Range-wide Population Structure Research Articles

Shared patterns of population genomic variation and phenotypic response across rapid range expansions in two invasive lady beetle species

Non-native lady beetle species have often been introduced, with variable success, into North America for biological control of aphids, scales, whiteflies, and other agricultural pests. Two predatory lady beetle species, Propylea quatuordecimpunctata and Hippodamia variegata, both originating from Eurasia, were first discovered near Montreal, Quebec, in North America in 1968 and 1984, respectively, and have since expanded into northeastern North America and the midwestern United States. In this study, we estimate the range-wide population structure, establishment and range-expansion, and recent evolutionary history of these lady beetle species using reduced-representation genotyping-by-sequencing via ddRADseq. In addition, we quantified the responses to a key abiotic factor, photoperiod, that regulates adult reproductive diapause in these two species and may influence their geographical range in North America. Our analyses detect: (1) non-significant genetic differentiation and divergence among North American populations that likely originated from a single accidental introduction, (2) evidence of reduced contemporary gene flow within the continental US, and (3) minor phenotypic differences in diapause induction between populations of the two species from the same location.

Genome-wide analysis of the harbour porpoise (Phocoena phocoena) indicates isolation-by-distance across the North Atlantic and potential local adaptation in adjacent waters

The harbour porpoise (Phocoena phocoena), a highly mobile cetacean species of the Northern Hemisphere, inhabits basins that vary broadly in salinity, temperature, and food availability; such variation can drive divergent adaptation among local populations. To shed light on range-wide population structure and local adaptation, we generated ddRAD sequencing data spanning the entire North Atlantic and the Baltic Sea, as well as the Black Sea as an outgroup, and mapped this data to the high-quality draft genome of the species. We identified 11,978 genome-wide SNPs from 150 individuals, which we used for population genetic inferences. Our results support genetic differentiation between North Atlantic and Baltic Sea populations, with Kattegat as a transition zone. Across the North Atlantic the population differentiation is subtle from west to east, congruent with an isolation-by-distance pattern, but indicates a separation of southern North Sea harbour porpoises. We identified genomic outlier regions, i.e., scaffold regions where SNPs with high FST across North Atlantic populations co-occur. Together with the draft genome annotation, these regions could point towards candidate genes for differential local adaptation processes among populations. Furthermore, they enable the development of a SNP panel for routine population assignment which will be useful in a conservation and management context. We identified six outlier loci putatively under positive selection, based on the population structure inferred from the complete SNP set. Our study highlights the value of genome resources in conservation and management and provides a crucial additional resource for the study of harbour porpoise evolution and phylogeny.

Weak range-wide population structure in the blackfin tuna (Thunnus atlanticus) revealed by analysis of genome-wide SNPs

Abstract Blackfin tuna (Thunnus atlanticus) is a small tuna distributed in the western Atlantic Ocean where it is exploited by growing recreational and commercial regional fisheries. In this work, genome-wide genetic variation was analysed to investigate the occurrence of stock subdivision. A de novo assembly of the blackfin tuna genome was generated using Illumina paired-end sequencing data and applied as a reference for population genomic analysis of specimens from nine localities (average sample size per locality n = 72) spanning most of the blackfin tuna distribution range. A total of 2139 single-nucleotide polymorphisms were discovered and genotyped using the double-digest restriction associated DNA sequencing. Pairwise exact homogeneity tests were significant in 24 out of 36 population pairs and significant spatial autocorrelation of genotypes was observed for specimens collected within 2250 km of each other. However, divergence among locality samples was very low (pairwise FST range 0.0002–0.0025) and significant temporal variations were detected in localities sampled multiple times. Approaches to detect cryptic groups de novo were unsuccessful. Additional sampling is warranted to determine if multiple stocks need to be defined for management and assess temporal and spatial patterns of gene flow connecting them.

Range-Wide Population Structure of 3 Deepwater Eteline Snappers Across the Indo-Pacific Basin.

