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opencc-zeroDec 2017View details →

Data from: Genotyping-by-sequencing of genome-wide microsatellite loci reveals fine-scale harvest composition in a coastal Atlantic salmon fishery

Individual assignment and genetic mixture analysis are commonly utilized in contemporary wildlife and fisheries management. Although microsatellite loci provide unparalleled numbers of alleles per locus, their use in assignment applications is increasingly limited. However, next-generation sequencing, in conjunction with novel bioinformatic tools allows large numbers of microsatellite loci to be simultaneously genotyped, presenting new opportunities for individual assignment and genetic mixture analysis. Here we scanned the published Atlantic salmon genome to identify 706 microsatellite loci, from which we developed a final panel of 101 microsatellites distributed across the genome (average 3.4 loci per chromosome). Using samples from 35 Atlantic salmon populations (n=1485 individuals) from coastal Labrador, Canada, a region characterized by low levels of differentiation in this species, this panel identified 844 alleles (average of 8.4 alleles per locus). Simulation-based evaluations of assignment and mixture identification accuracy revealed unprecedented resolution, clearly identifying 26 rivers or groups of rivers spanning 500 km of coastline. This baseline was used to examine the stock composition of 696 individuals harvested in the Labrador Atlantic salmon fishery and revealed that coastal fisheries largely targeted regional groups (<300km). This work suggests that the development and application of large sequenced microsatellite panels presents great potential for stock resolution in Atlantic salmon and more broadly in other exploited anadromous and marine species.

Data from: From animal tracks to fine-scale movement modes: a straightforward approach for identifying multiple, spatial movement patterns

1. Thanks to developments in animal tracking technology, detailed data on the movement tracks of individual animals are now attainable for many species. However, straightforward methods to decompose individual tracks into high-resolution, spatial modes are lacking but are essential to understand what an animal is doing. 2. We developed an analytical approach that combines separately-validated methods into a straightforward tool for converting animal GPS tracks to short-range movement modes. Our three-step analytical process comprises: (1) decomposing data into separate movement segments using behavioural change point analysis; (2) defining candidate movement modes and translating them into non-linear or linear equations between net squared displacement (NSD) and time; and (3) fitting each candidate equation to NSD segments and determining the best-fitting modes using Concordance Criteria, Akaike's Information Criteria and other fine-scale segment characteristics. We illustrate our approach for three sub-adults, male wild boar Sus scrofa tracked at 15 min intervals over 4 months using GPS collars. We defined five candidate movement modes based on previously published studies of short-term movements: encamped, ranging, round trips (complete and partial), and wandering. 3. Our approach successfully classified over 80% of the tracks into these movement modes lasting between 5 and 54 hours and covering between 300 m to 20 km. Repeated analyses of GPS data resampled at different rates indicated that one positional fix every 3-4 h was sufficient for >70% classification success. Classified modes were consistent with published observations of wild boar movement, further validating our method. 4. The proposed approach advances the status quo by permitting classification into multiple movement modes (where these are adequately discernable from spatial fixes) facilitating analyses at high temporal and spatial resolutions, and is straightforward, largely objective, and without restrictive assumptions, necessary parameterizations or visual interpretation. Thus, it should capture the complexity and variability of tracked animal movement mode for a variety of taxa across a wide range of spatial and temporal scales.

opencc-zeroDec 2017View details →

Data from: Landscape history confounds the ability of the NDVI to detect fine-scale variation in grassland communities

