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Figure 5 in Species diversity and endemism in the Daphnia of Argentina: a genetic investigation

Figure 5. NJ tree based on COI sequence variation among Argentine populations identified as D. laevis and D. gessneri. The identifications, based on head morphology, are indicated in this tree, followed by the collection site numbers. Sequences from the North American members of the D. laevis complex (D. dubia, D. laevis, and D. magniceps) were included for comparison. D. mendotae, a Hyalodaphnia species belonging to a different species complex (Colbourne & Hebert, 1996), was used to root the tree. The scale bar represents K2P distance.

Figure 4 in Species diversity and endemism in the Daphnia of Argentina: a genetic investigation

Figure 4. Collection sites for Argentine populations belonging to the subgenus Hyalodaphnia. Photographs are included to demonstrate the several head morphologies encountered. The morphological, not genetic, forms encountered at each site are indicated on the map.

Figure 3 in Species diversity and endemism in the Daphnia of Argentina: a genetic investigation

Figure 3. UPGMA tree based on allozyme variation at seven loci in three species of the Daphnia obtusa complex from Argentina. The scale bar represents Nei's genetic distance.

Figure 2 in Species diversity and endemism in the Daphnia of Argentina: a genetic investigation

Figure 2. NJ tree based on COI sequence variation among all unique haplotypes found in Argentine populations of the subgenus Daphnia. D. mendotae, a North American species belonging to the subgenus Hyalodaphnia, was included to root the tree. Bootstrap values for major clusters and among clusters are presented. The scale bar indicates K2P distances. D. obtusa 1 haplotype A was found at sites 1, 13, 15, 16, 17, 18, 20, 22, 26, 27, 40, 42, 46, 48, 122, 243, 249, 250, and 256; haplotype B was found at sites 132b, 169, 172, 183, 193, 194, and 195. D. 'pulicaria' haplotype C was found at sites 135, 156, 171, 202, and 205. All site codes are listed in Appendix 1. The NJ algorithm is used here for the purpose of clustering only; this tree is not intended to represent a phylogenetic hypothesis for the species assemblage.

opencc-zeroSep 2021View details →

Data from: Genetic diversity in a long-lived mammal is explained by the past's demographic shadow and current connectivity

Within-species genetic diversity is crucial for the persistence and integrity of populations and ecosystems. Conservation actions require an understanding of factors influencing genetic diversity, especially in the context of global change. Both population size and connectivity are factors greatly influencing genetic diversity; the relative importance of these factors can however change through time. Hence, quantifying the degree to which population size or genetic connectivity are shaping genetic diversity, and at which ecological time scale (past or present), is challenging, yet essential for the development of efficient conservation strategies. In this study, we estimated the genetic diversity of 42 colonies of Rhinolophus hipposideros, a long-lived mammal vulnerable to global change, sampling locations spanning its continental northern range. We present an integrative approach that disentangles and quantifies the contribution of different connectivity measures in addition to contemporary colony size and historic bottlenecks in shaping genetic diversity. In our study, the best model explained 64% of the variation in genetic diversity. It included historic bottlenecks, contemporary colony sizes, connectivity and a negative interaction between the latter two. Contemporary connectivity explained most genetic diversity when considering a 65 km radius around the focal colonies, emphasizing the large geographic scale at which the positive impact of connectivity on genetic diversity is most profound and hence the minimum scale at which conservation should be planned. Our results highlight that the relative importance of the two main factors shaping genetic diversity varies through time, emphasizing the relevance of disentangling them to ensure appropriate conservation strategies.

opencc-by-4.0Sep 2021View details →

Consequences of the Last Glacial Period on the Genetic Diversity of Southeast Asians

