scholarly journals Y-Chromosome Variation in Southern African Khoe-San Populations Based on Whole-Genome Sequences

2020 ◽  
Vol 12 (7) ◽  
pp. 1031-1039 ◽  
Author(s):  
Thijessen Naidoo ◽  
Jingzi Xu ◽  
Mário Vicente ◽  
Helena Malmström ◽  
Himla Soodyall ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Sequence Data ◽  
Demographic History ◽  
Data Sets ◽  
High Coverage ◽  
Hunter Gatherers ◽  
Data Set ◽  
Chromosome Sequence ◽  
Shared Ancestry ◽  
Chromosome Variant

Abstract Although the human Y chromosome has effectively shown utility in uncovering facets of human evolution and population histories, the ascertainment bias present in early Y-chromosome variant data sets limited the accuracy of diversity and TMRCA estimates obtained from them. The advent of next-generation sequencing, however, has removed this bias and allowed for the discovery of thousands of new variants for use in improving the Y-chromosome phylogeny and computing estimates that are more accurate. Here, we describe the high-coverage sequencing of the whole Y chromosome in a data set of 19 male Khoe-San individuals in comparison with existing whole Y-chromosome sequence data. Due to the increased resolution, we potentially resolve the source of haplogroup B-P70 in the Khoe-San, and reconcile recently published haplogroup A-M51 data with the most recent version of the ISOGG Y-chromosome phylogeny. Our results also improve the positioning of tentatively placed new branches of the ISOGG Y-chromosome phylogeny. The distribution of major Y-chromosome haplogroups in the Khoe-San and other African groups coincide with the emerging picture of African demographic history; with E-M2 linked to the agriculturalist Bantu expansion, E-M35 linked to pastoralist eastern African migrations, B-M112 linked to earlier east-south gene flow, A-M14 linked to shared ancestry with central African rainforest hunter-gatherers, and A-M51 potentially unique to the Khoe-San.

scholarly journals Limits and Convergence properties of the Sequentially Markovian Coalescent

2020 ◽  
Author(s):  
Thibaut Sellinger ◽  
Diala Abu Awad ◽  
Aurélien Tellier
Keyword(s):  
Sequence Data ◽  
Demographic History ◽  
Simulated Data ◽  
Simultaneous Estimation ◽  
Data Sets ◽  
Performance Limits ◽  
Biological Variables ◽  
Convergence Proofs ◽  
New Interpretation ◽  
Population Demographic

AbstractMany methods based on the Sequentially Markovian Coalescent (SMC) have been and are being developed. These methods make use of genome sequence data to uncover population demographic history. More recently, new methods have extended the original theoretical framework, allowing the simultaneous estimation of the demographic history and other biological variables. These methods can be applied to many different species, under different model assumptions, in hopes of unlocking the population/species evolutionary history. Although convergence proofs in particular cases have been given using simulated data, a clear outline of the performance limits of these methods is lacking. We here explore the limits of this methodology, as well as present a tool that can be used to help users quantify what information can be confidently retrieved from given datasets. In addition, we study the consequences for inference accuracy violating the hypotheses and the assumptions of SMC approaches, such as the presence of transposable elements, variable recombination and mutation rates along the sequence and SNP call errors. We also provide a new interpretation of the SMC through the use of the estimated transition matrix and offer recommendations for the most efficient use of these methods under budget constraints, notably through the building of data sets that would be better adapted for the biological question at hand.

scholarly journals Inferring the Demographic History of African Farmers and Pygmy Hunter–Gatherers Using a Multilocus Resequencing Data Set

PLoS Genetics ◽  
2009 ◽  
Vol 5 (4) ◽  
pp. e1000448 ◽  
Author(s):  
Etienne Patin ◽  
Guillaume Laval ◽  
Luis B. Barreiro ◽  
Antonio Salas ◽  
Ornella Semino ◽  
...  
Keyword(s):  
Demographic History ◽  
Hunter Gatherers ◽  
Data Set ◽  
History Of

scholarly journals Linking Branch Lengths across Sets of Loci Provides the Highest Statistical Support for Phylogenetic Inference

