Integrating GIS-based environmental data into evolutionary biology

A joint model for the estimation of species distributions and environmental characteristics from point-referenced data

BACKGROUND

Predicting and explaining species occurrence using environmental characteristics is essential for nature conservation and management. Species distribution models consider species occurrence as the dependent variable and environmental conditions as the independent variables. Suitable conditions are estimated based on a sample of species observations, where one assumes that the underlying environmental conditions are known. This is not always the case, as environmental variables at broad spatial scales are regularly extrapolated from point-referenced data. However, treating the predicted environmental conditions as accurate surveys of independent variables at a specific point does not take into account their uncertainty.

METHODS

We present a joint hierarchical Bayesian model where models for the environmental variables, rather than a set of predicted values, are input to the species distribution model. All models are fitted together based only on point-referenced observations, which results in a correct propagation of uncertainty. We use 50 plant species representative of the Dutch flora in natural areas with 8 soil condition predictors taken during field visits in the Netherlands as a case study. We compare the proposed model to the standard approach by studying the difference in associations, predicted maps, and cross-validated accuracy.

FINDINGS

We find that there are differences between the two approaches in the estimated association between soil conditions and species occurrence (correlation 0.64-0.84), but the predicted maps are quite similar (correlation 0.82-1.00). The differences are more pronounced in the rarer species. The cross-validated accuracy is substantially better for 5 species out of the 50, and the species can also help to predict the soil characteristics. The estimated associations tend to have a smaller magnitude with more certainty.

CONCLUSION

These findings suggests that the standard model is often sufficient for prediction, but effort should be taken to develop models which take the uncertainty in the independent variables into account for interpretation.

Variable intraspecific response to climate change in a medicinally important African tree species, Vachellia sieberiana (DC.) (paperbark thorn)

Climate change is predicted to disproportionately impact sub-Saharan Africa, with potential devastating consequences on plant populations. Climate change may, however, impact intraspecific taxa differently. The aim of the study was to determine the current distribution and impact of climate change on three varieties of Vachellia sieberiana, that is, var. sieberiana, var. villosa and var. woodii. Ensemble species distribution models (SDMs) were built in "biomod2" using 66, 45, and 137 occurrence records for var. sieberiana, var. villosa, and var. woodii, respectively. The ensemble SDMs were projected to 2041-2060 and 2081-2100 under three general circulation models (GCMs) and two shared socioeconomic pathways (SSPs). The three GCMs were the Canadian Earth System Model version 5, the Institut Pierre-Simon Laplace Climate Model version 6A Low Resolution, and the Model for Interdisciplinary Research on Climate version 6. The suitable habitat of var. sieberiana predominantly occurs in the Sudanian and Zambezian phytochoria while that of var. villosa largely occurs in the Sudanian phytochorion. The suitable habitat of var. woodii mainly occurs in the Zambezian phyotochorion. There is coexistence of var. villosa and var. sieberiana in the Sudanian phytochorion while var. sieberiana and var. woodii coexist in the Zambezian phytochorion. Under SSP2-4.5 in 2041-2060 and averaged across the three GCMs, the suitable habitat expanded by 33.8% and 119.7% for var. sieberiana and var. villosa, respectively. In contrast, the suitable habitat of var. woodii contracted by -8.4%. Similar trends were observed in 2041-2060 under SSP5-8.5 [var. sieberiana (38.6%), var. villosa (139.0%), and var. woodii (-10.4%)], in 2081-2100 under SSP2-4.5 [var. sieberiana (4.6%), var. villosa (153.4%), and var. woodii (-14.4%)], and in 2081-2100 under SSP5-8.5 [var. sieberiana (49.3%), var. villosa (233.4%), and var. woodii (-30.7%)]. Different responses to climate change call for unique management and conservation decisions for the varieties.

Predicting Quercus gilva distribution dynamics and its response to climate change induced by GHGs emission through MaxEnt modeling

Quercus gilva, an evergreen tree species in Quercus section Cyclobalanopsis, is an ecologically and economically valuable species in subtropical regions of East Asia. Predicting the impact of climate change on potential distribution of Q. gilva can provide a scientific basis for the conservation and utilization of its genetic resources, as well as for afforestation. In this study, 74 distribution records of Q. gilva and nine climate variables were obtained after data collection and processing. Current climate data downloaded from WorldClim and future climate data predicted by four future climate scenarios (2040s SSP1-2.6, 2040s SSP5-8.5, 2060s SSP1-2.6, and 2060s SSP5-8.5) mainly based on greenhouse gases emissions of distribution sites were used in MaxEnt model with optimized parameters to predict distribution dynamics of Q. gilva and its response to climate change. The results showed that the predicted current distribution was consistent with natural distribution of Q. gilva, which was mainly located in Hunan, Jiangxi, Zhejiang, Fujian, Guizhou, and Taiwan provinces of China, as well as Japan and Jeju Island of South Korea. Under current climate conditions, precipitation factors played a more significant role than temperature factors on distribution of Q. gilva, and precipitation of driest quarter (BIO17) is the most important restriction factor for its current distribution (contribution rate of 57.35%). Under future climate conditions, mean temperature of driest quarter (BIO9) was the essential climate factor affecting future change in potential distribution of Q. gilva. As the degree of climatic anomaly increased in the future, the total area of predicted distribution of Q. gilva showed a shrinking trend (decreased by 12.24%-45.21%) and Q. gilva would migrate to high altitudes and latitudes. The research results illustrated potential distribution range and suitable climate conditions of Q. gilva, which can provide essential theoretical references for the conservation, development, and utilization of Q. gilva and other related species.

Assessing the utility of SoilGrids250 for biogeographic inference of plant populations

Inclusion of edaphic conditions in biogeographical studies typically provides a better fit and deeper understanding of plant distributions. Increased reliance on soil data calls for easily accessible data layers providing continuous soil predictions worldwide. Although SoilGrids provides a potentially useful source of predicted soil data for biogeographic applications, its accuracy for estimating the soil characteristics experienced by individuals in small-scale populations is unclear. We used a biogeographic sampling approach to obtain soil samples from 212 sites across the midwestern and eastern United States, sampling only at sites where there was a population of one of the 22 species in Lobelia sect. Lobelia. We analyzed six physical and chemical characteristics in our samples and compared them with predicted values from SoilGrids. Across all sites and species, soil texture variables (clay, silt, sand) were better predicted by SoilGrids (R 2: .25-.46) than were soil chemistry variables (carbon and nitrogen, R 2 ≤ .01; pH, R 2: .19). While SoilGrids predictions rarely matched actual field values for any variable, we were able to recover qualitative patterns relating species means and population-level plant characteristics to soil texture and pH. Rank order of species mean values from SoilGrids and direct measures were much more consistent for soil texture (Spearman r S = .74-.84; all p < .0001) and pH (r S = .61, p = .002) than for carbon and nitrogen (p > .35). Within the species L. siphilitica, a significant association, known from field measurements, between soil texture and population sex ratios could be detected using SoilGrids data, but only with large numbers of sites. Our results suggest that modeled soil texture values can be used with caution in biogeographic applications, such as species distribution modeling, but that soil carbon and nitrogen contents are currently unreliable, at least in the region studied here.

