Gene Flow Research Articles

Connectivity differs by orders of magnitude among co-distributed corals, affecting spatial scales of eco-evolutionary processes.

Reef building corals are declining worldwide, yet the processes driving population connectivity remain poorly understood. Using complementary analyses, we provide quantitative estimates of ecologically relevant dispersal and evolutionarily important gene flow in co-distributed coral species on the Great Barrier Reef. We find dispersal distances across meters (23 to 102meters) in the brooding Stylophora pistillata and across kilometers (21 to 52 kilometers) in the broadcast spawning Pocillopora verrucosa, consistent with expectations based on their reproductive modes. Similarly, while gene flow rates averaged over the past ~400,000 generations are very low among S. pistillata populations, P. verrucosa populations are well connected. As a result, estimates of genetic diversity across multiple metrics and population sizes are smaller in S. pistillata compared to P. verrucosa. These results highlight the importance of spatial scales and reproductive modes in predicting coral adaptive responses and underscore the value of considering spatial connections between target populations in conservation and restoration.

Cyclic functional connectivity of Canada lynx (Lynx canadensis) populations across North American boreal landscapes.

Connectivity is determined by the degree to which inhospitable habitat matrices are permeable to gene flow. Successful gene flow requires that dispersing individuals travel to new populations, survive there, and finally, reproduce. Consequently, examinations of connectivity must consider both the permeability of the landscape and individual survival patterns, as surviving individuals are the only ones that have the potential to reproduce. We investigated functional connectivity of Canada lynx (Lynx canadensis) populations in the northwestern boreal forest using an unprecedented dataset of 207,957 relocations from 142 individual lynx. As a specialist predator of snowshoe hare (Lepus americanus), lynx populations follow a 10- to 12-year population cycle, which lags a few years behind the population cycles of hares. We used integrated step selection analyses to quantify habitat selection, and Bayesian counting process implementation of wrapped Cauchy survival models to evaluate mortality risk during dispersal. We compared movement patterns and survival across behavioral states and population phases, following the a population decline. Our results showed few complete physical barriers to dispersal in the study region, with many lynx dispersing greater than 3000 km. Step-selection analysis of lynx movement revealed a higher tolerance for poor quality habitats in dispersing lynx as compared to resident lynx, primarily in selection for rugged terrain and closer proximity to roads. These differences resulted in a higher estimate of landscape permeability for dispersing lynx compared to residents. When survival patterns were considered, there were increasingly stark differences between resident and dispersing lynx during population declines. Dispersing lynx faced markedly lower survival rates than resident lynx. Overall, this paints a picture of a more connected landscape during population highs, which becomes increasingly fragmented during population lows. Canada lynx populations appeared to have few impermeable barriers across the landscape, but they face periods of low functional connectivity driven by lower survival during population declines. This emphasizes the significance of maintaining high-quality refugia habitats from which population rebounds can occur following cyclic lows.

The interplay among space, environment, and gene flow drives genetic differentiation in endemic Baja California Agave sobria subspecies.

Research on neutral and adaptive processes that lead to the divergence of species and populations is a crucial component in evolutionary and conservation genetics. Agave sobria is an endemic group of subspecies scattered on canyons along a latitudinal gradient and distinct environments of the Baja California Peninsula, Mexico. Agave sobria represents a unique opportunity to study the process of genetic differentiation in a highly heterogeneous environment. Using genotyping-by-sequencing, we genotyped 8453 single-nucleotide polymorphisms (SNPs) in all A. sobria subspecies, including 19 A. sobria and three closely related A. cerulata ssp. subcerulata populations. We assessed neutral genetic structure and diversity at both the interspecific and intraspecific levels, evaluated the amount and direction of gene flow, and identified putatively adaptive SNPs. We found low support for the currently recognized subspecies. We detected neutral (i.e., isolation by distance) and adaptive divergence linked to eco-geographic characteristics of the habitat. High genetic connectivity indicated that gene flow between central and northern populations may have homogenizing effects preventing population differentiation. For the southernmost A. sobria ssp. frailensis, temperature and geographic isolation appear to be the main drivers of adaptive differentiation, with outlier SNPs located in coding regions involved in response to abiotic stress and immunology. In A. sobria, environmental isolation and geographic gradients affect the genetic structure, creating opportunities for local adaptation. Our results emphasize the importance of including neutral and adaptive perspectives, the combination of which allows a better understanding of the complexity of the processes that lead to population differentiation.

