Austronesian genetic signature in East African Madagascar and Polynesia

Genome Analysis Using Whole-Exome Sequencing of Non-Syndromic Cleft Lip and/or Palate from Malagasy Trios Identifies Variants Associated with Cilium-Related Pathways and Asian Genetic Ancestry

Background: Orofacial clefts (OFCs) are common congenital disabilities that can occur as isolated non-syndromic events or as part of Mendelian syndromes. OFC risk factors vary due to differences in regional environmental exposures, genetic variants, and ethnicities. In recent years, significant progress has been made in understanding OFCs, due to advances in sequencing and genotyping technologies. Despite these advances, very little is known about the genetic interplay in the Malagasy population. Methods: Here, we performed high-resolution whole-exome sequencing (WES) on non-syndromic cleft lip with or without palate (nCL/P) trios in the Malagasy population (78 individuals from 26 families (trios)). To integrate the impact of genetic ancestry admixture, we computed both global and local ancestries. Results: Participants demonstrated a high percentage of both African and Asian admixture. We identified damaging variants in primary cilium-mediated pathway genes WNT5B (one family), GPC4 (one family), co-occurrence in MSX1 (five families), WDR11 (one family), and tubulin stabilizer SEPTIN9 (one family). Furthermore, we identified an autosomal homozygous damaging variant in PHGDH (one family) gene that may impact metabiotic activity. Lastly, all variants were predicted to reside on local Asian genetic ancestry admixed alleles. Conclusion: Our results from examining the Malagasy genome provide limited support for the hypothesis that germline variants in primary cilia may be risk factors for nCL/P, and outline the importance of integrating local ancestry components better to understand the multi-ethnic impact on nCL/P.

Genetic characterization of populations in the Marquesas Archipelago in the context of the Austronesian expansion

Our exploration of the genetic constitution of Nuku Hiva (n = 51), Hiva Oa (n = 28) and Tahuata (n = 8) of the Marquesas Archipelago based on the analyses of genome-wide autosomal markers as well as high-resolution genotyping of paternal and maternal lineages provides us with information on the origins and settlement of these islands at the fringe of the Austronesian expansion. One widespread theme that emerges from this study is the genetic uniformity and relative isolation exhibited by the Marquesas and Society populations. This genetic homogeneity within East Polynesia groups is reflected in their limited average heterozygosity, uniformity of constituents in the Structure analyses, reiteration of complete mtDNA sequences, marked separation from Asian and other Oceanic populations in the PC analyses, limited differentiation in the PCAs and large number of IBD segments in common. Both the f3 and the Outgroup f3 results provide indications of intra-East Polynesian gene flow that may have promoted the observed intra-East Polynesia genetic homogeneity while ALDER analyses indicate that East Polynesia experienced two gene flow episodes, one relatively recent from Europe that coincides roughly with the European incursion into the region and an early one that may represent the original settlement of the islands by Austronesians. Median Network analysis based on high-resolution Y-STR loci under C2a-M208 generates a star-like topology with East Polynesian groups (especially from the Society Archipelago) in central stem positions and individuals from the different populations radiating out one mutational step away while several Samoan and outlier individuals occupy peripheral positions. This arrangement of populations is congruent with dispersals of C2a-M208 Y chromosomes from East Polynesia as a migration hub signaling dispersals in various directions. The equivalent ages of the C2a-M208 lineage of the populations in the Network corroborate an east to west flow of the most abundant Polynesian Y chromosome.

Genetic evidence and historical theories of the Asian and African origins of the present Malagasy population

The origin of the Malagasy population has been a subject of speculation since the 16th century. Contributions of African, Asian, Indian, Melanesian, Arabic and Persian populations have been suggested based on physical and cultural anthropology, oral tradition, linguistics and later also by archaeology. In the mid-20th century, increased knowledge of heredity rules and technical progress enabled the identification of African and Asian populations as main contributors. Recent access to the genomic landscape of Madagascar demonstrated pronounced regional variability in the relative contributions of these two ancestries, yet with significant presence of both African and Asian components throughout Madagascar. This article reviews the extent to which genetic results have settled historical questions concerning the origin of the Malagasy population. After an overview of the early literature, the genetic results of the 20th and 21th centuries are discussed and then complemented by the latest results in genome-wide analyses. While there is still much uncertainty regarding when, how and the circumstances under which the ancestors of the modern Malagasy population arrived on the island, we propose a scenario based on historical texts and genomic results.

