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opencc-zeroFeb 2023View details →

Data for: From rivers to ocean basins: The role of ocean barriers and philopatry in the genetic structuring of a cosmopolitan coastal predator

The Bull Shark (Carcharhinus leucas) faces varying levels of exploitation around the world due to its coastal distribution. Information regarding population connectivity is crucial to evaluate its conservation status and local fishing impacts. In this study, we sampled 922 putative Bull Sharks from 19 locations in the first global assessment of population structure of this cosmopolitan species. Using a recently developed DNA-capture approach (DArTcap), samples were genotyped for 3,400 nuclear markers. Additionally, full mitochondrial genomes of 384 Indo-Pacific samples were sequenced. Reproductive isolation was found between and across ocean basins (eastern Pacific, western Atlantic, eastern Atlantic, Indo-West Pacific) with distinct island populations in Japan and Fiji. Bull Sharks appear to maintain gene flow using shallow coastal waters as dispersal corridors, whereas large oceanic distances and historical land-bridges act as barriers. Females tend to return to the same area for reproduction, making them more susceptible to local threats and an important focus for management actions. Given these behaviours, the exploitation of Bull Sharks from insular populations, such as Japan and Fiji, may instigate local decline that cannot readily be replenished by immigration, which can in turn affect ecosystem dynamics and functions. These data also supported the development of a genetic panel to ascertain the population of origin, which will be useful in monitoring the trade of fisheries products and assessing population-level impacts of this harvest.

Fig. 1 in Socio-spatial organization and kin structure in ocelots from integration of camera trapping and noninvasive genetics

Fig. 1.—Map of Barro Colorado Island, Panama, showing the locations of camera traps placed along trails and at ocelot (Leopardus pardalis) latrines.

Fig. 2 in Socio-spatial organization and kin structure in ocelots from integration of camera trapping and noninvasive genetics

Fig. 2.—Cumulative frequency distributions of association index values among pairs of male versus female ocelots (Leopardus pardalis) on Barro Colorado Island, Panama. Half-weight association index values represent the strength of spatiotemporal overlap between same-sex dyads based on how often they were photographed at the same camera trap within the same 30-day interval.

Fig. 4 in Socio-spatial organization and kin structure in ocelots from integration of camera trapping and noninvasive genetics

Fig. 4.—Relatedness of individual ocelots (Leopardus pardalis) on Barro Colorado Island, Panama, depending on sex and overlap of space use. Values shown are observed mean differences in relatedness between dyads of individual ocelots with overlapping space use (vertical bold lines) versus all dyads in the sampled population, along with the cumulative distribution of simulated differences from 1,000,000 randomly generated bootstrap replicates. Reference lines represent quantiles from the simulated distribution. A) All dyads, B) male-female dyads, C) male-male dyads, and D) female-female dyads.

Fig. 3 in Socio-spatial organization and kin structure in ocelots from integration of camera trapping and noninvasive genetics

Fig. 3.—Half-weight association index values between pairs of a) female and b) male ocelots (Leopardus pardalis) from Barro Colorado Island, Panama, shown in both matrix and graphical format. Values and line weights represent the strength (on a scale of 0–1) of spatiotemporal overlap between pairs of individuals based on how often they were photographed at the same camera trap during the same 30-day period. Asterisks represent associations and double asterisks represent dissociations that differed from random expectations (P <0.05).

opencc-zeroApr 2023View details →

Phylogeography and population genetic structure of the cardinal tetra (Paracheirodon axelrodi) in the Orinoco basin and Negro River (Amazon basin): evaluating connectivity and historical patterns of diversification

The Neotropics contain one of the most diverse assemblages of freshwater fishes worldwide. Part of this diversity is shared between the Orinoco and Amazon basins. These basins have been separated for a long time due to the Vaupes Arch, rising between 10 - 11 Ma. Today, there is only one permanent connection between the Orinoco and Negro (Amazon) basins, known as the Casiquiare Canal. However, alternative corridors allowing fish dispersion between both basins have been proposed. The cardinal tetra (Paracheirodon axelrodi), the most important fish in the ornamental world market, is distributed in both basins. Here we investigated P. axelrodi phylogeography, population structure, and potential routes of migration and connectivity between the two basins. A total of 468 bp of the mitochondrial gene (COI), 555 bp of the nuclear gene fragment (MYH6), and 8 microsatellite loci were analyzed. As a result, we found two major genetic clusters as the most likely scenario (K=2), but they were not discreetly distributed between basins. A gradient of genetic admixture was observed in Cucui and São Gabriel da Cachoeira, between the upper Negro River and the upper Orinoco. Samples from the middle-lower Negro River were highly structured. Cucui (Negro basin) was more similar to the Orinoco than to the rest of the Negro basin populations. However, substructure was also observed by the discriminant analysis, fixation indices and other hierarchichal structure analyses (K=3-6), showing three major geographic clusters: Orinoco, Cucui, and the remaining of the Negro basin. Unidirectional migration patterns were detected between basins: via Cucui toward Orinoco and via the remaining of the Negro basin toward Orinoco. Results from the Relaxed Random Walk analysis support a very recent origin of this species in the headwater Orinoco basin (Western Guiana Shield, at late Pleistocene) with a later rapid colonization of the remaining Orinoco basin and almost simultaneously the Negro River via Cucui, between 0.115 until about 0.001 Ma. Historical biogeography and population genetic patterns observed here for Cardinal tetra, seem to be better explained by river capture, physical, or ecological barriers than due to the geographic distance.

