Relationship of genetic diversity and niche centrality: a survey and analysis

Niche modelling and landscape genetics of the yellow-legged hornet (Vespa velutina): An integrative approach for evaluating central-marginal population dynamics in Europe

Genetic diversity is an important biological trait for a successful invasion. During the expansion across a new territory, an invasive species may face unprecedented ecological conditions that will determine its demography and genetic diversity. The first record of the yellow-legged hornet (Vespa velutina) in Europe dates back to 2004 in France, from where it has successfully spread through a large territory in the continent, including Italy, Spain and Portugal. Integrative approaches offer a powerful strategy to detect and understand patterns of genetic variation in central and marginal populations. Here, we have analysed the relationship between genetic diversity parameters inferred from 15 V. velutina nuclear DNA microsatellite loci, and geographical and environmental drivers, such as the distance to the introduction focus, environmental suitability and distance to native and invasive niche centroids. Our results revealed a central-marginal dynamic, where allelic richness decreased towards the edge of the expansion range. The low environmental suitability of the territories invaded by marginal populations could prevent a diverse population from establishing and reducing the genetic diversity in populations at the expansion edge. Moreover, Markov chain Monte Carlo analysis showed both geographical and environmental distances were influencing population genetic differentiation. This study highlights the importance of combining genetic analysis with geographical and environmental drivers to understand genetic trends of invasive species to new environment.

Patterns and effects of gene flow on adaptation across spatial scales: implications for management

Gene flow can have rapid effects on adaptation and is an important evolutionary tool available when undertaking biological conservation and restoration. This tool is underused partly because of the perceived risk of outbreeding depression and loss of mean fitness when different populations are crossed. In this article, we briefly review some theory and empirical findings on how genetic variation is distributed across species ranges, describe known patterns of gene flow in nature with respect to environmental gradients, and highlight the effects of gene flow on adaptation in small or stressed populations in challenging environments (e.g., at species range limits). We then present a case study involving crosses at varying spatial scales among mountain populations of a trigger plant (Stylidium armeria: Stylidiaceae) in the Australian Alps to highlight how some issues around gene flow effects can be evaluated. We found evidence of outbreeding depression in seed production at greater geographic distances. Nevertheless, we found no evidence of maladaptive gene flow effects in likelihood of germination, plant performance (size), and performance variance, suggesting that gene flow at all spatial scales produces offspring with high adaptive potential. This case study demonstrates a path to evaluating how increasing sources of gene flow in managed wild and restored populations could identify some offspring with high fitness that could bolster the ability of populations to adapt to future environmental changes. We suggest further ways in which managers and researchers can act to understand and consider adaptive gene flow in natural and conservation contexts under rapidly changing conditions.

Leaf functional traits and ecological niche of Fagus grandifolia and Oreomunnea mexicana in natural forests and plantings as a proxy of climate change

PREMISE

Functional traits reflect species' responses to environmental variation and the breadth of their ecological niches. Fagus grandifolia and Oreomunnea mexicana have restricted distribution in upper montane cloud forests (1700-2000 m a.s.l.) in Mexico. These species were introduced into plantings at lower elevations (1200-1600 m a.s.l.) that have climates predicted for montane forests in 2050 and 2070. The aim was to relate morphological leaf traits to the ecological niche structure of each species.

METHODS

Leaf functional traits (leaf area, specific leaf area [SLA], thickness, and toughness) were analyzed in forests and plantings. Atmospheric circulation models and representative concentration pathways (RCPs: 2.6, 4.5, 8.5) were used to assess future climate conditions. Trait-niche relationships were analyzed by measuring the Mahalanobis distance (MD) from the forests and the plantings to the ecological niche centroid (ENC).

RESULTS

For both species, leaf area and SLA were higher and toughness lower in plantings at lower elevation relative to those in higher-elevation forests, and thickness was similar. Leaf traits varied with distance from sites to the ENC. Forests and plantings have different environmental locations regarding the ENC, but forests are closer (MD 0.34-0.58) than plantings (MD 0.50-0.70) for both species.

CONCLUSIONS

Elevation as a proxy for expected future climate conditions influenced the functional traits of both species, and trait patterns related to the structure of their ecological niches were consistent. The use of distances to the ENC is a promising approach to explore variability in species' functional traits and phenotypic responses in optimal versus marginal environmental conditions.

Niche-based approach to explore the impacts of environmental disturbances on biodiversity

Globally, species are increasingly at risk from compounding threatening processes, an increasingly prominent driver of which is environmental disturbances. To facilitate effective conservation efforts following such events, methods that evaluate potential impacts across multiple species and provide landscape-scale information are needed to guide targeted responses. Often, the geographic overlap between a disturbance and species' distribution is calculated and then used as a proxy for potential impact. However, such methods do not account for the important influence of environmental heterogeneity throughout species' ranges. To address this shortcoming, we quantified the effects of environmental disturbances on species' environmental niche space. Using the Australian 2019 and 2020 Black Summer fires as a case study, we applied a niche-centric approach to examine the potential impacts of these fires on 387 vertebrate species. We examined the utility of established and novel niche metrics to assess the potential impacts of large-scale disturbance events on species by comparing the potential effects of the fires as determined by our various niche measures to those derived from geographic-based measures of impact. We examined the quality of environmental space affected by the disturbance by quantifying the position in niche space where the disturbance occurred (center or margin), the uniqueness of the environmental space that was burned, and the degree to which the remaining, unburned portion of the niche differed from a species' original prefire niche. There was limited congruence between the proportion of geographic and niche space affected, which showed that geographic-based approaches in isolation may have underestimated the impact of the fires for 56% of modeled species. For each species, when combined, these metrics provided a greater indication of postdisturbance recovery potential than geographic-based measures alone. Accordingly, the integration of niche-based analyses into conservation assessments following large-scale disturbance events will lead to a more nuanced understanding of potential impacts and guide more informed and effective conservation actions.

Niche position and niche breadth effects on population abundances: A case study of New World Warblers (Parulidae)

Species abundance patterns are influenced by a myriad of factors, including habitat availability and ecological niche characteristics. However, the evidence concerning the specific impact factors such as niche position and niche breadth on mean and maximum abundances in vertebrates at a broad geographical scale remains inconclusive. In this study, we investigated the influence of niche position and breadth on the abundance of 47 species of birds belonging to the Parulidae family, commonly known as New World Warblers. We obtained data on abundance and presence records spanning the reproductive distribution of these species and employed the outlying mean index analysis to calculate niche position and niche breadth. We assessed the relationship between abundance metrics and niche descriptors using phylogenetic regressions to account for the non-independence resulting from phylogenetic ancestry. Initially, we developed individual models for each predictor and subsequently formulated a multi-predictor model encompassing niche position, niche breadth, and their interaction. Our findings revealed a negative relationship between niche position and both mean and maximum abundance, while niche breadth exhibited a positive relationship with these niche characteristics. Notably, the results of the multi-predictor models indicated that niche position exerted the most substantial influence on both mean and maximum abundance. Additionally, the interaction between niche position and niche breadth had the most positive and significant contribution to mean population abundance. This study underscores the need for future research in other vertebrates to delve into the mechanisms underlying these patterns. Such endeavors will not only enhance our understanding of ecological dynamics but also equip us with predictive capabilities to anticipate population responses to environmental changes effectively.

