Early replacement of West Eurasian male Y chromosomes from the east

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.

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Insights on The Morphological and Phylogenetic Delimitation of Dacrymyces Nees

10.21203/rs.3.rs-950799/v1 ◽

2021 ◽

Author(s):

Renato Lúcio Mendes Alvarenga ◽

Tatiana Baptista Gibertoni

Keyword(s):

New Species ◽

Phylogenetic Analyses ◽

Molecular Data ◽

Morphological Features ◽

New Combinations ◽

Dna Analyses ◽

Homogeneous Composition ◽

Morphological And Molecular Data

Abstract Dacrymycetes has four families and 13 genera, few of them with molecular data available and then usually polyphyletic in phylogenetic analyses. Dacrymyces Nees is one of the polyphyletic genera in Dacrymycetes and it was introduced to accommodate one species, D. stillatus Nees. The morphological features of the genus are a homogeneous composition of the intra-structure and an amphigenous or superior hymenium. In this study, we included Neotropical specimens in the phylogeny of the Dacrymycetes and Dacrymyces s.s. is emended to include species with resupinate basidiomata, unilateral hymenium and heterogeneous context. In this new delimitation, the new species Dacrymyces flavobrunneus is described using morphological and molecular data and three new combinations (D. ceraceus comb. nov., D. maxidorii comb. nov. and D. spathularia comb. nov.) are proposed based on DNA analyses.

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The Study of Tourist Movements in Tourist Historic Cities: A Comparative Analysis of the Applicability of Four Different Tools

Sustainability ◽

10.3390/su11195265 ◽

2019 ◽

Vol 11 (19) ◽

pp. 5265

Author(s):

Ana Muñoz-Mazón ◽

Laura Fuentes-Moraleda ◽

Angela Chantre-Astaiza ◽

Marlon-Felipe Burbano-Fernandez

Keyword(s):

Marketing Strategies ◽

Precise Data ◽

Time Period ◽

Tourist Flows ◽

Extensive Information ◽

Customer Services ◽

Destination Management Organizations ◽

Historic City ◽

Historic Cities ◽

Tourist Information

This paper presents the results of the application of four different tools (tourist card, questionarie, GPS and NFC) with the objective to study the movement of tourists in a tourist historic city (Popayán, Colombia). Given the need for these types of cities to manage tourism in a sustainable way, and considering that the management of tourist flows is a key aspect to achieve this, the aim was to find out which of the tools applied provides more precise data on the movement of tourists in the destination. For this, information was collected on the movement of tourists with four different tools, applying each tool in four different years (2011, 2012, 2013 and 2015) during the same time period (Holy Week). For the analysis of tourist movements, the Markov chain was obtained for each period. In order to study the generation of routes geo-location was used in each case. The results show that even though GPS technology provided more information on the visited places, NFC technology facilitates more extensive information. In addition, NFC technology allowed the extraction of important information about the places visited, showing a wide number of sites visited and, therefore, providing greater value for the study. Finally, the results of the study provide a better understanding of how destination management organizations could develop more suitable alternatives of the customer services systems, the delivery of tourist information and the identification of sites with heavy use. Conclusively, this study helps to identify how to take better advantage of the marketing strategies through different tools that analyses tourism movements.

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Cost Implications of Comorbidity for Autologous Stem Cell Transplantation in Elderly Patients with Multiple Myeloma Using SEER-Medicare

Bone Marrow Research ◽

10.1155/2016/3645623 ◽

2016 ◽

Vol 2016 ◽

pp. 1-6 ◽

Cited By ~ 2

Author(s):

Gunjan L. Shah ◽

Aaron Winn ◽

Pei-Jung Lin ◽

Andreas Klein ◽

Kellie A. Sprague ◽

...

Keyword(s):

Older Patients ◽

Early Period ◽

Early Time ◽

Cost Of Care ◽

Late Time ◽

Time Period ◽

Comorbidity Burden ◽

Impact On Survival ◽

The Difference ◽

Early Time Period

Comorbidity is more common in older patients and can increase the cost of care by increasing toxicity. Using the SEER-Medicare database from 2000 to 2007, we examined the costs and life-year benefit of Auto-HSCT for MM patients over the age of 65 by evaluating the difference over time relative to comorbidity burden. One hundred ten patients had an Auto-HSCT in the early time period (2000–2003) and 160 in the late time period (2004–2007). Patients were divided by a Charlson Comorbidity Index (CCI) of 0 or greater than 1 (CCI1+). Median overall survival was 53.5 months for the late time period patients compared to 40.3 months for the early time period patients (p=0.031). Median costs for CCI0 versus CCI1+ in the early period were, respectively, $70,900 versus $72,000 (100 d); $86,100 versus $98,300 (1 yr); and $139,200 versus $195,300 (3 yrs). Median costs for late period were, respectively, $58,400 versus $60,400 (100 d); $86,300 versus $77,700 (1 yr); and $124,400 versus $110,900 (3 yrs). Comorbidity had a significant impact on survival and cost among early time period patients but not among late time period patients. Therefore, older patients with some comorbidities can be considered for Auto-HSCT depending on clinical circumstances.