Development and field application of metabarcoding-adapted mt-ND4 markers shows substantial gene flow and varying local pressures on Haemonchus contortus and Teladorsagia circumcincta populations in the UK.

Gastrointestinal nematodes impose a significant burden on livestock production and public health by reducing animal productivity and increasing the environmental impact of farming. Modern sequencing techniques enable the efficient exploration of genetic diversity, necessary to inform effective parasite control. In this study, we developed and validated new mitochondrial ND4-based markers adapted for high-throughput sequencing. This enabled detailed analysis of genetic diversity in two important nematode species, Haemonchus contortus and Teladorsagia circumcincta. Laboratory validations confirmed that the assay reliably detected as little as 1% of larvae in mixed samples and accurately identified strain variants. Field application on 30 sheep farms across England and Scotland revealed 60 unique genetic variants in H. contortus and 35 in T. circumcincta. A single variant dominated the sequence reads in both species, particularly T. circumcincta. Regional comparisons showed that H. contortus exhibited fewer yet persistent variants in Scotland than in England; while phylogenetic analyses indicated a common origin and significant gene flow between regions. In contrast, T. circumcincta, despite being more prevalent across all farms, displayed lower overall diversity with a shared dominant variant; evidence of dual origins and marked regional differences in evolutionary pressures. Comparisons with publicly available global sequence data revealed distinct clustering of H. contortus isolates, separating Asian sequences from those in the United Kingdom and Australia. T. circumcincta isolates showed no apparent geographic clustering. These findings demonstrate the potential of high-throughput mitochondrial marker analysis to unravel complex parasite population dynamics, and to inform sustainable management strategies in the face of challenges such as drug resistance and climate change.

Movement phases make a difference in habitat selection: Iberian lynx diversity of responses to human-modified landscapes.

Wildlife conservation requires a comprehensive understanding of habitat and landscape conditions supporting viable and well-connected populations, especially for reintroduction efforts. Habitat selection depends on different life processes and behavioural states driving animal movements. However, habitat modelling often considers all species records together or distinguishes only between locations within and outside home ranges. We considered a more detailed characterization of movements, focusing on five distinct movement phases: home ranges, transient residences, excursions, post-release dispersals and dispersals. Utilizing GPS telemetry data from 124 Iberian lynxes (Lynx pardinus), mainly tracked during a reintroduction programme, we examined their habitat selection and adaptation to heterogeneous, human-modified and fragmented landscapes. We developed context-specific mixed-effects habitat selection models for each phase, incorporating two hierarchical selection scales: resident range and path selection functions at the landscape scale, and step selection functions at the local scale. All lynxes consistently avoided intensive non-tree cropland and selected mosaics of natural vegetation, including tree, shrubland and grassland cover. Resident lynxes selected areas with low road and human infrastructure densities locally, but no such pattern emerged at the landscape scale, likely due to constraints on establishing large home ranges where infrastructures are widespread and intertwined with natural cover. We observed significant differences in habitat selection among non-residential phases. During excursions, lynxes avoided areas with high human infrastructure, whereas during dispersals, this avoidance was less pronounced, indicating high behavioural plasticity. The post-release dispersal phase mirrored dispersals but showed infrastructure avoidance and a higher selection for sheltering features like rugged terrain and shrub cover. Our findings emphasize the importance of distinguishing specific movement phases, and particularly different movement phases outside home ranges, when assessing habitat selection, especially for translocated animals settling in the landscape. This differentiation is essential to (i) identify suitable reintroduction areas with habitat features supporting post-release movements and settlement; (ii) evaluate habitat conditions of temporary stopovers facilitating long-distance dispersals, and (iii) achieve accurate connectivity estimates among populations. True dispersal events, as the primary movements facilitating gene flow and range expansion, should be treated separately in landscape permeability studies to effectively guide related conservation efforts.

Foraging actively can be advantageous in heterogeneous environments.

A wealth of evidence indicates that behavioural polymorphism is widespread in nature. While some organisms search for food by moving almost continuously throughout their environment, other organisms forage in one place for long periods of time. Although such a dichotomy has been previously documented in Drosophila melanogaster, the question remains which foraging strategy is better suited to maximize energy intake in a particular environment. We designed an experiment to evaluate whether the configuration of food in the environment alters the foraging behaviour of two larval strains. Assuming that one of the strains acquires more food than the other in a given environment, we examined whether variation in growth occurred between them. Our results indicate that foraging behaviour is a plastic trait, shaped by the configuration of food in the environment. Regardless of the foraging strategy, we found that larvae generally increased their locomotion when food was patchy rather than clumped. Even though we observed that some individuals actively sought food while others stayed foraging at nearby sites, we found no differences in growth rate between them. However, we suggest that foraging actively may be advantageous in polymorphic populations because such behaviour facilitates local adaptation via founder effect and gene flow.

