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FIGURE 2. Haplotype network calculated from a 360 in A new species of Uroplatus (Gekkonidae) from Ankarana National Park Madagascar, of remarkably high genetic divergence

FIGURE 2. Haplotype network calculated from a 360 bp segment of the nuclear gene CMOS for the species in the Uroplatus ebenaui group.

FIGURE 1 in A new species of Uroplatus (Gekkonidae) from Ankarana National Park Madagascar, of remarkably high genetic divergence

FIGURE 1. Bayesian inference phylogenetic tree (50% majority-rule consensus tree) of the Uroplatus ebenaui group based on a 2686 bp alignment of five concatenated mitochondrial and nuclear gene fragments (ND4, 12S rRNA, 16S rRNA, COI, CMOS). Posterior probability values are shown on the nodes (omitted for most shallow nodes). Uroplatus alluaudi was used as the outgroup. The inset photo depicts a specimen of the new species, Uroplatus fetsy.

FIGURE 5 in A new species of Uroplatus (Gekkonidae) from Ankarana National Park Madagascar, of remarkably high genetic divergence

FIGURE 5. Photos in life of comparative specimens of Uroplatus ebenaui and views of their oral mucosa coloration. (a–d) specimens from Nosy Be (a, adult male, photographed in 2012; b, female, photographed in 1992; c–d, female specimen, photographed in 2009). (e–g) adult male from Forêt d'Ambre (MSZC 794), photographed 2017. (h–i) female from Forêt d'Ambre, photographed 2014; (j) female from Manongarivo, photographed 2003; (k) specimen from Berara (Sahamalaza Peninsula), photographed 2001; (l) male from Fanambana forest, photographed in 2012.

FIGURE 3 in A new species of Uroplatus (Gekkonidae) from Ankarana National Park Madagascar, of remarkably high genetic divergence

FIGURE 3. Map of northern Madagascar showing reliable locality records of Uroplatus ebenaui and U. fetsy sp. nov., based on molecular data.

opennotspecifiedSep 2010View details →

Fig. 4 in Genetic and morphological divergence among Gravel Bank Grasshoppers, Chorthippus pullus (Acrididae), from contrasting environments

Fig. 4 Discriminant function plot (group centroids ± SD for the first two discriminant func- tions) for the analysis presented in Table 7. Dark grey centroids: lowland heath populations; light grey centroids: alpine gravel bank populations

opencc-zeroDec 2014View details →

Data from: Population differentiation determined from putative neutral and divergent adaptive genetic markers in Eulachon (Thaleichthys pacificus, Osmeridae), an anadromous Pacific smelt.

Twelve eulachon (Thaleichthys pacificus, Osmeridae) populations ranging from Cook Inlet, Alaska and along the west coast of North America to the Columbia River were examined by restriction-site-associated DNA (RAD) sequencing to elucidate patterns of neutral and adaptive variation in this high geneflow species. A total of 4104 single-nucleotide polymorphisms (SNPs) were discovered across the genome, with 193 putatively adaptive SNPs as determined by FST outlier tests. Estimates of population structure in eulachon with the putatively adaptive SNPs were similar, but provided greater resolution of stocks compared with a putatively neutral panel of 3911 SNPs or previous estimates with 14 microsatellites. A cline of increasing measures of genetic diversity from south to north was found in the adaptive panel, but not in the neutral markers (SNPs or microsatellites). This may indicate divergent selective pressures in differing freshwater and marine environments between regional eulachon populations and that these adaptive diversity patterns not seen with neutral markers could be a consideration when determining genetic boundaries for conservation purposes. Estimates of effective population size (Ne) were similar with the neutral SNP panel and microsatellites and may be utilized to monitor population status for eulachon where census sizes are difficult to obtain. Greater differentiation with the panel of putatively adaptive SNPs provided higher individual assignment accuracy compared to the neutral panel or microsatellites for stock identification purposes. This study presents the first SNPs that have been developed for eulachon, and analyses with these markers highlighted the importance of integrating genome-wide neutral and adaptive genetic variation for the applications of conservation and management.

