Nuclear DNA diversity, population differentiation, and phylogenetic relationships in the California closed-cone pines based on RAPD and allozyme markers

Genome ◽  
1999 ◽  
Vol 42 (5) ◽  
pp. 893-908 ◽  
Author(s):  
J Wu ◽  
K V Krutovskii ◽  
S H Strauss
Keyword(s):  
Population Differentiation ◽  
Rapd Markers ◽  
Nuclear Dna ◽  
Gene Diversity ◽  
Phylogenetic Analyses ◽  
Nuclear Gene ◽  
Published Data ◽  
Data Set ◽  
Closed Cone ◽  
Allozyme Loci

We studied nuclear gene diversity and population differentiation using 91-98 randomly amplified polymorphic DNA (RAPD) loci in the California closed-cone pines knobcone (Pinus attenuata Lemm.), bishop (P. muricata D. Don), and Monterey (P. radiata D. Don) pines. A total of 384 trees from 13 populations were analyzed for RAPDs and another sample of 242 trees from 12 of these 13 populations were analyzed at 32-36 allozyme loci, using a published data set. Twenty-eight of 30 (93%) comigrating RAPD fragments tested were found to be homologous by Southern hybridization in all three species. Using an enriched mitochondrial DNA (mtDNA) preparation and a chloroplast DNA (cpDNA) library as probes, two fragments of cpDNA origin, and one of mtDNA origin present among RAPD profiles were excluded from analysis of nuclear gene diversity. RAPD markers revealed moderately higher intrapopulation gene diversity and substantially higher total genetic diversity and population differentiation than did allozyme markers for each species. We performed a simulation study using allozyme data, which showed that the dominant and biallelic nature of RAPD markers could explain the differences observed in differentiation parameters, but not in gene diversity; RAPD phenotypes appear to represent more underlying gene diversity than do allozyme phenotypes. Results of joint phylogenetic analyses of both the RAPD and allozyme markers strongly supported a common ancestor for P. radiata and P. attenuata pines, and south-to-north migration histories for all three species.Key words: allozymes, dominance, gene diversity, Pinus attenuata, Pinus muricata, Pinus radiata, phylogeny, RAPDs.

scholarly journals Measwring and Testing Genetic Differentiation With Ordered Versus Unordered Alleles

Genetics ◽  
1996 ◽  
Vol 144 (3) ◽  
pp. 1237-1245 ◽  
Author(s):  
O Pons ◽  
R J Petit
Keyword(s):  
Dna Sequences ◽  
Nuclear Dna ◽  
Mutation Rates ◽  
Phylogeographic Structure ◽  
Published Data ◽  
Data Set ◽  
Subdivided Populations ◽  
Two Measures ◽  
The Difference ◽  
Single Data

Abstract Estimates and variances of diversity and differentiation measures in subdivided populations are proposed that can be applied to haplotypes (ordered alleles such as DNA sequences, which may contain a record of their own histories). Hence, two measures of differentiation can be compared for a single data set: one (GST) that makes use only of the allelic frequencies and the other (NST) for which similarities between the haplotypes are taken into account in addition. Tests are proposed to compare NST and GST with zero and with each other. The difference between NST and GST can be caused by several factors, including sampling artefacts, unequal effect of mutation rates and phylogeographic structure. The method presented is applied to a published data set where a nuclear DNA sequence had been determined from individuals of a grasshopper distributed in 24 regions of Europe. Additional insights into the genetic subdivision of these populations are obtained by progressively combining related haplotypes and reanalyzing the data each time.

Squamate relationships based on C-mos nuclear DNA sequences: increased taxon sampling improves bootstrap support

2001 ◽  
Vol 22 (2) ◽  
pp. 235-242 ◽  
Author(s):  
J.C. Marshall ◽  
K.A. Crandall ◽  
D.J. Harris
Keyword(s):  
Dna Sequences ◽  
Nuclear Dna ◽  
Sequence Data ◽  
Nuclear Gene ◽  
Bootstrap Support ◽  
Published Data ◽  
Robust Estimate ◽  
Independent Evidence ◽  
Rapid Speciation ◽  
Mtdna Sequence

