Patterns Of Genetic Differentiation Research Articles

The reconstruction of invasion histories with genomic data in light of differing levels of anthropogenic transport.

Unravelling the history of range shifts is key for understanding past, current and future species distributions. Anthropogenic transport of species alters natural dispersal patterns and directly affects population connectivity. Studies have suggested that high levels of anthropogenic transport homogenize patterns of genetic differentiation and blur colonization pathways. However, empirical evidence of these effects remains elusive. We compared two range-shifting species (Microcosmus squamiger and Ciona robusta) to examine how anthropogenic transport affects our ability to reconstruct colonization pathways using genomic data. We first investigated shipping networks from the 18th century onwards, cross-referencing these with regions where the species have records to infer how each species has potentially been affected by different levels of anthropogenic transport. We then genotyped thousands of single-nucleotide polymorphisms from 280 M. squamiger and 190 C. robusta individuals collected across their extensive species' ranges and reconstructed colonization pathways. Differing levels of anthropogenic transport did not preclude the elucidation of population structure, though specific inferences of colonization pathways were difficult to discern in some of the considered scenario sets. We conclude that genomic data in combination with information of underlying introduction drivers provide key insights into the historic spread of range-shifting species.This article is part of the theme issue ‘Species’ ranges in the face of changing environments (part I)’.

GENETIC DIVERSITY OF NATURAL AND RESTORED API-API PUTIH (AVICENNIA ALBA) POPULATIONS IN THE WEST COAST OF PENINSULAR MALAYSIA

A large tract of mangrove forest in Malaysia has been lost due to increased anthropogenic activities. Restorative practices of mangrove forest have been adopted nationwide to re-establish ecosystem services in combating coastal erosion. However, genetic considerations in local mangrove restoration practices are still far lacking despite the vast literature on their genetic diversity. To understand whether the restored mangroves can impact the genetic diversity distribution among natural populations, we used eight microsatellite markers to assess the genetic diversity of the Api-api putih (Avicennia alba) between the natural and restored populations along the west coast of Peninsular Malaysia. We found no difference in terms of genetic diversity between these populations. Two genetic clusters were detected among A. alba along the west coast based on Bayesian clustering and discriminant analysis of principal components (DAPC). The southwest monsoon current circulation that coincides the timing of seed dispersal of A. alba may explain such pattern of genetic differentiation. Despite the minimal genetic structure, our results suggest that seed sourcing from either population is viable for the local mangrove restoration programs in the future.

Population genetics and independently replicated evolution of predator-associated burst speed ecophenotypy in mosquitofish.

Many species show replicated ecophenotypy due to recurring patterns of natural selection. Based on the presence or absence of pursuit predators, at least 17 species of fish repeatedly differentiated in body shape in a manner that increases burst swimming speed and the likelihood of predator escape. The predator-associated burst speed (PABS) ecophenotype is characterized by a small head and trunk and enlarged caudal region. Mechanisms promoting replicated phenotype-environment association include selection (without evolution), a single instance of adaptive evolution followed by biased habitat occupation, repeated instances of local adaptation, or adaptive phenotypic plasticity. Common garden rearing of mosquitofish, Gambusia affinis, demonstrated a likely heritable basis for PABS phenotypy, but it is unknown whether populations are otherwise genetically distinct or whether replicated ecophenotypy represents a single or replicated instances of adaptation. To genetically characterize the populations and test hypotheses of single or multiple adaptations, we characterized variation in 12 polymorphic DNA microsatellites in the previously studied G. affinis populations. Populations were genetically distinct by multilocus analysis, exhibited high allelic diversity, and were heterozygote deficient, which effects were attributed to G. affinis's shoaling nature and habitat patchiness. Genetic and phenotypic distances among populations were correlated for non-PABS but not PABS morphology. Multilocus analysis demonstrated ecophenotype polyphyly and scattered multivariate genetic structure which support only the replicated-adaptation model. As all of the diverse tests performed demonstrated lack of congruence between patterns of molecular genetic and PABS differentiation, it is likely that divergent natural selection drove multiple instances of adaptive evolution.

Genetic Polymorphism and Natural Selection of Apical Membrane Antigen-1 in Plasmodium falciparum Isolates from Vietnam.

