Population genomic evidence for radiative divergence of four Orychophragmus (Brassicaceae) species in eastern Asia

2019 ◽  
Vol 191 (1) ◽  
pp. 18-29 ◽  
Author(s):  
Linling Zhong ◽  
Huanhuan Liu ◽  
Dafu Ru ◽  
Huan Hu ◽  
Quanjun Hu
Keyword(s):  
Statistical Tests ◽  
Phylogenetic Analyses ◽  
Genomic Data ◽  
Gene Trees ◽  
Eastern Asia ◽  
Interspecific Relationships ◽  
Population Genomic ◽  
Interspecific Divergence ◽  
Alternative Hypotheses ◽  
Genetic Clusters

Abstract Radiation rather than bifurcating divergence has been inferred through a number of phylogenetic analyses using different DNA fragments. However, such inferences have rarely been tested by examining alternative hypotheses based on population genomic data. In this study, we sequenced the transcriptomes of 32 individuals from 13 populations of four Orychophragmus spp. (Brassicaceae) to investigate their divergence history. Cluster and population structure analyses recovered four distinct genetic clusters without any genetic mixture. Most orthologous genes produced unresolved bifurcating interspecific relationships with a star phylogeny. The resolved gene trees were highly inconsistent with each another in reconstructing interspecific relationships. Population genomic analyses suggested unexpectedly high genetic divergence and a lack of gene flow between the four species. We examined radiation vs. bifurcating divergence between these four species based on coalescent modelling tests of population genomic data. Our statistical tests supported a radiation of these species from a common ancestor at almost the same time, rejecting stepwise bifurcating interspecific divergence with time. This nearly simultaneous radiation was dated to the Quaternary, during which climate changes are suggested to have promoted species diversity in eastern Asia. Our results highlight the importance of population genomic data and statistical tests in deciphering interspecific relationships and tracing the divergence histories of closely related species.

scholarly journals Punctuated invasion of water, ice, snow and terrestrial ecozones by segmented worms (Oligochaeta: Enchytraeidae: Mesenchytraeus )

2017 ◽  
Vol 284 (1864) ◽  
pp. 20171081 ◽  
Author(s):  
Shirley A. Lang ◽  
Naim Saglam ◽  
Joseph Kawash ◽  
Daniel H. Shain
Keyword(s):  
North America ◽  
Phylogenetic Analyses ◽  
Extreme Environments ◽  
Gene Trees ◽  
Habitat Types ◽  
Rapid Radiation ◽  
Water Ice ◽  
Interspecific Divergence ◽  
The Pacific ◽  
Northwestern Region

Segmented worms (Annelida) are among the most successful animal inhabitants of extreme environments worldwide. An unusual group of enchytraeid oligochaetes of genus Mesenchytraeus are abundant in the Pacific northwestern region of North America and occupy geographically proximal ecozones ranging from low elevation rainforests and waterways to high altitude glaciers. Along this altitudinal transect, Mesenchytraeus representatives from disparate habitat types were collected and subjected to deep mitochondrial and nuclear phylogenetic analyses. Our data identify significant topological discordance among gene trees, and near equivalent interspecific divergence levels indicative of a rapid radiation event. Collectively, our results identify a Mesenchytraeus ‘explosion’ coincident with mountain building in the Pacific northwestern region that gave rise to closely related aquatic, ice, snow and terrestrial worms.

scholarly journals Population genomic data in spider mites point to a role for local adaptation in shaping range shifts

2020 ◽  
Vol 13 (10) ◽  
pp. 2821-2835
Author(s):  
Lei Chen ◽  
Jing‐Tao Sun ◽  
Peng‐Yu Jin ◽  
Ary A. Hoffmann ◽  
Xiao‐Li Bing ◽  
...  
Keyword(s):  
Local Adaptation ◽  
Genomic Data ◽  
Spider Mites ◽  
Range Shifts ◽  
Population Genomic

Elusive Relationships Within Order Fabales: Phylogenetic Analyses Using matK and rbcL Sequence Data

2009 ◽  
Vol 34 (1) ◽  
pp. 102-114 ◽  
Author(s):  
M. A. Bello ◽  
A. Bruneau ◽  
F. Forest ◽  
J. A. Hawkins
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Morphological Evidence ◽  
Taxon Sampling ◽  
Rapid Radiation ◽  
Bayesian Approaches ◽  
Molecular Studies ◽  
Alternative Hypotheses ◽  
The One ◽  
Good Support

The order Fabales, including Leguminosae, Polygalaceae, Quillajaceae and Surianaceae, represents a novel hypothesis emerging from angiosperm molecular phylogenies. Despite good support for the order, molecular studies to date have suggested contradictory, poorly supported interfamilial relationships. Our reappraisal of relationships within Fabales addresses past taxon sampling deficiencies, and employs parsimony and Bayesian approaches using sequences from the plastid regions rbcL (166 spp.) and matK (78 spp.). Five alternative hypotheses for interfamilial relationships within Fabales were recovered. The Shimodaira-Hasegawa test found the likelihood of a resolved topology significantly higher than the one calculated for a polytomy, but did not favour any of the alternative hypotheses of relationship within Fabales. In the light of the morphological evidence available and the comparative behavior of rbcL and matK, the topology recovering Polygalaceae as sister to the rest of the order Fabales with Leguminosae more closely related to Quillajaceae + Surianaceae, is considered the most likely hypothesis of interfamilial relationships of the order. Dating of selected crown clades in the Fabales phylogeny using penalized likelihood suggests rapid radiation of the Leguminosae, Polygalaceae, and (Quillajaceae + Surianaceae) crown clades.

