Self‐recruitment in a Caribbean reef fish: a method for approximating dispersal kernels accounting for seascape

Characterizing patterns of larval dispersal is essential to understanding the ecological and evolutionary dynamics of marine metapopulations. Recent research has measured local dispersal within populations, but the development of marine dispersal kernels from empirical data remains a challenge. We propose a framework to move beyond point estimates of dispersal towards the approximation of a simple dispersal kernel, based on the hypothesis that the structure of the seascape is a primary predictor of realized dispersal patterns. Using the coral reef fish Elacatinus lori as a study organism, we use genetic parentage analysis to estimate self‐recruitment at a small spatial scale (<1 km). Next, we determine which simple kernel explains the observed self‐recruitment, given the influx of larvae from reef habitat patches in the seascape at a large spatial scale (up to 35 km). Finally, we complete parentage analyses at six additional sites to test for export from the focal site and compare these observed dispersal data within the metapopulation to the predicted dispersal kernel. We find 4.6% self‐recruitment (CI_95%: ±3.0%) in the focal population, which is explained by the exponential kernel y = 0.915^x (CI_95%: y = 0.865^x, y = 0.965^x), given the seascape. Additional parentage analyses showed low levels of export to nearby sites, and the best‐fit line through the observed dispersal proportions also revealed a declining function y = 0.77^x. This study lends direct support to the hypothesis that the probability of larval dispersal declines rapidly with distance in Atlantic gobies in continuously distributed habitat, just as it does in the Indo‐Pacific damselfishes in patchily distributed habitat.     

Emergent patterns of population genetic structure for a coral reef community

What shapes variation in genetic structure within a community of codistributed species is a central but difficult question for the field of population genetics. With a focus on the isolated coral reef ecosystem of the Hawaiian Archipelago, we assessed how life history traits influence population genetic structure for 35 reef animals. Despite the archipelago's stepping stone configuration, isolation by distance was the least common type of genetic structure, detected in four species. Regional structuring (i.e. division of sites into genetically and spatially distinct regions) was most common, detected in 20 species and nearly in all endemics and habitat specialists. Seven species displayed chaotic (spatially unordered) structuring, and all were nonendemic generalist species. Chaotic structure also associated with relatively high global F_ST. Pelagic larval duration (PLD) was not a strong predictor of variation in population structure (R² = 0.22), but accounting for higher F_ST values of chaotic and invertebrate species, compared to regionally structured and fish species, doubled the power of PLD to explain variation in global F_ST (adjusted R² = 0.50). Multivariate correlation of eight species traits to six genetic traits highlighted dispersal ability, taxonomy (i.e. fish vs. invertebrate) and habitat specialization as strongest influences on genetics, but otherwise left much variation in genetic traits unexplained. Considering that the study design controlled for many sampling and geographical factors, the extreme interspecific variation in spatial genetic patterns observed for Hawaìi marine species may be generated by demographic variability due to species‐specific abundance and migration patterns and/or seascape and historical factors.     

Genetic assessment of connectivity in the common reef sponge, Callyspongia vaginalis (Demospongiae: Haplosclerida) reveals high population structure along the Florida reef tract

The genetic population structure of the common branching vase sponge, Callyspongia vaginalis, was determined along the entire length (465 km) of the Florida reef system from Palm Beach to the Dry Tortugas based on sequences of the mitochondrial cytochrome c oxidase subunit 1 (COI) gene. Populations of C. vaginalis were highly structured (overall Φ_ST = 0.33), in some cases over distances as small as tens of kilometers. However, nonsignificant pairwise Φ_ST values were also found between a few relatively distant sampling sites suggesting that some long distance larval dispersal may occur via ocean currents or transport in sponge fragments along continuous, shallow coastlines. Indeed, sufficient gene flow appears to occur along the Florida reef tract to obscure a signal of isolation by distance, but not to homogenize COI haplotype frequencies. The strong genetic differentiation among most of the sampling locations suggests that recruitment in this species is largely local source-driven, pointing to the importance of further elucidating general connectivity patterns along the Florida reef tract to guide the spatial scale of management efforts.     

