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763 results for “Mitochondrial DNA”
Mitochondrial DNA sequence phylogeny of Daucus
We explored the phylogenetic utility of mitochondrial DNA sequences in Daucus and compared the results with prior phylogenetic results using the same 36 accessions of Daucus (and two additional outgroups) with plastid DNA sequences and with other nuclear results. As in the plastid study we used Illumina HiSeq sequencer to obtain resequencing data of the same accessions of Daucus and outgroups, and analyzed the data with maximum parsimony and maximum likelihood. We obtained data from 47 of 71 total mitochondrial genes but only 17 of these 47 genes recovered major clades that were common in prior plastid and nuclear studies. Our phylogenetic trees of the concatenated data set of 47 genes were moderately resolved, with 100% bootstrap support for most of the external and many of the internal clades, except for the clade of D. carota and its most closely related species D. syrticus. There are areas of hard incongruence with phylogenies using plastid and nuclear data. In agreement with other studies, we conclude that mitochondrial sequences are generally poor phylogenetic markers, at least at the genus level, despite their utility in some other studies.
Data from: Molecular phylogeny of the Taeniapterini (Diptera: Micropezidae) using nuclear and mitochondrial DNA, with a reclassification of the genus Taeniaptera Macquart
DNA molecular data are used to generate a phylogeny for the micropezid subfamily Taeniapterinae. Thirty-two taeniapterine species were sampled, including 10 of the 20 New World genera recognized by Steyskal, as well as one genus formerly treated as a synonym of Poecilotylus Hennig (Hemichaeta Steyskal). Five species from the Micropezinae were included as outgroups. A total DNA dataset of 4705 bp, including mitochondrial genes (12S and cytochrome c oxidase I (COI)) and nuclear coding genes (wingless and CAD), was analysed using maximum parsimony and Bayesian inference. The genus Taeniaptera Macquart was found to be non-monophyletic with respect to the remainder of the Taeniapterini analysed here. Taeniaptera is restricted to the Taeniaptera trivittata Macquart species group, Mitromyia Cresson is resurrected to contain the Taeniaptera grata (Wulp) species group, and Paragrallomyia Hendel is resurrected to contain most species previously considered Taeniaptera. Poecilotylus is recognized as a paraphyletic group awaiting further research.
Data from: Nuclear introns outperform mitochondrial DNA in inter-specific phylogenetic reconstruction: Lessons from horseshoe bats (Rhinolophidae: Chiroptera)
Despite many studies illustrating the perils of utilising mitochondrial DNA in phylogenetic studies, it remains one of the most widely used genetic markers for this purpose. Over the last decade, nuclear introns have been proposed as alternative markers for phylogenetic reconstruction. However, the resolution capabilities of mtDNA and nuclear introns have rarely been quantified and compared. In the current study we generated a novel ∼5 kb dataset comprising six nuclear introns and a mtDNA fragment. We assessed the relative resolution capabilities of the six intronic fragments with respect to each other, when used in various combinations together, and when compared to the traditionally used mtDNA. We focused on a major clade in the horseshoe bat family (Afro-Palaearctic clade; Rhinolophidae) as our case study. This old, widely distributed and speciose group contains a high level of conserved morphology. This morphological stasis renders the reconstruction of the phylogeny of this group with traditional morphological characters complex. We sampled multiple individuals per species to represent their geographic distributions as best as possible (122 individuals, 24 species, 68 localities). We reconstructed the species phylogeny using several complementary methods (partitioned Maximum Likelihood and Bayesian and Bayesian multispecies-coalescent) and made inferences based on consensus across these methods. We computed pairwise comparisons based on Robinson–Foulds tree distance metric between all Bayesian topologies generated (27,000) for every gene(s) and visualised the tree space using multidimensional scaling (MDS) plots. Using our supported species phylogeny we estimated the ancestral state of key traits of interest within this group, e.g. echolocation peak frequency which has been implicated in speciation. Our results revealed many potential cryptic species within this group, even in taxa where this was not suspected a priori and also found evidence for mtDNA introgression. We demonstrated that by using just two introns one can recover a better supported species tree than when using the mtDNA alone, despite the shorter overall length of the combined introns. Additionally, when combining any single intron with mtDNA, we showed that the result is highly similar to the mtDNA gene tree and far from the true species tree and therefore this approach should be avoided. We caution against the indiscriminate use of mtDNA in phylogenetic studies and advocate for pilot studies to select nuclear introns. The selection of marker type and number is a crucial step that is best based on critical examination of preliminary or previously published data. Based on our findings and previous publications, we recommend the following markers to recover phylogenetic relationships between recently diverged taxa (<20 My) in bats and other mammals: ACOX2, COPS7A, BGN, ROGDI and STAT5A.
