Spatial differences in genetic diversity and northward migration suggest genetic erosion along the boreal caribou southern range limit and continued range retraction

With increasing human activities and associated landscape changes, distributions of terrestrial mammals become fragmented. These changes in distribution are often associated with reduced population sizes and loss of genetic connectivity and diversity (i.e., genetic erosion) which may further diminish a species' ability to respond to changing environmental conditions and lead to local population extinctions. We studied threatened boreal caribou (Rangifer tarandus caribou) populations across their distribution in Ontario/Manitoba (Canada) to assess changes in genetic diversity and connectivity in areas of high and low anthropogenic activity. Using data from >1,000 caribou and nine microsatellite loci, we assessed population genetic structure, genetic diversity, and recent migration rates using a combination of network and population genetic analyses. We used Bayesian clustering analyses to identify population genetic structure and explored spatial and temporal variation in those patterns by assembling networks based on R_ST and F_ST as historical and contemporary genetic edge distances, respectively. The Bayesian clustering analyses identified broad‐scale patterns of genetic structure and closely aligned with the R_ST network. The F_ST network revealed substantial contemporary genetic differentiation, particularly in areas presenting contemporary anthropogenic disturbances and habitat fragmentation. In general, relatively lower genetic diversity and greater genetic differentiation were detected along the southern range limit, differing from areas in the northern parts of the distribution. Moreover, estimation of migration rates suggested a northward movement of animals away from the southern range limit. The patterns of genetic erosion revealed in our study suggest ongoing range retraction of boreal caribou in central Canada.     

Urban land use limits regional bumble bee gene flow

Potential declines in native pollinator communities and increased reliance on pollinator‐dependent crops have raised concerns about native pollinator conservation and dispersal across human‐altered landscapes. Bumble bees are one of the most effective native pollinators and are often the first to be extirpated in human‐altered habitats, yet little is known about how bumble bees move across fine spatial scales and what landscapes promote or limit their gene flow. In this study, we examine regional genetic differentiation and fine‐scale relatedness patterns of the yellow‐faced bumble bee, Bombus vosnesenskii, to investigate how current and historic habitat composition impact gene flow. We conducted our study across a landscape mosaic of natural, agricultural and urban/suburban habitats, and we show that B. vosnesenskii exhibits low but significant levels of differentiation across the study system (F_ST = 0.019, D_est = 0.049). Most importantly, we reveal significant relationships between pairwise F_ST and resistance models created from contemporary land use maps. Specifically, B. vosnesenskii gene flow is most limited by commercial, industrial and transportation‐related impervious cover. Finally, our fine‐scale analysis reveals significant but declining relatedness between individuals at the 1–9 km spatial scale, most likely due to local queen dispersal. Overall, our results indicate that B. vosnesenskii exhibits considerable local dispersal and that regional gene flow is significantly limited by impervious cover associated with urbanization.     

Quantifying the lag time to detect barriers in landscape genetics

Understanding how spatial genetic patterns respond to landscape change is crucial for advancing the emerging field of landscape genetics. We quantified the number of generations for new landscape barrier signatures to become detectable and for old signatures to disappear after barrier removal. We used spatially explicit, individual‐based simulations to examine the ability of an individual‐based statistic [Mantel’s r using the proportion of shared alleles’ statistic (Dps)] and population‐based statistic (F_ST) to detect barriers. We simulated a range of movement strategies including nearest neighbour dispersal, long‐distance dispersal and panmixia. The lag time for the signal of a new barrier to become established is short using Mantel’s r (1–15 generations). F_ST required approximately 200 generations to reach 50% of its equilibrium maximum, although G’_ST performed much like Mantel’s r. In strong contrast, F_ST and Mantel’s r perform similarly following the removal of a barrier formerly dividing a population. Also, given neighbour mating and very short‐distance dispersal strategies, historical discontinuities from more than 100 generations ago might still be detectable with either method. This suggests that historical events and landscapes could have long‐term effects that confound inferences about the impacts of current landscape features on gene flow for species with very little long‐distance dispersal. Nonetheless, populations of organisms with relatively large dispersal distances will lose the signal of a former barrier within less than 15 generations, suggesting that individual‐based landscape genetic approaches can improve our ability to measure effects of existing landscape features on genetic structure and connectivity.     

