Population genetic structure and connectivity of the seagrass Thalassia hemprichii in the Western Indian Ocean is influenced by predominant ocean currents

This study is the first large‐scale genetic population study of a widespread climax species of seagrass, Thalassia hemprichii, in the Western Indian Ocean (WIO). The aim was to understand genetic population structure and connectivity of T. hemprichii in relation to hydrodynamic features. We genotyped 205 individual seagrass shoots from 11 sites across the WIO, spanning over a distance of ~2,700 km, with twelve microsatellite markers. Seagrass shoots were sampled in Kenya, Tanzania (mainland and Zanzibar), Mozambique, and Madagascar: 4–26°S and 33–48°E. We assessed clonality and visualized genetic diversity and genetic population differentiation. We used Bayesian clustering approaches (TESS) to trace spatial ancestry of populations and used directional migration rates (DivMigrate) to identify sources of gene flow. We identified four genetically differentiated groups: (a) samples from the Zanzibar channel; (b) Mozambique; (c) Madagascar; and (d) the east coast of Zanzibar and Kenya. Significant pairwise population genetic differentiation was found among many sites. Isolation by distance was detected for the estimated magnitude of divergence (D_EST), but the three predominant ocean current systems (i.e., East African Coastal Current, North East Madagascar Current, and the South Equatorial Current) also determine genetic connectivity and genetic structure. Directional migration rates indicate that Madagascar acts as an important source population. Overall, clonality was moderate to high with large differences among sampling sites, indicating relatively low, but spatially variable sexual reproduction rates. The strongest genetic break was identified for three sites in the Zanzibar channel. Although isolation by distance is present, this study suggests that the three regionally predominant ocean current systems (i.e., East African Coastal Current, North East Madagascar Current, and the South Equatorial Current) rather than distance determine genetic connectivity and structure of T. hemprichii in the WIO. If the goal is to maintain genetic connectivity of T. hemprichii within the WIO, conservation planning and implementation of marine protection should be considered at the regional scale—across national borders.     

Historical processes and contemporary ocean currents drive genetic structure in the seagrass Thalassia hemprichii in the Indo‐Australian Archipelago

Understanding spatial patterns of gene flow and genetic structure is essential for the conservation of marine ecosystems. Contemporary ocean currents and historical isolation due to Pleistocene sea level fluctuations have been predicted to influence the genetic structure in marine populations. In the Indo‐Australian Archipelago (IAA), the world's hotspot of marine biodiversity, seagrasses are a vital component but population genetic information is very limited. Here, we reconstructed the phylogeography of the seagrass Thalassia hemprichii in the IAA based on single nucleotide polymorphisms (SNPs) and then characterized the genetic structure based on a panel of 16 microsatellite markers. We further examined the relative importance of historical isolation and contemporary ocean currents in driving the patterns of genetic structure. Results from SNPs revealed three population groups: eastern Indonesia, western Indonesia (Sunda Shelf) and Indian Ocean; while the microsatellites supported five population groups (eastern Indonesia, Sunda Shelf, Lesser Sunda, Western Australia and Indian Ocean). Both SNPs and microsatellites showed asymmetrical gene flow among population groups with a trend of southwestward migration from eastern Indonesia. Genetic diversity was generally higher in eastern Indonesia and decreased southwestward. The pattern of genetic structure and connectivity is attributed partly to the Pleistocene sea level fluctuations modified to a smaller level by contemporary ocean currents.     

Fine- and regional-scale genetic structure of the exotic ascidian Styela clava (Tunicata) in southwest England, 50 years after its introduction

Styela clava , an ascidian native to the northwest Pacific, was first recorded in the Atlantic at Plymouth, southwest England, in 1953. It now ranges in the northeast Atlantic from Portugal to northern Denmark, and has colonized the east coast of North America. Within the region of first introduction, we aimed to characterize current genetic diversity in the species, elucidate the respective roles of human-aided vs. natural dispersal, and assess the extent of larval dispersal by looking for genetic differentiation at very small scales. Eight sites, mostly marinas, were studied along c . 200 km of coast in southwest England encompassing Plymouth. Five microsatellite loci were genotyped in 303 individuals to analyse gene flow at regional (among sites) and fine (within sites) scales. F -statistics and assignment tests were used to investigate regional genetic structure. At the fine scale, deviation from mutation–drift equilibrium was tested, and isolation by distance and genetic clustering analyses were undertaken. Significant genetic differentiation existed between sites, unrelated to geographical separation; migration between geographically distant marinas was inferred, highlighting the likely importance of human-mediated dispersal in range expansion and occupancy by S. clava . Fine-scale population structure was present within at least four sites, which may be explained by the limited dispersal ability of this ascidian and recruitment from differentiated pools of larvae. Populations in enclosed marinas had higher self-recruitment rates than those in open sites. Some marinas might therefore function as reservoirs of propagules for subsequent spread, whereas others might be sinks for migrants.     

