Species-genetic Diversity Correlations Research Articles

Neutral processes and taxonomic scale drive beta species-genetic diversity correlations in a submesophotic tropical reef fish.

If similar evolutionary forces maintain intra- and interspecific diversity, patterns of diversity at both levels of biological organization can be expected to covary across space. Although this prediction of a positive species-genetic diversity correlation (SGDC) has been tested for several taxa in natural landscapes, no study has yet evaluated the influence of the community delineation on these SGDCs. In this study, we focused on tropical fishes of the Indo-Pacific Ocean, using range-wide single nucleotide polymorphism data for a deep-sea fish (Etelis coruscans) and species presence data of 4878 Teleostei species. We investigated whether a diversity continuum occurred, for different community delineations (subfamily, family, order and class) and spatial extents, and which processes explained these diversity patterns. We found no association between genetic diversity and species richness (α-SGDC), regardless of the community and spatial extent. In contrast, we evidenced a positive relationship between genetic and species dissimilarities (β-SGDC) when the community was defined at the subfamily or family level of the species of interest, and when the Western Indian Ocean was excluded. This relationship was related to the imprint of dispersal processes across levels of biological organization in Lutjanidae. However, this positive β-SGDC was lost when considering higher taxonomic communities and at the scale of the entire Indo-Pacific, suggesting different responses of populations and communities to evolutionary processes at these scales. This study provides evidence that the taxonomic scale at which communities are defined and the spatial extent are pivotal to better understand the processes shaping diversity across levels of biological organization.

Community-wide correlations between species richness, abundance and population genomic diversity in a freshwater biodiversity hotspot.

Understanding patterns of diversity across macro (e.g. species-level) and micro (e.g. molecular-level) scales can shed light on community function and stability by elucidating the abiotic and biotic drivers of diversity within ecological communities. We examined the relationships among taxonomic and genetic metrics of diversity in freshwater mussels (Bivalvia: Unionidae), an ecologically important and species-rich group in the southeastern United States. Using quantitative community surveys and reduced-representation genome sequencing across 22 sites in seven rivers and two river basins, we surveyed 68 mussel species and sequenced 23 of these species to characterize intrapopulation genetic variation. We tested for the presence of species diversity-abundance correlations (i.e. the more-individuals hypothesis, MIH), species-genetic diversity correlations (SGDCs) and abundance-genetic diversity correlations (AGDCs) across all sites to evaluate relationships between different metrics of diversity. Sites with greater cumulative multispecies density (a standardized metric of abundance) had a greater number of species, consistent with the MIH hypothesis. Intrapopulation genetic diversity was strongly associated with the density of most species, indicating the presence of AGDCs. However, there was no consistent evidence for SGDCs. Although sites with greater overall densities of mussels had greater species richness, sites with higher genetic diversity did not always exhibit positive correlations with species richness, suggesting that there are spatial and evolutionary scales at which the processes influencing community-level diversity and intraspecific diversity differ. Our work reveals the importance of local abundance as indicator (and possibly a driver) of intrapopulation genetic diversity.

Spatial genetic differentiation correlates with species assemblage turnover across tropical reef fish lineages

AbstractAimEvaluating the similarity of diversity patterns across micro‐ to macroevolutionary scales in natural communities, such as species–genetic diversity correlations (SGDCs), may inform on processes shaping community assembly. However, whether SGDCs not only hold across communities but also across lineages has never been explored so far. Here we investigated SGDCs across co‐distributed taxa for different spatial components (α, β, γ), and formally tested the influence of dispersal traits on β‐SGDCs.LocationWestern Indian Ocean.Time period2016–2017.Major taxa studiedTropical reef fish species with contrasting dispersal traits.MethodsUsing double‐digest restriction‐site associated DNA sequencing (ddRADseq) Single Nucleotide Polymorphism data for 20 tropical reef fishes and distribution data of 2,446 species belonging to 12 families, we analysed the correlations between within‐species genetic diversity and within‐family species diversity (i.e., lineage diversity) for the three spatial components (α, β, γ‐SGDCs). We then related the strength of β‐SGDCs per species to proxies of larval dispersal abilities.ResultsWe detected positive and significant lineage‐based SGDC only for the β component, that is, the families showing the greatest level of species turnover among sites contain the species with the greatest levels of genetic differentiation. We showed that the Monsoon Drift mainly explained the β‐diversity patterns at both intraspecific and interspecific levels. Higher β‐SGDCs were found for species with short pelagic larval duration and weak larval swimming capacity.Main conclusionsOur study reveals a strong correlation between genetic and species β‐diversity, a result explained by the presence of a ‘soft’ barrier and mediated by larval dispersal processes. This suggests that vicariance and dispersal limitation are major processes shaping β‐diversity patterns from microevolutionary to macroevolutionary scales in tropical reef fishes.