Apical membrane antigen-1 of Plasmodium falciparum (PfAMA-1) is a leading malaria vaccine candidate antigen. However, the genetic diversity of pfama-1 and associated antigenic variation in global P. falciparum field isolates are major hurdles to the design of an efficacious vaccine formulated with this antigen. Here, we analyzed the genetic structure and the natural selection of pfama-1 in the P. falciparum population of Vietnam. A total of 37 distinct haplotypes were found in 131 P. falciparum Vietnamese isolates. Most amino acid changes detected in Vietnamese pfama-1 were localized in the ectodomain, domains I, II, and III. Overall patterns of major amino acid changes in Vietnamese pfama-1 were similar to those of global pfama-1, but the frequencies of the amino acid changes slightly differed by country. Novel amino acid changes were also identified in Vietnamese pfama-1. Vietnamese pfama-1 revealed relatively lower genetic diversity than currently analyzed pfama-1 in other geographical regions, and suggested a distinct genetic differentiation pattern. Evidence for natural selection was detected in Vietnamese pfama-1, but it showed purifying selection unlike the global pfama-1 analyzed so far. Recombination events were also found in Vietnamese pfama-1. Major amino acid changes that were commonly identified in global pfama-1 were mainly localized to predicted B-cell epitopes, RBC-binding sites, and IUR regions. These results provide important information for understanding the genetic nature of the Vietnamese pfama-1 population, and have significant implications for the design of a vaccine based on PfAMA-1.

Co-structure analysis and genetic associations reveal insights into pinworms (Trypanoxyuris) and primates (Alouatta palliata) microevolutionary dynamics

BackgroundIn parasitism arm race processes and red queen dynamics between host and parasites reciprocally mold many aspects of their genetics and evolution. We performed a parallel assessment of population genetics and demography of two species of pinworms with different degrees of host specificity (Trypanoxyuris multilabiatus, species-specific; and T. minutus, genus-specific) and their host, the mantled howler monkey (Alouatta palliata), based on mitochondrial DNA sequences and microsatellite loci (these only for the host). Given that pinworms and primates have a close co-evolutionary history, covariation in several genetic aspects of their populations is expected.ResultsMitochondrial DNA revealed two genetic clusters (West and East) in both pinworm species and howler monkeys, although population structure and genetic differentiation were stronger in the host, while genetic diversity was higher in pinworms than howler populations. Co-divergence tests showed no congruence between host and parasite phylogenies; nonetheless, a significant correlation was found between both pinworms and A. palliata genetic pairwise distances suggesting that the parasites’ gene flow is mediated by the host dispersal. Moreover, the parasite most infective and the host most susceptible haplotypes were also the most frequent, whereas the less divergent haplotypes tended to be either more infective (for pinworms) or more susceptible (for howlers). Finally, a positive correlation was found between pairwise p-distance of host haplotypes and that of their associated pinworm haplotypes.ConclusionThe genetic configuration of pinworm populations appears to be molded by their own demography and life history traits in conjunction with the biology and evolutionary history of their hosts, including host genetic variation, social interactions, dispersal and biogeography. Similarity in patterns of genetic structure, differentiation and diversity is higher between howler monkeys and T. multilabiatus in comparison with T. minutus, highlighting the role of host-specificity in coevolving processes. Trypanoxyuris minutus exhibits genetic specificity towards the most frequent host haplotype as well as geographic specificity. Results suggest signals of potential local adaptation in pinworms and further support the notion of correlated evolution between pinworms and their primate hosts.

Phylogeography of cicadas on continental and oceanic islands in the northwestern Pacific region

AbstractAimGenetic differentiation of terrestrial organisms among islands is assumed to be affected by the geological history of the islands, such as the time elapsed since the formation of islands or straits. Cicadas are generally poor dispersers, but some cicada groups have colonised continental and oceanic islands and evolved into endemic species. Here, we focused on a cicada group in the northwestern Pacific region to reveal the association between intra‐ and interspecific genetic differentiation and the geological history of islands for cicadas on continental islands. We also clarified whether colonisation of oceanic islands was achieved by long‐distance dispersal or artificial introduction.LocationJapanese Archipelago, Ogasawara Islands, Ryukyu Archipelago.TaxonCicadas of the genus Meimuna (Hemiptera: Cicadidae).MethodsWe performed phylogenetic analysis, divergence time estimation, and ancestral area reconstruction using two mitochondrial and four nuclear gene sequences and population genetics analyses, including Bayesian skyline plotting using a mitochondrial gene sequence.ResultsMeimuna opalifera in the Japanese Archipelago, which was connected to the continent during the glacial periods, diverged from the continental populations 0.4 million years ago (Ma). In the Ryukyu Archipelago, which became disconnected from the continent earlier, two endemic species Meimuna kuroiwae and M. oshimensis diverged 2.4 Ma; these species showed differences in intraspecific genetic differentiation and range expansion. Furthermore, Meimuna iwasakii colonised the South Ryukyus from Taiwan Island later than 1.4 Ma, whereas M. boninensis, which is endemic to the oceanic Ogasawara Islands, diverged from M. kuroiwae in the Middle Ryukyus 1.04 Ma.Main conclusionsGenetic divergence among Meimuna species was larger on the continental islands that disconnected earlier, as was expected from the geological history of the islands. However, the pattern of intraspecific genetic differentiation differed between species within the same island region, possibly due to their ecological characteristics. In addition, colonisation of oceanic islands was achieved by long‐distance (possibly wind‐borne) dispersal from the continental islands. Thus, the formation of island cicada fauna was affected by islands’ geological history and species’ ecological characteristics, as well as accidental long‐distance dispersal events.