A G219A hemagglutinin substitution increases pathogenicity and viral replication of Eurasian avian-like H1N1 swine influenza viruses.

A G219A hemagglutinin substitution increases pathogenicity and viral replication of Eurasian avian-like H1N1 swine influenza viruses.

Evolutionary rescue in a mixed beech–fir forest: insights from a quantitative‐genetics approach in a process‐based model

Questions have been raised about the ability of long‐lived organisms, such as trees, to adapt to rapid climate change, and to what extent forest management actions influence the evolutionary responses of tree species. Given the life history of trees and the time scales involved, these questions are often addressed through modeling approaches. Yet, most of these studies focus on single‐species case studies. The main objective and originality of our work is to explore the evolutionary responses of tree species to climate change using a process‐based model, in a multi‐specific context. This approach allows us to investigate the conditions necessary for evolutionary rescue in a mixed beech–fir forest. Furthermore, we explored how climate change adaptation and mitigation solutions, such as assisted gene flow and assisted migration, affect the conditions for evolutionary rescue in this forest type. To achieve these objectives, we integrated a quantitative genetic module into a process‐based forest gap model, enabling species‐specific parameters to evolve as quantitative traits under selective pressure and drift. Our results show that increased trait variability and heritability reduce the loss of forest cover following climatic warming in the short term (over a century). We also found that assisted gene flow had the expected effect of aiding species adapt to climate change. Finally, our study suggests that introducing new pre‐adapted species into the forest could improve recovery after climate change but could also hinder the evolutionary rescue of local species. We conclude that integrating evolutionary dynamics into process‐based models significantly enhances their predictive power by incorporating genetic adaptation scenarios that would otherwise be overlooked. This approach also allows us to test eco‐evolutionary hypotheses and better understand the potential consequences of adaptation measures to climate change for tree species.

From selection to resistance: Mitochondrial findings in hookworm evolution under drug pressure.

From selection to resistance: Mitochondrial findings in hookworm evolution under drug pressure.

The role of host sea turtles in the dispersal of amphipod epibionts

Abstract Epibiosis is an interspecific association whereby one organism lives on the surface of another, called the host or basibiont. One of the many advantages of epibiosis is that the interaction with the basibiont may increase the epibiont’s dispersal capacity, especially when the basibiont are highly migratory, such as sea turtles. Such hosts are known to harbour a broad diversity of epibiont communities, and crustacean amphipods are one of the most abundant. The increase in dispersal capacity due to the epibiont habit may be a strategic adaptation for amphipods, which are direct-developmental organisms. To understand the role of sea turtles on the dispersal of their epibionts, we combined mitochondrial (Cytb) and nuclear (ITS-1) markers to assess population genetic structure and evolutionary history of the amphipod species (Podocerus chelonophilus, Hyachelia tortugae and Hyachelia lowryi) known as obligate commensals of sea turtles. We obtained amphipod specimens from 33 sea turtles of three distinct species: loggerhead (Caretta caretta), green (Chelonia mydas), and hawksbill (Eretmochelys imbricata) sampled in six localities along the Brazilian coast. Our results show high genetic diversity, low genetic structure, and high gene flow among the different turtle species and localities for all epibiont species. Our findings suggest an overlap between the life histories of the hosts and their epibionts and a probable colonization event of a small number of mitochondrial DNA lineages, leading to high gene flow over long distances promoted by historical and present interaction with the host sea turtles.

Population genetic structure of Biomphalaria snails found in East Africa's river systems.