Demographic and ecological niche dynamics of the Vietnam warty newt, Paramesotriton deloustali: Historical climate influences

Quaternary climatic cycles strongly affected the genetic diversification and ranges of organisms, shaping current genetic structures and distribution patterns. Urodeles provide ideal examples for exploring these dynamics over time and across space. In this study, we integrated a phylogeographic approach and ensemble species distribution modeling (eSDM) to infer the historical demography and distribution patterns of the Vietnam warty newt, Paramesotriton deloustali. Mitochondrial data revealed two groups, West and East, which diverged approximately 1.92 million years ago (Mya). Diversification was likely driven by change in the climate during early stages of the Pleistocene, with increasing monsoon and drought intensities. Biogeographic analysis indicated that the newt's current distribution formed as a result of vicariance events. In addition, the two groups occupy distinct ecological niches. Demographic reconstruction showed signs of expansion in the effective population sizes of the two major groups beginning around 0.11 and 0.15 Mya, respectively. However, eSDM showed fluctuating predicted distributions during the last interglacial, last glacial maximum, mid-Holocene, and present. Mountain systems in northern Vietnam are likely to have served as climatic refuges and to have played a crucial role in safeguarding species from the effects of climate change.

Two Species Delimitation of Pseudaulacaspis (Hemiptera: Diaspididae) Based on Morphology, Molecular Clustering, and Niche Differentiation

Pseudaucalaspis pentagona and P. prunicola are notorious pests and commonly feed on various ornamental plants and fruit trees worldwide. The two species share many host-plant species, and are similar in morphological characteristics and life cycle, making it difficult to distinguish to distinguish between them. In this study, morphological characteristics, molecular evidence, and ecological niches were used to define these species. We performed PCA analysis on 22 morphological characteristics that allowed the delineation of the species. We then sequenced the COI gene of both species revealing five populations of P. pentagona and one population of P. prunicola, and the higher support rate could distinguish the two species. We also identified the potential distribution area of the two species based on the MaxEnt niche model, which showed that the degree of niche overlap was high, but that they occupied different niches. Ultimately, we combined three lines of evidence to show that the two species are distinctly different. This study supports species definition using combined morphology, genetics, and ecology and provides a theoretical basis for the effective control of these two pests in the future.

Meteorological data source comparison-a case study in geospatial modeling of potential environmental exposure to abandoned uranium mine sites in the Navajo Nation

Meteorological (MET) data is a crucial input for environmental exposure models. While modeling exposure potential using geospatial technology is a common practice, existing studies infrequently evaluate the impact of input MET data on the level of uncertainty on output results. The objective of this study is to determine the effect of various MET data sources on the potential exposure susceptibility predictions. Three sources of wind data are compared: The North American Regional Reanalysis (NARR) database, meteorological aerodrome reports (METARs) from regional airports, and data from local MET weather stations. These data sources are used as inputs into a machine learning (ML) driven GIS Multi-Criteria Decision Analysis (GIS-MCDA) geospatial model to predict potential exposure to abandoned uranium mine sites in the Navajo Nation. Results indicate significant variations in results derived from different wind data sources. After validating the results from each source using the National Uranium Resource Evaluation (NURE) database in a geographically weighted regression (GWR), METARs data combined with the local MET weather station data showed the highest accuracy, with an average R2 of 0.74. We conclude that local direct measurement-based data (METARs and MET data) produce a more accurate prediction than the other sources evaluated in the study. This study has the potential to inform future data collection methods, leading to more accurate predictions and better-informed policy decisions surrounding environmental exposure susceptibility and risk assessment.

Different GCMs yet similar outcome: predicting the habitat distribution of Shorea robusta C.F. Gaertn. in the Indian Himalayas using CMIP5 and CMIP6 climate models

Climate change impact on the habitat distribution of umbrella species presents a critical threat to the entire regional ecosystem. This is further perilous if the species is economically important. Sal (Shorea robusta C.F. Gaertn.), a climax forest forming Central Himalayan tree species, is one of the most valuable timber species and provides several ecological services. Sal forests are under threat due to over-exploitation, habitat destruction, and climate change. Sal's poor natural regeneration and its unimodal density-diameter distribution in the region illustrate the peril to its habitat. We, modelled the current as well as future distribution of suitable sal habitats under different climate scenarios using 179 sal occurrence points and 8 bioclimatic environmental variables (non-collinear). The CMIP5-based RCP4.5 and CMIP6-based SSP245 climate models under 2041-2060 and 2061-2080 periods were used to predict the impact of climate change on sal's future potential distribution area. The niche model results predict the mean annual temperature and precipitation seasonality as the most influential sal habitat governing variables in the region. The current high suitability region for sal was 4.36% of the total geographic area, which shows a drastic decline to 1.31% and 0.07% under SSP245 for 2041-60 and 2061-80, respectively. The RCP-based models predicted more severe impact than SSP; however, both RCP and SSP models showed complete loss of high suitability regions and overall shift of species northwards in the Uttarakhand state. We could identify the current and future suitable habitats for conserving sal population through assisted regeneration and management of other regional issues.

Potential dynamic changes of single-season rice planting suitability across China

As an important food crop in China, changes in suitable areas for rice planting are critical to agricultural production. In this study, the maximum entropy model (MaxEnt) was utilized to pick the main climatic factors affecting single-season rice planting distribution and project the potential changes under RCP4.5 and RCP8.5 scenarios. It was clear that rice planting distribution was significantly affected by annual total precipitation, the accumulated temperature during a period in which daily temperature was ≥ 10 °C, the moisture index, total precipitation during April-September, and continuous days during the period of daily temperature ≥ 18 °C, with their contribution being 97.6%. There was a continuous decrease in the area of good and high suitability for rice planting projected from 2021-2040 to 2061-2080, with a respective value ranging from 1.49 × 10⁶ km² to 0.93 × 10⁶ km² under the RCP4.5 scenario and from 1.42 × 10⁶ km² to 0.66 × 10⁶ km² under RCP8.5 scenarios. In 2081-2100, there was a bit increase in the area of good and high suitability under the RCP4.5 scenario. The most significant increases in good and high suitability were detected in Northeast China, while obvious decreases were demonstrated in the Yangtze River Basin which might be exposed to extreme temperature threat. The spatial potential planting center was characterized by the largest planting area in 25°N-37°N and 98°E-134°E. The north boundary and center of rice cultivation arose to 53.5°N and 37.52°N, respectively. These potential distributions for single-season rice under future climate change can provide a theoretical basis for optimizing rice planting layout, improving cultivation, and adjusting variety and management systems in response to climate change.

