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57 results for “phylogenetic markers”
GenBank accession numbers of the four marker genes and associated voucher specimens/tissues that were used in this study. For more details see Guo et al. (2014). Sequences of species in bold are unpublished and were provided by P. Guo as personal communication in Rediscovery of Andrea's keelback, Hebius andreae (Ziegler & Le, 2006): First country record for Laos and phylogenetic placement
GenBank accession numbers of the four marker genes and associated voucher specimens/tissues that were used in this study. For more details see Guo et al. (2014). Sequences of species in bold are unpublished and were provided by P. Guo as personal communication
Fig. 4 in Redescription And New Host Record Of Diplostamenides Sciaenae (Monogenea, Microcotylidae) And Its Phylogenetic Status Using Molecular Markers
Fig. 4. Phylogenetic tree topology of partial 18S rRNA nucleotide sequence data for different microcotylids and outgroup as diclidophorids through NJ and ME methods. The bootstrap values for 1000 replicates are shown as in the phylogram and branch length is genetic distance between taxa.
Fig. 3 in Redescription And New Host Record Of Diplostamenides Sciaenae (Monogenea, Microcotylidae) And Its Phylogenetic Status Using Molecular Markers
Fig. 3. Phylogenetic tree topology of parital 28S rRNA nucleotide sequence data for the members of microcotytlidae and outgroup of members of diclidophoridae through NJ and ME methods. The bootstrap values for 1000 replicates are shown as in the phylogram and branch length is genetic distance between taxa.
Fig. 1 in Redescription And New Host Record Of Diplostamenides Sciaenae (Monogenea, Microcotylidae) And Its Phylogenetic Status Using Molecular Markers
Fig. 1. Diplostamenides sciaenae: A — whole mount (ventral view): OS, oral sucker; P, pharyn×; OE, oesophagus; GA, genital atrium; IC, intestinal caecum; VI, vitellarium; H, haptor; C, clamp B — reproductive system: V, vas deferens; VD, vitelline duct; O, ovary; CVD, common vitelline duct; GIC, genitointestinal canal; OD, oviduct; OT, ootype; T, testes C — genital atrium and spines: AS, atrial spines; D — clamp and associated sclerites: SMD, scleritum marginal dorsale; SMV, scleritum marginal ventrale; SM, Scleritum median; SOB, scleritum obliqum basale; ETD, extreme terminal dorsale; ETV, extreme terminal ventrale.
Fig. 2 in Redescription And New Host Record Of Diplostamenides Sciaenae (Monogenea, Microcotylidae) And Its Phylogenetic Status Using Molecular Markers
Fig. 2. Diplostamenides sciaenae digital phototmicrographs (present study): A — whole mount; B — clamp and associated sclerites; C — gential atrium and spines; D — anterior region with oral suckers, pharyn× and oesophagus. Abbreviations are provided in figure 1.
Figure 1 in Phylogenetic relationships of the vulnerable wild cattle, Malayan gaur (Bos gaurus hubbacki), and its hybrid, the selembu, based on maternal markers
Figure 1. Neighbor-joining tree of the 12S rRNA gene. The numbers at the branches stand for bootstrap values (%) of 1000 replications.
Figure 4 in CHD genes: a reliable marker for bird populations and phylogenetic analysis? Case study of the superfamily Sylvioidea (Aves: Passeriformes)
Figure 4. Maximum clade credibility trees for three data sets obtained by BI analysis in BEAST v1.8.0. MCC genealogy based on a Yule speciation process, summarized from the output of a Markov chain Monte Carlo chain run for 10 million iterations and sampled every 1000 iterations.
Figure 3 in CHD genes: a reliable marker for bird populations and phylogenetic analysis? Case study of the superfamily Sylvioidea (Aves: Passeriformes)
Figure 3. The ML tree for myoglobin gene (in blue) and for CHD-Z gene (in red); both trees are scaled in substitutions and the length of each tree and different topologies indicate that both of them are improper for phylogeny using a single gene.
