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opencc-zeroDec 2009View details →

Data from: Strong population genetic structure in a broadcast-spawning Antarctic marine invertebrate

Although studies of population genetic structure are commonplace, a strong bias exists towards species from low latitudes and with relatively poor dispersal capabilities. Consequently, we used 280 Amplified Fragment Length Polymorphism (AFLP) bands to explore patterns of genetic differentiation among eight populations of a high latitude broadcast-spawning marine mollusc, the Antarctic limpet Nacella concinna. Over three hundred individuals were sampled along a latitudinal gradient spanning the Antarctic Peninsula from Adelaide Island to King George Island (67º–62º S), then to Signy Island (60ºS) and South Georgia (54ºS). Populations from the Antarctic Peninsula exhibited little genetic structure, but were themselves strongly differentiated from both Signy and South Georgia. This finding was analytically highly robust and implies the presence of significant oceanographic barriers to gene flow in a species long regarded as a classic example of a widely-dispersing broadcast-spawner.

opennotspecifiedOct 2001View details →

FIGURES 1-2. 1 in Taxonomic diagnosis of Dicyrtomina ornata and D. saundersi (Collembola: Dicyrtomidae) and analysis of their population genetic structure

FIGURES 1-2. 1, Dicyrtomina ornata, habitus; 2, Dicyrtomina saundersi, habitus.

opencc-zeroJan 2022View details →

Comparative biogeography and the evolution of population structure for bottlenose and common dolphins in the Indian Ocean

Abstract Aim: In the marine environment, where there are few physical boundaries to gene flow, there is often nevertheless intraspecific diversity with consequences for effective conservation and management. Here we compare two closely related dolphin species with a shared distribution in the Indian Ocean (IO) to better understand the biogeographic drivers of their population structure. Location: Global oceans and seas with a focus on the Indian Ocean Taxon: Tursiops sp. and Delphinus sp. Methods: Bayesian, ordination, assignment, statistical and phylogenetic analyses to assess phylogeography, connectivity and population structure using microsatellite and mitochondrial DNA genetic markers. Results: Both Tursiops sp. and Delphinus sp. showed population structure across the western IO and, in each case, populations in the Arabian Sea (off India, Pakistan and Oman) were most differentiated. Comparisons with other populations worldwide revealed independent lineages in this geographic region for both genera. For T. aduncus, (for which multiple sites within the IO could be compared), Bayesian modelling best supported a scenario of expansion southwards following a bottleneck event resulting in differentiation between the northern and western IO. For Delphinusthe same pattern is even more pronounced. Populations in the Arabian Sea region of the northwestern IO show genetic isolation for each of the two genera, consistent with other studies of cetacean species in this region. Main Conclusions: We propose that changes in the intensity of the southwest monsoon during the climate cycles of the Pleistocene could have affected regional patterns of productivity and represent an important biogeographic driver promoting the observed patterns of differentiation and population dynamics seen in our focal species. Patterns of population genetic structure are consistent with phenotypic differences, suggesting an influence from distinct habitats and resources, and emphasising the need for effective conservation measures in this geographic region.

opencc-zeroJan 2022View details →

Data from: Spatial familial networks to infer demographic structure of wild populations

In social species, reproductive success and rates of dispersal vary among individuals resulting in spatially structured populations. Network analyses of familial relationships may provide insights on how these parameters influence population-level demographic patterns. These methods have however rarely been applied to genetically-derived pedigree data from wild populations. Here we use parent-offspring relationships to construct familial networks 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 network measures, we assess the contribution of individual caribou to the population with several centrality measures and then determine which measures are best suited to inform on the population demographic structure. We investigate the centrality of individuals from eighteen different local areas, along with the entire population. 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 networks at different scales. The full network revealed that boreal caribou in Saskatchewan form a complex, interconnected familial network, as the removal of edges with high betweenness did not result in distinct subgroups. Alpha, betweenness, and eccentricity centrality were the most informative measures to characterize the population demographic structure and for spatially identifying areas of highest fitness levels and family cohesion across the range. We found varied levels of dispersal, fitness and cohesion in family groups. Synthesis and applications: Our results demonstrate the value of different network measures in assessing genetically-derived familial networks. The spatial application of the familial networks identified individuals presenting different fitness levels, short and long-distance dispersing ability across the range in support of population monitoring and recovery efforts.

opencc-by-4.0Mar 2022View details →

Figure 5 from: Zhao L, Wang S, Qu F, Liu Z, Gao T (2022) A genetic assessment of the population structure and demographic history of Odontamblyopus lacepedii (Perciformes, Amblyopinae) from the northwestern Pacific. ZooKeys 1088: 1-15. https://doi.org/10.3897/zookeys.1088.70860

Figure 5 Bayesian Skyline Plots based on the mtDNA partial control region sequences of Odontamblyopus lacepedii.

