Concordance of genetic divergence among sockeye salmon populations at allozyme, nuclear DNA, and mitochondrial DNA markers

Abstract.— We examined genetic variation at 21 polymorphic allozyme loci, 15 nuclear DNA loci, and mitochondrial DNA in four spawning populations of sockeye salmon ( Oncorhynchus nerka ) from Cook Inlet, Alaska, to test for differences in the patterns of divergence among different types of markers. We were specifically interested in testing the suggestion that natural selection at allozyme loci compromises the effectiveness of these markers for describing the amount and patterns of gene flow among populations. We found concordance among markers in the amount of genetic variation within and among populations, with the striking exception of one allozyme locus ( sAH ), which exhibited more than three times the amount of among-population differentiation as other loci. A consideration of reports of discordance between allozymes and other loci indicates that these differences usually result from one or two exceptional loci. We conclude that it is important to examine many loci when estimating genetic differentiation to infer historical amounts of gene flow and patterns of genetic exchange among populations. It is less important whether those loci are allozymes or nuclear DNA markers.     

Mitochondrial DNA products among RAPD profiles are frequent and strongly differentiated between races of Douglas-fir

Racial differentiation and genetic variability were studied between and within the coastal, north interior, and south interior races of Douglas-fir using RAPD and allozyme markers. Nearly half of all RAPD bands scored (13:45%) were found to be amplified from mitochondrial DNA. They exhibited maternal inheritance among hybrids and back-crosses between the races, and were much more highly differentiated (G_ST= 0.62 for haplotype frequencies) than were allozymes (G_ST= 0.26). No evidence of hybridization or introgression was detected where the coastal and interior races come into proximity in central Oregon.     

GEOGRAPHIC DISTRIBUTION OF MOLECULAR VARIANCE WITHIN THE BLUE MARLIN (MAKAIRA NIGRICANS): A HIERARCHICAL ANALYSIS OF ALLOZYME,SINGLE-COPY NUCLEAR DNA,AND MITOCHONDRIAL DNA MARKERS

This study presents a comparative hierarchical analysis of variance applied to three classes of molecular markers within the blue marlin (Makaira nigricans). Results are reported from analyses of four polymorphic allozyme loci, four polymorphic anonymously chosen single-copy nuclear DNA (scnDNA) loci, and previously reported restriction fragment length polymorphisms (RFLPs) of mitochondrial DNA (mtDNA). Samples were collected within and among the Atlantic and Pacific Oceans over a period of several years. Although moderate levels of genetic variation were detected at both polymorphic allozyme (H = 0.30) and scnDNA loci (H = 0.37), mtDNA markers were much more diverse (h = 0.85). Allele frequencies were significantly different between Atlantic and Pacific Ocean samples at three of four allozyme loci and three of four scnDNA loci. Estimates of allozyme genetic differentiation (θ_O) ranged from 0.00 to 0.15, with a mean of 0.08. The θ_O values for scnDNA loci were similar to those of allozymes, ranging from 0.00 to 0.12 with a mean of 0.09. MtDNA RFLP divergence between oceans (θ_O = 0.39) was significantly greater than divergence detected at nuclear loci (95% nuclear confidence interval = 0.04–0.11). The fourfold smaller effective population size of mtDNA and male-mediated gene flow may account for the difference observed between nuclear and mitochondrial divergence estimates.     

Estimation of Genetic Divergence in Meloidogyne Mitochondrial DNA

Restriction fragments from purified mitochondrial DNA can be readily detected following rapid end-labeling with [α-³²]nucleoside triphosphates and separation by gel electrophoresis. Mitochondrial DNA from 12 populations of Meloidogyne species was digested with 12 restriction enzymes producing more than 60 restriction fragments for each species. The mitochondrial genome of M. arenaria is the most genetically distinct of the four species compared. M. arenaria shows approximately 2.1-3.1% nucleotide sequence divergence from the mitochondrial genomes of M. javanica, M. incognita, and M. hapla. Among the latter three species, interspecific estimates of sequence divergence range from 0.7 to 2.3%. Relatively high intraspecific variation in mitochondrial restriction fragment patterns was observed in M. hapla. Intraspecific variation in M. incognita resulted in sequence divergence estimates of 0.5-1.0%. Such polymorphisms can serve as genetic markers for discerning mitochondrial DNA genotypes in nematode populations in the same way that allozymes have been used to discern nuclear DNA genotypes.     