Climatic and soil characteristics account for the genetic structure of the invasive cactus moth Cactoblastis cactorum, in its native range in Argentina

Background

Knowledge of the physical and environmental conditions that may limit the migration of invasive species is crucial to assess the potential for expansion outside their native ranges. The cactus moth, Cactoblastis cactorum, is native to South America (Argentina, Paraguay, Uruguay and Brazil) and has been introduced and invaded the Caribbean and southern United States, among other regions. In North America there is an ongoing process of range expansion threatening cacti biodiversity of the genus Opuntia and the commercial profits of domesticated Opuntia ficus-indica.

Methods

To further understand what influences the distribution and genetic structure of this otherwise important threat to native and managed ecosystems, in the present study we combined ecological niche modeling and population genetic analyses to identify potential environmental barriers in the native region of Argentina. Samples were collected on the host with the wider distribution range, O. ficus-indica.

Results

Significant genetic structure was detected using 10 nuclear microsatellites and 24 sampling sites. At least six genetic groups delimited by mountain ranges, salt flats and wetlands were mainly located to the west of the Dry Chaco ecoregion. Niche modeling supports that this region has high environmental suitability where the upper soil temperature and humidity, soil carbon content and precipitation were the main environmental factors that explain the presence of the moth. Environmental filters such as the upper soil layer may be critical for pupal survival and consequently for the establishment of populations in new habitats, whereas the presence of available hosts is a necessary conditions for insect survival, upper soil and climatic characteristics will determine the opportunities for a successful establishment.

Divergent mechanisms of reduced growth performance in Betula ermanii saplings from high-altitude and low-latitude range edges

The reduced growth performance of individuals from range edges is a common phenomenon in various taxa, and considered to be an evolutionary factor that limits the species' range. However, most studies did not distinguish between two mechanisms that can lead to this reduction: genetic load and adaptive selection to harsh conditions. To address this lack of understanding, we investigated the climatic and genetic factors underlying the growth performance of Betula ermanii saplings transplanted from 11 populations including high-altitude edge and low-latitude edge population. We estimated the climatic position of the populations within the overall B. ermanii's distribution, and the genetic composition and diversity using restriction-site associated DNA sequencing, and measured survival, growth rates and individual size of the saplings. The high-altitude edge population (APW) was located below the 95% significance interval for the mean annual temperature range, but did not show any distinctive genetic characteristics. In contrast, the low-latitude edge population (SHK) exhibited a high level of linkage disequilibrium, low genetic diversity, a distinct genetic composition from the other populations, and a high relatedness coefficient. Both APW and SHK saplings displayed lower survival rates, heights and diameters, while SHK saplings also exhibited lower growth rates than the other populations' saplings. The low heights and diameters of APW saplings was likely the result of adaptive selection to harsh conditions, while the low survival and growth rates of SHK saplings was likely the result of genetic load. Our findings shed light on the mechanisms underlying the reduced growth performance of range-edge populations.

Metabolome expression in Eucryphia cordifolia populations: Role of seasonality and ecological niche centrality hypothesis

The ecological niche centrality hypothesis states that population abundance is determined by the position in the ecological niche, expecting higher abundances towards the center of the niche and lower at the periphery. However, the variations in the conditions that favor the persistence of populations between the center and the periphery of the niche can be a surrogate of stress factors that are reflected in the production of metabolites in plants. In this study we tested if metabolomic similarity and diversity in populations of the tree species Eucryphia cordifolia Cav. vary according to their position with respect to the structure of the ecological niche. We hypothesize that populations growing near the centroid should exhibit lower metabolites diversity than plants growing at the periphery of the niche. The ecological niche of the species was modeled using correlative approaches and bioclimatic variables to define central and peripheral localities from which we chose four populations to obtain their metabolomic information using UHPLC-DAD-QTOF-MS. We observed that populations farther away from the centroid tend to have higher metabolome diversity, thus supporting our expectation of the niche centrality hypothesis. Nonetheless, the Shannon index showed a marked variation in metabolome diversity at the seasonal level, with summer and autumn being the periods with higher metabolite diversity compared to winter and spring. We conclude that both the environmental variation throughout the year in combination with the structure of the ecological niche are relevant to understand the variation in expression of metabolites in plants.

Conservation planning for the endemic and endangered medicinal plants under the climate change and human disturbance: a case study of Gentiana manshurica in China

Human activities and climate change have significantly impacted the quantity and sustainable utilization of medicinal plants. Gentiana manshurica Kitagawa, a high-quality original species of Gentianae Radix et Rhizoma, has significant medicinal value. However, wild resources have experienced a sharp decline due to human excavation, habitat destruction, and other factors. Consequently, it has been classified as an Endangered (EN) species on the IUCN Red List and is considered a third-level national key-protected medicinal material in China. The effects of climate change on G. manshurica are not yet known in the context of the severe negative impacts of climate change on most species. In this study, an optimized MaxEnt model was used to predict the current and future potential distribution of G. manshurica. In addition, land use data in 1980, 2000, and 2020 were used to calculate habitat quality by InVEST model and landscape fragmentation by the Fragstats model. Finally, using the above-calculated results, the priority protection areas and wild tending areas of G. manshurica were planned in ZONATION software. The results show that the suitable area is mainly distributed in the central part of the Songnen Plain. Bio15, bio03, bio01, and clay content are the environmental variables affecting the distribution. In general, the future potential distribution is expected to show an increasing trend. However, the species is expected to become threatened as carbon emission scenarios and years increase gradually. At worst, the high suitability area is expected to disappear completely under SSP585-2090s. Combined with the t-test, this could be due to pressure from bio01. The migration trends of climate niche centroid are inconsistent and do not all move to higher latitudes under different carbon emission scenarios. Over the past 40 years, habitat quality in the current potential distribution has declined yearly, and natural habitat has gradually fragmented. Existing reserves protect only 9.52% of G. manshurica's priority conservation area. To avoid extinction risk and increase the practicality of the results, we clarified the hotspot counties of priority protection area gaps and wild tending areas. These results can provide an essential reference and decision basis for effectively protecting G. manshurica under climate change.

Genetic variability and the ecology of geographic range: A test of the central-marginal hypothesis in Australian scincid lizards

For many species, both local abundance and regional occupancy are highest near the centre of their geographic distributions. One hypothesis for this pattern is that niche suitability declines with increasing distance from a species geographic centre, such that populations near range margins are characterized by reduced density and increased patchiness. In these smaller edge populations, genetic drift is more powerful, leading to the loss of genetic diversity. This simple verbal model has been formalized as the central-marginal hypothesis, which predicts that core populations should have greater genetic diversity than edge populations. Here, we tested the central-marginal hypothesis using a genomic data set of 25 species-level taxa of Australian scincid lizards in the genera Ctenotus and Lerista. A majority of taxa in our data set showed range-wide patterns of genetic variation consistent with central-marginal hypothesis, and eight of 25 taxa showed significantly greater genetic diversity in the centre of their range. We then explored biological, historical, and methodological factors that might predict which taxa support the central-marginal hypothesis. We found that taxa with the strongest evidence for range expansion were the least likely to follow predictions of the central-marginal hypothesis. The majority of these taxa had range expansions that originated at the range edge, which led to a gradient of decreasing genetic diversity from the range edge to the core, contrary to the central-marginal hypothesis.