Climatic factors and human disturbance influence ungulate species distribution on the Qinghai-Tibet Plateau

Due to human activities and climate change, the habitats of ungulate species on the Qinghai-Tibet Plateau have been greatly affected in recent decades. In this study, the distribution patterns of 19 ungulate species on the Qinghai-Tibet Plateau were identified based on MaxEnt model in the past (1960-1990) and current periods (2000-2015). Then the changes of their habitat distribution and the species richness in different periods were compared. Finally, the Zonation model was used to identify the key protected areas of ungulate species. The results show that the MaxEnt model can well predict the distribution of ungulate species. Most ungulate species are mainly distributed in the southeast of the Qinghai-Tibet Plateau. The distance to lakes and precipitation are the main factors affecting the distribution of most ungulate species. The habitats originally located in the southeast of the Qinghai-Tibet Plateau have mainly extended northeastwards, while the habitats originally located in the northwest has been largely lost. The changes in the habitats of ungulate species in the southeast and northwest are diametrically opposite. The key protected areas identified by Zonation model are mainly located in the southeast of the Qinghai-Tibet Plateau. The existing nature reserves can effectively protect the suitable habitats of the Tibetan antelope, Tibetan wild ass and wild yak. This research can provide scientific basis for coordinating the contradiction between development and protection and promoting the biodiversity conservation on the Qinghai-Tibet Plateau.

Facilitated Adaptation as A Conservation Tool in the Present Climate Change Context: A Methodological Guide

Climate change poses a novel threat to biodiversity that urgently requires the development of adequate conservation strategies. Living organisms respond to environmental change by migrating to locations where their ecological niche is preserved or by adapting to the new environment. While the first response has been used to develop, discuss and implement the strategy of assisted migration, facilitated adaptation is only beginning to be considered as a potential approach. Here, we present a review of the conceptual framework for facilitated adaptation, integrating advances and methodologies from different disciplines. Briefly, facilitated adaptation involves a population reinforcement that introduces beneficial alleles to enable the evolutionary adaptation of a focal population to pressing environmental conditions. To this purpose, we propose two methodological approaches. The first one (called pre-existing adaptation approach) is based on using pre-adapted genotypes existing in the focal population, in other populations, or even in closely related species. The second approach (called de novo adaptation approach) aims to generate new pre-adapted genotypes from the diversity present in the species through artificial selection. For each approach, we present a stage-by-stage procedure, with some techniques that can be used for its implementation. The associated risks and difficulties of each approach are also discussed.

Chill coma recovery of Ceratitis capitata adults across the Northern Hemisphere

The Mediterranean fruit fly, Ceratitis capitata (Diptera: Tephritidae), is an invasive pest, that is currently expanding its geographic distribution from the Mediterranean coasts to more temperate areas of Europe. Given that low temperature is a primary determinant of insect species' range boundaries especially in the Northern Hemisphere with pronounced seasonality, we used chill coma recovery time for assessing latitudinal clines in basal chill tolerance of C. capitata adults. We selected six populations obtained from areas with broad climatic variability based on the main bioclimatic variables of temperature and precipitation, spanning a latitudinal range of about 19° from Middle East to Central Europe. Adults were exposed to 0 °C for 4 h, and time to regain the typical standing position of a fly at 25 °C were recorded. The post-stress survival after a period of 8 days was also recorded. Results revealed that adults from Israel and Austria were less chill tolerant than those from Greece, resulting in curvilinear trends with latitude. Analysis of macroclimatic conditions revealed combined effects of latitude (as a proxy of photoperiod) and macroclimatic conditions on chill coma recovery time. Nonetheless, there was not a deleterious effect on post-recovery survival, except for flies obtained from the northern most point (Vienna, Austria). Overall, it seems that evolutionary patterns of basal chill coma recovery time of C. capitata adults are driven mainly by local climatic variability.

Prediction of the dynamic distribution for Eucheuma denticulatum (Rhodophyta, Solieriaceae) under climate change in the Indo-Pacific Ocean

Eucheuma is one of the most important commercial red seaweeds in Southeast Asia, and plays an important role in the global seaweed aquaculture. It is expected to exhibit great responses to ocean warming. Here, we used maximum entropy species distribution models (SDMs) to estimate the suitable habitat of Eucheuma denticulatum under present conditions, and to predict the future range dynamics under the four representative concentration pathway (RCP) scenarios. The best marine environmental factors for E. denticulatum distribution modeling were distance to shore, sea surface temperature and currents velocity. Our results showed that E. denticulatum' distributions would contract in the Central Indo-Pacific Ocean, especially the regions of the Sunda Shelf, while expanding poleward along the south coast of Australia in 2100. Our study provided important knowledge for the prediction of the tropical seaweed distribution, conservation and sustainable developments of E. denticulatum in the future.

Evaluation of tropical-temperate transitions: An example of climatic characterization in the Asian Palmate group of Araliaceae

PREMISE

There has been a great increase in using climatic data in phylogenetic studies over the past decades. However, compiling the high-quality spatial data needed to perform accurate climatic reconstructions is time-consuming and can result in poor geographical coverage. Therefore, researchers often resort to qualitative approximations. Our aim was to evaluate the climatic characterization of the genera of the Asian Palmate Group (AsPG) of Araliaceae as an exemplar lineage of plants showing tropical-temperate transitions.

METHODS

We compiled a curated worldwide spatial database of the AsPG genera and created five raster layers representing bioclimatic regionalizations of the world. Then, we crossed the database with the layers to climatically characterize the AsPG genera.

RESULTS

We found large disagreement in the climatic characterization of genera among regionalizations and little support for the climatic nature of the tropical-temperate distribution of the AsPG. Both results are attributed to the complexity of delimiting tropical, subtropical, and temperate climates in the world and to the distribution of the study group in regions with transitional climatic conditions.

CONCLUSIONS

The complexity in the climatic classification of this example of the tropical-temperate transitions calls for a general climatic revision of other tropical-temperate lineages. In fact, we argue that, to properly evaluate tropical-temperate transitions across the tree of life, we cannot ignore the complexity of distribution ranges.

Impacts of environment and human activity on grid-scale land cropping suitability and optimization of planting structure, measured based on the MaxEnt model

Making full use of agricultural resource endowment, determining the planting suitability of areas for different crops according to the environment and human activities, and optimizing planting structure are important ways to ensure stable increases in crop yield and improve food production capacity. Taking Songhua River Basin (SRB) as an example, this study used geographic distribution information on different crops and the Maximum Entropy (MaxEnt) model to determine the degree of suitability of land in SRB for cropping, and to optimize the layout of crop planting structure. The results showed that the main factors affecting land suitability for different crops, with a combined contribution >80%, were population density, Distance from road to cultivated land, normalized difference vegetation index, and total phosphorus. Under the joint influence of the environment and human activity, the total unsuitable area of the four crops became much more extensive, with the unsuitable area of soybean being the largest (173 thousand km²) and the smallest for wheat (128 thousand km²). The highly suitable area was largest for wheat (2 thousand km²), while the other three crops were less than 2 thousand km². Suitable distribution areas for all four crops were mainly located in the center of the basin (Songnen Plain) and in a wedge in the northeast corner (Sanjiang Plain). The relationships between different crops and environment and human activities revealed that crop suitability distribution is mainly determined by human activities, rather than the environment. These results provide a scientific basis for optimizing crop layout and improving the planting system, ensuring the security of food production.

