Abstract An illustration of the human footprint on biodiversity are the faunal movements that have accompanied commercial and cultural exchanges between civilizations throughout history. In this article, we provide an integrative review of biogeographical and archaeological knowledge to understand these processes for the Mediterranean tree frog (Hyla meridionalis), an African species that has reached several regions of south-western Europe and associated islands. By re-analysing molecular (multilocus mitochondrial and genome-wide markers) and bioclimatic (ecological niche modelling) data, we give a comprehensive picture of the genetic diversity, structure and environmental suitability of H. meridionalis across its natural and exotic ranges, which in turn offer specific clues to the putative routes of colonization and associated events. Long-term monitoring efforts suggest northwards shifts of local range margins, potentially due to global warming, and we further demonstrate that this species is the most frequent amphibian to travel via the food supply chain in Western Europe. High dispersal ability, ecological tolerance and proximity to human settlements have made H. meridionalis a recurrent witness to the complexity and diversity of the civilizations that ruled the Western Mediterranean.
Abstract The rich genetic and phenotypic diversity of species complexes is best recognized through formal taxonomic naming, but one must first assess the evolutionary history of phylogeographic lineages to identify and delimit candidate taxa. Using genomic markers, mitochondrial DNA barcoding, and morphometric analyses, we examined lineage diversity and distribution in the Iberian endemic frog Rana parvipalmata. We confirmed two deep phylogeographic lineages, one relatively homogenous genetically, found in Asturias and adjacent areas (T2), and one more fragmented and locally genetically impoverished, restricted to Galicia (T1). Analyses of their hybrid zone suggested a shallow transition characterized by far-ranging admixture, which was modelled by a wide geographic cline (~60 km for the genome average) and no obvious barrier loci (i.e. loci showing disproportionally restricted introgression). The relatively young T1 and T2 have thus remained reproductively compatible, which argues against their distinction as biological species, and we accordingly describe T2 as a new subspecies, Rana parvipalmata asturiensis ssp. nov. Remarkably, we highlight striking discordances between mitochondrial and nuclear distributions across their hybrid zones, as well as between their genetic and morphological differentiation. Our study illustrates how genomic-based phylogeographic frameworks can help decipher the high genetic and phenotypic variation of species complexes and substantiate the taxonomic assessment of candidate lineages.
Abstract The Bantu expansion, which started in West Central Africa around 5,000 BP, constitutes a major migratory movement involving the joint spread of peoples and languages across sub-Saharan Africa. Despite the rich linguistic and archaeological evidence available, the genetic relationships between different Bantu-speaking populations and the migratory routes they followed during various phases of the expansion remain poorly understood. Here, we analyze the genetic profiles of southwestern and southeastern Bantu-speaking peoples located at the edges of the Bantu expansion by generating genome-wide data for 200 individuals from 12 Mozambican and 3 Angolan populations using ∼1.9 million autosomal single nucleotide polymorphisms. Incorporating a wide range of available genetic data, our analyses confirm previous results favoring a “late split” between West and East Bantu speakers, following a joint passage through the rainforest. In addition, we find that Bantu speakers from eastern Africa display genetic substructure, with Mozambican populations forming a gradient of relatedness along a North-South cline stretching from the coastal border between Kenya and Tanzania to South Africa. This gradient is further associated with a southward increase in genetic homogeneity, and involved minimum admixture with resident populations. Together, our results provide the first genetic evidence in support of a rapid North-South dispersal of Bantu peoples along the Indian Ocean Coast, as inferred from the distribution and antiquity of Early Iron Age assemblages associated with the Kwale archaeological tradition.
Animal translocations provide striking examples of the human footprint on biodiversity. Combining continental-wide genomic and DNA-barcoding analyses, we reconstructed the historical biogeography of the Asian black-spined toad (Duttaphrynus melanostictus), a toxic commensal amphibian that currently threatens two biodiversity hotspots through biological invasions (Wallacea and Madagascar). The results emphasize a complex diversification shaped by speciation and mitochondrial introgression that comprises two distinct species. One species (true D. melanostictus) is distributed in the Indian subcontinent and is invasive in Wallacea. The other species, whose nomenclature remains unsettled, diverged from D. melanostictus in the Miocene era (~7 Mya) and diversified across Southeast Asia, from where it was introduced to Madagascar. Remarkably, the Indonesian population of D. melanostictus was recently established from India, which suggests historical, possibly human-assisted dispersal across the Bay of Bengal, reflecting the centuries-old connection between these regions. The Asian black-spined toad is a widespread, poisonous, invasive amphibian. Here, the authors use genomic and DNA-barcoding data from this toad to document its complex evolutionary history, two distinct species, and potential historic dispersal assisted by humans.