Linking ecological niche models and common garden experiments to predict phenotypic differentiation in stressful environments: Assessing the adaptive value of marginal populations in an alpine plant

Environmental variation within a species' range can create contrasting selective pressures, leading to divergent selection and novel adaptations. The conservation value of populations inhabiting environmentally marginal areas remains in debate and is closely related to the adaptive potential in changing environments. Strong selection caused by stressful conditions may generate novel adaptations, conferring these populations distinct evolutionary potential and high conservation value under climate change. On the other hand, environmentally marginal populations may be genetically depauperate, with little potential for new adaptations to emerge. Here, we explored the use of ecological niche models (ENMs) linked with common garden experiments to predict and test for genetically determined phenotypic differentiation related to contrasting environmental conditions. To do so, we built an ENM for the alpine plant Silene ciliata in central Spain and conducted common garden experiments, assessing flowering phenology changes and differences in leaf cell resistance to extreme temperatures. The suitability patterns and response curves of the ENM led to the predictions that: (1) the environmentally marginal populations experiencing less snowpack and higher minimum temperatures would have delayed flowering to avoid risks of late-spring frosts and (2) those with higher minimum temperatures and greater potential evapotranspiration would show enhanced cell resistance to high temperatures to deal with physiological stress related to desiccation and heat. The common garden experiments revealed the expected genetically based phenotypic differentiation in flowering phenology. In contrast, they did not show the expected differentiation for cell resistance, but these latter experiments had high variance and hence lower statistical power. The results highlight ENMs as useful tools to identify contrasting putative selective pressures across species ranges. Linking ENMs with common garden experiments provides a theoretically justified and practical way to study adaptive processes, including insights regarding the conservation value of populations inhabiting environmentally marginal areas under ongoing climate change.

A Closer Examination of the 'Abundant-Center' for Ectomycorrhizal Fungal Community Associated With Picea crassifolia in China

A long-standing hypothesis in biogeography predicts that a species' abundance is highest at the center of its geographical range and decreases toward its edges. In this study, we test the abundant-center hypothesis of ectomycorrhizal (ECM) fungal communities associated with Picea crassifolia, an endemic species widely distributed in northwest China. We analyzed the taxonomic richness and the relative abundance of ECM fungi in four main distribution areas, from center to edges. In total, 234 species of ECM fungi were detected, and of these, 137 species were shared among all four sites. Inocybe, Sebacina, Tomentella, and Cortinarius were the dominant genera. ECM fungal richness and biodiversity were highest at the central and lower at peripheral sites. Our results indicated that ECM fungal species richness was consistent with the abundant-center hypothesis, while the relative abundances of individual fungal genera shifted inconsistently across the plant's range.

Reduction of Genetic Variation When Far From the Niche Centroid: Prediction for Mangrove Species

The niche-centroid hypothesis states that populations that are distributed near the centroid of the species' ecological niche will have higher fitness-related attributes, such as population abundance and genetic diversity than populations near the edges of the niche. Empirical evidence based on abundance and, more recently, genetic diversity data support this hypothesis. However, there are few studies that test this hypothesis in coastal species, such as mangroves. Here, we focused on the black mangrove Avicennia germinans. We combined ecological, heterozygosity, and allelic richness information from 1,419 individuals distributed in 40 populations with three main goals: (1) test the relationship between distance to the niche centroid and genetic diversity, (2) determine the set of environmental variables that best explain heterozygosity and allelic richness, and (3) predict the spatial variation in genetic diversity throughout most of the species' natural geographic range. We found a strong correlation between the distance to the niche centroid and both observed heterozygosity (Ho; ρ2 = 0.67 P < 0.05) and expected heterozygosity (He; ρ2 = 0.65, P < 0.05). The niche variables that best explained geographic variation in genetic diversity were soil type and precipitation seasonality. This suggests that these environmental variables influence mangrove growth and establishment, indirectly impacting standing genetic variation. We also predicted the spatial heterozygosity of A. germinans across its natural geographic range in the Americas using regression model coefficients. They showed significant power in predicting the observed data (R2 = 0.65 for Ho; R2 = 0.60 for He), even when we considered independent data sets (R2= 0.28 for Ho; R2 = 0.25 for He). Using this approach, several genetic diversity estimates can be implemented and may take advantage of population genomics to improve genetic diversity predictions. We conclude that the level of genetic diversity in A. germinans is in agreement with expectations of the niche-centroid hypothesis, namely that the highest heterozygosity and allelic richness (the basic genetic units for adaptation) are higher at locations of high environmental suitability. This shows that this approach is a potentially powerful tool in the conservation and management of this species, including for modelling changes in the face of climate change.

Complex genetic patterns and distribution limits mediated by native congeners of the worldwide invasive red-eared slider turtle

Non-native (invasive) species offer a unique opportunity to study the geographic distribution and range limits of species, wherein the evolutionary change driven by interspecific interactions between native and non-native closely related species is a key component. The red-eared slider turtle, Trachemys scripta elegans (TSE), has been introduced and successfully established worldwide. It can coexist with its native congeners T. cataspila, T. venusta and T. taylori in Mexico. We performed comprehensive fieldwork, executed a battery of genetic analyses and applied a novel species distribution modeling approach to evaluate their historical lineage relationships and contemporary population genetic patterns. Our findings support the historical common ancestry between native TSE and non-native (TSE_alien ), while also highlighting the genetic differentiation of the exotic lineage. Genetic patterns are associated with their range size/endemism gradient, the microendemic T. taylori showed significant reduced genetic diversity and high differentiation, whereas TSE_alien showed the highest diversity and signals of population size expansion. Counter to our expectations, lower naturally occurring distribution overlap and little admixture patterns were found between TSE and its congeners, exhibiting reduced gene flow and clear genetic separation across neighboring species despite having zones of contact. We demonstrate that these native Trachemys species have distinct climatic niche suitability, likely preventing establishment of and displacement by the TSE_alien . Moreover, we found major niche overlap between TSE_alien and native species worldwide, supporting our prediction that sites with closer ecological optima to the invasive species have higher establishment risk than those that are closer to the niche-center of the native species.

