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140 results for “mitochondrial diversity”
Data from: Population structure of riverine and coastal dolphins Sotalia fluviatilis and Sotalia guianensis: PATTERNS of nuclear and mitochondrial diversity AND implications for conservation
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Data from: Congruent signals of population history but radically different patterns of genetic diversity between mitochondrial and nuclear markers in a mountain lizard
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Data from: Shotgun mitogenomics across body size classes in a local assemblage of tropical Diptera: phylogeny, species diversity and mitochondrial abundance spectrum
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Fig. 4. Mismatch distribution for mitochondrial haplotypes for 92 in Genetic diversity and population structure of Brycon nattereri (Characiformes: Bryconidae): a Neotropical fish under threat of extinction
Fig. 4. Mismatch distribution for mitochondrial haplotypes for 92 individuals of Brycon nattereri from the Laranjinha River.
A combined approach of mitochondrial DNA and anchored nuclear phylogenomics sheds light on unrecognized diversity, phylogeny, and historical biogeography of the cascade frogs, genus Amolops (Anura: Ranidae)
<p><i>Amolops</i> is one of the most species-rich genera in Ranidae, with 59 recognized species. This genus currently includes six species groups diagnosed mainly by morphology. Several recent molecular studies indicated that the classification of species groups within <i>Amolops</i> remains controversial, and key nodes in the phylogeny have been inadequately resolved. In addition, the diversity of cascade frogs remains poorly understood, especially for those from incompletely sampled regions. Herein, we investigate the species-level diversity within genus <i>Amolops</i> throughout southern China and Southeast Asia, and infer evolutionary relationships among the species using mtDNA data (16S, <i>COI</i>, and <i>ND2</i>). Molecular analyses indicate nine new unnamed species, mostly distributed in the Himalayas. We then utilized anchored hybrid enrichment to generate a dataset representing major mitochondrial lineages to resolve phylogenetic relationships, biogeography, and pattern of species diversification. Our resulting phylogeny strongly supports the monophyly of three previously identified species groups (the <i>A. ricketti</i>, <i>A. daiyunensis</i>,<i> </i>and <i>A. hainanensis</i> groups), the paraphyly of the <i>A. mantzorum</i> and <i>A. marmoratus</i> groups, as previously defined, and monophyly of the <i>A. monticola</i> group. We erect one new species group, the <i>A. viridimaculatus</i> group, and recognize Dubois (1992) 'subgenus' <i>Amo</i> as the <i>A. larutensis</i> species group. Biogeographic analysis suggests that <i>Amolops</i> originated on the Indo-Burma/Tai-Malay Peninsula at the Eocene/Oligocene boundary, and dispersed outward, exemplifying a common pattern observed for the origin of Asia's biodiversity. The early divergence within <i>Amolops</i> coincides with the Himalayas uplift, and the lateral extrusion of Indochina at the Oligocene/Miocene boundary. Our results show that paleoclimatic and geomorphological events have profoundly influenced the pattern of lineage diversification within <i>Amolops</i>.</p>
Data from: Tracking the origins of fly invasions; using mitochondrial haplotype diversity to identify potential source populations in two genetically intertwined fruit fly species (Bactrocera carambolae and Bactrocera dorsalis [Diptera: Tephritidae])
Bactrocera carambolae Drew and Hancock and B. dorsalis (Hendel) (Diptera: Tephritidae) are important pests of many fruits. These flies have been spread across the world through global travel and trade, and new areas are are at risk of invasion. Whenever new invasive populations are discovered, quick and accurate identification is needed to mitigate the damage they can cause. Determining invasive pathways can prevent further spread of pests as well as subsequent reinvasions through the same pathway. Molecular markers can be used for both species identification and pathway analysis. We analyzed 1601 individuals from 18 populations using 765 base pairs of the mitochondrial cytochrome oxidase I (COI) gene to infer the haplotype diversity and population structure within these flies from across their native and invasive ranges. We analyzed these samples by either grouping by species or geographic populations due to the genetic similarity in the mitochondrial genome. We found no genetic structure between B. dorsalis and B. carambolae and our findings suggest recent and most likely ongoing, genetic exchange between these two species in the wild. Hyper-diverse mitochondrial genetic diversity in the native range suggests large population sizes and relatively high mutation rates. Only 52% of the haplotypes found in the trap captures from California are shared with haplotypes from flies found in our global survey, indicating significant genetic diversity in the native range that is missing from our samples. However, these results provide a foundation for the accurate determination of the provenance of invasive populations around the world.
