scholarly journals Human origin and migration deciphered from a novel genomic footprints of mitochondrial sequences

2019 ◽  
Author(s):  
Aritra Mahapatra ◽  
Jayanta Mukherjee
Keyword(s):  
Phylogenetic Trees ◽  
Central Africa ◽  
Molecular Data ◽  
Modern Human ◽  
Human Migration ◽  
Genomic Feature ◽  
Genomic Studies ◽  
West And Central Africa ◽  
High Bootstrap ◽  
And Migration

AbstractThe origin of modern human and their migration across the world is one of the most debated topics for the decades. There exist two different hypotheses, recent African origin and multi-regional evolution, based on the genomic studies, haplogroups, archaeological records, cultural behaviors, palaeontology studies, etc. Various studies placed the modern humans in a phylogenetic tree to depict the relationships among them. The debate for determining those regions of Africa which witnessed the first origin of humans still exists. The conflicts between the results obtained from the molecular data and the archaeological and palaeontological reports still exist. We adopt a novel genomic feature derived from the whole mitochondrial sequence, and using a novel distance function the phylogenetic trees are constructed based on the feature which provide a new insight on human migration. We propose a new method to derive the bootstrap replica from the genome sequences by considering the genetic variance to demonstrate the robustness of the obtained trees. The results derived from the genomic feature are more consistent with the archaeological findings based on the time of origin of different communities. We find that west and central African communities are placed at the basal point with a very high bootstrap score. This study roughly estimates the existence of the archaic human at 800-900 kilo years ago and presence of human in Africa at 600-700 kilo years ago. This supports the presence of an ancestor in the west and central Africa much earlier than that of the fossils identified.

scholarly journals Evolutionary history of the Cameroon radiation of puddle frogs (Phrynobatrachidae: Phrynobatrachus), with descriptions of two critically endangered new species from the northern Cameroon Volcanic Line

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8393 ◽  
Author(s):  
Václav Gvoždík ◽  
Tadeáš Nečas ◽  
Matej Dolinay ◽  
Breda M. Zimkus ◽  
Andreas Schmitz ◽  
...  
Keyword(s):  
New Species ◽  
Phylogenetic Analyses ◽  
Central Africa ◽  
Molecular Data ◽  
Species Group ◽  
Critically Endangered ◽  
Cameroon Volcanic Line ◽  
Northern Cameroon ◽  
West And Central Africa ◽  
Mountain Chain

The Cameroon Volcanic Line, a mountain chain located between West and Central Africa, is a region of numerous endemic diversifications, including of puddle frogs (Phrynobatrachus). This study reviews the phylogeny and taxonomy of puddle frogs of the “Cameroon radiation,” which is a clade containing mainly montane but also at least three lowland species. Molecular data revealed a novel evolutionary lineage from high altitudes in the northern part of the mountains. Puddle frogs from the new, minute-sized (SVL < 20 mm) lineage are identified using molecular, morphological and acoustic data and described as two new species, Phrynobatrachus arcanus sp. nov. (Gotel Mountains, Cameroon–Nigeria) and P. mbabo sp. nov. (Tchabal Mbabo, Cameroon). The tadpole of the first species is also described. Phylogenetic analyses placed the new lineage to the proximity of the recently described lowland small-sized taxa (P. horsti, P. ruthbeateae). Based on the inferred phylogeny, we propose five species groups within the Cameroon radiation: P. arcanus, P. chukuchuku, P. ruthbeateae, P. steindachneri, and P. werneri. The taxonomically enigmatic P. hylaios is proposed to be a member of the P. ruthbeateae species group. The basal radiation evolved during the late Miocene with subsequent diversifications occurring during the Pliocene, while closely related terminal taxa originated during the Pleistocene. We recommend that the newly described species are categorized as Critically Endangered due to their limited ranges and because recent surveys did not identify any individuals at the type localities. This further supports the need for conservation interventions in the mountains of Cameroon and Nigeria.

scholarly journals Phylogeographic analysis reveals an ancient East African origin of the human herpes simplexvirus 2 dispersal out-of-Africa.

2022 ◽  
Author(s):  
Jennifer L. Havens ◽  
Sebastien Calvignac-Spencer ◽  
Kevin Merkel ◽  
Sonia Burrel ◽  
David Boutolleau ◽  
...  
Keyword(s):  
East Africa ◽  
Molecular Clock ◽  
Central Africa ◽  
Human Migration ◽  
Evolutionary Rates ◽  
Human Herpes ◽  
Phylogeographic Analysis ◽  
West And Central Africa ◽  
Out Of Africa ◽  
Competing Hypotheses