Microsatellite and mtDNA analysis of lake trout,Salvelinus namaycush,from Great Bear Lake,Northwest Territories: impacts of historical and contemporary evolutionary forces on Arctic ecosystems

Resolving the genetic population structure of species inhabiting pristine, high latitude ecosystems can provide novel insights into the post‐glacial, evolutionary processes shaping the distribution of contemporary genetic variation. In this study, we assayed genetic variation in lake trout (Salvelinus namaycush) from Great Bear Lake (GBL), NT and one population outside of this lake (Sandy Lake, NT) at 11 microsatellite loci and the mtDNA control region (d‐loop). Overall, population subdivision was low, but significant (global F_ST θ = 0.025), and pairwise comparisons indicated that significance was heavily influenced by comparisons between GBL localities and Sandy Lake. Our data indicate that there is no obvious genetic structure among the various basins within GBL (global F_ST = 0.002) despite the large geographic distances between sampling areas. We found evidence of low levels of contemporary gene flow among arms within GBL, but not between Sandy Lake and GBL. Coalescent analyses suggested that some historical gene flow occurred among arms within GBL and between GBL and Sandy Lake. It appears, therefore, that contemporary (ongoing dispersal and gene flow) and historical (historical gene flow and large founding and present‐day effective population sizes) factors contribute to the lack of neutral genetic structure in GBL. Overall, our results illustrate the importance of history (e.g., post‐glacial colonization) and contemporary dispersal ecology in shaping genetic population structure of Arctic faunas and provide a better understanding of the evolutionary ecology of long‐lived salmonids in pristine, interconnected habitats.     

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.     

Species‐level view of population structure and gene flow for a critically endangered primate (Varecia variegata)

Lemurs are among the world's most threatened mammals. The critically endangered black‐and‐white ruffed lemur (Varecia variegata), in particular, has recently experienced rapid population declines due to habitat loss, ecological sensitivities to habitat degradation, and extensive human hunting pressure. Despite this, a recent study indicates that ruffed lemurs retain among the highest levels of genetic diversity for primates. Identifying how this diversity is apportioned and whether gene flow is maintained among remnant populations will help to diagnose and target conservation priorities. We sampled 209 individuals from 19 sites throughout the remaining V. variegata range. We used 10 polymorphic microsatellite loci and ~550 bp of mtDNA sequence data to evaluate genetic structure and population dynamics, including dispersal patterns and recent population declines. Bayesian cluster analyses identified two distinct genetic clusters, which optimally partitioned data into populations occurring on either side of the Mangoro River. Localities north of the Mangoro were characterized by greater genetic diversity, greater gene flow (lower genetic differentiation) and higher mtDNA haplotype and nucleotide diversity than those in the south. Despite this, genetic differentiation across all sites was high, as indicated by high average F_ST (0.247) and Φ_ST (0.544), and followed a pattern of isolation‐by‐distance. We use these results to suggest future conservation strategies that include an effort to maintain genetic diversity in the north and restore connectivity in the south. We also note the discordance between patterns of genetic differentiation and current subspecies taxonomy, and encourage a re‐evaluation of conservation management units moving forward.     

Extensive sampling of polar bears (Ursus maritimus) in the Northwest Passage (Canadian Arctic Archipelago) reveals population differentiation across multiple spatial and temporal scales

As global warming accelerates the melting of Arctic sea ice, polar bears (Ursus maritimus) must adapt to a rapidly changing landscape. This process will necessarily alter the species distribution together with population dynamics and structure. Detailed knowledge of these changes is crucial to delineating conservation priorities. Here, we sampled 361 polar bears from across the center of the Canadian Arctic Archipelago spanning the Gulf of Boothia (GB) and M'Clintock Channel (MC). We use DNA microsatellites and mitochondrial control region sequences to quantify genetic differentiation, estimate gene flow, and infer population history. Two populations, roughly coincident with GB and MC, are significantly differentiated at both nuclear (F_ST = 0.01) and mitochondrial (Φ_ST = 0.47; F_ST = 0.29) loci, allowing Bayesian clustering analyses to assign individuals to either group. Our data imply that the causes of the mitochondrial and nuclear genetic patterns differ. Analysis of mtDNA reveals the matrilineal structure dates at least to the Holocene, and is common to individuals throughout the species’ range. These mtDNA differences probably reflect both genetic drift and historical colonization dynamics. In contrast, the differentiation inferred from microsatellites is only on the scale of hundreds of years, possibly reflecting contemporary impediments to gene flow. Taken together, our data suggest that gene flow is insufficient to homogenize the GB and MC populations and support the designation of GB and MC as separate polar bear conservation units. Our study also provide a striking example of how nuclear DNA and mtDNA capture different aspects of a species demographic history.     