La diversite genetique d’une population porte en elle la trace de pratiques culturelles et est un temoignage de certains elements passes. Ainsi, la langue, qui peut agir comme une barriere culturelle a la reproduction, et le systeme de parente, qui va determiner quand, ou et avec qui les individus se reproduisent, vont influencer la diversite genetique. L’objectif de cette these est de tenter de retracer les histoires demographiques de populations d’Asie du Sud et du Sud-Est, a plusieurs echelles culturelles, de la famille linguistique Austro-Asiatique aux groupes de filiation en utilisant des donnees genetiques. Dans un premier temps, nous nous sommes interesses a la famille linguistique Austro-Asiatique. Les langues appartenant a une meme famille linguistique descendent d’une meme langue « mere » et nous avons voulu savoir si en plus de cette parente linguistique, les locuteurs de ces langues partageaient une parente genetique. Nous avons etudie la diversite genetique autosomale de populations parlant des langues Austro-Asiatiques et nous les avons comparees a des populations voisines appartenant a d’autres familles linguistiques. Nous n’avons pas pu mettre en evidence de parente genetique particuliere entre les populations parlant des langues Austro-Asiatiques. Ces resultats excluent l’hypothese d’une origine commune des populations parlant des langues Austro-Asiatique et favorisent l’hypothese d’une diffusion culturelle des langues Austro-Asiatiques. Puis, nous avons etudie la parente genetique au sein de groupes de descendance dans huit populations d’Asie du Sud-Est. Les individus appartenant au meme groupe de filiation disent descendre d’un meme ancetre commun, paternel dans les populations patrilineaires ou maternel dans les populations matrilineaires. Nous avons voulu savoir si l’ancetre commun de ces populations est mythique ou biologique. Nous nous sommes interesses aux diversites genetiques du chromosome Y et de l’ADN mitochondrial de huit populations d’Asie du Sud-Est : quatre populations matrilineaires et quatre populations patrilineaires. Nos donnees montrent que des individus appartenant a un meme clan matrilineaire sont fortement apparentes genetiquement au niveau de leur lignee maternelle, visible au niveau de leur ADN mitochondrial. A l’inverse, les individus appartenant a un meme clan patrilineaire ne sont pas plus apparentes genetiquement entre eux que deux individus pris au hasard dans la population au niveau de leur lignee paternelle, visible au niveau du chromosome Y. Ces resultats temoignent de realites differentes entre les populations patrilineaires et matrilineaires d’Asie du Sud-Est avec un ancetre commun reel dans les populations matrilineaires et un ancetre commun mythique dans les clans patrilineaires. Pris ensemble, ces travaux rappellent la maniere dont differents processus culturels ont laisse des signatures genetiques sur les diversites genetiques uniparentales et autosomales et illustrent la maniere dont le geneticien des populations peut utiliser ces diversites genetiques pour retracer l’histoire demographique des populations.
The Bantu expansion, which started in West Central Africa around 5,000 BP, constitutes a major migratory movement involving the joint spread of peoples and languages across sub-Saharan Africa. Despite the rich linguistic and archaeological evidence available, the genetic relationships between different Bantu-speaking populations and the migratory routes they followed during various phases of the expansion remain poorly understood. Here, we analyze the genetic profiles of southwestern and southeastern Bantu-speaking peoples located at the edges of the Bantu expansion by generating genome-wide data for 200 individuals from 12 Mozambican and 3 Angolan populations using ∼1.9 million autosomal single nucleotide polymorphisms. Incorporating a wide range of available genetic data, our analyses confirm previous results favoring a "late split" between West and East Bantu speakers, following a joint passage through the rainforest. In addition, we find that Bantu speakers from eastern Africa display genetic substructure, with Mozambican populations forming a gradient of relatedness along a North-South cline stretching from the coastal border between Kenya and Tanzania to South Africa. This gradient is further associated with a southward increase in genetic homogeneity, and involved minimum admixture with resident populations. Together, our results provide the first genetic evidence in support of a rapid North-South dispersal of Bantu peoples along the Indian Ocean Coast, as inferred from the distribution and antiquity of Early Iron Age assemblages associated with the Kwale archaeological tradition.
Abstract Objectives Social organization plays a major role in shaping human population genetic diversity. In particular, matrilocal populations tend to exhibit less mitochondrial diversity than patrilocal populations, and the other way around for Y chromosome diversity. However, several studies have not replicated such findings. The objective of this study is to understand the reasons for such inconsistencies and further evaluate the influence of social organization on genetic diversity. Materials and Methods We explored uniparental diversity patterns using mitochondrial HV1 sequences and 17 Y‐linked short tandem repeats (STRs) in 12 populations ( n = 619) from mainland South–East Asia exhibiting a wide range of social organizations, along with quantitative ethno‐demographic information sampled at the individual level. Results MtDNA diversity was lower in matrilocal than in multilocal and patrilocal populations while Y chromosome diversity was similar among these social organizations. The reasons for such asymmetry at the genetic level were understood by quantifying sex‐specific migration rates from our ethno‐demographic data: while female migration rates varied between social organizations, male migration rates did not. This unexpected lack of difference in male migrations resulted from a higher flexibility in residence rule in patrilocal than in matrilocal populations. In addition, our data suggested an impact of clan fission process on uniparental genetic patterns. Conclusions The observed lack of signature of patrilocality on Y chromosome patterns might be attributed to the higher residence flexibility in the studied patrilocal populations, thus providing a potential explanation for the apparent discrepancies between social and genetic structures. Altogether, this study highlights the need to quantify the actual residence and descent patterns to fit social to genetic structures.
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