Data from: Evolutionary and dispersal history of Eurasian wild mice Mus musculus clarified by more extensive geographic sampling of mitochondrial DNA
We examined sequence variation of mitochondrial DNA control region and cytochrome b gene of the house mouse (Mus musculus sensu lato) drawn from ca. 200 localities, with 290 new samples drawn primarily from previously unsampled portions of their Eurasian distribution and with the objective of further clarifying evolutionary episodes of this species before and after the onset of human-mediated long-distance dispersals. Phylogenetic analysis of the expanded data detected five equally distinct clades, with geographic ranges of northern Eurasia (musculus, MUS), India and Southeast Asia (castaneus, CAS), Nepal (unspecified), western Europe (domesticus, DOM), and Yemen (gentilulus). Our results confirm previous suggestions of Southwestern Asia as the likely place of origin of M. musculus and the region of Iran, Afghanistan, Pakistan, and northern India, specifically as the ancestral homeland of CAS. The divergence of the subspecies lineages and of internal sublineage differentiation within CAS were estimated to be 0.37-0.47 and 0.14-0.23 million years ago (mya), respectively, assuming a split of M. musculus and Mus spretus at 1.7 mya. Of four CAS sublineages detected, only one extends to eastern parts of India, Southeast Asia, Indonesia, Philippines, South China, Northeast China, Primorye, Sakhalin and Japan, implying a dramatic range expansion of CAS out of its homeland during an evolutionary short time, perhaps associated with the spread of agricultural practices. Multiple and non-coincident eastward dispersal events of MUS sublineages to distant geographic areas, such as northern China, Russia, and Korea, are inferred, with the possibility of several different routes.
Data from: Glacial history of the European marine mussels Mytilus, inferred from distribution of mitochondrial DNA lineages
Mussels of the genus Mytilus have been used to assess the circumglacial phylogeography of the intertidal zone. These mussels are representative components of the intertidal zone and have rapidly evolving mitochondrial DNA, suitable for high resolution phylogeographic analyses. In Europe, the three Mytilus species currently share mitochondrial haplotypes, owing to the cases of extensive genetic introgression. Genetic diversity of Mytilus edulis, Mytilus trossulus and Mytilus galloprovincialis was studied using a 900-bp long part of the most variable fragment of the control region from one of their two mitochondrial genomes. To this end, 985 specimens were sampled along the European coasts, at sites ranging from the Black Sea to the White Sea. The relevant DNA fragments were amplified, sequenced and analyzed. Contrary to the earlier findings, our coalescence and nested cladistics results show that only a single M. edulis glacial refugium existed in the Atlantic. Despite that, the species survived the glaciation retaining much of its diversity. Unsurprisingly, M. galloprovincialis survived in the Mediterranean Sea. In a relatively short time period, around the climatic optimum at 10 ky ago, the species underwent rapid expansion coupled with population differentiation. Following the expansion, further contemporary gene flow between populations was limited.