Human herpes simplex virus 2 (HSV-2) is a globally ubiquitous, slow evolving DNA virus. HSV-2 genomic diversity can be divided into two main groups: an African lineage and worldwide lineage. Competing hypotheses have been put forth to explain the history of HSV-2. HSV-2 may have originated in Africa and then followed the first wave of human migration out of Africa between 50-100 kya. Alternatively, HSV-2 may have migrated out of Africa via the trans-Atlantic slave trade within the last 150-500 years. The lack of HSV-2 genomes from West and Central Africa, combined with a lack of molecular clock signal in HSV-2 has precluded robust testing of these competing hypotheses. Here, we expand the geographic sampling of HSV-2 genomes in order to resolve the geography and timing of divergence events within HSV-2. We analyze 65 newly sequenced HSV-2 genomes collected from primarily West and Central Africa along with 330 previously published genomes sampled over a 47-year period. Evolutionary simulations confirm that the molecular clock in HSV-2 is too slow to be detected using available data. However, phylogeographic analysis indicates that all biologically plausible evolutionary rates would place the ancestor of the worldwide lineage in East Africa, arguing against the trans-Atlantic slave trade as the source of worldwide diversity. The best supported evolutionary rates between 4.2x10-8 and 5.6x10-8 substitutions/site/year suggest a most recent common ancestor for HSV-2 around 90-120 kya and initial dispersal around 21.9-29.3 kya. These dates suggest HSV-2 left Africa during subsequent waves of human migration out of East Africa.

scholarly journals Ranking cancer drivers via betweenness-based outlier detection and random walks

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Cesim Erten ◽  
Aissa Houdjedj ◽  
Hilal Kazan
Keyword(s):  
Cancer Genomics ◽  
Interaction Network ◽  
Molecular Data ◽  
Alternative Methods ◽  
Patient Specific ◽  
Cancer Genes ◽  
Driver Genes ◽  
Cancer Driver ◽  
Protein Protein Interaction ◽  
Genomic Studies

Abstract Background Recent cancer genomic studies have generated detailed molecular data on a large number of cancer patients. A key remaining problem in cancer genomics is the identification of driver genes. Results We propose BetweenNet, a computational approach that integrates genomic data with a protein-protein interaction network to identify cancer driver genes. BetweenNet utilizes a measure based on betweenness centrality on patient specific networks to identify the so-called outlier genes that correspond to dysregulated genes for each patient. Setting up the relationship between the mutated genes and the outliers through a bipartite graph, it employs a random-walk process on the graph, which provides the final prioritization of the mutated genes. We compare BetweenNet against state-of-the art cancer gene prioritization methods on lung, breast, and pan-cancer datasets. Conclusions Our evaluations show that BetweenNet is better at recovering known cancer genes based on multiple reference databases. Additionally, we show that the GO terms and the reference pathways enriched in BetweenNet ranked genes and those that are enriched in known cancer genes overlap significantly when compared to the overlaps achieved by the rankings of the alternative methods.

scholarly journals Initial Upper Palaeolithic humans in Europe had recent Neanderthal ancestry

Nature ◽  
2021 ◽  
Vol 592 (7853) ◽  
pp. 253-257 ◽  
Author(s):  
Mateja Hajdinjak ◽  
Fabrizio Mafessoni ◽  
Laurits Skov ◽  
Benjamin Vernot ◽  
Alexander Hübner ◽  
...  
Keyword(s):  
Family History ◽  
East Asia ◽  
Late Pleistocene ◽  
Modern Human ◽  
Human Migration ◽  
Upper Palaeolithic ◽  
Modern Humans ◽  
Genome Wide ◽  
Genome Wide Data

AbstractModern humans appeared in Europe by at least 45,000 years ago1–5, but the extent of their interactions with Neanderthals, who disappeared by about 40,000 years ago6, and their relationship to the broader expansion of modern humans outside Africa are poorly understood. Here we present genome-wide data from three individuals dated to between 45,930 and 42,580 years ago from Bacho Kiro Cave, Bulgaria1,2. They are the earliest Late Pleistocene modern humans known to have been recovered in Europe so far, and were found in association with an Initial Upper Palaeolithic artefact assemblage. Unlike two previously studied individuals of similar ages from Romania7 and Siberia8 who did not contribute detectably to later populations, these individuals are more closely related to present-day and ancient populations in East Asia and the Americas than to later west Eurasian populations. This indicates that they belonged to a modern human migration into Europe that was not previously known from the genetic record, and provides evidence that there was at least some continuity between the earliest modern humans in Europe and later people in Eurasia. Moreover, we find that all three individuals had Neanderthal ancestors a few generations back in their family history, confirming that the first European modern humans mixed with Neanderthals and suggesting that such mixing could have been common.

How Should We Talk About Climate Change and Migration?

2020 ◽  
Author(s):  
James Morrissey
Keyword(s):  
Climate Change ◽  
Human Migration ◽  
Policy Response ◽  
Limited Capacity ◽  
Flexible Approach ◽  
Single Term ◽  
And Migration

Abstract This paper is a response Ferris (2020), specifically to the call for coalescence around a single term by which to talk about people migrating in response to climate change. While sympathetic to the imperative behind Ferris’ (2020) call, my overall argument is to reject this proposal. Instead I argue for less of focus on what we call people migrating in response to climate change, and more of a focus on how we talk about them. To justify this, I argue that a single term is inherently reductive and likely to play upon anti-immigrant sentiment due to the need to portray ‘migration as a problem’. At best this will result in a policy focus with limited capacity to address the challenge of migration in a context of climate change. At worst it will drive a policy response that is overtly counter-productive. As an alternative, I propose embracing a multitude of discourses, informed by principals that I argue will drive a humane climate agenda, and allow for a flexible approach that can account for the variety of concerns at the nexus of climate change and human migration.

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