Climate change and the future restructuring of Neotropical anuran biodiversity

Climate change is likely to impact multiple dimensions of biodiversity. Species range shifts are expected and may drive changes in the composition of species assemblages. In some regions, changes in climate may precipitate the loss of geographically restricted, niche specialists and facilitate their replacement by more widespread, niche generalists, leading to decreases in β-diversity and biotic homogenization. However, in other regions climate change may drive local extinctions and range contraction, leading to increases in β-diversity and biotic heterogenization. Regional topography should be a strong determinant of such changes as mountainous areas often are home to many geographically restricted species, whereas lowlands and plains are more often inhabited by widespread generalists. Climate warming, therefore, may simultaneously bring about opposite trends in β-diversity in mountainous highlands versus relatively flat lowlands. To test this hypothesis, we used species distribution modelling to map the present-day distributions of 2669 Neotropical anuran species, and then generated projections of their future distributions assuming future climate change scenarios. Using traditional metrics of β-diversity, we mapped shifts in biotic homogenization across the entire Neotropical region. We used generalized additive models to then evaluate how changes in β-diversity were associated with shifts in species richness, phylogenetic diversity and one measure of ecological generalism. Consistent with our hypothesis, we find increasing biotic homogenization in most highlands, associated with increased numbers of generalists and, to a lesser extent, losses of specialists, leading to an overall increase in alpha diversity, but lower mean phylogenetic diversity. In the lowlands, biotic heterogenization was more common, and primarily driven by local extinctions of generalists, leading to lower α-diversity, but higher mean phylogenetic diversity. Our results suggest that impacts of climate change on β-diversity are likely to vary regionally, but will generally lead to lower diversity, with increases in β-diversity offset by decreases in α-diversity.     

Genetic Structure and Evidence of a Local Bottleneck in Moose in Sweden

ABSTRACT The moose (Alces alces) is the most intensely managed game species in Sweden. Despite the biological and socioeconomical importance of moose, little is known of its population genetic structure. We analyzed 132 individuals from 4 geographically separate regions in Sweden for genetic variability at 6 microsatellite loci. We found evidence of strong substructuring and restricted levels of gene flow in this potentially mobile mammal. F_ST values were around 10%, and assignment tests indicated 3 genetically distinct populations over the study area. Spatial autocorrelation analysis provided a genetic patch size of approximately 420 km, implying that moose less than this distance apart are genetically more similar than 2 random individuals. Allele and genotype frequency distributions suggested a recent bottleneck in southern Sweden. Results indicate that moose may be more genetically divergent than currently anticipated, and therefore, the strong hunting pressure that is maintained over all of Sweden may have considerable local effects on genetic diversity. Sustainable moose hunting requires identification of spatial genetic structure to ensure that separate, genetically distinct subpopulations are not overharvested.     

The trouble with isolation by distance

The genetic population structure of many species is characterised by a pattern of isolation by distance (IBD): due to limited dispersal, individuals that are geographically close tend to be genetically more similar than individuals that are far apart. Despite the ubiquity of IBD in nature, many commonly used statistical tests are based on a null model that is completely non-spatial, the Island model. Here, I argue that patterns of spatial autocorrelation deriving from IBD present a problem for such tests as it can severely bias their outcome. I use simulated data to illustrate this problem for two widely used types of tests: tests of hierarchical population structure and the detection of loci under selection. My results show that for both types of tests the presence of IBD can indeed lead to a large number of false positives. I therefore argue that all analyses in a study should take the spatial dependence in the data into account, unless it can be shown that there is no spatial autocorrelation in the allele frequency distribution that is under investigation. Thus, it is urgent to develop additional statistical approaches that are based on a spatially explicit null model instead of the non-spatial Island model.     

Restricted gene flow in fragmented populations of a wind-pollinated tree

Fragmentation of natural populations can have negative effects at the genetic level, thus threatening their evolutionary potential. Many of the negative genetic impacts of population fragmentation can be ameliorated by gene flow and it has been suggested that in wind-pollinated tree species, high or even increased levels of gene flow are a feature of fragmented populations, although several studies have disputed this. We have used a combination of nuclear microsatellites and allele-specific PCR (AS-PCR) analysis of chloroplast single nucleotide polymorphisms (SNPs) to examine the levels and patterns of genetic diversity and population differentiation in fragmented populations of juniper (Juniperus communis) in Ireland and inform conservation programs for the species. Significant population differentiation was found for both chloroplast and nuclear markers, indicating restricted gene flow, particularly over larger geographic scales. For conservation purposes, the existence of genetically distinct clusters and geographically localised chloroplast haplotypes suggests that the concept of provenance should be taken into account when formulating augmentation or reintroduction strategies. Furthermore, the potential lack of seed dispersal and seedling establishment means that ex-situ approaches to seed and seedling management may have to be considered.     

