Mitochondrial DNA Variation in Black Rhinoceros (Diceros bicornis): Conservation Management Implications

Cell cultures have been established from 33 individual black rhinoceroses. These were from wild populations from various localities in southern Africa and include representatives from three geographical regions (southwestern, south-central, and eastern) corresponding to currently accepted conservation units, and include individuals previously attributed to one of the four subspecies, Diceros b. minor, D. b. bicornis, D. b. michaeli , and D. b. chobiensis (du Toit et al. 1987). Comparative mitochondrial DNA restriction maps were constructed using 16 restriction enzymes. These showed in each case two site differences between representative individuals from any two of the above geographical regions. Maps were monomorphic within geographical regions and, therefore, have the potential to provide diagnostic markers. The map from a single individual attributed to the D. b. chobiensis subspecies was identical to other individuals (attributed to D. b. minor ) in the south-central geographical region. The low amount of genetic diversity implied by these few differences renders it unlikely that problems with outbreeding depression will arise if, given the continuing decline in numbers of black rhinoceroses, it becomes necessary to supplement wild or captive populations with individuals from a different conservation unit in order to avoid inbreeding depression.     

Population Constraints Associated with the Use of Black Rhinos as an Umbrella Species for Desert Herbivores

The numerous tactics used to conserve biodiversity include the designation of protected areas, political change, and research and education, the latter involving paradigms such as insular biogeography and the "umbrella species concept." In Namibia lands removed from national park status in 1970 and currently under the jurisdiction of indigenous people now contain one of the few unfenced populations of black rhinos (Diceros bicornis) remaining in Africa. Theory predicts that the protection of umbrella species will ensure the survival of other biota that require(s) less space. To gauge how well biodiversity might be retained by examining the spatial needs of a small population of black rhinos, I used data gathered under various ecological conditions to estimate mean and minimum population sizes of six large herbivores of the Namib Desert ranging in size from giraffe (Giraffa camelopardalis) to springbok (Antidorcas marsupialis) and ostrich (Struthio camelus). My results indicate that annual differences in rainfall, both within and between seasons, resulted in wide fluctuations in herbivore population sizes for all species except rhino. Although other herbivores switched to areas of higher rainfall, rhinos did not. The data suggest that under conditions of extreme environmental variance the space used by rhinos alone was unlikely to assure the existence of populations of other species in excess of 250 individuals. Fifty percent of the species failed to exceed 150 individuals 50% of the time and one third of the species never attained populations in excess of 50 individuals. However, by employing assumptions about the spatial needs of rhino populations numbering up to 100 individuals, the mean minimum population sizes attained by any of four desert herbivores is 535. A future challenge in using rhinos and other large-bodied species as umbrellas for organisms of either similar or dissimilar trophic levels will be the refinement of estimates of population viability.     

DNA Fingerprinting Reveals a Lack of Genetic Variation in Northern Populations of the Western Pond Turtle (Clemmys marmorata)

I used DNA fingerprinting to provide the first analysis of the genetic composition of western pond turtle ( Clemmys marmorata ) populations in Washington, Oregon, and California. Populations of the western pond turtle in Washington and northern Oregon are rapidly approaching extinction. Genetic similarity within the largest northern populations, which are located inland, is high. An analysis of population substructure (F_st) revealed significant genetic divergence between inland populations, indicating a lack of dispersal and gene flow between sites. In contrast, northern coastal sites are not genetically distinct, but there are few if any viable populations remaining in this region. Genetic variability within southern California populations is a great deal higher than in northern inland sites. Similarly, a low F_st value indicated a lack of genetic differentiation between southern sites. An inter-regional analysis of population substructure (F_st = 0.24) revealed a significant degree of genetic divergence between geographical regions throughout the range. In addition, an estimate of western pond turtle phylogeny showed a genetic break in the species between northern and southern populations. Both population subdivision and phylogenetic analyses suggest a lack of appreciable gene flow between geographical regions for a considerable period of time. Genetic analyses support traditional subdivision based solely on the morphological variation of Clemmys marmorata into two subspecies: northern Clemmys marmorata marmorata and southern Clemmys marmorata pallida . Recovery of dwindling northern populations must combine demographic and genetic considerations. A first step should be to preserve local gene pools while augmenting population numbers, with the goal of preventing the extinction of this genetically and morphologically distinct subspecies.     

