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.
In boreal landscapes, emphasis is currently placed on close-to-nature management strategies, which aim to maintain the biodiversity and ecosystem services related to old-growth forests. The success of these strategies, however, depends on an accurate understanding of the dynamics within these forests. This study aims to reconstruct the disturbance and post-disturbance dynamics in boreal old-growth forests that are driven by recurrent moderate-severity disturbances. We studied eight old-growth forests in Québec, Canada, that has recorded recurrent and moderate to severe spruce budworm (Choristoneura fumiferana [Clem.]) outbreaks over the 20th century. To reconstruct the disturbance history and the post-disturbance dynamics of the study sites, we used dendrochronological data and k-means clustering to identify growth releases and growth patterns in the studied trees. We identified nine growth patterns; these patterns represented trees differing in age, size, and canopy layer, and indicated different tree histories. Spruce budworm outbreaks caused recurrent moderate-severity disturbances within the study sites. The canopy gaps created by these disturbances were filled mainly by understorey trees, which responded by single and significant increases in radial growth and height. In contrast, overstorey trees had little influence on gap filling; thus, trees were mostly from the dominant and codominant canopy layers. Our study underlines the resistance of boreal old-growth forests to recurrent and moderate-severity disturbances, as understorey trees can rapidly fill the resulting gaps. However, trees that are unable to attain the canopy following the disturbance then tend to remain in the lower canopy layers. Therefore, reaching the canopy represents a once-in-a-lifetime opportunity, where success or failure depends on a relatively short window of time. This gap-filling dynamic produces, however, a vertical structure that is often similar to the expected structure in even-aged forests. Our results highlight the efficacy of identifying tree growth patterns to reconstruct stand disturbance dynamics and contribute to developing closer to nature forest management strategies.
The diversity of butterflies is known to some extent in Nepal, but the study of their interactions with nectar plant sources and floral attributes is limited. This study was conducted along the periphery of Rupa Wetland, a Ramsar site, from February to November 2019 to assess butterfly species diversity and to identify the factors influencing their foraging choices at nectar plants. We assessed the number of butterfly species, their abundance, and their floral foraging behavior, from 28 linear transects (500 m long each) placed in a stratified and random manner throughout the study area. Five factors, i.e., category of plant, flower colour, corolla shape, corolla depth, and the proboscis length of butterfly species were taken into account to assess the nectar plant choices of butterfly families. Moreover, species diversity at the family level, and overall, were determined through several indices. When examining overall butterfly diversity and abundance, we recorded a total of 1,535 butterflies belonging to 138 species within six families. For our examination of butterfly-nectar plant observations, we recorded a total of 298 individuals belonging to 31 species of butterfly visiting a total of 28 nectar plant species. Among the recorded butterflies, Zemeros flegyas was found to be the most abundant (92 individuals), while only a single individual each of the species Troides helena, Gandaca herina and Belonois aurota were recorded. Of the 28 nectar host plant species, Biden pilosa was the most popular and was visited by 13 species of butterflies. Overall, total butterfly visitation was found to be significantly influenced by plant category (herbaceous preferred over woody), floral colour (yellow, white, and purple preferred over pink), and corolla shape (tubular preferred over non-tubular). Moreover, there was a significant positive correlation (r = 0.466) between the proboscis length of butterflies and the corolla tube length of flowers (p<0.001).
The geographical origin of watermelon (Citrullus lanatus) remains debated. While a first hypothesis suggests the center of origin to be west Africa, where a sister endemic species C. mucosospermus thrives, a second hypothesis suggests north-eastern Africa where the white-fleshed Sudanese Kordophan melon is cultivated. In this study, we infer biogeographical and haplotype genealogy for C. lanatus, C. mucosospermus, C. amarus, and C. colocynthis using non-coding cpDNA sequences (trnT-trnL and ndhF-rpl32 regions) from a global collection of 135 accessions. In total, we identified 38 haplotypes in C. lanatus, C. mucosospermus, C. amarus, and C. colocynthis; of these, 21 were found in Africa and 17 appear endemic to the continent. The least diverse species was C. mucosospermus (5 haplotypes) and the most diverse was C. colocynthis (16 haplotypes). Some haplotypes of C. mucosospermus were nearly exclusive to West-Africa, and C. lanatus and C. mucosospermus shared haplotypes that were distinct from those of both C. amarus and C. colocynthis. The results support previous findings C. mucosospermus to be the closest relative to C. lanatus (including subsp. cordophanus). West Africa, as a center of endemism of C. mucosospermus, is an area of interest in the search of the origin of C. lanatus. This calls for further historical and phylogeographical investigations and wider collection of samples in West and North-East Africa.
