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.
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.
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.
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
Arachnids are the most abundant land predators. Despite the importance of their functional roles as predators and the of necessity to understand their diet for conservation and nutrient fluxes, the trophic ecology of many arachnid species is not fully understood. In the case of the wandering spider, Phoneutria boliviensis F. O. Pickard-Cambridge, 1897, only selected field and laboratory observational studies about their diet exist. By using a DNA metabarcoding approach, we compared the prey found in the gut content of males and females from three distant Colombian populations of P. boliviensis. By DNA metabarcoding of the cytochrome c oxidase subunit I (COI), we detected and identiﬁed 234 prey records belonging to 96 operational taxonomic units (OTUs), as prey for this wandering predator. Our results broaden the known diet of P. boliviensis with at least 75 prey taxa not previously registered in fieldwork or laboratory experimental trials. These results suggest that P. boliviensis feeds predominantly on invertebrates (Diptera, Lepidoptera, Coleoptera and Orthoptera) and opportunistically on small squamates. Intersex and interpopulation differences are observed. Assuming that prey preference does not vary between populations, these differences are likely associated with a higher local prey availability. Finally, we suggest that DNA metabarcoding can be used for evaluating subtle differences in the diet of distinct populations of P. boliviensis, particularly when predation records in the field cannot be established or quantified using direct observation
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.
1. Worldwide bees provide an important ecosystem service of plant pollination. However, environmental pressures are threatening their survival. Information is lacking on how land-use systems and weather patterns in developing countries influence bee populations. 2. We investigated how environmental and land use mediated factors influence the abundance, diversity, and distribution of bees across seasons in a farming communal area of Zimbabwe. Bees were systematically sampled in five land-use types (natural woodlot, pastures, homestead, field, and garden) recording ground cover, grass height, flower abundance, and types, tree abundance, and recorded elevation, temperature, light intensity, wind speed, wind direction, and humidity. The hurdle model, general linear model, and PCA were conducted to understand the influence of explanatory variables on bee abundance and Shannon diversity. 3. We found out that bee abundance was highly positively influenced by the number of flower types P < 0.0001 and significantly positively correlated to tree abundance P = 0.0475. We also highlight the high sensitivity of bees to weather changes as wind speed increases, thus reducing the probability of finding bees (P = 0.033). Temperatures above 28.50C significantly lowered bee abundance (P < 0.001). 4. Bee diversity was highest in homesteads (coefficient 0.4438) and natural woodlots (coefficient 0.4172) than gardens with fields and pastures having a disproportionately high abundance of Apis. Bee species also showed tolerance to different land-use types with Megachile associated with homesteads and Nomia with grasslands. Homesteads however supported more diverse species (P = 0.0453) highlighting the importance of some of its components to bee conservation. 5. Synthesis and applications. Our study showed that land-use change reduced the diversity of species and proliferated species that could tolerate the changes. These results highlight the importance of setting aside bee-friendly habitats that can be refuge sites for species susceptible to land-use change.
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.
Morphometric research is being applied to a growing number and variety of organisms. Discoveries achieved via morphometric approaches are often considered highly transferable, in contrast to the tacit and idiosyncratic interpretation of discrete character states. The reliability of morphometric workflows in insect systematics has never been a subject of focused research, but such studies are sorely needed. In this paper, we assess the reproducibility of morphometric studies of ants where the mode of data collection is a shared routine. We compared datasets generated by eleven independent gaugers, i.e. collaborators, who measured 21 continuous morphometric traits on the same pool of individuals according to the same protocol. The gaugers possessed a wide range of morphometric skills, had varying expertise among insect groups, and differed in their facility with measuring equipment. We used Intraclass correlation coefficients (ICC) to calculate repeatability and reproducibility values (i.e., intra-, and inter-gauger agreements), and we performed a multivariate Permutational Multivariate Analysis of Variance (PERMANOVA) using the Morosita index of dissimilarity with 9999 iterations. The calculated average measure of intraclass correlation coefficients of different gaugers ranged from R = 0.784 to R = 0.9897 and a significant correlation was found between the repeatability and the morphometric skills of gaugers (p = 0.016). There was no significant association with the magnification of the equipment in the case of these rather small ants. The inter-gauger agreement, i.e. the reproducibility, varied between R=0.872 and R=0.471 (mean R=0.690), but all gaugers arrived at the same two-species conclusion. A PERMANOVA test revealed no significant gauger effect on species identity (R2 =0.69, p=0.58). Our findings show that morphometric studies are reproducible when observers follow the standard protocol; hence, morphometric findings are widely transferable, and will remain a valuable data source for alpha taxonomy.
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.
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.
Meta-analyses often encounter studies with incompletely reported variance measures (e.g. standard deviation values) or sample sizes, both needed to conduct weighted meta-analyses. Here, we first present a systematic literature survey on the frequency and treatment of missing data in published ecological meta-analyses showing that the majority of meta-analyses encountered incompletely reported studies. We then simulated meta-analysis data sets to investigate the performance of 14 options to treat or impute missing SDs and/or SSs. Performance was thereby assessed using results from fully informed weighted analyses on (hypothetically) complete data sets. We show that the omission of incompletely reported studies is not a viable solution. Unweighted and sample size-based variance approximation can yield unbiased grand means if effect sizes are independent of their corresponding SDs and SSs. The performance of different imputation methods depends on the structure of the meta-analysis data set, especially in the case of correlated effect sizes and standard deviations or sample sizes. In a best-case scenario, which assumes that SDs and/or SSs are both missing at random and are unrelated to effect sizes, our simulations show that the imputation of up to 90% of missing data still yields grand means and confidence intervals that are similar to those obtained with fully informed weighted analyses. We conclude that multiple imputation of missing variance measures and sample sizes could help overcome the problem of incompletely reported primary studies, not only in the field of ecological meta-analyses. Still, caution must be exercised in consideration of potential correlations and pattern of missingness.
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.
We conducted a comprehensive analysis of the phylogenetic, phylogeographic, and demographic relationships of Caspian cobra (Naja oxiana; Eichwald, 1831) populations based on a concatenated dataset of two mtDNA genes (cyt b and ND4) across the species’ range in Iran, Afghanistan, and Turkmenistan, along with other members of Asian cobras (i.e. subgenus Naja Laurenti, 1768). Our results provided strong support that N. oxiana is monophyletic and its divergence from its sister taxon, N. kaouthia, during early Pleistocene. Our results also highlight the existence of only one major evolutionary lineage in the Trans-Caspian region, suggesting a rapid expansion of the Caspian cobra from eastern to western Asia, coupled with a rapid range expansion from east of Iran to the northeast. However, the subdivision of eastern and northeastern populations in Iran was not supported; hence we propose only one evolutionary significant unit across the Iranian range of N. oxiana to be considered for conservation efforts.