Dark-colored Oncocyclus irises in Israel analyzed by AFLP, whole chloroplast genome sequencing and species distribution modeling

The Haynei is one of seven species aggregates (clusters of species having similar flower morphology) recognized in section Oncocyclus of genus Iris. This aggregate, characterized by dark-colored flowers, is represented by six species in Israel and adjacent Jordan. There is, however, no knowledge of the genetic relationship of these species making verification of their taxonomic status impossible. We investigated genetic variation in this group using analysis of whole chloroplast genomes and amplified fragment length polymorphism (AFLP). We also used species distribution modeling (SDM) to predict species ranges under current climatic conditions. We found some population groups within the currently recognized species of section Oncocyclus to represent dramatically different genetic entities which devaluates a general trend of merging many previously recognized species of section Oncocyclus based on their flower morphology. Despite the importance of homoploid hybridization in this group’s evolution and some apparently sporadically happening inter-specific gene flow, the main evolutionary forces in Oncocyclus appear to be vicariance and spatial isolation. Our findings suggest that some of the currently recognized species in section Oncocyclus need revision. A revision must be based on genetic analyses allowing the reconstruction of ancestry and recognition of the importance of vicariance and spatial isolation in the evolution of this group. The implications of the present findings for conservation are discussed.

Ecological niche modeling for reintroduction and conservation of Aristolochia cathcartii Hook.f. & Thomson (Aristolochiaceae), a threatened endemic plant in Assam, India

Aristolochia cathcartii Hook.f. & Thomson is a medicinal plant species native to Assam (India). Karbi people have traditionally used the plant to treat a variety of ailments. The population stock of this species has been rapidly depleting in its natural habitats due to over-utilization, habitat fragmentation, and other anthropogenic activities. Extensive field surveys were carried out to investigate the population status of A. cathcartii in various forest areas of Assam’s Karbi Anglong district. In 20 km of transects, a total of 36 quadrats were observed. A. cathcartii density, frequency of occurrence, and abundance were recorded to be 0.65, 17.8, and 3.81, respectively. Ecological niche modelling was used to identify suitable habitat for the reintroduction and conservation of this plant in Assam in order to prevent its extinction in the future. The maximum entropy distribution modelling algorithm was used to identify suitable areas and habitat for the species’ reintroduction and conservation. Primary data on the occurrence of A. cathcartii was gathered from the natural habitat of Karbi Anglong district, Assam, for modelling. The model identified various forest areas in northeastern India that have suitable climatic conditions for plant reinforcement. 

Adaptation and ecological speciation in seasonally varying environments at high latitudes: Drosophila virilis group

Living in high latitudes and altitudes sets specific requirements on species’ ability to forecast seasonal changes and to respond to them in an appropriate way. Adaptation into diverse environmental conditions can also lead to ecological speciation through habitat isolation or by inducing changes in traits that influence assortative mating. In this review, we explain how the unique time-measuring systems of Drosophila virilis group species have enabled the species to occupy high latitudes and how the traits involved in species reproduction and survival exhibit strong linkage with latitudinally varying photoperiodic and climatic conditions. We also describe variation in reproductive barriers between the populations of two species with overlapping distributions and show how local adaptation and the reinforcement of prezygotic barriers have created partial reproductive isolation between conspecific populations. Finally, we consider the role of species-specific chromosomal inversions and the X chromosome in the development of reproductive barriers between diverging lineages.

Niche Divergence at Intraspecific Level in the Hyrcanian Wood Frog, Rana pseudodalmatina: A Phylogenetic, Climatic, and Environmental Survey

The role of ecological niche divergence in lineage speciation has recently stimulated the interest of evolutionary biologists and ecologists. Phylogenetic analysis has revealed that the Hyrcanian wood frog, Rana pseudodalmatina, has diverged into two western and eastern regional clades (WRC and ERC) within the Hyrcanian forest. The goal of this study was to investigate whether the ecological niches of WRC and ERC are conserved or diverged, as well as to figure out what variables promote niche conservatism or divergence. For this purpose, the maximum entropy model was employed to assess environmental niche modeling in geographical (G) space utilizing climatic and macro-environmental data. The niche overlap, equivalency, and similarity tests based on PCAenv analyses were used to assess niche divergence or conservatism in environmental (E) space. The findings strongly support the hypothesis that WRC and ERC have undergone substantial niche divergence and are constrained by a unique set of climatic and macro-environmental conditions. This study by ecological niche comparisons based on phylogenetic data provides new insights into the exploration of species diversification processes in the Hyrcanian forests.

Assessing the Impact of Climate Change on Potential Distribution of Meconopsis punicea and Its Influence on Ecosystem Services Supply in the Southeastern Margin of Qinghai-Tibet Plateau

Meconopsis punicea is an iconic ornamental and medicinal plant whose natural habitat has degraded under global climate change, posing a serious threat to the future survival of the species. Therefore, it is critical to analyze the influence of climate change on possible distribution of M. punicea for conservation and sustainable utilization of this species. In this study, we used MaxEnt ecological niche modeling to predict the potential distribution of M. punicea under current and future climate scenarios in the southeastern margin region of Qinghai-Tibet Plateau. Model projections under current climate show that 16.8% of the study area is suitable habitat for Meconopsis. However, future projections indicate a sharp decline in potential habitat for 2050 and 2070 climate change scenarios. Soil type was the most important environmental variable in determining the habitat suitability of M. punicea, with 27.75% contribution to model output. Temperature seasonality (16.41%), precipitation of warmest quarter (14.01%), and precipitation of wettest month (13.02%), precipitation seasonality (9.41%) and annual temperature range (9.24%) also made significant contributions to model output. The mean elevation of suitable habitat for distribution of M. punicea is also likely to shift upward in most future climate change scenarios. This study provides vital information for the protection and sustainable use of medicinal species like M. punicea in the context of global environmental change. Our findings can aid in developing rational, broad-scale adaptation strategies for conservation and management for ecosystem services, in light of future climate changes.

Current and future distribution of the deciduous shrub Hydrangea macrophylla in China estimated by MaxEnt

Climate change has a significant impact on the growth and distribution of vegetation worldwide. Hydrangea macrophylla is widely distributed and considered a model species for studying the distribution and responses of shrub plants under climate change. These results can inform decision-making regarding shrub plant protection, management, and introduction of germplasm resources, and are of great importance for formulating ecological countermeasures to climate change in the future. We used the maximum entropy model to predict the change, scope expansion/reduction, centroid movement, and dominant climate factors that restrict the growth and distribution of H. macrophylla in China under current and future climate change scenarios. It was found that both precipitation and temperature affect the distribution of suitable habitat for H. macrophylla. Akaike information criterion (AICc) was used to select the feature combination (FC) and the regularization multiplier (RM). After the establishment of the optimal model (FC = QP, RM = 0.5), the complexity and over-fitting degree of the model were low (delta AICc = 0, omission rate = 0.026, difference between training and testing area under the curve values = 0.0009), indicating that it had high accuracy in predicting the potential geographical distribution of H. macrophylla (area under the curve = 0.979). Overall, from the current period to future, the potential suitable habitat of this species in China expanded to the north. The greenhouse effect caused by an increase in CO2 emissions would not only increase the area of high-suitability habitat in Central China, but also expand the area of total suitable habitat in the north. Under the maximum greenhouse gas emission scenario (RCP8.5), the migration distance of the centroid was the longest (e.g., By 2070s, the centroids of total and highly suitable areas have shifted 186.15 km and 89.84 km, respectively).