GENETIC STRUCTURE OF THE BLUE RIDGE DUSKY SALAMANDER (DESMOGNATHUS ORESTES): INFERENCES FROM ALLOZYMES, MITOCHONDRIAL DNA, AND BEHAVIOR

Abstract The plethodontid salamander Desmognathus orestes, a member of the D. ochrophaeus species complex, is distributed in southwestern Virginia, eastern Tennessee, and western North Carolina. Previous allozyme analyses indicate that D. orestes consists of two distinct groups of populations (D. orestes‘B’ and D. orestes‘C’) with extensive intergradation and probable gene flow between these two groups. Spatially varying allele frequencies can reflect historical associations, current gene flow, or a combination of population‐level processes. To differentiate among these processes, we use multiple markers to further characterize divergence among populations of D. orestes and assess the degree of intergradation between D. orestes‘B’ and D. orestes‘C’, specifically investigating variation in allozymes, mitochondrial DNA (mtDNA), and reproductive behavior among populations. On a broad scale, the mtDNA genealogies reconstruct haplotype clades that correspond to the species identified from previous allozyme analyses. However, at a finer geographic scale, the distributions of the allozyme and mtDNA markers for D. orestes‘B’ and D. orestes‘C’ are discordant. MtDNA haplotypes corresponding to D. orestes‘B’ are more broadly distributed across western North Carolina than predicted by allozyme data, and the region of intergradation with D. orestes‘C’ indicates asymmetric gene flow of these markers. Asymmetric mating may contribute to observed discordance in nuclear versus cytoplasmic markers. Results support describing D. orestes as a single species and emphasize the importance of using multiple markers to examine fine‐scale patterns and elucidate evolutionary processes affecting gene flow when making species‐level taxonomic decisions.     

Imprint of post-glacial history in a narrowly distributed endemic spruce, Picea alcoquiana, in central Japan observed in nuclear microsatellites and organelle DNA markers

Aim We aim to infer the post‐glacial history of the narrowly distributed endemic spruce Picea alcoquiana in Japan, and to assess the hypothesis that the existing narrow natural range of the species has resulted from the diminution of the past natural range since the last glacial period. Location Mountainous forests in central Honshu Island in Japan. Methods We assessed the geographical patterns of genetic variation across nine populations of P. alcoquiana across its natural range using five nuclear microsatellites and polymerase chain reaction–restriction fragment length polymorphism markers for chloroplast (cp) and mitochondrial (mt) DNA. This study focuses on the genetic differentiation between northern peripherally isolated and southern core populations within the natural range of the species in central Honshu. In addition, based on diagnostic morphological traits of the cone, we used reliable macrofossil evidence to gain further insight into the past natural range of the species. Results Picea alcoquiana shows a level of genetic differentiation among populations (Φ_ST = 0.082) that was higher than the levels observed in nuclear microsatellites for other anemophilous and widespread tree species in Japan. A notable finding for the nuclear microsatellites was the loss of rare alleles and strong evidence of a recent bottleneck in the peripherally isolated populations. Analysis of molecular variance in cpDNA and mtDNA markers showed an absence of genetic differentiation between the peripherally isolated and core populations. Macrofossil evidence indicated that the past natural range of the species extended to a lower elevation and c. 135 km north of the existing peripherally isolated populations during the last glacial period (c. 28,000 yr bp ). Main conclusions During the last glacial period, P. alcoquiana had a wider natural range in which the peripherally isolated and core populations could have been geographically continuous with each other, and effective gene flow by means of pollen and seeds might have occurred. The recent bottleneck and consequent loss of rare alleles in the peripherally isolated populations might have evolved during the diminution and retreat of the northern part of the past natural range southwards to the core area and during the subsequent separation of the peripherally isolated populations from the core area since the last glacial period.     

Species identification of Chilean Artemia populations based on mitochondrial DNA RFLP analysis

