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71 results for “Nuclear loci”
Genotype data of 10 nuclear microsatellite loci for 30 Quercus acutissima populations in China
<p>This dataset includes genotype data of 10 nuclear microsatellite loci for 707 individuals of Quercus acutissima from 30 natural populations in China.</p>
Genotype data of 970 Pedunculate oak trees (Quercus robur L.) in Russia and neighbouring countries at 385 gene loci covering the nuclear and organelle genome
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Data from: A new phylogeny of <em>Anastrepha</em> (Diptera: Tephritidae) based on nuclear loci obtained by phylogenomic methods
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Genotype data of 1970 Pedunculate oak trees (Quercus robur L.) in 13 European countries at 381 gene loci covering the nuclear and organelle genome
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Phylogeny and biogeography of Fagus (Fagaceae) based on 28 nuclear single/low‐copy loci
<p><i>Fagus</i> L. is a key component in temperate deciduous broadleaf forests of the Northern Hemisphere. However, its biogeographic history has not been examined under the framework of a fully resolved and reasonably time-calibrated phylogeny. In this study, we sequenced 28 nuclear single/low-copy loci (18,555 bp in total) of 11 <i>Fagus</i> species/segregates and seven outgroups. Phylogenetic trees were reconstructed using both concatenation-based (ML, MP, BI) and coalescent-based methods (StarBEAST2, ASTRAL). The monophyly of two subgenera (<i>Fagus</i> and <i>Engleriana</i>) and most sections was well supported, except for sect. <i>Lucida</i>, which was paraphyletic with respect to sect. <i>Longipetiolata</i>. We also found a major phylogenetic conflict among North American, East Asian and West Eurasian lineages of subgen. <i>Fagus</i>. Three segregates that have isolated distribution (<i>F. </i><i>mexicana</i>,<i> F. multinervis</i>, and <i>F. orientalis</i>) were independent evolutionary units. Biogeographic analysis with fossils suggested that <i>Fagus</i> could have originated in North Pacific region in late Early Eocene. Major diversifications coincided with a climate aberration at the Eocene/Oligocene boundary and the global cooling since Mid-Miocene. The Late Miocene accelerated global cooling and the Pleistocene glaciations would have driven beeches into East Asia, North America and West Eurasia. Meanwhile, range reduction and extinction in high latitudes, in central Asia and in western North America converged to form beech modern distribution pattern. This study provides a first attempt to disentangle the biogeographic history of beeches in the context of a nearly resolved and time-calibrated phylogeny, which may shed new insights into the formation of the temperate biome in the Northern Hemisphere.</p>
Data from: Species tree reconstruction of a poorly resolved clade of salamanders (Ambystomatidae) using multiple nuclear loci
The analysis of diverse data sets can yield different phylogenetic estimates that challenge systematists to explain the source of discordance. The mole salamanders (family Ambystomatidae) are a classic example of this phylogenetic conflict. Previous attempts to resolve the ambystomatid species tree using allozymic, morphological, and mitochondrial sequence data have yielded different estimates, making it unclear which data source best approximates ambystomatid phylogeny and which ones yield phylogenetically inaccurate reconstructions. To shed light on this conflict, we present the first multi-locus DNA sequence-based phylogenetic study of the Ambystomatidae. We utilized a range of analyses, including coalescent-based methods of species-tree estimation that account for incomplete lineage sorting within a locus and concordance-based methods that estimate the number of sampled loci that support a particular clade. We repeated these analyses with the removal of individual loci to determine if any locus has a disproportionate effect on our phylogenetic results. Collectively, these results robustly resolved many deep and relatively shallow clades within Ambystoma, including the placement of A. gracile and A. talpoideum as the sister clade to a clade containing all remaining ambystomatids, and the placement of A. maculatum as the sister lineage to all remaining ambystomatids excluding A. gracile and A. talpoideum. Both Bayesian coalescent and concordance methods produced similar results, highlighting strongly supported branches in the species tree. Furthermore, coalescent-based analyses that excluded loci produced overlapping species-tree posterior distributions, suggesting that no particular locus – including mtDNA – disproportionately contributed to our species-tree estimates. Overall, our phylogenetic estimates have greater similarity with previous allozyme and mitochondrial sequence-based phylogenetic estimates. However, intermediate depths of divergence in the ambystomatid species tree remain unresolved, potentially highlighting a region of rapid species radiation or a hard polytomy, which limits our ability to comment on previous morphologically-based taxonomic groups.