Data from: The hidden history of the snowshoe hare, Lepus americanus: extensive mitochondrial DNA introgression inferred from multilocus genetic variation
Hybridization drives the evolutionary trajectory of many species or local populations, and assessing the geographic extent and genetic impact of interspecific gene flow may provide invaluable clues to understand population divergence or the adaptive relevance of admixture. In North America, hares (Lepus spp.) are key species for ecosystem dynamics and their evolutionary history may have been affected by hybridization. Here we reconstructed the speciation history of the three most widespread hares in North America - the snowshoe hare (Lepus americanus), the white-tailed jackrabbit (L. townsendii) and the black-tailed jackrabbit (L. californicus) - by analyzing sequence variation at eight nuclear markers and one mitochondrial DNA (mtDNA) locus (6 240 bp; 94 specimens). A multilocus-multispecies coalescent-based phylogeny suggests that L. americanus diverged ~2.7 Mya and that L. californicus and L. townsendii split more recently (~1.2 Mya). Within L. americanus a deep history of cryptic divergence (~2.0 Mya) was inferred, which coincides with major speciation events in other North American species. While the isolation-with-migration model suggested that nuclear gene flow was generally rare or absent among species or major genetic groups, coalescent simulations of mtDNA divergence revealed historical mtDNA introgression from L. californicus into the Pacific Northwest populations of L. americanus. This finding marks a history of past reticulation between these species, which may have affected other parts of the genome and influence the adaptive potential of hares during climate change.
Data from: Phylogeny and biogeography of Poecilia (Cyprinodontiformes: Poeciliinae) across Central and South America based on mitochondrial and nuclear DNA markers
Poeciliids are a diverse group of small Neotropical fishes, and despite considerable research attention as models in ecology and evolutionary biology, our understanding of their biogeographic and phylogenetic relationships is still limited. We investigated the phylogenetic relationships of South and Central American Poecilia, by examining 2395 base pairs of mitochondrial DNA (ATPase 8/6, COI) and nuclear DNA (S7) for 18 species across six subgenera. Fifty-eight novel sequences were acquired from newly collected specimens and 20 sequences were obtained from previously published material. Analyses of concatenated and partitioned mitochondrial DNA and nuclear DNA sets resulted in a well-supported phylogeny that resolved several monophyletic groups corresponding to previously hypothesized subgenera and species complexes.
Data from: Differential migratory timing of western populations of Wilson's Warblers revealed by mitochondrial DNA and stable isotopes
Molecular markers and stable isotopes have provided important insights into the migratory connectivity of small landbirds. Research integrating these two methods has primarily focused on linking breeding and wintering sites, rather than focusing on timing of migratory movement of different breeding populations. We used mitochondrial DNA and isotopic markers to infer the timing of various breeding populations of migrating Wilson's Warblers (Cardellina pusilla) moving through a migratory stopover site, demonstrating the value of multiple sources of information in estimating the origin of migrants. Using mixed-stock analysis, we found that early spring migrants sampled in southwestern Arizona were dominated by warblers migrating to the West Coast of the contiguous United States, whereas later migrants included a large pulse of birds migrating to Alaska and western Canadian provinces. Stable hydrogen isotope data from individual birds showed the same timing pattern as genetic data. Had we used stable isotopes alone, we would not have been able to infer whether birds later in the migration season were most likely migrating to Alaska or the Interior West, given the large overlap in isotope values between those regions. The lack of mitochondrial group 2, common in the Interior West, in late-season migrants strongly suggests that these birds were migrating to breeding areas in Alaska or other northern regions. Studies that reveal the timing of migration of different breeding populations through stopover sites lay the foundation for more in-depth examination of seasonal interactions between migration and the stationary phases of the annual cycle.
Data from: Population genetics of overwintering monarch butterflies, Danaus plexippus (Linnaeus), from central Mexico inferred from mitochondrial DNA and microsatellite markers
Population genetic variation and demographic history in Danaus plexippus (L.), from Mexico were assessed based on analyses of mitochondrial cytochrome c oxidase subunit I (COI; 658 bp) and subunit II (COII; 503 bp) gene segments and seven microsatellite loci. The sample of 133 individuals included both migratory monarchs, mainly from four overwintering sites within the Monarch Butterfly Biosphere Reserve (MBBR) in central Mexico (states of Michoacán and México), and a nonmigratory population from Irapuato, Guanajuato. Haplotype (h) and nucleotide (π) diversities were relatively low, averaging 0.466 and 0.00073, respectively, for COI, and 0.629 and 0.00245 for COII. Analysis of molecular variance (AMOVA) of the COI data set, which included additional GenBank sequences from a nonmigratory Costa Rican population, showed significant population structure between Mexican migratory monarchs and nonmigratory monarchs from both Mexico and Costa Rica, suggesting limited gene flow between the two behaviorally distinct groups. Interestingly, while the COI haplotype frequencies of the nonmigratory populations differed from the migratory, they were similar to each other, despite the great physical distance between them. Microsatellite analyses, however, suggested a lack of structure between the two groups, possibly owing to the number of significant deviations from Hardy Weinberg equilibrium resulting from heterzoygote deficiencies found for most of the loci. Estimates of demographic history of the combined migratory MBBR monarch population, based on the mismatch distribution and Bayesian skyline analyses of the concatenated COI and COII data set (n = 89) suggested a population expansion dating to the late Pleistocene (~35,000 to 40,000 years before present) followed by a stable effective female population size (Nef) of about six million over the last 10,000 years.
Data from: Nuclear microsatellite and mitochondrial DNA analyses reveal the regional genetic structure and phylogeographical history of a sanguivorous land leech, Haemadipsa japonica, in Japan
Recent molecular studies have indicated that phylogeographical history of Japanese biota is likely shaped by geohistory along with biological events, such as distribution shifts, isolation, and divergence of populations. However, the genetic structure and phylogeographical history of terrestrial Annelida species, including leech species, are poorly understood. Therefore, we aimed to understand the genetic structure and phylogeographical history across the natural range of Haemadipsa japonica, a sanguivorous land leech species endemic to Japan, by using nine polymorphic nuclear microsatellites (nSSR) and cytochrome oxidase subunit one (COI) sequences of mitochondrial DNA (mtDNA). Analyses using nSSR revealed that H. japonica exhibited a stronger regional genetic differentiation among populations (G'ST = 0.77) than other animal species, probably because of the low mobility of land leech. Analyses using mtDNA indicated that H. japonica exhibited two distinct lineages (A and B), which were estimated to have diverged in the middle Pleistocene and probably because of range fragmentation resulting from climatic change and glacial and interglacial cycles. Lineage A was widely distributed across Japan, and lineage B was found in southwestern Japan. Analyses using nSSR revealed that lineage A was roughly divided into two population groups (i.e., northeastern and southwestern Japan); these analyses also revealed a gradual decrease in genetic diversity with increasing latitude in lineage A and a strong genetic drift in populations of northeastern Japan. Combined with the largely unresolved shallow polytomies from the mtDNA phylogeny, these results implied that lineage A may have undergone a rapid northward migration, probably during the Holocene. Then, the regional genetic structure with local unique gene pools may have been formed within each lineage because of the low mobility of this leech species.
Data from: Extensive mitochondrial introgression in North American Great Black-backed Gulls (Larus marinus) from the American Herring Gull (Larus smithsonianus) with little nuclear DNA impact
Recent genetic studies have shown that introgression rates among loci may greatly vary according to their location in the genome. In particular, several cases of mito-nuclear discordances have been reported for a wide range of organisms. In the present study, we examine the causes of discordance between mitochondrial (mtDNA) and nuclear DNA introgression detected in North American populations of the Great Black-backed Gull (Larus marinus), a Holarctic species, from the Nearctic North American Herring Gull (Larus smithsonianus). Our results show that extensive unidirectional mtDNA introgression from Larus smithsonianus into Larus marinus in North America cannot be explained by ancestral polymorphism but most likely results from ancient hybridization events occurring when Larus marinus invaded the North America. Conversely, our nuclear DNA results based on 12 microsatellites detected very little introgression from Larus smithsonianus into North American Larus marinus. We discuss these results in the framework of demographic and selective mechanisms that have been postulated to explain mito-nuclear discrepancies. We were unable to demonstrate selection as the main cause of mito-nuclear introgression discordance but cannot dismiss the possible role of selection in the observed pattern. Among demographic explanations, only drift in small populations and bias in mate choice in an invasive context may explain our results. As it is often difficult to demonstrate that selection may be the main factor driving the introgression of mitochondrial DNA in natural populations, we advocate that evaluating alternative demographic neutral hypotheses may help to indirectly support or reject hypotheses invoking selective processes.
Data from: Mitochondrial DNA (COI) analyses reveal that amphipod diversity is associated with environmental heterogeneity in deep-sea habitats
The relationship between species diversity and environmental parameters is poorly understood for the mobile macrofauna of deep-sea habitats due to under-sampling and subsequent lack of accurate taxonomic information. To redress this, cytochrome oxidase c subunit I (COI) DNA sequences were used to estimate species diversity and to compare phoxocephalid amphipod assemblages among 20 stations encompassing a range of environmental conditions. Two regions, east (Chatham Rise) and west (Challenger Plateau) of New Zealand were sampled to depths of 200 – 1200 m with an epibenthic sled. Using a comparison among identified morphospecies, we found a clear gap in sequence divergences between 6 and 13% and used a 6% threshold to designate molecular operational taxonomic units (MOTUs), as a surrogate to putative species. DNA sequences (n=297) revealed high total diversity (n=49 MOTUs), as well as high beta diversity (28 MOTUs found at single location only). Novel phoxocephalid MOTUs were found at most stations, especially on Challenger Plateau and the flanks of Chatham Rise. Analyses of inter-station assemblages revealed a major split between regions, indicating minimal overlap in taxon distributions. A cluster of highly similar stations was identified, broadly distributed over the crest of Chatham Rise, in association with elevated food availability, probably resulting from higher surface productivity and relatively shallow depth. Accordingly, multivariate analysis revealed a strong correlation between phoxocephalid assemblages and food supply. This study highlights the value of molecular approaches, in particular COI sequences, for quantifying and comparing diversity in under-sampled and/or under-studied taxa.
Data from: Complete mitochondrial DNA replacement in a Lake Tanganyika cichlid fish
We used nuclear and mitochondrial DNA sequences from specimens collected throughout Lake Tanganyika to clarify the evolutionary relationship between Lamprologus callipterus and Neolamprologus fasciatus. The nuclear data supports the reciprocal monophyly of these two shell breeding lamprologine cichlids. However, mitochondrial DNA (mtDNA) sequences show that 1) L. callipterus includes two divergent and geographically disjunct (North-South) mtDNA lineages; and that 2) N. fasciatus individuals cluster in a lineage sister group to the northern lineage of L. callipterus. The two mtDNA lineages of L. callipterus diverged c. 684 Kya to 1.2 Mya, coinciding with a major water level low stand in Lake Tanganyika, which divided the lake into isolated sub-lakes. This suggests that the two mtDNA lineages originated as the result of the separation of L. callipterus populations in different sub-basins. The incongruent phylogenetic position of N. fasciatus can best be explained by an ancient unidirectional introgression from L. callipterus into N. fasciatus. Remarkably, our data indicate that this event resulted in the complete mtDNA replacement in N. fasciatus. Our data suggest that hybridization occurred soon after the divergence of the two L. callipterus mtDNA lineages, probably still during the water level low stand, and that subsequently the invading mtDNA lineage spread throughout the lake.
Data from: Behavioral vs. molecular sources of conflict between nuclear and mitochondrial DNA: the role of male-biased dispersal in a Holarctic sea duck
Genetic studies of waterfowl (Anatidae) have observed the full spectrum of mitochondrial (mt) DNA population divergence, from panmixia to deep, reciprocally monophyletic lineages. Yet these studies generally found weak or no nuclear (nu) DNA structure which was often attributed to sex-biased gene flow (i.e., male dispersal and female philopatry), a common behavior within this family. An alternative explanation for this "conflict" is that the smaller effective population size and faster sorting rate of mtDNA relative to nuDNA leads to different signals of population structure. To test these alternatives, we simulated expected nuDNA differentiation based on mtDNA patterns of effective population sizes, gene flow, and divergence times in a Holarctic pair of waterfowl subspecies, the goosander (Mergus merganser merganser) and common merganser (M. m. americanus). We compared simulated results to empirical data from 12 nuDNA introns sampled from the species' global range. Between Europe and North America, nuDNA ФST was 3.4-fold lower than mtDNA ФST, a result consistent with differences in sorting rates. However, despite geographically structured and monophyletic mtDNA lineages within continents, nuDNA ФST values were generally < 0 and significantly lower than predicted. This between- and within-continent contrast held when comparing mtDNA and nuDNA among published studies of ducks. Thus, male-mediated gene flow is a better explanation than slower sorting rates for limited nuDNA differentiation within continents, which is also supported by non-molecular data. This study illustrates the value of quantitatively testing discrepancies between mtDNA and nuDNA to reject the null hypothesis that conflict simply reflects different sorting rates.