Data from: Elevated genetic diversity of mitochondrial genes in asexual populations of bark lice ("Psocoptera": Echmepteryx hageni)
Asexual reproduction is commonly thought to be associated with low genetic diversity in animals. Echmepteryx hageni (Insecta: "Psocoptera") is one of several psocopteran species that are primarily parthenogenetic, but also exists in small, isolated sexual populations. We used mitochondrial DNA sequences to investigate the population history and genealogical relationships between the sexual and asexual forms of this species. The asexual population of E. hageni exhibits extremely high mitochondrial haplotype diversity (H = 0.98), whereas the sexual forms had significantly lower haplotypic diversity (H = 0.25, after correcting for sample size). This diversity in asexuals represents one the greatest genetic diversities reported for asexual animals in the literature. Nucleotide diversities were also higher in asexual compared to sexual populations (π = 0.0071 vs. 0.00027). Compared to other reported estimates of π in insects, asexual nucleotide diversity is high, but not remarkably elevated. Three hypotheses might explain the elevated genetic diversity of asexual populations: 1) larger effective population size, 2) greater mutation rate, or 3) possible recent origin of sexuals. In addition, phylogeographic analysis revealed little geographic structure among asexual E. hageni, although specimens from the upper Midwest form a single clade and are genetically differentiated. The mismatch distribution and neutrality tests indicate a historical population size increase, possibly associated with expansion from glacial refugia.
Figures 2–3. Mitochondrial cytochrome c oxidase subunit 1 in Molecular confirmation of the occurrence of Anguilla interioris (Actinopterygii: Anguilliformes) in North Maluku of Indonesia and mitochondrial DNA haplotype diversity among existing specimens
Figures 2–3. Mitochondrial cytochrome c oxidase subunit 1 (CO1) 551 bp sequence analyses. (2) Phylogenetic analysis based on maximum likelihood algorithm with the sample codes, GenBank or BOLD accession numbers and sample sites shown. Bootstrap percentages are shown at the tree nodes. (3) Haplotype network with the haplotypes labelled as H1 to H9. The circle size is proportional to the number of samples, and different sample sites are represented by different colours. Small white circle represents median vector which is the hypothesized or missing haplotype. Each dash on the line symbolizes one mutational step.
Figure 3. a in Mitochondrial genetic diversity and structuring of northern white-breasted hedgehogs from the Central Balkans
Figure 3. a) Median-joining network of the mtDNA control region haplotypes of E. roumanicus and E. concolor. Circle sizes are proportional to haplotype frequencies, while circle colors correspond to defined regions as shown in the legend. Each branch represents one mutational step; if more than one mutation step is present, it is denoted by the numbers. The MJ network is presented as the shortest tree, while lost connections between haplotypes after MP processing are shown with dashed lines. Black circles represent median vectors (unsampled or ancestral haplotypes). b) Bayesian phylogenetic tree showing relationships among 30 haplotypes of E. roumanicus and E. concolor. The trees were rooted using E. europaeus as an out-group. Haplotype names correspond to those given in Table 1 and Table S1.
Figure 2 in Inferring phylogenetic relationships in the common vole (Microtus arvalis) based on mitochondrial and nuclear sequence diversities
Figure 2. Median-joining network obtained from CYTB haplotypes of Anatolian, Asian and European populations of M. arvalis. Number of mutations are shown by black lines on the branches.
Figure 3 in Mitochondrial DNA diversity and taxa delineation in the land snails of the Iberus gualtieranus (Pulmonata, Helicidae) complex
Figure 3. Relationships between the number of substitutions [Δ, transversion (Tv); ¥, transition (Ts)] and genetic distance (K80 distance) in the cytochrome oxidase subunit I (COI) fragment. A, considering the first, second, and third positions. B, considering the third position only.
Figure 2. A in Mitochondrial DNA diversity and taxa delineation in the land snails of the Iberus gualtieranus (Pulmonata, Helicidae) complex
Figure 2. A, collection sites of the specimens used in this study. B, detail of the south-eastern Iberian Peninsula localities (AL, Almería; GR, Granada; JA, Jaén; MU, Murcia). For abbreviations, see the legend to Figure 4.
Figure 3 from: Lukhtanov VA, Novikova AV (2015) Interpretation of mitochondrial diversity in terms of taxonomy: a case study of Hyponephele lycaon species complex in Israel (Lepidoptera, Nymphalidae, Satyrinae). ZooKeys 538: 21-34. https://doi.org/10.3897/zookeys.538.6689
Figure 3 - Wing pattern in haplogroup I and II samples from Mt Hermon, Israel. The pictures were taken using diffused daylight a sample CCDB-17969_A02, upperside b sample CCDB-17969_A02, underside c sample CCDB-17969_A09, upperside d sample CCDB-17969_A09, underside.
Figure 1 from: Lukhtanov VA, Novikova AV (2015) Interpretation of mitochondrial diversity in terms of taxonomy: a case study of Hyponephele lycaon species complex in Israel (Lepidoptera, Nymphalidae, Satyrinae). ZooKeys 538: 21-34. https://doi.org/10.3897/zookeys.538.6689
Figure 1 - The Bayesian tree of the Hyponephele lycaon species complex based on analysis of COI DNA barcodes. Numbers at nodes indicate Bayesian posterior probability values. Sympatric haplogroups I and II from Israel are highlighted. Scale bar = 0.2 substitutions per position.