Phylogeographic Subspecies Recognition in Leopards (Panthera pardus): Molecular Genetic Variation

The incorporation of precise definitions for taxonomic units into wildlife legislation has necessitated the reevaluation of the taxonomy of endangered and threatened species. We used the subspecies recognition criteria proposed by Avise and Ball (1990) and O'Brien and Mayr (1991) to examine the infraspecific taxonomy of the leopard, Panthera pardus , a geographically widespread species with 27 currently recognized trinomial designations. Samples from named subspecies revealed appreciable genetic diversity using three molecular methods: allozymes, mitochondrial DNA restriction sites, and feline-specific minisatellites. Continental populations and subspecies from Africa and Asia possessed the highest amount of molecular genetic variation, whereas relatively lower amounts of diversity were present in island populations. Molecular data were analyzed using three phylogenetic methods (distance-matrix, maximum parsimony, and maximum likelihood) to resolve genetic differentiation below the species level The combined results revealed phylogenetic distinction of six geographically isolated groups of leopards: (1) African, (2) central Asian, (3) Indian, (4) Sri Lankan, (5) Javan, and (6) east Asian. Based on the combined molecular analyses and supporting morphological data (Miththapala 1992), u,e recommend that subspecific leopard taxonomy be revised to comprise eight subspecies: (1) P. p. pardus , Africa; (2) P. p. saxicolor , central Asia; (3) P. p. fusca , Indian subcontinent; (4) P. p. kotiya , Sri Lanka; (5) P. p. melas , Java; (6) P. p. orientalis , Amur; (7) P. p. japonensis , northern China; and (8) P. p. delacouri , southern China. In most cases, designated subspecies conform to historic geological barriers that would have facilitated allopatric genetic divergence.     

Sympatry of distinct mitochondrial DNA lineages in a copepod inhabiting estuarine creeks in the southeastern USA

The population genetic structure of the meiobenthic harpacticoid copepod Microarthridion littorale (Poppe) was examined with a geographic survey of a 348 bp fragment of the mitochondrial cytochrome b gene. Copepods were collected from ten locations on the coast from North Carolina to Georgia, USA, from January 1997 to November 1998. Sequence divergence among 198 individuals was as much as 4.3%, and three divergent mitochondrial clades were uncovered that differed by six to nine nucleotide changes. A rapid assay was developed to distinguish among mitochondrial clades, and an additional 333 specimens were surveyed. The three lineages co-occurred in seven of ten sampling locations. Data analyses were carried out separately for individuals assayed by DNA sequencing as well as for a combined data set that included individuals typed by restriction endonuclease digestion. An analysis of molecular variance indicated that a significant proportion of the total genetic variance could be partitioned among populations, although no significant correlation between geographical and genetic distance was detected.     

Conservation Implications of Patterns of Horn Regeneration in Dehorned White Rhinos

