Model selection as a tool for phylogeographic inference: an example from the willow Salix melanopsis

Phylogeographic inference has typically relied on analyses of data from one or a few genes to provide estimates of demography and population histories. While much has been learned from these studies, all phylogeographic analysis is conditioned on the data, and thus, inferences derived from data that represent a small sample of the genome are unavoidably tenuous. Here, we demonstrate one approach for moving beyond classic phylogeographic research. We use sequence capture probes and Illumina sequencing to generate data from >400 loci in order to infer the phylogeographic history of Salix melanopsis, a riparian willow with a disjunct distribution in coastal and the inland Pacific Northwest. We evaluate a priori phylogeographic hypotheses using coalescent models for parameter estimation, and the results support earlier findings that identified post‐Pleistocene dispersal as the cause of the disjunction in S. melanopsis. We also conduct a series of model selection exercises using IMa2, Migrate‐n and ?a?i. The resulting ranking of models indicates that refugial dynamics were complex, with multiple regions in the inland regions serving as the source for postglacial colonization. Our results demonstrate that new sources of data and new approaches to data analysis can rejuvenate phylogeographic research by allowing for the identification of complex models that enable researchers to both identify and estimate the most relevant parameters for a given system.     

A global synthesis of climate vulnerability assessments on marine fisheries: Methods,scales, and knowledge co-production

Undertaking climate vulnerability assessments (CVAs) on marine fisheries is instrumental to the identification of regions, species, and stakeholders at risk of impacts from climate change, and the development of effective and targeted responses for fisheries adaptation. In this global literature review, we addressed three important questions to characterize fisheries CVAs: (i) what are the available approaches to develop CVAs in various social–ecological contexts, (ii) are different geographic scales and regions adequately represented, and (iii) how do diverse knowledge systems contribute to current understanding of vulnerability? As part of these general research efforts, we identified and characterized an inventory of frameworks and indicators that encompass a wide range of foci on ecological and socioeconomic dimensions of climate vulnerability on fisheries. Our analysis highlighted a large gap between countries with top research inputs and the most urgent adaptation needs. More research and resources are needed in low-income tropical countries to ensure existing inequities are not exacerbated. We also identified an uneven research focus across spatial scales and cautioned a possible scale mismatch between assessment and management needs. Drawing on this information, we catalog (1) a suite of research directions that could improve the utility and applicability of CVAs, particularly the examination of barriers and enabling conditions that influence the uptake of CVA results into management responses at multiple levels, (2) the lessons that have been learned from applications in data-limited regions, particularly the use of proxy indicators and knowledge co-production to overcome the problem of data deficiency, and (3) opportunities for wider applications, for example diversifying the use of vulnerability indicators in broader monitoring and management schemes. This information is used to provide a set of recommendations that could advance meaningful CVA practices for fisheries management and promote effective translation of climate vulnerability into adaptation actions.     

Latitudinal variation in global range-size of aquatic macrophyte species shows evidence for a Rapoport effect

