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263 results for “mitochondrial genetics”
FIGURE 28. A–O in Mitochondrial genetics of Ophiderini, with a new species from the Eudocima phalonia species group (Lepidoptera: Noctuidae: Calpinae)
FIGURE 28. A–O: Eudocima phalonia group and Calpini adults (dorsal aspect); P: Page 41, Plate 310, Figure A from Cramer (1782); Q: Page 58, Plate 12, Figure 11 from Stoll (1790).
Population genetics of Paramecium mitochondrial genomes; genome assemblies and annotation files
<p>Because of issues arising during submission to GenBank of Paramecium mitochondrial genomes due to the highly unconventional nature of the genetic code used in these genomes, we are initially making the genomes publicly available here (while we are still working on a submission to official databases).</p>
FIGURE 2 in High genetic variation within mitochondrial CO1 in Middle European Thanasimus formicarius (Linné, 1758) (Coleoptera: Cleridae)
FIGURE 2. Distribution of all Thanasimus clades in Europe. The light green areas are based on GBIF distributional data [https://www.gbif.org/] of both species.
Fig. 2 Mitochondrial haplotype network using the 590 in Differentiation of North African foxes and population genetic dynamics in the desert-insights into the evolutionary history of two sister taxa, Vulpes rueppellii and Vulpes vulpes
Fig. 2 Mitochondrial haplotype network using the 590-bp concatenated sequences from Cyt-b and D-loop and a total of 46 sequences (same as in Fig. 1, except for C. lupus not being used as an outgroup in the TCS network). a Neighbour-Net network based on uncorrected patristic distances as implemented in SPLITSTREE. Canis lupus (DQ480504) was used as an outgroup. Numbers indicate bootstrap values. Scale bar represents 0.01 sequence divergence. Highlighoed are the four species, the three V. vulpes clades and the location within the network of the V. vulpes sample from Egypt. Colour patterns are concordant with Fig. 1 and b. b Statistical parsimony network assuming a 95 % parsimony threshold, as constructed by TCS. Symbol size and branch lengths are proportional to the number of shared individuals per haplotype and the number of mutational steps amongst haplotypes, respectively. Numbers in black background also refer to the number of mutation steps between species and V. vulpes clades. Symbols and colours are concordant with Fig. 1 and a. Haplotype codes, sample origin and corresponding accession numbers are available in Online Resource Table S1
Fig. 2 Minimum-spanning network among 44 in Mitochondrial evidence for genetic diversity and low phylogeographic differentiation in the Marsh Warbler Acrocephalus palustris (Aves: Acrocephalidae)
Fig. 2 Minimum-spanning network among 44 COI haplotypes of Marsh Warbler (see Table S2). Size of circles represents the relative frequency of given haplotypes and each line between black nodes indicates a single mutational step
Fig. 3 in Mitochondrial evidence for genetic diversity and low phylogeographic differentiation in the Marsh Warbler Acrocephalus palustris (Aves: Acrocephalidae)
Fig. 3 Left: Mismatch distribution. Expected (solid line) and observed (broken line) mismatch distribution under population expansion model. Right: Bayesian skyline plot representing the historical demographic
Figure 3 in Mitochondrial genetic variation in long-eared hedgehogs, Hemiechinus auritus, from the Anatolian Peninsula and Cyprus
Figure 3: Median-joining network constructed using cyt-b sequences of Hemiechinus auritus. The size of each circle is proportional to the frequency of the haplotype in the sample. Median vectors are indicated by blank circles. Each mutation between haplotypes is represented by a bar. For the geographical origins of the sequences, see Figure 1, Table 1 and Supplementary Table S1.