Deep-sea habitats may drive unique dispersal and demographic patterns for fishes, but population genetic analyses to address these questions have rarely been conducted for fishes in these environments. This study investigates the population structure of 3 tropical deepwater snappers of the genus Etelis that reside at 100-400 m depth, with broad and overlapping distributions in the Indo-Pacific. Previous studies showed little population structure within the Hawaiian Archipelago for 2 of these species: Etelis coruscans and E. carbunculus. Here we extend sampling to the entire geographic range of each species to resolve the population genetic architecture for these 2 species, as well as a recently exposed cryptic species (Etelis sp.). One goal was to determine whether deepwater snappers are more dispersive than shallow-water fishes. A second goal was to determine whether submesophotic fishes have older, more stable populations than shallow reef denizens that are subject to glacial sea-level fluctuations. Both goals are pertinent to the management of these valuable food fishes. A total of 1153 specimens of E. coruscans from 15 geographic regions were analyzed, along with 1064 specimens of E. carbunculus from 11 regions, and 590 specimens of E. sp. from 16 regions. The first 2 species were analyzed with mtDNA and 9-11 microsatellite loci, while E. sp. was analyzed with mtDNA only. Etelis coruscans had a non-significant microsatellite global FST, but significant global mtDNA Ф ST = 0.010 (P = 0.0007), with the isolation of Seychelles in the western Indian Ocean, and intermittent signals of isolation for the Hawaiian Archipelago. Etelis carbunculus had a non-significant microsatellite global FST, and significant global mtDNA Ф ST = 0.021 (P = 0.0001), with low but significant levels of isolation for Hawai'i, and divergence between Tonga and Fiji. Etelis sp. had mtDNA Ф ST = 0.018 (P = 0.0005), with a strong pattern of isolation for both Seychelles and Tonga. Overall, we observed low population structure, shallow mtDNA coalescence (similar to near-shore species), and isolation at the fringes of the Indo-Pacific basin in Hawai'i and the western Indian Ocean. While most shallow-water species have population structure on the scale of biogeographic provinces, deepwater snapper populations are structured on the wider scale of ocean basins, more similar to pelagic fishes than to shallow-water species. This population structure indicates the capacity for widespread dispersal throughout the Indo-Pacific region.

High-throughput sequencing reveals distinct regional genetic structure among remaining populations of an endangered salt marsh plant in California

Conservation of rare species requires careful consideration to both preserve locally adapted traits and maintain genetic diversity, as species’ ranges fluctuate in response to a changing climate and habitat loss. Salt marsh systems in California have been highly modified and many salt marsh obligate species have undergone range reductions and habitat loss with concomitant losses of genetic diversity and connectivity. Remaining salt marshes are threatened by rising sea levels, and so these habitats will likely require active restoration and re-establishment efforts. This study aims to provide a reference point for the current status of genetic diversity and range-wide population structure of a federally and state listed endangered plant, salt marsh bird’s-beak (Chloropyron maritimum subsp. maritimum) that can inform future preservation and restoration efforts. We used historical data and current monitoring information to locate and sample all known occurrences throughout the range of this subspecies in southern California, and three additional occurrences from Baja California, Mexico. We used flow cytometry and single nucleotide polymorphic markers (SNPs), generated by double-digest restriction-site associated DNA sequencing (ddRAD), to assess relative ploidy, and estimate genetic diversity and population structure across the region. Overall, we found five distinct genetic clusters that coincide with geographic regions. Genetic diversity was greatest in the southern part of the range including Baja California and San Diego. These findings can bolster management and restoration efforts by identifying potentially isolated occurrences and areas that are the richest sources of allelic diversity, and by providing insight into the amount of genetic differentiation across the taxon’s range.

Atlantic coastwide population structure of striped bass Morone saxatilis using microsatellite DNA analysis

Striped bass Morone saxatilis support one of the most popular and important inshore recreational and commercial fisheries along the Atlantic Coast of North America. Populations at both extremes of its distribution are largely resident while those in the center of its range (Hudson River, New York, to Roanoke River, North Carolina) are seasonally migratory, ranging from the Bay of Fundy, Canada, to the Outer Banks of North Carolina. Historically, population abundances of striped bass fluctuated widely, sometimes resulting in the imposition of severe management measures to restrict their harvest. Detailed knowledge of its rangewide population structure would aid in more effective management; however, most genetic studies addressing the structure of the migratory coastal stock have largely failed to achieve this goal. To address this need, we used multi-loci microsatellite DNA analysis. We identified six, and posibly one more, genetically distinct populations across the species’ distribution, including the Miramichi, Shubenacadie, Hudson, Delaware-Chesapeake, Roanoke, and Santee-Cooper rivers. We also report significant genetic differentiation between the Nanticoke and Choptank rivers along the eastern shore of the Chesapeake Bay and collections from tributaries along the western shore of the Bay. The Annapolis and Saint John rivers, tributaries of the Bay of Fundy, historically hosted striped bass aggregations that were extirpated, or nearly so, by anthropogenic stressors in the late 20th century. No specimens with unique genotypes were found in collections from either river; instead the vast majority were admixed with genotypes of Shubenacadie River, Hudson River, Chesapeake Bay, and Roanoke River lineages. Finally, we show in simulations that these genetic markers should be informative in quantifying the contributions of the Hudson River, Chesapeake Bay-Delaware, and Roanoke River to mixed-stock harvests that occur within the range of the coastal migratory stock.