AbstractSequences of the nuclear gene C-mos from 16 new species have been combined with previously published data to produce an analysis of squamate relationships using 56 taxa, considerably more than in previous analyses. Support for many nodes is greatly increased, thus producing a more robust assessment of relationships. Sampling was concentrated within the families Iguanidae and Lacertidae, both of which have poorly supported phylogenies based on mtDNA sequence data. Our analysis supports a robust estimate of relationships within the Iguanidae. Within the Lacertidae relationships are only partially well resolved, and this provides independent evidence for rapid speciation within this family.

scholarly journals Phylogenomics With Hyb-Seq Unravels Korean Hosta Evolution

2021 ◽  
Vol 12 ◽  
Author(s):  
Mi-Jeong Yoo ◽  
Byoung-Yoon Lee ◽  
Sangtae Kim ◽  
Chae Eun Lim
Keyword(s):  
Phylogenetic Analyses ◽  
Ornamental Plants ◽  
Introgressive Hybridization ◽  
Nuclear Gene ◽  
Genomic Data ◽  
Data Set ◽  
History Of ◽  
Large Genome Size ◽  
Taxonomic Confusion ◽  
Do So

The genus Hosta (Agavoideae and Asparagaceae) is one of the most popular landscaping and ornamental plants native to temperate East Asia. Their popularity has led to extensive hybridization to develop various cultivars. However, their long history of hybridization, cultivation, and selection has brought about taxonomic confusion in the Hosta species delimitation along with their indistinguishable morphology. Here, we conducted the first broad phylogenetic analyses of Hosta species based on the most comprehensive genomic data set to date. To do so, we captured 246 nuclear gene sequences and plastomes from 55 accessions of Korean Hosta species using the Hyb-Seq method. As a result, this study provides the following novel and significant findings: (1) phylogenetic analyses of the captured sequences retrieved six species of Hosta in South Korea compared to five to eleven species based on the previous studies, (2) their phylogenetic relationships suggested that the large genome size was ancestral and the diversification of Korean Hosta species was accompanied by decreases in genome sizes, (3) comparison between nuclear genes and plastome revealed several introgressive hybridization events between Hosta species, and (4) divergence times estimated here showed that Hosta diverged 35.59 million years ago, while Korean Hosta species rapidly diversified during the late Miocene. Last, we explored whether these genomic data could be used to infer the origin of cultivars. In summary, this study provides the most comprehensive genomic resources to be used in phylogenetic, population, and conservation studies of Hosta, as well as for unraveling the origin of many cultivars.

scholarly journals Phylogenetic Estimation of Timescales Using Ancient DNA: The Effects of Temporal Sampling Scheme and Uncertainty in Sample Ages

2012 ◽  
Vol 30 (2) ◽  
pp. 253-262 ◽  
Author(s):  
Martyna Molak ◽  
Eline D. Lorenzen ◽  
Beth Shapiro ◽  
Simon Y.W. Ho
Keyword(s):  
Ancient Dna ◽  
Dna Sequences ◽  
Estimation Error ◽  
Phylogenetic Analyses ◽  
Published Data ◽  
Molecular Clocks ◽  
Data Sets ◽  
Data Set ◽  
Temporal Sampling ◽  
The Impact

Abstract In recent years, ancient DNA has increasingly been used for estimating molecular timescales, particularly in studies of substitution rates and demographic histories. Molecular clocks can be calibrated using temporal information from ancient DNA sequences. This information comes from the ages of the ancient samples, which can be estimated by radiocarbon dating the source material or by dating the layers in which the material was deposited. Both methods involve sources of uncertainty. The performance of Bayesian phylogenetic inference depends on the information content of the data set, which includes variation in the DNA sequences and the structure of the sample ages. Various sources of estimation error can reduce our ability to estimate rates and timescales accurately and precisely. We investigated the impact of sample-dating uncertainties on the estimation of evolutionary timescale parameters using the software BEAST. Our analyses involved 11 published data sets and focused on estimates of substitution rate and root age. We show that, provided that samples have been accurately dated and have a broad temporal span, it might be unnecessary to account for sample-dating uncertainty in Bayesian phylogenetic analyses of ancient DNA. We also investigated the sample size and temporal span of the ancient DNA sequences needed to estimate phylogenetic timescales reliably. Our results show that the range of sample ages plays a crucial role in determining the quality of the results but that accurate and precise phylogenetic estimates of timescales can be made even with only a few ancient sequences. These findings have important practical consequences for studies of molecular rates, timescales, and population dynamics.

scholarly journals Compositional heterogeneity and outgroup choice influence the internal phylogeny of the ants