Figure 1. Sex distribution for A. arundinaceus, A in CHD genes: a reliable marker for bird populations and phylogenetic analysis? Case study of the superfamily Sylvioidea (Aves: Passeriformes)
Figure 1. Sex distribution for A. arundinaceus, A. scirpaceus, and A. schoenobaenus, shown by sampling date.
Fig. 5 in Phylogenetic relationships of the bumblebees Bombus moderatus, B. albocinctus, B. burjaeticus, B. florilegus and B. cryptarum based on mitochondrial DNA markers: a complex of closely related taxa with circumpolar distribution (Hymenoptera: Apidae: Bombus))
Fig. 5: Tree topology calculated as Maximum-Likelihood tree using Bayesian MCMC analysis with the general time reversal model of base substitution and gamma distribution for degraded DNA of museum specimens, only parsimony informative triplets included.
Fig. 4 in Phylogenetic relationships of the bumblebees Bombus moderatus, B. albocinctus, B. burjaeticus, B. florilegus and B. cryptarum based on mitochondrial DNA markers: a complex of closely related taxa with circumpolar distribution (Hymenoptera: Apidae: Bombus))
Fig. 4: Observed diagnostic character changes with position numbers mapped onto the Maximum- Likelihood tree. Black box = unambiguous diagnostic charactercharacter change, grey box = ambiguous diagnostic charactercharacter change, and white box = character change.
Fig. 3 in Phylogenetic relationships of the bumblebees Bombus moderatus, B. albocinctus, B. burjaeticus, B. florilegus and B. cryptarum based on mitochondrial DNA markers: a complex of closely related taxa with circumpolar distribution (Hymenoptera: Apidae: Bombus))
Fig. 3: Alignment of all parsimonious informative triplets (with uninformative sites deleted -), and with a pointer for position number (numbered for total COI) and codon position. Diagnostic (= private) positions marked with colour green = Thymine, violet = Cytosine, red = Adenine and yellow = Guanine.
Fig. 2 in Phylogenetic relationships of the bumblebees Bombus moderatus, B. albocinctus, B. burjaeticus, B. florilegus and B. cryptarum based on mitochondrial DNA markers: a complex of closely related taxa with circumpolar distribution (Hymenoptera: Apidae: Bombus))
Fig. 2: Tree topology calculated as Maximum-Likelihood tree using Bayesian MCMC analysis with the general time reversal model of base substitutions with gamma distribution.
Data from: A RAD-sequencing approach to genome-wide marker discovery, genotyping, and phylogenetic inference in a diverse radiation of primates
Until recently, most phylogenetic and population genetics studies of nonhuman primates have relied on mitochondrial DNA and/or a small number of nuclear DNA markers, which can limit our understanding of primate evolutionary and population history. Here, we describe a cost-effective reduced representation method (ddRAD-seq) for identifying and genotyping large numbers of SNP loci for taxa from across the New World monkeys, a diverse radiation of primates that shared a common ancestor ~20-26 mya. We also estimate, for the first time, the phylogenetic relationships among 15 of the 22 currently-recognized genera of New World monkeys using ddRAD-seq SNP data using both maximum likelihood and quartet-based coalescent methods. Our phylogenetic analyses robustly reconstructed three monophyletic clades corresponding to the three families of extant platyrrhines (Atelidae, Pitheciidae and Cebidae), with Pitheciidae as basal within the radiation. At the genus level, our results conformed well with previous phylogenetic studies and provide additional information relevant to the problematic position of the owl monkey (Aotus) within the family Cebidae, suggesting a need for further exploration of incomplete lineage sorting and other explanations for phylogenetic discordance, including introgression. Our study additionally provides one of the first applications of next-generation sequencing methods to the inference of phylogenetic history across an old, diverse radiation of mammals and highlights the broad promise and utility of ddRAD-seq data for molecular primatology.