Fragility of nocturnal interactions: Pollination intensity increases with distance to light pollution sources but decreases with increasing environmental suitability

Light pollution represents a widespread long-established human-made disturbance and an important threat to nocturnal pollination. Distance from the niche centroid where optimal environmental conditions join may be related to species sensitivity to habitat change. We estimated the environmental suitability of the plant species Erythrostemon gilliesii and of its guild of hawkmoth pollinators. We considered the overlap of suitability maps of both partners as the environmental suitability of the interaction. We used a three-year record of ten E. gilliesii populations to calculate pollination intensity as the number of individuals that received pollen per population. In addition, for each population, we measured the distance to the high light pollution source around a buffer of 15 km radius. Finally, we predicted pollination intensity values for environmental suitability ranging from 0 to 1, and distance to high light pollution sources ranging from 0 to 56 Km. Pollination intensity decreased along an axis of increasing environmental suitability and increased with distance to sources of light pollution. The highest values of pollination intensity were observed at greatest distances to sources of light pollution and where environmental suitability of the interaction was lowest. The prediction model evidenced that, when environmental suitability was lowest, pollination intensity increased with distance to sources of high light pollution. However, when environmental suitability was intermediate or high, pollination intensity decreased away and until 28 km from the sources of high light pollution. Beyond 28 km from the sources of high light pollution, pollination intensity remained low and constant. Populations under conditions of low environmental suitability might be more likely to respond to disturbances that affect pollinators than populations under conditions of high environmental suitability.

Ecological niche differentiation among six annual Lythrum species in Mediterranean temporary pools

The ecological niche defines the favourable range of a species in a multidimensional space of ecological factors that determine the presence and function of individuals. This fundamental concept in ecology is widely used to understand plant species coexistence and segregation. In this study, we test for ecological differentiation among six annual Lythrum species that are characteristic of temporary pools in the South of France, where they either coexist or occur separately. We first analysed the co-occurrence of species at two different geographical scales: cluster analyses of species presence in 10 km grid cells and coexistence in 0.25 m² quadrats within populations of each species. Second, for three to nine populations of each species, we quantified a range of biotic and abiotic parameters using point contacts and soil measurements in five 0.25 m² quadrats per population. We performed PCA on all variables and analysed each variable separately to compare the ecological niche features of the six species. A phenological index was assessed for the plant community of each site. We detected highly localized niche differentiation in terms of soil pH (all species) and for a range of variables among pairs of species. The six species also showed marked differences in the flowering period relative to the mean and variability of flowering time in their local community. These fine-scaled niche differences are associated with phylogenetic distances among species and may contribute to species' coexistence. These results are integrated in a conservation management plan for the habitat of the rarest species in this group.

Ecologically coherent population structure of uncultivated bacterioplankton

Bacterioplankton are main drivers of biogeochemical cycles and important components of aquatic food webs. While sequencing-based studies have revealed how bacterioplankton communities are structured in time and space, relatively little is known about intraspecies diversity patterns and their ecological relevance. Here, we use the newly developed software POGENOM (POpulation GENomics from Metagenomes) to investigate genomic diversity and differentiation in metagenome-assembled genomes from the Baltic Sea, and investigate their genomic variation using metagenome data spanning a 1700 km transect and covering seasonal variation at one station. The majority of the investigated species, representing several major bacterioplankton clades, displayed population structures correlating significantly with environmental factors such as salinity and temperature. Population differentiation was more pronounced over spatial than temporal scales. We discovered genes that have undergone adaptation to different salinity regimes, potentially responsible for the populations' existence along with the salinity range. This in turn implies the broad existence of ecotypes that may remain undetected by rRNA gene sequencing. Our findings emphasize the importance of physiological barriers, and highlight the role of adaptive divergence as a structuring mechanism of bacterioplankton species.

The evolutionary genomics of species' responses to climate change

Climate change is a threat to biodiversity. One way that this threat manifests is through pronounced shifts in the geographical range of species over time. To predict these shifts, researchers have primarily used species distribution models. However, these models are based on assumptions of niche conservatism and do not consider evolutionary processes, potentially limiting their accuracy and value. To incorporate evolution into the prediction of species' responses to climate change, researchers have turned to landscape genomic data and examined information about local genetic adaptation using climate models. Although this is an important advancement, this approach currently does not include other evolutionary processes-such as gene flow, population dispersal and genomic load-that are critical for predicting the fate of species across the landscape. Here, we briefly review the current practices for the use of species distribution models and for incorporating local adaptation. We next discuss the rationale and theory for considering additional processes, reviewing how they can be incorporated into studies of species' responses to climate change. We summarize with a conceptual framework of how manifold layers of information can be combined to predict the potential response of specific populations to climate change. We illustrate all of the topics using an exemplar dataset and provide the source code as potential tutorials. This Perspective is intended to be a step towards a more comprehensive integration of population genomics with climate change science.

Genetic Diversity and Differentiation of Pedunculate Oak (Quercus robur L.) Populations at the Southern Margin of Its Distribution Range—Implications for Conservation

Understanding intraspecific genetic variation is one of the principal requirements for the evaluation of tree species capacity to cope with intensive climatic changes, as well as designing long-term conservation programs. Herein, we evaluated the genetic diversity and genetic structure of seven pedunculate oak (Quercus robur L.) populations, located at the southern margin of its distribution range on the Balkan Peninsula (Serbia). The objective of the study was to propose future in situ conservation measures aimed at protection of pedunculate oak adaptive and neutral genetic diversity at the species rear-edge. Genetic diversity and structure were estimated using twelve highly polymorphic simple sequence repeat (SSR) markers. The mean expected heterozygosity (He) was 0.769, allelic richness (AR) 9.63, and private allelic richness (pAR) 0.79, indicating high genetic diversity in the studied populations. Genetic differentiation among the populations was low (Fst = 0.032). Structure analysis, the unweighted pair group method with arithmetic mean (UPGMA) showed the existence of two gene pools unrelated to the populations’ area of occurrence. Taking into consideration the results of the current study and previous conservation activities on the pedunculate oak in Serbia, as well as the importance of rear-edge populations in the long-term conservation of the species genetic diversity, we suggested establishing three additional gene conservation units for securing long-term sustainability of the species.

Centre-periphery approaches based on geography, ecology and historical climate stability: what explains the variation in morphological traits of Bulnesia sarmientoi?

BACKGROUND AND AIMS

The centre-periphery hypothesis posits that higher species performance is expected in geographic and ecological centres rather than in peripheral populations. However, this is not the commonly found pattern; therefore, alternative approaches, including the historical dimension of species geographical ranges, should be explored. Morphological functional traits are fundamental determinants of species performance, commonly related to environmental stability and productivity. We tested whether or not historical processes may have shaped variations in tree and leaf traits of the Chaco tree Bulnesia sarmientoi.

METHODS

Morphological variation patterns were analysed from three centre-periphery approaches: geographical, ecological and historical. Tree (stem and canopy) and leaf (leaf size and specific leaf area) traits were measured in 24 populations across the species range. A principal component analysis was performed on morphological traits to obtain synthetic variables. Linear mixed-effects models were used to test which of the implemented centre-periphery approaches significantly explained trait spatial patterns.

KEY RESULTS

The patterns retrieved from the three centre-periphery approaches were not concordant. The historical approach revealed that trees were shorter in centre populations than in the periphery. Significant differences in leaf traits were observed between the geographical centre and the periphery, mainly due to low specific leaf area values towards the geographical centre. We did not find any pattern associated with the ecological centre-periphery approach.

