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140 results for “mitochondrial diversity”
FIGURE 1 in Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae)
FIGURE 1. Maximum likelihood mitochondrial phylogeny of the Naja melanoleuca complex. Node support values indicate % bootstrap support; support values for the most distal nodes not shown. Country abbreviations: CAR = Central African Republic, DRC = Democratic Republic of Congo, KZN = KwaZulu-Natal Province, South Africa, RoC = Republic of Congo. Mitochondrial candidate species (CS) are shown in the same colours as in Figures 2–4. For specimen information see Appendix 1.
FIGURE 5 in Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae)
FIGURE 5. Naja (Boulengerina) guineensis sp. nov. Left and top right: holotype, MNHN 1921.0485, dorsal and ventral view and side view of head. Note extensive mottling of throat and anterior ventral side and limited posterior extent of lighter ventral markings. Bottom right: live adult specimen measuring approximately 200 cm total length, from Sekondi-Takoradi, Western Region, Ghana, displaying dark suffusion of throat and anterior venter (not preserved; photo L. Chirio).
FIGURE 4 in Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae)
FIGURE 4. Ordination of individual specimens and OTU centroids of four of the mitochondrially defined candidate species of the N. melanoleuca complex along the first two canonical variates. CS5-peroescobari was omitted due to the small available sample size. Canonical variates 1 and 2 account for 57.9 and 22.8% of total variance, respectively. Enlarged symbols indicate OTU centroids.
FIGURE 3 in Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae)
FIGURE 3. Ordination of individual specimens in a Principal Coordinates Analysis of standardised multilocus distances of PRLR and UBN1 scnDNA sequence data. (a) All specimens; (b) Analysis repeated under exclusion of CS2 and CS3.
FIGURE 8 in Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae)
FIGURE 8. Naja (Boulengerina) melanoleuca. Adult specimens from Yaoundé, Cameroon (left—photo J.-F. Trape) and Tsibilé, Gabon (right—photo L. Chirio). Note the diffuse but distinct hood mark that is often present in this species, and the combination of broad main bands and narrow accessory bands on the ventral side.
FIGURE 9 in Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae)
FIGURE 9. Naja (Boulengerina) subfulva. Variation in colour and pattern. Top left: specimen from Kakamega, western Kenya, illustrating the typically deep black and white specimens with strong facial markings from the periphery of Lake Victoria. Bottom left: specimen from Chuka, Mount Kenya, Kenya, illustrating an extreme of the brown forebody and reduced facial pigmentation typical of the species in much of its range. Photos W. Wüster, courtesy Royjan Taylor / Bio-Ken snake farm live collection, Watamu, Kenya. Right: specimen from Bamenda, Cameroon, representing the form described by Stucki-Stirn (1979) as Naja melanoleuca aurata. Note the indistinct ventral bands and the lack of accessory ventral bands, as is typical of this species. Photo J.-F. Trape.
FIGURE 7 in Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae)
FIGURE 7. Naja (Boulengerina) savannula sp. nov. Top row and bottom left: holotype, MNHN 2018.0002. Bottom right: live specimen from Kindia, Guinea, showing conspicuous, broad dorsal bands and ventral banding, including narrow accessory bands (not vouchered). Photos J.-F. Trape.
FIGURE 2 in Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae)
FIGURE 2. Haplotype networks for single copy nuclear loci. (a) PRLR; (b) UBN1. Small black circles indicate unsampled haplotypes.
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
Fig. 3 in Spatial pattern of intraspecific mitochondrial diversity in the Northern Carpathian endemic spring snail, Bythinella pannonica (Frauenfeld, 1865) (Gastropoda: Hydrobiidae)
Fig. 3 Bythinella pannonica COI haplotype network. Circles Haplotypes occurring in the Karst (white) and in the Bükk Mts. (black). Circle sizes are proportional to the frequencies of the haplotypes. Haplotypes were nested into hierarchical clades following the rules of Templeton et al. (1987) and Templeton and Sing (1993). The two main clades, which could not be connected at the 95 % confidence level, are considered as distinct 4-step clades. For reasons of simplicity, only 2nd and higher step clades are indicated here. See Table 4 for phylogeographic inferences
Fig. 2 in Spatial pattern of intraspecific mitochondrial diversity in the Northern Carpathian endemic spring snail, Bythinella pannonica (Frauenfeld, 1865) (Gastropoda: Hydrobiidae)
Fig. 2 Constrained Bayesian tree of Bythinella pannonica mitochondrial cytochrome c oxidase subunit I gene (COI) haplotypes. The tree was rooted by Bythinella austriaca (FJ028978) (not illustrated). Numbers at branches are Bayesian posterior probabilities. For reasons of comparability, 2nd and higher step clades, defined by nested clade analysis, are indicated. Posterior probabilities above 95 % are given only for 2nd and higher step clades (see Fig. 3 for nested clade structure). Note that clade 2–7 is inferred to be paraphyletic by this analysis. This tree has been deposited in the TreeBase (http://purl.org/ phylo/treebase/phylows/study/ TB2:S10789)