Genome-wide SNPs resolve spatiotemporal patterns of connectivity within striped marlin (Kajikia audax), a broadly distributed and highly migratory pelagic species.

Genomic methodologies offer unprecedented opportunities for statistically robust studies of species broadly distributed in environments conducive to high gene flow, providing valuable information for wildlife conservation and management. Here, we sequence restriction site‐associated DNA to characterize genome‐wide single nucleotide polymorphisms (SNPs) in a broadly distributed and highly migratory large pelagic fish, striped marlin (Kajikia audax). Assessment of over 4,000 SNPs resolved spatiotemporal patterns of genetic connectivity throughout the species range in the Pacific and, for the first time, Indian oceans. Individual‐based cluster analyses identified six genetically distinct populations corresponding with the western Indian, eastern Indian, western South Pacific, and eastern central Pacific oceans, as well as two populations in the North Pacific Ocean (F ST = 0.0137–0.0819). F ST outlier analyses identified a subset of SNPs (n = 59) putatively under the influence of natural selection and capable of resolving populations separated by comparatively high degrees of genetic differentiation. Temporal collections available for some regions demonstrated the stability of allele frequencies over three to five generations of striped marlin. Relative migration rates reflected lower levels of genetic connectivity between Indian Ocean populations (m R ≤ 0.37) compared with most populations in the Pacific Ocean (m R ≥ 0.57) and highlight the importance of the western South Pacific in facilitating gene flow between ocean basins. Collectively, our results provide novel insights into rangewide population structure for striped marlin and highlight substantial inconsistencies between genetically distinct populations and stocks currently recognized for fisheries management. More broadly, we demonstrate that species capable of long‐distance dispersal in environments lacking obvious physical barriers to movement can display substantial population subdivision that persists over multiple generations and that may be facilitated by both neutral and adaptive processes. Importantly, surveys of genome‐wide markers enable inference of population‐level relationships using sample sizes practical for large pelagic fishes of conservation concern.

Range-wide genetic structure of a cooperative mouse in a semi-arid zone: Evidence for panmixia.

Landscape topography and the mobility of individuals will have fundamental impacts on a species' population structure, for example by enhancing or reducing gene flow and therefore influencing the effective size and genetic diversity of the population. However, social organization will also influence population genetic structure. For example, species that live and breed in cooperative groups may experience high levels of inbreeding and strong genetic drift. The western pebble-mound mouse (Pseudomys chapmani), which occupies a highly heterogeneous, semi-arid landscape in Australia, is an enigmatic social mammal that has the intriguing behaviour of working cooperatively in groups to build permanent pebble mounds above a subterranean burrow system. Here, we used both nuclear (microsatellite) and mitochondrial (mtDNA) markers to analyse the range-wide population structure of western pebble-mound mice sourced from multiple social groups. We observed high levels of genetic diversity at the broad scale, very weak genetic differentiation at a finer scale and low levels of inbreeding. Our genetic analyses suggest that the western pebble-mound mouse population is both panmictic and highly viable. We conclude that high genetic connectivity across the complex landscape is a consequence of the species' ability to permeate their environment, which may be enhanced by "boom-bust" population dynamics driven by the semi-arid climate. More broadly, our results highlight the importance of sampling strategies to infer social structure and demonstrate that sociality is an important component of population genetic structure.