Watershed‐level brook trout genetic structuring: Evaluation and application of riverscape genetics models

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Detection of environmental and morphological adaptation despite high landscape genetic connectivity in a pest grasshopper (Phaulacridium vittatum)

Widespread species that exhibit both high gene flow and the capacity to occupy heterogeneous environments make excellent models for examining local selection processes along environmental gradients. Here we evaluate the influence of temperature and landscape variables on genetic connectivity and signatures of local adaptation in Phaulacridium vittatum, a widespread agricultural pest grasshopper, endemic to Australia. With sampling across a 900‐km latitudinal gradient, we genotyped 185 P. vittatum from 19 sites at 11,408 single nucleotide polymorphisms (SNPs) using ddRAD sequencing. Despite high gene flow across sites (pairwise F_ST = 0.0003–0.08), landscape genetic resistance modelling identified a positive nonlinear effect of mean annual temperature on genetic connectivity. Urban areas and water bodies had a greater influence on genetic distance among sites than pasture, agricultural areas and forest. Together, F_ST outlier tests and environmental association analysis (EAA) detected 242 unique SNPs under putative selection, with the highest numbers associated with latitude, mean annual temperature and body size. A combination of landscape genetic connectivity analysis together with EAA identified mean annual temperature as a key driver of both neutral gene flow and environmental selection processes. Gene annotation of putatively adaptive SNPs matched with gene functions for olfaction, metabolic detoxification and ultraviolet light shielding. Our results imply that this widespread agricultural pest has the potential to spread and adapt under shifting temperature regimes and land cover change.     

Development of genetic diversity,differentiation and structure over 500 years in four ponderosa pine populations

Population history plays an important role in shaping contemporary levels of genetic variation and geographic structure. This is especially true in small, isolated range‐margin populations, where effects of inbreeding, genetic drift and gene flow may be more pronounced than in large continuous populations. Effects of landscape fragmentation and isolation distance may have implications for persistence of range‐margin populations if they are demographic sinks. We studied four small, disjunct populations of ponderosa pine over a 500‐year period. We coupled demographic data obtained through dendroecological methods with microsatellite data to discern how and when contemporary levels of allelic diversity, among and within‐population levels of differentiation, and geographic structure, arose. Alleles accumulated rapidly following initial colonization, demonstrating proportionally high levels of gene flow into the populations. At population sizes of approximately 100 individuals, allele accumulation saturated. Levels of genetic differentiation among populations (F_ST and Jost's D_est) and diversity within populations (F_IS) remained stable through time. There was no evidence of geographic genetic structure at any time in the populations' history. Proportionally, high gene flow in the early stages of population growth resulted in rapid accumulation of alleles and quickly created relatively homogenous genetic patterns among populations. Our study demonstrates that contemporary levels of genetic diversity were formed quickly and early in population development. How contemporary genetic diversity accumulates over time is a key facet of understanding population growth and development. This is especially relevant given the extent and speed at which species ranges are predicted to shift in the coming century.     

Fine scale patterns of migration and gene flow in the endangered mound spring snail, <Emphasis Type="Italic">Fonscochlea accepta</Emphasis> (Mollusca:Hydrobiidae) in arid Australia