1. To test hypotheses concerning the applicability of the Rapoport effect (RE: “species that occur at higher latitudes tend to have greater geographical range-size than species which have ranges limited to latitudes closer to the equator”) to aquatic macrophytes at global scale, we analysed the world latitudinal distribution and range-size of 1,083 vascular aquatic macrophyte species, from 91 genera in 11 families. We targeted macrophyte families strongly associated with inland aquatic habitats (i.e. with a zero, or only very low, proportion of constituent species which occur also in non-aquatic habitats), and which are distributed across a substantial latitudinal gradient, a necessary condition to test our hypotheses.
2. The macrophyte species present in these families include plants from all the normally accepted life form-defined functional groups of macrophytes, namely submerged, free-floating, floating-leaf rooted and emergent species, and represent the three major vascular taxonomic groups occurring as aquatic macrophytes (ferns/fern allies, monocots, and dicots). For the analysis, we used both latitude-only and areal measures of macrophyte species geographic range-size, within a 10 × 10° (latitude × longitude) grid of 238 grid cells, covering the six world ecozones (Palaearctic, Orient, Australasia, Nearctic, Neotropics, Afrotropics) that primarily contain inland freshwater and brackish macrophyte habitats.
3. The results provide new insight into the relationships between global range-size of macrophytes, latitude, and other potential spatio-environmental and anthropogenic drivers acting upon these plants at world scale. In particular, the outcomes indicated that: (1) the range-size versus latitude distribution of macrophytes shows evidence of a strong RE influence, with significantly greater species range-size at higher latitudes; and (2) the β-diversity pattern of species distribution along this latitudinal gradient is poorly explained by nestedness organisation, and species turnover is a more likely explanation of the observed changes in species distribution with latitude.
4. Spatio-environmental and anthropogenic variables other than latitude may also influence the observed global geographical pattern of macrophyte range-size, although their importance as predictors varies between individual families. Extent of agricultural land use, altitude, and historic (post-Quaternary) climate change velocity were all significant predictor variables for some families. However, interestingly, neither the area of land nor the area of waterbody present per grid cell were major influences on macrophyte range-size distribution.
5. Our finding of evidence for an RE, acting at global scale in aquatic macrophytes, contributes to increasing the generality of conclusions so far reached about the large-scale factors that drive patterns of species range-size at global scale. The study also provides a baseline for future macroecological work on aquatic plants, and potentially other freshwater organisms, particularly in the context of predicting how the world ranges of freshwater biota will respond to ongoing global environmental change.

     

Widespread parallel population adaptation to climate variation across a radiation: implications for adaptation to climate change

Global warming will impact species in a number of ways, and it is important to know the extent to which natural populations can adapt to anthropogenic climate change by natural selection. Parallel microevolution within separate species can demonstrate natural selection, but several studies of homoplasy have not yet revealed examples of widespread parallel evolution in a generic radiation. Taking into account primary phylogeographic divisions, we investigate numerous quantitative traits (size, shape, scalation, colour pattern and hue) in anole radiations from the mountainous Lesser Antillean islands. Adaptation to climatic differences can lead to very pronounced differences between spatially close populations with all studied traits showing some evidence of parallel evolution. Traits from shape, scalation, pattern and hue (particularly the latter) show widespread evolutionary parallels within these species in response to altitudinal climate variation greater than extreme anthropogenic climate change predicted for 2080. This gives strong evidence of the ability to adapt to climate variation by natural selection throughout this radiation. As anoles can evolve very rapidly, it suggests anthropogenic climate change is likely to be less of a conservation threat than other factors, such as habitat loss and invasive species, in this, Lesser Antillean, biodiversity hot spot.     

Runoff and the longitudinal distribution of macroinvertebrates in a glacier‐fed stream: implications for the effects of global warming

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Landscape fluidity – a unifying perspective for understanding and adapting to global change

Rapid, human-induced global change presents major challenges to researchers, policy-makers and land managers. Addressing these challenges requires an appreciation of the dynamics of ecological systems. Here, we propose 'landscape fluidity' as a perspective and research agenda from which to consider landscapes in the process of changing rapidly through both time and space. We define landscape fluidity as the ebb and flow of different organisms within a landscape through time. A range of existing ideas, themes and practical approaches are relevant to landscape fluidity, and we use a case study of scattered tree landscapes in south-eastern Australia to illustrate the benefits of a landscape fluidity perspective. We suggest that a focus on landscape fluidity can bring a renewed emphasis on change in landscapes and so help unify a range of currently separate research themes in biogeography, ecology, palaeoecology and conservation biology.     

The effects of climate change on a mega‐diverse country: predicted shifts in mammalian species richness and turnover in continental Ecuador

Ecuador has some of the greatest biodiversity in the world, sheltering global biodiversity hotspots in lowland and mountain regions. Climate change will likely have a major effect on these regions, but the consequences for faunal diversity and conservation remain unclear. To address this issue, we used an ensemble of eight species distribution models to predict future shifts and identify areas of high changes in species richness and species turnover for 201 mammals. We projected the distributions using two different climate change scenarios at the 2050 horizon and contrasted two extreme dispersal scenarios (no dispersal vs. full dispersal). Our results showed extended distributional shifts all over the country. For most groups, our results predicted that the current diversity of mammals in Ecuador would decrease significantly under all climate change scenarios and dispersal assumptions. The Northern Andes and the Amazonian region would remain diversity hotspots but with a significant decrease in the number of species. All predictions, including the most conservative scenarios in terms of dispersal and climate change, predicted major changes in the distribution of mammalian species diversity in Ecuador. Primates might be the most severely affected because they would have fewer suitable areas, compared with other mammals. Our work emphasizes the need for sound conservation strategies in Ecuador to mitigate the effects of climate change     