1. The NDVI is a remotely-sensed vegetation index that is frequently used in ecological studies. There is, however, a lack of studies that evaluate the ability of the NDVI to detect fine-scale variation in grassland plant community composition and species richness. Ellenberg indicators characterize the environmental preferences of plant species – and community-mean Ellenberg values have been used to explore the environmental drivers of community assembly. 2. We used variation partitioning to test the ability of satellite-based NDVI to explain community-mean Ellenberg nutrient (mN) and moisture (mF) indices, and the richness of habitat-specialist species in dry grasslands of different ages. The grasslands represent a gradient of decreasing soil nutrient status. 3. If community composition is determined by the responses of individual species to the underlying environmental conditions and if, at the same time, community composition determines the optical characteristics of the vegetation canopy, then positive relationships between the NDVI and mN and mF are expected. Many grassland specialists are intolerant of nutrient-rich soils. If specialist richness is negatively related to soil-nutrient levels, then a negative association between the NDVI and specialist richness is expected. However, because grassland community composition is not only influenced by abiotic variables but also by other spatial and temporal drivers, we included spatial variables and grassland age in the statistical analyses. 4. The NDVI explained the majority of the variation in mF, and also contributed to a substantial proportion of the variation in mN. However, variation in specialist richness and the lowest values of mN were explained by grassland age and spatial variables – but were poorly explained by the NDVI. 5. Synthesis and applications. The NDVI showed a good ability to detect variation in plant community composition, and should provide a valuable tool for assessing fine-scale environmental variation in grasslands or for monitoring changes in grassland habitat properties. However, because the concentration of grassland specialists not only depends on environmental variables but also on the age and spatial context of the grasslands, the NDVI is unlikely to allow the identification of grasslands with high numbers of specialist species.

Data from: Fine-scale movement responses of free-ranging harbour porpoises to capture, tagging, and short-term noise pulses from a single airgun

Knowledge about the impact of anthropogenic disturbances on the behavioural responses of cetaceans is constrained by lack of data on fine-scale movements of individuals. We equipped five free-ranging harbour porpoises (Phocoena phocoena) with high-resolution location and dive loggers and exposed them to a single 10 in3 underwater airgun producing high-intensity noise pulses (2−3 second intervals) for one minute. All five porpoises responded to capture and tagging with longer, faster and more directed movements as well as with shorter, shallower, less wiggly dives immediately after release, with natural behaviour resumed in ≤24 hours. When we exposed porpoises to airgun pulses at ranges of 420−690 m with noise level estimates of 135−147 dB re 1µPa2s (SEL), one individual displayed rapid and directed movements away from the exposure site and two individuals used shorter and shallower dives compared to natural behaviour immediately after exposure. Noise-induced movement typically lasted for ≤8 hours with an additional 24-hour recovery period until natural behaviour was resumed. The remaining individuals did not show any quantifiable responses to the noise exposure. Changes in natural behaviour following anthropogenic disturbances may reduce feeding opportunities and evaluating potential population-level consequences should be a priority research area.

Data from: Arctic fungal communities associated with roots of Bistorta vivipara do not respond to the same fine-scale edaphic gradients as the above-ground vegetation

Soil conditions and microclimate are important determinants of the fine-scale distribution of plant species in the Arctic, creating locally heterogeneous vegetation. We hypothesize that root-associated fungal (RAF) communities respond to the same fine-scale environmental gradients as the aboveground vegetation, creating a coherent pattern between aboveground vegetation and RAF. We explored how RAF communities of the ectomycorrhizal (ECM) plant Bistorta vivipara and aboveground vegetation structure of arctic plants were affected by biotic and abiotic variables at 0.3–3.0-m scales. RAF communities were determined using pyrosequencing. Composition and spatial structure of RAF and aboveground vegetation in relation to collected biotic and abiotic variables were analysed by ordination and semi-variance analyses. The vegetation was spatially structured along soil C and N gradients, whereas RAF lacked significant spatial structure. A weak relationship between RAF community composition and the cover of two ECM plants, B. vivipara and S. polaris, was found, and RAF richness increased with host root length and root weight. Results suggest that the fine-scale spatial structure of RAF communities of B. vivipara and the aboveground vegetation are driven by different factors. At fine spatial scales, neighbouring ECM plants may affect RAF community composition, whereas soil nutrients gradients structure the vegetation.

Data from: Fine-scale population genetic structure of the Bengal tiger (Panthera tigris tigris) in a human-dominated western Terai Arc Landscape, India