2019 ◽  
Vol 37 (4) ◽  
pp. 1202-1210 ◽  
Author(s):  
David A Duchêne ◽  
K Jun Tong ◽  
Charles S P Foster ◽  
Sebastián Duchêne ◽  
Robert Lanfear ◽  
...  
Keyword(s):  
Empirical Data ◽  
Sequence Data ◽  
Branch Length ◽  
Data Sets ◽  
Gene Trees ◽  
Data Set ◽  
Branch Lengths ◽  
Statistical Support ◽  
Distinct Branch ◽  
Consistent Support

Abstract Evolution leaves heterogeneous patterns of nucleotide variation across the genome, with different loci subject to varying degrees of mutation, selection, and drift. In phylogenetics, the potential impacts of partitioning sequence data for the assignment of substitution models are well appreciated. In contrast, the treatment of branch lengths has received far less attention. In this study, we examined the effects of linking and unlinking branch-length parameters across loci or subsets of loci. By analyzing a range of empirical data sets, we find consistent support for a model in which branch lengths are proportionate between subsets of loci: gene trees share the same pattern of branch lengths, but form subsets that vary in their overall tree lengths. These models had substantially better statistical support than models that assume identical branch lengths across gene trees, or those in which genes form subsets with distinct branch-length patterns. We show using simulations and empirical data that the complexity of the branch-length model with the highest support depends on the length of the sequence alignment and on the numbers of taxa and loci in the data set. Our findings suggest that models in which branch lengths are proportionate between subsets have the highest statistical support under the conditions that are most commonly seen in practice. The results of our study have implications for model selection, computational efficiency, and experimental design in phylogenomics.

Assessing the usefulness of histone H3, U2 snRNA and 28S rDNA in analyses of polychaete relationships

1999 ◽  
Vol 47 (5) ◽  
pp. 499 ◽  
Author(s):  
S. Brown ◽  
G. Rouse ◽  
P. Hutchings ◽  
D. Colgan
Keyword(s):  
Maximum Parsimony ◽  
Sequence Data ◽  
Histone H3 ◽  
28S Rdna ◽  
Maximum Parsimony Analysis ◽  
Data Sets ◽  
Data Set ◽  
U2 Snrna ◽  
Dna Sequence Data ◽  
Combined Data

DNA sequence data from for histone H3 (34 species), U2 snRNA (34 species) and two segments (D1 and D9–10 expansion regions) of 28S rDNA (28 and 26 species, respectively) have been collected to investigate the relationships of polychaetes. Representatives of all of the major morphologically identified clades were used, as well as members of the Sipuncula, Echiura, Turbellaria, Clitellata and Siboglinidae (formerly the phyla Pogonophora and Vestimentifera). Maximum parsimony analyses of the separate data sets gave conflicting results and none conformed closely to previous results based on morphology. Instead each data set provided corroboration of a few of the morphological groupings, usually pairing, though inconsistently, members of the same family. Higher groupings proposed on morphological grounds were rarely recovered. Maximum parsimony analysis of the combined data, excluding areas of uncertain alignment, recovered some morphological groupings such as Cirratulidae, Terebellidae, scale worms and eunicimorphs, and did not significantly contradict others. However, some expected groupings were not recovered. Surprisingly, the fanworms (Sabellidae and Serpulidae) were not shown as sister taxa, and monophyly of Phyllodocida, a morphologically well corroborated clade, required four more steps than most parsimonious trees. Aciculata was not seen in our analyses, although it was the most strongly supported large clade in Rouse and Fauchald (1997, Cladistics and polychaetes. Zoologica Scripta 26, 138–204). Trees constrained to show Aciculata as monophyletic were 18 steps longer than the most parsimonious trees. If trees are rooted on sipunculans rather than the nematode, Aciculata is nearly recovered, being rendered paraphyletic by the inclusion of the sister-pair of Oweniidae and Chaetopteridae. As suggested by some recent morphological and molecular analyses, Siboglinidae and Clitellata may well have sister groups among polychaetes. The morphologically aberrant Sternaspidae are closest to members of Terebellida in the present analyses, supporting the placement of Rouse and Fauchald. Interesting results deserving further assessment concern the placement of Chaetopteridae, Oweniidae and Sipuncula.