Gene amplification in mammalian cells: strategies for protein production.

Gene amplification is an experimental strategy for increasing protein production in mammalian cells. Co-amplification of the target gene by genetically linking it to one or more selectable and amplifiable genetic markers is a particularly successful strategy. A number of papers published in the past year or two illustrate the use of gene amplification to achieve high levels of expression.     

Niche breadth and geographical range: ecological compensation for geographical rarity in rainforest frogs

We investigated the relationship between diet specialization and geographical range in Cophixalus, a genus of microhylid frogs from the Wet Tropics of northern Queensland, Australia. The geographical ranges of these species vary from a few square kilometres in species restricted to a single mountain top to the entire region for the widespread species. Although macroecological theory predicts that species with broad niches should have the largest geographical ranges, we found the opposite: geographically rare species were diet generalists and widespread species were diet specialists. We argue that this pattern is a product of extinction filtering, whereby geographically rare and therefore extinction-prone species are more likely to persist if they are diet generalists.     

Mate recognition in a freshwater fish: geographical distance, genetic differentiation, and variation in female preference for local over foreign males

It often is assumed that more distant allopatry should reflect reduced rates of contemporary gene flow and/or greater divergence in mate recognition systems. This assumption, however, is rarely tested and may not always be appropriate. Here we investigated female preference for local and foreign males in a morphologically variable Australian freshwater fish, the Pacific blue-eye Pseudomugil signifer. Using a multidisciplinary approach that combined molecular phylogeography with conventional mate choice experiments, we found female blue-eyes spent more time in association with local males only when the alternative was a foreigner from a geographically and genetically more distant population. When offered the choice between two foreign males, females associated more with males from the population that was more closely adjacent to their own. Our results suggest that female preference for local over foreign males in blue-eyes may depend on how genetically and geographically separated populations are from one another.     

Presence-absence versus presence-only modelling methods for predicting bird habitat suitability

Habitat suitability models can be generated using methods requiring information on species presence or species presence and absence. Knowledge of the predictive performance of such methods becomes a critical issue to establish their optimal scope of application for mapping current species distributions under different constraints. Here, we use breeding bird atlas data in Catalonia as a working example and attempt to analyse the relative performance of two methods: the Ecological Niche factor Analysis (ENFA) using presence data only and Generalised Linear Models (GLM) using presence/absence data. Models were run on a set of forest species with similar habitat requirements, but with varying occurrence rates (prevalence) and niche positions (marginality). Our results support the idea that GLM predictions are more accurate than those obtained with ENFA. This was particularly true when species were using available habitats proportionally to their suitability, making absence data reliable and useful to enhance model calibration. Species marginality in niche space was also correlated to predictive accuracy, i.e. species with less restricted ecological requirements were modelled less accurately than species with more restricted requirements. This pattern was irrespective of the method employed. Models for wide‐ranging and tolerant species were more sensitive to absence data, suggesting that presence/absence methods may be particularly important for predicting distributions of this type of species. We conclude that modellers should consider that species ecological characteristics are critical in determining the accuracy of models and that it is difficult to predict generalist species distributions accurately and this is independent of the method used. Being based on distinct approaches regarding adjustment to data and data quality, habitat distribution modelling methods cover different application areas, making it difficult to identify one that should be universally applicable. Our results suggest however, that if absence data is available, methods using this information should be preferably used in most situations.     

