Wolf spiders are typically the most common group of arthropod predators on both lake and marine shorelines, because of the high prey availability in these habitats. However, shores are also harsh environments due to flooding and, in proximity to marine waters, to toxic salinity levels. Here, we describe the spider community, prey availabilities and spider diets between shoreline sites with different salinities, albeit with comparatively small differences (5 vs. 7‰). Despite the small environmental differences, spider communities between low and higher saline sites showed an almost complete species turnover. At the same time, differences in prey availability or spider gut contents did not match changes in spider species composition but rather changed with habitat characteristics within region, where spiders collected at sites with thick wrack beds had a different diet than sites with little wrack. These data suggest that shifts in spider communities are due to habitat characteristics rather than prey availabilities, and the most likely candidate restricting species in high salinity would be saline sensitivity. At the same time, species absences from low-saline habitats remain unresolved.

The Philippine native pig (PhNP) is a unique genetic resource with complex genetics due to multiple ancestries and hybridizations with wild pigs. No prior study has determined the population structure and genetic diversity of PhNPs on multiple islands and provinces, which is essential for establishing conservation priorities. In this study, we explore the population structure and genetic diversity of various PhNP populations in Luzon and the Visayas, Philippines, to identify conservation priorities. We analyzed 157 native pigs representing 7 populations (Benguet (B), Kalinga (K), Nueva Vizcaya, Isabela (I), Quezon (Q), Marinduque (M), and Samar (S)) and 39 pigs of transboundary distribution (Duroc, Large White, Landrace, and Berkshire). The pigs were compared against a panel of 21 ISAG–FAO recommended microsatellite markers. We tested for population structure at the island, administrative region and province levels. Strong genetic differentiation between native and transboundary breeds was confirmed by analysis of molecular variance (Frt: 0.08; F’st: 0.288-0.728), Bayesian clustering (k = 2) and Nei’s DA genetic distance (98% bootstrap support for the PhNP cluster). PhNP exhibited high heterozygosity (Ho: 0.72), a high allele count (Na: 9.24) and a low inbreeding coefficient (Fis: -0.022 to 0.150). Bayesian clustering supported genetic differentiation at the island (k = 2; North Luzon and South Luzon-Visayas cluster), administrative region (k = 4) and population (k= 9) levels. The pairwise F’st between PhNP populations ranged from 0.130 (Q and M) to 0.427 (Q and K), confirming that PhNP populations exhibited sufficient genetic distance to be considered separate populations. This study shows that the seven previously assigned PhNP populations, roughly delimited by provincial origin, are unique genetic units for conservation. Furthermore, the small effective population sizes of B, Q, I, and S (Ne: 5, 17, 24, and 26, respectively) necessitate immediate conservation actions, such as incentivizing the farming of PhNP.

During litter decomposition, part of the water-soluble components of the material dissolve (leach) rapidly into available water in the environment. Studies on litter decomposition that quantify mass-loss from litterbags integrate leaching and mineralization. In contrast to Lind et al. (2022), we believe that correcting for leaching in (terrestrial) litterbags studies such as the Tea Bag Index will result in more uncertainties than it resolves. This is mainly because leaching is a continuous process and because leached material can still be mineralized after leaching. Further, amount of material that potentially leaches from tea is comparable to other litter types. When correcting for leaching, it is key to be specific about the employed method, just like being specific about the study specific definition of decomposition.

Aim: To test whether the occupancy of shorebirds has changed in the eastern Canadian Arctic, and whether these changes could indicate that shorebird distributions are shifting in response to long-term climate change Location: Foxe Basin and Rasmussen Lowlands, Nunavut, Canada Methods: We used a unique set of observations, made 25 years apart, using general linear models to test if there was a relationship between changes in shorebird species’ occupancy and their Species Temperature Index, a simple version of a species climate envelope. Results: Changes in occupancy and density varied widely across species, with some increasing and some decreasing. This is despite that overall population trends are known to be negative for all of these species, based on surveys during migration. The changes in occupancy that we observed were positively related to the Species Temperature Index, such that the warmer-breeding species appear to be moving into these regions, while colder-breeding species appear to be shifting out of the regions, likely northwards. Main Conclusions: Our results suggest that we should be concerned about declining breeding habitat availability for bird species whose current breeding ranges are centred on higher and colder latitudes.