The Marquesans at the fringes of the Austronesian expansion

In the present study, 87 unrelated individuals from the Marquesas Archipelago in French Polynesia were typed using mtDNA, Y-chromosome and autosomal (STRs) markers and compared to key target populations from Island South East Asia (ISEA), Taiwan, and West and East Polynesia to investigate their genetic relationships. The Marquesas, located at the eastern-most fringes of the Austronesian expansion, offer a unique opportunity to examine the effects of a protracted population expansion wave on population structure. We explore the contribution of Melanesian, Asian and European heritage to the Marquesan islands of Nuku-Hiva, Hiva-Oa and Tahuata. Overall, the Marquesas Islands are genetically homogeneous. In the Marquesan Archipelago all of the mtDNA haplogroups are of Austronesian origin belonging to the B4a1 subhaplogroup as the region marks the end of a west to east decreasing cline of Melanesian mtDNA starting with the West Polynesian population of Tonga. Genetic discrepancies are less pronounced between the Marquesan and Society islands, and among the Marquesan islands. Interestingly, a number of Melanesian, Polynesian and European Y-chromosome haplogroups exhibit very different distribution between the Marquesan islands of Nuku Hiva and Hiva Oa, likely resulting from drift, differential migration involving various source populations and/or unique trading routes.

Evidence for Host-Bacterial Co-evolution via Genome Sequence Analysis of 480 Thai Mycobacterium tuberculosis Lineage 1 Isolates

Tuberculosis presents a global health challenge. Mycobacterium tuberculosis is divided into several lineages, each with a different geographical distribution. M. tuberculosis lineage 1 (L1) is common in the high-burden areas in East Africa and Southeast Asia. Although the founder effect contributes significantly to the phylogeographic profile, co-evolution between the host and M. tuberculosis may also play a role. Here, we reported the genomic analysis of 480 L1 isolates from patients in northern Thailand. The studied bacterial population was genetically diverse, allowing the identification of a total of 18 sublineages distributed into three major clades. The majority of isolates belonged to L1.1 followed by L1.2.1 and L1.2.2. Comparison of the single nucleotide variant (SNV) phylogenetic tree and the clades defined by spoligotyping revealed some monophyletic clades representing EAI2_MNL, EAI2_NTM and EAI6_BGD1 spoligotypes. Our work demonstrates that ambiguity in spoligotype assignment could be partially resolved if the entire DR region is investigated. Using the information to map L1 diversity across Southeast Asia highlighted differences in the dominant strain-types in each individual country, despite extensive interactions between populations over time. This finding supported the hypothesis that there is co-evolution between the bacteria and the host, and have implications for tuberculosis disease control.

Human population history revealed by a supertree approach

Over the past two decades numerous new trees of modern human populations have been published extensively but little attention has been paid to formal phylogenetic synthesis. We utilized the "matrix representation with parsimony" (MRP) method to infer a composite phylogeny (supertree) of modern human populations, based on 257 genetic/genomic, as well as linguistic, phylogenetic trees and 44 admixture plots from 200 published studies (1990-2014). The resulting supertree topology includes the most basal position of S African Khoisan followed by C African Pygmies, and the paraphyletic section of all other sub-Saharan peoples. The sub-Saharan African section is basal to the monophyletic clade consisting of the N African-W Eurasian assemblage and the consistently monophyletic Eastern superclade (Sahul-Oceanian, E Asian, and Beringian-American peoples). This topology, dominated by genetic data, is well-resolved and robust to parameter set changes, with a few unstable areas (e.g., West Eurasia, Sahul-Melanesia) reflecting the existing phylogenetic controversies. A few populations were identified as highly unstable "wildcard taxa" (e.g. Andamanese, Malagasy). The linguistic classification fits rather poorly on the supertree topology, supporting a view that direct coevolution between genes and languages is far from universal.

Genome-wide evidence of Austronesian-Bantu admixture and cultural reversion in a hunter-gatherer group of Madagascar

Linguistic and cultural evidence suggest that Madagascar was the final point of two major dispersals of Austronesian- and Bantu-speaking populations. Today, the Mikea are described as the last-known Malagasy population reported to be still practicing a hunter-gatherer lifestyle. It is unclear, however, whether the Mikea descend from a remnant population that existed before the arrival of Austronesian and Bantu agriculturalists or whether it is only their lifestyle that separates them from the other contemporary populations of South Madagascar. To address these questions we have performed a genome-wide analysis of >700,000 SNP markers on 21 Mikea, 24 Vezo, and 24 Temoro individuals, together with 50 individuals from Bajo and Lebbo populations from Indonesia. Our analyses of these data in the context of data available from other Southeast Asian and African populations reveal that all three Malagasy populations are derived from the same admixture event involving Austronesian and Bantu sources. In contrast to the fact that most of the vocabulary of the Malagasy speakers is derived from the Barito group of the Austronesian language family, we observe that only one-third of their genetic ancestry is related to the populations of the Java-Kalimantan-Sulawesi area. Because no additional ancestry components distinctive for the Mikea were found, it is likely that they have adopted their hunter-gatherer way of life through cultural reversion, and selection signals suggest a genetic adaptation to their new lifestyle.