Aim Two species of the brine shrimp, namely Artemia franciscana Kellogg and A. persimilis Piccinelli and Prosdocimi, inhabit Chile. Most studies so far have shown that A. franciscana is the most widely distributed species in Chile, with A. persimilis present only in Chilean Patagonia. In general, there is good agreement between morphological and genetic comparisons of Chilean populations with respect to species discrimination. However, a number of results indicate an overlap with some populations tending to diverge from A. franciscana and/or resembling A. persimilis. Prior to the mid 90's the use of DNA markers in Artemia was rather limited, despite their successful application in numerous other species. In this study, we investigate whether the conclusions drawn from traditional comparative tools are congruent with the pattern of genetic divergence depicted by DNA analysis at the mitochondrial level. Location Eight sites in Chile and two reference samples of A. franciscana and A. persimilis from San Francisco Bay (USA) and Buenos Aires (Argentina), respectively. Methods Restriction fragment length polymorphism (RFLP) analysis of a 535 bp segment of the mitochondrial 16S rRNA gene with nine restriction enzymes in 240 individuals. Results No haplotype was shared between the two species. Five restriction enzymes produced species‐specific patterns, enabling the unambiguous assignment of populations to species. Very high (100%) bootstrap values supported the clustering of haplotypes in two groups corresponding to the two species. The two species were clearly differentiated with average sequence divergence of 12.3%. High genetic differentiation was also found among con‐specific populations of A. franciscana with an F_ST estimate of 91%. Main conclusions The mitochondrial DNA (mtDNA) results of this study show a broadly similar pattern to those of previous allozyme and nuclear DNA analyses, with the two New World species appearing as highly divergent. The presence of A. persimilis in southern Chile (Chilean Patagonia) was confirmed. Hence, a species previously regarded as geographically restricted mainly to Argentina, appears to have expanded its range. Populations of A. franciscana appear highly structured with a level of inter‐population genetic differentiation much higher for mtDNA than previously reported with allozymes. Clustering of these populations does not follow a clear geographic pattern. The identification of population‐specific genetic markers for A. persimilis and A. franciscana will help to tackle further aspects of the speciation patterns of these species.     

Random amplified polymorphic DNA (RAPD) and quantitative trait analyses across a major phylogeographical break in the Mediterranean ragwort Senecio gallicus Vill. (Asteraceae)

Random amplified polymorphic DNA (RAPD) and quantitative trait variation of the widespread and ephemeral Senecio gallicus were surveyed in 11 populations sampled from the Iberian Peninsula and southern France. The aim of the study was to compare population relationships and levels of geographical differentiation with chloroplast (cp) DNA and allozyme variation assessed previously in the same populations. Employing multivariate statistics, a moderate level of intraspecific differentiation was observed among populations from Iberian coastal and inland regions for both RAPDs and quantitative traits. However, RAPDs provided greater resolution in identifying additional population structure within the hypothesized, Pleistocene refugial source area of the species in coastal Iberia. A major part of the geographical subdivision in RAPD and quantitative traits was concordant with the coastal vs. inland divergence as previously inferred from cpDNA haplotype frequencies, but strongly contrasted with the geographical uniformity of the species for allozymes. This concordance across various nuclear and cytoplasmic markers (RAPDs/quantitative traits, cpDNA) suggests that geographical uniformity for allozymes is more attributable to low rates of evolution and/or small genome sampling rather than high rates of pollen dispersal, slow rates of nuclear lineage sorting, or indirect balancing selection. The present study underscores the value of using additional classes of nuclear markers for narrowing the numbers of competing causal hypotheses about intraspecific cpDNA-allozyme discrepancies and their underlying evolutionary processes.     

Restriction fragment length polymorphisms in satellite DNA distinguish chromosomal races of the white-footed mouse Peromyscus leucopus

We describe a polymorphism revealed by a high-copy-number tandem repeat which serves to distinguish most individuals sampled (96%) from two chromosomal races of Peromyscus leucopus. Classical morphology, allozymes, mtDNA, and rDNA have all failed to provide fixed markers which separate these two chromosomal races. Data from P. leucopus further documents the utility of DNA polymorphisms to establish the natal origin (DNA ‘zipcodes’) of populations or individuals.     

Population Genetic Structuring in <Emphasis Type="Italic">Acanthopagrus butcheri</Emphasis> (Pisces: Sparidae): Does Low Gene Flow Among Estuaries Apply to Both Sexes?

Acanthopagrus butcheri completes its entire life history within estuaries and coastal lakes of southern Australia, although adults occasionally move between estuaries via the sea. Consequently, it is expected that populations of A. butcheri in different estuaries will be genetically distinct, with the magnitude of genetic divergence increasing with geographic isolation. However, previous genetic studies of A. butcheri from southeast Australia yielded conflicting results; allozyme variation exhibited minimal spatial structuring (θ = 0.012), whereas mitochondrial DNA distinguished the majority of populations analyzed (θ = 0.263) and genetic divergence was positively correlated with geographic isolation. This discrepancy could reflect high male gene flow, which impacts nuclear but not mitochondrial markers. Here we estimated allele frequencies at five nuclear microsatellite loci across 11 southeast Australian populations (595 individuals). Overall structuring of microsatellite variation was weaker (θ = 0.088) than that observed for mitochondrial DNA, but was able to distinguish a greater number of populations and was positively correlated with geographic distance. Therefore, we reject high male gene flow and invoke a stepping-stone model of infrequent gene flow among estuaries for both sexes. Likewise, management of A. butcheri within the study range should be conducted at the scale of individual or geographically proximate estuaries for both sexes. The lack of allozyme structuring in southeast Australia reflects either the large variance in structuring expected among loci under neutral conditions and the low number of allozymes surveyed or a recent colonization of estuaries such that some but not all nuclear loci have approached migration-drift equilibrium.     