Genetic structure and ecological niche segregation of Indian gray mongoose (Urva edwardsii) in Iran

Combining genetic data with ecological niche models is an effective approach for exploring climatic and nonclimatic environmental variables affecting spatial patterns of intraspecific genetic variation. Here, we adopted this combined approach to evaluate genetic structure and ecological niche of the Indian gray mongoose (Urva edwardsii) in Iran, as the most western part of the species range. Using mtDNA, we confirmed the presence of two highly differentiated clades. Then, we incorporated ensemble of small models (ESMs) using climatic and nonclimatic variables with genetic data to assess whether genetic differentiation among clades was coupled with their ecological niche. Climate niche divergence was also examined based on a principal component analysis on climatic factors only. The relative habitat suitability values predicted by the ESMs for both clades revealed their niche separation. Between-clade climate only niche comparison revealed that climate space occupied by clades is similar to some extent, but the niches that they utilize differ between the distribution ranges of clades. We found that in the absence of evidence for recent genetic exchanges, distribution models suggest the species occurs in different niches and that there are apparent areas of disconnection across the species range. The estimated divergence time between the two Iranian clades (4.9 Mya) coincides with the uplifting of the Zagros Mountains during the Early Pliocene. The Zagros mountain-building event seems to have prevented the distribution of U. edwardsii populations between the western and eastern parts of the mountains as a result of vicariance events. Our findings indicated that the two U. edwardsii genetic clades in Iran can be considered as two conservation units and can be utilized to develop habitat-specific and climate change-integrated management strategies.

Brassica rapa Domestication: Untangling Wild and Feral Forms and Convergence of Crop Morphotypes

The study of domestication contributes to our knowledge of evolution and crop genetic resources. Human selection has shaped wild Brassica rapa into diverse turnip, leafy, and oilseed crops. Despite its worldwide economic importance and potential as a model for understanding diversification under domestication, insights into the number of domestication events and initial crop(s) domesticated in B. rapa have been limited due to a lack of clarity about the wild or feral status of conspecific noncrop relatives. To address this gap and reconstruct the domestication history of B. rapa, we analyzed 68,468 genotyping-by-sequencing-derived single nucleotide polymorphisms for 416 samples in the largest diversity panel of domesticated and weedy B. rapa to date. To further understand the center of origin, we modeled the potential range of wild B. rapa during the mid-Holocene. Our analyses of genetic diversity across B. rapa morphotypes suggest that noncrop samples from the Caucasus, Siberia, and Italy may be truly wild, whereas those occurring in the Americas and much of Europe are feral. Clustering, tree-based analyses, and parameterized demographic inference further indicate that turnips were likely the first crop type domesticated, from which leafy types in East Asia and Europe were selected from distinct lineages. These findings clarify the domestication history and nature of wild crop genetic resources for B. rapa, which provides the first step toward investigating cases of possible parallel selection, the domestication and feralization syndrome, and novel germplasm for Brassica crop improvement.

Of pandas, fossils, and bamboo forests: ecological niche modeling of the giant panda (Ailuropoda melanoleuca) during the Last Glacial Maximum

The giant panda (Ailuropoda melanoleuca) is the most basal living species in the phylogeny of the family Ursidae, with a specialized diet composed of a variety of bamboo species. The evolutionary history and past distribution patterns of the giant panda remain poorly understood. Our aim was to integratively apply distinct methods to evaluate the evolutionary history and distributional patterns of the giant panda; these included phylogeography, ecological niche modeling (ENM), and fossil data. To this end, we characterized the panda’s past and present ecological niches and the environmental conditions that define them. To estimate the panda’s phylogeographic patterns and the environmental conditions (precipitation and temperature) available across its historical geographic range, we evaluated its past distribution during the Last Glacial Maximum (LGM). Considering that modeling biotic interactions (e.g., foraging, predation) is still an enormous challenge, we propose a novel modeling strategy based on the panda’s specialized diet, using an ensemble of three bamboo genera with distribution across the panda’s historical geographic range. Finally, we tested the accuracy of our approach by evaluating its ability to predict the LGM fossils. Our results support that the panda’s diversification across its distribution happened ca. 2.7 million years (Mya), coinciding with the likely period when the panda changed from a carnivorous to a vegetarian diet (from the Pleistocene to the Pliocene), acquiring its exclusively bamboo-feeding habits until the mid-Holocene. Our findings provide evidence of a historical directional niche change along which the panda has currently reached the lower limits of temperature and precipitation conditions existing on the geography where its food is available. Our proposed ENM based on the panda’s food habits accurately predicted 85.7% of the LGM fossils, in stark contrast with the traditional approach of modeling the distribution of species by using exclusively its own occurrences. These results provide insights on how to include Eltonian components to undertake more robust ENM when only abiotic variables are available. We emphasize the importance of integrating fossil information, whenever available, into the niche modeling process to include the historical component when estimating species ecological niches.

Multiple paths to cold tolerance: the role of environmental cues, morphological traits and the circadian clock gene vrille

Background

Tracing the association between insect cold tolerance and latitudinally and locally varying environmental conditions, as well as key morphological traits and molecular mechanisms, is essential for understanding the processes involved in adaptation. We explored these issues in two closely-related species, Drosophila montana and Drosophila flavomontana, originating from diverse climatic locations across several latitudes on the coastal and mountainous regions of North America. We also investigated the association between sequence variation in one of the key circadian clock genes, vrille, and cold tolerance in both species. Finally, we studied the impact of vrille on fly cold tolerance and cold acclimation ability by silencing it with RNA interference in D. montana.

Results

We performed a principal component analysis (PCA) on variables representing bioclimatic conditions on the study sites and used latitude as a proxy of photoperiod. PC1 separated the mountainous continental sites from the coastal ones based on temperature variability and precipitation, while PC2 arranged the sites based on summer and annual mean temperatures. Cold tolerance tests showed D. montana to be more cold-tolerant than D. flavomontana and chill coma resistance (CT_min) of this species showed an association with PC2. Chill coma recovery time (CCRT) of both species improved towards northern latitudes, and in D. flavomontana this trait was also associated with PC1. D. flavomontana flies were darkest in the coast and in the northern mountainous populations, but coloration showed no linkage with cold tolerance. Body size decreased towards cold environments in both species, but only within D. montana populations largest flies showed fastest recovery from cold. Finally, both the sequence analysis and RNAi study on vrille suggested this gene to play an essential role in D. montana cold resistance and acclimation, but not in recovery time.

Conclusions

Our study demonstrates the complexity of insect cold tolerance and emphasizes the need to trace its association with multiple environmental variables and morphological traits to identify potential agents of natural selection. It also shows that a circadian clock gene vrille is essential both for short- and long-term cold acclimation, potentially elucidating the connection between circadian clock system and cold tolerance.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-021-01849-y.