Ascertaining the role of Taiwan as a source for the Austronesian expansion

Taiwanese aborigines have been deemed the ancestors of Austronesian speakers which are currently distributed throughout two-thirds of the globe. As such, understanding their genetic distribution and diversity as well as their relationship to mainland Asian groups is important to consolidating the numerous models that have been proposed to explain the dispersal of Austronesian speaking peoples into Oceania. To better understand the role played by the aboriginal Taiwanese in this diaspora, we have analyzed a total of 451 individuals belonging to nine of the tribes currently residing in Taiwan, namely the Ami, Atayal, Bunun, Paiwan, Puyuma, Rukai, Saisiyat, Tsou, and the Yami from Orchid Island off the coast of Taiwan across 15 autosomal short tandem repeat loci. In addition, we have compared the genetic profiles of these tribes to populations from mainland China as well as to collections at key points throughout the Austronesian domain. While our results suggest that Daic populations from Southern China are the likely forefathers of the Taiwanese aborigines, populations within Taiwan show a greater genetic impact on groups at the extremes of the current domain than populations from Indonesia, Mainland, or Southeast Asia lending support to the "Out of Taiwan" hypothesis. We have also observed that specific Taiwanese aboriginal groups (Paiwan, Puyuma, and Saisiyat), and not all tribal populations, have highly influenced genetic distributions of Austronesian populations in the pacific and Madagascar suggesting either an asymmetric migration out of Taiwan or the loss of certain genetic signatures in some of the Taiwanese tribes due to endogamy, isolation, and/or drift.

The Soliga, an isolated tribe from Southern India: genetic diversity and phylogenetic affinities

India's role in the dispersal of modern humans can be explored by investigating its oldest inhabitants: the tribal people. The Soliga people of the Biligiri Rangana Hills, a tribal community in Southern India, could be among the country's first settlers. This forest-bound, Dravidian speaking group, lives isolated, practicing subsistence-level agriculture under primitive conditions. The aim of this study is to examine the phylogenetic relationships of the Soligas in relation to 29 worldwide, geographically targeted, reference populations. For this purpose, we employed a battery of 15 hypervariable autosomal short tandem repeat loci as markers. The Soliga tribe was found to be remarkably different from other Indian populations including other southern Dravidian-speaking tribes. In contrast, the Soliga people exhibited genetic affinity to two Australian aboriginal populations. This genetic similarity could be attributed to the 'Out of Africa' migratory wave(s) along the southern coast of India that eventually reached Australia. Alternatively, the observed genetic affinity may be explained by more recent migrations from the Indian subcontinent into Australia.

High prevalence of hepatitis B virus genotype E in Northern Madagascar indicates a West-African lineage

The prevalence of hepatitis B virus (HBV) markers was investigated in 563 inhabitants aged 15-55 years from a sugar cane region, Sirama, and from a village, Mataipako, in Northern Madagascar. Serological markers of past or present infection were significantly higher in Sirama, 74% versus 45%. There was no difference in the prevalence of chronic HBsAg carriers, 8.7% versus 8.5% between the two regions. Sequencing the S gene in 45 strains revealed a predominance of genotype E, in 53%, followed by subgenotype A1 in 22%, and genotype D in 18%. Phylogenetic analyses of the genotype E strains showed homology with West African strains. All A1 isolates were similar to Malawi strains. Most genotype D strains were subgenotype D7 and related to strains from Somalia and Tunisia. One genotype D strain formed a branch between Pacific D4 and African D7 strains at neighbor-joining analysis. The pre-core stop mutant was found in 33% of the genotype D strains, 17% of E but not in any A1 strain. The high prevalence and low variability of genotype E strains in only two villages, indicates a rather recent introduction of this genotype into Madagascar from West Africa, possibly through migration or slave trade. The wider spread and genetic relationship of genotype D with East African and Austronesian strains indicate an earlier introduction of this genotype. Molecular epidemiology of HBV may thus be used to complement linguistic and genetic studies on past human migrations in Africa.