scholarly journals Mosaic Genomes of the Six Major Primate Lentivirus Lineages Revealed by Phylogenetic Analyses

2003 ◽  
Vol 77 (13) ◽  
pp. 7202-7213 ◽  
Author(s):  
Marco Salemi ◽  
Tulio De Oliveira ◽  
Valerie Courgnaud ◽  
Vincent Moulton ◽  
Barbara Holland ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Statistical Tests ◽  
Phylogenetic Analyses ◽  
Decomposition Analysis ◽  
Phylogeny Reconstruction ◽  
Origin And Evolution ◽  
Immunodeficiency Virus ◽  
Primate Lentiviruses ◽  
Recombinant Fragments ◽  
Clustering Patterns

ABSTRACT To clarify the origin and evolution of the primate lentiviruses (PLVs), which include human immunodeficiency virus types 1 and 2 as well as their simian relatives, simian immunodeficiency viruses (SIVs), isolated from several host species, we investigated the phylogenetic relationships among the six supposedly nonrecombinant PLV lineages for which the full genome sequences are available. Employing bootscanning as an exploratory tool, we located several regions in the PLV genome that seem to have uncertain or conflicting phylogenetic histories. Phylogeny reconstruction based on distance and maximum-likelihood algorithms followed by a number of statistical tests confirms the existence of at least five putative recombinant fragments in the PLV genome with different clustering patterns. Split decomposition analysis also shows that phylogenetic relationships among PLVs may be better represented by network-based graphs, such as the ones produced by SplitsTree. Our findings not only imply that the six so-called pure PLV lineages have in fact mosaic genomes but also make more unlikely the hypothesis of cospeciation of SIVs and their simian hosts.

scholarly journals Early replacement of West Eurasian male Y chromosomes from the east

2019 ◽  
Author(s):  
Pille Hallast ◽  
Anastasia Agdzhoyan ◽  
Oleg Balanovsky ◽  
Yali Xue ◽  
Chris Tyler-Smith
Keyword(s):  
Phylogenetic Analyses ◽  
Early Period ◽  
South East Asia ◽  
Eastern Asia ◽  
Population Movements ◽  
Dna Analyses ◽  
Y Chromosomes ◽  
Time Period ◽  
African Populations ◽  
Extensive Information

AbstractThe genomes of humans outside Africa originated almost entirely from a single migration out ∼50,000-60,000 years ago1,2, followed closely by mixture with Neanderthals contributing ∼2% to all non-Africans3,4. However, the details of this initial migration remain poorly-understood because no ancient DNA analyses are available from this key time period, and present-day autosomal data are uninformative due to subsequent population movements/reshaping5. One locus, however, does retain extensive information from this early period: the Y-chromosome, where a detailed calibrated phylogeny has been constructed6. Three present-day Y lineages were carried by the initial migration: the rare haplogroup D, the moderately rare C, and the very common FT lineage which now dominates most non-African populations6,7. We show that phylogenetic analyses of haplogroup C, D and FT sequences, including very rare deep-rooting lineages, together with phylogeographic analyses of ancient and present-day non-African Y-chromosomes, all point to East/South-east Asia as the origin 50,000-55,000 years ago of all known non-African male lineages (apart from recent migrants). This implies that the initial Y lineages in populations between Africa and eastern Asia have been entirely replaced by lineages from the east, contrasting with the expectations of the serial-founder model8,9, and thus informing and constraining models of the initial expansion.

scholarly journals Inferring Adaptive Introgression Using Hidden Markov Models

2020 ◽  
Author(s):  
Jesper Svedberg ◽  
Vladimir Shchur ◽  
Solomon Reinman ◽  
Rasmus Nielsen ◽  
Russell Corbett-Detig
Keyword(s):  
Markov Models ◽  
Hidden Markov ◽  
Genomic Data ◽  
Diverse Populations ◽  
Powerful Method ◽  
Adaptive Genetic Variation ◽  
Adaptive Introgression ◽  
Population Genomic ◽  
Significant Interest ◽  
Selection Parameters