********* Observed data ********* The file ObsData.arp contains the sequences of the mtDNA hypervariable I region from 720 individuals belonging to 25 Southeast Asian populations used as input file to compute the summary statistics with Arlequin. For further details on the format and available Summary statistics see the manual of Arlequin.   ********* Input files for simulations ********* For each evolutionary scenario (NONE, LGP, LDD and LGP&LDD) find a folder (named after the scenario) containing the input files to perform 100 simulations. To run the simulations one should access the command line and execute:  ./ABCsampler abc_sensitivity.input Input files for SPLATCHE3, Arlequin and ABCtoolbox are included (for further details on them see the manual of these software). ********* Selection of the best-fitting evolutionary scenario ********* The R script (ModelSelection.R) can be used to select the evolutionary scenario that better fits the observed data, using the multinomial logistic regression method and the neural networks based method. Firstly, one will need the summary statistics obtained from observed data (the file entitled ObsSS.txt). Then, one will need the files containing the output files of the simulations under each scenario, i.e., the genetic parameters used under each simulation and the computed summary statistics. Please, note that the output of the ABCtoolbox is a single file containing all this information, but we prefer to use a file with the summary statistics and another with the parameters. Here, we provide example files obtained from 100 simulations of each scenario: - ssNONE.txt, the summary statistics computed from 100 simulations under the scenario NONE - parNONE.txt, the genetic and demographic parameters per simulation under the scenario NONE - ssLGP.txt, the summary statistics computed from 100 simulations under the scenario LGP - parLGP.txt, the genetic and demographic parameters per simulation under the scenario LGP - ssLDD.txt, the summary statistics computed from 100 simulations under the scenario LDD - parLDD.txt, the genetic and demographic parameters per simulation under the scenario LDD - ssLGP_LDD.txt, the summary statistics computed from 100 simulations under the scenario LGP&LDD - parLGP_LDD.txt, the genetic and demographic parameters per simulation under the scenario LGP&LDD To run the script the directory containing these files has to be specified in the script. For details see Csilléry, et al. (2012): "Approximate Bayesian computation (ABC) in R: a Vignette." ********* Parameters estimation ********* The folder named ParametersEstimation contains all the input files to estimate the genetic and demographic parameters under the selected evolutionary scenario (LGP&LDD). Within the folder, one will find the summary statistics obtained under the selected scenario and the corresponding parameters (completeEstimator_LGP-LDD.txt), the summary statists from observed data (obs11SS.txt) and all the remaining input files to run ABCestimator (for further detail on these files see the manual of ABCtoolbox).

opencc-zeroOct 2021View details →

Species ecology explains the various spatial components of genetic diversity in tropical reef fishes

Generating genomic data for 19 tropical reef fish species of the Western Indian Ocean, we investigate how species ecology influences genetic diver- sity patterns from local to regional scales. We distinguish between the α, β and γ components of genetic diversity, which we subsequently link to six ecological traits. We find that the α and γ components of genetic diversity are strongly correlated so that species with a high total regional genetic diversity display systematically high local diversity. The α and γ diversity components are negatively associated with species abundance recorded using underwater visual surveys and positively with body size. Pelagic larval duration is found to be negatively related to genetic β diversity supporting its role as a dispersal trait in marine fishes. Deviation from the neutral theory of molecular evolution motivates further effort to understand the processes shaping genetic diversity and ultimately the diversification of the exceptional diversity of tropical reef fishes.

opencc-zeroJan 2023View details →

Whole genome demographic models indicate divergent effective population size histories shape contemporary genetic diversity gradients in a montane bumble bee

Understanding historical range shifts and population size variation provides important context for interpreting contemporary genetic diversity. Methods to predict changes in species distributions and model changes in effective population size (Ne) using whole genomes make it feasible to examine how temporal dynamics influence diversity across populations. We investigate Ne variation and climate-associated range shifts to examine the origins of a previously observed latitudinal heterozygosity gradient in the bumble bee Bombus vancouverensis Cresson (Hymenoptera: Apidae: Bombus Latreille) in western North America. We analyze whole genomes from a latitude-elevation cline using sequentially Markovian coalescent models of Ne through time to test whether relatively low diversity in southern high-elevation populations is a result of long-term differences in Ne. We use Maxent models of the species range over the last 130,000 years to evaluate range shifts and stability. Ne fluctuates with climate across populations, but more genetically diverse northern populations have maintained greater Ne over the late Pleistocene and experienced larger expansions with climatically favorable time periods. Northern populations also experienced larger bottlenecks during the last glacial period which matched the loss of range area near these sites, however, bottlenecks were not sufficient to erode diversity maintained during periods of large Ne. A genome sampled from an island population indicated a severe postglacial bottleneck, indicating that large recent post-glacial declines are detectable if they have occurred. Genetic diversity was not related to niche stability or glacial-period bottleneck size. Instead, spatial expansions and increased connectivity during favorable climates likely maintain diversity in the north while restriction to high elevations maintains relatively low diversity despite greater stability in southern regions. Results suggest genetic diversity gradients reflect long-term differences in Ne dynamics and also emphasize the unique effects of isolation on insular habitats for bumble bees. Patterns are discussed in the context of conservation under climate change.