Species–genetic diversity correlations through the lens of spatial autocorrelation: insights from high Andean wetlands

Species–genetic diversity correlations through the lens of spatial autocorrelation: insights from high Andean wetlands

Species–genetic diversity correlations depend on ecological similarity between multiple moorland plant species

Species diversity (SD) and genetic diversity (GD) are fundamental aspects of biodiversity and are dependent because they are sympatrically affected by biotic and abiotic factors. Species–genetic diversity correlations (SGDCs) range from positive to negative among multiple focal species even across same communities. As determinant mechanisms of SGDCs, previous studies identified neutral processes related with habitat size and connectivity, environmental filtering and interspecific interactions. Theoretically, similar responses of SD and GD to these mechanisms can lead to positive SGDCs. The quantitative evaluation and comparison of similarity in each mechanism have not been performed. Here, we tested whether α‐ and β‐SGDCs could be determined by similarity in ecological characteristics (ecological similarity), such as environmental responses (responses of GD to moorland area, altitude, pH, electric conductivity and spatial autocorrelation based on regression analysis), dispersal ability (seed dispersal and pollination mode) and functional traits associated with competitions (leaf height, leaf size and specific leaf area (SLA)). We investigated SD and GD of 11 species based on single nucleotide polymorphisms across 20 moorland plant communities in northern Japan, and evaluated correlations between SGDCs and principal components of the ecological characteristics across the focal species. α‐SGDCs varied from positive to negative, which was explained by ecological similarity in the response of GD to pH, seed dispersal and pollination mode, leaf height and SLA. In contrast, β‐SGDCs were almost consistently positive, which resulted from spatial autocorrelation and could not be explained by ecological similarity. We emphasized that not only environmental filtering and neutral process via dispersal limitation but also competitions can contribute to SGDCs. The incorporation of trait‐based approaches is effective for understanding spatial patterns of combinations of SD and GD. Evaluating SGDCs and spectrums of functional traits highly related to community assembly may lead to spatial predictions of GD in whole members of communities.

Community genomics: a community-wide perspective on within-species genetic diversity.

Community genomics: a community-wide perspective on within-species genetic diversity.

Species–genetic diversity correlation in phyllostomid bats of the Bodoquena plateau, Brazil

Recent theories suggest that processes shaping species diversity are the same shaping genetic diversity, leading to a correlation between the two levels of diversity. Using Neotropical bat assemblages, and considering the genetic diversity of two co-distributed Chiroptera species with distinct life-history traits, Artibeus planirostris and Carollia perspicillata, we evaluated the correlation between metrics of taxonomic (species richness, evenness, and community divergence) and genetic diversity (number of haplotypes, haplotype diversity, allelic richness, expected heterozygosity and genetic divergence) in these two species. Landscape variables potentially affecting those correlations (distance to the nearest conservation unit, forest area, forest border length and number of forest fragments) were also analysed. For A. planirostris, we found a negative correlation between evenness and expected heterozygosity and also between mean presence-absence assemblage divergence and mean genetic divergence based on microsatellites. Our results indicate that the genetic diversity in A. planirostris is not explained by the landscape variables considered. For C. perspicillata, we found a positive correlation between species richness and haplotype richness and between evenness and expected heterozygosity. Genetic differentiation based on microsatellites in C. perspicillata was positively related to geographic distance and landscape differentiation. Allelic richness and expected heterozygosity in C. perspicillata were negatively related to distance from the conservation unit and forest area, but significance changed according to the spatial scale. We conclude that species-genetic diversity correlations may vary according to the species under study. Thus, A. planirostris appears to be ecologically different to other species in assemblages, while C. perspicillata seems to be ecologically similar.