Gradients of genetic diversity and differentiation across the distribution range of a Mediterranean coral: Patterns, processes and conservation implications

AbstractAimHow historical and contemporary eco‐evolutionary processes shape the patterns of genetic diversity and differentiation across species’ distribution range remains an open question with strong conservation implications. Focusing on the orange stony coral, Astroides calycularis, we (a) characterized the pattern of neutral genetic diversity across the distribution range; (b) gave insights into the underlying processes; and (c) discussed conservation implications with emphasis on a national park located on a hotspot of genetic diversity.LocationSouth Mediterranean Sea and Zembra National Park.MethodsWe combined new data from 12 microsatellites in 13 populations located in the Centre and in the Western Periphery of the distribution range with a published dataset including 16 populations from the Western and Eastern Peripheries. We analysed the relationship among parameters of genetic diversity (He, Ar(g)) and structure (population‐specific FST) and two measures of geographic peripherality. We compared two estimators of pairwise genetic structure (GST, DEST) across the distribution range. The evolutionary and demographic history of the populations following the Last Glacial Maximum was reconstructed using approximate Bayesian computations and maximum‐likelihood analyses. We inferred the contemporary connectivity among populations from Zembra National Park and with the neighbouring area of Cap Bon.ResultsWe demonstrate a decrease in genetic diversity and an increase in genetic differentiation from the Centre to the Eastern and Western Peripheries of the distribution range. Populations from Zembra show the highest genetic diversity reported in the species. We identified a spillover effect towards Cap Bon.Main conclusionsThe patterns of genetic diversity and differentiation are most likely explained by “the postglacial range expansion hypothesis” rather than the “central–peripheral hypothesis.” Enforcement of conservation measures should be considered to protect this genetic diversity pattern, in particular when considering the low effective population size inferred at many sites.

Evolutionary history of the roan antelope across its African range

AbstractAimPhylogeographic studies on savanna ungulates have extensively evaluated genetic patterns mostly related to Pleistocene climatic oscillations. We address this subject through a comprehensive assessment across the pan‐African range of the roan antelope, assessing whether climatic oscillations or natural physical barriers play a predominant role in the evolutionary history of the species. We also address the spatial concordance of the genetic structure with the currently recognized subspecies.LocationSub‐Saharan Africa.TaxonRoan antelope (Hippotragus equinus).MethodsWe genotyped 43 microsatellite loci and sequenced whole‐mitochondrial genomes for 131 individuals across the species' entire African range. We performed spatial analyses of genetic diversity for contemporary and historical samples and calculated overall patterns of genetic differentiation and structure for both marker types. We also estimated the timing of divergence events and demographic trends, correlating these with the species’ biotic attributes as well as abiotic features shaping African savanna habitats.ResultsOur analyses uncovered highly structured clusters and contact zones across the distribution of the roan antelope, including five nuclear groups and four mitochondrial lineages. The north‐west group had the highest level of intra‐group diversity as well as inter‐group divergence and represents the oldest vicariant event. The central and southern groups had the lowest intra‐group diversity with low divergence values separating them, suggesting a more recent ancestry for these groups. All population groups showed signals of demographic stability over time showed signals of demographic stability over a demographic decline during the Holocene.Main conclusionsThe roan antelope exhibits significant population structure across its African range. This structure is largely associated with natural physical barriers, whereas contact zones could more easily be explained by climatic events. Based on estimates of genetic diversity, we propose a West African ancestry for this species with subsequent eastward and southern range expansions, as well as the persistence of stable population numbers within refugia. A general trend of population size decreases likely reflects Holocene extreme climatic events and increased human pressure.