scholarly journals Mitochondrial Evidence on the Phylogenetic Position of Caecilians (Amphibia: Gymnophiona)

Genetics ◽  
2000 ◽  
Vol 155 (2) ◽  
pp. 765-775
Author(s):  
Rafael Zardoya ◽  
Axel Meyer
Keyword(s):  
Tandem Repeats ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Maximum Parsimony Analysis ◽  
Bootstrap Support ◽  
Phylogenetic Position ◽  
Trna Genes ◽  
Data Sets ◽  
Data Set ◽  
Protein Coding

Abstract The complete nucleotide sequence (17,005 bp) of the mitochondrial genome of the caecilian Typhlonectes natans (Gymnophiona, Amphibia) was determined. This molecule is characterized by two distinctive genomic features: there are seven large 109-bp tandem repeats in the control region, and the sequence for the putative origin of replication of the L strand can potentially fold into two alternative secondary structures (one including part of the tRNACys). The new sequence data were used to assess the phylogenetic position of caecilians and to gain insights into the origin of living amphibians (frogs, salamanders, and caecilians). Phylogenetic analyses of two data sets—one combining protein-coding genes and the other combining tRNA genes—strongly supported a caecilian + frog clade and, hence, monophyly of modern amphibians. These two data sets could not further resolve relationships among the coelacanth, lungfishes, and tetrapods, but strongly supported diapsid affinities of turtles. Phylogenetic relationships among a larger set of species of frogs, salamanders, and caecilians were estimated with a mitochondrial rRNA data set. Maximum parsimony analysis of this latter data set also recovered monophyly of living amphibians and favored a frog + salamander (Batrachia) relationship. However, bootstrap support was only moderate at these nodes. This is likely due to an extensive among-site rate heterogeneity in the rRNA data set and the narrow window of time in which the three main groups of living amphibians were originated.

scholarly journals Polygenic adaptation and convergent evolution on growth and cardiac genetic pathways in African and Asian rainforest hunter-gatherers

2018 ◽  
Vol 115 (48) ◽  
pp. E11256-E11263 ◽  
Author(s):  
Christina M. Bergey ◽  
Marie Lopez ◽  
Genelle F. Harrison ◽  
Etienne Patin ◽  
Jacob A. Cohen ◽  
...  
Keyword(s):  
Body Size ◽  
Positive Selection ◽  
Cardiac Development ◽  
Sequence Data ◽  
Small Body ◽  
Human Populations ◽  
High Coverage ◽  
Hunter Gatherers ◽  
Genetic Changes ◽  
Evolutionary Pattern

Different human populations facing similar environmental challenges have sometimes evolved convergent biological adaptations, for example, hypoxia resistance at high altitudes and depigmented skin in northern latitudes on separate continents. The “pygmy” phenotype (small adult body size), characteristic of hunter-gatherer populations inhabiting both African and Asian tropical rainforests, is often highlighted as another case of convergent adaptation in humans. However, the degree to which phenotypic convergence in this polygenic trait is due to convergent versus population-specific genetic changes is unknown. To address this question, we analyzed high-coverage sequence data from the protein-coding portion of the genomes of two pairs of populations: Batwa rainforest hunter-gatherers and neighboring Bakiga agriculturalists from Uganda and Andamanese rainforest hunter-gatherers and Brahmin agriculturalists from India. We observed signatures of convergent positive selection between the rainforest hunter-gatherers across the set of genes with “growth factor binding” functions (P<0.001). Unexpectedly, for the rainforest groups, we also observed convergent and population-specific signatures of positive selection in pathways related to cardiac development (e.g., “cardiac muscle tissue development”; P=0.001). We hypothesize that the growth hormone subresponsiveness likely underlying the adult small body-size phenotype may have led to compensatory changes in cardiac pathways, in which this hormone also plays an essential role. Importantly, in the agriculturalist populations, we did not observe similar patterns of positive selection on sets of genes associated with growth or cardiac development, indicating our results most likely reflect a history of convergent adaptation to the similar ecology of rainforests rather than a more general evolutionary pattern.