Nuclear and chloroplast DNA phylogeography reveals Pleistocene divergence and subsequent secondary contact of two genetic lineages of the tropical rainforest tree species Shorea leprosula (Dipterocarpaceae) in South‐East Asia

Tropical rainforests in South‐East Asia have been affected by climatic fluctuations during past glacial eras. To examine how the accompanying changes in land areas and temperature have affected the genetic properties of rainforest trees in the region, we investigated the phylogeographic patterns of a widespread dipterocarp species, Shorea leprosula. Two types of DNA markers were used: expressed sequence tag‐based simple sequence repeats and chloroplast DNA (cpDNA) sequence variations. Both sets of markers revealed clear genetic differentiation between populations in Borneo and those in the Malay Peninsula and Sumatra (Malay/Sumatra). However, in the south‐western part of Borneo, genetic admixture of the lineages was observed in the two marker types. Coalescent simulation based on cpDNA sequence variation suggested that the two lineages arose 0.28–0.09 million years before present and that following their divergence migration from Malay/Sumatra to Borneo strongly exceeded migration in the opposite direction. We conclude that the genetic structure of S. leprosula was largely formed during the middle Pleistocene and was subsequently modified by eastward migration across the subaerially exposed Sunda Shelf.     

Population structure delineated with microsatellite markers in fragmented populations of a tropical tree, carapa guianensis (Meliaceae)

Deforestation and selective logging in the tropics may have serious consequences on genetic processes in tropical tree populations, affecting long-term survival of a given species as well as tropical forest communities. Because understanding the effects of human-induced changes on genetic processes is of utmost importance in formulating sound conservation and management plans for tropical forest communities, we developed microsatellite or simple sequence repeat (SSR) markers for the tropical tree Carapa guianensis (Meliaceae) and assessed the polymorphism of SSRs in adult and sapling populations in a large contiguous forest and in selectively logged and fragmented forests. The number of alleles in polymorphic loci ranged between 4 and 28. No inbreeding was detected in saplings or adult cohorts, but the allelic richness was lower in the sapling cohort of the isolated fragment. Genetic distances, Nei's D and (delta&mgr;)2, and RST values among saplings were greater than among adult cohorts, suggesting restriction of gene flow due to deforestation and habitat fragmentation. These SSR loci may be used to address many related questions regarding the population and conservation genetics of tropical trees.     

Strong population structure despite evidence of recent migration in a selfing hermaphroditic vertebrate, the mangrove killifish (Kryptolebias marmoratus)

We employ a battery of 33 polymorphic microsatellite loci to describe geographical population structure of the mangrove killifish (Kryptolebias marmoratus), the only vertebrate species known to have a mixed-mating system of selfing and outcrossing. Significant population genetic structure was detected at spatial scales ranging from tens to hundreds of kilometres in Florida, Belize, and the Bahamas. The wealth of genotypic information, coupled with the highly inbred nature of most killifish lineages due to predominant selfing, also permitted treatments of individual fish as units of analysis. Genetic clustering algorithms, neighbour-joining trees, factorial correspondence, and related methods all earmarked particular killifish specimens as products of recent outcross events that could often be provisionally linked to specific migration events. Although mutation is the ultimate source of genetic diversity in K. marmoratus, our data indicate that interlocality dispersal and outcross-mediated genetic recombination (and probably genetic drift also) play key proximate roles in the local 'clonal' dynamics of this species.     