There is a need for current and more detailed information on the population genetic structure of Biomphalaria snails in East Africa's river systems. Here, we examine the population genetic structure of Biomphalaria populations in East Africa using the mitochondrial cytochrome oxidase 1 (CO1) gene and the internal transcribed spacer 2 (ITS-2) region of nuclear ribosomal DNA. Biomphalaria snails were found at 31 of the 172 sites surveyed, with B. pfeifferi snails found at 23 sites and snails of the Biomphalaria 'Nilotic Species Complex' found at 9 sites. Biomphalaria pfeifferi formed a monophyletic group in both CO1 and ITS-2 phylogenetic trees. Similarly, the 'Nilotic Species Complex' also formed a monophyletic group in both CO1 and ITS-2 trees but while some individual species within the 'Nilotic Species Complex' were monophyletic, others were not monophyletic and intermingled in the trees. A total of 17 CO1 haplotypes (3 shared haplotypes and 14 private haplotypes) were identified for B. pfeifferi populations with a haplotype diversity of 0.798 and nucleotide diversity of 0.004. For ITS-2, a total of 27 B. pfeifferi haplotypes (3 shared haplotypes and 24 private haplotypes) were identified, with a haplotype diversity of 0.471 and nucleotide diversity of 0.002. For the 'Nilotic Species Complex', a total of 21 CO1 haplotypes (all private) were identified, with a haplotype diversity of 0.897 and nucleotide diversity of 0.018. For ITS-2, a total of 23 'Nilotic Species Complex' ITS-2 haplotypes (3 shared haplotypes and 20 private haplotypes) were identified with a haplotype diversity of 0.951 and nucleotide diversity of 0.008. Analysis of Molecular Variance (AMOVA) revealed low genetic variation within B. pfeifferi populations (between 4.83 % and 5.86 %) and high genetic differentiation among populations (between 94.14 % and 95.17 %). For the 'Nilotic Species Complex', the genetic diversity was moderate within populations (between 27.83 % and 31.96 %) and among populations (between 68.04 % and 72.17 %). Geographical distance plays a role in bringing about genetic differentiation among Biomphalaria populations in East Africa's river systems, with sequences from Biomphalaria populations that were found at sites close to each other geographically, taking positions close to each other in the phylogenetic trees. B. pfeifferi populations studied herein were characterised by low intra-population genetic diversity and high inter-population genetic diversity suggestive of low levels of gene flow and high levels of inbreeding. In the case of the 'Nilotic Species Complex', there was moderate to high levels of intra-population genetic diversity and moderate to high levels of inter-population genetic differentiation suggestive of high levels of gene flow. It was established that the population genetic structure of Biomphalaria snails is a possible determinant of the success of S. mansoni infections in the snails.

Nested admixture during and after the Trans-Atlantic Slave Trade on the island of São Tomé.

Human genetic admixture, involving the contact between two or more previously isolated populations, can be a complex process influenced by social dynamics. In this study, we aim to reconstruct complex admixture histories in São Tomé, an island in the Gulf of Guinea where the Portuguese established one of the first plantation-based slave societies. Since the 15th century, migration waves from Africa and Europe, slavery, marooning and indentured labour, led to profound demographic shifts and social stratification on the island. Examining 2.5 million SNPs newly genotyped in 96 São Toméans, we observed patterns of genetic differentiation that were more complex than those of other populations descended from enslaved Africans on either side of the Atlantic. Using local ancestry inference and Identical-by-Descent methods, we identified five genetic clusters in São Tomé and reconstructed shared ancestries between each cluster and 70 African and European population samples, including an extensive sample from the Cabo Verde archipelago. Our findings align with historical records, retracing the major slave trade routes and labour-driven migrations after the abolition of slavery. We also identified gene flow between recently admixed groups that were previously isolated on the island. We call this process, creating multiple layers of genetic ancestry in admixed genomes, nested admixture. We suggest that changing social structures in São Tomé transformed the genetic structure of its population and influenced the admixture process. This study demonstrates how successive admixture and isolation events during and after the Trans-Atlantic Slave Trade shaped extant genetic diversity patterns at local scale in Africa.

Hybrid incompatibility emerges at the one-cell stage in interspecies Caenorhabditis embryos.

Hybrid incompatibility emerges at the one-cell stage in interspecies Caenorhabditis embryos.

Whole genome data demonstrate that episodic population expansion and secondary contact shaped population genetic structure in the North American water vole (Microtus richardsoni)

Abstract Over the last several million years, geological events have influenced temperate forests and the animals that inhabit them in the Pacific Northwest of North America. We use whole genome data collected from the North American water vole (Microtus richardsoni) to infer population demographic change over time, identify the most likely model of historical demography, and infer potential migration routes. These estimates provide greater detail of the historical demography in M. richardsoni. For example, they indicate that both coastal and inland populations experienced a population bottleneck during the last glaciation of the Pleistocene, with a subsequent expansion that coincided roughly with glacial retreat. Our analyses provide strong evidence that coastal and inland populations diverged well before the Last Glacial Maximum of the Pleistocene but have experienced secondary contact and changes in population size since this divergence. Using species distribution modelling, we support these inferences by demonstrating that suitable habitat has been present in both the coastal and inland regions. Estimation of effective migration surfaces supports the Okanogan Highlands as a possible area of historical gene flow. This project highlights the increased resolution that whole genome data can bring to phylogeographical analyses and suggests that a refined understanding of historical demography is possible.