Climate variables explain neutral and adaptive variation within salmonid metapopulations: the importance of replication in landscape genetics

Understanding how environmental variation influences population genetic structure is important for conservation management because it can reveal how human stressors influence population connectivity, genetic diversity and persistence. We used riverscape genetics modelling to assess whether climatic and habitat variables were related to neutral and adaptive patterns of genetic differentiation (population‐specific and pairwise F_ST) within five metapopulations (79 populations, 4583 individuals) of steelhead trout (Oncorhynchus mykiss) in the Columbia River Basin, USA. Using 151 putatively neutral and 29 candidate adaptive SNP loci, we found that climate‐related variables (winter precipitation, summer maximum temperature, winter highest 5% flow events and summer mean flow) best explained neutral and adaptive patterns of genetic differentiation within metapopulations, suggesting that climatic variation likely influences both demography (neutral variation) and local adaptation (adaptive variation). However, we did not observe consistent relationships between climate variables and F_ST across all metapopulations, underscoring the need for replication when extrapolating results from one scale to another (e.g. basin‐wide to the metapopulation scale). Sensitivity analysis (leave‐one‐population‐out) revealed consistent relationships between climate variables and F_ST within three metapopulations; however, these patterns were not consistent in two metapopulations likely due to small sample sizes (N = 10). These results provide correlative evidence that climatic variation has shaped the genetic structure of steelhead populations and highlight the need for replication and sensitivity analyses in land and riverscape genetics.     

Oceanic dispersal barriers in a holoplanktonic gastropod

Pteropods, a group of holoplanktonic gastropods, are regarded as bioindicators of the effects of ocean acidification on open ocean ecosystems, because their thin aragonitic shells are susceptible to dissolution. While there have been recent efforts to address their capacity for physiological acclimation, it is also important to gain predictive understanding of their ability to adapt to future ocean conditions. However, little is known about the levels of genetic variation and large‐scale population structuring of pteropods, key characteristics enabling local adaptation. We examined the spatial distribution of genetic diversity in the mitochondrial cytochrome c oxidase I (COI) and nuclear 28S gene fragments, as well as shell shape variation, across a latitudinal transect in the Atlantic Ocean (35°N–36°S) for the pteropod Limacina bulimoides. We observed high levels of genetic variability (COI π = 0.034, 28S π = 0.0021) and strong spatial structuring (COI Φ_ST = 0.230, 28S Φ_ST = 0.255) across this transect. Based on the congruence of mitochondrial and nuclear differentiation, as well as differences in shell shape, we identified a primary dispersal barrier in the southern Atlantic subtropical gyre (15–18°S). This barrier is maintained despite the presence of expatriates, a gyral current system, and in the absence of any distinct oceanographic gradients in this region, suggesting that reproductive isolation between these populations must be strong. A secondary dispersal barrier supported only by 28S pairwise Φ_ST comparisons was identified in the equatorial upwelling region (between 15°N and 4°S), which is concordant with barriers observed in other zooplankton species. Both oceanic dispersal barriers were congruent with regions of low abundance reported for a similar basin‐scale transect that was sampled 2 years later. Our finding supports the hypothesis that low abundance indicates areas of suboptimal habitat that result in barriers to gene flow in widely distributed zooplankton species. Such species may in fact consist of several populations or (sub)species that are adapted to local environmental conditions, limiting their potential for adaptive responses to ocean changes. Future analyses of genome‐wide diversity in pteropods could provide further insight into the strength, formation and maintenance of oceanic dispersal barriers.     

Do plant populations on distinct inselbergs talk to each other? A case study of genetic connectivity of a bromeliad species in an Ocbil landscape

Here, we explore the historical and contemporaneous patterns of connectivity among Encholirium horridum populations located on granitic inselbergs in an Ocbil landscape within the Brazilian Atlantic Forest, using both nuclear and chloroplast microsatellite markers. Beyond to assess the E. horridum population genetic structure, we built species distribution models across four periods (current conditions, mid‐Holocene, Last Glacial Maximum [LGM], and Last Interglacial) and inferred putative dispersal corridors using a least‐cost path analysis to elucidate biogeographic patterns. Overall, high and significant genetic divergence was estimated among populations for both nuclear and plastid DNA (Φ_ST(n) = 0.463 and Φ_ST(plastid) = 0.961, respectively, p < .001). For nuclear genome, almost total absence of genetic admixture among populations and very low migration rates were evident, corroborating with the very low estimates of immigration and emigration rates observed among E. horridum populations. Based on the cpDNA results, putative dispersal routes in Sugar Loaf Land across cycles of climatic fluctuations in the Quaternary period revealed that the populations’ connectivity changed little during those events. Genetic analyses highlighted the low genetic connectivity and long‐term persistence of populations, and the founder effect and genetic drift seemed to have been very important processes that shaped the current diversity and genetic structure observed in both genomes. The genetic singularity of each population clearly shows the need for in situ conservation of all of them.     