Data from: The first set of universal nuclear protein-coding loci markers for avian phylogenetic and population genetic studies
Multiple nuclear markers provide genetic polymorphism data for molecular systematics and population genetic studies. They are especially required for the coalescent-based analyses that can be used to accurately estimate species trees and infer population demographic histories. However, in avian evolutionary studies, these powerful coalescent-based methods are hindered by the lack of a sufficient number of markers. In this study, we designed PCR primers to amplify 136 nuclear protein-coding loci (NPCLs) by scanning the published Red Junglefowl (Gallus gallus) and Zebra Finch (Taeniopygia guttata) genomes. To test their utility, we amplified these loci in 41 bird species representing 23 Aves orders. The sixty-three best-performing NPCLs, based on high PCR success rates, were selected which had various mutation rates and were evenly distributed across 17 avian autosomal chromosomes and the Z chromosome. To test phylogenetic resolving power of these markers, we conducted a Neoavian phylogenies analysis using 63 concatenated NPCL markers derived from 48 whole genomes of birds. The resulting phylogenetic topology, to a large extent, is congruence with results resolved by previous whole genome data. To test the level of intraspecific polymorphism in these makers, we examined the genetic diversity in four populations of the Kentish Plover (Charadrius alexandrinus) at 17 of NPCL markers chosen at random. Our results showed that these NPCL markers exhibited a level of polymorphism comparable with mitochondrial loci. Therefore, this set of pan-avian nuclear protein-coding loci has great potential to facilitate studies in avian phylogenetics and population genetics.
Data from: A phylogeny of the genus Amaranthus (Amaranthaceae), based on several low-copy nuclear loci and chloroplast regions
The genus Amaranthus (pigweeds) is a group of ∼74 monoecious or dioecious annual species native to every continent but Antarctica, frequently associated with natural and human disturbance, with several economically important domesticated and weedy species. We set out to reconstruct the phylogeny of Amaranthus, with broad geographic sampling, in order to answer questions about biogeographic relationships in the genus and the monophyly of the subgenera. Fifty-eight species were included inmaximum parsimony and Bayesian phylogenetic analyses based on ITS and three low-copy nuclear genes (A36, G3PDH, and Waxy), as well as two chloroplast regions (trnL5′-trnL3′ and matK/trnK). Topology tests were also employed to test taxonomic hypotheses about incongruence between trees and the monophyly of clades containing Galápagos species. Our analyses support the origin of the genus in the Americas, with a single long-distance dispersal event to the Old World, and both nuclear and chloroplast trees recover three to fourmajor clades, roughly corresponding to three subgenera recognized based on morphology. However, there are species in all of these clades that were not predicted based on morphology, and we discover previously unsuspected relationships between Galápagos species and species from the North American Southwest, which comprise small monophyletic groups outside of the three recognized subgenera. Additionally, an important herbicide resistant weed species (A. palmeri) and its sister species are placed into different large clades based on nuclear or chloroplast data, suggesting a chloroplast capture event. These results will provide a basis for further exploration of the evolution of weedy ecological strategies in the group.
Data from: Development of nuclear microsatellite loci and mitochondrial single nucleotide polymorphisms for the natterjack toad, Bufo (Epidalea) calamita (Bufonidae), using next generation sequencing and Competitive Allele Specific PCR (KASPar)
Amphibians are undergoing a major decline worldwide and the steady increase in the number of threatened species in this particular taxa highlights the need for conservation genetics studies using high-quality molecular markers. The natterjack toad, Bufo (Epidalea) calamita, is a vulnerable pioneering species confined to specialized habitats in Western Europe. To provide efficient and cost-effective genetic resources for conservation biologists, we developed and characterized 22 new nuclear microsatellite markers using next-generation sequencing. We also used sequence data acquired from Sanger sequencing to develop the first mitochondrial markers for KASPar assay genotyping. Genetic polymorphism was then analyzed for 95 toads sampled from 5 populations in France. For polymorphic microsatellite loci, number of alleles and expected heterozygosity ranged from 2 to 14 and from 0.035 to 0.720, respectively. No significant departures from panmixia were observed (mean multilocus F IS = −0.015) and population differentiation was substantial (mean multilocus F ST = 0.222, P < 0.001). From a set of 18 mitochondrial SNPs located in the 16S and D-loop region, we further developed a fast and cost-effective SNP genotyping method based on competitive allele-specific PCR amplification (KASPar). The combination of allelic states for these mitochondrial DNA SNP markers yielded 10 different haplotypes, ranging from 2 to 5 within populations. Populations were highly differentiated (G ST = 0.407, P < 0.001). These new genetic resources will facilitate future parentage, population genetics and phylogeographical studies and will be useful for both evolutionary and conservation concerns, especially for the set-up of management strategies and the definition of distinct evolutionary significant units.
