Influence of habitat discontinuity, geographical distance, and oceanography on fine-scale population genetic structure of copper rockfish (Sebastes caurinus)

The copper rockfish is a benthic, nonmigratory, temperate rocky reef marine species with pelagic larvae and juveniles. A previous range-wide study of the population-genetic structure of copper rockfish revealed a pattern consistent with isolation-by-distance. This could arise from an intrinsically limited dispersal capability in the species or from regularly-spaced extrinsic barriers that restrict gene flow (offshore jets that advect larvae offshore and/or habitat patchiness). Tissue samples were collected along the West Coast of the contiguous USA between Neah Bay, WA and San Diego, CA, with dense sampling along Oregon. At the whole-coast scale (approximately 2200 km), significant population subdivision (F(ST) = 0.0042), and a significant correlation between genetic and geographical distance were observed based on 11 microsatellite DNA loci. Population divergence was also significant among Oregon collections (approximately 450 km, F(ST) = 0.001). Hierarchical amova identified a weak but significant 130-km habitat break as a possible barrier to gene flow within Oregon, across which we estimated that dispersal (N(e)m) is half that of the coast-wide average. However, individual-based Bayesian analyses failed to identify more than a single population along the Oregon coast. In addition, no correlation between pairwise population genetic and geographical distances was detected at this scale. The offshore jet at Cape Blanco was not a significant barrier to gene flow in this species. These findings are consistent with low larval dispersal distances calculated in previous studies on this species, support a mesoscale dispersal model, and highlight the importance of continuity of habitat and adult population size in maintaining gene flow.     

Spatial genetic patterns indicate mechanism and consequences of large carnivore cohabitation within development

Patterns of human development are shifting from concentrated housing toward sprawled housing intermixed with natural land cover, and wildlife species increasingly persist in close proximity to housing, roads, and other anthropogenic features. These associations can alter population dynamics and evolutionary trajectories. Large carnivores increasingly occupy urban peripheries, yet the ecological consequences for populations established entirely within urban and exurban landscapes are largely unknown. We applied a spatial and landscape genetics approach, using noninvasively collected genetic data, to identify differences in black bear spatial genetic patterns across a rural‐to‐urban gradient and quantify how development affects spatial genetic processes. We quantified differences in black bear dispersal, spatial genetic structure, and migration between differing levels of development within a population primarily occupying areas with >6 houses/km² in western Connecticut. Increased development disrupted spatial genetic structure, and we found an association between increased housing densities and longer dispersal. We also found evidence that roads limited gene flow among bears in more rural areas, yet had no effect among bears in more developed ones. These results suggest dispersal behavior is condition‐dependent and indicate the potential for landscapes intermixing development and natural land cover to facilitate shifts toward increased dispersal. These changes can affect patterns of range expansion and the phenotypic and genetic composition of surrounding populations. We found evidence that subpopulations occupying more developed landscapes may be sustained by male‐biased immigration, creating potentially detrimental demographic shifts.     

Theoretical limits to the correlation between pelagic larval duration and population genetic structure

Increasing dispersal duration should result in increasing dispersal distance, facilitating higher gene flow among populations. As such, it has long been predicted that genetic structure (e.g. F(ST) ) among populations of marine species should be strongly correlated with pelagic larval duration (PLD). However, previous studies have repeatedly shown a surprisingly poor correspondence. This result has been frequently interpreted as evidence for larval behaviours or physical oceanographic processes that result in larvae failing to reach their dispersal potential, or error inherent in estimating PLD and F(ST) . This study employed a computer modelling approach to explore the impacts of various uncertainties on the correlation between measures of genetic differentiation such as F(ST) and PLD. Results indicate that variation resulting from PLD estimation error had minor impacts on the correlation between genetic structure and PLD. However, variation in effective population size between species, errors in F(ST) estimation and non-equilibrium F(ST) values all had major impacts, resulting in dramatically weaker correlations between PLD and F(ST) . These results suggest that poor correlations between PLD and F(ST) may result from variation and uncertainty in the terms associated with the calculation of F(ST) values. As such, PLD may be a much stronger determinant of realized larval dispersal than suggested by the weak-to-moderate correlations between PLD and F(ST) reported in empirical studies.     