Genetic imprints of Brosimum alicastrum Sw. in Mexico.

The mechanisms generating the geographical distributions of genetic diversity are a central theme in evolutionary biology. The amount of genetic diversity and its distribution are controlled by several factors, including dispersal abilities, physical barriers, and environmental and climatic changes. We investigated the patterns of genetic diversity and differentiation among populations of the widespread species Brosimum alicastrum in Mexico. Using nuclear DNA microsatellite data, we tested whether the genetic structure of B. alicastrum was associated with the roles of the Trans-Mexican Volcanic Belt and the Isthmus of Tehuantepec as geographical barriers to gene flow and to infer the role of past events in the genetic diversity patterns. We further used a maximum-likelihood population-effects mixed model (MLPE) to identify the main factor affecting population differentiation in B. alicastrum. Our results suggested that Mexican B. alicastrum is well differentiated into three main lineages. Patterns of the genetic structure at a finer scale did not fully correspond to the current geographical barriers to gene flow. According to the MLPE mixed model, isolation by distance is the best model for explaining the genetic differentiation of B. alicastrum in Mexico. We propose that the differentiation patterns might reflect (1) an ancient differentiation that occurred in Central and South America, (2) the effects of past climatic changes, and (3) the functions of some physical barriers to gene flow. This study provides insights into the possible mechanisms underlying the geographic genetic variation of B. alicastrum along a moisture gradient in tropical lowland forests.

Genetic Differentiation and Demographic History of Three Cerris Oak Species in China Based on Nuclear Microsatellite Makers

Knowledge of interspecific divergence and population expansions/contractions of dominant forest trees in response to geological events and climatic oscillations is of major importance to understand their evolution and demography. However, the interspecific patterns of genetic differentiation and spatiotemporal population dynamics of three deciduous Cerris oak species (Q. acutissima, Q. variabilis and Q. chenii) that are widely distributed in China remain poorly understood. In this study, we genotyped 16 nuclear loci in 759 individuals sampled from 44 natural populations of these three sibling species to evaluate the plausible demographical scenarios of the closely related species. We also tested the hypothesis that macro- and microevolutionary processes of the three species had been triggered and molded by Miocene–Pliocene geological events and Quaternary climatic change. The Bayesian cluster analysis showed that Q. acutissima and Q. chenii were clustered in the same group, whereas Q. variabilis formed a different genetic cluster. An approximate Bayesian computation (ABC) analyses suggested that Q. variabilis and Q. acutissima diverged from their most common ancestor around 19.84 Ma, and subsequently Q. chenii diverged from Q. acutissima at about 9.6 Ma, which was significantly associated with the episodes of the Qinghai–Tibetan Plateau (QTP). In addition, ecological niche modeling and population history analysis showed that these three Cerris oak species repeatedly underwent considerable ‘expansion–contraction’ during the interglacial and glacial periods of the Pleistocene, although they have varying degrees of tolerance for the climatic change. Overall, these findings indicated geological and climatic changes during the Miocene–Pliocene and Pleistocene as causes of species divergence and range shifts of dominant tree species in the subtropical and warm temperature areas in China.

Genetic analyses reveal demographic decline and population differentiation in an endangered social carnivore, Asiatic wild dog

Deforestation and agricultural intensification have resulted in an alarming change in the global land cover over the past 300 years, posing a threat to species conservation. Dhole is a monophyletic, social canid and, being an endangered and highly forest-dependent species, is more prone to the loss of favorable habitat in the Anthropocene. We determined the genetic differentiation and demographic history of dhole across the tiger reserves of Maharashtra using the microsatellite data of 305 individuals. Simulation-based analyses revealed a 77–85% decline in the major dhole sub-populations. Protected areas have provided refuge to the historically declining dhole population resulting in clustering with strong genetic structure in the remnant dhole population. The historical population decline coincides with the extreme events in the landscape over the past 300 years. The study highlights the pattern of genetic differentiation and diversity of a highly forest-dependent species which can be associated with the loss of forest cover outside tiger reserves. It also warrants attention to develop conservation plans for the remnant surviving population of dholes in India.