Biocrust lichen and moss species most suitable for restoration projects

Reintroducing lichens and mosses to areas slated for restoration or rehabilitation may prove integral to project success by filling the biocrust component (niche) of arid ecosystems. In doing so, it is important to select appropriate species and genetic source material. Some bryophyte and lichen species are early pioneers and are potentially well‐suited for restoration projects. Species traits such as high reproductive rates, rapid establishment rates, and large asexual reproductive propagules can be beneficial for restoration. For instance, the large number of spores produced by some mosses are beneficial for reproductive success in arid environments. In addition to identifying the benefit of reproductive strategies, it is important to take habitat needs into consideration; lichen and moss species that are wide‐ranging both geographically and ecologically are recommended over geographically and edaphically restricted species that occur only in specific habitats, such as calcareous soils. Biocrusts used in specific restoration areas should have similar genetic source material (local provenance), and harsh environmental conditions should be ameliorated.     

Heterosis in an isolated, effectively small, and self-fertilizing population of the flowering plant Leavenworthia alabamica

Mildly deleterious mutations are thought to play a major role in the extinction of natural populations, especially those that are small, isolated, or inbred. Self-fertilization should reduce the effective size of populations and simultaneously reduce migration between populations. A history of self-fertilization should therefore cause a population to harbor a substantial "local drift load" caused by the fixation of mildly deleterious mutations. This hypothesis was tested in Leavenworthia alabamica, which contains large, self-incompatible populations and smaller self-compatible populations with adaptations for self-fertilization. The fitness of offspring from within- and between-population crosses was compared to quantify heterosis caused by the masking of deleterious alleles in the heterozygous state. Little heterosis was observed in crosses between five large, self-incompatible populations and two of the three small, self-fertilizing populations of L. alabamica. However, the most geographically isolated and genetically divergent self-fertilizing population (Tuscumbia) exhibited a 110.2% increase in germination and a 73.6% increase in fitness, which is consistent with a sizeable local drift load. The finding of substantial heterosis for fitness supports the idea that small effective size, reproductive isolation, and self-fertilization can make populations particularly vulnerable to mutation accumulation.     

Missing the rarest: is the positive interspecific abundance–distribution relationship a truly general macroecological pattern?

Lepidopterists have long acknowledged that many uncommon butterfly species can be extremely abundant in suitable locations. If this is generally true, it contradicts the general macroecological pattern of the positive interspecific relationship between abundance and distribution, i.e. locally abundant species are often geographically more widespread than locally rare species. Indeed, a negative abundance–distribution relationship has been documented for butterflies in Finland. Here we show, using the Finnish butterflies as an example, that a positive abundance–distribution relationship results if the geographically restricted species are missed, as may be the case in studies based on random or restricted sampling protocols, or in studies that are conducted over small spatial scales. In our case, the abundance–distribution relationship becomes negative when approximately 70 per cent of the species are included. This observation suggests that the abundance–distribution relationship may in fact not be linear over the entire range of distributions. This intriguing possibility combined with some taxonomic biases in the literature may undermine the generalization that for a given taxonomic assemblage there is a positive interspecific relationship between local abundance and regional distribution.     

Genetic differentiation of the millipede Pycnotropis epiclysmus inhabiting seasonally inundated and non-flooded Amazonian forests

The millipede Pycnotropis epiclysmus Hoffman, 1995 (Diplopoda: Polydesmida: Platyrhacidae) is frequently found in Central Amazonian white-and mixed-water inundation forests along the Solimöes-Amazon River near Manaus, Brazil. It also inhabits non-flooded disturbed forest areas adjacent to this river. Populations from both biotopes were genetically studied. The specific pPeP172 satellite DNA family identified in P. epiclysmus has been analyzed in order to elucidate the systematic rank of morphologically indistinguishable individuals from the different habitat types. Nucleotide sequence data, sequence variability and copy number estimates of the pPeP172 satellite DNA do not discriminate the respective populations into genetically different ecotypes. The study of enzyme variability, however, revealed genotypic differences among the three populations: the populations from two geographically more distant inundation forests are genetically rather similar; and the geographically closer populations, one found in a non-flooded and the other in an inundation forest, have a genetic distance which is of similar magnitude to that of the two geographically more distant populations. The genetic data suggest that individuals from different habitats belong to populations of a single species. Genotypic structuring among and within local populations indicates processes of genetic differentiation which can be the result of the migration ability of this millipede.     