Species and genetic diversity are not congruent in fragmented dry grasslands.

Biological diversity comprises both species diversity (SD) and genetic diversity (GD), and it has been postulated that both levels of diversity depend on similar mechanisms. Species‐genetic diversity correlations (SGDC) are therefore supposed to be generally positive. However, in contrast to theory, empirical data are contradictory. Furthermore, there is a pronounced lack of multispecies studies including also the ecological factors potentially driving species and genetic diversity. We analyzed the relationship between the species diversity of dry grasslands and the genetic diversity of several dry grassland plant species, therefore, in the context of habitat fragmentation and habitat conditions. Our study revealed a lack of correlation between species and genetic diversity. We demonstrated previously that SD mainly depends on habitat conditions (vegetation height and cover of litter), whereas GD is significantly affected by habitat fragmentation (distance to the nearest dry grassland in 1830 and connectivity in 2013). This seems to be the main reason why SD and GD are not congruent in fragmented grasslands. Our results support, hence, the observation that positive SGDCs can mainly be found in natural, island‐like study systems in equilibrium and at similar levels of heterogeneity. In fragmented dry grassland ecosystems, which differ in heterogeneity, this state of equilibrium may not have been reached mitigating the positive relationship between SD and GD. From our study, it can be concluded that in fragmented dry grasslands, the protection of SD does not necessarily ensure the conservation of GD.

Partitioning genetic and species diversity refines our understanding of species-genetic diversity relationships.

Disentangling the origin of species–genetic diversity correlations (SGDCs) is a challenging task that provides insight into the way that neutral and adaptive processes influence diversity at multiple levels. Genetic and species diversity are comprised by components that respond differently to the same ecological processes. Thus, it can be useful to partition species and genetic diversity into their different components to infer the mechanisms behind SGDCs. In this study, we applied such an approach using a high‐elevation Andean wetland system, where previous evidence identified neutral processes as major determinants of the strong and positive covariation between plant species richness and AFLP genetic diversity of the common sedge Carex gayana. To tease apart putative neutral and non‐neutral genetic variation of C. gayana, we identified loci putatively under selection from a dataset of 1,709 SNPs produced using restriction site‐associated DNA sequencing (RAD‐seq). Significant and positive relationships between local estimates of genetic and species diversities (α‐SGDCs) were only found with the putatively neutral loci datasets and with species richness, confirming that neutral processes were primarily driving the correlations and that the involved processes differentially influenced local species diversity components (i.e., richness and evenness). In contrast, SGDCs based on genetic and community dissimilarities (β‐SGDCs) were only significant with the putative non‐neutral datasets. This suggests that selective processes influencing C. gayana genetic diversity were involved in the detected correlations. Together, our results demonstrate that analyzing distinct components of genetic and species diversity simultaneously is useful to determine the mechanisms behind species–genetic diversity relationships.

Deciphering the drivers of negative species-genetic diversity correlation in Alpine amphibians.

The evolutionary and ecological importance of neutral and adaptive genetic diversity is widely recognized. Nevertheless, genetic diversity is rarely assessed for conservation planning, which often implicitly assumes a positive correlation between species and genetic diversity. Multiple drivers can cause the co-variation between the genetic diversity of one species and the richness of the whole communities, and explicit tests are needed to identify the processes that can determine species-genetic diversity correlations (SGDCs). Here, we tested whether intrapopulation genetic diversity (at neutral loci) and species richness co-vary in the amphibian communities of a southern Alpine region (Trentino, Italy), using the common frog (Rana temporaria) as focal species for the study of genetic diversity. We also analysed ecological similarity, niche overlap and interspecific interactions between the species, to unravel the processes determining SGDC. The neutral genetic diversity of common frogs was negatively related to species richness. The negative SGDC was probably due to an opposite influence of environmental gradients on the two levels of biodiversity, since the focal species and the other amphibians differ in ecological preferences, particularly in terms of thermal optimum. Conversely, we did not find evidence for a role of interspecific interactions in the negative SGDC. Our findings stress that species richness cannot be used as a universal proxy for genetic diversity, and only combining SGDC with analyses on the determinants of biodiversity can allow to identify the processes determining the relationships between genetic and species diversity.