Range-wide population structure and dynamics of a serotinous conifer, knobcone pine (Pinus attenuata L.), under an anthropogenically-altered disturbance regime

There is growing concern that populations of fire-adapted species around the world are at risk of extirpation due to 20th century fire exclusion (i.e. senescence risk). Concurrently, increasing fire activity in many regions is prompting concern that repeated, short-interval fire poses a risk to young stands before trees reach reproductive maturity (i.e. immaturity risk). Conceptual models assessing vulnerability to both risks exist, yet there is a lack of empirically-based studies that assess the effects of anthropogenically-altered fire regimes across the entire range of a fire-adapted species. We used geospatial data on fire occurrence (1900–2015) and a systematic sample of recently re-measured (∼2005–2015) forest inventory plots across the range of a serotinous conifer, knobcone pine (Pinus attenuata), in California and southwestern Oregon, U.S.A. to assess the relative threat of immaturity and senescence risk. We base our assessment on: (1) recent trends in area burned, (2) geographic variability and changes in stand-scale population structure, and (3) patterns of local colonization, extirpation, and population change. The area burned across the species range was lowest during the early and mid-20th century and increased in the early 1980s. Approximately 39% of the range burned between 1984 and 2015 and fire rotation was 81 years for the 25-year period ending in 2015. During this period, approximately 6% of the range of knobcone pine experienced repeated fire, and only 4% of the reburned area (∼0.25% of the entire range) experienced multiple fires at an interval less than 10 years. Most populations of knobcone pine currently exist in a mature or decadent state and we found evidence of recent senescence-related extirpation across approximately 15% of its range. However, we also observed a cumulative expansion of knobcone pine during the last decade, and the rate of colonization (less than half of which was associated with fire) was almost double that of extirpation. Despite high rates of colonization and expansion of knobcone pine in response to recent fires, vulnerability to extirpation varies geographically and remains high in some parts of the species range where wildfire activity has been low. This study provides a rare empirically-based look at the contribution of extirpation and colonization to the range-wide dynamics of a serotinous tree. Our findings underlie the importance of recognizing the different temporal and spatial scales at which contemporary disturbance regimes threaten fire-adapted species, and highlight the potential for alternative pathways of persistence and expansion of serotinous species.

Population structure, genetic connectivity, and adaptation in the Olympia oyster (Ostrea lurida) along the west coast of North America.

Effective management of threatened and exploited species requires an understanding of both the genetic connectivity among populations and local adaptation. The Olympia oyster (Ostrea lurida), patchily distributed from Baja California to the central coast of Canada, has a long history of population declines due to anthropogenic stressors. For such coastal marine species, population structure could follow a continuous isolation‐by‐distance model, contain regional blocks of genetic similarity separated by barriers to gene flow, or be consistent with a null model of no population structure. To distinguish between these hypotheses in O. lurida, 13,424 single nucleotide polymorphisms (SNPs) were used to characterize rangewide population structure, genetic connectivity, and adaptive divergence. Samples were collected across the species range on the west coast of North America, from southern California to Vancouver Island. A conservative approach for detecting putative loci under selection identified 235 SNPs across 129 GBS loci, which were functionally annotated and analyzed separately from the remaining neutral loci. While strong population structure was observed on a regional scale in both neutral and outlier markers, neutral markers had greater power to detect fine‐scale structure. Geographic regions of reduced gene flow aligned with known marine biogeographic barriers, such as Cape Mendocino, Monterey Bay, and the currents around Cape Flattery. The outlier loci identified as under putative selection included genes involved in developmental regulation, sensory information processing, energy metabolism, immune response, and muscle contraction. These loci are excellent candidates for future research and may provide targets for genetic monitoring programs. Beyond specific applications for restoration and management of the Olympia oyster, this study lends to the growing body of evidence for both population structure and adaptive differentiation across a range of marine species exhibiting the potential for panmixia. Computational notebooks are available to facilitate reproducibility and future open‐sourced research on the population structure of O. lurida.

Unexpected population fragmentation in an endangered seabird: the case of the Peruvian diving-petrel