opencc-zeroDec 2015View details →

Data from: Habitat discontinuities separate genetically divergent populations of a rocky shore marine fish

Habitat fragmentation has been suggested to be responsible for major genetic differentiations in a range of marine organisms. In this study, we combined genetic data and environmental information to unravel the relative role of geography and habitat heterogeneity on patterns of genetic population structure of corkwing wrasse (Symphodus melops), a rocky shore species at the northern limit of its distribution range in Scandinavia. Our results revealed a major genetic break separating populations inhabiting the western and southern coasts of Norway. This genetic break coincides with the longest stretch of sand in the whole study area, suggesting habitat fragmentation as a major driver of genetic differentiation of this obligate rocky shore benthic fish in Scandinavia. The complex fjords systems extending along the western coast of Norway appeared responsible for further regional genetic structuring. Our findings indicate that habitat discontinuities may lead to significant genetic fragmentation over short geographical distances, even for marine species with a pelagic larval phase, as for this rocky shore fish.

opencc-zeroDec 2010View details →

Data from: Quantitative genetic inheritance of morphological divergence in a lake-stream stickleback ecotype pair: implications for reproductive isolation

Ecological selection against hybrids between populations occupying different habitats might be an important component of reproductive isolation during the initial stages of speciation. The strength and directionality of this barrier to gene flow depends on the genetic architecture underlying divergence in ecologically relevant phenotypes. We here present line cross analyses of inheritance for two key foraging-related morphological traits involved in adaptive divergence between stickleback ecotypes residing parapatrically in lake and stream habitats within the Misty Lake watershed (Vancouver Island, Canada). One main finding is striking genetic dominance of the lake phenotype for body depth. Selection associated with this phenotype against first and later generation hybrids should therefore be asymmetric, hindering introgression from the lake to the stream population but not vice versa. Another main finding is that divergence in gill raker number is inherited additively and should therefore contribute symmetrically to reproductive isolation. Our study suggests that traits involved in adaptation might contribute to reproductive isolation qualitatively differently, depending on their mode of inheritance.

opencc-zeroDec 2010View details →

Data from: Convergence and non-convergence in ecological, phenotypic, and genetic divergence across replicate population pairs of lake and stream stickleback

Convergent (or parallel) evolution provides strong evidence for a deterministic role of natural selection: similar phenotypes evolve when independent populations colonize similar environments. In reality, however, independent populations in similar environments always show some differences: some non-convergent evolution is present. It is therefore important to explicitly quantify the convergent and non-convergent aspects of trait variation, and to investigate the ecological and genetic explanations for each. We performed such an analysis for threespine stickleback (Gasterosteus aculeatus) populations inhabiting lake and stream habitats in independent watersheds. Morphological traits differed in the degree to which lake-stream divergence was convergent across watersheds. Some aspects of this variation were correlated with ecological variables related to diet, presumably reflecting the strength and specifics of divergent selection. Furthermore, a genetic scan revealed some markers that diverged between lakes and streams in many of the watersheds and some that diverged in only a few watersheds. Moreover, some of the lake-stream divergence in genetic markers was associated within some of the lake-stream divergence in morphological traits. Our results suggest that convergent evolution, and deviations from it, are primarily the result of natural selection, which corresponds in only some respect to the dichotomous habitat classifications frequently used in such studies.

opencc-zeroDec 2017View details →

Data from: Phylogeography of African locust bean (Parkia biglobosa) reveals genetic divergence and spatially structured populations in West and Central Africa