opencc-by-4.0Mar 2022View details →

Figure 2 from: Zhao L, Wang S, Qu F, Liu Z, Gao T (2022) A genetic assessment of the population structure and demographic history of Odontamblyopus lacepedii (Perciformes, Amblyopinae) from the northwestern Pacific. ZooKeys 1088: 1-15. https://doi.org/10.3897/zookeys.1088.70860

Figure 2 Maximum Likelihood tree is shown based on the control region haplotypes of Odontamblyopus lacepedii. The species of O. rebecca was used as the outgroup.

opencc-by-4.0Mar 2022View details →

Figure 4 from: Zhao L, Wang S, Qu F, Liu Z, Gao T (2022) A genetic assessment of the population structure and demographic history of Odontamblyopus lacepedii (Perciformes, Amblyopinae) from the northwestern Pacific. ZooKeys 1088: 1-15. https://doi.org/10.3897/zookeys.1088.70860

Figure 4 Mismatch distribution for demographic expansion based on mtDNA partial control region sequences of Odontamblyopus lacepedii.

opencc-zeroMar 2022View details →

Micro-endemic species of snails and amphipods show population genetic structure across very small geographic ranges

Understanding variation in population genetic structure, even across small distances and for species with extremely limited ranges, is critical for conservation planning and the development of effective management strategies for imperiled species. Organisms that occupy the same geographic extent can maintain different population structures, ranging from highly diverged to panmictic. Such differences can result from differences in biological characteristics such as dispersal ability or demographic history. We used microsatellite loci to evaluate population genetic structure and variation of four desert spring invertebrates having high to low dispersal ability: the lung snail Physa acuta, two species of gilled snails (Juturnia kosteri and Pyrgulopsis roswellensis; family Hydrobiidae) and the amphipod Gammarus desperatus. The study location represents entire species ranges for the micro-endemic hydrobiids and G. desperatus, while P. acuta is ubiquitous throughout much of North America. We found little evidence of significant population genetic structure for P. acuta and J. kosteri, but much more for P. roswellensis and G. desperatus. Our results demonstrate differences in habitat preference and/or dispersal ability between the species. While significant isolation-by-distance was detected in the two hydrobiids, dispersal is likely more limited in P. roswellensis than J. kosteri. This information provides insight into how gene flow shapes varying population genetic structure between species across small spatial scales (<100 km2). Most importantly, our results suggest that conservation agencies should not consider these microendemic species to be composed of single populations, but rather, that management plans for such species should account for population genetic variation across the species' ranges.

opencc-zeroMar 2022View details →

Age-specific habitat preference, carrying capacity, and landscape structure determine the response of population spatial variability to fishing-driven age truncation

1. Understanding the mechanisms underlying spatial variability of exploited fish is critical for the sustainable management of fish stocks. Empirical studies suggest that size-selective fishing can elevate fish population spatial variability (i.e., more heterogeneous distribution) through age truncation, making the population less resilient to changing environment. However, species differ in how their spatial variability respond to age truncation and the underlying mechanisms remain unclear. 2. We hypothesize that age-specific habitat preference, together with environmental carrying capacity and landscape structure, determines the response of population spatial variability to fishing-induced age truncation. To test these hypotheses, we design an individual-based model of an age-structured fish population on a two-dimensional landscape under size-selective fishing. Individual fish reproduces and survives, and moves between habitats according to age-specific habitat preference and density-dependent habitat selection. 3. Population spatial variability elevates with increasing age truncation and the response is stronger for populations with stronger age-specific habitat preference. On a gradient landscape, reducing carrying capacity elevates the relative importance of density-dependence in habitat selection, which weakens the response of spatial variability to age truncation for populations with strong age-specific habitat preference. On a fragmented landscape, both populations with strong and weak age-specific habitat preferences are restricted at local optimal habitats, and reducing carrying capacity weakens the responses of spatial variability to age truncation for both populations. 4. Synthesis and applications. We demonstrate that to track and predict the changes in population spatial variability under exploitation, it is essential to consider the interactive effects of age-specific habitat preference, carrying capacity, and landscape structure. To improve spatial management in fisheries, it is crucial to enhance empirical and theoretical developments in the methodology to quantify age-specific habitat preference of marine fish, and to understand how climatic change influences carrying capacity and landscape continuity.

opencc-zeroDec 2014View details →

Data from: Genetic diversity and population structure of wild/weedy eggplant (Solanum insanum L., Solanaceae) in southern India: implications for conservation

[No abstract entered]

opencc-zeroDec 2013View details →

Data from: Causes and consequences of fine-scale population structure in a critically endangered freshwater seal

[No abstract entered]

opencc-zeroJul 2022View details →

Microsatellite genotyping data for habitat-linked genetic structure for white-crowned sparrow (Zonotrichia leucophrys): local factors shape population genetic structure