Data from: Molecular phylogeny of Tragopogon L. (Asteraceae) based on seven nuclear loci (Adh, GapC, LFY, AP3, PI, ITS, and ETS)
Tragopogon is a large Eurasian genus of approximately 150 species. Despite the use of 6910 aligned bp of sequence data representing seven loci, relationships within the genus remain largely unresolved. The young age of the genus in combination with rapid diversification may be the best explanation for this poor resolution. Our studies have revealed that Geropogon is well supported as the immediate sister to Tragopogon. Sections Tragopogon, Brevirostris, Chromopappus, and Hebecarpus of traditional taxonomic treatments are largely monophyletic; sections Angustissimi, Majores, Collini, and Profundisulcati are non-monophyletic. The monotypic sections Macropogon, Dasypogon, and Dybjanskya appear within other sections and no longer merit recognition. Our molecular investigations of geographically widespread species in Europe, including T. crocifolius, T. pratensis, T. porrifolius, and T. orientalis, indicate that each may be non-monophyletic, comprising several cryptic species. These widespread diploids are the proposed parents of some of the Eurasian allopolyploids, as well as the parents of the recently formed T. mirus and T. miscellus from North America
Data from: Primers for Castilleja and their utility across Orobanchaceae: II. Single-copy nuclear loci
Premise of the study: We developed primers targeting nuclear loci in Castilleja with the goal of reconstructing the evolutionary history of this challenging clade. These primers were tested across other major clades in Orobanchaceae to assess their broader utility. Methods and Results: We assembled low-coverage genomes for three taxa in Castilleja and developed primer combinations for the single-copy conserved ortholog set (COSII) and the pentatricopeptide repeat (PPR) gene family. These primer combinations were designed to take advantage of the Fluidigm microfluidic PCR platform and are well suited for high-throughput sequencing applications. Eighty-seven primers were designed for Castilleja, and 27 were found to have broader utility in Orobanchaceae. Conclusions: These results demonstrate the utility of these primers, not only across Castilleja, but for other lineages within Orobanchaceae as well. This expanded molecular toolkit will be an asset to future phylogenetic studies in Castilleja and throughout Orobanchaceae.
12 nuclear microsatellite loci scores for 543 adult trees of Tilia cordata in Lithuainia
<p>Genetic signature of the natural genepool of <i>Tilia cordata</i> Mill. in Lithuania: compound evolutionary and anthropogenic effects</p> <p><i>Tilia cordata</i> Mill. is a valuable tree species enriching the ecological values of the coniferous dominated boreal forests in Europe. Following the historical decline, spreading of <i>Tilia</i> sp. is challenged by the elevated inbreeding and habitat fragmentation. We studied the geographical distribution of genetic diversity of <i>Tilia cordata</i> populations in Lithuania. We used 14 genomic microsatellite markers to genotype 543 individuals from 23 wild growing populations. We found that <i>Tilia cordata</i> retained high levels of genetic diversity (population F<sub>is</sub> = 0 to 0.15, H<sub>o </sub>= 0.53 to 0.69, H<sub>e </sub>= 0.56 to 0.75). AMOVA, Bayesian clustering and Monmonier's barrier detection indicate weak but significant differentiation among the populations (F<sub>st</sub> = 0.037***) into geographically interpretable clusters of (a) western Lithuania with high genetic heterogeneity but low genetic diversity, bottleneck effects, (b) relatively higher genetic diversity of <i>Tilia cordata</i> on rich and most soils of midland lowland, and (c) the most differentiated populations on poor soils of the coolest north-eastern highland possessing the highest rare allele frequency but elevated inbreeding and bottleneck effects. Weak genetic differentiation among the <i>Tilia cordata</i> populations in Lithuania implies common ancestry, absence of strong adaptive gradients and effective genetic exchange possible mediated via the riparian networks. A hypothesis on riparian networks as geneflow mediators in <i>Tilia cordata</i> was raised based on results of this study.</p>
The phylogeny of Triticeae Dumort. (Poaceae): resolution and reticulation based on a genome-wide selection of nuclear loci.