Identification of adults and larvae in Spiochaetopterus (Polychaeta, Chaetopteridae): consequences for larval transport and recruitment

This work is based on recent studies describing new species in Spiochaetopterus (Annelida Polychaeta). New morphological features were brought to light in studies of adults from widely separate areas. A parallel study of planktonic larvae in three areas (northern Atlantic Ocean, Gulf of California, Mediterranean Sea) led to the isolation of several larval categories, each related to an already described species. The large number of species already described shows that the founder species has been subjected to an intense adaptive radiation and that in spite of the ability of larvae to disseminate, each species now inhabits only a limited geographical area. Teleplanic larvae are thus not as effective as is generally supposed in controlling the adult area. The new paradigm implies that individuals from widely separate areas belong to species other than Spiochaetopterus costarum. Although larvae of each species are capable of covering long distances, larval transport may be interrupted at various stages of the life cycle for a variety of reasons. The most powerful causes of failure are not linked to the lifespan of planktonic larvae, but rather to constraints on the ability to realize physiological functions, including fecundation. The putative cosmopolitanism of S. costarum, before new species were described, was the result of both inadequate morphological examination and the use of questionable ecological arguments linked to larval dispersal.     

Global patterns in marine dispersal estimates: the influence of geography, taxonomic category and life history

We examine estimates of dispersal in a broad range of marine species through an analysis of published values, and evaluate how well these values represent global patterns through a comparison with correlates of dispersal. Our analysis indicates a historical focus in dispersal studies on low-dispersal/low-latitude species, and we hypothesize that these studies are not generally applicable and representative of global patterns. Large-scale patterns in dispersal were examined using a database of correlates of dispersal such as planktonic larval duration (PLD, 318 species) and genetic differentiation (FST, 246 species). We observed significant differences in FST (p<0.001) and PLD (p<0.001) between taxonomic groups (e.g. fishes, cnidarians, etc.). Within marine fishes (more than 50% of datasets), the prevalence of demersal eggs was negatively associated with PLD (R2=0.80, p<0.001) and positively associated with genetic structure (R2=0.74, p<0.001). Furthermore, dispersal within marine fishes (i.e. PLD and FST) increased with latitude, adult body size and water depth. Of these variables, multiple regression identified latitude and body size as persistent predictors across taxonomic levels. These global patterns of dispersal represent a first step towards understanding and predicting species-level and regional differences in dispersal, and will be improved as more comprehensive data become available.     

Islands increase genetic subdivision and disrupt patterns of connectivity of intertidal snails in a complex archipelago

The view that marine species with planktonic dispersal have highly connected, demographically open populations is giving way to recognition that populations may often be largely self-recruiting, or demographically closed. This raises the question of what local conditions might favor isolation of populations. To test the importance of islands for local isolation in species with planktonic larvae, we examined allozyme variation among 35 populations of the intertidal snail Austrocochlea constricta in the Houtman Abrolhos Islands, Western Australia, spanning 60 km. Heterogeneity of allozyme frequencies among populations was high, with average F(ST) of 0.237, indicating highly localized populations. Increased subdivision was associated with islands at different scales: between island groups, separated by deep water gaps, and between disconnected sets of islands within groups. At short distances, up to two km, subdivision increased fivefold between islands compared with that between populations on the same island. Along 11 km of continuous, sheltered shore, there was isolation by distance but among a linear series of islands over similar distance, there was greater subdivision at short distances but no association with distance. These patterns had been seen previously in the direct-developing snail Bembicium vittatum, but its finding in A. constricta confirms for a planktonic disperser the importance of this complex archipelago for both retention of locally produced larvae and disruption of patterns of connectivity. Taken together, these results indicate that islands can increase both the "open" and the "closed" components of recruitment and that applicable models of genetic connectivity depend substantially on local conditions.     

Landscape effects on the contemporary genetic structure of Ruffed Grouse (Bonasa umbellus) populations

The amount of dispersal that occurs among populations can be limited by landscape heterogeneity, which is often due to both natural processes and anthropogenic activity leading to habitat loss or fragmentation. Understanding how populations are structured and mapping existing dispersal corridors among populations is imperative to both determining contemporary forces mediating population connectivity, and informing proper management of species with fragmented populations. Furthermore, the contemporary processes mediating gene flow across heterogeneous landscapes on a large scale are understudied, particularly with respect to widespread species. This study focuses on a widespread game bird, the Ruffed Grouse (Bonasa umbellus), for which we analyzed samples from the western extent of the range. Using three types of genetic markers, we uncovered multiple factors acting in concert that are responsible for mediating contemporary population connectivity in this species. Multiple genetically distinct groups were detected; microsatellite markers revealed six groups, and a mitochondrial marker revealed four. Many populations of Ruffed Grouse are genetically isolated, likely by macrogeographic barriers. Furthermore, the addition of landscape genetic methods not only corroborated genetic structure results, but also uncovered compelling evidence that dispersal resistance created by areas of unsuitable habitat is the most important factor mediating population connectivity among the sampled populations. This research has important implications for both our study species and other inhabitants of the early successional forest habitat preferred by Ruffed Grouse. Moreover, it adds to a growing body of evidence that isolation by resistance is more prevalent in shaping population structure of widespread species than previously thought.     