AbstractAdaptive introgression - the flow of adaptive genetic variation between species or populations - has attracted significant interest in recent years and it has been implicated in a number of cases of adaptation, from pesticide resistance and immunity, to local adaptation. Despite this, methods for identification of adaptive introgression from population genomic data are lacking. Here, we present Ancestry_HMM-S, a Hidden Markov Model based method for identifying genes undergoing adaptive introgression and quantifying the strength of selection acting on them. Through extensive validation, we show that this method performs well on moderately sized datasets for realistic population and selection parameters. We apply Ancestry_HMM-S to a dataset of an admixed Drosophila melanogaster population from South Africa and we identify 17 loci which show signatures of adaptive introgression, four of which have previously been shown to confer resistance to insecticides. Ancestry_HMM-S provides a powerful method for inferring adaptive introgression in datasets that are typically collected when studying admixed populations. This method will enable powerful insights into the genetic consequences of admixture across diverse populations. Ancestry_HMM-S can be downloaded from https://github.com/jesvedberg/Ancestry_HMM-S/.

scholarly journals Estimating Seven Coefficients of Pairwise Relatedness Using Population-Genomic Data

Genetics ◽  
2017 ◽  
Vol 206 (1) ◽  
pp. 105-118 ◽  
Author(s):  
Matthew S. Ackerman ◽  
Parul Johri ◽  
Ken Spitze ◽  
Sen Xu ◽  
Thomas G. Doak ◽  
...  
Keyword(s):  
Genomic Data ◽  
Population Genomic

Redescription and SSU rRNA gene-based phylogeny of an anaerobic ciliate, Plagiopyla ovata Kahl, 1931 (Ciliophora, Plagiopylea)

2021 ◽  
Vol 71 (8) ◽  
Author(s):  
Ran Li ◽  
Wenbao Zhuang ◽  
Congcong Wang ◽  
Hamed El-Serehy ◽  
Saleh A. Al-Farraj ◽  
...  
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Small Subunit ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Gene Trees ◽  
Ssu Rrna Gene ◽  
Anaerobic Ciliate ◽  
Pr China

The morphology and molecular phylogeny of Plagiopyla ovata Kahl, 1931, a poorly known anaerobic ciliate, were investigated based on a population isolated from sand samples collected from the Yellow Sea coast at Qingdao, PR China. Details of the oral ciliature are documented for the first time to our knowledge and an improved species diagnosis is given. The small subunit ribosomal RNA (SSU rRNA) gene was newly sequenced and phylogenetic analyses revealed that P. ovata clusters within the monophyletic family Plagiopylidae. However, evolutionary relationships within both the family Plagiopylidae and the genus Plagiopyla remain obscure owing to undersampling, the lack of sequence data from known species and low nodal support or unstable topologies in gene trees. A key to the identification of the species of the genus Plagiopyla with validly published names is also supplied.

scholarly journals Equitable Expanded Carrier Screening Needs Indigenous Clinical and Population Genomic Data

2020 ◽  
Vol 107 (2) ◽  
pp. 175-182
Author(s):  
Simon Easteal ◽  
Ruth M. Arkell ◽  
Renzo F. Balboa ◽  
Shayne A. Bellingham ◽  
Alex D. Brown ◽  
...  
Keyword(s):  
Genomic Data ◽  
Carrier Screening ◽  
Expanded Carrier Screening ◽  
Population Genomic

scholarly journals Genomic Characterization and Curation of UCEs Improves Species Tree Reconstruction

2020 ◽  
Author(s):  
Matthew H Van Dam ◽  
James B Henderson ◽  
Lauren Esposito ◽  
Michelle Trautwein
Keyword(s):  
Marine Invertebrates ◽  
Phylogenetic Analyses ◽  
Single Gene ◽  
Gene Tree ◽  
Single Copy ◽  
Species Tree ◽  
Bootstrap Support ◽  
Gene Trees ◽  
Species Trees ◽  
Tree Reconstruction

Abstract Ultraconserved genomic elements (UCEs) are generally treated as independent loci in phylogenetic analyses. The identification pipeline for UCE probes does not require prior knowledge of genetic identity, only selecting loci that are highly conserved, single copy, without repeats, and of a particular length. Here, we characterized UCEs from 11 phylogenomic studies across the animal tree of life, from birds to marine invertebrates. We found that within vertebrate lineages, UCEs are mostly intronic and intergenic, while in invertebrates, the majority are in exons. We then curated four different sets of UCE markers by genomic category from five different studies including: birds, mammals, fish, Hymenoptera (ants, wasps, and bees), and Coleoptera (beetles). Of genes captured by UCEs, we find that many are represented by two or more UCEs, corresponding to nonoverlapping segments of a single gene. We considered these UCEs to be nonindependent, merged all UCEs that belonged to a particular gene, constructed gene and species trees, and then evaluated the subsequent effect of merging cogenic UCEs on gene and species tree reconstruction. Average bootstrap support for merged UCE gene trees was significantly improved across all data sets apparently driven by the increase in loci length. Additionally, we conducted simulations and found that gene trees generated from merged UCEs were more accurate than those generated by unmerged UCEs. As loci length improves gene tree accuracy, this modest degree of UCE characterization and curation impacts downstream analyses and demonstrates the advantages of incorporating basic genomic characterizations into phylogenomic analyses. [Anchored hybrid enrichment; ants; ASTRAL; bait capture; carangimorph; Coleoptera; conserved nonexonic elements; exon capture; gene tree; Hymenoptera; mammal; phylogenomic markers; songbird; species tree; ultraconserved elements; weevils.]

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