Benthic species of the Kerguelen Plateau show contrasting distribution shifts in response to environmental changes

Marine life of the Southern Ocean has been facing environmental changes and the direct impact of human activities during the past decades. Benthic communities have particularly been affected by such changes although we only slowly understand the effect of environmental changes on species physiology, biogeography, and distribution. Species distribution models (SDM) can help explore species geographic responses to main environmental changes. In this work, we modeled the distribution of four echinoid species with contrasting ecological niches. Models developed for [2005–2012] were projected to different time periods, and the magnitude of distribution range shifts was assessed for recent‐past conditions [1955–1974] and for the future, under scenario RCP 8.5 for [2050–2099]. Our results suggest that species distribution shifts are expected to be more important in a near future compared to the past. The geographic response of species may vary between poleward shift, latitudinal reduction, and local extinction. Species with broad ecological niches and not limited by biogeographic barriers would be the least affected by environmental changes, in contrast to endemic species, restricted to coastal areas, which are predicted to be more sensitive.     

Human impact signals from peat bogs – a combined palynological and geochemical approach

This research compares palynological evidence for changes in land use histories with a geochemical method for reconstructing past soil erosion. Changes in land use have significant effects on soil erosion. It has been shown elsewhere that silicon (Si) and titanium (Ti) are good proxies for soil erosion. Ombrotrophic peat bogs are useful archives in which to measure Si and Ti depositions as they only receive inorganic erosional inputs through atmospheric deposition and they contain very low background levels of mineral matter. The correlation between geochemical and pollen analytical reconstructions of past human activity from three raised bog sites in Great Britain and Ireland is discussed here, with reference to examples from four particular time periods: the mid-to-late Bronze Age/Iron Age, the late Iron Age/Roman period, the Middle Ages/Tudor period and the more recent past. The results generally indicate a close correlation between the palynological and geochemical proxies, with the combination of both methods allowing a more comprehensive interpretation of the palaeoenvironmental record. Plantago lanceolata and Poaceae pollen frequencies appear to correlate particularly well with the geochemical proxies. A multi-proxy approach such as this may be particularly useful for identifying and interpreting low-level prehistoric human impact.     

A comparison of levels of genetic polymorphism and self-compatibility in geographically restricted and widespread plant congeners

Summary Evolutionary theory predicts low levels of genetic polymorphism and high levels of self-compatibility in plant species with small ranges and few individuals. To test these predictions, I compared published data on electrophoretically detectable genetic variation and breeding systems for geographically restricted and widespread congeners in eleven genera. The restricted species exhibit significantly fewer polymorphic loci and alleles per polymorphic locus than do their widespread congeners. Although some rare species are genetically impoverished, others are nearly as polymorphic as their widespread congeners. The restricted species and their widespread congeners do not differ consistently with respect to breeding systems.     

Intrinsic determinants of a population trend in timing of breeding in the wandering albatross

Numerous studies of wild animal species have documented that population level responses to environmental change are underpinned by individual level phenotypic plasticity. However, where the relationship between an individual trait and a climate variable occurs when both show a trend over time, phenotypic plasticity may be confounded by ageing. We investigated between and within individual change in laying date in the wandering albatross Diomedea exulans, a long‐lived species experiencing a dramatic decline in population size. Laying date has advanced over the last three decades. A mean‐centering analysis demonstrated that this pattern was driven by within‐individual changes as opposed to appearance or disappearance of phenotypes. Furthermore, a lack of between individual effect suggested the change resulted from ageing as opposed to phenotypic plasticity. Females varied significantly in rate of advance, such that those with low past reproductive rates exhibited a negative temporal trend in laying date, whereas birds with moderate to high past reproductive performance showed little change. The population trend was therefore driven by a subset with low past breeding success. An analysis of effects of timing of breeding on breeding success revealed stabilizing selection for relative laying date. Furthermore, current breeding success was positively related to past success rate, which suggests that there may be indirect selection against plasticity in this population. Our results show that population trends can arise from individual level change unrelated to prevailing environmental conditions, thus demonstrating the importance of longitudinal analyses in the interpretation of climate change effects.     

Incorporating the effects of changes in vegetation functioning and CO2 on water availability in plant habitat models

The direct effects of CO2 level changes on plant water availability are usually ignored in plant habitat models. We compare traditional proxies for water availability with changes in soil water (fAWC) predicted by a process-based ecosystem model, which simulates changes in vegetation structure and functioning, including CO2 physiological effects. We modelled current and future habitats of 108 European tree species using ensemble forecasting, comprising six habitat models, two model evaluation methods and two climate change scenarios. The fAWC models' projections are generally more conservative. Potential habitats shrink significantly less for boreo-alpine and alpine species. Changes in vegetation functioning and CO2 on plant water availability should therefore be taken into account in plant habitat change projections.     