Naturally patchy ecosystems are models for other systems currently undergoing anthropogenic habitat fragmentation. Understanding patterns of gene flow in these model systems can help us manage species and ecosystems threatened by human impacts. The mound springs of central Australia represent such a natural model ecosystem, supporting a unique aquatic fauna distributed within an inhospitable arid landscape. Moreover, these springs are being impacted by over extraction of groundwater, providing a unique opportunity to look at dispersal in a patchy habitat that is changing. The present study represents the first fine scale analysis of gene flow under different scenarios of habitat connectivity for the endangered mound spring snail, Fonscochlea accepta. Within a single spring group pairwise estimates of F _ST between springs were very low (ave 0.015) with no association found between genetic distance and a series of geographical distance matrices based on the degree of habitat connectivity among the springs: results implying unstructured dispersal and limited population isolation. However, results from Bayesian assignment tests showed that on average approximately 97% of snails were assigned to their spring of origin. In a preliminary analysis at broader geographic scales (among spring groups) the results from F _ST estimates, Mantel correlation analyses and assignment tests all suggest much stronger and geographically correlated population structuring. While varying results from F-statistics and Bayesian analyses stem from the different information they utilise, together they provide data on contemporary and historical estimates of gene flow and the influence of landscape dynamics on the spatial genetic patterning of the springs.     

Directional gene flow patterns in disjunct populations of the black ratsnake (Pantheropis obsoletus) and the Blanding’s turtle (Emydoidea blandingii)

The estimation and maintenance of connectivity among local populations is an important conservation goal for many species at risk. We used Bayesian statistics and coalescent theory to estimate short- and long-term directional gene flow among subpopulations for two reptiles that occur in Canada as peripheral populations that are geographically disjunct from the core of their respective species’ ranges: the black ratsnake and the Blanding’s turtle. Estimates of directional gene flow were used to examine population connectivity and potential genetic source-sink dynamics. For both species, our estimates of directional short- and long-term gene flow were consistently lower than estimates inferred previously from F _ST measures. Short- and long-term gene flow estimates were discordant in both species, suggesting that population dynamics have varied temporally in both species. These estimates of directional gene flow were used to identify specific subpopulations in both species that may be of high conservation value because they are net exporters of individuals to other subpopulations. Overall, our results show that the use of more sophisticated methods to evaluate population genetic data can provide valuable information for the conservation of species at risk, including bidirectional estimates of subpopulation connectivity that rely on fewer assumptions than more traditional analyses. Such information can be used by conservation practitioners to better understand the geographic scope required to maintain a functional metapopulation, determine which habitat corridors within a working landscape may be most important to maintain connectivity among subpopulations, and to prioritize subpopulations with respect to their potential to act as genetic sources within the metapopulation.     

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.     

Contemporary human‐altered landscapes and oceanic barriers reduce bumble bee gene flow

Much of the world's terrestrial landscapes are being altered by humans in the form of agriculture, urbanization and pastoral systems, with major implications for biodiversity. Bumble bees are one of the most effective pollinators in both natural and cultivated landscapes, but are often the first to be extirpated in human‐altered habitats. Yet, little is known about the role of natural and human‐altered habitats in promoting or limiting bumble bee gene flow. In this study, I closely examine the genetic structure of the yellow‐faced bumble bee, Bombus vosnesenskii, across the southwestern US coast and find strong evidence that natural oceanic barriers, as well as contemporary human‐altered habitats, limit bee gene flow. Heterozygosity and allelic richness were lower in island populations, while private allelic richness was higher in island populations compared to mainland populations. Genetic differentiation, measured for three indices across the 1000 km study region, was significantly greater than the null expectation (F_ST = 0.041, F’_ST = 0.044 and D_est = 0.155) and correlated with geographic distance. Furthermore, genetic differentiation patterns were most strongly correlated with contemporary (2011) not past (2006, 2001) resistance maps calibrated for high dispersal limitation over oceans, impervious habitat and croplands. Despite the incorporation of dramatic elevation gradients, the analyses reveal that oceans and contemporary human land use, not mountains, are the primary dispersal barriers for B. vosnesenskii gene flow. These findings reinforce the importance of maintaining corridors of suitable habitat across the distribution range of native pollinators to promote their persistence and safeguard their ability to provide essential pollination services.     