Riverine fish diversity varies according to geographical isolation and land use modification.

Understanding the environmental factors driving species‐genetic diversity correlations (SGDCs) is critical for designing appropriate conservation and management strategies to protect biodiversity. Yet, few studies have explored the impact of changing land use patterns on SGDCs specifically in aquatic communities. This study examined patterns of genetic diversity in roach (Rutilus rutilus L.) together with fish species composition across 19 locations in a large river catchment, spanning a gradient in land use. Our findings show significant correlations between some, but not all, species and genetic diversity end points. For example, genetic and species differentiation showed a weak but significant linear relationship across the Thames catchment, but additional diversity measures such as allelic richness and fish population abundance did not. Further examination of patterns in species and genetic diversity indicated that land use intensification has a modest effect on fish diversity compared to the combined influence of geographical isolation and land use intensification. These results indicate that environmental changes in riparian habitats have the potential to amplify shifts in the composition of stream fish communities in poorly connected river stretches. Conservation and management strategies for fish populations should, therefore, focus on enhancing connectivity between river stretches and limit conversion of nearby land to arable or urban use to maintain current levels of biodiversity.

The contribution of species–genetic diversity correlations to the understanding of community assembly rules

Community genetics aims at understanding how within‐species variation, species diversity and environmental factors interact to shape community assembly. An approach that emerged a few years ago has been to quantify the correlation between the neutral genetic diversity of a focal species and species diversity of the surrounding community (species–genetic diversity correlations, or SGDCs). We here review this approach and discuss its interpretative framework in a community ecology context. First, we show that the case for mostly positive SGDCs is probably overstated due to publication bias – only 11% are significantly positive, a fraction comparable to the significantly negative ones. This suggests that variation in area and connectivity among habitat patches, theoretically leading to positive SGDCs, is not the only factor affecting SGDCs. Second, building upon previous contributions, we propose a general framework to identify the multiple factors underpinning SGDCs, and argue that it will help deepen our understanding of community assembly, especially with regard to the ecological factors playing at metacommunity scale. Our framework distinguishes between site and community factors which can affect SGDCs either positively or negatively, depending on whether the focal species and the rest of the community are similar or dissimilar, in terms of realized niches and dispersal abilities. Empirical studies should thus go beyond simply computing SGDCs, and we provide statistical methods (e.g. structural equation modelling) to decompose SGDCs into the multiple contributions of site and community factors. As an example, we use a published dataset (freshwater snail metacommunity), and show how the role of focal population size on SGDCs had hitherto not been detected. We further discuss how considering several focal species and various delimitations of the community may help one to identify clusters of ecologically similar species. We eventually highlight the benefit that SGDC studies would get from integrating β‐diversities.

Genetic variation of loci potentially under selection confounds species-genetic diversity correlations in a fragmented habitat.

Positive species-genetic diversity correlations (SGDCs) are often thought to result from the parallel influence of neutral processes on genetic and species diversity. Yet, confounding effects of non-neutral mechanisms have not been explored. Here, we investigate the impact of non-neutral genetic diversity on SGDCs in high Andean wetlands. We compare correlations between plant species diversity and genetic diversity (GD) calculated with and without loci potentially under selection (outlier loci). The study system includes 2188 specimens from five species (three common aquatic macroinvertebrate and two dominant plant species) that were genotyped for 396 amplified fragment length polymorphism loci. We also appraise the importance of neutral processes on SGDCs by investigating the influence of habitat fragmentation features. Significant positive SGDCs were detected for all five species (mean SGDC=0.52±0.05). While only a few outlier loci were detected in each species, they resulted in significant decreases in GD and in SGDCs. This supports the hypothesis that neutral processes drive species-genetic diversity relationships in high Andean wetlands. Unexpectedly, the effects on genetic diversity GD of the habitat fragmentation characteristics in this study increased with the presence of outlier loci in two species. Overall, our results reveal pitfalls in using habitat features to infer processes driving SGDCs and show that a few loci potentially under selection are enough to cause a significant downward bias in SGDC. Investigating confounding effects of outlier loci thus represents a useful approach to evidence the contribution of neutral processes on species-genetic diversity relationships.