CONCLUSIONS

The decoupled response between leaf and tree traits suggests that these sets of traits respond differently to processes occurring at different times. The geographical and historical approaches showed centres with extreme environments in relation to their respective peripheries, but the historical centre has also been a climatically stable area since the Last Glacial Maximum. The historical approach allowed for the recovery of historical processes underlying variation in tree traits, highlighting that centre-periphery delimitations should be based on a multi-approach framework.

How is adaptive potential distributed within species ranges?

Quantitative genetic variation (QGV) represents a major component of adaptive potential and, if reduced toward range-edge populations, could prevent a species' expansion or adaptive response to rapid ecological change. It has been hypothesized that QGV will be lower at the range edge due to small populations-often the result of poor habitat quality-and potentially decreased gene flow. However, whether central populations are higher in QGV is unknown. We used a meta-analytic approach to test for a general QGV-range position relationship, including geographic and climatic distance from range centers. We identified 35 studies meeting our criteria, yielding nearly 1000 estimates of QGV (including broad-sense heritability, narrow-sense heritability, and evolvability) from 34 species. The relationship between QGV and distance from the geographic range or climatic niche center depended on the focal trait and how QGV was estimated. We found some evidence that QGV declines from geographic centers but that it increases toward niche edges; niche and geographic distances were uncorrelated. Nevertheless, few studies have compared QGV in both central and marginal regions or environments within the same species. We call for more research in this area and discuss potential research avenues related to adaptive potential in the context of global change.

Adaptation across geographic ranges is consistent with strong selection in marginal climates and legacies of range expansion

Every species experiences limits to its geographic distribution. Some evolutionary models predict that populations at range edges are less well adapted to their local environments due to drift, expansion load, or swamping gene flow from the range interior. Alternatively, populations near range edges might be uniquely adapted to marginal environments. In this study, we use a database of transplant studies that quantify performance at broad geographic scales to test how local adaptation, site quality, and population quality change from spatial and climatic range centers toward edges. We find that populations from poleward edges perform relatively poorly, both on average across all sites (15% lower population quality) and when compared to other populations at home (31% relative fitness disadvantage), consistent with these populations harboring high genetic load. Populations from equatorial edges also perform poorly on average (18% lower population quality) but, in contrast, outperform foreign populations (16% relative fitness advantage), suggesting that populations from equatorial edges have strongly adapted to unique environments. Finally, we find that populations from sites that are thermally extreme relative to the species' niche demonstrate strong local adaptation, regardless of their geographic position. Our findings indicate that both nonadaptive processes and adaptive evolution contribute to variation in adaptation across species' ranges.

Comparing Genetic Diversity in Three Threatened Oaks

Genetic diversity is a critical resource for species’ survival during times of environmental change. Conserving and sustainably managing genetic diversity requires understanding the distribution and amount of genetic diversity (in situ and ex situ) across multiple species. This paper focuses on three emblematic and IUCN Red List threatened oaks (Quercus, Fagaceae), a highly speciose tree genus that contains numerous rare species and poses challenges for ex situ conservation. We compare the genetic diversity of three rare oak species—Quercus georgiana, Q. oglethorpensis, and Q. boyntonii—to common oaks; investigate the correlation of range size, population size, and the abiotic environment with genetic diversity within and among populations in situ; and test how well genetic diversity preserved in botanic gardens correlates with geographic range size. Our main findings are: (1) these three rare species generally have lower genetic diversity than more abundant oaks; (2) in some cases, small population size and geographic range correlate with genetic diversity and differentiation; and (3) genetic diversity currently protected in botanic gardens is inadequately predicted by geographic range size and number of samples preserved, suggesting non-random sampling of populations for conservation collections. Our results highlight that most populations of these three rare oaks have managed to avoid severe genetic erosion, but their small size will likely necessitate genetic management going forward.

When ecological marginality is not geographically peripheral: exploring genetic predictions of the centre-periphery hypothesis in the endemic plant Lilium pomponium

Background

Quantifying variation of genetic traits over the geographical range of species is crucial for understanding the factors driving their range dynamics. The center-periphery hypothesis postulates, and many studies support, the idea that genetic diversity decreases and genetic differentiation increases toward the geographical periphery due to population isolation. The effects of environmental marginality on genetic variation has however received much less attention.

Methods

We tested the concordance between geographical and environmental gradients and the genetic predictions of center-periphery hypothesis for endemic Lilium pomponium in the southern Alps.

Results

We found little evidence for concordance between genetic variation and both geographical and environmental gradients. Although the prediction of increased differentiation at range limits is met, genetic diversity does not decrease towards the geographical periphery. Increased differentiation among peripheral populations, that are not ecologically marginal, may be explained by a decrease in habitat availability that reduces population connectivity. In contrast, a decrease of genetic diversity along environmental but not geographical gradients may be due to the presence of low quality habitats in the different parts of the range of a species that reduce effective population size or increase environmental constraints. As a result, environmental factors may affect population dynamics irrespective of distance from the geographical center of the range. In such situations of discordance between geographical and environmental gradients, the predictions of decreasing genetic diversity and increasing differentiation toward the geographical periphery may not be respected.

Implications of genetic heterogeneity for plant translocation during ecological restoration

Ecological restoration often requires translocating plant material from distant sites. Importing suitable plant material is important for successful establishment and persistence. Yet, published guidelines for seed transfer are available for very few species. Accurately predicting how transferred plants will perform requires multiyear and multi-environment field trials and comprehensive follow-up work, and is therefore infeasible given the number of species used in restoration programs. Alternative methods to predict the outcomes of seed transfer are valuable for species without published guidelines. In this study, we analyzed the genetic structure of an important shrub used in ecological restoration in the Southern Rocky Mountains called alder-leaf mountain mahogany (Cercocarpus montanus). We sequenced DNA from 1,440 plants in 48 populations across a broad geographic range. We found that genetic heterogeneity among populations reflected the complex climate and topography across which the species is distributed. We identified temperature and precipitation variables that were useful predictors of genetic differentiation and can be used to generate seed transfer recommendations. These results will be valuable for defining management and restoration practices for mountain mahogany.

Life history, climate and biogeography interactively affect worldwide genetic diversity of plant and animal populations

Understanding how biological and environmental factors interactively shape the global distribution of plant and animal genetic diversity is fundamental to biodiversity conservation. Genetic diversity measured in local populations (GDP) is correspondingly assumed representative for population fitness and eco-evolutionary dynamics. For 8356 populations across the globe, we report that plants systematically display much lower GDP than animals, and that life history traits shape GDP patterns both directly (animal longevity and size), and indirectly by mediating core-periphery patterns (animal fecundity and plant dispersal). Particularly in some plant groups, peripheral populations can sustain similar GDP as core populations, emphasizing their potential conservation value. We further find surprisingly weak support for general latitudinal GDP trends. Finally, contemporary rather than past climate contributes to the spatial distribution of GDP, suggesting that contemporary environmental changes affect global patterns of GDP. Our findings generate new perspectives for the conservation of genetic resources at worldwide and taxonomic-wide scales.