Genetic connectivity among swarming sites in the wide ranging and recently declining little brown bat (Myotis lucifugus)

Characterizing movement dynamics and spatial aspects of gene flow within a species permits inference on population structuring. As patterns of structuring are products of historical and current demographics and gene flow, assessment of structure through time can yield an understanding of evolutionary dynamics acting on populations that are necessary to inform management. Recent dramatic population declines in hibernating bats in eastern North America from white‐nose syndrome have prompted the need for information on movement dynamics for multiple bat species. We characterized population genetic structure of the little brown bat, Myotis lucifugus, at swarming sites in southeastern Canada using 9 nuclear microsatellites and a 292‐bp region of the mitochondrial genome. Analyses of F_ST, Φ_ST, and Bayesian clustering (STRUCTURE) found weak levels of genetic structure among swarming sites for the nuclear and mitochondrial genome (Global F_ST = 0.001, P < 0.05, Global Φ_ST = 0.045, P < 0.01, STRUCTURE K = 1) suggesting high contemporary gene flow. Hierarchical AMOVA also suggests little structuring at a regional (provincial) level. Metrics of nuclear genetic structure were not found to differ between males and females suggesting weak asymmetries in gene flow between the sexes. However, a greater degree of mitochondrial structuring does support male‐biased dispersal long term. Demographic analyses were consistent with past population growth and suggest a population expansion occurred from approximately 1250 to 12,500 BP, following Pleistocene deglaciation in the region. Our study suggests high gene flow and thus a high degree of connectivity among bats that visit swarming sites whereby mainland areas of the region may be best considered as one large gene pool for management and conservation.     

Population structure and connectivity of the mountainous star coral,Orbicella faveolata,throughout the wider Caribbean region

As coral reefs continue to decline worldwide, it becomes ever more necessary to understand the connectivity between coral populations to develop efficient management strategies facilitating survival and adaptation of coral reefs in the future. Orbicella faveolata is one of the most important reef‐building corals in the Caribbean and has recently experienced severe population reductions. Here, we utilize a panel of nine microsatellite loci to evaluate the genetic structure of O. faveolata and to infer connectivity across ten sites spanning the wider Caribbean region. Populations are generally well‐mixed throughout the basin (F_ST = 0.038), although notable patterns of substructure arise at local and regional scales. Eastern and western populations appear segregated with a genetic break around the Mona Passage in the north, as has been shown previously in other species; however, we find evidence for significant connectivity between Curaçao and Mexico, suggesting that the southern margin of this barrier is permeable to dispersal. Our results also identify a strong genetic break within the Mesoamerican Barrier Reef System associated with complex oceanographic patterns that promote larval retention in southern Belize. Additionally, the diverse genetic signature at Flower Garden Banks suggests its possible function as a downstream genetic sink. The findings reported here are relevant to the ongoing conservation efforts for this important and threatened species, and contribute to the growing understanding of large‐scale coral reef connectivity throughout the wider Caribbean.     

Phylogeography of Chinese cherry (Prunus pseudocerasus Lindl.) inferred from chloroplast and nuclear DNA: insights into evolutionary patterns and demographic history

Chinese cherry (Prunus pseudocerasus Lindl.) is a commercially valuable fruit crop in China. In order to obtain new insights into its evolutionary history and provide valuable recommendations for resource conservation, phylogeographic patterns of 26 natural populations (305 total individuals) from six geographic regions were analyzed using chloroplast and nuclear DNA fragments. Low levels of haplotype and nucleotide diversity were found in these populations, especially in landrace populations. It is likely that a combined effect of botanical characteristics impact the effective population size, such as inbreeding mating system, long life span, as well as vegetative reproduction. In addition, strong bottleneck effect caused by domestication, together with founder effect after dispersal and subsequent demographic expansion, might also accelerate the reduction of the genetic variation in landrace populations. Interestingly, populations from Longmen Mountain (LMM) and Daliangshan Mountain (DLSM) exhibited relatively higher levels of genetic diversity, inferring the two historical genetic diversity centers of the species. Moreover, moderate population subdivision was also detected by both chloroplast DNA (G_ST = 0.215; N_ST = 0.256) and nuclear DNA (G_ST = 0.146; N_ST = 0.342), respectively. We inferred that the episodes of efficient gene flow through seed dispersal, together with features of long generation cycle and inbreeding mating system, were likely the main contributors causing the observed phylogeographic patterns. Finally, factors that led to the present demographic patterns of populations from these regions and taxonomic varieties were also discussed.     

