the effect of temporal variation in these pressures may help determine why these types of social systems form. Our goal was to examine the degree of temporal variability in inter-unit associations in a multi-level society of Rwenzori Angolan colobus monkey (Colobus angolensis ruwenzorii), and to determine whether social or ecological factors correlated with association patterns. Using social network analyses, we described the association patterns of 12-13 core units over 21-months and investigated the effect of changes in rainfall, food availability, and inter-unit dispersals. We found that core unit networks were denser and more clustered when fruit was abundant, likely due to reduced food competition. Male dispersals also occurred more at these times, suggesting that greater band cohesion allowed males to prospect for dispersal opportunities. Within the band, we observed the formation of an all-male unit and the transfer of one core unit between clans. Our findings highlight how ecological conditions can influence association patterns, interunit relationships, and ultimately social organization.

Understanding niche overlap with other wild species and domestic cattle is useful to conserve and manage the wildlife in their natural habitat. We assessed habitat niche breadth and overlap among the two sympatric wild ungulates: spotted deer (Axis axis) and swamp deer (Cervus duvaucelii) and, indigenous intermediate ruminants, and domestic cattle in Shuklaphanta National Park, Nepal during the dry season. Our objective was to explore the interspecific competition by studying the habitat use by these species. The assumption was made that the presence of pellets is a proof for habitat used by species. Grid based surveys with total 96 sample plots each of size 20 m * 20 m in 6 sample grids (2 * 2 km2) with 24 sub-grids (500 * 500 m2) were used for locating pellets group. Levin’s niche breadth and Morisita’s overlap index were calculated to determine the niche breadth, and the habitat overlap respectively. The Levin’s measure of niche breadth suggested that spotted deer had the highest adaptability with an index value of 0.94 followed by domestic cattle 0.50, and swamp deer 0.33 in our study area. Thus, it was concluded that spotted deer is a habitat generalist whereas swamp deer are specialists and mostly preferred grasslands after a fire. Also, there was high habitat overlap index value of 0.83 between domestic cattle and spotted deer whereas the swamp deer and the spotted deer showed moderate habitat overlap of 0.57. The swamp deer had low habitat overlap as well as spatial overlap with domestic cattle. Grassland management should be carried out for the benefit of ungulate species as the study showed the preference of swamp deer on grassland after a fire. Similar studies should be conducted including seasons and places prior to implementing appropriate habitat management activities intended to reduce interspecific competition for co-existence.

Several studies have attempted to understand the origin and evolution of single exon genes (SEGs) in eukaryotic organisms including fishes, but few have examined the functional and evolutionary relationships between SEG and multiple exon gene (MEG) orthologs, in particular the conservation of promoter regions. Given that SEGs originate via the reverse transcription of mRNA from a “parental” MEG, such comparisons may enable identifying evolutionarily-related SEG/MEG orthologs, which might fulfill equivalent physiological functions. Here, the relationship of SEG proportion with MEG count, gene density, intron count and chromosome size was assessed for the genome of sea bass, Dicentrarchus labrax. Then, SEGs with an MEG parent were identified, and promoter sequences of SEG/MEG orthologs compared, to identify highly conserved functional motifs. The results revealed a total proportion of 1585 (8.3%) SEGs evenly distributed in the sea bass genome, which was correlated with MEG count but not with gene density. These results suggest that SEGs are continuously and independently generated after species divergence over evolutionary time, as is evident from the significant proportion of SEGs with an MEG parent. Functional annotation showed that the majority of SEGs are functional, as is evident from their expression in RNA-seq data used to support homology-based genome annotation. Differences in 5’UTR and 3’UTR lengths between SEG/MEG orthologs observed in this study may contribute to gene expression divergence between them, and therefore lead to the emergence of new SEG functions. The comparison of nonsynonymous to synonymous changes (Ka/Ks) between SEG/MEG parents showed that 74 of them are under positive selection (Ka/Ks > 1; P = 0.0447). An additional fifteen of SEGs with a MEG parent have a common promoter, which implies that they are under the influence of common regulatory networks and may be involved in equivalent functions.