Despite massive global conservation strategies, tiger populations continued to decline until recently, mainly due to habitat loss, human-animal conflicts, and poaching. These factors are known to affect the genetic characteristics of tiger populations and decrease local effective population sizes. The Terai Arc Landscape (TAL) at the foothills of the Himalaya is one of the 42 source sites of tigers around the globe. Therefore, information on how landscape features and anthropogenic factors affect the fine-scale spatial genetic structure and variation of tigers in TAL is needed to develop proper management strategies for achieving long-term conservation goals. We document, for the first time, the genetic characteristics of this tiger population by genotyping 71 tiger samples using 13 microsatellite markers from the western region of TAL (WTAL) (1800 km2). Specifically, we aimed to estimate the genetic variability, population structure, and gene flow. The microsatellite markers indicated that the levels of allelic diversity (MNA = 6.6) and genetic variation (Ho =0.50, HE = 0.64) were slightly lower than those reported previously in other Bengal tiger populations. We observed moderate gene flow and significant genetic differentiation (FST= 0.060), and identified the presence of cryptic genetic structure using Bayesian and non-Bayesian approaches. There was low and significantly asymmetric migration between the two main subpopulations of the Rajaji Tiger Reserve and the Corbett Tiger Reserve in WTAL. Sibship relationships indicated that the functionality of the corridor between these subpopulations may be retained if the quality of the habitat does not deteriorate. However, we found that gene flow is not adequate in view of changing land use matrices. We discuss the need to maintain connectivity by implementing the measures that have been suggested previously to minimize the level of human disturbance, including relocation of villages and industries, prevention of encroachment, and banning sand and boulder mining in the corridors.

opencc-zeroDec 2012View details →

Data from: From fine-scale foraging to home ranges: a semi-variance approach to identifying movement modes across spatiotemporal scales

Understanding animal movement is a key challenge in ecology and conservation biology. Relocation data often represent a complex mixture of different movement behaviors, and reliably decomposing this mix into its component parts is an unresolved problem in movement ecology. Traditional approaches, such as composite random walk models, require that the timescales characterizing the movement are all similar to the usually arbitrary data-sampling rate. Movement behaviors such as long-distance searching and fine-scale foraging, however, are often intermixed but operate on vastly different spatial and temporal scales. An approach that integrates the full sweep of movement behaviors across scales is currently lacking. Here we show how the semivariance function (SVF) of a stochastic movement process can both identify multiple movement modes and solve the sampling rate problem. We express a broad range of continuous-space, continuous-time stochastic movement models in terms of their SVFs, connect them to relocation data via variogram regression, and compare them using standard model selection techniques. We illustrate our approach using Mongolian gazelle relocation data and show that gazelle movement is characterized by ballistic foraging movements on a 6-h timescale, fast diffusive searching with a 10-week timescale, and asymptotic diffusion over longer timescales.

opencc-zeroDec 2015View details →

Data from: Fine-scale spatial genetic structure in the frankincense tree Boswellia papyrifera (Del.) Hochst. and implications for conservation

The fine-scale genetic structure and how it varies between generations depends on the spatial scale of gene dispersal and other fundamental aspects of species' biology, such as the mating system. Such knowledge is crucial for the design of genetic conservation strategies. This is particularly relevant for species that are increasingly fragmented such as Boswellia papyrifera. This species occurs in dry tropical forests from Ethiopia, Eritrea and Sudan and is an important source of frankincense, a highly valued aromatic resin obtained from the bark of the tree. This study assessed the genetic diversity and fine-scale spatial genetic structure (FSGS) of two cohorts (adults and seedlings) from two populations (Guba-Arenja and Kurmuk) in Western Ethiopia and inferred intra-population gene dispersal in the species, using microsatellite markers. The expected heterozygosity (HE) was 0.664–0.724. The spatial analyses based on kinship coefficient (Fij) revealed a significant positive genetic correlation up to a distance of 130 m. Spatial genetic structure was relatively weak (Sp = 0.002–0.014) indicating that gene dispersal is extensive within the populations. Based on the FSGS patterns found, we estimate indirectly gene dispersal distances of 103 and 124 m for the two populations studied. The high heterozygosity, the low fixation index and the low Sp values found in this study are consistent with outcrossing as the (predominant) mating system in B. papyrifera. We suggest that seed collection for ex situ conservation and reforestation programmes of B. papyrifera should use trees separated by distances of at least 100 m but preferably 150 m to limit genetic relatedness among seeds from different trees.