Figure 5 from: Lukhtanov VA, Novikova AV (2015) Interpretation of mitochondrial diversity in terms of taxonomy: a case study of Hyponephele lycaon species complex in Israel (Lepidoptera, Nymphalidae, Satyrinae). ZooKeys 538: 21-34. https://doi.org/10.3897/zookeys.538.6689
Figure 5 - Typical male genitalia in haplogroups I (a, b) and II (c, d) from Mt Hermon, Israel. Lateral view. Brachia are indicated by arrow a specimen CCDB-17969_A10 b specimen CCDB-17969_A01 c specimen CCDB-17968_D10 d specimen CCDB-17968_D09.
Figure 4 from: Lukhtanov VA, Novikova AV (2015) Interpretation of mitochondrial diversity in terms of taxonomy: a case study of Hyponephele lycaon species complex in Israel (Lepidoptera, Nymphalidae, Satyrinae). ZooKeys 538: 21-34. https://doi.org/10.3897/zookeys.538.6689
Figure 4 - Pattern of the wing underside in haplogroups I and II samples. The pictures were taken using a flash a CCDB-17969_A01 b CCDB-17969_A02 c CCDB-17969_A03 d CCDB-17969_A06 e CCDB-17969_A10 f CCDB-17969_A05 g CCDB-17968_C11 h CCDB-17968_D09 i CCDB-17968_G01 j CCDB-17969_A07 k CCDB-17969_A08 l CCDB-17969_A09 m CCDB-17968_C11.
Figure 6 from: Shapoval NA, Lukhtanov VA (2015) Taxonomic interpretation of chromosomal and mitochondrial DNA variability in the species complex close to Polyommatus (Agrodiaetus) dama (Lepidoptera, Lycaenidae). In: Lukhtanov VA, Kuznetsova VG, Grozeva S, Golub NV (Eds) Genetic and cytogenetic structure of biological diversity in insects. ZooKeys 538: 1-20. https://doi.org/10.3897/zookeys.538.6559
Figure 6 - Underside and upperside of the Polyommatus (Agrodiaetus) karindus saravandi ssp. n. wings. A upperside (left) and underside (right) of the male wings B upperside (left) and underside (right) of the female wings.
Figure 4 from: Shapoval NA, Lukhtanov VA (2015) Taxonomic interpretation of chromosomal and mitochondrial DNA variability in the species complex close to Polyommatus (Agrodiaetus) dama (Lepidoptera, Lycaenidae). In: Lukhtanov VA, Kuznetsova VG, Grozeva S, Golub NV (Eds) Genetic and cytogenetic structure of biological diversity in insects. ZooKeys 538: 1-20. https://doi.org/10.3897/zookeys.538.6559
Figure 4 - COI Haplotype analysis. A geographical distribution of haplogroups. Number of studied individuals sharing the same haplogroup is given in parentheses B most parsimonious COI haplotype network; h01–h12 are COI haplotypes; GH1–GH5 are COI haplogroups. Number of studied individuals sharing the same haplotype is given in parentheses.
Figure 5 from: Shapoval NA, Lukhtanov VA (2015) Taxonomic interpretation of chromosomal and mitochondrial DNA variability in the species complex close to Polyommatus (Agrodiaetus) dama (Lepidoptera, Lycaenidae). In: Lukhtanov VA, Kuznetsova VG, Grozeva S, Golub NV (Eds) Genetic and cytogenetic structure of biological diversity in insects. ZooKeys 538: 1-20. https://doi.org/10.3897/zookeys.538.6559
Figure 5 - Holotype of Polyommatus (Agrodiaetus) karindus saravandi, sample W064. Upperside (left) and underside (right) of the male wings.
Figure 3 from: Shapoval NA, Lukhtanov VA (2015) Taxonomic interpretation of chromosomal and mitochondrial DNA variability in the species complex close to Polyommatus (Agrodiaetus) dama (Lepidoptera, Lycaenidae). In: Lukhtanov VA, Kuznetsova VG, Grozeva S, Golub NV (Eds) Genetic and cytogenetic structure of biological diversity in insects. ZooKeys 538: 1-20. https://doi.org/10.3897/zookeys.538.6559
Figure 3 - The Bayesian tree of Polyommatus (Agrodiaetus) dama and Polyommatus (Agrodiaetus) karindus based on analysis of the cytochrome c oxidase subunit I gene from 57 specimens. Numbers at nodes indicate Bayesian posterior probability. Agrodiaetus karindus karindus and Agrodiaetus karindus saravandi clusters highlighted in pink and blue respectively.
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