<p>Chloroplast-genome and nuclear-locus phylogenetic datasets for the wheat tribe Triticeae.</p>
Genotype data of 14 nuclear microsatellite loci for 18 Quercus chenii populations in China
<p>This dataset includes genotype data of 14 nuclear microsatellite loci for 419 individuals of Quercus chenii from 18 natural populations in China.</p>
Phylogeny of Crataegus (Rosaceae) based on 257 nuclear loci and chloroplast genomes: evaluating the impact of hybridization
<p>Assembled sequence alignments and phylogenetic trees for plastomes and nuclear loci for 24 samples of Crataegus.</p>
Fig. 1 in Phylogeny of Celastraceae subfamily Hippocrateoideae inferred from morphological characters and nuclear and plastid loci
Fig. 1. Simultaneous-analysis parsimony JK tree of all morphological and molecular characters with parsimony JK values above each branch, and likelihood BS values (for the matrix of all nucleotide characters) below each branch. Clades in the parsimony JK tree that were contradicted by clades in the likelihood BS tree are indicated by XX, with BS support for the highest contradictory likelihood clade listed.
Phylogenetic relationships of Tilia (Malvaceae) inferred from multiple nuclear loci and plastid genomes
<p class="MsoNormal"><em><span>Premise of research.</span></em><strong><span> </span></strong><em><span>Tilia</span></em><span> is a<strong> </strong>Eurasian-eastern North American disjunct plant genus with great economic and ecological importance. However, a robust phylogeny has not been established with a comprehensive taxon sampling and a large amount of data. </span></p> <p class="MsoNormal"><em><span>Methodology</span></em><span>. We obtained DNA sequences of plastomes and multiple nuclear loci using the anchored hybrid enrichment technique and next generation sequencing technology. Orthologous nuclear loci were inferred using tree-based methods. Phylogenetic analyses were performed using maximum parsimony, Bayesian, and coalescence-based species tree methods. Parentages of polyploids were inferred from the nuclear and plastid phylogenies. </span></p> <p class="MsoNormal"><em><span>Pivotal results</span></em><span>. <em>Craigia yunnanensis</em> is sister to <em>Tilia</em>, within which <em>T.</em> <em>endochrysea</em> endemic to southern China is the earliest lineage diverging followed by the European species <em>T. platyphyllos</em>. The European <em>T. cordata</em> and eastern Asian <em>T. amurensis</em> and <em>T. kiusiana </em>form a clade, while the North American <em>T. americana</em> is most closely related to the eastern and western Asian species complex including <em>T. chingiana</em>, <em>T. mandshurica</em>, <em>T. oliver</em>, and western Asian <em>T. tomentosa</em>. Significant incongruence exists between nuclear and plastid phylogenies.</span></p> <p class="MsoNormal"><em><span>Conclusions</span></em><span>. Our phylogenetic results<em> </em>suggest that there are six distinctive lineages or species complexes in the genus including 1) T. <em>endochrysea</em>, 2) <em>T. platyphyllos</em>, 3) <em>T. kiusiana</em>, 4) <em>T. cordata </em>and<em> T. amurensis</em>, 5) <em>T. chingiana</em>, <em>T. miqueliana</em>, <em>T. oliveri</em>, and 6) <em>T. tomentosa</em>, and <em>T. americana</em>. They may be divided into two sections (<em>Trichophilyra</em> and <em>Tilia</em>) and three subsections (<em>Tilia</em>, <em>Lindnera</em>, and <em>Trabeculares</em>). The prevalent incongruence between nuclear and plastid confirms the importance of ancient hybridization and introgression in the evolutionary history of the genus. Polyploid species in Eurasia and their corresponding diploid parental lineages may have formed a hybrid swarm in the region.</span></p>
Data from: A phylogeny of the genus Amaranthus (Amaranthaceae), based on several low-copy nuclear loci and chloroplast regions
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Data from: Phylogenetic relationships and character evolution in Heuchera (Saxifragaceae) on the basis of multiple nuclear loci
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Data from: Species tree reconstruction of a poorly resolved clade of salamanders (Ambystomatidae) using multiple nuclear loci
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