Figure 2 in Mitochondrial genetic variation in long-eared hedgehogs, Hemiechinus auritus, from the Anatolian Peninsula and Cyprus
Figure 2: Results of MP, ML and BI analyses combined on an ML tree based on cyt-b sequences of Hemiechinus auritus. Numbers at nodes indicate bootstrap support values (MP and ML)/posterior probabilities (BI). Bootstrap values ≥ 90 % and Bayesian posterior probabilities ≥0.90 are shown. For the geographical origins of the sequences, see Figure 1, Table 1 and Supplementary Table S1.
Figure 1 in Mitochondrial genetic variation in long-eared hedgehogs, Hemiechinus auritus, from the Anatolian Peninsula and Cyprus
Figure 1: Map showing the distribution range of the five main geographical lineages (I.–V. MGL) we discussed based on cyt-b data. It shows the match of the mitochondrial genetic structuring with named sub-species that have previously been described. Location numbers on the map for Hemiechinus auritus samples sequenced for the present study are listed in Table 1. For the geographical origins of the published sequences, see Supplementary Table S1.
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>
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.
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.
How long is 3 kilometres for a butterfly? Ecological constraints and functional traits explain high mitochondrial genetic diversity between Sicily and the Italian Peninsula
<p>1. Populations inhabiting Mediterranean islands often show contrasting genetic lineages, even on islands that were connected to the mainland during glacial maxima. This pattern is generated by forces acting in historical and contemporary times. Understanding these phenomena requires comparative studies relating genetic structure, functional traits and dispersal constraints.</p> <p>2. Using as a model the butterfly species living across the Messina strait separating Sicily from the Italian Peninsula (3 km wide), we aimed to unravel the mechanisms limiting the dispersal of matrilines across a narrow sea strait and producing genetic differentiation. </p> <p>3. We analysed the mitochondrial COI gene of 84 butterfly species out of 90 documented in Sicily and compared them with populations from the neighbouring southern Italian Peninsula (1398 sequences) and from the entire Palearctic region (8093 sequences). For each species, we regressed 13 functional traits and two ecological constraints to dispersal (winds experienced at the strait and climatic suitability) against genetic differentiation between Sicily and Italian Peninsula to understand the factors limiting dispersal.</p> <p>4. More than a third of the species showed different haplogroups across the strait and most of them also represented endemic haplogroups for this island. One fifth of Sicilian populations (and 32.3% of endemic lineages) had their closest relatives in distant areas, instead of the neighbouring Italian Peninsula, which suggests high relictuality. Haplotype diversity was significantly explained by length of the flight period, an intrinsic phenology trait, while genetic differentiation was explained by both intrinsic traits (wingspan and degree of generalism) and contemporary local constraints (winds experienced at the strait and climatic suitability).</p> <p>5. A relatively narrow sea strait can produce considerable differentiation among butterfly matrilines and this phenomenon showed a largely deterministic fingerprint. Because of unfavourable winds, populations of the less dispersive Sicilian butterflies tended to differentiate into endemic variants or to maintain relict populations. Understanding these phenomena required the integration of DNA sequences, species traits and physical constraints for a large taxon at continental scale. Future studies may reveal if the patterns here shown for mitochondrial DNA are also reflected in the nuclear genome or, alternatively, are the product of limited female dispersal.</p>
Data from: Mitochondrial genetic structure and matrilineal origin of white sharks, Carcharodon carcharias, in the Northeastern Pacific: implications for their conservation
White sharks (Carcharodon carcharias, WS henceforth) are globally and regionally threatened. Understanding their patterns of abundance and connectivity, as they relate to habitat use, is central for delineating conservation units and identifying priority areas for conservation. We analyzed mitochondrial data to test the congruence between patterns of genetic connectivity and of individual movements in the Northeastern Pacific (NEP) and to trace the matrilineal origin of immature WS from coastal California and Baja California to adult aggregation areas. We analyzed 186 mitochondrial control region sequences from sharks sampled in Central California (CC; n = 61), Southern California Bight (SCB; n = 25), Baja California Pacific coast (BCPC; n = 9), Bahía Vizcaíno (BV; n = 39), Guadalupe Island (GI; n = 45), and the Gulf of California (GC; n = 7). Significant mitochondrial differentiation between adult aggregation areas (CC, GI) revealed two reproductive populations in the NEP. We found general concordance between movement patterns of young and adult WS with genetic results. Young sharks from coastal California and Baja California were more likely born from females from GI. Mitochondrial differentiation of young-of-the-year from SCB and BV suggests philopatry to nursery areas in females from GI. These results provide a genetic basis of female reproductive behavior at a regional scale and point to a preponderance of sharks from GI in the use of the sampled coastal region as pupping habitat. These findings should be considered in Mexican and US management and conservation strategies of the WS NEP population.