Supraspecific units in correlative niche modeling improves the prediction of geographic potential of biological invasions

BACKGROUND

Biological invasions rank among the most significant threats to biodiversity and ecosystems. Correlative ecological niche modeling is among the most frequently used tools with which to estimate potential distributions of invasive species. However, when areas accessible to the species across its native distribution do not represent the full spectrum of environmental conditions that the species can tolerate, correlative studies often underestimate fundamental niches.

METHODS

Here, we explore the utility of supraspecific modeling units to improve the predictive ability of models focused on biological invasions. Taking into account phylogenetic relationships in correlative ecological niche models, we studied the invasion patterns of three species (Aedes aegypti, Pterois volitans and Oreochromis mossambicus).

RESULTS

Use of supraspecific modeling units improved the predictive ability of correlative niche models in anticipating potential distributions of three invasive species. We demonstrated that integrating data on closely related species allowed a more complete characterization of fundamental niches. This approach could be used to model species with invasive potential but that have not yet invaded new regions.

Effects of environmental heterogeneity on phenotypic variation of the endemic plant Lilium pomponium in the Maritime and Ligurian Alps

Geographical limits of species’ distributions are assumed to be coincident with ecological margins, although this assumption might not always be true. Indeed, harsh environments such as Alpine and Mediterranean ecosystems may favour high phenotypic variability among populations, especially those in peripheral sites. Floral traits are often found to be less variable and less affected by environmental heterogeneity than vegetative traits because variation in the former may have negative effects on fitness. For this reason, it is important to quantify variation in floral traits and plant fecundity in study range limits. The objective of the study is to examine phenotypic variation and differences in reproduction in endemic Lilium pomponium in the Maritime and Ligurian Alps in relation to environmental variation across its distribution range. In this species, marginal climatic populations occur both in the peripheral and central geographical locations of the distribution range; hence, geographical and ecological gradients are not concordant. Floral trait variation is related to local environmental conditions with an array of interactions among resource availability, potential pollen limitation and population size that are differentially related to floral traits. Contrary to the general expectation, all central and peripheral populations had similar, moderate seed production with each group limited by different factors acting on different stages of the life-history strategy. Our results are in line with the idea that general expectations are confirmed only when its assumptions are met and that the differences in pollination environment along an environmental gradient may not be the main determinant of the distribution limit.

Niche divergence of evolutionarily significant units with implications for repopulation programs of the world's largest amphibians

The niche divergence and potential climate change-induced loss of evolutionarily significant units (ESUs) of flagship amphibian species in China, the Chinese giant salamander clade, were investigated. We tested niche-related ecological hypotheses and identified suitable habitats that are essential for the conservation of ESUs in response to future climate change according to ecological niche models (ENMs). We predicted the localized habitat loss crisis of ESUs induced by global climate heating using the predicted climate derived from two representative concentration pathway (RCP) scenarios 2.6 and 8.5, respectively. In our study, a niche conservatism pattern was found between the two distinctive northern and southern ESUs with sufficient distributional records, but their niches were not equivalent. Furthermore, there was neither abrupt environmental change in nor remarkable biogeographic barriers between the suitable habitats of the species, as indicated by random linear, blob and ribbon range-breaking tests. Under the low-emission scenario RCP2.6, the northern ESU had a moderate loss of suitable range, while the southern ESU had range expansion in the 2070s. The climatic velocities were low in the ranges of both ESUs. However, under the high-emission scenario RCP8.5, the climatic velocities were found to become larger in the suitable ranges of both ESUs. Moreover, the northern ESU had severe habitat loss, bringing it to the edge of extinction, while the southern ESU also had intensified range loss. Considering this, climatic velocity can be an effective indicator of range loss. We argued conclusively that conservation prioritization of ESUs should effectively take into account the underlying geographic and ecological mechanisms driving the speciation process. The conservation of ESUs should consider the conservation of both evolutionary potential and ecological adaptation capacity of each lineage. The present study provided practical guidelines for repopulation programs for endangered species and the conservation of evolutionary diversity.

Evaluation of the Minimum Sampling Design for Population Genomic and Microsatellite Studies: An Analysis Based on Wild Maize

Massive parallel sequencing (MPS) is revolutionizing the field of molecular ecology by allowing us to understand better the evolutionary history of populations and species, and to detect genomic regions that could be under selection. However, the economic and computational resources needed generate a tradeoff between the amount of loci that can be obtained and the number of populations or individuals that can be sequenced. In this work, we analyzed and compared two simulated genomic datasets fitting a hierarchical structure, two extensive empirical genomic datasets, and a dataset comprising microsatellite information. For all datasets, we generated different subsampling designs by changing the number of loci, individuals, populations, and individuals per population to test for deviations in classic population genetics parameters (H_S, F_IS, F_ST). For the empirical datasets we also analyzed the effect of sampling design on landscape genetic tests (isolation by distance and environment, central abundance hypothesis). We also tested the effect of sampling a different number of populations in the detection of outlier SNPs. We found that the microsatellite dataset is very sensitive to the number of individuals sampled when obtaining summary statistics. F_IS was particularly sensitive to a low sampling of individuals in the simulated, genomic, and microsatellite datasets. For the empirical and simulated genomic datasets, we found that as long as many populations are sampled, few individuals and loci are needed. For the empirical datasets, we found that increasing the number of populations sampled was important in obtaining precise landscape genetic estimates. Finally, we corroborated that outlier tests are sensitive to the number of populations sampled. We conclude by proposing different sampling designs depending on the objectives.

Leaf size variations in a dominant desert shrub, Reaumuria soongarica, adapted to heterogeneous environments

The climate in arid Central Asia (ACA) has changed rapidly in recent decades, but the ecological consequences of this are far from clear. To predict the impacts of climate change on ecosystem functioning, greater attention should be given to the relationships between leaf functional traits and environmental heterogeneity. As a dominant constructive shrub widely distributed in ACA, Reaumuria soongarica provided us with an ideal model to understand how leaf functional traits of desert ecosystems responded to the heterogeneous environments of ACA. Here, to determine the influences of genetic and ecological factors, we characterized species-wide variations in leaf traits among 30 wild populations of R. soongarica and 16 populations grown in a common garden. We found that the leaf length, width, and leaf length to width ratio (L/W) of the northern lineage were significantly larger than those of other genetic lineages, and principal component analysis based on the in situ environmental factors distinguished the northern lineage from the other lineages studied. With increasing latitude, leaf length, width, and L/W in the wild populations increased significantly. Leaf length and L/W were negatively correlated with altitude, and first increased and then decreased with increasing mean annual temperature (MAT) and mean annual precipitation (MAP). Stepwise regression analyses further indicated that leaf length variation was mainly affected by latitude. However, leaf width was uncorrelated with altitude, MAT, or MAP. The common garden trial showed that leaf width variation among the eastern populations was caused by both local adaptation and phenotypic plasticity. Our findings suggest that R. soongarica preferentially changes leaf length to adjust leaf size to cope with environmental change. We also reveal phenotypic evidence for ecological speciation of R. soongarica. These results will help us better understand and predict the consequences of climate change for desert ecosystem functioning.