2017 ◽  
Author(s):  
Marek L. Borowiec ◽  
Christian Rabeling ◽  
Seán G. Brady ◽  
Brian L. Fisher ◽  
Ted R. Schultz ◽  
...  
Keyword(s):  
Molecular Phylogenetics ◽  
Phylogenetic Analyses ◽  
Nuclear Gene ◽  
Phylogenetic Inference ◽  
Death Process ◽  
Compositional Heterogeneity ◽  
Data Set ◽  
Key Species ◽  
Divergence Dating ◽  
Birth Death

AbstractKnowledge of the internal phylogeny and evolutionary history of ants (Formicidae), the world’s most species-rich clade of eusocial organisms, has dramatically improved since the advent of molecular phylogenetics. A number of relationships at the subfamily level, however, remain uncertain. Key unresolved issues include placement of the root of the ant tree of life and the relationships among the so-called poneroid subfamilies. Here we assemble a new data set to attempt a resolution of these two problems and carry out divergence dating, focusing on the age of the root node of crown Formicidae. For the phylogenetic analyses we included data from 110 ant species, including the key species Martialis heureka. We focused taxon sampling on non-formicoid lineages of ants to gain insight about deep nodes in the ant phylogeny. For divergence dating we retained a subset of 62 extant taxa and 42 fossils in order to approximate diversified sampling in the context of the fossilized birth-death process. We sequenced 11 nuclear gene fragments for a total of ~7.5 kb and investigated the DNA sequence data for the presence of among-taxon compositional heterogeneity, a property known to mislead phylogenetic inference, and for its potential to affect the rooting of the ant phylogeny. We found sequences of the Leptanillinae and several outgroup taxa to be rich in adenine and thymine (51% average AT content) compared to the remaining ants (45% average). To investigate whether this heterogeneity could bias phylogenetic inference we performed outgroup removal experiments, analysis of compositionally homogeneous sites, and a simulation study. We found that compositional heterogeneity indeed appears to affect the placement of the root of the ant tree but has limited impact on more recent nodes. We put forward a novel hypothesis regarding the rooting of the ant phylogeny, in which Martialis and the Leptanillinae together constitute a clade that is sister to all other ants. After correcting for compositional heterogeneity this emerges as the best-supported hypothesis of relationships at deep nodes in the ant tree. The results of our divergence dating under the fossilized birth-death process and diversified sampling suggest that the crown Formicidae originated during the Albian or Aptian ages of the Lower Cretaceous (103–124 Ma). In addition, we found support for monophyletic poneroids comprising the subfamilies Agroecomyrmecinae, Amblyoponinae, Apomyrminae, Paraponerinae, Ponerinae, and Proceratiinae, and well-supported relationships among these subfamilies except for the placement of Proceratiinae and (Amblyoponinae + Apomyrminae). Our phylogeny also highlights the non-monophyly of several ant genera, including Protanilla and Leptanilla in the Leptanillinae, Proceratium in the Proceratiinae, and Cryptopone, Euponera, and Mesoponera within the Ponerinae.

scholarly journals Phylogenetic relationships in the southern African genus Drosanthemum (Ruschioideae, Aizoaceae)

2019 ◽  
Author(s):  
Sigrid Liede-Schumann ◽  
Guido W. Grimm ◽  
Nicolai M. Nürk ◽  
Alastair J. Potts ◽  
Ulrich Meve ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Nuclear Dna ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Cape Floristic Region ◽  
Rapid Radiation ◽  
Data Set ◽  
Widespread Species ◽  
Dna Sequence Data ◽  
Phylogenetic Affinities

AbstractBackgroundDrosanthemum, the only genus of the tribe Drosanthemeae, is widespread over the Greater Cape Floristic Region in southern Africa. With 114 recognized species, Drosanthemum together with the highly succulent and species-rich tribe Ruschieae constitute the ‘core ruschioids’ in Aizoaceae. Within Drosanthemum, nine subgenera have been described based on flower and fruit morphology. Their phylogenetic relationships, however, have not yet been investigated, hampering understanding of monophyletic entities and patterns of geographic distribution.MethodsUsing chloroplast and nuclear DNA sequence data, we performed network- and tree-based phylogenetic analyses of 73 species represented by multiple accessions of Drosanthemum. A well-curated, geo-referenced occurrence data set comprising the phylogenetically studied and 867 further accessions was used to describe the distributional ranges of intrageneric lineages and the genus as a whole.ResultsPhylogenetic inference supports nine clades within Drosanthemum, seven of them group in two major clades, while the remaining two show ambiguous affinities. The nine clades are generally congruent to previously described subgenera within Drosanthemum, with exceptions such as (pseudo-) cryptic species. In-depth analyses of sequence patterns in each gene region revealed phylogenetic affinities not obvious in the phylogenetic tree. We observe a complex distribution pattern including widespread, species-rich clades expanding into arid habitats of the interior (subgenera Drosanthemum p.p., Vespertina, Xamera) that are molecular and morphologically diverse. In contrast, less species-rich, molecularly less divergent, and morphologically unique lineages are restricted to the central Cape region and more mesic conditions (Decidua, Necopina, Ossicula, Quastea, Quadrata, Speciosa). Our results suggest initial rapid radiation generating the main lineages, with some clades showing subsequent diversification.