Linking population-level and microevolutionary processes to understand speciation dynamics at the macroevolutionary scale

Although speciation dynamics have been described for several taxonomic groups in distinct geographic regions, most macroevolutionary studies still lack a detailed mechanistic view on how or why speciation rates change. To help partially fill this gap, we suggest that the interaction between the time taken by a species to geographically expand and the time populations take to evolve reproductive isolation should be considered when we are trying to understand macroevolutionary patterns. We introduce a simple conceptual index to guide our discussion on how demographic and microevolutionary processes might produce speciation dynamics at macroevolutionary scales. Our framework is developed under different scenarios: when speciation is mediated by geographical or resource-partitioning opportunities, and when diversity is limited or not. We also discuss how organismal intrinsic properties and different overall geographical settings can influence the tempo and mode of speciation. We argue that specific conditions observed at the microscale might produce a pulse in speciation rates even without a pulse in either climate or physical barriers. We also propose a hypothesis to reconcile the apparent inconsistency between speciation measured at the microscale and macroscale, and emphasize that diversification rates are better seen as an emergent property. We hope to bring the reader's attention to interesting mechanisms to be further studied, to motivate the development of new theoretical models that connect microevolution and macroevolution, and to inspire new empirical and methodological approaches to more adequately investigate speciation dynamics either using neontological or paleontological data.

Niche differentiation in a postglacial colonizer, the bank vole Clethrionomys glareolus

Species-level environmental niche modeling has been crucial in efforts to understand how species respond to climate variation and change. However, species often exhibit local adaptation and intraspecific niche differences that may be important to consider in predicting responses to climate. Here, we explore whether phylogeographic lineages of the bank vole originating from different glacial refugia (Carpathian, Western, Eastern, and Southern) show niche differentiation, which would suggest a role for local adaptation in biogeography of this widespread Eurasian small mammal. We first model the environmental requirements for the bank vole using species-wide occurrences (210 filtered records) and then model each lineage separately to examine niche overlap and test for niche differentiation in geographic and environmental space. We then use the models to estimate past [Last Glacial Maximum (LGM) and mid-Holocene] habitat suitability to compare with previously hypothesized glacial refugia for this species. Environmental niches are statistically significantly different from each other for all pairs of lineages in geographic and environmental space, and these differences cannot be explained by habitat availability within their respective ranges. Together with the inability of most of the lineages to correctly predict the distributions of other lineages, these results support intraspecific ecological differentiation in the bank vole. Model projections of habitat suitability during the LGM support glacial survival of the bank vole in the Mediterranean region and in central and western Europe. Niche differences between lineages and the resulting spatial segregation of habitat suitability suggest ecological differentiation has played a role in determining the present phylogeographic patterns in the bank vole. Our study illustrates that models pooling lineages within a species may obscure the potential for different responses to climate change among populations.

Phylogeography and demographic expansion in the widely distributed horned passalus beetle, Odontotaenius disjunctus (coleoptera: Passalidae)

Dynamic climatic oscillations during the Pleistocene had profound effects on the distribution of species across North America. Although the role of historical climate change on speciation remains controversial, the impact on genetic variation within species has been well documented. Analyses of mtDNA sequences from the cytochrome oxidase I gene (911 bp) for 115 individuals of Odontotaenius disjunctus was combined with ecological niche modelling (ENM) to infer the demographic and population differentiation scenarios under present and past conditions. We inferred three lineages that diverged during the Pleistocene and replace each other geographically across the eastern United States. One of these lineages traverses previously identified genetic barriers for terrestrial animals including the Mississippi and Apalachicola Rivers and the Appalachian Mountains. We observed overlapping ranges between two haplotype groups as well as a region of secondary contact associated with ecological transition zone in northern Florida. The two continental lineages depict a genetic signature of a recent population increase associated with expanding niche envelope, whereas the clade restricted to peninsular Florida shows stable populations in a shrinking niche envelope. Given the lack of ecological separation, overlapping distribution of haplogroups and the presence of secondary contact zones, the taxonomic status of these lineages must await robust testing using multilocus DNA data to assess species boundaries.

An escape-to-radiate model for explaining the high plant diversity and endemism in campos rupestres†

With extraordinary levels of plant diversity and endemism, the Brazilian campos rupestres across the Espinhaço Range have a species/area ratio 40 times higher than the lowland Amazon. Although diversification drivers in campos rupestres remain a matter of debate, the Pleistocene refugium hypothesis (PRH) is often adopted as the most plausible explanation for their high diversity. The PRH has two main postulates: highland interglacial refugia and a species pump mechanism catalysed by climatic changes. We critically assessed studies on campos rupestres diversification at different evolutionary levels and conclude that most of them are affected by sampling biases, unrealistic assumptions or inaccurate results that do not support the PRH. By modelling the palaeo-range of campos rupestres based on the distribution of 1123 species of vascular plants endemic to the Espinhaço Range and using climate and edaphic variables, we projected a virtually constant suitable area for campos rupestres across the last glacial cycle. We challenge the great importance placed on Pleistocene climatic oscillations in campos rupestres plant diversification and offer an alternative explanation named escape-to-radiate model, which emphasizes niche shifts. Under this biogeographic model of diversification, the long-term fragmentation of campos rupestres combined with recurrent extinctions after genetic drift and sporadic events of adaptive radiation may provide an explanation for the current diversity and endemism in the Espinhaço Range. We conclude that long-term diversification dynamics in campos rupestres are mainly driven by selection, while most endemic diversity is ephemeral, extremely fragile and mainly driven by drift.

Niche differentiation between deeply divergent phylogenetic lineages of an endemic newt: implications for Species Distribution Models

Species distribution models (SDMs) treat species as a single unit, neglecting intraspecific variation. Few studies address the impact of intraspecific variation on SDM performance, and none of them account for the well-known inter-algorithm variability in prediction performance. The endemic Iberian amphibian Lissotriton boscai comprises two geographically highly structured phylogenetic lineages, which allowed us to explore how intraspecific variation affects the overall performance of SDMs and the predicted ecological niche. We built species and lineage distribution models using three different presence-only algorithms. We also tested for niche overlap, niche equivalency and niche similarity, using an ordination technique. We found differences in the predicted potential distribution of the two lineages and the underlying environmental factors. Moreover, intraspecific differences in model predictive capacity existed irrespective of which algorithm was used to build the distribution models. This was coupled with lineages showing a low degree of niche overlap and occurring in relatively different environmental niches spaces. The intraspecific variation observed in L. boscai led to an improved intraspecific predictivity of the lineage level based-distribution models. There was partial spatial agreement between the niche overlap and independently reported secondary contact zones. Thus SDMs built only at the species level may be too naive to predict impacts of global change on species distributions.

Hybridization and hybrid zone stability between two lizards explained by population genetics and niche quantification

Understanding the factors that affect hybridization is an important issue in the study of species evolution. In this work, we analyse the genetic structure of two lizard species, Salvator merianae and Salvator rufescens, at a microscale within a climatic niche analysis framework, to reveal the main factors that contribute to the stability of their hybrid zone. We assess the effect of climate in hybridization by quantifying and decomposing the niche overlap of both species. Using a mitochondrial and a nuclear marker, we find that hybridization is frequent and is not restricted to the sympatric region. The gene flow is mainly from S. rufescens to S. merianae, with introgression into the range of S. merianae. Also, S. merianae would have long been present in the area, while S. rufescens appears to be a recent colonizer. The climate contributes to the population structure of S. merianae, but not to that of S. rufescens. The niches occupied by S. rufescens in the hybrid zone and the non-hybrid zone are similar, while the niches of S. merianae are different. Our results do not fit previous models of hybrid zone stability, suggesting the need to develop new models that consider the evolutionary factors that can differentially affect parental species and hybrids.