Spatial patterns of genetic structure among populations of a stone‐cased caddis (Trichoptera: Tasimiidae) in south‐east Queensland,Australia

1. Gene flow and dispersal among populations of a stone‐cased caddis (Tasimiidae: Tasimia palpata) were estimated indirectly using a 460 bp region of the cytochrome oxidase I gene of mitochondrial DNA. 2. There was no significant differentiation at the largest spatial scale (between catchments) and no correlation between genetic distance and geographic distance. These results are consistent with widespread adult dispersal. 3. Conversely, significant genetic differentiation was detected at the smallest spatial scale examined (among reaches within streams). This pattern was primarily because of significant F_ST values in a single stream (Bundaroo Creek). 4. Bundaroo Creek also had the lowest mean number of haplotypes per population (n = 7) suggesting that a limited number of females may be responsible for recruitment at these sites. Significant F_ST's at the reach scale may be a result of this ‘patchy’ recruitment. However, additional evidence regarding the long‐range dispersal ability and fecundity of T. palpata females is needed to test this hypothesis fully.     

Molecular genetics of peripheral populations of Nova Scotian Unionidae (Mollusca: Bivalvia)

Peripheral populations of eight species of freshwater bivalves (Unionidae.) extending their geographic ranges into Nova Scotia, Canada, were examined electrophoretically to determine both the extent of genetic variability within such populations, and whether the hypothesized pathway of colonization across the Isthmus of Chignecto is reflected in patterns of genetic resemblance among these populations. The Nova Scotian species examined could be separated into two groups based on levels of observed heterozygosity and levels of variability in allele frequencies. The first group is characterized by low levels of heterozygosity and polymorphism compared with north-eastern American populations, and in the case of one species, Elliptio complanala, considerable variability in allele frequencies among populations occurring in similar habitats in different drainages. Populations of E. complanata from Nova Scotia can be differentiated from conspecific populations on the southern Atlantic Slope by possession of fast alleles at two loci. Multivariate analyses define subgroups within populations of E. complanata consistent with hypothesis that the species invaded Nova Scotia by way of the Isthmus of Chignecto, and then split into two groups, one of which colonized Cape Breton to the north and the other of which colonized southern areas of the Province. The second group of Nova Scotian species is characterized by little reduction in heterozygosity and polymorphism compared with values observed among north-eastern American conspecifics or congeners, little variability in allele frequencies from population to population, and little evidence to suggest that these species were dependent on the land bridge to invade the Province. The type of dispersal is hypothesized to be responsible, in part, for these differences: larvae of species in the first group rely on a parasitic attachment to fish with territorial habits limited to fresh water, and are thus likely to invade new drainages separated by salt water by chance, in small numbers, and in stepping-stone fashion. Species in the second group parasitize anadromous or saltwater tolerant hosts, are likely to be introduced into new habitats in greater numbers and/or receive greater amounts of gene flow subsequent to colonization, and seem less dependent on land-bridges to colonize new habitats.     

Temporal and spatial analyses disclose consequences of habitat fragmentation on the genetic diversity in capercaillie (Tetrao urogallus)

As a result of habitat fragmentation, the capercaillie ( Tetrao urogallus ) population in the Black Forest mountain range in southwestern Germany has declined rapidly during the last decades and now persists in patchy isolated fragments. To study the effects of fragmentation, we quantified dispersal patterns by genotyping 213 individuals in four subpopulations. We used a landscape genetics approach to analyse individual genetic variation, and despite overall low genetic structure, we found strong indications for a major boundary separating the northern part of the Black Forest area from the other subpopulations. Males and females display different gene flow patterns across the landscape. Females tend to disperse across longer distances than do males. We additionally studied the effects of the population decline on genetic diversity during the last hundred years. Although the population has dramatically declined from over 4000 to 250 males over a few decades, genetic diversity was not affected in the same way. We found two haplotypes that were present only in historic samples but microsatellite markers revealed no significant reduction in genetic diversity. Among historic samples, genetic differentiation was very low, indicating that the current genetic structure is caused by recent habitat fragmentation. We argue that inferences about reduced genetic diversity are drawn cautiously and recommend sampling over different temporal scales.     