Na+ and Cl– are the most abundant dissolved ions in seawater, constituting ~85% of total ions. They significantly affect the osmolality of body fluids of marine invertebrates. Seawater also contains minor ions such as Mg2+, Ca2+, K+, and SO42–, but their effects on marine organisms are unclear. This study analyzed the effects of Mg2+, Ca2+, and K+ (ambient minor cations) on survival, hemolymph ionic composition, and gene expression in the gills of three euryhaline crabs: Helice tridens, Macrophthalmus japonicus, and Chiromantes dehaani. Ambient minor cations were required for survival of H. tridens and M. japonicus under isosmotic conditions with seawater. The ambient minor cations also affected the osmolality and ionic composition of hemolymph by regulating expressions of specific genes in the gills required for Na+ uptake, such as Na+/K+ ATPase, cytoplasmic carbonic anhydrase, and Na+/H+ exchanger. Administration of carbonic anhydrase and Na+/H+ exchanger inhibitors increased the survival rate even if ambient minor cations did not exist. In contrast, under hypo-osmotic conditions, ambient minor cations had different effects on crabs; a lethal effect on M. japonicus, and an increase of the hemolymph K+ concentration in H. tridens and M. japonicus. It is thus concluded that the effects of ambient minor cations are osmolality–dependent. In contrast, in C. dehaani, the hemolymph ionic composition and survival rate were hardly affected by ambient minor cations, probably reflecting the habitat of this species. These results strongly indicated that C. dehaani is less susceptive to ambient minor cations compared to H. tridens and M. japonicus.
1. The metric of functional evenness FEve is an example of how approaches to conceptualizing and measuring functional variability may go astray. 2. The index of functional evenness FEve has critical conceptual and practical drawbacks: a) Different values of the FEve index for the same community can be obtained if the species have unequal species abundances; this result is highly likely if most of the traits are categorical. b) Very minor differences in even one pairwise distance can result in very different values of FEve. c) FEve uses only a fraction of the information contained in the matrix of species distances. Counterintuitively, this can cause very similar FEve scores for communities with substantially different patterns of species dispersal in trait space. d) FEve is a valid metric only if all species have exactly the same abundances. However, the meaning of FEve in such an instance is unclear as the purpose of the metric is to measure the variability of abundances in trait space. 3. We recommend not using FEve metric in studies of functional variability. Given the wide usage of FEve index over the last decade, the validity of the conclusions based on those estimates are in question. 4. Instead, we suggest three alternative metrics that combines variability in species distances in trait space with abundance in various ways, and more broadly recommend that researchers think about which community properties (e.g., trait-distances of a focus species to the nearest neighbor or all other species, variability of pairwise interactions between species) they want to measure and pick from among the appropriate metrics.
Ambrosia artemisiifolia and Ambrosia trifida are two species of very harmful and invasive plants of the same genus. However, it remains unclear why A. artemisiifolia is more widely distributed than A. trifida worldwide. Distribution and abundance of these two species were surveyed and measured from 2010 to 2017 in the Yili Valley, Xinjiang, China. Soil temperature and humidity, main companion species, the biological characteristics in farmland ecotone, residential area, roadside and grassland, and water demand of the two species were determined and studied from 2017 to 2018. The area occupied by A. artemisiifolia in the Yili Valley was more extensive than that of A. trifida, while the abundance of A. artemisiifolia in grassland was less than that of A. trifida at eight years after invasion. The interspecific competitive ability of two species were stronger than those of companion species in farmland ecotone, residential, and roadside. In addition, A. trifida had greater interspecific competitive ability than other plant species in grassland. The seed size and seed weight of A. trifida were five times or eight times those of A.artemisiifolia. When comparing the changes under simulated annual precipitation of 840 mm versus 280 mm, the seed yield per m2 of A. trifida decreased from 50,185 to 19, while that of A. artemisiifolia decreased from 15,579 to 530. The differences in the distribution of the two species are mainly due to differences in interspecific competitive ability, seed size, and water dependence. The two species have stronger interspecific competitive ability than that of companion species, but A. artemisiifolia has a smaller seed size and stronger drought tolerance, which allows A. artemisiifolia to spread farther than A. trifida. The reason for wider distribution of A. trifida in grassland is that A. trifida has stronger interspecific competitive ability than A. artemisiifolia under sufficient water.
Tree spatial patterns in dry coniferous forests of the western US, and analogous ecosystems globally, were historically aggregated, comprising a mixture of single trees and groups of trees. Modern forests, in contrast, are generally more homogeneous and overstocked than their historical counterparts. As these modern forests lack regular fire, pattern formation and maintenance is generally attributed to fire. Accordingly, fires in modern forests may not yield historically analogous patterns. However, direct observations on how selective tree mortality among pre-existing forest structure shapes tree spatial patterns is limited. In this study, we (1) simulated fires in historical and contemporary counterpart plots in a Sierra Nevadan mixed-conifer forest, (2) estimated tree mortality, and (3) examined tree spatial patterns of live trees before and after fire, and of fire-killed trees. Tree mortality in the historical period was clustered and density-dependent, because trees were aggregated and segregated by tree size before fire. Thus, fires maintained an aggregated distribution of tree groups. Tree mortality in the contemporary period was widespread, except for dispersed large trees, because most trees were a part of large, interconnected tree groups. Thus, post-fire tree patterns were more uniform and devoid of moderately sized tree groups. Post-fire tree patterns in the historical period, unlike the contemporary period, were within the historical range of variability identified for the western US. This divergence suggests that decades of forest dynamics without significant disturbances has altered the historical means of pyric pattern formation. Our results suggest that ecological silvicultural treatments, such as forest restoration thinnings, which emulate qualities of historical forests may facilitate the reintroduction of fire as a means to reinforce forest structural heterogeneity.