Genomic analysis of a cardinalfish with larval homing potential reveals genetic admixture in the Okinawa Islands

Discrepancies between potential and observed dispersal distances of reef fish indicate the need for a better understanding of the influence of larval behaviour on recruitment and dispersal. Population genetic studies can provide insight on the degree to which populations are connected, and the development of restriction site‐associated sequencing (RAD‐Seq) methods has made such studies of nonmodel organisms more accessible. We applied double‐digest RAD‐Seq methods to test for population differentiation in the coral reef‐dwelling cardinalfish, Siphamia tubifer, which based on behavioural studies, have the potential to use navigational cues to return to natal reefs. Analysis of 11,836 SNPs from fish collected at coral reefs in Okinawa, Japan, from eleven locations over 3 years reveals little genetic differentiation between groups of S. tubifer at spatial scales from 2 to 140 km and between years at one location: pairwise F_ST values were between 0.0116 and 0.0214. These results suggest that the Kuroshio Current largely influences larval dispersal in the region, and in contrast to expectations based on studies of other cardinalfishes, there is no evidence of population structure for S. tubifer at the spatial scales examined. However, analyses of outlier loci putatively under selection reveal patterns of temporal differentiation that indicate high population turnover and variable larval supply from divergent source populations between years. These findings highlight the need for more studies of fishes across various geographic regions that also examine temporal patterns of genetic differentiation to better understand the potential connections between early life‐history traits and connectivity of reef fish populations.     

Unraveling hierarchical genetic structure in a marine metapopulation: A comparison of three high‐throughput genotyping approaches

Marine metapopulations often exhibit subtle population structure that can be difficult to detect. Given recent advances in high‐throughput sequencing, an emerging question is whether various genotyping approaches, in concert with improved sampling designs, will substantially improve our understanding of genetic structure in the sea. To address this question, we explored hierarchical patterns of structure in the coral reef fish Elacatinus lori using a high‐resolution approach with respect to both genetic and geographic sampling. Previously, we identified three putative E. lori populations within Belize using traditional genetic markers and sparse geographic sampling: barrier reef and Turneffe Atoll; Glover's Atoll; and Lighthouse Atoll. Here, we systematically sampled individuals at ~10 km intervals throughout these reefs (1,129 individuals from 35 sites) and sequenced all individuals at three sets of markers: 2,418 SNPs; 89 microsatellites; and 57 nonrepetitive nuclear loci. At broad spatial scales, the markers were consistent with each other and with previous findings. At finer spatial scales, there was new evidence of genetic substructure, but our three marker sets differed slightly in their ability to detect these patterns. Specifically, we found subtle structure between the barrier reef and Turneffe Atoll, with SNPs resolving this pattern most effectively. We also documented isolation by distance within the barrier reef. Sensitivity analyses revealed that the number of loci (and alleles) had a strong effect on the detection of structure for all three marker sets, particularly at small spatial scales. Taken together, these results illustrate empirically that high‐throughput genotyping data can elucidate subtle genetic structure at previously‐undetected scales in a dispersive marine fish.     