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Phylogeography of Aedes (Stegomyia) aegypti (L.) and Aedes (Stegomyia) albopictus (Skuse) (Diptera: Culicidae) based on mitochondrial DNA variations

Genetics Research ◽

10.1017/s0016672305007627 ◽

2005 ◽

Vol 86 (1) ◽

pp. 1-11 ◽

Cited By ~ 124

Author(s):

LAURENCE MOUSSON ◽

CATHERINE DAUGA ◽

THOMAS GARRIGUES ◽

FRANCIS SCHAFFNER ◽

MARIE VAZEILLE ◽

...

Keyword(s):

Mitochondrial Dna ◽

Genetic Variation ◽

East Asia ◽

Ivory Coast ◽

Nadh Dehydrogenase ◽

South East Asia ◽

Nadh Dehydrogenase Subunit ◽

African Populations ◽

The Tropics ◽

Dna Variations

Aedes (Stegomyia) aegypti (L.) and Aedes (Stegomyia) albopictus (Skuse) are the most important vectors of the dengue and yellow-fever viruses. Both took advantage of trade developments to spread throughout the tropics from their native area: A. aegypti originated from Africa and A. albopictus from South-East Asia. We investigated the relationships between A. aegypti and A. albopictus mosquitoes based on three mitochondrial-DNA genes (cytochrome b, cytochrome oxidase I and NADH dehydrogenase subunit 5). Little genetic variation was observed for A. albopictus, probably owing to the recent spreading of the species via human activities. For A. aegypti, most populations from South America were found to be genetically similar to populations from South-East Asia (Thailand and Vietnam), except for one sample from Boa Vista (northern Amazonia), which was more closely related to samples from Africa (Guinea and Ivory Coast). This suggests that African populations of A. aegypti introduced during the slave trade have persisted in Boa Vista, resisting eradication campaigns.

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A comparison of chloroplast genome sequences in Aconitum (Ranunculaceae): a traditional herbal medicinal genus

10.7287/peerj.preprints.3360v1 ◽

2017 ◽

Author(s):

Hanghui Kong ◽

Wanzhen Liu ◽

Gang Yao ◽

Wei Gong

Keyword(s):

Chloroplast Genome ◽

Phylogenetic Analyses ◽

Eastern Asia ◽

Genome Sequences ◽

Protein Coding ◽

Nucleotide Variability ◽

Intergenic Regions ◽

Molecular Information ◽

Herbal Medicinal ◽

Cp Genome

The herbal medicinal genus Aconitum L., belonging to the Ranunculaceae family, represents the earliest diverging lineage within the eudicots. It currently comprises of two subgenera, A. subgenus Lycoctonum and A. subg. Aconitum. The complete chloroplast (cp) genome sequences were characterized in three species: A. angustius, A. finetianum, and A. sinomontanum in subg. Lycoctonum and compared to other Aconitum species to clarify their phylogenetic relationship and provide molecular information for utilization of Aconitum species particularly in Eastern Asia. The length of the chloroplast genome sequences were 156,109 bp in A. angustius, 155,625 bp in A. finetianum and 157,215 bp in A. sinomontanum, with each species possessing 126 genes with 84 protein coding genes (PCGs). While genomic rearrangements were absent, structural variation was detected in the LSC/IR/SSC boundaries. Five pseudogenes were identified, among which Ψrps19 and Ψycf1 were in the LSC/IR/SSC boundaries, Ψrps16 and ΨinfA in the LSC region, and Ψycf15 in the IRb region. The nucleotide variability (Pi) of Aconitum was estimated to be 0.00549, with comparably higher variations in the LSC and SSC than the IR regions. Eight intergenic regions were revealed to be highly variable and a total of 58 – 62 simple sequence repeats (SSRs) were detected in all three species. More than 80% of SSRs were present in the LSC region. Altogether, 64.41% and 46.81% of SSRs are mononucleotides in subg. Lycoctonum and subg. Aconitum, respectively, while a higher percentage of di-, tri-, tetra-, and penta- SSRs were present in subg. Aconitum. Most species of subg. Aconitum in Eastern Asia were first used for phylogenetic analyses. The availability of the complete cp genome sequences of these species in subg. Lycoctonum will benefit future phylogenetic analyses and aid in germplasm utilization in Aconitum species.