Environmental correlates of body size influence range size and extinction risk: A global study in rodents

Aim

Species-level traits, such as body and range sizes, are important correlates of extinction risk. However, both are often related and are driven by environmental factors. Here, we elucidated links between environmental factors, body size, range size and susceptibility to extinction, across the whole order of rodents.

Location

Global.

Time period

Current.

Major taxa studied

Rodents (order Rodentia).

Methods

We compiled an unprecedentedly large database of rodent morphology, phylogeny, range size, conservation status, global climate and normalized difference vegetation index (NDVI), comprising >86% of all described species. Using phylogenetic regressions, we initially explored the environmental factors driving body size. Next, we modelled the relationship between body size and range size. From this relationship, we computed and mapped (at the assemblage level) an index of relative range size, corresponding to the deviation from the expected range size of each species, given its body size. Finally, we tested whether relative range was correlated with the risk of extinction of the species derived from an assessment by the International Union for Conservation of Nature.

Results

We found that, contrary to the expectations of Bergmann's rule, the body size of rodents was mostly influenced by variation in NDVI (rather than latitude/temperature). Body size, in turn, imposed a constraint on species range size, as evidenced by a triangular relationship that was segmented at the lower bound. The relative species range size derived from this relationship highlighted four geographical regions where rodents with small relative range were concentrated globally. We demonstrated that lower relative range size was associated with increased risk of extinction.

Main conclusions

Species that, given their body size, are distributed across ranges that are smaller than expected have elevated extinction risk. Therefore, investigating the relationships between environmental drivers, body size and range size might help to detect species that could become threatened in the near future.     

Islands of water in a sea of dry land: hydrological regime predicts genetic diversity and dispersal in a widespread fish from Australia's arid zone, the golden perch (Macquaria ambigua)

Rivers provide an excellent system to study interactions between patterns of biodiversity structure and ecological processes. In these environments, gene flow is restricted by the spatial hierarchy and temporal variation of connectivity within the drainage network. In the Australian arid zone, this variability is high and rivers often exist as isolated waterholes connected during unpredictable floods. These conditions cause boom/bust cycles in the population dynamics of taxa, but their influence on spatial genetic diversity is largely unknown. We used a landscape genetics approach to assess the effect of hydrological variability on gene flow, spatial population structure and genetic diversity in an Australian freshwater fish, Macquaria ambigua. Our analysis is based on microsatellite data of 590 samples from 26 locations across the species range. Despite temporal isolation of populations, the species showed surprisingly high rates of dispersal, with population genetic structure only evident among major drainage basins. Within drainages, hydrological variability was a strong predictor of genetic diversity, being positively correlated with spring-time flow volume. We propose that increases in flow volume during spring stimulate recruitment booms and dispersal, boosting population size and genetic diversity. Although it is uncertain how the hydrological regime in arid Australia may change under future climate scenarios, management strategies for arid-zone fishes should mitigate barriers to dispersal and alterations to the natural flow regime to maintain connectivity and the species' evolutionary potential. This study contributes to our understanding of the influence of spatial and temporal heterogeneity on population and landscape processes.     

UV effects that come and go: a global comparison of marine benthic community level impacts

Ambient UV radiation has substantially increased during the last decades, but its impact on marine benthic communities is hardly known. The aim of this study was to globally compare and quantify how shallow hard‐bottom communities are affected by UV during early succession. Identical field experiments in 10 different coastal regions of both hemispheres produced a consistent but unexpected pattern: (i) UV radiation affected species diversity and community biomass in a very similar manner, (ii) diversity and biomass were reduced to a larger extent by UVA than UVB radiation, (iii) ambient UV levels did not affect the composition of the communities, and (iv) any UV effects disappeared during species succession after 2–3 months. Thus, current levels of UV radiation seem to have small, predictable, and transient effects on shallow marine hard‐bottom communities.     