Disentangling the effects of geographic peripherality and habitat suitability on neutral and adaptive genetic variation in Swiss stone pine

It is generally accepted that the spatial distribution of neutral genetic diversity within a species' native range mostly depends on effective population size, demographic history, and geographic position. However, it is unclear how genetic diversity at adaptive loci correlates with geographic peripherality or with habitat suitability within the ecological niche. Using exome-wide genomic data and distribution maps of the Alpine range, we first tested whether geographic peripherality correlates with four measures of population genetic diversity at > 17,000 SNP loci in 24 Alpine populations (480 individuals) of Swiss stone pine (Pinus cembra) from Switzerland. To distinguish between neutral and adaptive SNP sets, we used four approaches (two gene diversity estimates, F_ST outlier test, and environmental association analysis) that search for signatures of selection. Second, we established ecological niche models for P. cembra in the study range and investigated how habitat suitability correlates with genetic diversity at neutral and adaptive loci. All estimates of neutral genetic diversity decreased with geographic peripherality, but were uncorrelated with habitat suitability. However, heterozygosity (H_e ) at adaptive loci based on Tajima's D declined significantly with increasingly suitable conditions. No other diversity estimates at adaptive loci were correlated with habitat suitability. Our findings suggest that populations at the edge of a species' geographic distribution harbour limited neutral genetic diversity due to demographic properties. Moreover, we argue that populations from suitable habitats went through strong selection processes, are thus well adapted to local conditions, and therefore exhibit reduced genetic diversity at adaptive loci compared to populations at niche margins.

Genetic patterns and changes in availability of suitable habitat support a colonisation history of a North American perennial plant

Climatic fluctuations during the Pleistocene influenced the geographical distribution of plant species across the southern region of California. Following an integrative approach, we combined genetic data analysis with Environmental Niche Models (ENMs) to assess the historical range expansion of Yucca schidigera, a long-lived desert perennial native of the Baja California Peninsula. We genotyped 240 individuals with seven nuclear microsatellite to investigate genetic diversity distribution across 13 populations. Indeed, we used Environmental Niche Models to examine the changes on the distribution of suitable climatic conditions for this species during the LIG (~120 ka), LGM (~22 ka) and Mid Holocene (~6 ka). We detected high genetic diversity across Y. schidigera populations (A_R = 9.94 ± 0.38 SE; H_exp = 0.791 ± 0.011 SE) with genetic variation decreasing significantly with latitude (allelic richness: R ²  = 0.38, P = 0.023; expected heterocigosity: R²  = 0.32, P = 0.042). We observed low, but significant genetic differentiation (F_ST  = 0.0678; P < 0.001) which was consistent with the parapatric distribution of the three genetic groupings detected by the Bayesian clustering algorithm. The ENMs suggest that suitable habitat for this species increased since the LGM. Our results support a range expansion of Y. schidigera across northwestern Baja California during the late Quaternary. Genetic data suggest that colonization of the current distribution followed a southward directionality as suitable climatic conditions became widely available in this region. High genetic variation across our sample suggests large historic effective population sizes for this section of the geographical range.

Is the central-marginal hypothesis a general rule? Evidence from three distributions of an expanding mangrove species, Avicennia germinans (L.) L

The central-marginal hypothesis (CMH) posits that range margins exhibit less genetic diversity and greater inter-population genetic differentiation compared to range cores. CMH predictions are based on long-held "abundant-centre" assumptions of a decline in ecological conditions and abundances towards range margins. Although much empirical research has confirmed CMH, exceptions remain almost as common. We contend that mangroves provide a model system to test CMH that alleviates common confounding factors and may help clarify this lack of consensus. Here, we document changes in black mangrove (Avicennia germinans) population genetics with 12 nuclear microsatellite loci along three replicate coastlines in the United States (only two of three conform to underlying "abundant-centre" assumptions). We then test an implicit prediction of CMH (reduced genetic diversity may constrain adaptation at range margins) by measuring functional traits of leaves associated with cold tolerance, the climatic factor that controls these mangrove distributional limits. CMH predictions were confirmed only along the coastlines that conform to "abundant-centre" assumptions and, in contrast to theory, range margin A. germinans exhibited functional traits consistent with greater cold tolerance compared to range cores. These findings support previous accounts that CMH may not be a general rule across species and that reduced neutral genetic diversity at range margins may not be a constraint to shifts in functional trait variation along climatic gradients.

Relationships between population densities and niche-centroid distances in North American birds

Correlational ecological niche models have seen intensive use and exploration as a means of estimating the limits of actual and potential geographic distributions of species, yet their application to explaining geographic abundance patterns has been debated. We developed a detailed test of this latter possibility based on the North American Breeding Bird Survey. Correlations between abundances and niche-centroid distances were mostly negative, as per expectations of niche theory and the abundant niche-centre relationship. The negative relationships were not distributed randomly among species: terrestrial, non-migratory, small-bodied, small-niche-breadth and restricted-range species had the strongest negative associations. Distances to niche centroids as estimated from correlational analyses of presence-only data thus offer a unique means by which to infer geographic abundance patterns, which otherwise are enormously difficult to characterise.

Geography alone cannot explain Tetranychus truncatus (Acari: Tetranychidae) population abundance and genetic diversity in the context of the center-periphery hypothesis

The center-periphery hypothesis (CPH) states that the genetic diversity, genetic flow, and population abundance of a species are highest at the center of the species' geographic distribution. However, most CPH studies have focused on the geographic distance and have ignored ecological and historical effects. Studies using niche models to define the center and periphery of a distribution and the interactions among geographical, ecological, and historical gradients have rarely been done in the framework of the CPH, especially in biogeographical studies of animal species. Here, we examined the CPH for a widely distributed arthropod, Tetranychus truncatus (Acari: Tetranychidae), in eastern China using three measurements: geographic distance to the center of the distribution (geography), ecological suitability based on current climate data (ecology), and historical climate data from the last glacial maximum (history). We found that the relative abundances of different populations were more strongly related to ecology than to geography and history. Genetic diversity within populations and genetic differentiation among populations based on mitochondrial marker were only significantly related to history. However, the genetic diversity and population differentiation based on microsatellites were significantly related to all three CPH measurements. Overall, population abundance and genetic pattern cannot be explained very well by geography alone. Our results show that ecological gradients explain the variation in population abundance better than geographic gradients and historical factors, and that current and historical factors strongly influence the spatial patterns of genetic variation. This study highlights the importance of examining more than just geography when assessing the CPH.

A Practical Guide to the Study of Distribution Limits

Factors that limit the geographic distribution of species are broadly important in ecology and evolutionary biology, and understanding distribution limits is imperative for predicting how species will respond to environmental change. Good data indicate that factors such as dispersal limitation, small effective population size, and isolation are sometimes important. But empirical research highlights no single factor that explains the ubiquity of distribution limits. In this article, we outline a guide to tackling distribution limits that integrates established causes, such as dispersal limitation and spatial environmental heterogeneity, with understudied causes, such as mutational load and genetic or developmental integration of traits limiting niche expansion. We highlight how modeling and quantitative genetic and genomic analyses can provide insight into sources of distribution limits. Our practical guide provides a framework for considering the many factors likely to determine species distributions and how the different approaches can be integrated to predict distribution limits using eco-evolutionary modeling. The framework should also help predict distribution limits of invasive species and of species under climate change.