The evolutionary history of African savannah tree species is crucial for the management of their genetic resources. In this study, we investigated the phylogeography of Parkia biglobosa and its modelled distribution under past and present climate conditions. This tree species is very valued and widespread in West Africa, providing edible and medicinal products. A large sample of 1 610 individuals from 84 populations, distributed across 12 countries in Western and Central Africa, were genotyped using eight nuclear microsatellites. Individual-based assignments clearly distinguished three genetic clusters, extreme West Africa (EWA), centre of West Africa CWA), and Central Africa (CA). Overall, estimates of genetic diversity were moderate to high, with lower values for populations in EWA (AR=6.4, HE=0.78 and HO=0.7) and CA (AR=5.9, HE=0.67 and HO=0.61) compared to populations in CWA (AR=7.3, HE=0.79 and HO=0.75). The overall population differentiation was found to be moderate (FST=0.09). A highly significant isolation-by-distance pattern was detected, with a marked phylogeographic signature suggesting possible effects of past climate and geographic barriers to migration. Modelling the potential distribution of the species showed a contraction during the last glaciations followed by expansion events. The exploratory Approximate Bayesian Computation conducted suggests a best-supported scenario in which the cluster CWA traced back to the ancestral populations and a first split between EWA and CWA took place about 160 000 years BP, then a second split divided CA and CWA, about 100 000 years BP. However, our genetic data do not enable to conclusively distinguish among a few alternative possible scenarios.

opencc-zeroDec 2015View details →

Data from: Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis)

The evolutionary mechanisms generating the tremendous biodiversity of islands have long fascinated evolutionary biologists. Genetic drift and divergent selection are predicted to be strong on islands and both could drive population divergence and speciation. Alternatively, strong genetic drift may preclude adaptation. We conducted a genomic analysis to test the roles of genetic drift and divergent selection in causing genetic differentiation among populations of the island fox (Urocyon littoralis). This species consists of six subspecies, each of which occupies a different California Channel Island. Analysis of 5293 SNP loci generated using Restriction-site Associated DNA (RAD) sequencing found support for genetic drift as the dominant evolutionary mechanism driving population divergence among island fox populations. In particular, populations had exceptionally low genetic variation, small Ne (range = 2.1–89.7; median = 19.4), and significant genetic signatures of bottlenecks. Moreover, islands with the lowest genetic variation (and, by inference, the strongest historical genetic drift) were most genetically differentiated from mainland grey foxes, and vice versa, indicating genetic drift drives genome-wide divergence. Nonetheless, outlier tests identified 3.6–6.6% of loci as high FST outliers, suggesting that despite strong genetic drift, divergent selection contributes to population divergence. Patterns of similarity among populations based on high FST outliers mirrored patterns based on morphology, providing additional evidence that outliers reflect adaptive divergence. Extremely low genetic variation and small Ne in some island fox populations, particularly on San Nicolas Island, suggest that they may be vulnerable to fixation of deleterious alleles, decreased fitness and reduced adaptive potential.

opennotspecifiedApr 2012View details →

FIGURE 4 in Genetic and shell-shape analyses of Orlitia borneensis (Testudines: Geoemydidae) reveal limited divergence among founders of the European zoo population

FIGURE 4. PCA for plastron shape. Specimens are marked according to haplotype group. A—haplotype group 1, B—group 2, C—group 3, D—haplotype 61, U—unknown. The first axis PC1 explains 29.79% and second axis PC2 explains 14.14% of the total variance in the shapes.

opennotspecifiedApr 2012View details →

FIGURE 3 in Genetic and shell-shape analyses of Orlitia borneensis (Testudines: Geoemydidae) reveal limited divergence among founders of the European zoo population

FIGURE 3. Bayesian skyline plot demonstrating changes in effective population size in Orlitia borneensis based on mitochondrial data. Thick solid line represents median of the estimate, borders of grey area delineate the highest 95% posterior density interval.

opennotspecifiedApr 2012View details →

FIGURE 2 in Genetic and shell-shape analyses of Orlitia borneensis (Testudines: Geoemydidae) reveal limited divergence among founders of the European zoo population

FIGURE 2. Median-joining network indicating relationships among haplotypes of Orlitia borneensis based on cytochrome b sequences. Haplotypes are denoted as circles, their size is proportional to number of individuals carrying respective haplotype. Numbers at branches represent numbers of mutational steps (displayed for n> 1). Three main haplogroups are marked by ovals.