Genetic architecture of host use in a widely distributed, polyphagous butterfly (Lepidoptera: Papilionidae): adaptive inferences based on comparison of spatio-temporal populations

Genetic variance-covariance structure of larval performance within and among spatio-temporal populations of the widely distributed, polyphagous tiger swallowtail butterfly, Papilio glaucus , is described. Performance traits were assessed for full-sibling families on three host species: Liriodendron tulipifera, Magnolia virginiana and Prunus serotina . Mean performance varied across hosts, indicating these hosts present unique developmental environments. Although full-sibling families significantly differed in plasticity of across-hosts response in three of the five spatio-temporal populations, additive genetic variation was mostly associated with P. serotina or pupal mass. The relative lack of heritable variation in rate and length of larval development on L. tulipifera and M. virginiana was consistent with an earlier study that established host-associated geographic differentiation of P. glaucus populations. Performance appeared relatively independent across hosts and thus genetic constraints cannot be casually invoked to explain persistence of local adaptation and host specialization in the face of extensive gene flow. I promote the hypothesis that gene flow among geographically distant populations is relatively restricted and that previously established, allozyme-based estimates of panmixia are confounded by effects of Pleistocene glaciations. Significant heterogeneity of variance-covariance structure among spatio-temporal P. glaucus populations supports an interpretation of restricted gene flow and relative evolutionary independence. Despite low precision of estimates of genetic parameters, local variance-covariance structure was remarkably consistent with expectations given the presumed evolutionary history of regional populations.     

High levels of gene flow among song dialect populations of the Puget Sound white‐crowned sparrow

Populations within a species can show geographic variation in behavioral traits that affect mating decisions or limit dispersal. This may lead to restricted gene flow, resulting in a correlation between behavioral variation and genetic differentiation. Populations of a songbird that differ in a learned behavioral trait, their song dialects, may also differ genetically. If song dialects function as mating barriers, evolutionary processes such as genetic drift should lead to divergence in allele frequencies among dialect populations. The Puget Sound white‐crowned sparrow (Zonotrichia leucophrys pugetensis) is an excellent study system with a well‐defined series of song dialects along the Pacific Northwest coast. A previous study found low genetic differentiation based on four microsatellite loci; however, available loci and analyses techniques have since dramatically improved and allow us to reassess gene flow in this species. We also add extra samples to fill in gaps and add a new level of analysis of geographic variation. Based on acoustic similarities, we group six song dialects into two geographically larger “northern” and “southern” song themes. One southern dialect is acoustically more similar to dialects in the north, which makes the genetic profile of birds singing this dialect particularly interesting. Traditional F‐statistics, analysis of molecular variance as well as Bayesian techniques confirmed the earlier result that geographic variation in song does not correlate with the neutral genetic structure of the sampled dialect populations. The song themes also did not differ genetically, and the origin of the extralimital northern‐theme dialect cannot be determined. We compare this result to findings in several other species and discuss how the timing of learning and dispersal allow vocalizations to vary independently of patterns of genetic divergence.     

Robustness despite uncertainty: regional climate data reveal the dominant role of humans in explaining global extinctions of Late Quaternary megafauna

Debate over the Late Quaternary megafaunal extinctions has focussed on whether human colonisation or climatic changes were more important drivers of extinction, with few extinctions being unambiguously attributable to either. Most analyses have been geographically or taxonomically restricted and the few quantitative global analyses have been limited by coarse temporal resolution or overly simplified climate reconstructions or proxies. We present a global analysis of the causes of these extinctions which uses high‐resolution climate reconstructions and explicitly investigates the sensitivity of our results to uncertainty in the palaeological record. Our results show that human colonisation was the dominant driver of megafaunal extinction across the world but that climatic factors were also important. We identify the geographic regions where future research is likely to have the most impact, with our models reliably predicting extinctions across most of the world, with the notable exception of mainland Asia where we fail to explain the apparently low rate of extinction found in in the fossil record. Our results are highly robust to uncertainties in the palaeological record, and our main conclusions are unlikely to change qualitatively following minor improvements or changes in the dates of extinctions and human colonisation.