Northern Hemisphere origin,transoceanic dispersal,and diversification of Ranunculeae DC. (Ranunculaceae) in the Cenozoic

Aim The role of dispersal versus vicariance for plant distribution patterns has long been disputed. We study the temporal and spatial diversification of Ranunculeae, an almost cosmopolitan tribe comprising 19 genera, to understand the processes that have resulted in the present inter‐continental disjunctions. Location All continents (except Antarctica). Methods Based on phylogenetic analyses of nuclear and chloroplast DNA sequences for 18 genera and 89 species, we develop a temporal–spatial framework for the reconstruction of the biogeographical history of Ranunculeae. To estimate divergence dates, Bayesian uncorrelated rates analyses and four calibration points derived from geological, fossil and external molecular information were applied. Parsimony‐based methods for dispersal–vicariance analysis (diva and Mesquite ) and a maximum likelihood‐based method (Lagrange ) were used for reconstructing ancestral areas. Six areas corresponding to continents were delimited. Results The reconstruction of ancestral areas is congruent in the diva and maximum likelihood‐based analyses for most nodes, but Mesquite reveals equivocal results at deep nodes. Our study suggests a Northern Hemisphere origin for the Ranunculeae in the Eocene and a weakly supported vicariance event between North America and Eurasia. The Eurasian clade diversified between the early Oligocene and the late Miocene, with at least three independent migrations to the Southern Hemisphere. The North American clade diversified in the Miocene and dispersed later to Eurasia, South America and Africa. Main conclusions Ranunculeae diversified between the late Eocene and the late Miocene. During this time period, the main oceanic barriers already existed between continents and thus dispersal is the most likely explanation for the current distribution of the tribe. In the Southern Hemisphere, a vicariance model related to the break‐up of Gondwana is clearly rejected. Dispersals between continents could have occurred via migration over land bridges, such as the Bering Land Bridge, or via long‐distance dispersal.     

Inbreeding and population structure of the potato cyst nematode (Globodera pallida) in its native area (Peru)

The dispersal abilities and the population genetic structure of nematodes living in the soil are poorly known. In the present study, we have pursued these issues in the potato cyst nematode Globodera pallida, which parasitizes potato roots and is indigenous to South America. A hierarchical sampling regime was conducted in Peru to investigate gene flow on regional, field and plant scales. Multilocus genotypes of single individuals were obtained using eight polymorphic microsatellites markers. Large heterozygote deficiencies were observed at most loci. The limited active dispersal of larvae from their cyst, which favours mating between (half) siblings, could be responsible for this pattern. Within fields, as well as among fields within regions (even 35 km apart), low F(ST) values suggest extensive gene flow. Among fields within regions, only 1.5-4.4% genetic variability was observed. Passive dispersal of cysts by natural means (wind, running water, or wild animals) or by anthropogenic means (tillage, movement of infected seed tubers) is probably responsible for the results observed. Among regions, high F(ST) values were observed. Thus long-range dispersal (more than 320 km apart) is probably limited by major biogeographical barriers such as the mountains found in the Andean Cordillera. These results provide useful information for the management of resistant varieties, to slow down the emergence and spread of resistance-breaking pathotypes.     

Microsatellite DNA analysis of genetic effects of harvesting in old-growth eastern white pine (Pinus strobus) in Ontario, Canada

Microsatellite DNA markers from 13 simple sequence repeat (SSR) loci were used to compare genetic diversity between preharvest pristine and postharvest residual gene pools of two adjacent virgin, old-growth ( approximately 250 years) stands of eastern white pine (Pinus strobus L.) in Ontario. There was concurrence in genetic diversity changes in the postharvest gene pools of the two stands. The total and mean numbers of alleles detected in each stand were reduced by approximately 26% after tree density reductions of approximately 75%. Approximately 18 and 21% of the low-frequency (0. 25 > P > or = 0.01) alleles and 76 and 92% of the rare (P < 0.01) alleles were lost from residual stands A and B, respectively, after harvesting. Multilocus gametic diversity was reduced by 38 and 85% and genotype additivity by approximately 50% in the residual stands after harvesting. Latent genetic potential of each stand was reduced by approximately 40%. Although heterozygosity was reduced (1-5%) in the postharvest residual stands, the reductions were not substantial and not comparable to those using other genetic diversity measures. The reductions in genetic diversity measures were slightly higher than those theoretically expected in postbottleneck populations according to drift theory. In the absence of substantial gene migration that could ameliorate the genetic losses, the ability of the postharvest white pine gene pools to adapt to changing environmental and disease conditions may have been compromised. The microsatellite DNA results for genetic effects of harvesting in old-growth eastern white pine stands were similar to those that we reported earlier from allozyme analysis (Buchert et al. 1997). The results indicate that silvicultural practices should ensure that the gene pools of remaining pristine old-growth stands are reconstituted in the regenerating stands.     