opencc-zeroApr 2023View details →

Genotype and genetic diversity data for: Contrasts in riverscape patterns of intraspecific genetic variation in a diverse Neotropical fish community of high conservation value

Spatial patterns in genetic variation compared across species provide information about the predictability of genetic diversity of natural populations and areas requiring conservation measures. Due to their remarkable fish diversity, rivers in Neotropical regions are ideal systems to confront theory with observations and would benefit greatly from such approaches given their increasing vulnerability to anthropogenic pressures. We used SNP data from 18 fish species with contrasting life-history traits, co-sampled across 12 sites in the Maroni – a major river system from the Guiana Shield – to compare patterns of intraspecific genetic variation and identify their underlying drivers. Analyses of covariance revealed a decrease in genetic diversity as distance from the river outlet increased for 5 of the 18 species, illustrating a pattern commonly observed in riverscapes for species with low-to-medium dispersal abilities. However, mean within-site genetic diversity was lowest in the two easternmost tributaries of the Upper Maroni and around an urbanized location downstream, indicating the need to address the potential influence of local pressures in these areas, such as goldmining or fishing. Finally, the relative influence of isolation by stream distance, isolation by discontinuous river flow and isolation by spatial heterogeneity in effective size on pairwise genetic differentiation varied across species. Species with similar dispersal and reproductive guilds did not necessarily display shared patterns of population structure. Increasing the knowledge of specific life history traits and ecological requirements of fish species in these remote areas should help further understand factors that influence their current patterns of genetic variation.

opencc-zeroApr 2023View details →

Density and genetic diversity of grizzly bears at the northern edge of their distribution

Species at the periphery of their range are typically limited in density by lower habitat quality. As a result, the Central-Marginal Hypothesis (CMH) predicts a decline in genetic diversity of populations towards the periphery of a species' range. Grizzly bears (Ursus arctos) once ranged throughout most of North America but have been extirpated from nearly half of their former range, mainly in the south. They are considered a species at risk even in Canada's remote North, where they occupy the northernmost edge of the species' continental distribution in a low-productivity tundra environment. With climate change, one of their main food items in the tundra (caribou), which has always shown yearly fluctuations, is declining, but simultaneously, grizzlies appear to be expanding their range northward, in tundra environment. Yet, a lack of population density estimates across the North is hindering effective conservation action. The CMH has implications for the viability of peripheral populations, and the links between population fluctuations, potential bottlenecks and genetic diversity need to be determined to contribute to species' conservation. Using non-invasive genetic sampling from 2012 to 2014, and autosomal DNA genotyping (via-microsatellites), we estimated bear density using a spatial capture-recapture framework and analysed genetic diversity using observed heterozygosity (Ho), Allelic Richness (AR), and expected heterozygosity (He). We compared our findings to other studies that used comparable methodologies on this and a related species (Black bears; Ursus americanus). We found densities of grizzly bears that were low for the species but characteristic for the region (5.9 ± 0.4 bears/1000 km2), but with high Ho (0.81 ± 0.05), AR (7 ± 0.78) and He (0.71 ± 0.03), despite a signal of recent bottlenecks. In both species, peripherality was not correlated with Ho but was negatively correlated with density. We suggest that the apparent growth of this expanding population of grizzlies offsets the negative impacts of recent bottlenecks on Ho. Indigenous Knowledge provides historical context (on the order of centuries – e.g., arctic large mammal fluctuations, grizzly bear bottlenecks) for the current bear population dynamics (on the order of decades – e.g., climate change, northern grizzly bear expansion).

opencc-by-4.0Jun 2011View details →

Fig. 2 in Genetic diversity of Maghrebian Hottentotta (Scorpiones: Buthidae) scorpions based on CO1: new insights on the genus phylogeny and distribution

Fig. 2. Phylogram showing phylogenetic relationships estimated using Bayesian Inference as described in the text. Numbers at branches are Bayesian posterior probabilities and ML bootstrap percentages respectively. The tree was rooted with Scorpio fuliginosus (not shown). Codes refer to Table 1.

opencc-by-4.0Jun 2011View details →

Fig. 1 in Genetic diversity of Maghrebian Hottentotta (Scorpiones: Buthidae) scorpions based on CO1: new insights on the genus phylogeny and distribution