The demand for rhino horn has led to drastic declines in numbers of rhinos in Asia and Africa. Although all trade in rhino products has been illegal since the mid-1970s, a lucrative illegal market flourishes and poaching continues. Horn removal from African rhinos has been conducted in Zimbabwe, Namibia, and Swaziland to deter poaching. Regeneration of horns following dehorning has created the potential for a sustainable harvest of rhino horn through dehorning programs. Establishment of a regulated legal market for rhino horn has been suggested to help fund rhino conservation programs in African countries. However, evaluation of an economic harvest of rhino horn from dehorning programs has been limited because few data on rates and form of horn regeneration exist. Because rate of horn regeneration will determine the interval at which rhino horns could be harvested profitably, we measured horn regrowth for two white rhino (Ceratotherium simum) populations studied in Zimbabwe between 1991–1995. Measurements of horn sizes were collected before and after dehorning, and mass to volume relationships were calculated. Von Bertalanffy growth curves were used to model horn size and rates of horn regrowth relative to age. Adult males had larger horn bases (p < 0.001) and faster rates of horn regrowth than adult females. Regenerated horn mass for adult males (>1.3 kg/yr) was almost twice the mass of adult females. Based on an economic model for profit maximization, intervals for dehorning range from 1.16 to 1.51 years and vary with both sex and age. We suggest managers use these values as minimum dehorning intervals to balance profits with longer-term management goals. Rates of horn regeneration are likely to be less important than law enforcement in determining the efficacy of dehorning as a deterrent to rhino poaching.     

Rapid sperm evolution in the bluethroat (Luscinia svecica) subspecies complex

Spermatozoa are among the most variable animal cell types, and much research is currently directed towards explaining inter- and intraspecific variation in sperm form and function. Recent comparative studies in passerine birds have found associations between the level of sperm competition and both sperm length and sperm velocity. In species with sperm competition, postcopulatory sexual selection may shape the morphology of sperm as adaptations to the female environment. The speed of evolutionary change in sperm morphology at the species level is largely unknown. In this study, we analysed variation in sperm morphology among morphologically distinct and geographically isolated bluethroat subspecies in Europe. Consistent with previous studies, our analyses of mtDNA and nuclear introns suggest recent divergence and lack of lineage sorting among the subspecies. We found significant divergence in total sperm length and in the length of some sperm components (i.e. head and midpiece). There was a significantly positive relationship between pairwise divergences in sperm morphology and mitochondrial DNA, suggesting a role for genetic drift in sperm divergence. The magnitude of sperm length divergence was considerably higher than that in other geographically structured passerines, and even higher than that observed between several pairs of sister species. We hypothesize that the rapid sperm evolution in bluethroats is driven by sperm competition, and that strong postcopulatory sexual selection on sperm traits can lead to rapid speciation through reproductive incompatibilities.     

Erosion of Heterozygosity in Fluctuating Populations

Abstract: Demographic, environmental, and genetic stochasticity threaten the persistence of isolated populations. The relative importance of these intertwining factors remains unresolved, but a common view is that random demographic and environmental events will usually drive small populations to the brink of extinction before genetic deterioration poses a serious threat. To evaluate the potential importance of genetic factors, we analyzed a model linking demographic and environmental conditions to the loss of genetic diversity in isolated populations undergoing natural levels of fluctuation. Nongenetic processes—environmental stochasticity and population demography—were modeled according to a bounded diffusion process. Genetic processes were modeled by quantifying the rate of drift according to the effective population size, which was predicted from the same parameters used to describe the nongenetic processes. We combined these models to predict the heterozygosity remaining at the time of extinction, as predicted by the nongenetic portion of the model. Our model predicts that many populations will lose most or all of their neutral genetic diversity before nongenetic random events lead to extinction. Given the abundant evidence for inbreeding depression and recent evidence for elevated extinction rates of inbred populations, our findings suggest that inbreeding may be a greater general threat to population persistence than is generally recognized. Therefore, conservation biologists should not ignore the genetic component of extinction risk when assessing species endangerment and developing recovery plans.     