Insects as a piece of the puzzle to mitigate global problems: an opportunity for ecologists

Although scientists have studied and touted the importance of insects to many ecosystem services for decades, insects and insect science are often poorly perceived by the public and by policy makers. Because insects do have important influences on many ecosystem services, they have even greater potential to be used to solve some anthropogenically-caused current global problems. We give several examples where insects are currently being used, or are being considered for future use, as a part of the solution to a global problem, including their potential roles as a part of the solution to sustainable fuel and food systems, deforestation and other environmental degradation, and global inequities. Ecologists have an important role to play in assessing how many of the proposed uses of insects will alter ecological processes and ecosystem services, or how their use may be effectively implemented.     

Development and validation of an experimental life support system for assessing the effects of global climate change and environmental contamination on estuarine and coastal marine benthic communities

An experimental life support system (ELSS) was constructed to study the interactive effects of multiple stressors on coastal and estuarine benthic communities, specifically perturbations driven by global climate change and anthropogenic environmental contamination. The ELSS allows researchers to control salinity, pH, temperature, ultraviolet radiation (UVR), tidal rhythms and exposure to selected contaminants. Unlike most microcosms previously described, our system enables true independent replication (including randomization). In addition to this, it can be assembled using commercially available materials and equipment, thereby facilitating the replication of identical experimental setups in different geographical locations. Here, we validate the reproducibility and environmental quality of the system by comparing chemical and biological parameters recorded in our ELSS with those prevalent in the natural environment. Water, sediment microbial community and ragworm (the polychaete Hediste diversicolor) samples were obtained from four microcosms after 57 days of operation. In general, average concentrations of dissolved inorganic nutrients (NO₃^?; NH₄⁺ and PO₄^?3) in the water column of the ELSS experimental control units were within the range of concentrations recorded in the natural environment. While some shifts in bacterial community composition were observed between in situ and ELSS sediment samples, the relative abundance of most metabolically active bacterial taxa appeared to be stable. In addition, ELSS operation did not significantly affect survival, oxidative stress and neurological biomarkers of the model organism Hediste diversicolor. The validation data indicate that this system can be used to assess independent or interactive effects of climate change and environmental contamination on benthic communities. Researchers will be able to simulate the effects of these stressors on processes driven by microbial communities, sediment and seawater chemistry and to evaluate potential consequences to sediment toxicity using model organisms such as Hediste diversicolor.     

Validation of a physician global assessment tool for vitiligo extent: Results of an international vitiligo expert meeting

Currently, vitiligo lacks a validated Physician Global Assessment (PGA) for disease extent. This PGA can be used to stratify and interpret the numeric scores obtained by the Vitiligo Extent Score (VES). We investigated the interrater reliability of a 5‐point PGA scale during an international vitiligo workshop. Vitiligo experts from five different continents rated photographs of non‐segmental vitiligo patients with varying degrees of extent with the PGA score. Good interrater agreements (intraclass correlation coefficient >0.6) were observed between the raters overall and within each continent. All hypotheses to evaluate construct validity were confirmed. Median VES values per category were for limited 1.10 [IQR: 0.21–1.67], moderate 3.17 [IQR: 1.75–6.21], extensive 9.58 [IQR: 6.21–13.03] and very extensive 42.67 [IQR: 21.20–42.67]. Defined categories for vitiligo extent can be valuable for inclusion criteria and may impact future reimbursement criteria.     