Fig. 1. Map showing the sampling locations of Hottentotta from Morocco included in this study. The estimated distribution of both Hottentotta species proposed by Vachon (1952) is indicated. The clades resolved in Fig. 2 are noted. Specimen codes follow Table 1.

opencc-zeroMay 2023View details →

Sexual recombination and temporal gene flow maintain host resistance and genetic diversity

Infectious disease can threaten host populations. Hosts can rapidly evolve resistance during epidemics, with this evolution often modulated by fitness trade-offs (e.g., between resistance and fecundity). However, many organisms switch between asexual and sexual reproduction, and this shift in reproductive strategy can also alter how resistance in host populations persists through time. Recombination can shuffle alleles selected for during an asexual phase, uncoupling the combinations of alleles that facilitated resistance to parasites and altering the distribution of resistance phenotypes in populations. Furthermore, in host species that produce diapausing propagules (e.g., seeds, spores, or resting eggs) after sex, accumulation of propagules into and gene flow out of a germ bank introduce allele combinations from past populations. Thus, recombination and gene flow might shift populations away from the trait distribution reached after selection by parasites. To understand how recombination and gene flow alter host population resistance, we tracked the genotypic diversity and resistance distributions of two wild populations of cyclical parthenogens. In one population, resistance and genetic diversity increased after recombination whereas, in the other, recombination did not shift already high resistance and genetic diversity. In both lakes, resistance remained high after temporal gene flow. This observation surprised us: due to costs to resistance imposed by a fecundity-resistance trade-off, we expected that high population resistance would be a transient state that would be eroded through time by recombination and gene flow. Instead, low resistance was the transient state, while recombination and gene flow re-established or maintained high resistance to this virulent parasite. We propose this outcome may have been driven by the joint influence of fitness trade-offs, genetic slippage after recombination, and temporal gene flow via the egg bank.

opencc-by-4.0Mar 2023View details →

Figure 4 in Genetic diversity, phylogenetic and phylogeographic analyses of Oncideres impluviata (Germar, 1823) (Coleoptera: Cerambycidae) in Rio Grande do Sul state, Brazil

Figure 4 Phylogenetic tree summarizing the results of Bayesian inference (BI) and Maximum likelihood (ML). Tree shows the relationships among species of Oncideres along with the haplotype network of five populations of Oncideres impluviata from Rio Grande do Sul, Brazil. A, B and C depicts clades within Oncideres impluviata. The circle areas in the haplotype network are proportional to the frequencies of each haplotype and hatch markers represent the number of differences among haplotypes.

opencc-by-4.0Mar 2023View details →

Figure 2 in Genetic diversity, phylogenetic and phylogeographic analyses of Oncideres impluviata (Germar, 1823) (Coleoptera: Cerambycidae) in Rio Grande do Sul state, Brazil

Figure 2 Injuries caused by Oncideres impluviata to Acacia mearnsii in the State of Rio Grande do Sul, Brazil. Girdled fallen branches in a Acacia plantation in General Câmara.Red arrows show branches girdled by O. impluviata (a). Adults of O. impluviata copulating and girdling the main trunk of a young Acacia tree in Encruzilhada do Sul (b).

opencc-by-4.0Nov 2022View details →

Reference datasets for consistency tests of GENAPOPOP 1.0 software: a user-friendly software to analyse genetic diversity and structure in partially clonal and selfed polyploid organisms.

Datasets companion of the manuscript entitled GenAPoPop 1.0: a user-friendly software to analyse genetic diversity and structure in partially clonal and selfed polyploid organisms, used to achieve consistency test with Spagedi 1.5 software, and used as reference datasets to demonstrate the new possibilities allowed by GenAPoPop software. Raw datasets used for testing GenAPoPop 1.0, A user-friendly software for easily compute genetic analyses of autopolyploid populations packaged for Linux, MacOS and Windows; Results obtained from Spagedi 1.5 (Hardy & Vekemans 2001) and GenAPoPop1.0. Four pseudo-observed genotyping autotetrapolyploid SNP datasets, corresponding respectively to panmictic (A), highly clonal (B), highly selfed (C) and half-clonal-half-selfed (D) reproductive mode scenario. In all these four scenarios, we simulated two populations of 100 individuals each, connected with a migration rate of 0.01 and mutating at a rate of 0.01, genotyped at 10 SNPs. Datasets were recorded 1000 generations after an initial randomly drawing population with equal allele frequencies. One SNP tetraploid genotyping dataset from two French Ludwigia grandiflora subsp. hexapetala populations (aquatic plant from the Angiosperm clade): two populations in which we collected 75 individuals, each genotyped with 36 SNPs using the Hiplex method allowing confident allele dosage (Delord et al. 2018). One microsatellite tetraploid genotyping dataset on two Aulactinia stella populations (sea-anemone from the Cnidaria phylum), sampled on the coast of the arctic ocean. One population of 21 individuals and one population of 15 individuals, both genotyped with 10 microsatellites. We also report here the consistency tests with GenAlex and Spagedi, results of analyses (GPP tab) on 6300 independant simulations and inferences of the quantitative reproductive modes using the bayesian method on CEMP tab made on 6300 another independant simulations.