Bacterial evolution in the oral microbiome: the role of conjugative elements and horizontal gene transfer.

As one of the most diverse bacterial populations within the human body, the oral microbiome encodes a wealth of genetic information. Horizontal gene transfer, driven by mobile genetic elements, takes advantage of this information to influence bacterial evolution and the spread of phenotypes (antibiotic resistances, virulence attributes, and metabolic capabilities) among oral microbes. Although widespread within microbial communities, fundamental aspects of the mobile elements that drive horizontal gene transfer within the oral cavity remain poorly understood. In this review, we explore what is known about the role of horizontal gene transfer in bacterial evolution within the oral microbiome and the elements that facilitate this transfer, with a specific focus on conjugative DNA transfer. Conjugative elements are found in virtually all bacterial phylogenetic clades, and some can mediate genetic exchange between distantly related organisms. This is of particular interest in the diverse microcosm of the oral cavity, specifically how it drives the evolution and virulence of dental pathogens. Finally, we highlight advances in our understanding of the unique biology within dental plaque and how these might influence our understanding of bacterial gene transfer, and thus human health and disease.

Genome analyses suggest recent speciation and postglacial isolation in the Norwegian lemming

The Norwegian lemming (Lemmus lemmus) is a small rodent distributed across the Fennoscandian mountain tundra and the Kola Peninsula. The Norwegian lemming likely evolved during the Late Pleistocene and inhabited Fennoscandia shortly prior to the Last Glacial Maximum. However, the exact timing and origins of the species, and its phylogenetic position relative to the closely related Siberian lemming (Lemmus sibiricus) remain disputed. Moreover, the presence of ancient or contemporary gene flow between both species is largely untested. The Norwegian lemming displays characteristic phenotypic and behavioral adaptations (e.g., coat color, aggression) that are not present in other Lemmus species. We generated a de novo genome assembly for the Norwegian lemming and resequenced nine modern and two ancient Lemmus spp. genomes. We show that all Lemmus species form distinct monophyletic clades, with concordant topology between the mitochondrial and nuclear genome phylogenies. The Siberian lemming is divided into two distinct but paraphyletic clades, one in the east and one in the west, where the western clade represents a sister taxon to the Norwegian lemming. We estimate that the Norwegian and western Siberian lemming diverged shortly before the Last Glacial Maximum, making the Norwegian lemming one of the youngest known mammalian species. We did not find any indication of gene flow between L. lemmus and L. sibiricus, suggesting postglacial isolation of L. lemmus. Furthermore, we identify species-specific genomic differences in genes related to coat color and fat transport, which are likely associated with the distinctive coloration and overwintering behavior observed in the Norwegian lemming.

Madagascar Speciation on Mountains: Pleistocene Glaciation Cycles Promote Genetic Divergence, Secondary Contact, and Morphological Diversification in Sympatric Lineages of the Pelican Spider Eriauchenus workmani (Archaeidae).

Habitat contraction and expansion around montane areas, caused by climatic cycles, can allopatrically isolate lineages and then put them back into secondary contact. When closely related lineages come back into coexistence, competition for similar resources may be strong, promoting niche partitioning via ecological character displacement. Eriauchenus workmani is an endemic spider species of the montane rainforest areas of Madagascar, with high morphological variation in somatic features. In this study, we address whether this variation is attributed to diverging populations, some of which co-occur in sympatry, and what role did mountains play in creating this divergence. Sampling individuals across the distribution range of this species, we gather hundreds of loci per specimen and then implement population genetic analyses, species delimitation methods, demographic models, ecological niche models, and morphological multivariate analyses. Findings show population contraction around montane areas during warm periods, when the distributions become fragmented, and population expansion during the last glacial maximum, when distributions become continuous. Further, we found four genetically distinct populations, three of which cohabitate in sympatry; however, gene flow is low considering populations are sympatric. There are significant differences in body size between populations. Within a population there are significant morphological differences, including a reduction in disparity when comparing allopatric with sympatric individuals. In conclusion, we hypothesise that the repeated cycles of isolation and secondary contact that occur in montane areas due to glacial cycles are fuelling speciation via allopatric divergence followed by ecological character displacement upon secondary contact.