Genetics of Lactose Intolerance: An Updated Review and Online Interactive World Maps of Phenotype and Genotype Frequencies

In humans the ability to digest milk lactose is conferred by a β-galactosidase enzyme called lactase-phlorizin hydrolase (LPH). While in some humans (approximately two-thirds of humankind) the levels of this enzyme decline drastically after the weaning phase (a trait known as lactase non-persistence (LNP)), some other individuals are capable of maintaining high levels of LPH lifelong (lactase persistence (LP)), thus being able to digest milk during adulthood. Both lactase phenotypes in humans present a complex genetic basis and have been widely investigated during the last decades. The distribution of lactase phenotypes and their associated single nucleotide polymorphisms (SNPs) across human populations has also been extensively studied, though not recently reviewed. All available information has always been presented in the form of static world maps or large dimension tables, so that it would benefit from the newly available visualization tools, such as interactive world maps. Taking all this into consideration, the aims of the present review were: (1) to gather and summarize all available information on LNP and LP genetic mechanisms and evolutionary adaptation theories, and (2) to create online interactive world maps, including all LP phenotype and genotype frequency data reported to date. As a result, we have created two online interactive resources, which constitute an upgrade over previously published static world maps, and allow users a personalized data exploration, while at the same time accessing complete reports by population or ethnicity.

Optimized Maxent Model Predictions of Climate Change Impacts on the Suitable Distribution of Cunninghamia lanceolata in China

Climate change significantly influences changes in ecological phenomena and processes, such as species distribution and phenology, thus accelerating the rate of species extinction or prosperity. Climate change is considered to be one of the most important threats to global biodiversity in the 21st century and will pose significant challenges to biodiversity conservation in the future. The use of niche modelling to predict changes in the suitable distribution of species under climate change scenarios is becoming a hot topic of biological conservation. In this study, we use data from China’s National Forest Continuous Inventory as well as specimen collection data of Cunninghamia lanceolata (Lamb.) Hook to run optimized Maxent models to predict potential suitable distribution of the species in the present day, 2050s, and 2070s under different climate change scenarios in China. In the modeling process, the most important uncorrelated variables were chosen, and the sample-size-adjusted Akaike information criterion (AICc) was used to select the optimal combination of feature type and regularization multiplier. Variable selection reduced the number of variables used and the complexity of the model, and the use of the AICc reduced overfitting. Variables relating to precipitation were more important than temperature variables in predicting C. lanceolata distribution in the optimal model. The predicted suitable distribution areas of C. lanceolata were different for the different periods under different climate change scenarios, with the centroids showing a degree of northward movement. The suitable distribution area is predicted to become more fragmented in the future. Our results reveal the climate conditions required for the suitable distribution of C. lanceolata in China and the likely changes to its distribution pattern in the future, providing a scientific basis for the sustainable management, protection, and restoration of the suitable habitat of this economically important tree species in the context of climate change.

Comparative studies on population genetic structure of two closely related selfing and outcrossing Zingiber species in Hainan Island

How mating system impacts the genetic diversity of plants has long fascinated and puzzled evolutionary biologists. Numerous studies have shown that self-fertilising plants have less genetic diversity at both the population and species levels than outcrossers. However, the phylogenetic relationships between species and correlated ecological traits have not been accounted for in these previous studies. Here, we conduct a comparative population genetic study of two closely related selfing and outcrossing Zingiber species, with sympatric distribution in Hainan Island, and obtain a result contrary to previous studies. The results indicate that selfing Z. corallinum can maintain high genetic diversity through differentiation intensified by local adaptation in populations across the species’ range. In contrast, outcrossing Z. nudicarpum preserves high genetic diversity through gene exchange by frequent export of pollen within or among populations. Contrary to expectations, the major portion of genetic variation of outcrossing Z. nudicarpum may exist among populations, depending on the dispersal ability of pollen and seed. Our results also reveal that the main factor affecting population structure of selfing Z. corallinum is mountain ranges, followed by a moist climate, while that of outcrossing Z. nudicarpum is likely moisture, but not mountain ranges, due to gene flow via pollen.

Do selfing species have greater niche breadth? Support from ecological niche modeling

We explore the relationship between plant mating system (selfing or outcrossing) and niche breadth to gain new insights into processes that drive species distributions. Using a comparative approach with highly selfing versus highly outcrossing sister species, we test the extent to which: (1) species pairs have evolved significant niche divergence and less niche overlap, (2) selfers have wider niche breadths than outcrossers or vice versa, and (3) niches of selfers and outcrossers are defined by significant differences in environmental variables. We applied predictive ecological niche modeling approaches to estimate and contrast niche divergence, overlap and breadth, and to identify key environmental variables associated with each species' niche for seven sister species with divergent mating systems. Data from 4862 geo-referenced herbarium occurrence records were compiled for 14 species in Collinsia and Tonella (Plantaginaceae) and 19 environmental variables associated with each record. We found sister species display significant niche divergence, though not as a function of divergence time, and overall, selfers have significantly wider niche breadths compared to their outcrossing sisters. Our results suggest that a selfing mating system likely contributes to the greater capacity to reach, reproduce, establish, and adapt to new habitats, which increases niche breadth of selfers.

Sufficient versus optimal climatic stability during the Late Quaternary: using environmental quality to guide phylogeographic inferences in a Neotropical montane system

Quaternary climatic oscillations affected species distributions worldwide, creating cycles of connectivity and isolation that impacted population demography and promoted lineage divergence. These effects have been well studied in temperate regions. Taxa inhabiting mesic montane habitats in tropical ecosystems show high levels of endemism and diversification in the distinct mountain ranges they inhabit; such a pattern has commonly been ascribed to past climatic oscillations, but few phylogeographic studies have tested this hypothesis. Here, we combine ecological niche models of species distributions with molecular data to study phylogeographic patterns in two rodents endemic to the highlands of Costa Rica and western Panama (Reithrodontomys creper and Nephelomys devius). In so doing, we apply a novel approach that incorporates a basic ecological principle: the expected positive relationship between environmental suitability and population abundance. Specifically, we use niche models to predict potential patterns of population connectivity and stability of different suitability levels during climatic extremes of the last glacial–interglacial cycle; we then test these predictions with population genetic analyses of a mitochondrial and a nuclear marker. The detailed predictions arising from the different levels of suitability were moderately to highly congruent with the molecular data depending on the species. Overall, results suggest that in these tropical montane ecosystems, cycles of population connectivity and isolation followed a pattern opposite to that typically described for temperate or lowland tropical ecosystems: namely, higher connectivity during the colder glacials, with isolation in montane refugia during the interglacials, including today. Nevertheless, the individualistic patterns for each species indicate a potentially wide gamut of phylogeographic histories reflecting particularities of their niches. Taken together, this study illustrates how phylogeographic inferences may benefit from niche model outputs that provide more detailed predictions of connectivity and finer characterizations of potential refugia through time.