Microsatellite analysis of genetic structure in the mangrove species Avicennia marina (Forsk.) Vierh. (Avicenniaceae)

The level of genetic variation throughout the entire worldwide range of the mangrove species Avicennia marina (Forsk.) Vierh. was examined using microsatellite markers. Three microsatellite loci detected high levels of allelic diversity (70 alleles in total), essential for an accurate estimation of population genetic parameters. The informativeness of the microsatellite loci tended to increase with increasing average number of repeats. The levels of heterozygosity detected for each population, over all loci, ranged from 0.0 to 0.8, with an average of 0.407, indicating that some populations had little or no genetic variation, whereas others had a large amount. Populations at the extremes of the distribution range showed reduced levels of heterozygosity, and significant levels of inbreeding. This is not unexpected as these populations may be subject to founder effects and environmental constraints. The presence of genetic structure was tested in A. marina populations using three models: (i) a single panmictic model; (ii) the discrete subpopulation model; and (iii) the isolation by distance model. The discrete subpopulations model was supported by the overall measures of population differentiation based on the infinite alleles model (F-statistics), and the stepwise mutation model (R statistics). In addition, an analysis of molecular variance (AMOVA), using both theoretical models, found that most of the variation was between populations (41-71%), and within individuals in the total population (31-49%). There was little variation among individuals within populations (0-10%). There was no significant isolation by distance. The high levels of genetic differentiation observed among populations of A. marina may be due to environmental and ecological factors, particularly past sea level and climatic changes.     

Fine-scale population structure in a desert amphibian: landscape genetics of the black toad (Bufo exsul)

Environmental variables can strongly influence a variety of intra- and inter-population processes, including demography, population structure and gene flow. When environmental conditions are particularly harsh for a certain species, investigating these effects is important to understanding how populations persist under difficult conditions. Furthermore, species inhabiting challenging environments present excellent opportunities to examine the effects of complex landscapes on population processes because these effects will often be more pronounced. In this study, I use 16 microsatellite loci to examine population structure, gene flow and demographic history in the black toad, Bufo exsul , which has one of the most restricted natural ranges of any amphibian. Bufo exsul inhabits four springs in the Deep Springs Valley high desert basin and has never been observed more than several meters from any source of water. My results reveal limited gene flow and moderately high levels of population structure ( F _ST = 0.051–0.063) between all but the two closest springs. I found that the geographic distance across the arid scrub habitat between springs is significantly correlated with genetic structure when distance accounts for topography and barriers to dispersal. I also found very low effective population sizes ( N _e = 7–30) and substantial evidence for historical population bottlenecks in all four populations. Together, these results suggest that the desert landscape and B.   exsul 's high habitat specificity contribute significantly to population structure and demography in this species and emphasize the importance of considering behavioural and landscape data in conservation genetic studies of natural systems.     

Population genetic structure and approximate Bayesian computation analyses reveal the southern origin and northward dispersal of the oriental fruit moth Grapholita molesta (Lepidoptera: Tortricidae) in its native range

The oriental fruit moth (OFM) Grapholita molesta is one of the most destructive orchard pests. Assumed to be native to China, the moth is now distributed throughout the world. However, the evolutionary history of this moth in its native range remains unknown. In this study, we explored the population genetic structure, dispersal routes and demographic history of the OFM in China and South Korea based on mitochondrial genes and microsatellite loci. The Mantel test indicated a significant correlation between genetic distance and geographical distance in the populations. Bayesian analysis of population genetic structure (baps ) identified four nested clusters, while the geneland analysis inferred five genetic groups with spatial discontinuities. Based on the approximate Bayesian computation approach, we found that the OFM was originated from southern China near the Shilin area of Yunnan Province. The early divergence and dispersal of this moth was dated to the Penultimate glaciation of Pleistocene. Further dispersal from southern to northern region of China occurred before the last glacial maximum, while the expansion of population size in the derived populations in northern region of China occurred after the last glacial maximum. Our results indicated that the current distribution and structure of the OFM were complicatedly influenced by climatic and geological events and human activities of cultivation and wide dissemination of peach in ancient China. We provide an example on revealing the origin and dispersal history of an agricultural pest insect in its native range as well as the underlying factors.     