Eastern wild turkeys (Meleagris gallopavo silvestris) exhibit social hierarchies wherein dominance is established through agnostic interactions within social groups. When dominant individuals effectively monopolize reproductive opportunities, asynchronous breeding can occur, which may disproportionately influence individual fitness within social groups. For females, higher ranked individuals may witness reproductive advantages associated with earlier nesting than subordinate conspecifics. We evaluated reproductive synchrony within and between presumed social groups of GPS-tagged female eastern wild turkeys by inferring female social rank based on timing of nest initiation. We examined 30 social groups with an average of 7 females per group (range 2 - 15) during 2014-2019 in west-central Louisiana. We found that the estimated number of days between first nest initiation across females within social groups varied between 3-7 days across years, and the number of days between nest attempts was lower for successful than failed attempts. Our findings suggest that social hierarchies may influence reproductive success in female wild turkeys, and we postulate that social constraints could cause variation in timing of nest initiation for females within social groups.

Very little is known about factors determining the assemblage structure of megadiverse polyphagous-herbivore scarab chafers in the tropics (Coleoptera: Scarabaeidae). Here, we examined the composition of Sri Lankan chafer assemblages and investigated whether it is influenced more by the general ecoclimatic situation, macrohabitat, of indetermined stochastic biotic and abiotic factors of each locality. We also explored the influence of the latter on separate lineages and general body size. Based on dedicated field surveys conducted during the dry and wet seasons, we examined 4847 chafer individuals of 105 species sampled using multiple UV-light traps in 11 localities covering different forest types and altitudinal zones. Assemblages were assessed for compositional similarity, species diversity, and abundance within four major eco-spatial partitions: forest types, elevational zones, localities, and macrohabitats. Our results revealed that assemblages were shaped mainly by locality stochastics, and to a minor extent by ecoclimatic conditions. Macrohabitat had little effect on the assemblage composition. This was true for the entire chafer assemblage as well as for all single lineages or different body size classes. However, in medium and large specimens the contrasts between localities were less pronounced, which was not the case for individual lineages of the assemblage. Contrasts of assemblage similarity between localities were much more evident than those for forest types and elevation zones. Significant correlation between species composition and geographic distance was found only for the assemblage of small-bodied specimens. Seasonal change (dry-wet) in species composition was minor and only measurable in a few localities.

Diospyros (Ebenaceae) is a widely distributed genus of trees and shrubs native to tropical and subtropical regions, with numerous species valued for their fruits (persimmons), timber, and medicinal values. However, information regarding their plastomes and chloroplast evolution is scarce. The present study performed comparative genomic and evolutionary analyses on plastomes of 18 accepted Diospyros species, including three newly sequenced ones. Our study showed a highly conserved genomic structure across the species, with plastome size ranging from 157,321 bp (D. jinzaoshi) to 157,934 bp (D. deyangensis). These plastomes encoded 134–138 genes, including 89–91 protein-coding genes, 1–2 pseudogenes (Ψycf1 for all, Ψrps19 for a few), 37 tRNA genes, and 8 rRNA genes. Comparative analysis of Diospyros identified the intergenic regions (trnH-psbA, rps16-trnQ, trnT-psbD, petA-psbJ, trnL-trnF-ndhJ) as the mutational hotspots in these species. Phylogenomic analyses identified three main groups within the genus designated as the evergreen, deciduous, and island groups. The codon usage analysis identified 30 codons with relative synonymous codon usage (RSCU) values greater than 1 and 29 codons ending with A and U bases. A total of three codons (UUA, GCU, and AGA) with highest (RSCU) values were identified as the optimal codons. ENC-plot indicated the significant role of mutational pressure in shaping codon usage, while most protein-coding genes in Diospyros experienced relaxed purifying selection (Ka/Ks < 1). Additionally, the ndhG, rpoC1, and ycf3 genes showed positive selection (Ka/Ks > 1) in the island, deciduous, and both deciduous and evergreen species, respectively. Thus, the results provide a foundation for elaborating Diospyros’s genetic architecture and taxonomy, conserving genetic diversity and enriching genetic resources.