Phylogeny of the water strider genus Aquarius Schellenberg (Heteroptera: Gerridae) based on nuclear and mitochondrial DNA sequences and morphology

2000 ◽  
Vol 31 (1) ◽  
pp. 71-90 ◽  
Author(s):  
Nils Møller Andersen ◽  
Jakob Damgaard ◽  
Felix A.H. Sperling
Keyword(s):  
Dna Sequences ◽  
Sequence Data ◽  
Mitochondrial Gene ◽  
Nuclear Gene ◽  
Molecular Data ◽  
Morphological Data ◽  
Published Data ◽  
Data Sets ◽  
Gene Encoding ◽  
Data Set

AbstractWe examined phylogenetic relationships among gerrid water striders of the genus Aquarius Schellenberg using molecular and morphological characters. The molecular data sets included 780 bp sequence data from the mitochondrial gene encoding cytochrome oxidase subunit I (COI), and 515 bp sequence data from the nuclear gene encoding elongation factor I alpha (EF-1α). The morphological data set was a slightly modified version of a previously published data set. We included all 17 known species and one subspecies of Aquarius as well as five species from three related genera, Gigantometra gigas, Limnoporus esakii, L. rufoscutellatus, Gerris pingreensis, and G. lacustris. Unweighted parsimony analyses of the COI data set gave a single most parsimonious tree (MPT) with a topology quite similar to the morphological tree. Parsimony analyses of the EF-1α data set gave 3 MPT's and a strict consensus of these trees gave a tree with a slightly different topology. A combined analysis of the three data sets gave a single MPT with the same topology as for the morphological data set alone. The phylogeny of Aquarius presented here supports the monophyly of the A. najas, remigis, conformis and paludum species groups as well as previous hypotheses about their relationships. On the other hand, the inclusion of molecular data weakens the support for the monophyly of the genus Aquarius, and questions the specific status of the eastern North American A. nebularis (as separate from A. conformis) and members of the Nearctic A. remigis group. Finally, we discuss the implications of the reconstructed phylogeny in the biogeography and ecological phylogenetics of Aquarius.

scholarly journals Phylogenetic relationships of xenodermid snakes (Squamata: Serpentes: Xenodermidae), with the description of a new genus

2021 ◽  
Vol 71 ◽  
pp. 747-763
Author(s):  
V. Deepak ◽  
Samuel Lalronunga ◽  
Esther Lalhmingliani ◽  
Abhijit Das ◽  
Surya Narayanan ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Nuclear Gene ◽  
Morphological Data ◽  
Data Set ◽  
Molecular Phylogenetic ◽  
East And Southeast Asia ◽  
Nuclear Gene Sequence

Xenodermidae is a generally poorly known lineage of caenophidian snakes found in South, East and Southeast Asia. We report molecular phylogenetic analyses for a multilocus data set comprising all five currently recognised genera and including new mitochondrial and nuclear gene sequence data for the recently described Stoliczkia vanhnuailianai. Our phylogenetic results provide very strong support for the non-monophyly of Stoliczkia, as presently constituted, with S. borneensis being more closely related to Xenodermus than to the Northeast Indian S. vanhnuailianai. Based on phylogenetic relationships and morphological distinctiveness, we transfer Stoliczkia borneensis to a new monotypic genus endemic to Borneo, Paraxenodermusgen. nov. We also present new morphological data for P. borneensis.

scholarly journals Risk of cardiac manifestations in adult mitochondrial disease caused by nuclear genetic defects