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Electricity Generation and Real Output in Asia: A Panel Co-Integration Approach

Review of Economics and Development Studies ◽

10.26710/reads.v3i1.163 ◽

2017 ◽

Vol 3 (1) ◽

pp. 13-28

Author(s):

Furrukh Bashir ◽

Tusawar Iftikhar Ahmad ◽

Ismat Nasim ◽

Kishwar Parveen

Keyword(s):

East Asia ◽

South Asia ◽

Central Asia ◽

Electricity Production ◽

South East Asia ◽

Real Output ◽

Long Run ◽

Time Period ◽

Integration Test ◽

Relationship Of

Purpose: The present study concentrates on the relationship of electricity with real output in Asia. The paper analyzes this connection individually among all regions of Asia. Some countries are selected from Central Asia, East Asia, South Asia and South East Asia. Time period of 1990 - 2015 has been chosen for the analysis. We have considered Solow growth model and have taken labor and capital as necessary variables for growth. After confirmation of integration of order as 1 for all variables, Kao Co-integration test infers presence of long run relationship in all models. FM-OLS suggests that labor and capital are positively significant factors for the development of real output in all the regions of Asia. Electricity Production is positively influencing real output in Central Asia, South Asia and South East Asia; For East Asia, it has been stated as negative. On the basis of results, study suggests that government should develop more skilled labor, cheap investment opportunities, efficient and cheap electricity production.

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Multilocus phylogeny reveals taxonomic misidentification of the Schizopora paradoxa (KUC8140) representative genome

MycoKeys ◽

10.3897/mycokeys.38.28497 ◽

2018 ◽

Vol 38 ◽

pp. 121-127 ◽

Cited By ~ 4

Author(s):

Javier Fernández-López ◽

María P. Martín ◽

Margarita Dueñas ◽

M. Teresa Telleria

Keyword(s):

Geographical Distribution ◽

Phylogenetic Analyses ◽

White Rot ◽

White Rot Fungus ◽

Eastern Asia ◽

Wrong Identification ◽

European Distribution ◽

Fungal Genomes ◽

Nuclear Regions ◽

Multilocus Phylogeny

Schizoporaparadoxa, current name Xylodonparadoxus, is a white-rot fungus with certain useful biotechnological properties. The representative genome of Schizoporaparadoxa strain KUC8140 was published in 2015 as part of the 1000 Fungal Genomes Project. Multilocus phylogenetic analyses, based on three nuclear regions (ITS, LSU and rpb2), confirmed a misidentification of S.paradoxa strain KUC8140 which should be identified as Xylodonovisporus. This wrong identification explains the unexpected geographical distribution of S.paradoxa, since this species has a European distribution, whereas the strain KUC8140 was recorded from Korea, Eastern Asia.

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

Botanical Journal of the Linnean Society ◽

10.1093/botlinnean/boz026 ◽

2019 ◽

Vol 191 (1) ◽

pp. 18-29 ◽

Cited By ~ 1

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.

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Phylogenetic analyses of Searsia (Anacardiaceae) from eastern Asia and its biogeographic disjunction with its African relatives

South African Journal of Botany ◽

10.1016/j.sajb.2016.05.021 ◽

2016 ◽

Vol 106 ◽

pp. 129-136 ◽

Cited By ~ 4

Author(s):

Ying-Ying Yang ◽

Ying Meng ◽

Jun Wen ◽

Hang Sun ◽

Ze-Long Nie

Keyword(s):

Phylogenetic Analyses ◽

Eastern Asia

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Phylogeny of the fern family Aspleniaceae in Australasia and the south-western Pacific

Australian Systematic Botany ◽

10.1071/sb14043 ◽

2014 ◽

Vol 27 (6) ◽

pp. 355 ◽

Cited By ~ 23

Author(s):

Daniel J. Ohlsen ◽

Leon R. Perrie ◽

Lara D. Shepherd ◽

Patrick J. Brownsey ◽

Michael J. Bayly

Keyword(s):

New Zealand ◽

East Asia ◽

Phylogenetic Analyses ◽

Western Pacific ◽

South East Asia ◽

The South ◽

Widespread Species ◽

Species Complexes ◽

The Family

Aspleniaceae is one of the largest fern families. It is species-rich in Australasia and the south-western Pacific (ASWP), where approximately 115 species occur. In the current study, the chloroplast regions rbcL, trnL–trnF and rps4–trnS were sequenced for 100 Aspleniaceae samples from ASWP. These data were combined with published sequences for species from New Zealand and other regions for phylogenetic analyses. Species of Aspleniaceae from ASWP were placed in six of the eight previously identified inter-continental clades. The majority of species from ASWP were placed in two of these clades, with the remaining four clades each being represented by three or fewer species. Strong biogeographic affinities with South-east Asia were observed and immigration, rather than local radiations of endemic taxa, appears to have made a more important contribution to patterns of diversity in ASWP. This study supports the current taxonomic practice of recognising two genera, Asplenium L. and Hymenasplenium Hayata, in Aspleniaceae, and identifies future taxonomic work required for the family in this region, including potential synonymising of species, and revision of species complexes or widespread species that are demonstrably non-monophyletic.

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