In less than one century, the once-abundant Peruvian diving petrel has become the first endangered seabird of the Humboldt Current System (HCS). This small endemic petrel of the South American Pacific coast is now an important indicator of ongoing habitat loss and of the success of local conservation policies in the HCS - an ecoregion designated as a priority for the conservation of global biodiversity. Yet so far, poorly understood life history traits such as philopatry or dispersal ability may strongly influence the species’ response to ecosystem changes, but also our capacity to assess and interpret this response. To address this question, we explore the range-wide population structure of the Peruvian diving petrel, and show that this small seabird exhibits extreme philopatric behavior at the island level. Mitochondrial DNA sequences and genome-wide SNP data reveal significant isolation and low migration at very short distances, and provide strong evidence for questioning the alleged recovery in the Peruvian and Chilean populations of this species. Importantly, the full demographic independence between colonies makes local population rescue through migration unlikely. As a consequence, the Peruvian diving petrel appears to be particularly vulnerable to ongoing anthropogenic pressure. By excluding immigration as a major factor of demographic recovery, our results highlight the unambiguously positive impact of local conservation measures on breeding populations; yet at the same time they also cast doubt on alleged range-wide positive population trends. Overall, the protection of independent breeding colonies, and not only of the species as a whole, remains a major element in the conservation strategy for endemic seabirds. Finally, we underline the importance of considering the philopatric behavior and demographic independence of breeding populations, even at very fine spatial scales, in spatial planning for marine coastal areas.

Genetic population structure of the spotted seatrout (Cynoscion nebulosus): simultaneous examination of the mtDNA control region and microsatellite marker results

The spotted seatrout, Cynoscion nebulosus (Cuvier, 1830), lives almost entirely within natal estuaries, and although many genetic studies identify fine-scale population structure, they do not provide a consensus as to the number of stocks, the stock boundaries, or their connectivity. Two perceived limitations of previous studies were addressed. To address a presumption of limited sampling, we assembled a large sample size with broad geographic range: 547 specimens from 18 sampling areas (mean inter-area distance = 270 km) between Texas and North Carolina, representing the majority of this species' range. To address the presumptive limitations of genetic markers, two genetic marker types were compared: a 335-base-pair segment of the mitochondrial DNA (mtDNA) control region and 38 microsatellite loci. MtDNA haplotype frequencies were different only between populations of the Gulf of Mexico (GoM) and the Atlantic Ocean, but not between the western GoM and the eastern GoM. In contrast, the microsatellite loci characterized the species' range-wide population structure as three geographically non-overlapping clusters. These clusters were defined by two genetic breaks: one at the Apalachicola River, on Florida's Gulf Coast, and another in the Atlantic Ocean between Miami and Palm Beach on Florida's east coast. Moreover, within each genetic cluster (identified by microsatellite markers), a pattern of isolation by distance was evident. This new characterization of spotted seatrout population structure supports assessment and management of the species by individual states and defines distinct stock boundaries in Florida, the only state with multiple genetic stocks, as defined by either genetic marker type.

Range-wide phylogeographic structure of the vernal pool fairy shrimp (Branchinecta lynchi).

Wetland habitats across the world are experiencing rapid modification and loss due to accelerating habitat conversion. Impacts to wetland habitats are particularly acute in California where up to 90% of wetland habitats have been modified or lost. Vernal pool ecosystems have therefore undergone a dramatic loss in habitat and along with them an entire endemic fauna is under threat of extinction. Recent efforts to conserve vernal pool habitat and associated species have involved restoration and creation of vernal pools as well as translocations of threatened species. The vernal pool fairy shrimp, Branchinecta lynchi, is one of several endemic and federally listed species being targeted for translocations. To guide reintroduction and conservation, detailed information on range-wide population structure and diversity is needed. We collected genetic data from two mitochondrial genes throughout the known extant range of B. lynchi to elucidate population structure and diversity of the species. We found support for phylogeographic structure throughout the range of B. lynch associated with isolated watersheds and vernal pool regions previously identified in the recovery plan for the species. The underlying mechanisms responsible for this broad pattern of genetic structure have yet to be identified. However, the evidence of only a few haplotypes being shared across the species range and patterns of isolation by distance within vernal pool regions suggests dispersal limitation may play a role. These results stress that conservation programs, at a minimum, should consider using individuals from regional populations as sources for reintroductions to maintain historical patterns of genetic differentiation. Additionally, because genetic structure is associated with vernal pool regions which are based on local hydrology and geology, translocations should proceed considering the distance between donor and recipient sites.

Persistence of historical population structure in an endangered species despite near-complete biome conversion in California's San Joaquin Desert.