Genetic differentiation between two varieties of Oreocharis benthamii (Gesneriaceae) in sympatric and allopatric regions

The pattern of genetic differentiation between diverging species receives much attention as one of the key observable features of speciation. It has often been suggested that introgression between closely related species occurs commonly where their distributions overlap, leading to their becoming more morphologically and genetically similar, but there are a few opposite results. However, most of these studies have been carried out with animals and separate species; few have looked at intraspecific cases, especially in plants. Here, we conduct a comparative study on patterns of genetic differentiation among populations of two varieties of Oreocharis benthamii in allopatry and sympatry based on ISSR data for 754 individuals from 26 populations, in order to understand the processes leading to speciation. Contrary to expectations, the facultative xenogamy (mixed mating) species O. benthamii has a relatively low genetic diversity within populations (H = 0.1014, I = 0.1528) and high genetic differentiation among populations (G_ST = 0.5867, Ф_ST = 0.659), as is typically found for selfing species. Genetic variance between the two varieties in sympatric populations (44%, Ф_ST = 0.444) is significantly more than that in allopatric populations (14%, Ф_ST = 0.138). Consistent with the taxonomical delimitation of the two varieties, all sampled individuals of O. benthamii clustered into two genetic groups. Moreover, the genetic structures of populations of both varieties are correlated with their different geographical origins. Our studies show that significant divergence between sympatric populations of the two varieties could be attributed primarily to reinforcement by genetic divergent selection in sympatry where secondary contact had occurred. The major proportion of the genetic variation in outcrossing and mixed mating plants may exist among populations when the populations are distributed in fragmented habitats, due to the paucity of suitable habitat combined with inefficient seed dispersal mechanism and limited pollinator foraging area that may limit the gene flow.     

High genetic differentiation and cross-shelf patterns of genetic diversity among Great Barrier Reef populations of Symbiodinium

The resilience of Symbiodinium harboured by corals is dependent on the genetic diversity and extent of connectivity among reef populations. This study presents genetic analyses of Great Barrier Reef (GBR) populations of clade C Symbiodinium hosted by the alcyonacean coral, Sinularia flexibilis. Allelic variation at four newly developed microsatellite loci demonstrated that Symbiodinium populations are genetically differentiated at all spatial scales from 16 to 1,360 km (pairwise Φ_ST = 0.01–0.47, mean = 0.22); the only exception being two neighbouring populations in the Cairns region separated by 17 km. This indicates that gene flow is restricted for Symbiodinium C hosted by S. flexibilis on the GBR. Patterns of population structure reflect longshore circulation patterns and limited cross-shelf mixing, suggesting that passive transport by currents is the primary mechanism of dispersal in Symbiodinium types that are acquired horizontally. There was no correlation between the genetic structure of Symbiodinium populations and their host S. flexibilis, most likely because different factors affect the dispersal and recruitment of each partner in the symbiosis. The genetic diversity of these Symbiodinium reef populations is on average 1.5 times lower on inshore reefs than on offshore reefs. Lower inshore diversity may reflect the impact of recent bleaching events on Sinularia assemblages, which have been more widespread and severe on inshore reefs, but may also have been shaped by historical sea level fluctuations or recent migration patterns. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. Communicated by Biology Editor Dr. Ruth Gates.     

The population genetic structure of a common tropical damselfish on the Great Barrier Reef and eastern Papua New Guinea

Understanding patterns of connectivity in marine species is vital for the management and conservation of marine biodiversity. Here, the population genetic structure of a common and abundant tropical reef damselfish, Pomacentrus amboinensis, is reported. Using nine polymorphic microsatellite loci, the genetic structure at both small (i.e., around Lizard Island, Great Barrier Reef [GBR]) and large (GBR and Papua New Guinea [PNG]) spatial and temporal scales (2–1,600 km; 28 days– 6 years; n = 1,119) was analyzed. Temporal analyses found no evidence of genetic differentiation within or between Lizard Island recruitment pulses (R _ST = −0.001, P = 0.788), or corresponding established adult populations separated by 6 years of sampling (R _ST = 0.003, P = 0.116). The spatial analysis revealed that P. amboinensis populations are largely panmictic on the GBR and eastern PNG (R _ST = 0.001, P = 0.913), the only genetic discontinuity being between Kimbe Bay to the north of PNG and all populations south of PNG (R _ST = 0.077, P < 0.0001). Despite assumed high levels of self-recruitment based on previous tagging studies (15–60%), data presented here indicate that enough recruits are dispersing to impede the evolution of genetic structure over distances as great as 1,600 kms in this species. Data therefore indicate that the temporal genetic stability recorded here is maintained by high levels of gene flow.     