Phylogeography of surfclams,<Emphasis Type="Italic"> Spisula solidissima</Emphasis>, in the western North Atlantic based on mitochondrial and nuclear DNA sequences

The Atlantic surfclam, Spisula solidissima (Dillwyn), is broadly distributed in sandy sediments of the western North Atlantic between the Gulf of St. Lawrence and the Gulf of Mexico. In the United States, a substantial commercial fishery between Long Island and Cape Hatteras harvests offshore populations of one subspecies, S. s. solidissima. A smaller coastal form, S. s. similis Say (also known as S. s. raveneli Conrad), has a partially sympatric geographic distribution, but differs in several life-history characteristics. DNA sequence variation in mitochondrial cytochrome oxidase I (COI) and in introns at two nuclear calmodulin loci was examined to measure genetic divergence between the two subspecies and to test for population structure among populations of S. s. solidissima. Surfclams were collected from seven localities between 1994 and 2001. Based on both mitochondrial and nuclear DNA variation, the two subspecies of S. solidissima are reciprocally monophyletic, with a net COI divergence of 13.9%, indicating long-term reproductive isolation. The only significant differentiation among populations of S. s. solidissima (based on an AMOVA analysis of COI sequences) was between the Gulf of St. Lawrence and more southerly populations. A long internal branch in the S. s. solidissima genealogy coupled with low haplotype diversity in the northern-most population suggests that populations north and south of Nova Scotia have been isolated from each other in the past, with gene exchange more recently. Populations of S. s. similis from Atlantic and Gulf of Mexico coasts had a net COI divergence of 9.2%. Thus, diversification of Spisula spp. clams in the western North Atlantic involved an early adaptive divergence between coastal and offshore forms, with later barriers to dispersal emerging in the offshore form from north to south and in the coastal form between Atlantic and Gulf of Mexico populations.     

Phenotypic Alterations, Evolutionarily Significant Structures, and Rhino Conservation

To slow the impending loss of wild black ( Diceros bicornis ) and white ( Ceratotherium simum ) rhinos, three African countries have resorted to dehorning, a practice designed to remove the incentive for poachers to kill the hornless animals. The efficacy of this controversial conservation action remains unknown, in part because much uncertainty exists about the functional significance of rhino horns. We assessed the current utility of horns in Namibian black rhinos from phenotypically altered and intact populations in the Namib Desert, and we collated data on mortal fighting among horned females living in Etosha National Park. Infant mortality was 100% when dehorned mothers were sympatric with spotted hyenas ( Crocuta crocuta ). In contrast, infant survival was 100% for both horned mothers living with hyenas and occasional lions ( Panthera leo ) and 100% for dehorned mothers in the absence of dangerous carnivores. These data suggest that female horns can have direct fitness benefits in terms of calf survival. However, because lethal wounding due to fighting may account for up to 33% of the mortality of horned females, dehorning may improve adult survivorship. Our results (1) suggest that, where the aim of conservation programs is to improve population viability through juvenile recruitment, dehorning is unlikely to be a prudent strategy if practiced in areas with dangerous predators, and (2) illustrate the value of experimental approaches to onerous problems in conservation.     

Phylogeography of the sub-Antarctic notothenioid fish Eleginops maclovinus: evidence of population expansion

Phylogeography studies add insights into the geographic and evolutionary processes that underline the genetic divergence of populations. This work examines the geographic genetic structure of the Patagonian blennie, Eleginops maclovinus, a notothenioid (Perciformes) endemic to South American temperate and sub-Antarctic waters, using mitochondrial DNA cytochrome b sequences. We found 58 haplotypes in the analysis of 261 individual sequences of 833 base pairs in length. Among-population variance was very low (1.62%) and many haplotypes were shared between several populations across the species geographic range. Genetic differentiation was not consistent with a simple model of isolation by distance, possibly suggesting a lack of equilibrium between gene flow and local genetic drift. The analysis of mismatch distributions, neutrality tests, and the Bayesian Skyline Plot showed a pattern consistent with a recent population expansion event that may have taken place during the Middle Pleistocene.     