Catchment‐scale modeling of riverine species diversity using hydrological simulation: application to tests of species‐genetic diversity correlation

AbstractSpecies distribution models were developed to predict the spatial patterns of the species diversity and the genetic diversity of stream organisms using a distributed hydrological model. We derived annual metrics of water depth and flow velocity in rivers using a hydrological model covering an entire catchment in northeastern Japan. We acquired geospatial data throughout the catchment and the presence records of six taxa within the part of the catchment. Subsequently we derived habitat suitability indices (HSIs) for these taxa using a frequency analysis or the maximum‐entropy approach (MaxEnt) to predict three metrics of species diversity. The Shannon‐Wiener's diversity index based on MaxEnt (Shannon_MaxE) most effectively represented empirical taxon richness. Subsequently, by comparing Shannon_MaxE and empirical genetic diversity for the four species of stream insects, we evaluated species‐genetic diversity correlations (SGDCs). Of the four species, only one caddisfly species (Hydropsyche orientalis) displayed significant positive SGDCs. The result reflects the broad habitat range of this taxon throughout the catchment and its poor dispersal ability, whereas the other three species lacked SGDCs and displayed either a strong dispersal potential (Stenopsyche marmorata and Ephemera japonica) or a narrower habitat range within upstream domains (Hydropsyche albicephala). Finally, we estimated the spatial distribution of genetic diversity of H. orientalis populations based on the calculated Shannon_MaxE using the positive SGDC. This framework is promising for projecting future biodiversity in the context of anthropogenic perturbations such as climate change.

Limited erosion of genetic and species diversity from small forest patches: Sacred forest groves in an Afrotropical biodiversity hotspot have high conservation value for butterflies

Sacred forest groves are often located in some of the world's hottest hotspots of biodiversity, and consequently have high potential conservation value. Recent efforts to quantify their value have focused nearly exclusively on a single component of diversity, species diversity within communities, which may or may not be an effective proxy for a second fundamental component of diversity, genetic diversity within populations. We studied fruit-feeding butterfly communities to simultaneously assess to what extent five small sacred groves have retained the level of species and genetic diversity found in two much larger forest reserves. We additionally evaluate whether measures correlate across habitat fragments to investigate how closely these two components of diversity mirror each other. We quantified the diversity and composition of the fruit-feeding butterfly communities at each site and also the haplotype diversity within three specific species that differ with respect to their sensitivity to habitat fragmentation. Of the multiple measures of species and genetic diversity computed, only rarefied species richness was correlated with forest fragment size and even in this case the relationship was weak. Importantly, the limited decline in species richness documented in the sacred groves was not due to species replacements, whereby common, broadly distributed, generalists supplanted more vulnerable species in these communities. Although similar processes are known to drive declines in both species and gene diversity, we found only limited evidence of positive species-genetic diversity correlations (SGDCs), and only in the species most sensitive to fragmentation. Thus, a conservation strategy that emphasizes species complementarity or richness may be ineffective at capturing other critical levels of biodiversity. Overall, our findings demonstrate that even very small forest patches can have a conservation value that rivals that of much larger forest reserves. The implementation of official national and international initiatives that preserve and strengthen existing community-based conservation practices is critically needed to ensure that indigenous conservation areas persist into the future.

Species–genetic diversity correlations in habitat fragmentation can be biased by small sample sizes

Predicted parallel impacts of habitat fragmentation on genes and species lie at the core of conservation biology, yet tests of this rule are rare. In a recent article in Ecology Letters, Struebig et al. (2011) report that declining genetic diversity accompanies declining species diversity in tropical forest fragments. However, this study estimates diversity in many populations through extrapolation from very small sample sizes. Using the data of this recent work, we show that results estimated from the smallest sample sizes drive the species-genetic diversity correlation (SGDC), owing to a false-positive association between habitat fragmentation and loss of genetic diversity. Small sample sizes are a persistent problem in habitat fragmentation studies, the results of which often do not fit simple theoretical models. It is essential, therefore, that data assessing the proposed SGDC are sufficient in order that conclusions be robust.