Data from: Fine-scale environmental specialization of reef- building corals might be limiting reef recovery in the Florida Keys

Despite decades of monitoring global reef decline, we are still largely unable to explain patterns of reef deterioration at local scales, which precludes the development of effective management strategies. Offshore reefs of the Florida Keys, USA, experience milder temperatures and lower nutrient loads in comparison to inshore reefs yet remain considerably more degraded than nearshore patch reefs. A year-long reciprocal transplant experiment of the mustard hill coral (Porites astreoides) involving four source and eight transplant locations reveals that corals adapt and/or acclimatize to their local habitat on a <10-km scale. Surprisingly, transplantation to putatively similar environmental types (e.g., offshore corals moved to a novel offshore site, or along-shore transplantation) resulted in greater reductions in fitness proxies, such as coral growth, than cross-channel transplantation between inshore and offshore reefs. The only abiotic factor showing significantly greater differences between along-shore sites was daily temperature range extremes (rather than the absolute high or low temperatures reached), providing a possible explanation for this pattern. Offshore-origin corals exhibited significant growth reductions at sites with greater daily temperature ranges, which explained up to 39% of the variation in their mass gain. In contrast, daily temperature range explained at most 9% of growth variation in inshore-origin corals, suggesting that inshore corals are more tolerant of high-frequency temperature fluctuations. Finally, corals incur trade-offs when specializing to their native reef. Across reef locations the coefficient of selection against coral transplants was 0.07 ± 0.02 (mean ± SE). This selection against immigrants could hinder the ability of corals to recolonize devastated reefs, whether through assisted migration efforts or natural recruitment events, providing a unifying explanation for observed patterns of coral decline in this reef system.

Data from: Applications of random forest feature selection for fine-scale genetic population assignment

Genetic population assignment used to inform wildlife management and conservation efforts requires panels of highly informative genetic markers and sensitive assignment tests. We explored the utility of machine-learning algorithms (random forest, regularized random forest, and guided regularized random forest) compared with FST ranking for selection of single nucleotide polymorphisms (SNP) for fine-scale population assignment. We applied these methods to an unpublished SNP dataset for Atlantic salmon (Salmo salar) and a published SNP data set for Alaskan Chinook salmon (Oncorhynchus tshawytscha). In each species, we identified the minimum panel size required to obtain a self-assignment accuracy of at least 90% using each method to create panels of 50-700 markers Panels of SNPs identified using random forest-based methods performed up to 7.8 and 11.2 percentage points better than FST-selected panels of similar size for the Atlantic salmon and Chinook salmon data, respectively. Self-assignment accuracy ≥90% was obtained with panels of 670 and 384 SNPs for each dataset, respectively, a level of accuracy never reached for these species using FST-selected panels. Our results demonstrate a role for machine-learning approaches in marker selection across large genomic datasets to improve assignment for management and conservation of exploited populations.

Data from: Fine-scale refuges can buffer demographic and genetic processes against short-term climatic variation and disturbance: a 22 year case study of an arboreal marsupial

Ecological disturbance and climate are key drivers of temporal dynamics in the demography and genetic diversity of natural populations. Microscale refuges are known to buffer species' persistence against environmental change, but the effects of such refuges on demographic and genetic patterns in response to short-term environmental variation are poorly understood. We quantified demographic and genetic responses of mountain brushtail possums (Trichosurus cunninghami) to rainfall variability (1992–2013) and to a major wildfire. We hypothesized that there would be underlying differences in demographic and genetic processes between an unburnt mesic refuge and a topographically exposed zone that was burnt in 2009. Fire caused a 2-year decrease in survival in the burnt zone, but the population grew after the fire due to immigration, leading to increased expected heterozygosity. We documented a fire-related behavioural shift, where the rate of movement by individuals in the unburnt refuge to the burnt zone decreased after fire. Irrespective of the fire, there were long-term differences in demographic and genetic parameters between the mesic/unburnt refuge and the nonmesic/burnt zone. Survival was high and unaffected by rainfall in the refuge, but lower and rainfall-dependent in the nonmesic zone. Net movement of individuals was directional, from the mesic refuge to the nonmesic zone, suggesting fine-scale source–sink dynamics. There were higher expected heterozygosity (HE) and temporal genetic stability in the refuge, but lower HE and marked temporal genetic structure in the exposed habitat, consistent with reduced generational overlap caused by elevated mortality and immigration. Thus, fine-scale refuges can mediate the short-term demographic and genetic effects of climate and ecological disturbance.