High connectivity on a global scale in the pelagic wahoo,Acanthocybium solandri (tuna family Scombridae)

The population genetic structure and phylogeography of wahoo, Acanthocybium solandri, were investigated on a global scale with intron six of lactate dehydrogenase‐A (ldhA6, 8 locations, N = 213) and mtDNA cytochrome b (Cytb, 10 locations, N = 322). Results show extensive sharing of haplotypes across the wahoo's entire global range, and analyses were unable to detect significant structure (nuclear F_ST = 0.0125, P = 0.106; mtDNA Φ_ST < 0.0001, P = 0.634). Power analyses indicated 95% confidence in detecting nuclear F_ST ≥ 0.0389 and mtDNA Φ_ST ≥ 0.0148. These findings appear unique, as most other tunas, billfishes, and oceanic sharks exhibit significant population structure on the scale of East–West Atlantic, Atlantic vs. Indian‐Pacific, or East–West Pacific. Overall nuclear heterozygosity (H = 0.714) and mtDNA haplotype diversity (h = 0.918) are both high in wahoo, while overall mtDNA nucleotide diversity (π= 0.006) and nuclear nucleotide diversity (π=0.004) are uniformly low, indicating a recent increase in population size. Coalescence analyses yield an estimate of effective female population size (N_eF) at ~816 000, and a population bottleneck ~690 000 years ago. However, conclusions about population history from our Cytb data set are not concordant with a control region survey, a finding that will require further investigation. This is the first example of a vertebrate with a single globally distributed population, a finding we attribute to extensive dispersal at all life stages. The indications of a worldwide stock for wahoo reinforce the mandate for international cooperation on fisheries issues.     

Familial social structure and socially driven genetic differentiation in Hawaiian short‐finned pilot whales

Social structure can have a significant impact on divergence and evolution within species, especially in the marine environment, which has few environmental boundaries to dispersal. On the other hand, genetic structure can affect social structure in many species, through an individual preference towards associating with relatives. One social species, the short‐finned pilot whale (Globicephala macrorhynchus), has been shown to live in stable social groups for periods of at least a decade. Using mitochondrial control sequences from 242 individuals and single nucleotide polymorphisms from 106 individuals, we examine population structure among geographic and social groups of short‐finned pilot whales in the Hawaiian Islands, and test for links between social and genetic structure. Our results show that there are at least two geographic populations in the Hawaiian Islands: a Main Hawaiian Islands (MHI) population and a Northwestern Hawaiian Islands/Pelagic population (F_ST and Φ_ST p < .001), as well as an eastern MHI community and a western MHI community (F_ST p = .009). We find genetically driven social structure, or high relatedness among social units and clusters (p < .001), and a positive relationship between relatedness and association between individuals (p < .0001). Further, socially organized clusters are genetically distinct, indicating that social structure drives genetic divergence within the population, likely through restricted mate selection (F_ST p = .05). This genetic divergence among social groups can make the species less resilient to anthropogenic or ecological disturbance. Conservation of this species therefore depends on understanding links among social structure, genetic structure and ecological variability within the species.     

Genetic diversity in fragmented populations of the critically endangered spider orchid Caladenia huegelii: implications for conservation

The Orchidaceae is characterised by a diverse range of life histories, reproductive strategies and geographic distribution, reflected in a variety of patterns in the population genetic structure of different species. In this study, the genetic diversity and structure was assessed within and among remnant populations of the critically endangered sexually deceptive orchid, Caladenia huegelii. This species has experienced severe recent habitat loss in a landscape marked by ancient patterns of population fragmentation within the Southwest Australian Floristic Region, a global biodiversity hotspot. Using seven polymorphic microsatellite loci, high levels of within-population diversity (mean alleles/locus = 6.73; mean H _E = 0.690), weak genetic structuring among 13 remnant populations (F _ST = 0.047) and a consistent deficit of heterozygotes from Hardy–Weinberg expectation were found across all populations (mean F _IS = 0.22). Positive inbreeding coefficients are most likely due to Wahlund effects and/or inbreeding effects from highly correlated paternity and typically low fruit set. Indirect estimates of gene flow (Nm = 5.09 using F _ST; Nm = 3.12 using the private alleles method) among populations reflects a historical capacity for gene flow through long distance pollen dispersal by sexually deceived wasp pollinators and/or long range dispersal of dust-like orchid seed. However, current levels of gene flow may be impacted by habitat destruction, fragmentation and reduced population size. A genetically divergent population was identified, which should be a high priority for conservation managers. Very weak genetic differentiation indicates that the movement and mixing of seeds from different populations for reintroduction programs should result in minimal negative genetic effects.     