Fig. 4 in Spatial pattern of intraspecific mitochondrial diversity in the Northern Carpathian endemic spring snail, Bythinella pannonica (Frauenfeld, 1865) (Gastropoda: Hydrobiidae)
Fig. 4 Mismatch frequency distributions of pairwise mutational differences for different datasets of Bythinella pannonica samples. a Whole dataset, b clade-A (see Figs. 2 and 3) c Clade-B d Subset of Clade-A sampled in the Karst, e Subset of Clade-A sampled in the Bükk Mts. Thick solid lines Observed frequency of pairwise differences, dashed lines expected distribution under the sudden expansion model, thin lines lower and upper bounds of the 95 % confidence interval
Fig. 1 in Spatial pattern of intraspecific mitochondrial diversity in the Northern Carpathian endemic spring snail, Bythinella pannonica (Frauenfeld, 1865) (Gastropoda: Hydrobiidae)
Fig. 1 Relief map of the northeastern part of the Carpathian Basin showing collection sites and the geographic distribution of intraspecific clades [at the level at which significant phylogenetic structure was found by nested clade phylogeographic analysis (NCPA)]. Clade names correspond to those in Figs. 2 and 3. More precise locality data are given in Table 1. Thick solid line Political border between Hungary and Slovakia
Fig. 2 in Pauesia species (Hymenoptera: Braconidae: Aphidiinae) attacking Eulachnini aphids (Hemiptera: Aphididae: Lachninae) on coniferous plants in Lithuania: ecological and mitochondrial COI diversity
Fig. 2 Haplotype networks of Pauesia species attacking Eulachnini aphids in Lithuania based on partial COI fragment
Data from: Population structure of riverine and coastal dolphins Sotalia fluviatilis and Sotalia guianensis: PATTERNS of nuclear and mitochondrial diversity AND implications for conservation
Coastal and freshwater cetaceans are particularly vulnerable due to their proximity to human activity, localized distributions and small home ranges. These species include Sotalia guianensis, found in the Atlantic and Caribbean coastal areas of central and South America, and Sotalia fluviatilis, distributed in the Amazon River and tributaries. We investigated the population structure and genetic diversity of these two species by analyses of mtDNA control region and 8-10 microsatellite loci. MtDNA analyses revealed strong regional structuring for S. guianensis (i.e. Colombian Caribbean vs. Brazilian Coast, FST= 0.807, ΦST = 0.878, P <0.001) especially north and south of the Amazon River mouth. For S. fluviatilis, population structuring was detected between the western and eastern Amazon (i.e. Colombian Amazon vs. Brazilian Amazon, FST= 0.085, ΦST = 0.277, P <0.001). Haplotype and nucleotide diversity were higher for S. fluviatilis. Population differentiation was supported by analysis of the microsatellite loci (S. guianensis, northern South America vs. southern South America FST= 0.275, Jost´s D = 0.476, P<0.001; S. fluviatilis, western and eastern Amazon FST= 0.197, Jost´s D = 0.364, P<0.001). Most estimated migration rates in both species overlapped with zero, suggesting no measurable migration between most of the sampling locations. However, for S. guianensis, there was measurable migration in neighboring sampling locations. These results indicate that the small home ranges of these species may act to restrict gene flow between populations separated by relatively short distances, increasing the risk of extirpation of some localized populations in the future if existing threats are not minimized.
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>
Figure 5. Maximum likelihood trees constructed from mitochondrial cytochrome c oxidase subunit I in Cryptic diversity in coastal Australasia: a morphological and mitonuclear genetic analysis of habitat-forming sibling species
Figure 5. Maximum likelihood trees constructed from mitochondrial cytochrome c oxidase subunit I (left; log likelihood: -399.5730) and nuclear adenine nucleotide transporter intron (right; log likelihood: -12170.8682) sequences of Pyura praeputialis and Pyura doppelgangera sp. nov. Nodal support from 1000 bootstrap replications (> 75%) is indicated next to some branches. Circles indicate regions in which a particular allele was present. For simplicity, allele frequencies are not indicated.
FIGURE 2. The Neighbor-Joining tree for the cytochrome oxidase c subunit 1 in Mitochondrial diversity of the white-toothed shrews (Mammalia, Eulipotyphla, Crocidura) in Vietnam
FIGURE 2. The Neighbor-Joining tree for the cytochrome oxidase c subunit 1 (COI) gene fragment. The bootstrap values (≥ 50 %) obtained from 1000 pseudoreplications are presented above the branches. Crocidura olivieri is used as outgroup.
FIGURE 3. The Neighbor-Joining tree for the cytochrome b in Mitochondrial diversity of the white-toothed shrews (Mammalia, Eulipotyphla, Crocidura) in Vietnam
FIGURE 3. The Neighbor-Joining tree for the cytochrome b (cytb) gene fragment. Designations as on the Fig. 2. Suncus murinus and S. stoliczkanus are used as outgroup.
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
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The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
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