Data from: Whole-genome patterns of linkage disequilibrium across flycatcher populations clarify the causes and consequences of fine-scale recombination rate variation in birds

Recombination rate is heterogeneous across the genome of various species, and so are genetic diversity and differentiation as a consequence of linked selection. However, we still lack a clear picture of the underlying mechanisms for regulating recombination. Here we estimated fine-scale population recombination rate based on the patterns of linkage disequilibrium (LD) across the genomes of multiple populations of two closely related flycatcher species (Ficedula albicollis and F. hypoleuca). This revealed an overall conservation of the recombination landscape between these species at the scale of 200-kb, but we also identified differences in the local rate of recombination despite their recent divergence (<1 million years). Genetic diversity and differentiation were associated with recombination rate in a lineage-specific manner, indicating differences in the extent of linked selection between species. We detected 400-3,085 recombination hotspots per population. Location of hotspots was conserved between species, but the intensity of hotspot activity varied between species. Recombination hotspots were primarily associated with CpG islands (CGIs), regardless of whether CGIs were at promoter regions or away from genes. Recombination hotspots were also associated with specific transposable elements (TEs), but this association appears indirect due to shared preferences of the transposition machinery and the recombination machinery for accessible open chromatin regions. Our results suggest that CGIs are a major determinant of the localization of recombination hotspots, and we propose that both the distribution of TEs and fine-scale variation in recombination rate may be associated with the evolution of the epigenetic landscape.

opencc-zeroJul 2019View details →

Data from: Genetic rescue by distant trees mitigates qualitative pollen limitation imposed by fine-scale spatial genetic structure

Restricted seed dispersal frequently leads to fine-scale spatial genetic structure (i.e., FSGS) within plant populations. Depending on its spatial extent and the mobility of pollinators, this inflated kinship at the immediate neighbourhood can critically impoverish pollen quality. Despite the common occurrence of positive FSGS within plant populations, our knowledge regarding the role of long-distance pollination preventing reproductive failure is still limited. Using microsatellite markers, we examined the existence of positive FSGS in two low-density populations of the tree Pyrus bourgaeana. We also designed controlled crosses among trees differing in their kinship to investigate the effects of increased local kinship on plant reproduction. We used six pollination treatments and fully monitored fruit production, fruit and seed weight, proportion of mature seeds per fruit, and seed germination. Our results revealed positive FSGS in both study populations and lower fruit initiation in flowers pollinated with pollen from highly-genetically related individuals within the neighbourhood, with this trend intensifying as the fruit development progressed. Besides, open-pollinated flowers exhibited lower performance of compared to those pollinated by distant pollen donors, suggesting intense qualitative pollen limitation in natural populations. We found positive fine-scale spatial genetic structure is translated into impoverished pollen quality from nearby pollen donors which negatively impacts the reproductive success of trees in low-density populations. Under this scenario of intrapopulation genetic rescue by distant pollen donors, the relevance of highly-mobile pollinators for connecting spatially and genetically distant patches of trees may be crucial to safeguarding population recruitment.

opencc-zeroJan 2020View details →

Resolving fine-scale population structure and fishery exploitation using sequenced microsatellites in a northern fish

<p>The resiliency of populations and species to environmental change is dependent on the maintenance of genetic diversity, and as such quantifying diversity is central to combatting ongoing wide spread reductions in biodiversity. With the advent of next-generation sequencing, several methods now exist for resolving fine-scale population structure, but the comparative performance of these methods for genetic assignment has rarely been tested. Here we evaluate the performance of sequenced microsatellites and a single nucleotide polymorphism (SNP) array to resolve fine-scale population structure in a critically important salmonid in northeastern Canada, Arctic charr (<i>Salvelinus alpinus</i>). We also assess the utility of sequenced microsatellites for fisheries applications by quantifying the spatial scales of movement and exploitation through genetic assignment of fishery samples to rivers of origin and comparing these results with a 29-year tagging dataset. Self-assignment and simulation-based analyses of 111 genome-wide microsatellite loci and 500 informative SNPs from 28 populations of Arctic charr in northeastern Canada identified largely river-specific genetic structure. Despite large differences (~4X) in the number of loci surveyed between panels, mean self-assignment accuracy was similar with the SNP panel and with the microsatellite loci (>90%). Subsequent analysis of 996 fishery-collected samples using the microsatellite panel revealed that larger rivers contribute greater numbers of individuals to the fishery, and that coastal fisheries largely exploit individuals originating from nearby rivers, corroborating results from traditional tagging experiments. Our results demonstrate the efficacy of sequence-based microsatellite genotyping to advance understanding of fine-scale population structure and harvest composition in northern and understudied species.</p>