Mitochondrial DNA variability in viviparous and ovoviviparous populations of the urodele Salamandra salamandra

Mitochondrial DNA analysis of 13 populations of S. salamandra along a transect across the North of the Iberian Peninsula showed values of divergence between haplotypes ranging from d = 0.41% to 5.91%. Phenetic and cladistic analysis grouped the isofemale lineages into two main clusters with contrasting phylogeographic patterns. The first group encompasses populations located at each extreme of the Iberian Peninsula. Despite the large geographic distance separating these populations, they exhibit only a minor degree of divergence among haplotypes. In contrast, much higher diversification, in both number of distinct haplotypes, and overall genetic divergence, was observed in the second group of phylogenetically related populations. Surprisingly, this process of radiation and divergence in mtDNA haplotypes occurred in populations in close geographic proximity. All populations sampled in this group are located within a 300 km range, in the central part of our transect across the Northern edge of the Peninsula. Most populations in the central range of our transect exhibit viviparous reproduction — which is derived and highly unusual among urodeles. The genetic distances measured among Asturian (central portion of our transect), viviparous populations are higher than the distances measured between the two main taxonomic clusters. A viviparous population showing an unusual level of mtDNA heterogenetiy is reported and the potential implications of this focus of localized variability are discussed. The dynamics of isofemale lineages among the two reproductive modes was further explored in combination with the previous allozyme data. Several nuclear markers suggest that major mtDNA divergences could be explained by long-term extrinsic barriers to gene flow. Isofemale lineages indicate a narrow secondary contact zone among populations with different reproductive patterns. The existence of viviparous and ovovivparous populations sharing a common haplotype suggests that reproductive transition in S. salamandra could have arisen in absence of genetic mtDNA differentiation. We finally outline a genetic model system where the acquisition of water independence from a primitively aquatic dependent amphibian life cycle can be analyzed from a microevolutionary perspective.     

Genetic structure of avian populations--allozymes revisited

Selection on allozymes has sometimes been advanced as one explanation for the low levels of population differentiation detected in avian populations by the use of enzymatic markers. Comparisons of the amount of population subdivision (estimated by FST values or analogous indices) measured by enzymatic and mitochondrial DNA (mtDNA) markers in birds were seen as evidence for this because mtDNA typically produces a more structured picture of population subdivisions. In fact, when taking into account the smaller effective population size of mtDNA, nuclear and mitochondrial markers give concordant results. Some discrepancies still exist, but I suggest that some might originate from different amounts of nuclear vs. mitochondrial gene flow due to partial reproductive isolation. Variable number of tandem repeat (VNTR) loci do not provide a dramatically different picture of population structures in birds compared to allozymes. Although more tests are needed, such as comparing the amount of genetic structure detected in the same populations with allozymes and microsatellites, the low levels of population subdivision measured with allozymes in birds seem to reflect historical and demographic processes and would not appear to result from any peculiarities of bird enzymatic loci.     

Nuclear microsatellite and mitochondrial DNA analyses reveal the regional genetic structure and phylogeographical history of a sanguivorous land leech,Haemadipsa japonica,in Japan