Sex-biased genetic component distribution among populations: additive genetic and maternal contributions to phenotypic differences among populations of Chinook salmon

An approach frequently used to demonstrate a genetic basis for population-level phenotypic differences is to employ common garden rearing designs, where observed differences are assumed to be attributable to primarily additive genetic effects. Here, in two common garden experiments, we employed factorial breeding designs between wild and domestic, and among wild populations of Chinook salmon (Oncorhynchus tshawytscha). We measured the contribution of additive (V(A)) and maternal (V(M)) effects to the observed population differences for 17 life history and fitness-related traits. Our results show that, in general, maternal effects contribute more to phenotypic differences among populations than additive genetic effects. These results suggest that maternal effects are important in population phenotypic differentiation and also signify that the inclusion of the maternal source of variation is critical when employing models to test population differences in salmon, such as in local adaptation studies.     

The origins of larval forms: what the data indicate,and what they don't

What is a larva, if it is not what survives of an ancestor's adult, compressed into a transient pre‐reproductive phase, as suggested by Haeckel's largely disreputed model of evolution by recapitulation? A recently published article hypothesizes that larva and adult of holometabolous insects are developmental expressions of two different genomes coexisting in the same animal as a result of an ancient hybridization event between an onychophoran and a primitive insect with eventless post‐embryonic development. More likely, however, larvae originated from late embryonic or early post‐embryonic stages of ancestors with direct development. Evolutionary novelties would thus be intercalary rather than terminal, with respect to the ancestor's ontogenetic schedule. This scenario, supported by current research on holometabolous insects and marine invertebrates with complex life cycles, offers a serious alternative to the traditional scenario (‘what is early in ontogeny is also early in phylogeny’) underlying the current perception of the evolution of genetic regulatory networks.     

Spatial genetic analyses reveal strong genetic structure in two populations of the outcrossing tree fern Alsophila firma (Cyatheaceae)

The development of spatial genetic structure (SGS) in seed plants has been linked to several biological attributes of species, such as breeding system and life form. However, little is known about SGS in ferns, which together with lycopods are unique among land plants in having two free‐living life stages. We combined spatial aggregation statistics and spatial genetic autocorrelation analyses using five plastid microsatellites and one nuclear gene to investigate SGS in two populations of the outcrossing tree fern Alsophila firma (Cyatheaceae). We assessed how the observed patterns compare with those estimated for other ferns and seed plants. Populations of A. firma exhibited strong SGS, spatial clustering of individuals, substantial clonal diversity and no inbreeding. SGS in ferns appears to be higher than in most seed plants analysed to date. Contrary to our expectations, an outcrossing breeding system, wind dispersal and an arborescent life form did not translate into weak or no SGS. In ferns, SGS is probably being affected by the life cycle with two free‐living life stages. The reproductive biology of ferns appears to be more complex than previously thought. This implies that SGS in ferns is affected by some factors that cannot be inferred from the study of flowering plants. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 177 , 439–449.     

The influence of coastal topography, circulation patterns, and rafting in structuring populations of an intertidal alga

Understanding the dispersal processes that influence genetic structure in marine species requires estimating gene flow in a dynamic, fluid environment that is often poorly characterized at scales relevant to multiple dispersive stages (e.g. spores, gametes, zygotes, larvae, adults). We examine genetic structure in the marine alga Fucus vesiculosus L., which inhabits moderately exposed shores in the northern Atlantic but releases gametes only under sunny, calm conditions. We predicted genetic structure would correlate with coastal topography because weather frequently varies across coastal promontories on the Maine shore when F. vesiculosus is reproductive, which causes one side to experience high levels of water motion (= no gamete release) while one side is calm (= gamete release). Furthermore, we expected that the effect of low dispersal capacities of gametes and zygotes would result in spatial genetic structure over short distances. Using surface drifters, we characterized near-shore circulation patterns around the study sites to investigate whether directionality of gene flow was correlated with directionality of currents. We found significant genetic differentiation among sites sampled at two different peninsulas, but patterns of differentiation were unrelated to coastal topography and there was no within-site spatial structuring. Our genetic and near-shore circulation data, combined with an examination of gamete longevity, support the dependency of gene flow on storm-detached, rafting, reproductive adults. This study highlights the significance of rafting as a mechanism for structuring established populations of macroalgae and associated biota and demonstrates the importance of coupling population genetics' research with relevant hydrodynamic studies.     