When Thailand was an island – the phylogeny and biogeography of mite harvestmen (Opiliones,Cyphophthalmi, Stylocellidae) in Southeast Asia

Aim To develop a comprehensive explanation for the biological diversity of Southeast Asia, especially in the Wallacea and Sundaland regions. This study focuses on a group of arachnids, mite harvestmen, which are thought to be an extremely old group of endemic animals that have been present in the region since most of its land supposedly formed part of the northern rim of the supercontinent Gondwana. Location Eastern Himalayas, Thai‐Malay Peninsula, Sumatra, Borneo, Java, Sulawesi, and New Guinea. Methods  Approximately 5.6 kb of sequence data were obtained from 110 South‐east Asian Cyphophthalmi specimens. Phylogenetic analyses were conducted under a variety of methods and analytical parameters, and the optimal tree was dated using calibration points derived from fossil data. Event based and paralogy‐free subtree biogeographical analyses were conducted. Results The Southeast Asian family Stylocellidae was recovered as monophyletic, arising on what is now the Thai‐Malay Peninsula and diversifying into three main clades. One clade (Meghalaya, here formally placed in Stylocellidae) expanded north as far as the eastern Himalayas, a second clade entered Borneo and later expanded back across the Sundaland Peninsula to Sumatra, and a third clade expanded out of Borneo into the entire lower part of Sundaland. Molecular dating suggested that Stylocellidae separated from other Cyphophthalmi 295 Ma and began diversifying 258 Ma, and the lineage that inhabits mostly Borneo today began diversifying between 175 and 150 Ma. Main conclusions The topology and molecular dating of our phylogenetic hypothesis suggest that Stylocellidae originated on Gondwana, arrived in Southeast Asia via the Cimmerian palaeocontinent, and subsequently diversified north, then south. Their present distribution in the Indo‐Malay Archipelago is explained largely by a diversification over the Sundaland Peninsula before western Sulawesi departed and the peninsula was extensively inundated.     

Clonality strongly affects the spatial genetic structure of the nurse species Aechmea nudicaulis (L.) Griseb. (Bromeliaceae)

Aechmea nudicaulis is a clonal bromeliad common to the Brazilian Atlantic forest complex and is found abundantly in the sandy coastal plain vegetation (restinga) on the north coast of Rio de Janeiro state, Brazil. This restinga site is structured in vegetation islands, and the species plays a key role as a nurse plant, much favoured by its clonality. We studied the clonal structure and consequences of clonality on the population spatial genetic structure (SGS) of this species using six nuclear microsatellites. Spatial autocorrelation analysis was performed to study the effects of sexual and clonal reproduction on the dispersal of A. nudicaulis. Analyses were performed at the genet (i.e. excluding clonal repeats) and ramet levels. Genotypic richness was moderate (R = 0.32), mostly as a result of the dominance of a few clones. The spatial distribution of genets was moderately intermingled, the mean clone size was 4.9 clonal fragments per genet and the maximum clonal spread was 25 m. Expected heterozygosities were high and comparable with those found in other clonal plants. SGS analyses at the genet level revealed significantly restricted gene dispersal (Sp = 0.074), a strong SGS compared with other herbaceous species. The clonal subrange extended across 23 m where clonality had a significant effect on SGS. The restricted dispersal and SGS pattern in A. nudicaulis, coupled with high levels of genetic diversity, indicated a recruitment at windows of opportunity (RWO) strategy. Moreover, the spatial distribution of genetic variation and the habitat occupation pattern in A. nudicaulis were dependent not only on the intrinsic biological traits of the species (such as spacer size and mating system), but also on biotic interactions with neighbouring species that determined suitable habitats for germination and the establishment of new genets. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 178 , 329–342.     

Population genetic structure and migration patterns of Dendrothrips minowai (Thysanoptera: Thripidae) in Guizhou,China

Dendrothrips minowai Priesner (Thysanoptera: Thripidae) is one of the most destructive insect pests on tea plants. Although outbreaks of this pest occur annually in South China, especially in Guizhou Province, little is known about its population genetics, such as genetic diversity and gene flow. To investigate its population genetic structure and migration routes in Guizhou Province, we analyzed 24 D. minowai populations across Guizhou using six microsatellite loci. We detected the moderate genetic diversity and the population genetic structure of this thrip species. Neighbor‐joining (NJ) phylogenetic tree and STRUCTURE analyses recognized two clusters within the studied populations. No correlation between genetic and geographical distances (r = 0.0139, P = 0.5830) was detected and more than 89% of the variation occurred among samples within populations. Gene flow analysis revealed high migration rates (74.0 – 894.1) among D. minowai populations. Overall, the trend of asymmetrical gene flow was from northeast to southwest. Our analyses demonstrated that D. minowai derived or originated from multiple sites and could be eventually divided into two groups in Guizhou.     