Ecological, environmental, and geographic factors all influence genetic structure. Species with broad distributions are ideal systems because they cover a range of ecological and environmental conditions allowing us to test which components predict genetic structure. This study presents a novel, broad geographic approach using molecular markers, morphology, and habitat modelling to investigate rangewide and local barriers causing contemporary genetic differentiation within the geographical range of three white-crowned sparrow (Zonotrichia leucophrys) subspecies: Z. l. gambelii, Z. l. oriantha, and Z. l. pugetensis. Three types of genetic markers showed geographic distance between sampling sites, elevation, and ecosystem type are key factors contributing to population genetic structure. Microsatellite markers revealed white-crowned sparrows do not group by subspecies, but instead indicated four groupings at a rangewide scale and two groupings based on coniferous and deciduous ecosystems at a local scale. Our analyses of morphological variation also revealed habitat differences; sparrows from deciduous ecosystems are larger than individuals from coniferous ecosystems based on principal component analyses. Habitat modeling showed isolation by distance was prevalent in describing genetic structure, but isolation by resistance also had a small but significant influence. Not only do these findings have implications concerning the accuracy of subspecies delineations, they also highlight the critical role of local factors such as habitat in shaping contemporary population genetic structure of species with high dispersal ability.

Figure 5 from: Pupillo P, Astuti G (2017) Population structure of Erythronium dens-canis L. (Liliaceae) in the northern Apennines (Italy). Italian Botanist 4: 1-14. https://doi.org/10.3897/ib.4.12439

Figure 5 - Discoloration: loss of red pigment from red-brown spots in E. dens-canis leaves. Time course of the discoloration in A adult plants (FLO and MNF), and B JUV plants.

Figure 4 from: Pupillo P, Astuti G (2017) Population structure of Erythronium dens-canis L. (Liliaceae) in the northern Apennines (Italy). Italian Botanist 4: 1-14. https://doi.org/10.3897/ib.4.12439

Figure 4 - Different patterns of E. dens-canis leaves. A Silvery pictorial pattern (SLV-PC) characterized by red-brown (and later green) drawings on a grey-silvery background (Feb. 27, 2015) B Silvery-and-green chess-like leaves with red-brown spots (S&G-CH, Feb. 13, 2016) C Green-mottled leaves with red-brown spots (GRN-MO, Feb. 24th, 2016) D A rare rusty variant of SLV with red-brown leaves (Mt. Adone, 550 m of altitude, March 15, 2015) E A juvenile leaf with clear-silvery spots on green background (GRN-CS, April 11, 2015) F Juvenile lanceolate (JUV-LA) uniformly green (GRN-UN) leaf. Photos taken at Farneto (except D).

Figure 3 from: Pupillo P, Astuti G (2017) Population structure of Erythronium dens-canis L. (Liliaceae) in the northern Apennines (Italy). Italian Botanist 4: 1-14. https://doi.org/10.3897/ib.4.12439

Figure 3 - Leaf shape in new plants of E. dens-canis. Histograms of A mature non-flowering individuals (MNF) with oval (OV), shield-like (SH) and elongate (EL) leaf shapes, and B juvenile (JUV) plants with oval (OV), elongate (EL) and lanceolate (LA) leaf shapes.

Figure 1 from: Pupillo P, Astuti G (2017) Population structure of Erythronium dens-canis L. (Liliaceae) in the northern Apennines (Italy). Italian Botanist 4: 1-14. https://doi.org/10.3897/ib.4.12439

Figure 1 - Number of individuals of Erythronium dens-canis during spring 2015 in Farneto-C. The histograms show the number of flowering (FLO), mature non-flowering (MNF) and juvenile (JUV) plants. A New plants and B all plants.

Figure 2 from: Pupillo P, Astuti G (2017) Population structure of Erythronium dens-canis L. (Liliaceae) in the northern Apennines (Italy). Italian Botanist 4: 1-14. https://doi.org/10.3897/ib.4.12439

Figure 2 - Survivorship of MNF E. dens-canis plants in March 2015. The three major cohorts are shown: Cohort 10 (in blue) with 94 new plants found on March 8th (week 10); Cohort 11 (in red) with 127 new plants found on March 12th (week 11); Cohort 12 (in green) with 82 new plants found on March 19th (week 12).

opencc-by-4.0Nov 2015View details →

Supplementary material 7 from: Virgilio M, Delatte H, Nzogela YB, Simiand C, Quilici S, De Meyer M, Mwatawala M (2015) Population structure and cryptic genetic variation in the mango fruit fly, Ceratitis cosyra (Diptera, Tephritidae). In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 525-538. https://doi.org/10.3897/zookeys.540.9618

STRUCTURE sequential assignments:

opencc-by-4.0Nov 2015View details →

Supplementary material 5 from: Virgilio M, Delatte H, Nzogela YB, Simiand C, Quilici S, De Meyer M, Mwatawala M (2015) Population structure and cryptic genetic variation in the mango fruit fly, Ceratitis cosyra (Diptera, Tephritidae). In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 525-538. https://doi.org/10.3897/zookeys.540.9618

Estimated null allele proportions: