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307 results for “Nuclear DNA”
Data from: Developing nuclear DNA phylogenetic markers in the angiosperm genus Leucadendron (Proteaceae): a next-generation sequencing transcriptomic approach
Despite the recent advances in generating molecular data, reconstructing species-level phylogenies for non-models groups remains a challenge. The use of a number of independent genes is required to resolve phylogenetic relationships, especially for groups displaying low polymorphism. In such cases, low-copy nuclear exons and non-coding regions, such as 3′ untranslated regions (3′-UTRs) or introns, constitute a potentially interesting source of nuclear DNA variation. Here, we present a methodology meant to identify new nuclear orthologous markers using both public-nucleotide databases and transcriptomic data generated for the group of interest by using next generation sequencing technology. To identify PCR primers for a non-model group, the genus Leucadendron (Proteaceae), we adopted a framework aimed at minimizing the probability of paralogy and maximizing polymorphism. We anchored when possible the right-hand primer into the 3′-UTR and the left-hand primer into the coding region. Seven new nuclear markers emerged from this search strategy, three of those included 3′-UTRs. We further compared the phylogenetic potential between our new markers and the ribosomal internal transcribed spacer region (ITS). The sequenced 3′-UTRs yielded higher polymorphism rates than the ITS region did. We did not find strong incongruences with the phylogenetic signal contained in the ITS region and the seven new designed markers but they strongly improved the phylogeny of the genus Leucadendron. Overall, this methodology is efficient in isolating orthologous loci and is valid for any non-model group given the availability of transcriptomic data.
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.
Murine polyomavirus DNA transitions through spatially distinct nuclear replication subdomains during infection
<p>The replication of small DNA viruses requires both host DNA replication and repair factors that are often recruited to subnuclear domains termed viral replication centers (VRCs). Aside from serving as a spatial focus for viral replication, little is known about these dynamic areas in the nucleus. We investigated the organization and function of VRCs during murine polyomavirus (MuPyV) infection using 3D structured illumination microscopy (3D-SIM). We localized MuPyV replication center components, such as the viral large T-antigen (LT) and the cellular replication protein A (RPA), to spatially distinct subdomains within VRCs. We found that viral DNA (vDNA) trafficked sequentially through these subdomains post-synthesis, suggesting their distinct functional roles in vDNA processing. Additionally, we observed disruption of VRC organization and vDNA trafficking during mutant MuPyV infections or inhibition of DNA synthesis. These results reveal a dynamic organization of VRC components that coordinates virus replication.</p>
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: Strong nuclear differentiation contrasts with widespread sharing of plastid DNA haplotypes across taxa in European purple saxifrages (Saxifraga sect. Porphyrion subsect. Oppositifoliae)
The purple saxifrages, Saxifraga sect. Porphyrion subsect. Oppositifoliae, comprise the closest relatives of the arctic-alpine model plant S. oppositifolia and have a centre of diversity in the central and southern European mountain ranges. A multitude of taxa has been described and taxonomic concepts vary among different treatments. Using amplified fragment length polymorphism (AFLP) fingerprinting we show that some taxa indeed form strongly supported genetic entities best recognized on the species level (S. biflora, S. blepharophylla, S. retusa, S. rudolphiana, S. speciosa), while others (S. murithiana, S. paradoxa) are not genetically divergent at all. Saxifraga oppositifolia s. s. is phylogenetically incoherent. Plastid DNA sequence data show very limited congruence with the predominantly nuclear-derived AFLPs. Several co-distributed taxa (S. biflora, S. blepharophylla, S. oppositifolia s. s., S. retusa) share the same set of haplotypes. In the widespread species S. oppositifolia and S. retusa, highly divergent haplotype lineages were discovered, which exhibit a geographic rather than taxonomic structure. Recent and ancient hybridization and/or lineage sorting are likely responsible for the strong incongruence between data derived from nuclear and plastid genomes. Hybridization, which is known to occur among almost all taxa of this group when growing in sympatry, seems, however, insufficient to break down species barriers.
Data from: New DNA data from a Transthyretin nuclear intron suggest an Oligocene to Miocene diversification of living South America opossums (Marsupialia: Didelphidae).
Phylogenetic relationships of 19 species of didelphid marsupials were studied using two nuclear markers, the non-coding transthyretin intron 1 (TTR) and the coding interphotoreceptor retinoid binding protein exon 1 (IRBP), and two mitochondrial genes, the protein-coding cytochrome b (cyt-b) and the structural 12S ribosomal DNA (12S rDNA). Evolutionary dynamics of these four markers were compared to each other, revealing the appropriate properties presented by TTR intron 1 together with its well supported and resolved phylogenetic signal. Nuclear markers supported the monophyly of medium and large-sized opossums Metachirus+(Chironectes, Lutreolina, Didelphis, Philander), and the paraphyly of mouse-sized opossums, with the genera Gracilinanus, Thylamys, and Marmosops as a sister group to medium and large-sized didelphids. Conflicting branching patterns between mitochondrial and nuclear data involved the phylogenetic position of Marmosa-Micoureus-Monodelphis relative to other mouse-sized opossums. Nuclear phylogenetic inferences among genera were confirmed by the presence of synapomorphic indels observed in TTR intron 1. A Bayesian relaxed molecular clock dating of didelphid evolution using nuclear markers estimated their origin in the Middle Eocene (39.8 million years ago), with subsequent diversification during the Oligocene (Deseadan) and Miocene.
FIGURE 17 in The identity of the Javan Krait, Bungarus javanicus Kopstein, 1932 (Squamata: Elapidae): evidence from mitochondrial and nuclear DNA sequence analyses and morphology
FIGURE 17. Black adult male Bungarus candidus (UK B15) from near Losarang (Kabupaten Indramayu, West Java, Indonesia). Like the type specimen of Bungarus javanicus, it has a yellow ventral colouration and yellow spots on the vertebrals. Note unpigmented internasals and 5th and 6th supralabials of the right head side. Photo by Ulrich Kuch.
FIGURE 16 in The identity of the Javan Krait, Bungarus javanicus Kopstein, 1932 (Squamata: Elapidae): evidence from mitochondrial and nuclear DNA sequence analyses and morphology
FIGURE 16. Close-up of a black adult male Bungarus candidus (UK BP4) from the area of Purwokerto, Central Java, Indonesia. Photo by Ulrich Kuch.
FIGURE 15 in The identity of the Javan Krait, Bungarus javanicus Kopstein, 1932 (Squamata: Elapidae): evidence from mitochondrial and nuclear DNA sequence analyses and morphology
FIGURE 15. The most frequently encountered colour morph of "black" Bungarus candidus on Java represented by an adult male (UK BX3) from near Losarang (Kabupaten Indramayu, West Java, Indonesia). Photo by Ulrich Kuch.
FIGURE 13 in The identity of the Javan Krait, Bungarus javanicus Kopstein, 1932 (Squamata: Elapidae): evidence from mitochondrial and nuclear DNA sequence analyses and morphology
FIGURE 13. Adult female Bungarus candidus (UK B34) from the area of Losarang (Kabupaten Indramayu, West Java, Indonesia) with reduced black bands on the anterior body and mosaic-like dark stippling on the posterior body and tail. Photo by Ulrich Kuch.
FIGURE 11 in The identity of the Javan Krait, Bungarus javanicus Kopstein, 1932 (Squamata: Elapidae): evidence from mitochondrial and nuclear DNA sequence analyses and morphology
FIGURE 11. Adult male Bungarus candidus (UK B38) from the area of Losarang (Kabupaten Indramayu, West Java, Indonesia) with reduced black bands on the posterior half of the body. Photo by Ulrich Kuch.
FIGURE 14 in The identity of the Javan Krait, Bungarus javanicus Kopstein, 1932 (Squamata: Elapidae): evidence from mitochondrial and nuclear DNA sequence analyses and morphology
FIGURE 14. Adult male Bungarus candidus (UK B35) from the area of Losarang (Kabupaten Indramayu, West Java, Indonesia) with reduced bands on the posterior body and heavy pigmentation of all light interspaces and ventrolateral areas (opaque colouration is due to imminent shedding). Photo by Ulrich Kuch.
FIGURE 10 in The identity of the Javan Krait, Bungarus javanicus Kopstein, 1932 (Squamata: Elapidae): evidence from mitochondrial and nuclear DNA sequence analyses and morphology
FIGURE 10. Regularly black-and-white banded juvenile Bungarus candidus from Desa Songgon, about 20 km SW of Banyuwangi, East Java, Indonesia. Note the characteristic light head pattern of juvenile specimens. Photo by Andrea Glässer-Trobisch and Dietmar Trobisch.
FIGURE 9 in The identity of the Javan Krait, Bungarus javanicus Kopstein, 1932 (Squamata: Elapidae): evidence from mitochondrial and nuclear DNA sequence analyses and morphology
FIGURE 9. Black juvenile Bungarus candidus (ZMB 57702) from Banjar Berawa, Desa Canggu, Denpasar, Bali, Indonesia. Photo by Frank Tillack.
FIGURE 8 in The identity of the Javan Krait, Bungarus javanicus Kopstein, 1932 (Squamata: Elapidae): evidence from mitochondrial and nuclear DNA sequence analyses and morphology
FIGURE 8. Ventral view of the partially leucistic juvenile Bungarus candidus (UK 96-1) from Linggarjati. Photo by Ulrich Kuch.
FIGURE 7 in The identity of the Javan Krait, Bungarus javanicus Kopstein, 1932 (Squamata: Elapidae): evidence from mitochondrial and nuclear DNA sequence analyses and morphology
FIGURE 7. Juvenile Bungarus candidus (UK 96-1) from Linggarjati (Kabupaten Cirebon, West Java, Indonesia; 400– 500 m above sea level) with white snout, reduced black bands on anterior body, and white dorsals with dark tips on the rest of the body. Photo by Ulrich Kuch.
FIGURE 6 in The identity of the Javan Krait, Bungarus javanicus Kopstein, 1932 (Squamata: Elapidae): evidence from mitochondrial and nuclear DNA sequence analyses and morphology
FIGURE 6. Contour map of Java and Madura (Bali, adjacent to the east, not shown). Capital letters indicate collecting areas: A, Losarang (near Indramayu); B, area of the type locality of Bungarus javanicus (near Mt. Ciremai, e.g., Linggarjati); C, Purwokerto basin; D, coastal plain near Cilacap. Dots and circles, respectively, mark collecting localities of additional examined specimens and literature records of black-and-white banded Bungarus candidus.
FIGURE 5 in The identity of the Javan Krait, Bungarus javanicus Kopstein, 1932 (Squamata: Elapidae): evidence from mitochondrial and nuclear DNA sequence analyses and morphology
FIGURE 5. Black adult female Bungarus candidus (SMF 76271) from Linggarjati (Kabupaten Cirebon, West Java, Indonesia; 400–500 m above sea level). The colour pattern of this snake closely resembles that of the type specimen of Bungarus javanicus. Photo by Ulrich Kuch.
FIGURE 4 in The identity of the Javan Krait, Bungarus javanicus Kopstein, 1932 (Squamata: Elapidae): evidence from mitochondrial and nuclear DNA sequence analyses and morphology
FIGURE 4. Kopstein's (1936) third specimen of Bungarus javanicus, the 'intermediary' snake from Linggarjati (ZRC 2.4379). Photo by Ulrich Kuch.
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