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opennotspecifiedNov 2021View details →

Fig. 4 in DNA barcoding in Dorcadionini (Coleoptera, Cerambycidae) uncovers mitochondrial-morphological discordance and the hybridogenic origin of several subspecies

Fig. 4 Comparison between interspecific and intraspecific pairwise genetic distances in Dorcadionini based on the DNA barcode. Distances were calculated once with all sequences from a species included (graphs on left side) or after excluding taxa resulted from introgression and mitochondrial capture (graphs on right side). With introgression removed, the grey area of overlap between intraspecific and interspecific distances decreases, the number of uncertain cases dropping from 16 to 4 (one square represents one mean pairwise distance)

FIGURE 6. T in Molecular phylogenetic and historical biogeographical relationships of Laudakia (Squamata: Agamidae) and intraspecific differentiation of L. stoliczkana inferred from mitochondrial DNA sequences

FIGURE 6. T-test results for morphological indicators. (F = females, M = males, N = northern Xinjiang, S = south Xinjiang)

FIGURE 5 in Molecular phylogenetic and historical biogeographical relationships of Laudakia (Squamata: Agamidae) and intraspecific differentiation of L. stoliczkana inferred from mitochondrial DNA sequences

FIGURE 5. The morphology and tail of Laudakia stoliczkana subspecies. (A & a: L. s. altaica; B & b: L. s. stoliczkana)

FIGURE 4 in Molecular phylogenetic and historical biogeographical relationships of Laudakia (Squamata: Agamidae) and intraspecific differentiation of L. stoliczkana inferred from mitochondrial DNA sequences

FIGURE 4. The estimation of divergence time for Laudakia. (Note: Values are estimated divergence times, and the blue bars are 95% confidence intervals HPD)

FIGURE 3 in Molecular phylogenetic and historical biogeographical relationships of Laudakia (Squamata: Agamidae) and intraspecific differentiation of L. stoliczkana inferred from mitochondrial DNA sequences

FIGURE 3. Bayesian phylogenetic trees of Laudakia species on tandem sequences (CO1 and 16S). (note: the values of nodes near is BPP/BS).

FIGURE 2 in Molecular phylogenetic and historical biogeographical relationships of Laudakia (Squamata: Agamidae) and intraspecific differentiation of L. stoliczkana inferred from mitochondrial DNA sequences

FIGURE 2. Bayesian phylogenetic trees of Laudakia on the sequenced of COI. (note: the values of nodes near is BPP/BS).

FIGURE 1 in Molecular phylogenetic and historical biogeographical relationships of Laudakia (Squamata: Agamidae) and intraspecific differentiation of L. stoliczkana inferred from mitochondrial DNA sequences

FIGURE 1. Bayesian phylogenetic trees of Laudakia on the sequenced of 16S. (note: the values of nodes near is BPP/BS).

FIGURE 9. Antennablennius variopunctatus. A in Mitochondrial DNA-based reassessment of Antennablennius Fowler (Blenniidae: Salariini) from the north-western Indian Ocean, with resurrection of A. persicus (Regan)

FIGURE 9. Antennablennius variopunctatus. A: 42.0 mm SL, Masirah Island, Oman; B: ZMFUM-BLE-0132, 54.0 mm SL, Kish Island, Iran, Persian Gulf. Photos by J.E. Randall (A), S. Estekani (B & C).

FIGURE 8. Antennablennius simonyi. A in Mitochondrial DNA-based reassessment of Antennablennius Fowler (Blenniidae: Salariini) from the north-western Indian Ocean, with resurrection of A. persicus (Regan)

FIGURE 8. Antennablennius simonyi. A: USNM 217360, 44 mm SL, male, Muscat, Oman; B: SMF uncatalogued (tissue sample SOC18-033), 45.0 mm SL, male, Di Hamri, Socotra Island; C: SMF uncatalogued (tissue sample SOC18-025), 29.0 mm SL, female, Di Hamri, Socotra Island. Photos by J.E. Randall (A), S.V. Bogorodsky (B & C).

FIGURE 6. Antennablennius hypenetes, A in Mitochondrial DNA-based reassessment of Antennablennius Fowler (Blenniidae: Salariini) from the north-western Indian Ocean, with resurrection of A. persicus (Regan)

FIGURE 6. Antennablennius hypenetes, A: male, Obhur, Jeddah, Saudi Arabia; B: SMF 35918 (tissue sample 14-585), 35.0 mm SL, female, Obhur, Jeddah, Saudi Arabia; C: SMF 39710 (tissue sample KAU17-129), 45.0 mm SL, male, Farasan Island, Saudi Arabia; D: 40.0 mm SL, Obhur, Jeddah, Saudi Arabia. Photos by S.V. Bogorodsky.