Molecular population structure of the kuruma shrimp <Emphasis Type="Italic">Penaeus</Emphasis><Emphasis Type="Italic"> japonicus</Emphasis> species complex in western Pacific

In a previous study on the kuruma shrimp Penaeus japonicus from the South China Sea, we detected high genetic divergence between two morphologically similar varieties (I and II) with distinct color banding patterns on the carapace, indicating the occurrence of cryptic species. In the present study, we clarify the geographical distribution of the two varieties in the western Pacific by investigating the genetic differentiation of the shrimp from ten localities. Two Mediterranean populations are also included for comparison. Based on the mitochondrial DNA sequence data, the shrimps are separated into two distinct clades representing the two varieties. Variety I comprises populations from Japan and China (including Taiwan), while variety II consists of populations from Southeast Asia (Vietnam, Singapore and the Philippines), Australia and the Mediterranean. Population differentiation is evident in variety II, as supported by restriction profiles of two mitochondrial markers and analysis of two microsatellite loci. The Australian population is genetically diverged from the others, whereas the Southeast Asian and Mediterranean populations show a close genetic relationship. Variety I does not occur in these three localities, while a small proportion of variety II is found along the northern coast of the South China Sea and Taiwan, which constitute the sympatric zone of the two varieties. The present study reveals high genetic diversity of P. japonicus. Further studies on the genetic structure of this species complex, particularly the populations in the Indian Ocean and Mediterranean, are needed not only to understand the evolutionary history of the shrimp, but also to improve the knowledge-based fishery management and aquaculture development programs of this important biological resource.     

Phylogenetic Reanalysis of the Saudi Gazelle and Its Implications for Conservation

Abstract: The identification of taxonomically appropriate populations of endangered species for captive breeding and reintroduction programs is fundamental to the success of those programs. The Saudi gazelle (   Gazella saudiya ) was endemic to the Arabian peninsula but is now considered extinct in the wild and is potentially a candidate for captive breeding and reintroduction. Using 375 base pairs of mitochondrial DNA (mtDNA) cytochrome b gene derived from museum samples collected from the wild prior to the presumed extinction of this species, we show that G. saudiya is the sister taxon of the African dorcas gazelle (  G. dorcas ). Reciprocal monophyly of G. saudiya mtDNA haplotypes with G. dorcas , coupled with morphological distinctiveness, suggests that it is an evolutionarily significant unit. These data indicate that captive populations identified previously as potential sources of G. saudiya for captive breeding appear incorrectly designated and are irrelevant to the conservation of G. saudiya. The polymerase chain reaction–restriction fragment length polymorphism ( PCR-RFLP) analysis of several private collections of living gazelles in Saudi Arabia provides no evidence for the survival of G. saudiya. We recommend that field surveys be undertaken to establish whether G. saudiya is indeed extinct in the wild and that other private collections within the Arabian peninsula be screened genetically. We urge caution when captive animals of unknown provenance are used to investigate the phylogenetics of cryptic species groups.     

Genetics, Taxonomy, and Conservation of the Threatened California Gnatcatcher

Abstract: The California Gnatcatcher (   Polioptila californica ) has become a flagship species in the dispute over development of southern California's unique coastal sage scrub habitat, a fragile, geographically restricted ecosystem with high endemism. One aspect of the controversy concerns the status of the subspecies of this bird in southern California coastal sage scrub that is currently listed as threatened under the U.S. Endangered Species Act. To investigate the recent population history of this species and the genetic distinctiveness of subspecies and to inform conservation planning, we used direct sequencing of mitochondrial DNA (mtDNA) for 64 individuals from 13 samples taken throughout the species' range. We found that coastal sage scrub populations of California Gnatcatchers are not genetically distinct from populations in Baja California, which are dense and continuously distributed throughout the peninsula. Rather, mtDNA sequences from this species contain the signatures of population growth and support a hypothesis of recent expansion of populations from a southern Baja California refugium northward into the southern coastal regions of California. During this expansion, stochastic events led to a reduction in genetic variation in the newly occupied range. Thus, preservation of coastal sage scrub cannot be linked to maintaining the genetic diversity of northern gnatcatcher populations, despite previous recognition of subspecies. Our study suggests that not all currently recognized subspecies are equivalent to evolutionarily significant units and illustrates the danger of focusing conservation efforts for threatened habitats on a single species.     