Contrasting relationships between species diversity and genetic diversity in natural and disturbed forest tree communities

• This study aimed to reveal species-genetic diversity correlations (SGDCs) and their underlying mechanisms in natural and disturbed forests. • A community survey and molecular analyses were carried out to compare species diversity (SD), the genetic diversity of the dominant tree species Euptelea pleiospermum (GD), the altitudinal patterns of SD and GD, SGDC, genetic differentiation (F(ST) ), community divergence (F(ST) -C), effective population size (N(e) ), and recent migration rate between mountain riparian forests along the Yandu (natural) and Nan (disturbed) rivers. • In natural forests, both SD and GD showed a unimodal altitudinal pattern and GD was positively correlated with SD, whereas a unimodal pattern and positive SGDC were not found in the disturbed forests. SD and F(ST) at the natural sites were higher than those at the disturbed sites. However, there were no significant differences in GD, F(ST) -C, N(e) or recent migration rate between the natural and disturbed sites. • A correlation between the patterns of SD and GD along a geographical gradient (e.g. altitude) is an important driver of positive SGDC. The absence of positive SGDC in the disturbed forests may result from reduced SD but unaffected GD, indicating nonparallel changes in SD and GD. This study furthermore cautions against generalizations about changes in SD and GD following disturbance.

Species Diversity and Genetic Diversity: Parallel Processes and Correlated Patterns

Species diversity and genetic diversity may be correlated as a result of processes acting in parallel at the two levels. However, no theories predict the conditions under which different relationships between species diversity and genetic diversity might arise and therefore when one level of diversity may be predicted using the other. I used simulation models to investigate the parallel influence of locality area, immigration rate, and environmental heterogeneity on species diversity and genetic diversity. The most common pattern was moderate to strong positive species-genetic diversity correlations (SGDCs). Such correlations may be driven by any one of the three locality characteristics examined, but important exceptions and patterns emerged. Genetic diversity and species diversity were more weakly correlated when genetic diversity was measured for rare versus common species. Environmental heterogeneity not only imposes spatially varying selection on populations and communities but also causes changes in species' population sizes and therefore genetic diversity; these interacting processes can create positive, negative, or unimodal relationships of genetic diversity with species diversity. When species are considered as part of multispecies communities, predictions from single-species models of genetic diversity apply in some instances (effects of area and immigration) but often not in others (effects of environmental heterogeneity).

PARALLEL EFFECTS OF LAND-USE HISTORY ON SPECIES DIVERSITY AND GENETIC DIVERSITY OF FOREST HERBS

The two most fundamental levels of biodiversity, species diversity and genetic diversity, are seldom studied simultaneously despite a strikingly similar set of processes that underlie patterns at the two levels. Agricultural land use drastically reduces populations of forest herbs in the north-temperate zone, so that bottlenecks or founder events in forests on abandoned agricultural land (i.e., secondary forests) may have a long-term impact on both species diversity and genetic diversity. Using forest-herb community surveys and molecular-genetic analysis of populations of Trillium grandiflorum, a representative species of forest herb, I investigated the influence of land-use history, landscape context, and environmental conditions on diversity and divergence at the population and community levels. Secondary forests (70–100 years old) had reduced diversity of both genes and species relative to primary forests (i.e., stands never cleared for agriculture). The community in secondary forests had an overrepresentation of the most common species in the landscape, though divergence in species' relative abundances within stands suggested an influence of community drift via local bottlenecks. Secondary-forest populations of T. grandiflorum were more genetically divergent than those in primary forests, again indicating drift in small populations. Land-use history and the size of populations and communities drove correlations between species diversity and genetic diversity (and community divergence × genetic divergence), though the strength of correlations was relatively weak. These results extend the generality of positive species–genetic diversity correlations previously observed for islands, and they demonstrate a long-term legacy of land-use history at multiple levels of biodiversity.