Major aridification events in Australia during the Pliocene may have had significant impact on the distribution and structure of widespread species. To explore the potential impact of Pliocene and Pleistocene climate oscillations we estimated the timing of population fragmentation and past connectivity of the currently isolated but morphologically similar subspecies of the widespread brushtail possum (Trichosurus vulpecula). We use ecological niche modelling (ENM) with the current fragmented distribution of brushtail possum to estimate the environmental envelope of this marsupial. We projected the ENM on models of past climatic conditions in Australia to infer the potential distribution of brushtail possums over six million years. D-loop haplotypes were used to describe population structure. From shotgun sequencing we assembled whole mitochondrial DNA genomes and estimated timing of intraspecific divergence. Our projections of ENMs suggest current possum populations were unlikely to have been in contact during the Pleistocene. Although lowered sea level during glacial periods enabled colonisation of Tasmania, climate fluctuation during this time would not have facilitated gene flow. The most recent common ancestor of sampled intraspecific diversity dates to the early Pliocene when continental aridification caused significant changes to Australian ecology and Trichosurus vulpecula distribution was likely fragmented. Phylogenetic analysis revealed that the subspecies T. v. hypoleucus (koomal; southwest), T. v. arnhemensis (langkurr; north) and T. v. vulpecula (bilda; southeast) correspond to distinct mitochondrial lineages. Despite little phenotypic differentiation, Trichosurus vulpecula populations probably experienced little gene flow with one another since the Pliocene, supporting the recognition of several subspecies and explaining their adaptations to the regional plant assemblages on which they feed.

Quantifying space use and segregation, as well as the extrinsic and intrinsic factors affecting them, is crucial to increase our knowledge of species-specific movement ecology and to design effective management and conservation measures. This is particularly relevant in the case of species that are highly mobile and dependent on sparse and unpredictable trophic resources, such as vultures. Here, we used the GPS-tagged data of 127 adult Griffon Vultures Gyps fulvus captured at five different breeding regions in Spain to describe the movement patterns (home-range size and fidelity, and monthly cumulative distance). We also examined how individual sex, season and breeding region determined the cumulative distance travelled and the size and overlap between consecutive monthly home-ranges. Overall, Griffon Vultures exhibited very large annual home-range sizes of 5,027 ± 2,123 km2, mean monthly cumulative distances of 1,776 ± 1,497 km, and showed a monthly home-range fidelity of 67.8 ± 25.5 %. However, individuals from northern breeding regions showed smaller home-ranges and travelled shorter monthly distances than those from southern ones. In all cases, home-ranges were larger in spring and summer than in winter and autumn. Moreover, females showed larger home-ranges and less monthly fidelity than males, indicating that the latter tended to use the similar areas throughout the year. Overall, our results indicate that both extrinsic and intrinsic factors modulate the home-range the social Griffon Vulture and that spatial segregation depend on sex and season at the individual level, without relevant differences between breeding regions in individual site fidelity.

Phenotypic divergence is an important consequence of restricted gene flow in insular populations. This divergence can be challenging to detect when it occurs through subtle shifts in morphological traits, particularly in traits with complex geometries, like insect wing venation. Here, we employed geometric morphometrics to assess the extent of variation in wing venation patterns across reproductively isolated populations of the social sweat bee, Halictus tripartitus. We examined wing morphology of specimens sampled from a reproductively isolated population of H. tripartitus on Santa Cruz Island (Channel Islands, Southern California). Our analysis revealed significant differentiation in wing venation in this island population relative to conspecific mainland populations. We additionally found that this population-level variation was less pronounced than the species-level variation in wing venation among three sympatric congeners native to the region, Halictus tripartitus, Halictus ligatus, and Halictus farinosus. Together, these results provide evidence for subtle phenotypic divergence in an island bee population. More broadly, these results emphasize the utility and potential of wing morphometrics for large-scale assessment of insect population structure.