Molecular Evidence for a Unique Evolutionary Lineage of Endangered Sonoran Desert Fish (Genus Poeciliopsis)

Efforts to restore an endangered species in its former range should be based on a sound understanding of evolutionary relationships among remaining natural populations. In this study mitochondrial (mt) DNA diversity within and among Gila River drainage populations of the endangered Sonoran topminnow ( Poeciliopsis occidentalis ) in Arizona was compared to that from neighboring populations in Sonora, Mexico, where the species remains locally abundant. No mtDNA diversity was detected within or among samples from the Gila River basin in Arizona. But considerable variation was found within and among populations from several river systems in Sonora. Examination of mtDNA from a population that inhabits the upper reaches of the Río Yaqui in southeastern Arizona revealed substantial divergence between it and all other populations examined. We comment on the implications of this divergent population for topminnow management in Arizona and argue for more-detailed genetic and morphological studies to determine the distributional limits and specific status of this highly divergent form.     

Conservation Implications of Genetic Differentiation in Southern African Populations of Black Rhinoceros (Diceros bicornis)

We analyzed 30 protein-coding loci of four southern African black rhinoceros populations in order to calculate fixation indices and genetic distances for the different populations. We concluded that one of these populations is of the subspecies Diceros bicornis bicornis and the other three of Diceros bicornis minor. No evidence of inbreeding within populations was found. F- statistics revealed significant differentiation between populations. Small genetic distances found among the four populations reveal that they are conspecific, and no evidence was found to support the claim that the populations belong to discrete subspecies. Rather, an east-west cline in genetic characteristics appears to exist with G6pd and HB-2 alleles peculiar to western populations and Es-2 and GP-3 alleles peculiar to eastern populations.     

Implications from Mitochondrial DNA for Management to Conserve the Eastern Barred Bandicoot (Perameles gunnii)

On mainland Australia, the eastern barred bandicoot, Perameles gunnii , is confined to a relic wild population numbering less than 100 individuals in the city of Hamilton. Animals derived from this population are being bred in captivity in order to promote their recovery. The species also exists in Tasmania, where tittle is known of its conservation and taxonomic status. Mitochondrial DNA variability was compared within and between populations of P. gunnii using restriction fragment length polymorphisms. Genetic variability was found to be high among P. gunnii in Hamilton compared to those in Tasmania (higher diversity index, nucleotide sequence divergence, and greater number of haplotypes), despite the known decline and subdivision of the Hamilton population. Restriction fragment length polymorphisms distinguished animals from the east and the west of Hamilton and from the north and south of Tasmania. Nucleotide sequence divergence was substantial (2.2–2.5%) between Hamilton and Tasmania. Implications are that captive breeding and reintroduction should be designed to genetically represent the structure within Hamilton in order to minimize inbreeding and that the introduction of Tasmanian P. gunnii would not benefit the Hamilton population. It is concluded that mitochondrial DNA markers clearly can provide useful information about the history and current status of endangered marsupial populations, to the benefit of conservation management.     