Figure 3 in Mitochondrial genetic variation within and between Holbrookia lacerata lacerata and Holbrookia lacerata subcaudalis, the spot-tailed earless lizards of Texas
Figure 3. Hind limb blotches of (a) Holbrookia lacerata lacerata (UTA R 63333) and (b) H. l. subcaudalis (UTA R 63303). In H. l. lacerata, most blotches are oblong and fused into bands. In H. l. subcaudalis, blotches are ellipsoid.
Figure 2 in Mitochondrial genetic variation within and between Holbrookia lacerata lacerata and Holbrookia lacerata subcaudalis, the spot-tailed earless lizards of Texas
Figure 2. Bayesian phylogeny of whole mitochondrial genomes from Holbrookia lacerata lacerata and H. l. subcaudalis, with H. maculata and H. propinqua as outgroup taxa. Numerical values are Bayesian posterior probabilities; all other nodes represent values> 0.95. The scale bar represents percent genetic divergence.
Figure 1 in Mitochondrial genetic variation within and between Holbrookia lacerata lacerata and Holbrookia lacerata subcaudalis, the spot-tailed earless lizards of Texas
Figure 1. Sampling map of the focal taxa (Holbrookia lacerata lacerata and H. l. subcaudalis) and outgroup taxa (H. maculata and H. propinqua). The sampling ranges for the nominal taxa are representative of their current distributions. The historical distribution of H. lacerata is represented by the dotted line, while the Balcones Fault/Escarpment, the natural biogeographic barrier between the two subspecies, is represented by the solid black line.
Figure 2 in Complete mitochondrial genome of Tetraophasis szechenyii Madarász, 1885 (Aves: Galliformes: Phasianidae), and its genetic variation as inferred from the mitochondrial DNA Control Region
Figure 2. Median-joining network of all the control region haplotypes found in Tetraophasis szechenyii. Notes: Missing haplotypes in the network are represented by black dots; circle sizes are proportional to the number of individuals sharing the same haplotypes (n); each mutation step is shown as a short line connecting neighbouring haplotypes; numbers of mutations between haplotypes are indicated near branches if greater than 1.
Figure 1 in Complete mitochondrial genome of Tetraophasis szechenyii Madarász, 1885 (Aves: Galliformes: Phasianidae), and its genetic variation as inferred from the mitochondrial DNA Control Region
Figure 1. Molecular phylogenetic tree derived from the complete DNA sequences of 12 mitochondrial protein-coding genes using Bayesian inference and maximum likelihood analyses. Notes:The numbers beside the nodes are Bayesian posterior probabilities (≥ 0.9 retained) and bootstrap proportions of maximum likelihood analyses calculated with 100 replicates (≥ 50% retained); Anas platyrhynchos and Alectura lathami were set as outgroups; *clades not supported by Bayesian inference.
Figure 3. Ninety-five per cent maximum parsimony networks obtained for the 12 in Mitochondrial DNA genetic variation and phylogeography of the recently described vole species Proedromys liangshanensis Liu, Sun, Zeng and Zhao, 2007 (Rodentia: Arvicolinae)
Figure 3. Ninety-five per cent maximum parsimony networks obtained for the 12 haplotypes in Proedromys liangshanensis. Circle sizes are proportional to haplotype frequencies.
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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