Data from: A RAD-sequencing approach to genome-wide marker discovery, genotyping, and phylogenetic inference in a diverse radiation of primates
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Development of novel, Exon-Primed Intron-Crossing (EPIC) markers from EST databases and evaluation of their phylogenetic utility in Commiphora (Burseraceae)
Premise of the study: Novel nuclear exon-primed intron-crossing (EPIC) markers were developed to increase phylogenetic resolution among recently diverged lineages in the frankincense and myrrh family, Burseraceae, using Citrus, Arabidopsis, and Oryza genome resources. Methods and Results: Primer pairs for 48 nuclear introns were developed using the genome resource IntrEST and were screened using species of Commiphora and other Burseraceae taxa. Four putative intron regions (RPT6A, BXL2, mtATP Synthase D, and Rab6) sequenced successfully for multiple taxa and recovered phylogenies consistent with those of existing studies. In some cases, these regions yielded informative sequence variation on par with that of the nrDNA internal transcribed spacer. Conclusions: The combination of freely available genome resources and our design criteria have uncovered four, single-copy nuclear intron regions that are useful for phylogenetic reconstruction of Burseraceae taxa. Because our EPIC primers also amplify Arabidopsis, we recommend their trial in other rosid and eudicot lineages.
Data from: Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in phylogenetic trees of phylogenetic marker genes
BACKGROUND: Most of our knowledge about the ancient evolutionary history of organisms has been derived from data associated with specific known organisms (i.e., organisms that we can study directly such as plants, metazoans, and culturable microbes). Recently, however, a new source of data for such studies has arrived: DNA sequence data generated directly from environmental samples. Such metagenomic data has enormous potential in a variety of areas including, as we argue here, in studies of very early events in the evolution of gene families and of species. METHODOLOGY/PRINCIPAL FINDINGS: We designed and implemented new methods for analyzing metagenomic data and used them to search the Global Ocean Sampling (GOS) Expedition data set for novel lineages in three gene families commonly used in phylogenetic studies of known and unknown organisms: small subunit rRNA and the recA and rpoB superfamilies. Though the methods available could not accurately identify very deeply branched ss-rRNAs (largely due to difficulties in making robust sequence alignments for novel rRNA fragments), our analysis revealed the existence of multiple novel branches in the recA and rpoB gene families. Analysis of available sequence data likely from the same genomes as these novel recA and rpoB homologs was then used to further characterize the possible organismal source of the novel sequences. CONCLUSIONS/SIGNIFICANCE: Of the novel recA and rpoB homologs identified in the metagenomic data, some likely come from uncharacterized viruses while others may represent ancient paralogs not yet seen in any cultured organism. A third possibility is that some come from novel cellular lineages that are only distantly related to any organisms for which sequence data is currently available. If there exist any major, but so-far-undiscovered, deeply branching lineages in the tree of life, we suggest that methods such as those described herein currently offer the best way to search for them.
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: 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.
FIGURE. (A) Summary phylogeny showing relations between genera in tribe Phyllantheae from Bayesian and Maximum Likelihood analysis of five markers (ITS, PHYC, accD–psaI, trnS–trnG, matK), modified from Appendix 1. Classification is shown of genera (right column), subgenera (middle column) and sections (except for the genus Phyllanthus. Sections not included in phylogenetic analyses and those for the genus Flueggea were omitted. (B) summary phylogeny of the genus Phyllanthus as envisioned here with subgenera and sections of groups included in phylogenetic studies shown. in A revised phylogenetic classification of tribe Phyllantheae (Phyllanthaceae)
FIGURE. (A) Summary phylogeny showing relations between genera in tribe Phyllantheae from Bayesian and Maximum Likelihood analysis of five markers (ITS, PHYC, accD–psaI, trnS–trnG, matK), modified from Appendix 1. Classification is shown of genera (right column), subgenera (middle column) and sections (except for the genus Phyllanthus. Sections not included in phylogenetic analyses and those for the genus Flueggea were omitted. (B) summary phylogeny of the genus Phyllanthus as envisioned here with subgenera and sections of groups included in phylogenetic studies shown.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
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
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.