Echoes of a distant time: effects of historical processes on contemporary genetic patterns in Galaxias platei in Patagonia

Interpreting the genetic structure of a metapopulation as the outcome of gene flow over a variety of timescales is essential for the proper understanding of how changes in landscape affect biological connectivity. Here we contrast historical and contemporary connectivity in two metapopulations of the freshwater fish Galaxias platei in northern and southernmost Patagonia where paleolakes existed during the Holocene and Pleistocene, respectively. Contemporary gene flow was mostly high and asymmetrical in the northern system while extremely reduced in the southernmost system. Historical migration patterns were high and symmetric in the northern system and high and largely asymmetric in the southern system. Both systems showed a moderate structure with a clear pattern of isolation by distance (IBD). Effective population sizes were smaller in populations with low contemporary gene flow. An approximate Bayesian computation (ABC) approach suggests a late Holocene colonization of the lakes in the northern system and recent divergence of the populations from refugial populations from east and west of the Andes. For the southern system, the ABC approach reveals that some of the extant G. platei populations most likely derive from an ancestral population inhabiting a large Pleistocene paleolake while the rest derive from a higher‐altitude lake. Our results suggest that neither historical nor contemporary processes individually fully explain the observed structure and geneflow patterns and both are necessary for a proper understanding of the factors that affect diversity and its distribution. Our study highlights the importance of a temporal perspective on connectivity to analyse the diversity of spatially complex metapopulations.     

Islands within islands: two montane palaeo‐endemic birds impacted by recent anthropogenic fragmentation

Anthropogenic habitat fragmentation of species that live in naturally patchy metapopulations such as mountaintops or sky islands experiences two levels of patchiness. Effects of such multilevel patchiness on species have rarely been examined. Metapopulation theory suggests that patchy habitats could have varied impacts on persistence, dependent on differential migration. It is not known whether montane endemic species, evolutionarily adapted to natural patchiness, are able to disperse between anthropogenic fragments at similar spatial scales as natural patches. We investigated historic and contemporary gene flow between natural and anthropogenic patches across the distribution range of a Western Ghats sky‐island‐endemic bird species complex. Data from 14 microsatellites for 218 individuals detected major genetic structuring by deep valleys, including one hitherto undescribed barrier. As expected, we found strong effects of historic genetic differentiation across natural patches, but not across anthropogenic fragments. Contrastingly, contemporary differentiation (D_PS) was higher relative to historic differentiation (F_ST) in anthropogenic fragments, despite the species’ ability to historically traverse shallow valleys. Simulations of recent isolation resulted in high D_PS/F_ST values, confirming recent isolation in Western Ghats anthropogenic fragments and also suggesting that this ratio can be used to identifying recent fragmentation in the context of historic connectedness. We suggest that in this landscape, in addition to natural patchiness affecting population connectivity, anthropogenic fragmentation additionally impacts connectivity, making anthropogenic fragments akin to islands within natural islands of montane habitat, a pattern that may be recovered in other sky‐island systems.     

Examination of ten thousand years of mitochondrial DNA diversity and population demographics in bowhead whales (Balaena mysticetus) of the Central Canadian Arctic

Mitochondrial DNA (mtDNA) sequences were analyzed from 106 bowhead whale (Balaena mysticetus) specimens dating 471 ± 44 ¹⁴C b.p. –10,290 ± 150 ¹⁴C b.p. to evaluate whether historical changes in distribution and connectivity were detectable in levels of diversity and population structuring in the Central Canadian Arctic. The species has maintained levels of mtDNA diversity over 10,000 yr comparable to other nonbottlenecked large whale species. When compared to data from the Holocene East Greenland/Spitsbergen and contemporary Bering‐Chuckchi‐Beaufort populations, differentiation was low (F_ST≤ 0.005, Φ_ST≤ 0.003) and no temporal or geographical genetic structuring was evident. A combination of analyses suggests that the population has expanded over the past 30,000 ¹⁴C yr. This genetic signature of expansion could result from population growth, admixture of multiple gene pools, or a combination of both scenarios. Despite known climatic change that altered bowhead distribution and led to isolation of populations, there is no detectable population structuring or change in genetic diversity during the Holocene. This may be due to long generation time, occasional population connectivity and a historically large global population. These characteristics warrant caution when interpreting contemporary bowhead whale DNA data, as it is unlikely that any population will be in mutation‐drift equilibrium.     