Phylogeography of colonially nesting seabirds, with special reference to global matrilineal patterns in the sooty tern (Sterna fuscata)

Sooty tern (Sterna fuscata) rookeries are scattered throughout the tropical oceans. When not nesting, individuals wander great distances across open seas, but, like many other seabirds, they tend to be site-faithful to nesting locales in successive years. Here we examine the matrilineal history of sooty terns on a global scale. Assayed colonies within an ocean are poorly differentiated in mitochondrial DNA sequence, a result indicating tight historical ties. However, a shallow genealogical partition distinguishes Atlantic from Indo-Pacific rookeries. Phylogeographic patterns in the sooty tern are compared to those in other colonially nesting seabirds, as well as in the green turtle (Chelonia mydas), an analogue of tropical seabirds in some salient aspects of natural history. Phylogeographic structure within an ocean is normally weak in seabirds, unlike the pronounced matrilineal structure in green turtles. However, the phylogeographic partition between Atlantic and Indo-Pacific rookeries in sooty terns mirrors, albeit in shallower evolutionary time, the major matrilineal subdivision in green turtles. Thus, global geology has apparently influenced historical gene movements in these two circumtropical species.     

基于转录组数据高通量发掘扶桑绵粉蚧微卫星引物

【目的】扶桑绵粉蚧Phenacoccus solenopsis Tinsley是我国重要的检疫性害虫。简单重复序列(simple sequence repeat,SSR)研究在遗传图谱和物理图谱的构建、分子标记辅助育种、品种鉴定、基因定位、遗传多样性、动植物分类和进化等方面具有重要意义。筛选的SSR引物将为扶桑绵粉蚧遗传多样性分析、进化分析及入侵生物学等奠定基础。【方法】利用高通量搜索的方法对扶桑绵粉蚧转录组中28 120条unigenes的数据进行搜索。【结果】共找到1 781个SSR位点。扶桑绵粉蚧转录组中SSRs的主要重复类型是单核苷酸重复,占SSR总数的89.44%;其次是三核苷酸重复,占SSR总数的7.52%。单核苷酸重复里主要是A/T基序,占了总量的87.42%。基于筛选的SSRs,运用Primer 3软件进行引物的批量设计,共有481个unigenes成功设计引物,共设计出1 228对引物。【结论】研究表明利用扶桑绵粉蚧转录组数据开发SSR标记是可行的,本研究开发的引物将为扶桑绵粉蚧遗传多样性分析、进化分析及入侵生物学等奠定基础。     

Colonization patterns and genetic structure of peripheral populations of the trumpeter finch (Bucanetes githagineus) from Northwest Africa, the Canary Islands and the Iberian Peninsula

Aim This paper has three aims: (1) to reconstruct the colonization history of two peripheral populations of the trumpeter finch (Bucanetes githagineus) presumably originating from the same source, one the result of an ancient expansion process and the other recently established and still expanding; (2) to estimate the importance of key events, such as past and current gene flow and bottlenecks, in both expansion processes and their contribution to the present population structure and genetic diversity; and (3) to find out whether two peripheral populations that established at widely differing times also differ in terms of genetic diversity. Location Northwest Africa (assumed source population), Canary Islands (long‐established peripheral) and south‐eastern Iberian Peninsula (recently established peripheral). Methods Bayesian analysis of population structure, individual assignment tests, F‐statistics, maximum likelihood migration estimates, genetic diversity indices and bottleneck tests were calculated with microsatellite data from 194 trumpeter finches from five breeding and two seasonal non‐breeding sites. Results Our data support the existence of two subpopulations (Canary Island and Ibero‐African) as the most likely population structure. Seasonal sites in the Iberian Peninsula had the highest percentage of birds assigned to other, mainly Iberian, sites. Pairwise F_ST values showed that the Canary Island localities were very similar to each other, but differed from the rest. Gene flow estimates within subpopulations were only slightly higher in the Canary Island population than in the Ibero‐African one. Gene diversity indices were similar at all localities. Canary Island sites show evidence of bottlenecks, whereas the Ibero‐African sites do not. Main conclusions Our data show that, at present, birds from the Canary Islands are genetically differentiated from those in North Africa and continental Spain. We could not unequivocally confirm the African origin of Canary populations because the contrary is also plausible. The Iberian Peninsula seems to have repeatedly received individuals from North Africa, which would have led to the relatively high genetic diversity found in these recently established localities and prevented bottlenecks. Movements of individuals towards sites outside their current range during the non‐breeding season are likely to precede the establishment of new breeding sites at the periphery of the distribution range.