opencc-by-4.0May 2023View details →

Data for Selfing species has greater genetic diversity and less structure than related outcrossing species due to seed dispersal and population history in Roscoea (Zingiberaceae)

Data matrix of two species with nexus format.

opennotspecifiedMay 2023View details →

Fig. 3. STRUCTURE plot for Leucotaraxis argenticollis genotyped with 15 in Prey-associated genetic differentiation in two species of silver fly (Diptera: Chamaemyiidae), Leucotaraxis argenticollis and L. piniperda

Fig. 3. STRUCTURE plot for Leucotaraxis argenticollis genotyped with 15 microsatellite loci.The height of each bar represents the proportion of an individual′s genotype assigned to each of K = 4 clusters.The names of the clusters correspond to those in Fig. 1C. Vertical black lines separate groups of individuals collected in different states or provinces and on different adelgid host plant genera.

opennotspecifiedMay 2023View details →

Fig. 4. STRUCTURE plot for Leucotaraxis piniperda genotyped with 16 in Prey-associated genetic differentiation in two species of silver fly (Diptera: Chamaemyiidae), Leucotaraxis argenticollis and L. piniperda

Fig. 4. STRUCTURE plot for Leucotaraxis piniperda genotyped with 16 microsatellite loci. The height of each bar represents the proportion of an individual′s genotype assigned to: A) each of K = 2 clusters for analysis of all individuals, and B) each of K = 2 clusters for analysis of only western individuals.The names of the clusters correspond to those in Fig. 1D. Vertical black lines separate groups of individuals collected in different states or provinces and on different adelgid host plant genera.

opencc-zeroJun 2023View details →

Assessment of genetic diversity, population structure and wolf-dog hybridisation in the Eastern Romanian Carpathian wolf population

The Carpathian Mountains were always inhabited by grey wolves and present one of the largest distribution areas in Europe, comprising between 2,300 to 2,700 individuals in Romania. To date, however, relatively little is known about the Romanian wolf population. We aimed to provide a first assessment of genetic diversity, population structure and wolf-dog hybridisation based on 444 mostly non-invasively collected samples in the Eastern Romanian Carpathians. Pack reconstruction and analysis of population genetic parameters were performed with mitochondrial DNA control-region sequencing and microsatellite genotyping. We found relatively high levels of genetic diversity, which is similar to values found in previous studies on Carpathian wolves from Poland and Slovakia, as well as to the long-lasting Dinaric-Balkan wolf population. We found no significant population structure in our study region, suggesting effective dispersal and admixture. Analysis of wolf-dog hybridisation using a Single Nucleotide Polymorphism panel optimised for hybrid detection revealed low rates of admixture between wolves and domestic dogs. Our results provide evidence for the existence of a genetically viable wolf population in the Romanian Carpathians. The genetic data obtained in this study may serve as valuable baseline information for the elaboration of monitoring standards and management plans for wolves in Romania.

opencc-zeroJun 2023View details →

An evaluation of isolation by distance (IBD) and isolation by resistance (IBR) on genetic structure of the Persian squirrel (Sciurus anomalus) in the Zagros forests of Iran

For conservation of wild species, it is important to understand how landscape change and land management can affect gene flow and movement. Landscape genetic analyses provide a powerful approach to infer effects of various landscape factors on gene flow, thereby informing conservation actions. The Persian squirrel is a keystone species in the woodlands and oak forests of Western Asia, where it has experienced recent habitat loss and fragmentation. We conducted landscape genetic analyses of individuals sampled in the northern Zagros Mountains of Iran (provinces of Kurdistan, Kermanshah, and Ilam), focusing on evaluation of isolation by distance (IBD) and isolation by resistance (IBR), using 16 microsatellite markers. The roles of geographical distance and landscape features including roads, rivers, developed areas, farming and agriculture, forests, lakes, plantation forests, rangelands, shrublands and rocky areas of varying canopy cover, and swamp margins on genetic structure were quantified using individual-based approaches and resistance surface modelling. We found a significant pattern of IBD but only weak support for an effect of forest cover on genetic structure and gene flow. It seems that geographical distance is an important factor limiting the dispersal of the Persian squirrel in this region. The results of the current study inform ongoing conservation programs for the Persian squirrel in the Zagros oak forest.

opennotspecifiedAug 2023View details →

FIGURE 3. Genetic structure between N. lobata and N in Molecular phylogeny and taxonomy of the genus Nanocnide (Urticaceae) with particular attention to the Ryukyu Islands endemic N. lobata

FIGURE 3. Genetic structure between N. lobata and N. pilosa based on averaged MIG-seq data inferred using structure. The sample 1–4 and 5–9 correspond to N. lobata and N. pilosa. More precisely, the numbers correspond to the samples as follows: 1: R2. 2: R9. 3: R10. 4: R19. 5: R23. 6: KY18. 7: 33028. 8: H30528. 9: H30337.