Genomic responses to habitat conversion can be rapid, providing wildlife managers with time-limited opportunities to enact recovery efforts that use population connectivity information that reflects predisturbance landscapes. Despite near-complete biome conversion, such opportunities may still exist for the endemic fauna and flora of California's San Joaquin Desert, but comprehensive genetic data sets are lacking for nearly all species in the region. To fill this knowledge gap, we studied the rangewide population structure of the endangered blunt-nosed leopard lizard Gambelia sila, a San Joaquin Desert endemic, using restriction site-associated DNA (RAD), microsatellite and mtDNA data to test whether admixture patterns and estimates of effective migration surfaces (EEMS) can identify land areas with high population connectivity prior to the conversion of native xeric habitats. Clustering and phylogenetic analyses indicate a recent shared history between numerous isolated populations and EEMS reveals latent signals of corridors and barriers to gene flow over areas now replaced by agriculture and urbanization. Conflicting histories between the mtDNA and nuclear genomes are consistent with hybridization with the sister species G.wislizenii, raising important questions about where legal protection should end at the southern range limit of G.sila. Comparative analysis of different data sets also adds to a growing list of advantages in using RAD loci for genetic studies of rare species. We demonstrate how the results of this work can serve as an evolutionary guidance tool for managing endemic, arid-adapted taxa in one of the world's most compromised landscapes.

Very Low Population Structure in a Highly Mobile and Wide-Ranging Endangered Bird Species.

The loss of biodiversity following fragmentation and degradation of habitat is a major issue in conservation biology. As competition for resources increases following habitat loss and fragmentation, severe population declines may occur even in common, highly mobile species; such demographic decline may cause changes within the population structure of the species. The regent honeyeater, Anthochaera phrygia, is a highly nomadic woodland bird once common in its native southeast Australia. It has experienced a sharp decline in abundance since the late 1970s, following clearing of large areas of its preferred habitat, box-ironbark woodland, within the last 200 years. A captive breeding program has been established as part of efforts to restore this species. This study used genetic data to examine the range-wide population structure of regent honeyeaters, including spatial structure, its change through time, sex differences in philopatry and mobility, and genetic differences between the captive and wild populations. There was low genetic differentiation between birds captured in different geographic areas. Despite the recent demographic decline, low spatial structure appears to have some temporal consistency. Both sexes appear to be highly mobile, and there does not seem to be significant genetic differentiation between the captive and wild populations. We conclude that management efforts for survival of this species, including habitat protection, restoration, and release of captive-bred birds into the wild, can treat the species as effectively a single genetic population.

Comparative Population Genetic Analysis of Bocaccio Rockfish Sebastes paucispinis Using Anonymous and Gene-Associated Simple Sequence Repeat Loci

Comparative population genetic analyses of traditional and emergent molecular markers aid in determining appropriate use of new technologies. The bocaccio rockfish Sebastes paucispinis is a high gene-flow marine species off the west coast of North America that experienced strong population decline over the past 3 decades. We used 18 anonymous and 13 gene-associated simple sequence repeat (SSR) loci (expressed sequence tag [EST]-SSRs) to characterize range-wide population structure with temporal replicates. No F(ST)-outliers were detected using the LOSITAN program, suggesting that neither balancing nor divergent selection affected the loci surveyed. Consistent hierarchical structuring of populations by geography or year class was not detected regardless of marker class. The EST-SSRs were less variable than the anonymous SSRs, but no correlation between F(ST) and variation or marker class was observed. General linear model analysis showed that low EST-SSR variation was attributable to low mean repeat number. Comparative genomic analysis with Gasterosteus aculeatus, Takifugu rubripes, and Oryzias latipes showed consistently lower repeat number in EST-SSRs than SSR loci that were not in ESTs. Purifying selection likely imposed functional constraints on EST-SSRs resulting in low repeat numbers that affected diversity estimates but did not affect the observed pattern of population structure.

Range-Wide Genetic Connectivity of the Hawaiian Monk Seal and Implications for Translocation

The Hawaiian monk seal (Monachus schauinslandi) is one of the most critically endangered marine mammals. Less than 1200 individuals remain, and the species is declining at a rate of approximately 4% per year as a result of juvenile starvation, shark predation, and entanglement in marine debris. Some of these problems may be alleviated by translocation; however, if island breeding aggregates are effectively isolated subpopulations, moving individuals may disrupt local adaptations. In these circumstances, managers must balance the pragmatic need of increasing survival with theoretical concerns about genetic viability. To assess range-wide population structure of the Hawaiian monk seal, we examined an unprecedented, near-complete genetic inventory of the species (n =1897 seals, sampled over 14 years) at 18 microsatellite loci. Genetic variation was not spatially partitioned ((w) =-0.03, p = 1.0), and a Bayesian clustering method provided evidence of one panmictic population (K =1). Pairwise F(ST) comparisons (among 7 island aggregates over 14 annual cohorts) did not reveal temporally stable, spatial reproductive isolation. Our results coupled with long-term tag-resight data confirm seal movement and gene flow throughout the Hawaiian Archipelago. Thus, human-mediated translocation of seals among locations is not likely to result in genetic incompatibilities.