Parallel evolution and adaptation to environmental factors in a marine flatfish: Implications for fisheries and aquaculture management of the turbot (Scophthalmus maximus)

Unraveling adaptive genetic variation represents, in addition to the estimate of population demographic parameters, a cornerstone for the management of aquatic natural living resources, which, in turn, represent the raw material for breeding programs. The turbot (Scophthalmus maximus) is a marine flatfish of high commercial value living on the European continental shelf. While wild populations are declining, aquaculture is flourishing in southern Europe. We evaluated the genetic structure of turbot throughout its natural distribution range (672 individuals; 20 populations) by analyzing allele frequency data from 755 single nucleotide polymorphism discovered and genotyped by double-digest RAD sequencing. The species was structured into four main regions: Baltic Sea, Atlantic Ocean, Adriatic Sea, and Black Sea, with subtle differentiation apparent at the distribution margins of the Atlantic region. Genetic diversity and effective population size estimates were highest in the Atlantic populations, the area of greatest occurrence, while turbot from other regions showed lower levels, reflecting geographical isolation and reduced abundance. Divergent selection was detected within and between the Atlantic Ocean and Baltic Sea regions, and also when comparing these two regions with the Black Sea. Evidence of parallel evolution was detected between the two low salinity regions, the Baltic and Black seas. Correlation between genetic and environmental variation indicated that temperature and salinity were probably the main environmental drivers of selection. Mining around the four genomic regions consistently inferred to be under selection identified candidate genes related to osmoregulation, growth, and resistance to diseases. The new insights are useful for the management of turbot fisheries and aquaculture by providing the baseline for evaluating the consequences of turbot releases from restocking and farming.

Climate complexity in the migratory cycle of Ammodramus bairdii

One way to understand the ecology of bird migration is to analyze how birds use their ecological niche during their annual cycle. Ammodramus bairdii is a grassland specialist sparrow that breeds in southern Canada and the northern U.S.A. and winters in the Chihuahuan Desert. A continuous and alarming decrease of its populations has been observed over the last 50 years, and studying its seasonal distribution and associated climatic niches could help improve strategies for its conservation. We analyzed the temporal use of its Grinnellian niche (GN) -set of environmental conditions under which a species can establish and persist; in this case the climatic attributes-. We modeled the GN for the reproductive and winter seasons and projected them onto each other (inter-prediction), and also onto transient migratory periods. To measure niche breadth and their overlap, minimum convex polygons (MCP) were calculated for the climatic space. The niches of each of the two seasons were tested for similarity using the PCA axes of climatic variables. The geographic areas with optimal, suboptimal and marginal conditions were identified, based on the distance to the centroid of the GN. The models for each season revealed no geographic inter-prediction among them, with the exception of winter to migratory seasons. The niche breadth of the winter was greater than that of the reproductive season, with an overlap of 22.47% and 45.18%, respectively. The similarity analyses showed a value of zero between seasons. The climate conditions for the records during the migratory months corresponded with suboptimal and marginal conditions of the sparrow's winter niche. These results suggest that A. bairdii uses different climate conditions within ecological niches of each season during its migratory cycle.

Summary results of the 2014-2015 DARPA Chikungunya challenge

Background: Emerging pathogens such as Zika, chikungunya, Ebola, and dengue viruses are serious threats to national and global health security. Accurate forecasts of emerging epidemics and their severity are critical to minimizing subsequent mortality, morbidity, and economic loss. The recent introduction of chikungunya and Zika virus to the Americas underscores the need for better methods for disease surveillance and forecasting.

Methods: To explore the suitability of current approaches to forecasting emerging diseases, the Defense Advanced Research Projects Agency (DARPA) launched the 2014–2015 DARPA Chikungunya Challenge to forecast the number of cases and spread of chikungunya disease in the Americas. Challenge participants (n=38 during final evaluation) provided predictions of chikungunya epidemics across the Americas for a six-month period, from September 1, 2014 to February 16, 2015, to be evaluated by comparison with incidence data reported to the Pan American Health Organization (PAHO). This manuscript presents an overview of the challenge and a summary of the approaches used by the winners.

Results: Participant submissions were evaluated by a team of non-competing government subject matter experts based on numerical accuracy and methodology. Although this manuscript does not include in-depth analyses of the results, cursory analyses suggest that simpler models appear to outperform more complex approaches that included, for example, demographic information and transportation dynamics, due to the reporting biases, which can be implicitly captured in statistical models. Mosquito-dynamics, population specific information, and dengue-specific information correlated best with prediction accuracy.

Conclusion: We conclude that with careful consideration and understanding of the relative advantages and disadvantages of particular methods, implementation of an effective prediction system is feasible. However, there is a need to improve the quality of the data in order to more accurately predict the course of epidemics.

Predictable invasion dynamics in North American populations of the Eurasian collared dove Streptopelia decaocto

Species invasions represent a significant dimension of global change yet the dynamics of invasions remain poorly understood and are considered rather unpredictable. We explored interannual dynamics of the invasion process in the Eurasian collared dove (Streptopelia decaocto) and tested whether the advance of the invasion front of the species in North America relates to centrality (versus peripherality) within its estimated fundamental ecological niche. We used ecological niche modelling approaches to estimate the dimensions of the fundamental ecological niche on the Old World distribution of the species, and then transferred that model to the New World as measures of centrality versus peripherality within the niche for the species. Although our hypothesis was that the invasion front would advance faster over more favourable (i.e. more central) conditions, the reverse was the case: the invasion expanded faster in areas presenting less favourable (i.e. more peripheral) conditions for the species as it advanced across North America. This result offers a first view of a predictive approach to the dynamics of species' invasions, and thereby has relevant implications for the management of invasive species, as such a predictive understanding would allow better anticipation of coming steps and advances in the progress of invasions, important to designing and guiding effective remediation and mitigation efforts.

Understanding population structure and historical demography of Litsea auriculata (Lauraceae), an endangered species in east China

Detecting how historical and contemporary factors contribute to genetic divergence and genetic structure is a central question in ecology and evolution. We examine this question by intergrating population genetics with ecological niche modelling of Litsea auriculata (Lauraceae), which is endangered and native to east China. Geographical and environmental factors including climatic fluctuations since the last glacial maximum (LGM) have also contribute to population demography and patterns of genetic structure. L. auriculata populations underwent expansion after divergence and dramatically decreased to the current small size with relative population bottlenecks due to climate changes. Populations separated by physical geographical barrier including geographic distance and Yangtze River, as a result contemporary gene flow among L. auriculata populations showed drastic declines in comparison with historical gene flow, resulting in a high level of population divergence. Thus, patterns of genetic structure of L. auriculata can result from both geographic and environmental factors including climate changes. This information is helpful in forming conservation strategies for L. auriculata in China.