Seed germination responses to seasonal temperature and drought stress are species‐specific but not related to seed size in a desert steppe: Implications for effect of climate change on community structure

Investigating how seed germination of multiple species in an ecosystem responds to environmental conditions is crucial for understanding the mechanisms for community structure and biodiversity maintenance. However, knowledge of seed germination response of species to environmental conditions is still scarce at the community level. We hypothesized that responses of seed germination to environmental conditions differ among species at the community level, and that germination response is not correlated with seed size. To test this hypothesis, we determined the response of seed germination of 20 common species in the Siziwang Desert Steppe, China, to seasonal temperature regimes (representing April, May, June, and July) and drought stress (0, ?0.003, ?0.027, ?0.155, and ?0.87 MPa). Seed germination percentage increased with increasing temperature regime, but Allium ramosum, Allium tenuissimum, Artemisia annua, Artemisia mongolica, Artemisia scoparia, Artemisia sieversiana, Bassia dasyphylla, Kochia prastrata, and Neopallasia pectinata germinated to >60% in the lowest temperature regime (April). Germination decreased with increasing water stress, but Allium ramosum, Artemisia annua, Artemisia scoparia, Bassia dasyphylla, Heteropappus altaicus, Kochia prastrata, Neopallasia pectinata, and Potentilla tanacetifolia germinated to near 60% at ?0.87 MPa. Among these eight species, germination of six was tolerant to both temperature and water stress. Mean germination percentage in the four temperature regimes and the five water potentials was not significantly correlated with seed mass or seed area, which were highly correlated. Our results suggest that the species‐specific germination responses to environmental conditions are important in structuring the desert steppe community and have implications for predicting community structure under climate change. Thus, the predicted warmer and dryer climate will favor germination of drought‐tolerant species, resulting in altered proportions of germinants of different species and subsequently change in community composition of the desert steppe.     

Smaller,more diverse and on the way to the top: Rapid community shifts of montane wild bees within an extraordinary hot decade

Aim

Global warming is assumed to restructure mountain insect communities in space and time. Theory and observations along climate gradients predict that insect abundance and richness, especially of small-bodied species, will increase with increasing temperature. However, the specific responses of single species to rising temperatures, such as spatial range shifts, also alter communities, calling for intensive monitoring of real-world communities over time.

Location

German Alps and pre-alpine forests in south-east Germany.

Methods

We empirically examined the temporal and spatial change in wild bee communities and its drivers along two largely well-protected elevational gradients (alpine grassland vs. pre-alpine forest), each sampled twice within the last decade.

Results

We detected clear abundance-based upward shifts in bee communities, particularly in cold-adapted bumble bee species, demonstrating the speed with which mobile organisms can respond to climatic changes. Mean annual temperature was identified as the main driver of species richness in both regions. Accordingly, and in large overlap with expectations under climate warming, we detected an increase in bee richness and abundance, and an increase in small-bodied species in low- and mid-elevations along the grassland gradient. Community responses in the pre-alpine forest gradient were only partly consistent with community responses in alpine grasslands.

Main Conclusion

In well-protected temperate mountain regions, small-bodied bees may initially profit from warming temperatures, by getting more abundant and diverse. Less severe warming, and differences in habitat openness along the forested gradient, however, might moderate species responses. Our study further highlights the utility of standardized abundance data for revealing rapid changes in bee communities over only one decade.     

An experimental test of the role of environmental temperature variability on ectotherm molecular, physiological and life-history traits: implications for global warming

Global climate change is one of the greatest threats to biodiversity; one of the most important effects is the increase in the mean earth surface temperature. However, another but poorly studied main characteristic of global change appears to be an increase in temperature variability. Most of the current analyses of global change have focused on mean values, paying less attention to the role of the fluctuations of environmental variables. We experimentally tested the effects of environmental temperature variability on characteristics associated to the fitness (body mass balance, growth rate, and survival), metabolic rate (VCO(2)) and molecular traits (heat shock protein expression, Hsp70), in an ectotherm, the terrestrial woodlouse Porcellio laevis. Our general hypotheses are that higher values of thermal amplitude may directly affect life-history traits, increasing metabolic cost and stress responses. At first, results supported our hypotheses showing a diversity of responses among characters to the experimental thermal treatments. We emphasize that knowledge about the cellular and physiological mechanisms by which animals cope with environmental changes is essential to understand the impact of mean climatic change and variability. Also, we consider that the studies that only incorporate only mean temperatures to predict the life-history, ecological and evolutionary impact of global temperature changes present important problems to predict the diversity of responses of the organism. This is because the analysis ignores the complexity and details of the molecular and physiological processes by which animals cope with environmental variability, as well as the life-history and demographic consequences of such variability.     