Microsatellite DNA markers to resolve population structure and hybridization of two closely related surgeonfish species, Acanthurus nigricans and Acanthurus leucosternon

Ten polymorphic microsatellite loci were developed for sister surgeonfish species: the white cheek surgeonfish (Acanthurus nigricans) which occurs primarily in the Pacific Ocean, and the powder blue tang (Acanthurus leucosternon) in the Indian Ocean. All loci were scored for widely separated collections (A. nigricans, N = 30, French Polynesia; A. leucosternon, N = 27, Republic of Seychelles; hybrids, N = 17, Cocos/Keeling Island, eastern Indian Ocean). For A. nigricans, A. leucosternon, and hybrids, respectively, the mean number of alleles per locus is A = 17.80, A = 16.60, and A = 14.60, while observed heterozygosity ranges from HO = 0.78–1.00, HO = 0.74–0.96, and HO = 0.69–1.00. With the exception of locus Ahy54, all loci conformed to Hardy–Weinberg expectations, most loci were in linkage equilibrium, and there was little evidence for confounding null alleles. These markers will be used to resolve range-wide population structure and patterns of hybridization.

Phylogeography of North African Atlas cedar (Cedrus atlantica, Pinaceae): Combined molecular and fossil data reveal a complex Quaternary history

Northwest Africa is a major hotspot of plant biodiversity, but very little is known about the Quaternary range dynamics of plant species in this region. Here we investigate the range-wide population structure and phylogeography of Atlas cedar (Cedrus atlantica), an emblematic forest tree endemic to Morocco and Algeria. We genotyped 261 individuals from 11 populations using AFLP markers. Data were analyzed using both conventional F(ST)-based techniques and Bayesian clustering. Overall population differentiation was high (F(ST) = 0.25). Two major groups of populations were identified, one distributed through the Rif and Middle Atlas mountains in Morocco and the other through the Algerian Tell Atlas and Aurès mountains as well as the Middle Atlas. Combined molecular and fossil data indicate that C. atlantica survived the Last Glacial Maximum in at least three disjunct refugia along the coast of the Mediterranean Sea, whereas the Middle Atlas, today the core of the species range, has been colonized relatively recently (<10000 yr BP). The colonization history of individual populations has left clear imprints in their present-day diversity, which may vary greatly even between nearby stands. Our study illustrates how integrating different data sources and analytical approaches can help elucidate complex range dynamics that would otherwise remain undeciphered.

Range-wide phylogeography of Juniperus thurifera L., a presumptive keystone species of western Mediterranean vegetation during cold stages of the Pleistocene

We investigate the range-wide population structure and phylogeography of thuriferous juniper (Juniperus thurifera L.), a species with a highly disjunct distribution in the western Mediterranean. We genotyped a total of 327 individuals from 20 populations using amplified fragment length polymorphisms (AFLP). Different analyses such as principal co-ordinate analysis (PCoA), nonmetric multidimensional scaling of FST distances among populations, unweighted pair group method with arithmetic mean (UPGMA), and Bayesian clustering revealed that the Strait of Gibraltar acted as an efficient barrier against gene flow between the Moroccan and European populations for a very long time, and consequently support that the Moroccan populations should be recognised as a distinct subspecies (J. thurifera L. subsp. africana (Maire) Romo and Boratyńsky). The Algerian population was genetically more closely related to the European than to the Moroccan ones, probably due to dispersal events from Europe to Algeria. With respect to the mainland European populations, our data are not conclusive to reject any of the two following hypotheses: (1) the Iberian Peninsula was subdivided into different gene pools, and was the source for the colonisation of the Pyrenees and the Alps; and (2) the pattern we see today is partly the result of immigration into the Iberian Peninsula, e.g. from the Alps. Finally, the Corsican population was closely related genetically to two northern Iberian populations most probably due to relatively recent long-distance dispersal.