FIGURE 4. A in Mitochondrial DNA-based reassessment of Antennablennius Fowler (Blenniidae: Salariini) from the north-western Indian Ocean, with resurrection of A. persicus (Regan)

FIGURE 4. A: Antennablennius adenensis, BPBM 34470, 35.0 mm SL, Musandam, Oman. Antennablennius aff. adenensis 2, SMF 34097 (tissue sample SOC18-006), 23.2 mm SL, male, Di Hamri, Socotra Island, B: fresh specimen; C: live specimen. Antennablennius aff. adenensis 1, D & E: ZMFUM-BLE-0104, 40.0 mm SL, male, Kish Island, Iran, Persian Gulf; F: ZMFUMBLE-0110, 31.0 mm SL, female, Kish Island, Iran, Persian Gulf. Photos by J.E. Randall (A), S.V. Bogorodsky (B & C), S. Estekani (D–F).

FIGURE 1 in Mitochondrial DNA-based reassessment of Antennablennius Fowler (Blenniidae: Salariini) from the north-western Indian Ocean, with resurrection of A. persicus (Regan)

FIGURE 1. Map of the distributional ranges and sampled localities of phylogenetic lineages identified on the basis of mitochondrial DNA analyses.

FIGURE 2 in Mitochondrial DNA-based reassessment of Antennablennius Fowler (Blenniidae: Salariini) from the north-western Indian Ocean, with resurrection of A. persicus (Regan)

FIGURE 2. Bayesian tree resulting from the data set of COI gene. Posterior probability values of the Bayesian Inference analysis are indicated by asterisk at the> 99% (**) and> 95% (*) significance levels. Numbers on the branch indicate posterior probability values of the Maximum Likelihood analysis (values greater than 50% were shown).

FIGURE 7 in Mitochondrial DNA-based reassessment of Antennablennius Fowler (Blenniidae: Salariini) from the north-western Indian Ocean, with resurrection of A. persicus (Regan)

FIGURE 7. Antennablennius persicus, Chabahar, Iran, Gulf of Oman. A: ZMFUM-BLE-0124, 60.7 mm SL, male; B: ZMFUMBLE-0113, 61.0 mm SL, male; C: ZMFUM-BLE-0122, 56.0 mm SL, female; D: ZMFUM-BLE-0119, 59.0 mm SL, female. Photos by S. Estekani.

FIGURE 3. TCS haplotype network obtained for 521 in Mitochondrial DNA-based reassessment of Antennablennius Fowler (Blenniidae: Salariini) from the north-western Indian Ocean, with resurrection of A. persicus (Regan)

FIGURE 3. TCS haplotype network obtained for 521 bp fragment of mitochondrial COI of the genus Antennablennius. Numbers between haplotypes represent mutational steps between them.

opennotspecifiedNov 2000View details →

Table 2. Genetic distances for mitochondrial DNA partial cytochrome c oxidase subunit I and cytochrome b in Molecular phylogeny of the Aplodactylidae (Perciformes: Cirrhitoidea), a group of Southern Hemisphere marine ® shes

<p>Table 2. Genetic distances for mitochondrial DNA partial cytochrome <i>c</i> oxidase subunit I and cytochrome <i>b</i> sequences when combined. Values are Kimura (1980) two-parameter percentage sequence divergences, obtained when using the optimum expected transition±transversion nucleotide substitution ratio of 3.0 from maximum likelihood analysis (fi gure 3).</p><table><tbody><tr><th></th><th></th><th>1</th><th>2</th><th>3</th><th>4</th><th>5</th><th>6</th><th>7</th></tr></tbody><tbody><tr><th>1</th><td><i>Aplodactylus arctidens</i></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>2</th><td><i>Aplodactylus punctatus</i></td><td>6.1</td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>3</th><td><i>Aplodactylus westralis</i></td><td>7.8</td><td>7.6</td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>4</th><td><i>Aplodactylus etheridgii</i></td><td>10.0</td><td>10.3</td><td>10.0</td><td></td><td></td><td></td><td></td></tr><tr><th>5</th><td><i>Aplodactylus lophodon</i></td><td>11.8</td><td>11.9</td><td>12.4</td><td>11.1</td><td></td><td></td><td></td></tr><tr><th>6</th><td><i>Chironemus marmoratus</i></td><td>20.0</td><td>18.7</td><td>18.3</td><td>19.3</td><td>19.5</td><td></td><td></td></tr><tr><th>7</th><td><i>Cheilodactylus fasciatus</i></td><td>21.8</td><td>21.0</td><td>20.5</td><td>22.6</td><td>20.2</td><td>21.2</td><td></td></tr><tr><th>8</th><td><i>Cirrhitus splendens</i></td><td>22.6</td><td>20.7</td><td>21.0</td><td>23.1</td><td>22.0</td><td>23.1</td><td>22.8</td></tr></tbody></table>

opencc-zeroDec 2010View details →

Data from: Scale-specific sex-biased dispersal in the Valais shrew unveiled by genetic variation on the Y chromosome, autosomes, and mitochondrial DNA