Open Heart ◽  
2021 ◽  
Vol 8 (1) ◽  
pp. e001510
Author(s):  
Albert Zishen Lim ◽  
Daniel M Jones ◽  
Matthew G D Bates ◽  
Andrew M Schaefer ◽  
John O'Sullivan ◽  
...  
Keyword(s):  
Mitochondrial Disease ◽  
Nuclear Dna ◽  
Laboratory Data ◽  
Nuclear Genome ◽  
Nuclear Gene ◽  
Left Ventricular ◽  
Adult Patients ◽  
Limited Information ◽  
Cardiac Abnormalities ◽  
Cardiac Manifestations

ObjectiveRegular cardiac surveillance is advocated for patients with primary mitochondrial DNA disease. However, there is limited information to guide clinical practice in mitochondrial conditions caused by nuclear DNA defects. We sought to determine the frequency and spectrum of cardiac abnormalities identified in adult mitochondrial disease originated from the nuclear genome.MethodsAdult patients with a genetically confirmed mitochondrial disease were identified and followed up at the national clinical service for mitochondrial disease in Newcastle upon Tyne, UK (January 2009 to December 2018). Case notes, molecular genetics reports, laboratory data and cardiac investigations, including serial electrocardiograms and echocardiograms, were reviewed.ResultsIn this cohort-based observational study, we included 146 adult patients (92 women) (mean age 53.6±18.7 years, 95% CI 50.6 to 56.7) with a mean follow-up duration of 7.9±5.1 years (95% CI 7.0 to 8.8). Eleven different nuclear genotypes were identified: TWNK, POLG, RRM2B, OPA1, GFER, YARS2, TYMP, ETFDH, SDHA, TRIT1 and AGK. Cardiac abnormalities were detected in 14 patients (9.6%). Seven of these patients (4.8%) had early-onset cardiac manifestations: hypertrophic cardiomyopathy required cardiac transplantation (AGK; n=2/2), left ventricular (LV) hypertrophy and bifascicular heart block (GFER; n=2/3) and mild LV dysfunction (GFER; n=1/3, YARS2; n=1/2, TWNK; n=1/41). The remaining seven patients had acquired heart disease most likely related to conventional cardiovascular risk factors and presented later in life (14.6±12.8 vs 55.1±8.9 years, p<0.0001).ConclusionsOur findings demonstrate that the risk of cardiac involvement is genotype specific, suggesting that routine cardiac screening is not indicated for most adult patients with nuclear gene-related mitochondrial disease.

scholarly journals The Complete DNA Sequence of the Mitochondrial Genome of a “Living Fossil,” the Coelacanth (Latimeria chalumnae)

Genetics ◽  
1997 ◽  
Vol 146 (3) ◽  
pp. 995-1010 ◽  
Author(s):  
Rafael Zardoya ◽  
Axel Meyer
Keyword(s):  
Mitochondrial Genome ◽  
Tandem Repeats ◽  
Phylogenetic Analyses ◽  
Large Data ◽  
Molecular Data ◽  
Phylogenetic Position ◽  
Data Set ◽  
Living Fossil ◽  
Latimeria Chalumnae ◽  
Relationship Of

The complete nucleotide sequence of the 16,407-bp mitochondrial genome of the coelacanth (Latimeria chalumnae) was determined. The coelacanth mitochondrial genome order is identical to the consensus vertebrate gene order which is also found in all ray-finned fishes, the lungfish, and most tetrapods. Base composition and codon usage also conform to typical vertebrate patterns. The entire mitochondrial genome was PCR-amplified with 24 sets of primers that are expected to amplify homologous regions in other related vertebrate species. Analyses of the control region of the coelacanth mitochondrial genome revealed the existence of four 22-bp tandem repeats close to its 3′ end. The phylogenetic analyses of a large data set combining genes coding for rRNAs, tRNA, and proteins (16,140 characters) confirmed the phylogenetic position of the coelacanth as a lobe-finned fish; it is more closely related to tetrapods than to ray-finned fishes. However, different phylogenetic methods applied to this largest available molecular data set were unable to resolve unambiguously the relationship of the coelacanth to the two other groups of extant lobe-finned fishes, the lungfishes and the tetrapods. Maximum parsimony favored a lungfish/coelacanth or a lungfish/tetrapod sistergroup relationship depending on which transversion:transition weighting is assumed. Neighbor-joining and maximum likelihood supported a lungfish/tetrapod sistergroup relationship.

Sign in / Sign up

Export Citation Format

Share Document