Spatial genetic structure of the mountain pine beetle (Dendroctonus ponderosae) outbreak in western Canada: historical patterns and contemporary dispersal

Environmental change has a wide range of ecological consequences, including species extinction and range expansion. Many studies have shown that insect species respond rapidly to climatic change. A mountain pine beetle epidemic of record size in North America has led to unprecedented mortality of lodgepole pine, and a significant range expansion to the northeast of its historic range. Our goal was to determine the spatial genetic variation found among outbreak population from which genetic structure, and dispersal patterns may be inferred. Beetles from 49 sampling locations throughout the outbreak area in western Canada were analysed at 13 microsatellite loci. We found significant north-south population structure as evidenced by: (i) Bayesian-based analyses, (ii) north-south genetic relationships and diversity gradients; and (iii) a lack of isolation-by-distance in the northernmost cluster. The north-south structure is proposed to have arisen from the processes of postglacial colonization as well as recent climate-driven changes in population dynamics. Our data support the hypothesis of multiple sources of origin for the outbreak and point to the need for population specific information to improve our understanding and management of outbreaks. The recent range expansion across the Rocky Mountains into the jack/lodgepole hybrid and pure jack pine zones of northern Alberta is consistent with a northern British Columbia origin. We detected no loss of genetic variability in these populations, indicating that the evolutionary potential of mountain pine beetle to adapt has not been reduced by founder events. This study illustrates a rapid range-wide response to the removal of climatic constraints, and the potential for range expansion of a regional population.     

Population genetic structure, gene flow and sex-biased dispersal in frillneck lizards (Chlamydosaurus kingii)

By using both mitochondrial and nuclear multiloci markers, we explored population genetic structure, gene flow and sex-specific dispersal of frillneck lizards ( Chlamydosaurus kingii ) sampled at three locations, separated by 10 to 50 km, in a homogenous savannah woodland in tropical Australia. Apart from a recombinant lizard, the mitochondrial analyses revealed two nonoverlapping haplotypes/populations, while the nuclear markers showed that the frillneck lizards represented three separate clusters/populations. Due to the small population size of the mtDNA, fixation may occur via founder effects and/or drift. We therefore suggest that either of these two processes, or a combination of the two, are the most likely causes of the discordant results obtained from the mitochondrial and the nuclear markers. In contrast to the nonoverlapping mitochondrial haplotypes, in 12 out of 74 lizards, mixed nuclear genotypes were observed, hence revealing a limited nuclear gene flow. Although gene flow should ultimately result in a blending of the populations, we propose that the distinct nuclear population structure is maintained by frequent fires resulting in local bottlenecks, and concomitant spatial separation of the frillneck lizard populations. Limited mark–recapture data and the difference in distribution of the mitochondrial and nuclear markers suggest that the mixed nuclear genotypes were caused by juvenile male-biased dispersal.     

Compound eyes and ocular pigments of crustacean larvae (Stomatopoda and decapoda,brachyura)

Larvae of decapod and stomatopod crustaceans possess paired compound eyes not unlike those of adult crustaceans. However, the visual demands of larval and adult life differ considerably. Furthermore, the eyes of adult stomatopods appear to be far more specialized than those of the larvae. We examined eyes of several stomatopod species just before and after larval metamorphosis. At this time, the entire larval retina is joined by a new, adult‐type retinal array which gradually replaces the remnants of the larval retina. The new retina of the postlarva is anatomically similar to that of the full‐grown adult, and has virtually identical assemblages of intrarhabdomal filters. We determined the photopigments of Gonodactylus aloha, the only species for which we were able to obtain both larval and adult specimens, using microspectrophotometry. The single middle‐wavelength larval rhodopsin (λ_max= 499 nm) disappears at metamorphosis; none of the 10 classes of adult rhodopsins has λ_max between 473 and 510 nm. This metamorphic change of visual pigment does not occur in a comparison species of decapod crustacean, the blue crab Callinectes sapidus. Here, rhodopsins both of the megalops larva and the adult had λ_max at 503–504 nm. The difference between these two species can be explained by the varying ecological requirements of their larvae and adults, and more study of visual pigments in retinas of larval and adult crustaceans is warranted.     