We investigated sex-specificities in the evolutionary processes shaping Y chromosome, autosomes and mitochondrial DNA patterns of genetic structure in the Valais shrew (Sorex antinorii), a mountain dwelling species with a hierarchical distribution. Both hierarchical analyses of variance and isolation-by-distance analyses revealed patterns of population structure that were not consistent across maternal, paternal and bi-parentally inherited markers. Differentiation on a Y microsatellite was lower than expected from the comparison with autosomal microsatellites and mtDNA, and it was mostly due to genetic variance among populations within valleys, while the opposite was observed on other markers. In addition, there was no pattern of isolation-by-distance for the Y, while there was strong isolation-by-distance on mtDNA and autosomes. We use a hierarchical island model of coancestry dynamics to discuss the relative roles of the micro-evolutionary forces that may induce such patterns. We conclude that sex-biased dispersal is the most important driver of the observed genetic structure, but with an intriguing twist: it seems that dispersal is strongly male-biased at large spatial scale, while it is mildly biased in favour of females at local scale. These results add to recent reports of scale-specific sex-biased dispersal patterns, and emphasize the usefulness of the Y chromosome in conjunction with mtDNA and autosomes to infer sex-specificities.

opencc-zeroDec 2013View details →

Data from: Population genetic structure and demographic history of Atrina pectinata based on mitochondrial DNA and microsatellite markers

The pen shell, Atrina pectinata, is one of the commercial bivalves in East Asia and thought to be recently affected by anthropogenic pressure (habitat destruction and/or fishing pressure). Information on its population genetic structure is crucial for the conservation of A. pectinata. Considering its long pelagic larval duration and iteroparity with high fecundity, the genetic structure for A. pectinata could be expected to be weak at a fine scale. However, the unusual oceanography in the coasts of China and Korea suggests potential for restricted dispersal of pelagic larvae and geographical differentiation. In addition, environmental changes associated with Pleistocene sea level fluctuations on the East China Sea continental shelf may also have strongly influenced historical population demography and genetic diversity of marine organisms. Here, partial sequences of the mitochondrial Cytochrome c oxidase subunit I (COI) gene and seven microsatellite loci were used to estimate population genetic structure and demographic history of seven samples from Northern China coast and one sample from North Korea coast. Despite high levels of genetic diversity within samples, there was no genetic differentiation among samples from Northern China coast and low but significant genetic differentiation between some of the Chinese samples and the North Korean sample. A late Pleistocene population expansion, probably after the Last Glacial Maximum, was also demonstrated for A. pectinata samples. No recent genetic bottleneck was detected in any of the eight samples. We concluded that both historical recolonization (through population range expansion and demographic expansion in the late Pleistocene) and current gene flow (through larval dispersal) were responsible for the weak level of genetic structure detected in A. pectinata.

opencc-zeroJul 2019View details →

Data from: Integrating three comprehensive datasets shows that mitochondrial DNA variation is linked to species traits and paleogeographic events in European butterflies.

Understanding the dynamics of biodiversity, including the spatial distribution of genetic diversity, is critical for predicting responses to environmental changes, as well as for effective conservation measures. This task requires tracking changes in biodiversity at large spatial scales and correlating with species functional traits. We provide three comprehensive resources to understand the determinants for mitochondrial DNA differentiation represented by i) 15,609 COI sequences and ii) 14 traits belonging to 307 butterfly species occurring in Western-Central Europe and iii) the first multi-locus phylogenetic tree of all European butterfly species. By applying phylogenetic regressions we show that mitochondrial DNA spatial differentiation (as measured with Gst, G'st, D and Dst) is negatively correlated with species traits determining dispersal capability and colonization ability. Thanks to the high spatial resolution of the COI data, we also provide the first zoogeographic regionalization maps based on intraspecific genetic variation. The overall pattern obtained by averaging the spatial differentiation of all Western-Central European butterflies shows that the paradigm of long-term glacial isolation followed by rapid pulses of post-glacial expansion has been a pervasive phenomenon in European butterflies. The results and the extensive datasets we provide here constitute the basis for genetically-informed conservation plans for a charismatic group in a continent where flying insects are under alarming decline.