Molecular Characterization of Vancomycin-Resistant Enterococcus spp. from Clinical Samples and Identification of a Novel Sequence Type in Mexico

Background:Enterococcus spp. is the third leading cause of healthcare-associated infections in the American continent, often because of the virulence factors that protect the bacterium against host defenses and facilitate tissue attachment and genetic material exchange. In addition, vancomycin, considered a last-resort treatment, has shown reduced efficacy in Enterococcus spp. strains. However, the relationship between bacterial resistance and virulence factors remains unclear. This study intends to evaluate the prevalence of glycopeptide-resistant genotypes and virulence factors in Enterococcus spp. strains. Methods: Over six months, 159 Enterococcus spp. strains causing nosocomial infections were analyzed. Multiplex PCR was performed to identify species, glycopeptide-resistant genotypes, and 12 virulence factors. Results: The most abundant species identified were Enterococcus faecalis and E. faecium. Vancomycin resistance was observed in 10.7% of the isolates, and the vanA genotype was present in 47% of resistant samples. The main virulence factors detected were acm (54%), which is related to cell adhesion; gel E (66%), a metalloproteinase linked to tissue damage; and the sex pheromones cpd (64%) and ccf (84%), which are involved in horizontal gene transfer. A significant association was found between the prevalence of acm, ccf, and cpd in VRE isolates, indicating the potential dissemination of genes to emerging strains via horizontal gene transfer. In addition, a new E. faecium, which displayed five virulence factors and harbored the vanA sequence type, was identified and registered as ST2700. Conclusions:Enterococcus faecalis and E. faecium are clinically critical due to multidrug resistance and virulence factors like acm, which aids host colonization. Genes ccf and cpd promote resistance spread via horizontal transfer, while the emerging ST2700 strain requires urgent monitoring to curb its virulent, drug-resistant spread.

Population Genetic Structure in the Invasive Ant Tapinoma indicum (Forel) (Hymenoptera: Formicidae) in Penang Island, Malaysia

Tapinoma indicum (Forel, 1895) (Hymenoptera: Formicidae) is a common household ant in Southeast Asia and has become increasingly dominant in urban environments on Penang Island, Malaysia. Its ability to establish persistent infestations indoors presents a growing concern. As its presence expands, understanding its genetic structure and dispersal patterns becomes increasingly important to uncover how it colonizes new areas and maintains high population densities. This study presents the first population genetic analysis of T. indicum using seven polymorphic microsatellite markers. A total of 300 individuals from 30 residential sites across three districts were analyzed to assess genetic diversity and population structure. All loci exhibited high polymorphism, with an average of 31 alleles per locus and high expected heterozygosity (mean HE = 0.926), indicating substantial genetic variation. However, observed heterozygosity was lower (mean HO = 0.437), and some loci showed signs of null alleles and inbreeding. F-statistics revealed moderate inbreeding within populations (mean FIS = 0.490) and low genetic differentiation between districts (FST = 0.075). Principal Coordinates Analysis and STRUCTURE results showed weak spatial genetic structuring and evidence of admixture, suggesting widespread gene flow. These findings indicate that T. indicum populations on Penang Island are genetically diverse but not strongly differentiated, forming a largely interconnected population across the island.

Dissecting the Genetic Affinity Between the Orang Asli and Southeast Asian Native Populations.

Southeast Asia (SEA) is a region with enriched human diversity and complex population history. Despite numerous small-scale population genetics studies being carried out, the map of human migration in this landmass remains fragmentary. Notably, the genetic affinities of the Orang Asli from Peninsular Malaysia and other SEA natives have not been comprehensively assessed. In this study, publicly available genotypic datasets were gathered and imputed. The genetic relationships and ancestry make-up of 19 SEA native populations, covering Peninsular Malaysia, Indonesia, Papua New Guinea, the Philippines, Vietnam, and Andaman, were comprehended and benchmarked with 14 global populations. With ∼20 million SNPs coverage, we provided supporting evidence to (i) a possible ancient genetic link between the Andamanese, Papuan and the Philippines and Peninsular Negrito; (ii) gene flow from the ancestors of Andamanese to Papuan, and the Negrito from Peninsular Malaysia and the Philippines; (iii) different genetic structures between the island SEA (iSEA) and mainland (mSEA) populations; (iv) close genetic affinity between the Proto-Malay Seletar with the iSEA populations and (v) close genetic affinity between the Senoi Mah Meri with the Proto-Malays. To our knowledge, this study reported the highest genomic sequence coverage and the most comprehensive SEA native populations covered thus far. Our results not only have provided strong supporting evidence to the earlier hypothesis, but also novel insights into the genetic diversity of the SEA native populations.