Recent molecular studies have indicated that phylogeographical history of Japanese biota is likely shaped by geohistory along with biological events, such as distribution shifts, isolation, and divergence of populations. However, the genetic structure and phylogeographical history of terrestrial Annelida species, including leech species, are poorly understood. Therefore, we aimed to understand the genetic structure and phylogeographical history across the natural range of Haemadipsa japonica, a sanguivorous land leech species endemic to Japan, by using nine polymorphic nuclear microsatellites (nSSR) and cytochrome oxidase subunit one (COI) sequences of mitochondrial DNA (mtDNA). Analyses using nSSR revealed that H. japonica exhibited a stronger regional genetic differentiation among populations (G'_ST = 0.77) than other animal species, probably because of the low mobility of land leech. Analyses using mtDNA indicated that H. japonica exhibited two distinct lineages (A and B), which were estimated to have diverged in the middle Pleistocene and probably because of range fragmentation resulting from climatic change and glacial and interglacial cycles. Lineage A was widely distributed across Japan, and lineage B was found in southwestern Japan. Analyses using nSSR revealed that lineage A was roughly divided into two population groups (i.e., northeastern and southwestern Japan); these analyses also revealed a gradual decrease in genetic diversity with increasing latitude in lineage A and a strong genetic drift in populations of northeastern Japan. Combined with the largely unresolved shallow polytomies from the mtDNA phylogeny, these results implied that lineage A may have undergone a rapid northward migration, probably during the Holocene. Then, the regional genetic structure with local unique gene pools may have been formed within each lineage because of the low mobility of this leech species.     

Cryptic diversity in an endemic rainforest skink (Gnypetoscincus queenslandiae)

Gynpetoscincus is a monotypic genus of skink endemic to the ancient and biogeographically complex wet tropical rainforests of northern Queensland. Surveys of variation in mitochondrial DNA and allozymes inG. queenslandiae revealed a major genetic break within the skink's 275 km range, clearly dividing it into northern and southern populations. The genetic differences between the two groups of populations are several-fold greater than differences between similarly separated localities within the southern group. The presence of two strongly differentiated evolutionary lineages within this narrowly distributed species highlights the value of genetic surveys to estimate evolutionary diversity in old, biogeographically complex biomes such as these rainforests.     

Patterns of population genetic variation in sympatric chiltoniid amphipods within a calcrete aquifer reveal a dynamic subterranean environment

Calcrete aquifers from the Yilgarn region of arid central Western Australia contain an assemblage of obligate groundwater invertebrate species that are each endemic to single aquifers. Fine-scale phylogeographic and population genetic analyses of three sympatric and independently derived species of amphipod (Chiltoniidae) were carried out to determine whether there were common patterns of population genetic structure or evidence for past geographic isolation of populations within a single calcrete aquifer. Genetic diversity in amphipod mitochondrial DNA (cytochrome c oxidase subunit I gene) and allozymes were examined across a 3.5 km² region of the Sturt Meadows calcrete, which contains a grid of 115 bore holes (=wells). Stygobiont amphipods were found to have high levels of mitochondrial haplotype diversity coupled with low nucleotide diversity. Mitochondrial phylogeographic structuring was found between haplogroups for one of the chiltoniid species, which also showed population structuring for nuclear markers. Signatures of population expansion in two of the three species, match previous findings for diving beetles at the same site, indicating that the system is dynamic. We propose isolation of populations in refugia within the calcrete, followed by expansion events, as the most likely source of intraspecific genetic diversity, due to changes in water level influencing gene flow across the calcrete.     

The postglacial history of Scots pine (Pinus sylvestris L.) in western Europe: evidence from mitochondrial DNA variation

The geographical structure of mitochondrial (mt)DNA variants (mitotypes) was investigated in 38 western European populations of Scots pine Pinus sylvestris using restriction fragment length polymorphism (RFLP) analysis of total DNA and a homologous cox1 probe. Three major mitotypes (designated a, b and d ) were detected. Within Spain all three major mitotypes were found, gene diversity was high, H_T = 0.586, and this diversity was distributed predominantly among rather than within populations (F_ST(M) = 0.813 for the seven Spanish populations). Mitotype d was present only in the most southerly population from the Sierra Nevada . Elsewhere in Europe, populations showed little or no mtDNA diversity within regions, but there were marked differences between regions. Italian populations were fixed for mitotype b ; populations from northern France, Germany, Poland, Russia and southern Sweden were fixed for mitotype a ; while populations in northern Fennoscandia were fixed for mitotype b . The isolated Scottish populations were predominantly of mitotype a , but mitotype b was present in three of the 20 populations scored. In Scotland, UK gene diversity (H_T = 0.120) and genetic differentiation among populations (F_ST(M) = 0.37) was much lower than in Spain. When interpreted in the light of complementary data from pollen analysis and nuclear genetic markers, the results suggest that present-day populations of P. sylvestris in western Europe have been derived from at least three different sources after glaciation.     