Biophysical connectivity explains population genetic structure in a highly dispersive marine species

Connectivity, the exchange of individuals among locations, is a fundamental ecological process that explains how otherwise disparate populations interact. For most marine organisms, dispersal occurs primarily during a pelagic larval phase that connects populations. We paired population structure from comprehensive genetic sampling and biophysical larval transport modeling to describe how spiny lobster (Panulirus argus) population differentiation is related to biological oceanography. A total of 581 lobsters were genotyped with 11 microsatellites from ten locations around the greater Caribbean. The overall F _ST of 0.0016 (P = 0.005) suggested low yet significant levels of structuring among sites. An isolation by geographic distance model did not explain spatial patterns of genetic differentiation in P. argus (P = 0.19; Mantel r = 0.18), whereas a biophysical connectivity model provided a significant explanation of population differentiation (P = 0.04; Mantel r = 0.47). Thus, even for a widely dispersing species, dispersal occurs over a continuum where basin-wide larval retention creates genetic structure. Our study provides a framework for future explorations of wide-scale larval dispersal and marine connectivity by integrating empirical genetic research and probabilistic modeling.

     

Combined analyses of kinship and FST suggest potential drivers of chaotic genetic patchiness in high gene‐flow populations

We combine kinship estimates with traditional F‐statistics to explain contemporary drivers of population genetic differentiation despite high gene flow. We investigate range‐wide population genetic structure of the California spiny (or red rock) lobster (Panulirus interruptus) and find slight, but significant global population differentiation in mtDNA (Φ_ST = 0.006, P = 0.001; D_{est_Chao} = 0.025) and seven nuclear microsatellites (F_ST = 0.004, P < 0.001; D_{est_Chao} = 0.03), despite the species’ 240‐ to 330‐day pelagic larval duration. Significant population structure does not correlate with distance between sampling locations, and pairwise F_ST between adjacent sites often exceeds that among geographically distant locations. This result would typically be interpreted as unexplainable, chaotic genetic patchiness. However, kinship levels differ significantly among sites (pseudo‐F_16,988 = 1.39, P = 0.001), and ten of 17 sample sites have significantly greater numbers of kin than expected by chance (P < 0.05). Moreover, a higher proportion of kin within sites strongly correlates with greater genetic differentiation among sites (D_{est_Chao}, R² = 0.66, P < 0.005). Sites with elevated mean kinship were geographically proximate to regions of high upwelling intensity (R² = 0.41, P = 0.0009). These results indicate that P. interruptus does not maintain a single homogenous population, despite extreme dispersal potential. Instead, these lobsters appear to either have substantial localized recruitment or maintain planktonic larval cohesiveness whereby siblings more likely settle together than disperse across sites. More broadly, our results contribute to a growing number of studies showing that low F_ST and high family structure across populations can coexist, illuminating the foundations of cryptic genetic patterns and the nature of marine dispersal.     

Multilocus genetic analyses and spatial modeling reveal complex population structure and history in a widespread resident North American passerine (Perisoreus canadensis)

An increasing body of studies of widely distributed, high latitude species shows a variety of refugial locations and population genetic patterns. We examined the effects of glaciations and dispersal barriers on the population genetic patterns of a widely distributed, high latitude, resident corvid, the gray jay (Perisoreus canadensis), using the highly variable mitochondrial DNA (mtDNA) control region and microsatellite markers combined with species distribution modeling. We sequenced 914 bp of mtDNA control region for 375 individuals from 37 populations and screened seven loci for 402 individuals from 27 populations across the gray jay range. We used species distribution modeling and a range of phylogeographic analyses (haplotype diversity, Φ_ST, SAMOVA, F_ST, Bayesian clustering analyses) to examine evolutionary history and population genetic structure. MtDNA and microsatellite markers revealed significant genetic differentiation among populations with high concordance between markers. Paleodistribution models supported at least five potential areas of suitable gray jay habitat during the last glacial maximum and revealed distributions similar to the gray jay's contemporary during the last interglacial. Colonization from and prolonged isolation in multiple refugia is evident. Historical climatic fluctuations, the presence of multiple dispersal barriers, and highly restricted gene flow appear to be responsible for strong genetic diversification and differentiation in gray jays.