A combination of short-read paired-end and mate-pair libraries of large insert sizes is used as a standard method to generate genome assemblies with high contiguity. The third-generation sequencing techniques also are used to improve the quality of assembled genomes. However, both mate-pair libraries and the third-generation libraries require high-molecular-weight DNA, making the use of these libraries inappropriate for samples with only degraded DNA. An in silico method that generates mate-pair libraries using a reference genome was devised for the task of assembling target genomes. Although the contiguity and completeness of assembled genomes were significantly improved by this method, a high level of errors manifested in the assembly, further to which the methods for using reference genomes were not optimized. Here, we tested different strategies for using reference genomes to generate in silico mate-pairs. The results showed that using a closely related reference genome from the same genus was more effective than using divergent references. Conservation of in silico mate-pairs by comparing two references and using those to guide genome assembly reduced the number of misassemblies (18.6% – 46.1%) and increased the contiguity of assembled genomes (9.7% – 70.7%), while maintaining gene completeness at a level that was either similar or marginally lower than that obtained via the current method. Finally, we developed a pipeline of optimized method and compared it with another reference-guided assembler, Ragtag. We found that Ragtag produced longer scaffolds (17.8 Mbp vs. 3.0 Mbp), but resulted in a much higher misassembly rate (85.68%) than our optimized in silico mate-pair method. This optimized in silico pipeline developed in this study should facilitate further studies on genomics, population genetics and conservation of endangered species.

Conservation and management professionals often works across jurisdictional boundaries to identify broad ecological patterns. These collaborations help to protect populations whose distributions span political borders. One common limitation to multijurisdictional collaboration is consistency in data recording and reporting. This limitation can impact genetic research which relies on data about specific markers in an organism’s genome. Incomplete overlap of markers between separate studies can prevent direct comparisons. Standardized marker panels can reduce the impact this issue and provide a common starting place for new research. Genotyping-in-thousands (GTSeq) is one approach used to create standardized marker panels for non-model organisms. Here we describe the development, optimization, and early assessments of a new GTSeq panel for use with walleye (Sander vitreus) from the Great Lakes region of North America. High genome-coverage sequencing conducted using RAD-capture provided genotypes for thousands of single nucleotide polymorphisms (SNPs). From these markers, SNP and microhaplotype makers were chosen that were informative for genetic stock identification (GSI) and kinship analysis. The final GTSeq panel contained 500 markers, including 197 microhaplotypes and 303 SNPs. Leave-one-out GSI simulations indicated that GSI accuracy should be greater than 80% in most jurisdictions. The false-positive rates of parent-offspring and full-sibling kinship identification was found to be low. Finally, genotypes could be consistently scored among separate sequencing runs >94% of the time. Results indicate that the GTSeq panel we developed should perform well for multijurisdictional research throughout the Great Lakes region.

Siraitia grosvenorii, an economically important plant species with high medicinal value, is endemic to subtropical China. To determine the population structure and origin of cultivated S. grosvenorii, we examined the variation in three chloroplast DNA regions (trnR-atpA, trnH-psbA, trnL-trnF) and two nuclear gene orthologs (CHS and EDL2) of S. grosvenorii in 130 individuals, selected from 13 wild populations across its natural distribution range, and 21 cultivated accessions using a phylogeographic approach. The results showed non-overlapping distribution of chlorotypes, three distinct chloroplast genetic groups restricted to different mountain ranges, and comparable nuclear diversity among the distinct geographical groups, suggesting the existence of at least three separate refugia. The current phylogeographic patterns of S. grosvenorii probably resulted from long-term survival in multiple refugia and limited expansion. Our results also demonstrated that wild populations in northeastern Guangxi share the same gene pool as cultivated S. grosvenorii accessions, suggesting that the current cultivars originated from wild populations distributed in northeastern Guangxi. The results of this study provide insight into improving the efficiency of S. grosvenorii breeding using a genetic approach, and outline measures for the conservation of its genetic resources.

Ecuador has both high richness and high endemism of species which are increasingly threatened by anthropic pressures, including roads. However, research evaluating the effects of roads remains scarce, making it difficult to develop mitigation plans. Here we present the first national assessment of wildlife mortality that allow us to 1) identify species and areas where mortality occurs due to collision with vehicles and 2) reveal knowledge gaps. We bring together data from systematic surveys and citizen science efforts in Ecuador to present a dataset with >5000 wildlife roadkill records from 454 species. Systematic surveys were reported by ten studies conducted in five out of the 24 Ecuadorian provinces. Collectively they revealed 282 species with mortality rates ranging from 0.008 to 95.56 ind./km/year. The highest rates were for the yellow warbler Setophaga petechia in Galápagos (95.56 ind./km/year), the cane toad Rhinella marina in Napo (16.91 ind./km/year), and the small ground-finch Geospiza fuliginosa in Galápagos (14.11 ind./km/year). Citizen science and other no systematic monitoring provided 1705 roadkill records representing all the 24 provinces of Ecuador and 299 species. The common opossum Didelphis marsupialis, the Andean white-eared opossum Didelphis pernigra, and the yellow warbler Setophaga petechia were more commonly reported (250, 104, and 81 individuals respectively). Across all sources, we found 15 species listed as Threatened and six as Data Deficient by the IUCN. We suggest stronger research efforts on areas where mortality of endemic or threatened species could be critical for populations, such as in Galápagos. This first assessment of wildlife mortality on Ecuadorian roads represents contributions from several sectors including academia, members of the public, and government underlining the value of wider engagement and collaboration. We hope these findings and the compiled dataset will guide sustainable planning of infrastructure in Ecuador and ultimately, contribute to reduce wildlife mortality on roads.