Phylogeography of a salmonid fish,masu salmon Oncorhynchus masou subspecies-complex,with disjunct distributions across the temperate northern Pacific

1. Climate oscillations during the Pleistocene had profound effects on the evolutionary history of freshwater fishes now distributed across northern temperate regions. The extent of continental glaciation on the western side of the North Pacific, including areas of East Asia, was more limited as compared with regions of North America, Europe and high-latitude areas of the North Pacific. Therefore, the effects of climate oscillations might have influenced species in dissimilar ways depending on the species' distribution.
2. We used mitochondrial DNA (mtDNA) and microsatellite DNA (msDNA) markers to clarify the evolutionary history of masu salmon Oncorhynchus masou subspecies-complex (family Salmonidae) distributed in historically non-glaciated regions in the western North Pacific.
3. No marked regional or subspecies-specific mtDNA haplotype associations were recognised, except for O. masou subsp., a lacustrine form endemic to Lake Biwa, an ancient lake in central Honshu. The landlocked subspecies O. masou formosanus, with a disjunct distribution on Taiwan Island, exhibited no diagnostic population features differing from the other subspecies, in either mtDNA or msDNA markers. Mismatch distribution and Bayesian skyline plot analyses indicated relatively recent range expansion and rapid population growth for masu salmon during the last glacial period (c. 0.1–0.15 Ma).
4. Contrary to the mtDNA genealogy, Bayesian clustering using msDNA showed two main genetic clusters, mainly northern populations of the subspecies O. m. masou and populations of the subspecies O. m. ishikawae in southern areas of the Japanese Archipelago. Notably, O. m. formosanus on Taiwan Island was included in the O. m. masou group, and O. masou subsp. was included in the O. m. ishikawae group.
5. Our results suggest that the masu salmon subspecies-complex in historically non-glaciated regions of the Temperate Northern Pacific is characterised by weak population structuring and shallow genetic differentiation among the subspecies, except for O. masou subsp. owing to its long isolation in Lake Biwa. Incomplete lineage sorting and historical inter-subspecies hybridisation, possibly due to secondary contact, seem to be plausible explanations for discrepancies in the mitochondrial DNA genealogy and nuclear DNA genetic structure.

     

Longtail tuna Thunnus tonggol (Bleeker, 1851) shows genetic partitioning across,but not within,basins of the Indo‐Pacific based on mitochondrial DNA

Genetic stock structure is atypical in tuna species, with most species demonstrating geographically‐broad, panmictic populations. Here, genetic data suggest a distinct pattern for Thunnus tonggol across the Indo‐Pacific region. The genetic variation in the coastal tuna T. tonggol sampled from across the South China Sea was examined using the highly variable mitochondrial DNA displacement loop (D‐loop) gene region. One hundred and thirty‐nine specimens were sampled from four locations in Indonesia, Vietnam and the Philippines. Phylogenetic reconstruction of genetic relationships revealed no significant ?_ST statistics and hence no population structure within the South China Sea. However, subsequent analysis with sequence data from coastal northwest India infers discrete genetic stocks between the Indian Ocean and the South China Sea. Consistent with previous genetic analyses of tuna species in the Indo‐Pacific, the findings in this study infer no population structure within each basin, but rather show a significant partitioning across the wider region. Furthermore, these results have implications for the management of the commercially valuable Thunnus tonggol across national boundaries, and thus requiring collaboration among countries to ensure its sustainable use.     

Population structure,connectivity, and demographic history of an apex marine predator,the bull shark Carcharhinus leucas

Knowledge of population structure, connectivity, and effective population size remains limited for many marine apex predators, including the bull shark Carcharhinus leucas. This large‐bodied coastal shark is distributed worldwide in warm temperate and tropical waters, and uses estuaries and rivers as nurseries. As an apex predator, the bull shark likely plays a vital ecological role within marine food webs, but is at risk due to inshore habitat degradation and various fishing pressures. We investigated the bull shark's global population structure and demographic history by analyzing the genetic diversity of 370 individuals from 11 different locations using 25 microsatellite loci and three mitochondrial genes (CR, nd4, and cytb). Both types of markers revealed clustering between sharks from the Western Atlantic and those from the Western Pacific and the Western Indian Ocean, with no contemporary gene flow. Microsatellite data suggested low differentiation between the Western Indian Ocean and the Western Pacific, but substantial differentiation was found using mitochondrial DNA. Integrating information from both types of markers and using Bayesian computation with a random forest procedure (ABC‐RF), this discordance was found to be due to a complete lack of contemporary gene flow. High genetic connectivity was found both within the Western Indian Ocean and within the Western Pacific. In conclusion, these results suggest important structuring of bull shark populations globally with important gene flow occurring along coastlines, highlighting the need for management and conservation plans on regional scales rather than oceanic basin scale.