Migration, isolation and hybridization in island crop populations: the case of Madagascar rice

Understanding how crop species spread and are introduced to new areas provides insights into the nature of species range expansions. The domesticated species Oryza sativa or Asian rice is one of the key domesticated crop species in the world. The island of Madagascar off the coast of East Africa was one of the last major Old World areas of introduction of rice after the domestication of this crop species and before extensive historical global trade in this crop. Asian rice was introduced in Madagascar from India, the Malay Peninsula and Indonesia approximately 800-1400 years ago. Studies of domestication traits characteristic of the two independently domesticated Asian rice subspecies, indica and tropical japonica, suggest two major waves of migrations into Madagascar. A population genetic analysis of rice in Madagascar using sequence data from 53 gene fragments provided insights into the dynamics of island founder events during the expansion of a crop species' geographic range and introduction to novel agro-ecological environments. We observed a significant decrease in genetic diversity in rice from Madagascar when compared to those in Asia, likely the result of a bottleneck on the island. We also found a high frequency of a unique indica type in Madagascar that shows clear population differentiation from most of the sampled Asian landraces, as well as differential exchange of alleles between Asia and Madagascar populations of the tropical japonica subspecies. Finally, despite partial reproductive isolation between japonica and indica, there was evidence of indica/japonica recombination resulting from their hybridization on the island.

Genetic diversity on the Comoros Islands shows early seafaring as major determinant of human biocultural evolution in the Western Indian Ocean

The Comoros Islands are situated off the coast of East Africa, at the northern entrance of the channel of Mozambique. Contemporary Comoros society displays linguistic, cultural and religious features that are indicators of interactions between African, Middle Eastern and Southeast Asian (SEA) populations. Influences came from the north, brought by the Arab and Persian traders whose maritime routes extended to Madagascar by 700-900 AD. Influences also came from the Far East, with the long-distance colonisation by Austronesian seafarers that reached Madagascar 1500 years ago. Indeed, strong genetic evidence for a SEA, but not a Middle Eastern, contribution has been found on Madagascar, but no genetic trace of either migration has been shown to exist in mainland Africa. Studying genetic diversity on the Comoros Islands could therefore provide new insights into human movement in the Indian Ocean. Here, we describe Y chromosomal and mitochondrial genetic variation in 577 Comorian islanders. We have defined 28 Y chromosomal and 9 mitochondrial lineages. We show the Comoros population to be a genetic mosaic, the result of tripartite gene flow from Africa, the Middle East and Southeast Asia. A distinctive profile of African haplogroups, shared with Madagascar, may be characteristic of coastal sub-Saharan East Africa. Finally, the absence of any maternal contribution from Western Eurasia strongly implicates male-dominated trade and religion as the drivers of gene flow from the North. The Comoros provides a first view of the genetic makeup of coastal East Africa.

The genetic structure of populations from Haiti and Jamaica reflect divergent demographic histories

The West Indies represent an amalgamation of African, European and in some cases, East Asian sources, but the contributions from each ethnic group remain relatively unexplored from a genetic perspective. In the present study, we report, for the first time, allelic frequency data across the complete set of 15 autosomal STR loci for general collections from Haiti and Jamaica, which were subsequently used to examine the genetic diversity present in each island population. Our results indicate that although both Haiti and Jamaica display genetic affinities with the continental African collections, a stronger African signal is detected in Haiti than in Jamaica. Although only minimal contributions from non-African sources were observed in Haiti, Jamaica displays genetic input from both European and East Asian sources, an admixture profile similar to other New World collections of African descent analyzed in this report. The divergent genetic signatures present in these populations allude to the different migratory events of Africans, Europeans, and East Asians into the New World.

The genetic legacy of the Transatlantic Slave Trade in the island of New Providence

The Bahamian archipelago has been influenced by a wide array of settlers (Lucayans, Eleutherian Adventurers, British Loyalists, Creoles from the United States and African slaves) throughout its short but dynamic history. Nevertheless, the Bahamas remains poorly characterized genetically and little is known about each group's contribution to the island chain. In the current study, the population of New Providence was analyzed based on 15 autosomal STR loci routinely employed in forensic DNA fingerprinting applications. A comparison of this collection with African groups reveals similar genetic profiles to West African populations from Equatorial Guinea and Angola, possibly resulting from the importation of slaves from West African ports during the Transatlantic Slave Trade. Although the New Providence collection exhibits strong genetic affinities to the two US African American reference populations, the detection of unique alleles among them may necessitate the utilization of population-specific databases in forensic cases especially when the STR profiles include these specific variants.