Oceanic dispersal in a sedentary reef shark (Triaenodon obesus): genetic evidence for extensive connectivity without a pelagic larval stage

Aim Most reef fishes are site‐attached, but can maintain a broad distribution through their highly dispersive larval stage. The whitetip reef shark (Triaenodon obesus) is site‐attached, yet maintains the largest Indo‐Pacific distribution of any reef shark while lacking the larval stage of bony (teleost) fishes. Here we use mitochondrial DNA (mtDNA) sequence data to evaluate the enigma of the sedentary reef shark that maintains a distribution across two‐thirds of the planet. Location Tropical Pacific and Indian Oceans. Methods We analysed 1025 base pairs of the mtDNA control region in 310 individuals from 25 locations across the Indian and Pacific Oceans. Phylogeographic and population genetic analyses were used to reveal the dispersal and recent evolutionary history of the species. Results We resolved 15 mtDNA control region haplotypes, but two comprised 87% of the specimens and were detected at nearly every location. Similar to other sharks, genetic diversity was low (h = 0.550 ± 0.0254 and π = 0.00213 ± 0.00131). Spatial analyses of genetic variation demonstrated strong isolation across the Indo‐Pacific Barrier and between western and central Pacific locations. Pairwise Φ_ST comparisons indicated high connectivity among archipelagos of the central Pacific but isolation across short distances of contiguous habitat (Great Barrier Reef) and intermittent habitat (Hawaiian Archipelago). In the eastern Pacific only a single haplotype (the most common one in the central Pacific) was observed, indicating recent dispersal (or colonization) across the East Pacific Barrier. Main conclusions The shallow haplotype network indicates recent expansion of modern populations within the last half million years from a common ancestor. Based on the distribution of mtDNA diversity, this began with an Indo‐West Pacific centre of origin, with subsequent dispersal to the Central Pacific and East Pacific. Genetic differences between Indian and Pacific Ocean populations are consistent with Pleistocene closures of the Indo‐Pacific Barrier associated with glacial cycles. Pairwise population comparisons reveal weak but significant isolation by distance, and notably do not indicate the high coastal connectivity observed in other shark species. The finding of population structure among semi‐contiguous habitats, but population connectivity among archipelagos, may indicate a previously unsuspected oceanic dispersal behaviour in whitetip reef sharks.     

Biogeographic patterns and current distribution of molecular-genetic variation among populations of speckled dace, Rhinichthys osculus (Girard)

We examined genetic diversity within- and among-populations of speckled dace (Rhinichthys osculus) in five major drainage systems in the state of Oregon in western North America. Analysis of sequence variation in a 670-bp segment of the mitochondrial cytochrome b gene revealed deep divergence among basins and high genetic diversity within basins. Application of a molecular clock indicated that the divergence time among basins reflects vicariant events during the late Miocene to early Pliocene. The high levels of genetic diversity observed within basins is likely due to large historic population sizes, in particular, within the Klamath Basin. Two highly divergent mtDNA lineages were found to co-occur in populations in the Klamath Basin. This result may be indicative of a complex history of isolation and reconnection in this basin and/or multiple colonization events. Based on the observed level of mtDNA divergence these lineages may represent two reproductively isolated sympatric taxa. We recommend that major basins be regarded as distinct ESUs based on high levels of subdivision, deep divergences, and reciprocal monophyly among basins.     

Significant genetic differentiation among populations of Anomalocardia brasiliana (Gmelin, 1791): A bivalve with planktonic larval dispersion

Four Brazilian populations of Anomalocardia brasiliana were tested for mutual genetic homogeneity, using data from 123 sequences of the mtDNA cytochrome oxidase c subunit I gene. A total of 36 haplotypes were identified, those shared being H3 (Canela Island, Prainha and Acupe) and both H5 and H9 (Prainha and Acupe). Haplotype diversity values were high, except for the Camurupim population, whereas nucleotide values were low in all the populations, except for that of Acupe. Only the Prainha population showed a deviation from neutrality and the SSD test did not reject the demographic expansion hypothesis. Fst values showed that the Prainha and Acupe populations represent a single stock, whereas in both the Canela Island and Camurupim stocks, population structures are different and independent. The observed structure at Canela Island may be due to the geographic distance between this population and the remainder. The Camurupim population does not share any haplotype with the remaining populations in northeastern Brazil. The apparent isolation could be due to the rocky barrier located facing the mouth of the Mamanguape River. The results highlight the importance of wide-scale studies to identify and conserve local genetic diversity, especially where migration is restricted.