Desiccation resistance and pigmentation variation reflects bioclimatic differences in the Drosophila americana species complex

Background

Disentangling the selective factors shaping adaptive trait variation is an important but challenging task. Many studies—especially in Drosophila—have documented trait variation along latitudinal or altitudinal clines, but frequently lack resolution about specific environmental gradients that could be causal selective agents, and often do not investigate covariation between traits simultaneously. Here we examined variation in multiple macroecological factors across geographic space and their associations with variation in three physiological traits (desiccation resistance, UV resistance, and pigmentation) at both population and species scales, to address the role of abiotic environment in shaping trait variation.

Results

Using environmental data from collection locations of three North American Drosophila species—D. americana americana, D. americana texana and D. novamexicana—we identified two primary axes of macroecological variation; these differentiated species habitats and were strongly loaded for precipitation and moisture variables. In nine focal populations (three per species) assayed for each trait, we detected significant species-level variation for both desiccation resistance and pigmentation, but not for UV resistance. Species-level trait variation was consistent with differential natural selection imposed by variation in habitat water availability, although patterns of variation differed between desiccation resistance and pigmentation, and we found little evidence for pleiotropy between traits.

Conclusions

Our multi-faceted approach enabled us to identify potential agents of natural selection and examine how they might influence the evolution of multiple traits at different evolutionary scales. Our findings highlight that environmental factors influence functional trait variation in ways that can be complex, and point to the importance of studies that examine these relationships at both population- and species-levels.

Integrating natural history collections and comparative genomics to study the genetic architecture of convergent evolution

Evolutionary convergence has been long considered primary evidence of adaptation driven by natural selection and provides opportunities to explore evolutionary repeatability and predictability. In recent years, there has been increased interest in exploring the genetic mechanisms underlying convergent evolution, in part, owing to the advent of genomic techniques. However, the current 'genomics gold rush' in studies of convergence has overshadowed the reality that most trait classifications are quite broadly defined, resulting in incomplete or potentially biased interpretations of results. Genomic studies of convergence would be greatly improved by integrating deep 'vertical', natural history knowledge with 'horizontal' knowledge focusing on the breadth of taxonomic diversity. Natural history collections have and continue to be best positioned for increasing our comprehensive understanding of phenotypic diversity, with modern practices of digitization and databasing of morphological traits providing exciting improvements in our ability to evaluate the degree of morphological convergence. Combining more detailed phenotypic data with the well-established field of genomics will enable scientists to make progress on an important goal in biology: to understand the degree to which genetic or molecular convergence is associated with phenotypic convergence. Although the fields of comparative biology or comparative genomics alone can separately reveal important insights into convergent evolution, here we suggest that the synergistic and complementary roles of natural history collection-derived phenomic data and comparative genomics methods can be particularly powerful in together elucidating the genomic basis of convergent evolution among higher taxa. This article is part of the theme issue 'Convergent evolution in the genomics era: new insights and directions'.

Admixture between ancient lineages, selection, and the formation of sympatric stickleback species-pairs

Ecological speciation has become a popular model for the development and maintenance of reproductive isolation in closely related sympatric pairs of species or ecotypes. An implicit assumption has been that such pairs originate (possibly with gene flow) from a recent, genetically homogeneous ancestor. However, recent genomic data has revealed that currently sympatric taxa are often a result of secondary contact between ancestrally allopatric lineages. This has sparked an interest in the importance of initial hybridization upon secondary contact, with genomic re-analysis of classic examples of ecological speciation often implicating admixture in speciation. We describe a novel occurrence of unusually well-developed reproductive isolation in a model system for ecological speciation: the three-spined stickleback (Gasterosteus aculeatus), breeding sympatrically in multiple lagoons on the Scottish island of North Uist. Using morphological data, targeted genotyping and genome-wide single nucleotide polymorphism (SNP) data we show that lagoon resident and anadromous ecotypes are strongly reproductively isolated with an estimated hybridization rate of only ∼1%. We use palaeoecological and genetic data to test three hypotheses to explain the existence of these species-pairs. Our results suggest that recent, purely ecological speciation from a genetically homogeneous ancestor is probably not solely responsible for the evolution of species-pairs. Instead we reveal a complex colonisation history with multiple ancestral lineages contributing to the genetic composition of species-pairs, alongside strong disruptive selection. Our results imply a role for admixture upon secondary contact and are consistent with the recent suggestion that the genomic underpinning of ecological speciation often has an older, allopatric origin.

Spread of the non-native anemone Anemonia alicemartinae Häussermann & Försterra, 2001 along the Humboldt-current large marine ecosystem: an ecological niche model approach

The geographical expansion of invasive species depends mainly on its dispersal potential, and the abiotic and biotic factors affecting it. Knowing the invasive dynamic of non-native species, as well as its behavior at different natural or anthropogenic scenarios, is fundamental for planning conservation management policies and control plans. The invasive sea anemone Anemonia alicemartinae in habits from the north (18°S) to the south-central (36°S) coast of Chile and its distribution range has expanded by approximately 1,928 km in the last 50 years. Previous works have proposed that human-mediated southward transport associated with regional-scale maritime activities could explain its rapid spread. To evaluate this hypothesis, we used ecological niche models (ENM) to evaluate the potential colonization of the southernmost area of South America. Additionally, we conducted a post hoc analysis to evaluate the relationship between the prediction of the ENM and human activity measured as the number of landings of ships in ports. The models were built based on presence records of A. alicemartinae, and oceanographic variables. Results showed that sea surface salinity and annual sea surface temperature (variance) are the best predictor variables to explain the distribution of A. alicemartinae. There was a positive and significant relationship between the geographical distribution of the sea anemone predicted by the ENM and the number of landings, as a proxy of anthropogenic activity. The most susceptible areas to invasion were those that showed the highest variability in both oceanographic predictors. These areas included the Biobío region, Chiloé´s inland sea, Aysén, and Chacabuco regions, which together comprise two biogeographical provinces. These results sustain the proposed hypothesis and, overall, the results suggest that along with the characteristics of the life history of A. alicemartinae, oceanographic conditions and maritime transport as vector contribute to the southern range expansion of this invasive cryptogenic species in the Humboldt-current large marine ecosystem.

Markers in time and space: A review of the last decade of plant phylogeographic approaches

Plant studies comprise a relatively small proportion of the phylogeographic literature, likely as a consequence of the fundamental challenges posed by the complex genomic structures and life history strategies of these organisms. Comparative plastomics (i.e., comparisons of mutation rates within and among regions of the chloroplast genome) across plant lineages has led to an increased understanding of which markers are likely to provide the most information at low taxonomic levels. However, the extent to which the results of such work have influenced the literature has not been fully assessed, nor has the extent to which plant phylogeographers explicitly analyse markers in time and space, both of which are integral components of the field. Here, we reviewed more than 400 publications from the last decade of plant phylogeography to specifically address the following questions: (i) What is the phylogenetic breadth of studies to date? (ii) What molecular markers have been used, and why were they chosen? (iii) What kinds of markers are most frequently used and in what combinations? (iv) How frequently are divergence time estimation and ecological niche modelling used in plant phylogeography? Our results indicate that chloroplast DNA sequence data remain the primary tool of choice, followed distantly by nuclear DNA sequences and microsatellites. Less than half (42%) of all studies use divergence time estimation, while even fewer use ecological niche modelling (14%). We discuss the implications of our findings, as well as the need for community standards on data reporting.