opencc-zeroOct 2021View details →

Microsatellites data set: Correlated population genetic structure in a three-tiered host-parasite system: the potential for coevolution and adaptive divergence

Three subspecies of Northern Bahamian Rock Iguanas, Cyclura cychlura, are currently recognized: C. c. cychlura,restricted to Andros Island, and C. c. figginsi and C. c. inornata, native to the Exuma Island chain. Populations on Andros are genetically distinct from Exuma Island populations, yet genetic divergence among populations in the Exumas is inconsistent with the two currently recognized subspecies from those islands. The potential consequences of this discrepancy might include the recognition of a single subspecies throughout the Exumas rather than two. That inference also ignores evidence that populations of C. cychlura are potentially adaptively divergent. We compared patterns of population relatedness in a three-tiered host-parasite system: C. cychlura iguanas, their ticks (genus Amblyomma, preferentially parasitizing these reptiles), and Rickettsia spp. endosymbionts (within tick ectoparasites). Our results indicate that while C. c. cychlura on Andros is consistently supported as a separate clade, patterns of relatedness among populations of C. c. figginsi and C. c. inornata within the Exuma Island chain are more complex. The distribution of the hosts, different tick species, and Rickettsia spp., supports the evolutionary independence of C. c. inornata. Further, these patterns are also consistent with two independent evolutionarily significant units within C. c. figginsi. Our findings suggest coevolutionary relationships between the reptile hosts, their ectoparasites, and rickettsial organisms, suggesting local adaptation. This work also speaks to the limitations of using neutral molecular markers from a single focal taxon as the sole currency for recognizing evolutionary novelty in populations of endangered species.

Figure 5 in Morphological trends and genetic divergence in anacondas, genus Eunectes Wagler, 1830 (Serpentes: Boidae)

Figure 5. Phylogenetic tree (left) and haplotype network (right) based on the analysis of mitochondrial Cytochrome b sequences. Bayesian inference tree is shown; the nodes with the posterior probability support below 0.5 are shown as unresolved. Above the nodes, posterior probabilities are shown, and bootstrap values inferred from ML analysis with RaxML if exceeding 50. The boxes indicate 95% HPD intervals for the estimated split times. Haplotype/ allele networks: size of the pies are proportional to the number of individuals/ alleles.

Figure 1 in Morphological trends and genetic divergence in anacondas, genus Eunectes Wagler, 1830 (Serpentes: Boidae)

Figure 1. Sampling locations of Eunectes spp. Sampling locations of specimens used for genetic analysis pointed, and the individual sample numbers, indicated in supplementary table S1 and figs 4 and 5 shown in frames. Outlines depict ranges of the Eunectes species, after the IUCN Red List website: green – E. murinus, orange – E. deschauenseei, yellow – E. notaeus, red – E. beniensis.

Figure 4 in Morphological trends and genetic divergence in anacondas, genus Eunectes Wagler, 1830 (Serpentes: Boidae)

Figure 4. Assignment of the 20 individuals in the RAPD dataset to genetic groups using STRUCTURE analyses for K = 3 optimal number of clusters (L(K) = -914.64). Each individual is represented by a column, which is partitioned in K coloured segments that represent the genetically based membership to each species cluster. The labels below indicate the species and specimens labels used in the RAPD (and partly sequencing) analysis.

Figure 3 in Morphological trends and genetic divergence in anacondas, genus Eunectes Wagler, 1830 (Serpentes: Boidae)

Figure 3. Dendrogram (between-group average linkage) based on the squared Euclidean distance between population centroids based on the first two discriminant scores.

Figure 2 in Morphological trends and genetic divergence in anacondas, genus Eunectes Wagler, 1830 (Serpentes: Boidae)

Figure 2. Principal Component analyses based on 23 morphological traits, depicting the separation of E. murinus from the other three species of Eunectes along the first two PCA axes.