opencc-zeroAug 2023View details →

Population genomic evidence that stream networks structure genetic diversity in the narrowly endemic patch-nosed salamander (Urspelerpes brucei)

Described in 2009, the Patch-nosed Salamander (Urspelerpes brucei) is a miniature species of lungless salamander with a geographic range of only ~45 km2. This species is endemic to the foothills of the Appalachian Mountains in extreme northeastern Georgia and northwestern South Carolina. The Tugaloo River—a waterway of some 50 m in width that forms the political boundary between the two states—bisects the tiny range of U. brucei and likely acts as a barrier to gene flow. Using RADcap data and a suite of complementary population genomic analyses, we evaluated the role that this river and its tributaries may play in enabling and/or interrupting gene flow among populations of U. brucei, and we investigated patterns of within-population and between-population genetic variation. Our results revealed a general pattern of isolation-by-stream distance and indicated that a population separated by the Tugaloo River is moderately more differentiated than what is explainable by stream distance alone. Unique in both its physiography and geologic history, this region in which U. brucei lives also harbors more than a dozen other species of lungless salamanders. Therefore, the genetic patterns that we have elucidated may have larger implications for differentiation among populations of other species with similar dispersal abilities.

opencc-zeroSep 2023View details →

Data from: Phenotypic plasticity and genetic diversity shed light on endemism of rare Boechera perstellata and its potential vulnerability to climate warming

Premise of the study: The rapid pace of contemporary environmental change puts many species at risk, especially rare species constrained by limited capacity to adapt or migrate due to low genetic diversity and/or fitness. But the ability to acclimate can provide another way to persist through change. We compared the capacity of rare Boechera perstellata (Braun's rockcress) and widespread B. laevigata to acclimate to change. Methods: We investigated the phenotypic plasticity of growth, biomass allocation, and leaf morphology of individuals of B. perstellata and B. laevigata propagated from seed collected from several populations throughout their ranges in a growth chamber experiment to assess their capacity to acclimate. Concurrently, we assessed the genetic diversity of sampled populations using 17 microsatellite loci to assess evolutionary potential. Key results: Plasticity was limited in both rare B. perstellata and widespread B. laevigata, but differences in the plasticity of root traits between species suggest that B. perstellata may have less capacity to acclimate to change. In contrast to its widespread congener, B. perstellata exhibited no plasticity in response to temperature and weaker plastic responses to water availability. As expected, B. perstellata also had lower levels of observed heterozygosity than B. laevigata at the species level, but population-level trends in diversity measures were inconsistent due to high heterogeneity among B. laevigata populations. Conclusions: Overall, the ability of phenotypic plasticity to broadly explain the rarity of B. perstellata vs. commonness of B. laevigata is limited. However, some contextual aspects of our plasticity findings compared with its relatively low genetic variability may shed light on the narrow range and habitat associations of B. perstellata and suggest its vulnerability to climate warming due to acclimatory and evolutionary constraints.

opencc-by-4.0Dec 2018View details →

Fig. 1 in High Genetic Diversity of Amoebae Belonging to the Genus Mayorella (Amoebozoa, Discosea, Dermamoebida) in Natural Habitats

Fig. 1. Diversity of locomotive and floating forms of studied strains: A–E – Mayorella sp. strain Belaya; F–J – Mayorella sp. strain 2Th5; K–O – Mayorella sp. strain FE 16; P–S – Mayorella sp. strain JJP2003. DIC and phase contrast images, scale bar is 20 μm.