Genomic introgression from a distant congener in the Levant fritillary butterfly, Melitaea acentria

Introgressive hybridization is more common in nature than previously thought, and its role and creative power in evolution is hotly discussed but not completely understood. Introgression occurs more frequently in sympatry between recently diverged taxa, or when the speciation process has not yet been completed. However, there are relatively few documented cases of hybridization that erodes reproductive barriers between distantly related species. Here, we use whole genome and mitochondrial data to examine how introgression from a distant congener affects pattern of genetic differentiation in the Levant fritillary butterfly Melitaea acentria. We show that this local taxon has evolved as a peripatric geographic isolate of the widespread Melitaea persea, and that there has been significant unidirectional gene flow from the sympatric, nonclosely related Melitaea didyma to M.acentria. We found direct evidence of ongoing sporadic hybridization between M.didyma and M.acentria, which are separated by at least 5million years of independent evolution. Elevated differentiation and lower level of introgression on the sex Z chromosome compared to autosomes suggest that the Z chromosome has accumulated loci acting as intrinsic postzygotic barriers. Our results show that introgression from M.didyma has been an additional source of nucleotide diversity in the M.acentria population, providing material for drift and selection.

Adaptive and nonadaptive causes of heterogeneity in genetic differentiation across the Mimulus guttatus genome.

Genetic diversity becomes structured among populations over time due to genetic drift and divergent selection. Although population structure is often treated as a uniform underlying factor, recent resequencing studies of wild populations have demonstrated that diversity in many regions of the genome may be structured quite dissimilar to the genome-wide pattern. Here, we explored the adaptive and nonadaptive causes of such genomic heterogeneity using population-level, whole genome resequencing data obtained from annual Mimulus guttatus individuals collected across a rugged environment landscape. We found substantial variation in how genetic differentiation is structured both within and between chromosomes, although, in contrast to other studies, known inversion polymorphisms appear to serve only minor roles in this heterogeneity. In addition, much of the genome can be clustered into eight among-population genetic differentiation patterns, but only two of these clusters are particularly consistent with patterns of isolation by distance. By performing genotype-environment association analysis, we also identified genomic intervals where local adaptation to specific climate factors has accentuated genetic differentiation among populations, and candidate genes in these windows indicate climate adaptation may proceed through changes affecting specialized metabolism, drought resistance, and development. Finally, by integrating our findings with previous studies, we show that multiple aspects of plant reproductive biology may be common targets of balancing selection and that variants historically involved in climate adaptation among populations have probably also fuelled rapid adaptation to microgeographic environmental variation within sites.

Complex spatial patterns of genetic differentiation in the Caribbean mustard hill coral Porites astreoides

Complex spatial patterns of genetic differentiation in the Caribbean mustard hill coral Porites astreoides

The least‐cost path analysis of landscape genetics identifies two dispersal routes for the threatened Kaiser's mountain newt (Caudata: Salamandridae)

Variation in landscape features plays an important role in shaping the distribution of species in natural populations. These can influence population connectivity, gene flow, genetic drift, and ultimately the genetic structure and diversity of isolated populations. In this study, we aimed to identify the impact of landscape heterogeneity on the dispersal patterns of the threatened Kaiser’s mountain newt, Neurergus kaiseri. We integrated population genetics and geospatial data to predict the rates and patterns of genetic differentiation as well as to identify potential movement corridors among populations. For this purpose, we used two mitochondrial DNA markers and combined data on genetic subdivision (θST) and least-cost path (LCP) analyses from 15 fragmented highland streams and spring-ponds representing the entire species distribution area. Five possible dispersal routes used in this study were straight-line, stepping-stone, least cost slope, stream likelihood and combination least cost slope/stream likelihood. Genetic and LCP analyses indicated that two clades in the northern and southern distribution range have experienced two differing dispersal routes. The newts identified through the northern populations with high genetic diversity have dispersed with stepping-stone movements. In contrast, the southern populations are more isolated and dispersal might be facilitated by aquatic corridors in the least cost slope. We suggest that this study allows new implications for the conservation priorities of N. kaiseri by estimating the potential dispersal activity of the species in the face of climate change and ongoing habitat destruction relating to human activities in the southern Zagros mountains of Iran.

Fresh start after rough rides: understanding patterns of genetic differentiation upon human-mediated translocations

Fresh start after rough rides: understanding patterns of genetic differentiation upon human-mediated translocations

Genetic differentiation in Eurasian Woodcock (Scolopax rusticola) from the Azores

The Eurasian Woodcock Scolopax rusticola is a widespread Palaearctic migratory wader, with purportedly sedentary populations occurring in the Macaronesian archipelago of the Azores. Here we used microsatellite markers to investigate patterns of genetic diversity and differentiation in these insular birds, and compared Azorean populations with those from mainland Europe. Azorean populations show a (non‐significant) trend for reduced diversity, and low but consistent differentiation from mainland populations; evidence for widespread over‐water migration (in either direction) is weak but must occasionally occur given the recovery of an Azorean ringed bird in France. It is thus likely that the Azorean populations diverged recently from their mainland counterparts, but gene flow is currently restricted.