A document by Hongyong Wang. Click on the document to view its contents.

Plant and soil biodiversity can have significant effects on herbivore resistance mediated by plant metabolites. Here, we disentangled the independent effects of plant diversity and soil legacy on constitutive and herbivore-induced plant metabolomes of three plant species in two complementary microcosm experiments. First, we grew plants in sterile soil with three different plant diversity levels. Second, single plant species were grown on soil with different plant diversity-induced soil legacies. We infested a subset of all plants with Spodoptera exigua larvae, a generalist leaf-chewing herbivore, and assessed foliar and root metabolomes. Neither plant diversity nor soil legacy had significant effects on overall foliar, root, or herbivore-induced metabolome composition. Herbivore-induced metabolomes, however, differed from those of control plants. We also detected 139 significantly regulated metabolites by comparing plants grown in monocultures with conspecifics growing in plant or soil legacy mixtures. Moreover, plant-plant and plant-soil interactions regulated 141 metabolites in herbivore-induced plants. Taken together, plant diversity and soil legacy independently alter the concentration and induction of plant metabolites, thus affecting the plant's defensive capability. This is a first step towards disentangling plant and soil biodiversity effects on herbivore resistance, thereby improving our understanding of the mechanisms that govern ecosystem functioning.

1. Describing and explaining patterns of individual animal behaviors in situ, and their repeatability over the annual cycle, is an emerging field in ecology owing largely to advances in tagging technology. 2. We describe individual movements of adult Sakhalin taimen Parahucho perryi, an endangered salmonid fish, in the headwaters of a river in northern Japan during the spring spawning season over two years. 3. Migration timing, separated into stages prior to, during, and following the spawning period, was found to be more consistent and repeatable for females than males. 4. We hypothesized that the observed coordinated movement within seasons, and repeatability in migration timing across seasons, could result from 1) individual-specific responsiveness resulting from endogenous, biological traits that are mediated by environmental factors, or 2) social interactions among comigrating individuals. 5. We found that water temperature and water level experienced by fish near the river mouth approximately a week before arrival at the spawning ground explained variability in run timing between years for females but not males. 6. We found no evidence of conspecific attraction or repulsion resulting from social interactions among the spawners and post-spawners. 7. We conclude that individual-specific responsiveness to environmental cues was the likely mechanism underpinning the observed migration timing and movement patterns. 8. Determining the importance of these environmental and social factors not only during spawning but also during non-breeding life-history stages would contribute to a more comprehensive understanding of migratory connectivity in this species.

Myriad ecological and evolutionary factors can influence whether a particular parasite successfully transmits to a new host during a disease outbreak, with consequences for the structure and diversity of parasite populations. However, even though the diversity and evolution of parasite populations is of clear fundamental and applied importance, we have surprisingly few studies that track how genetic structure of parasites changes during naturally occurring outbreaks in non-human populations. Here, we used population genetic approaches to reveal how genotypes of a bacterial parasite, Pasteuria ramosa, change over time, focusing on how infecting P. ramosa genotypes change during the course of epidemics in Daphnia populations in two lakes. We found evidence for genetic change – and, therefore, evolution – of the parasite during outbreaks. In one lake, P. ramosa genotypes structured by sampling date; in both lakes, genetic distance between groups of P. ramosa isolates increased with time between sampling. Diversity in parasite populations remained constant over epidemics, though one epidemic (which was large) had low genetic diversity while the other epidemic (which was small) had high genetic diversity. Our findings demonstrate that patterns of parasite evolution differ between outbreaks; future studies exploring the feedbacks between epidemic size, host diversity, and parasite genetic diversity would improve our understanding of parasite dynamics and evolution.