Environmental factors affecting population level genetic divergence of the striped field mouse (<Emphasis Type="Italic">Apodemus agrarius</Emphasis>) in South Korea

The cognizing of connectivity among small mammal populations across heterogeneous landscapes is complicated due to complex influences of landscape and anthropogenic factors on gene flow. A landscape genetics approach offers inferences on how landscape features drive population structure. Through a landscape genetics approach, we investigated influences of geographical, environmental, and anthropogenic features on populations of Apodemus agrarius, the striped field mouse, the prime vector of hemorrhagic fever by a landscape genetic approach. We identified landscape features that might affect the population structure of striped field mice by analyzing microsatellite markers of 197 striped field mice from 21 populations throughout South Korea. We developed Maximum-likelihood population effects models based on landscape distances and resistance matrices and pairwise F_ST values for meta-populations of striped field mouse. We also conducted Mantel and partial Mantel tests to investigate geographic patterns of genetic similarities. In Mantel and partial Mantel tests, the F_ST was significantly correlated with all three models of movement; movement cost, Euclidian distance and least-cost distance, although the magnitudes of correlations varied. The 4 top-ranked models included three variables; temperature, precipitation and one human disturbance factor (population). We did not attain a significant effect for anthropogenic factors on genetic similarities among populations in the Korean striped field mouse, but we confirmed a significant association for genetic similarity with climatic features (temperature and precipitation).     

Diversity and genetic connectivity among populations of a threatened tree (<Emphasis Type="Italic">Dalbergia nigra</Emphasis>) in a recently fragmented landscape of the Brazilian Atlantic Forest

In this study we evaluated the influence of recent landscape fragmentation on the dynamics of remnant fragments from the Brazilian Atlantic Forest. This biome is one of the richest in the world and has been extensively deforested and fragmented. We sampled five populations of the threatened Dalbergia nigra, a tree endemic to the Brazilian Atlantic Forest, two located in a large reserve of continuous forest and three in fragments of different sizes and levels of disturbance. In order to assess historical changes, considering the longevity of the analyzed species, 119 adults and 116 saplings were genotyped for six microsatellite loci. Lower levels of genetic diversity were found in the most impacted fragments when compared to the most preserved population located inside the reserve, and there was significant genetic structure among the populations studied (pairwise F _ST = 0.031–0.152; pairwise D _EST = 0.039–0.301). However, genetic structure among saplings (F _ST = 0.056; D _EST = 0.231) was significantly lower than among adults (F _ST = 0.088; D _EST = 0.275). Estimates of contemporary gene flow based on assignment tests corroborated this result, suggesting that fragmentation led to an increase in gene flow. This connectivity among remnant fragments could mitigate the loss of genetic diversity through a metapopulation dynamic, but the high rate of habitat loss and the unknown long-term genetic effects add uncertainty. These results, taken together with the presence of private alleles in disturbed populations, highlight the importance of preserving the extant fragments.     

Limited genetic connectivity of Pavona gigantea in the Mexican Pacific

Coral reefs are the most complex and diverse of aquatic ecosystems. Their vulnerability and deterioration in the face of anthropogenic disturbance require the adoption of conservation and restoration efforts to maintain their resilience, for which connectivity is of paramount importance. Dispersal of meroplanktonic larval stages drives the levels of connectivity among coral populations and is influenced by the local current regime, the synchronization of spawning events, and the capacity of larvae to reach recruitment sites. This research aims to quantify the levels of connectivity among Pavona gigantea populations in the Mexican Pacific, using two mitochondrial genes and a nuclear gene. Mitochondrial genes were insufficiently variable to test geographical heterogeneity, whereas the more variable (h ≥ 0.86) nuclear rDNA indicated significant geographic differentiation (Φ _ST  = 0.159, P < 0.001) among five locations along the Mexican Pacific, but no evidence of isolation by distance. Gene flow was limited among most sampled locales, and the largest estimate suggested moderate and unidirectional gene flow from Huatulco Bays to La Paz Bay and Marietas Islands. We found partial agreement between the patterns of connectivity among localities and the general pattern of superficial oceanographic circulation of the region, particularly in reference with the expected influence of the northward flowing West Mexican Current. These results suggest a limited demographic connectivity among Pavona gigantea populations along the Mexican Pacific, mediated by passive larval transport, and highlight the difficulty of predicting connectivity patterns on the basis of highly variable oceanographic regimes and reproductive events. The limited connectivity is of consequence for the viability and vulnerability of local populations and should be considered in the management and conservation strategies in the region.