Data from: Speciation processes in putative island endemic sister bat species: false impressions from mitochondrial DNA and microsatellite data
Cases of geographically restricted co-occurring sister taxa are rare and may point to potential divergence with gene flow. The two bat species Murina gracilis and M. recondita are both endemic to Taiwan and are putative sister species. To test for non-allopatric divergence and gene flow in these taxa, we generated sequences using Sanger and Next Generation Sequencing, and combined these with microsatellite data for coalescent-based analyses. MtDNA phylogenies supported the reciprocally monophyletic sister relationship between M. gracilis and M. recondita, however, clustering of microsatellite genotypes revealed several cases of species admixture suggesting possible introgression. Sequencing of microsatellite flanking regions revealed that admixture signatures stemmed from microsatellite allele homoplasy rather than recent introgressive hybridization, and also uncovered an unexpected sister relationship between M. recondita and the continental species M. eleryi, to the exclusion of M. gracilis. To dissect the basis of these conflicts between ncDNA and mtDNA, we analysed sequences from 10 anonymous ncDNA loci with *BEAST and isolation-with-migration (IM) and found two distinct clades of M. eleryi, one of which was sister to M. recondita. We conclude that Taiwan was colonized by the ancestor of M. gracilis first, followed by the ancestor of M. recondita after a period of allopatric divergence. After colonization, the mitochondrial genome of M. recondita was replaced by that of the resident M. gracilis. This study illustrates how apparent signatures of sympatric divergence can arise from complex histories of allopatric divergence, colonization and hybridization, thus highlighting the need for rigorous analyses to distinguish between such scenarios.
Mitochondrial DNA tree for COI sequences (DNA barcode) of the goby genus Trimma.
<p>Mitochondrial DNA tree for COI sequences (DNA barcode) of the goby genus Trimma</p>
FIGURES 2A–E. Diamesa aculeata new species. A in New species of Diamesa (Diptera: Chironomidae) from Tibet: conspecific males and females associated with mitochondrial DNA
FIGURES 2A–E. Diamesa aculeata new species. A, male genitalia in dorsal view. B, ventral view of pars ventralis, aedeagal lobe, basal plate and ventromesal margin of gonocoxite IX. C, ventral view of cuspidate microtrichia along dorsomesal edge of medial field. D, apex of anal point. E, female genitalia in lateral view.
FIGURES 3A–C. Diamesa spp., female genitalia. A–B in New species of Diamesa (Diptera: Chironomidae) from Tibet: conspecific males and females associated with mitochondrial DNA
FIGURES 3A–C. Diamesa spp., female genitalia. A–B, Diamesa sp. Himalaya1 in ventral and lateral view. C, Diamesa sp. Himalaya2 in ventral view.
FIGURES 1A–E. Diamesa solhoyi new species. A, male tentorium. B in New species of Diamesa (Diptera: Chironomidae) from Tibet: conspecific males and females associated with mitochondrial DNA
FIGURES 1A–E. Diamesa solhoyi new species. A, male tentorium. B, male genitalia in dorsal view. C, ventral view of pars ventralis (pv), basal plate (bp), basimedial setal cluster (bs) and aedeagal lobe (al). D, female genitalia in lateral view. E, female genitalia in ventral view. Scale bars (C–D) are 250 µm.
FIGURE 8 in Description of a new Tityus species (Scorpiones: Buthidae) from Sierra de Portuguesa, western Venezuela, based on morphological and mitochondrial DNA evidence
FIGURE 8. MALDITOF MS analysis of venom from Tityus imei sp. nov. in the 6000–8000 Da range. Spectrum is representative of at least three analyses of independent venom pools.
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