Data from: Contrasting patterns of clonality and fine-scale genetic structure in two rare sedges with differing geographic distributions

For plants with mixed reproductive capabilities, asexual reproduction is more frequent in rare species and is considered a strategy for persistence when sexual recruitment is limited. We investigate whether asexual reproduction contributes to the persistence of two co-occurring, rare sedges that both experience irregular seed set and if their differing geographic distributions have a role in the relative contribution of clonality. Genotypic richness was high (R=0.889±0.02) across the clustered populations of Lepidosperma sp. Mt Caudan and, where detected, clonal patches were small, both in ramet numbers (less than or equal to3 ramets/genet) and physical size (1.3±0.1 m). In contrast, genotypic richness was lower in the isolated L. sp. Parker Range populations, albeit more variable (R=0.437±0.13), with genets as large as 17 ramets and up to 5.8 m in size. Aggregated clonal growth generated significant fine-scale genetic structure in both species but to a greater spatial extent and with additional genet-level structure in L. sp. Parker Range that is likely due to restricted seed dispersal. Despite both species being rare, asexual reproduction clearly has a more important role in the persistence of L. sp. Parker Range than L. sp. Mt Caudan. This is consistent with our prediction that limitations to sexual reproduction, via geographic isolation to effective gene exchange, can lead to greater contributions of asexual reproduction. These results demonstrate the role of population isolation in affecting the balance of alternate reproductive modes and the contextual nature of asexual reproduction in rare species.

opencc-zeroDec 2011View details →

Data from: Fine-scale spatiotemporal patterns of genetic variation reflect budding dispersal coupled with strong natal philopatry in a cooperatively breeding mammal

The relatedness structure of animal populations is thought to be a critically important factor underlying the evolution of mating systems and social behaviours. While previous work has shown that population structure is shaped by many biological processes, few studies have investigated how these factors vary over time. Consequently, we explored the fine-scale spatiotemporal genetic structure of an intensively studied population of cooperatively breeding banded mongooses (Mungos mungo) over a ten-year period. Overall population structure was strong (average Fst = 0.129) but groups with spatially overlapping territories were not more genetically similar to one another than non-contiguous groups. Instead, genetic differentiation was associated with historical group-fission (budding) events, with new groups diverging from their parent groups over time. Within groups, relatedness was high within but not between the sexes, although the latter increased over time since group formation due to group founders being replaced by philopatric young. This trend was not mirrored by a decrease in average offspring heterozygosity over time, suggesting that close inbreeding may often be avoided, even when immigration into established groups is virtually absent and opportunities for extra-group matings are rare. Fine-scale spatiotemporal population structure could have important implications in social species, where relatedness between interacting individuals is a vital component in the evolution of patterns of inbreeding avoidance, reproductive skew and kin-selected helping and harming.

Data from: Population genomic footprints of fine-scale differentiation between habitats in Mediterranean blue tits

Linking population genetic variation to the spatial heterogeneity of the environment is of fundamental interest to evolutionary biology and ecology, in particular when phenotypic differences between populations are observed at biologically small spatial scales. Here, we applied restriction-site associated DNA sequencing (RAD-Seq) to test whether phenotypically differentiated populations of wild blue tits (Cyanistes caeruleus) breeding in a highly heterogeneous environment exhibit genetic structure related to habitat type. Using 12106 SNPs in 197 individuals from deciduous and evergreen oak woodlands, we applied complementary population genomic analyses, which revealed that genetic variation is influenced by both geographical distance and habitat type. A fine-scale genetic differentiation supported by genome- and transcriptome-wide analyses was found within Corsica, between two adjacent habitats where blue tits exhibit marked differences in breeding time while nesting less than 6 km apart. Using redundancy analysis (RDA), we show that genomic variation remains associated with habitat type when controlling for spatial and temporal effects. Finally, our results suggest that the observed patterns of genomic differentiation were not driven by a small proportion of highly differentiated loci, but rather emerged through a process such as habitat choice, which reduces gene flow between habitats across the entire genome. The pattern of genomic isolation-by-environment closely matches differentiation observed at the phenotypic level, thereby offering significant potential for future inference of phenotype-genotype associations in a heterogeneous environment.