Range position and climate sensitivity: The structure of among‐population demographic responses to climatic variation

Species’ distributions will respond to climate change based on the relationship between local demographic processes and climate and how this relationship varies based on range position. A rarely tested demographic prediction is that populations at the extremes of a species’ climate envelope (e.g., populations in areas with the highest mean annual temperature) will be most sensitive to local shifts in climate (i.e., warming). We tested this prediction using a dynamic species distribution model linking demographic rates to variation in temperature and precipitation for wood frogs (Lithobates sylvaticus) in North America. Using long‐term monitoring data from 746 populations in 27 study areas, we determined how climatic variation affected population growth rates and how these relationships varied with respect to long‐term climate. Some models supported the predicted pattern, with negative effects of extreme summer temperatures in hotter areas and positive effects on recruitment for summer water availability in drier areas. We also found evidence of interacting temperature and precipitation influencing population size, such as extreme heat having less of a negative effect in wetter areas. Other results were contrary to predictions, such as positive effects of summer water availability in wetter parts of the range and positive responses to winter warming especially in milder areas. In general, we found wood frogs were more sensitive to changes in temperature or temperature interacting with precipitation than to changes in precipitation alone. Our results suggest that sensitivity to changes in climate cannot be predicted simply by knowing locations within the species’ climate envelope. Many climate processes did not affect population growth rates in the predicted direction based on range position. Processes such as species‐interactions, local adaptation, and interactions with the physical landscape likely affect the responses we observed. Our work highlights the need to measure demographic responses to changing climate.     

Intra-Annual Variability in Responses of a Canopy Forming Kelp to Cumulative Low Tide Heat Stress: Implications for Populations at the Trailing Range Edge

Anthropogenic climate change is driving the redistribution of species at a global scale. For marine species, populations at trailing edges often live very close to their upper thermal limits and, as such, poleward range contractions are one of the most pervasive effects of ongoing and predicted warming. However, the mechanics of processes driving such contractions are poorly understood. Here, we examined the response of the habitat forming kelp, Laminaria digitata, to realistic terrestrial heatwave simulations akin to those experienced by intertidal populations persisting at the trailing range edge in the northeast Atlantic (SW England). We conducted experiments in both spring and autumn to determine temporal variability in the effects of heatwaves. In spring, heatwave scenarios caused minimal stress to L. digitata but in autumn all scenarios tested resulted in tissue being nonviable by the end of each assay. The effects of heatwave scenarios were only apparent after consecutive exposures, indicating erosion of resilience over time. Monthly field surveys corroborated experimental evidence as the prevalence of bleaching (an indication of physiological stress and tissue damage) in natural populations was greatest in autumn and early winter. Overall, our data showed that L. digitata populations in SW England persist close to their upper physiological limits for emersion stress in autumn. As the intensity of extreme warming events is likely to increase with anthropogenic climate change, thermal conditions experienced during periods of emersion will soon exceed physiological thresholds and will likely induce widespread mortality and consequent changes at the population level.     

A comparative study of allozyme variation of peripheral and central populations of Silene nutans L. (Caryophyllaceae) from Western Europe: implications for conservation

In Belgium, at the western border of its continental distribution range, the perennial herb S. nutans has evolved two parapatric ecotypes (calcicolous or silicicolous), which show contrasted allozyme, morphological and adaptive patterns, and isolating reproductive barriers. We examined allozyme variation in 21 populations close to Belgium (from France and Luxemburg) in relation to their peripheral or central geographical position, and investigated their genetic relationships with the Belgian ecotypes. Both peripheral and central populations showed high genetic variation. They were differentiated from each other, but not in relation to the substrate (calcareous or siliceous). The peripheral and central populations were related to the Belgian silicicolous and calcicolous ecotype, respectively. This suggests an ancient differentiation and different past histories for the Belgian ecotypes, and parapatric speciation processes. This study exemplifies the high evolutionary potential of populations at range peripheries and the need for considering them in conservation strategies.