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.

Morphological data, molecular data, and total evidence in phylogenetic analysis

1995 ◽  
Vol 73 (S1) ◽  
pp. 667-676 ◽  
Author(s):  
Anders Tehler
Keyword(s):  
Molecular Phylogeny ◽  
Sequence Data ◽  
Molecular Data ◽  
Sister Species ◽  
Total Evidence ◽  
Morphological Data ◽  
Data Sets ◽  
Data Set ◽  
Morphological And Molecular Data ◽  
Congruence Test

Two data sets, one morphological and one molecular, for ascolocular fungi have been analysed separately for taxonomic congruence and in combination for total evidence. Data were analysed with cladistic parsimony, the total support test, and the congruence test. The morphological data set comprised 15 characters and four species, Arthonia radiata, Dendrographa leucophaea, Lecanactis abietina, and Schismatomma pericleum (Arthoniales). The molecular data include the same species and comprised sequence data with 21 informative sites from approximately half of the 18S ribosomal RNA gene. The morphological phylogeny is corroborated by the molecular phylogeny with regard to relationships of Arthonia radiata, Schismatomma pericleum, and Dendrographa leucophaea. But in the molecular phylogeny Lecanactis abietina is placed as a sister species to the former three species. In the phylogeny inferred from morphological data Lecanactis abietina and Dendrographa leucophaea constitute a sister pair with Schismatomma pericleum followed by Arthonia radiata as subsequent sister taxa. The consensus obtained from the taxonomic congruence method was fully collapsed and uninformative. The combined morphological and molecular data in total evidence produced one most parsimonious cladogram. In total evidence Lecanactis abietina is placed as sister species to Schismatomma pericleum and Dendrographa leucophaea all with Arthonia radiata as sister species. The most resolved and phylogenetically informative hypothesis was obtained from cladistic parsimony analysis using total evidence. A review of congruence between morphological and molecular data in determining gross relationships within the Eumycota and Ascomycetes is also given. Key words: Ascomycetes, Arthoniales, phylogeny, cladistics, taxonomic congruence, total evidence, 18SrDNA.

scholarly journals Refining the Y chromosome phylogeny with southern African sequences

2015 ◽  
Author(s):  
Chiara Barbieri ◽  
Alexander Hübner ◽  
Enrico Macholdt ◽  
Shengyu Ni ◽  
Sebastian Lippold ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Large Scale ◽  
Sequence Data ◽  
Population Expansion ◽  
Branch Length ◽  
Paternal Age ◽  
Effective Population ◽  
Chromosome Sequence ◽  
Human Y Chromosome ◽  
Major Haplogroups

The recent availability of large-scale sequence data for the human Y chromosome has revolutionized analyses of and insights gained from this non-recombining, paternally inherited chromosome. However, the studies to date focus on Eurasian variation, and hence the diversity of early-diverging branches found in Africa has not been adequately documented. Here we analyze over 900 kb of Y chromosome sequence obtained from 547 individuals from southern African Khoisan and Bantu-speaking populations, identifying 232 new sequences from basal haplogroups A and B. We find new branches within haplogroups A2 and A3b1 and suggest that the prehistory of haplogroup B2a is more complex than previously suspected; this haplogroup is likely to have existed in Khoisan groups before the arrival of Bantu-speakers, who brought additional B2a lineages to southern Africa. Furthermore, we estimate older dates than obtained previously for both the A2-T node within the human Y chromosome phylogeny and for some individual haplogroups. Finally, there is pronounced variation in branch length between major haplogroups; haplogroups associated with Bantu-speakers have significantly longer branches. This likely reflects a combination of biases in the SNP calling process and demographic factors, such as an older average paternal age (hence a higher mutation rate), a higher effective population size, and/or a stronger effect of population expansion for Bantu-speakers than for Khoisan groups.

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