opencc-zeroDec 2013View details →

Data from: Fine-scale spatial genetic dynamics over the life-cycle of the tropical tree Prunus africana

Studying fine-scale spatial genetic patterns across life stages is a powerful approach to identify ecological processes acting within tree populations. We investigated spatial genetic dynamics across five life stages in the insect-pollinated and vertebrate-dispersed tropical tree Prunus africana in Kakamega Forest, Kenya. Using six highly polymorphic microsatellite loci, we assessed genetic diversity and spatial genetic structure (SGS) from seed rain and seedlings, and different sapling stages to adult trees. We found significant SGS in all stages, potentially caused by limited seed dispersal and high recruitment rates in areas with high light availability. SGS decreased from seed and early seedling stages to older juvenile stages. Interestingly, SGS was stronger in adults than in late juveniles. The initial decrease in SGS was probably driven by both random and non-random thinning of offspring clusters during recruitment. Intergenerational variation in SGS could have been driven by variation in gene flow processes, overlapping generations in the adult stage or local selection. Our study shows that complex sequential processes during recruitment contribute to SGS of tree populations.

Data from: Life-history characteristics and landscape attributes as drivers of genetic variation, gene flow and fine-scale population structure in Northern Dolly Varden (Salvelinus malma malma) in Canada

The Northern Dolly Varden (Salvelinus malma malma) displays variable life-history types and occupies freshwater habitats with varying levels of connectivity. Here, we assayed microsatellite DNA variation in Northern Dolly Varden from the western Canadian Arctic to resolve landscape and life history variables driving variation in genetic diversity and population structure. Overall, genetic variation was highest in anadromous populations and lowest in those isolated above waterfalls with stream-resident forms intermediate between the two. Anadromous and isolated populations were genetically divergent from each other while no genetic differentiation was detectable between sympatric anadromous and stream-resident forms. Population structure was stable over 25 years, hierarchically organized and conformed to an isolation-by-distance pattern, but stream-isolated forms often deviated from these patterns. Gene flow occurred primarily among Yukon North Slope populations and between sympatric anadromous and resident forms. These results were sex-dependent to some extent, but were influenced more by reproductive status and life history. Our study provides novel insights into the life history, population demographic and habitat variables that shape the distribution of genetic variation and population structure in Arctic fluvial habitats while providing a spatial context for management and conservation.

Data from: RAD sequencing resolves fine-scale population structure in a benthic invertebrate: implications for understanding phenotypic plasticity

The field of molecular ecology is transitioning from the use of small panels of classical genetic markers such as microsatellites to much larger panels of single nucleotide polymorphisms (SNPs) generated by approaches like RAD sequencing. However, few empirical studies have directly compared the ability of these methods to resolve population structure. This could have implications for understanding phenotypic plasticity, as many previous studies of natural populations may have lacked the power to detect genetic differences, especially over micro-geographic scales. We therefore compared the ability of microsatellites and RAD sequencing to resolve fine-scale population structure in a commercially important benthic invertebrate by genotyping great scallops (Pecten maximus) from nine populations around Northern Ireland at 13 microsatellites and 10 539 SNPs. The shells were then subjected to morphometric and colour analysis in order to compare patterns of phenotypic and genetic variation. We found that RAD sequencing was superior at resolving population structure, yielding higher Fst values and support for two distinct genetic clusters, whereas only one cluster could be detected in a Bayesian analysis of the microsatellite dataset. Furthermore, appreciable phenotypic variation was observed in size-independent shell shape and coloration, including among localities that could not be distinguished from one another genetically, providing support for the notion that these traits are phenotypically plastic. Taken together, our results suggest that RAD sequencing is a powerful approach for studying population structure and phenotypic plasticity in natural populations.