Local climate adaptation and gene flow in the native range of two co-occurring fruit moths with contrasting invasiveness.

Invasive species pose increasing threats to global biodiversity and ecosystems. While previous studies have characterized successful invaders based on ecological traits, characteristics related to evolutionary processes have rarely been investigated. Here we compared gene flow and local adaptation using demographic analyses and outlier tests in two co-occurring moth pests across their common native range of China, one of which (the peach fruit moth, Carposina sasakii) has maintained its native distribution, while the other (the oriental fruit moth, Grapholita molesta) has expanded its range globally during the past century. We found that both species showed a pattern of genetic differentiation and an evolutionary history consistent with a common southwestern origin and northward expansion in their native range. However, for the noninvasive species, genetic differentiation was closely aligned with the environment, and there was a relatively low level of gene flow, whereas in the invasive species, genetic differentiation was associated with geography. Genome scans indicated stronger patterns of climate-associated loci in the noninvasive species. While strong local adaptation and reduced gene flow across its native range may have decreased the invasiveness of C. sasakii, this requires further validation with additional comparisons of invasive and noninvasive species across their native range.

Incomplete reproductive isolation and low genetic differentiation despite floral divergence across varying geographic scales in Castilleja.

Divergence depends on the strength of selection and frequency of gene flow between taxa, while reproductive isolation relies on mating barriers and geographic distance. Less is known about how these processes interact at early stages of speciation. Here, we compared population-level differentiation in floral phenotype and genetic sequence variation among recently diverged Castilleja to explore patterns of diversification under different scenarios of reproductive isolation. Using target enrichment enabled by the Angiosperms353 probe set, we assessed genetic distance among 50 populations of four Castilleja species. We investigated whether patterns of genetic divergence are explained by floral trait variation or geographic distance in two focal groups: the widespread C. sessiliflora and the more restricted C. purpurea species complex. We document that C. sessiliflora and the C. purpurea complex are characterized by high diversity in floral color across varying geographic scales. Despite phenotypic divergence, groups were not well supported in phylogenetic analyses, and little genetic differentiation was found across targeted Angiosperms353 loci. Nonetheless, a principal coordinate analysis of single nucleotide polymorphisms revealed differentiation within C. sessiliflora across floral morphs and geography and less differentiation among species of the C. purpurea complex. Patterns of genetic distance in C. sessiliflora suggest species cohesion maintained over long distances despite variation in floral traits. In the C. purpurea complex, divergence in floral color across narrow geographic clines may be driven by recent selection on floral color. These contrasting patterns of floral and genetic differentiation reveal that divergence can arise via multiple eco-evolutionary paths.

Ethiopian indigenous goats offer insights into past and recent demographic dynamics and local adaptation in sub-Saharan African goats.

Knowledge on how adaptive evolution and human socio‐cultural and economic interests shaped livestock genomes particularly in sub‐Saharan Africa remains limited. Ethiopia is in a geographic region that has been critical in the history of African agriculture with ancient and diverse human ethnicity and bio‐climatic conditions. Using 52K genome‐wide data analysed in 646 individuals from 13 Ethiopian indigenous goat populations, we observed high levels of genetic variation. Although runs of homozygosity (ROH) were ubiquitous genome‐wide, there were clear differences in patterns of ROH length and abundance and in effective population sizes illustrating differences in genome homozygosity, evolutionary history, and management. Phylogenetic analysis incorporating patterns of genetic differentiation and gene flow with ancestry modelling highlighted past and recent intermixing and possible two deep ancient genetic ancestries that could have been brought by humans with the first introduction of goats in Africa. We observed four strong selection signatures that were specific to Arsi‐Bale and Nubian goats. These signatures overlapped genomic regions with genes associated with morphological, adaptation, reproduction and production traits due possibly to selection under environmental constraints and/or human preferences. The regions also overlapped uncharacterized genes, calling for a comprehensive annotation of the goat genome. Our results provide insights into mechanisms leading to genome variation and differentiation in sub‐Saharan Africa indigenous goats.