Genetic Variability in Swayne's Hartebeest, an Endangered Antelope of Ethiopia

Abstract: Swayne's hartebeest ( Alcelaphus buselaphus swaynei ) is an endangered antelope that survives in four or five relict populations in Ethiopia. We examined the two main populations (Senkele and Nechisar) for mitochondrial (D-loop) and nuclear (microsatellite) variability in order to measure levels of genetic variation within the subspecies and degree of differentiation between populations. For comparison, we examined samples from a large population of red hartebeest ( Alcelaphus buselaphus caama ). Both swaynei and caama exhibited high levels of variation. There was significant differentiation between the populations of swaynei at Senkele and Nechisar, and gene diversity in Nechisar, the smaller of the two populations, was significantly lower than that in Senkele. Many mitochondrial haplotypes and microsatellite alleles present at high frequencies among the Senkele individuals were missing in Nechisar, suggesting that the translocation of animals from Senkele undertaken in 1974 did not contribute notably to the gene pool in Nechisar. Subsamples taken from Senkele in 1988 and 1995 showed a significant change in allele frequencies, a change that probably can be attributed to a massive population decline during this period. We recommend that both populations be protected in situ to maintain as much as possible of the diversity that exists within the taxon and that a breeding program be established. In spite of the earlier unsuccessful attempt, we argue that translocation of animals for enhancement of population size as well as genetic variation in Nechisar should be considered.     

Darwin's Fox: A Distinct Endangered Species in a Vanishing Habitat

The temperate rain forest of Chiloé Island, Chile, is inhabited by an endemic fox ( Dusicyon fulvipes ) first described by Charles Darwin and now designated Darwin's fox. Despite morphological differences, Darwin's fox has been considered only an insular subspecies of the mainland chilla fox ( D. griseus ). This follows the assumption that the island population, with an estimated population of less than 500, has been separated from the mainland chilla fox for only about 15,000 years and may have received occasional immigrants from the mainland. Consequently, this island population has not been protected as endangered or bred in captivity. Recently, a population of Darwin's fox was discovered on the Chilean mainland 600 km north of Chiloé Island. This population exists in sympatry with chilla and possibly culpeo ( D. culpaeus ) foxes, which suggests that Darwin's fox may be reproductively isolated. To clarify the phylogenetic position of Darwin's fox, we analyzed 344 bp of mitochondrial DNA control-region sequence of the three species of Chilean foxes. Darwin's foxes from the island and mainland populations compose a monophyletic group distinct from the two other Chilean fox species. This indicates that Darwin's fox was probably an early inhabitant of central Chile, and that its present distribution on the mainland may be a relict of a once much wider distribution. Our results highlight the ability of molecular genetic techniques to uncover historical relationships masked by recent events, such as local extinctions. The "rediscovery" of Darwin's fox as a distinct species implies that greater significance should be given to the protection of this species and its unique habitat and to documenting the extent of its mainland distribution.     

Population structure of the planktonic copepod Calanus pacificus in the North Pacific Ocean

The pelagic copepod Calanus pacificus ranges nearly continuously across temperate-boreal regions of the North Pacific Ocean and is currently divided into three subspecies—C. pacificus oceanicus, C. pacificus californicus, C. pacificus pacificus—based on subtle morphological differences and geographic location. The relation between geography and genetic differentiation was examined for 398 C. pacificus individuals sampled from six widely distributed locations across the North Pacific, including an open ocean site and coastal sites on both sides of the North Pacific basin. For each individual copepod, the DNA sequence was determined for a 421-bp region of the mitochondrial coxI gene (mtCOI). A total of sixty-three different mtCOI sequences, or haplotypes, were detected, with a sequence divergence between haplotypes of 0.2–3.1%. The number and distribution of haplotypes varied with sampling location; 12 haplotypes were distributed across multiple sampling locations, and 51 occurred at only one location. Five genetically distinct populations were detected based on F _ST values. Haplotype minimum spanning networks, nucleotide divergence and F _ST values indicated that individuals from coastal sites in the North Pacific Ocean were more closely related to each other than to individuals from the open ocean site at Station P. These results provide genetic support for the designation of two subspecies—a coastal subspecies that consists of what is currently referred to as C. p. pacificus and C. p. californicus and an open ocean subspecies C. p. oceanicus. This work also indicates that planktonic copepods with potentially high dispersal capacity can develop genetically structured populations in the absence of obvious geographic barriers between proximate locales within an ocean basin.