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Antonelli A, Hettling H, Condamine F, Vos K, Nilsson R, Sanderson M et al. (2016)
Toward a Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa
Systematic Biology syw066.
Rapidly growing biological data –including molecular sequences and fossils– hold an unprecedented potential to reveal how evolutionary processes generate and maintain biodiversity. However, researchers often have to develop their own idiosyncratic workflows to integrate and analyse these data for reconstructing time-calibrated phylogenies. In addition, divergence times estimated under different methods and assumptions, and based on data of various quality and reliability, should not be combined without proper correction. Here we introduce a modular framework termed SUPERSMART (Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa), and provide a proof of concept for dealing with the moving targets of evolutionary and biogeographical research. This framework assembles comprehensive datasets of molecular and fossil data for any taxa and infers dated phylogenies using robust species tree methods, also allowing for the inclusion of genomic data produced through next-generation sequencing techniques. We exemplify the application of our method by presenting phylogenetic and dating analyses for the mammal order Primates and for the plant family Arecaceae (palms). We believe that this framework will provide a valuable tool for a wide range of hypothesis-driven research questions in systematics, biogeography, and evolution. SUPERSMART will also accelerate the inference of a “Dated Tree of Life” where all node ages are directly comparable.
Keywords: Bayesian phylogenetics, GenBank, data mining, divide-and-conquer methods, multilocus multispecies coalescent, next-generation sequencing, palms, primates, tree calibration
Bacon C, Look S, Gutiérrez-Pinto N, Antonelli A, Tan H, Kumar P et al. (2016)
Botanical Journal of the Linnean Society.
Four species are recognized in the understorey palm genus Johannesteijsmannia (Arecaceae), all of which occur in close geographical proximity in the Malay Peninsula. We hypothesize that overlapping distributions are maintained by a lack of gene flow among species and that segregation along morphological trait or environmental axes confers ecological divergence and, hence, defines species limits. Although some species have sympatric distributions, differentiation was detected among species in morphological and genetic data, corroborating current species delimitation. Differences in niche breadth were not found to explain the overlapping distribution and co-existence of Johannesteijsmannia spp. Four species formed over the last 3 Mya, showing that diversity accumulated within a short time frame and wide range expansion has not occurred, potentially due to a lack of time for dispersal or the evolution of traits to facilitate movement. An assessment of genetic diversity is presented and, as expected, the widest distribution in the genus harbours the highest genetic diversity.
Keywords: Malesia, Palmae, niche, phylogenetics, speciation
Fourcade Y (2016)
Comparing species distributions modelled from occurrence data and from expert-based range maps. Implication for predicting range shifts with climate change
Ecological Informatics 36 8-14.
Species range and climate change risk are often assessed using species distribution models (SDM) that model species niche from presence points and environmental variables and project it in space and time. These presence points frequently originate from occurrence data downloaded from public biodiversity databases, but such data are known to suffer from high biases. There is thus a need to find alternative sources of information to train these models. In this regard, expert-based range maps such as those provided by the International Union for Conservation of Nature (IUCN) have the potential to be used as a source of species presence in a SDM workflow. Here, I compared the predictions of SDM built using true occurrences provided by GBIF or iNaturalist, or using pseudo-occurrences sampled from IUCN expert-based range maps, in current and future climate. I found that the agreement between both types of SDM did not depend on the spatial resolution of environmental data but instead were affected by the number of points sampled from range maps and even more by the spatial congruence between input data. A strong agreement between occurrence data and range maps resulted in very similar SDM outputs, which suggests that expert knowledge can be a valuable alternative source of data to feed SDM and assess potential range shifts when the only available occurrences are biased or fragmentary.
Keywords: Biodiversity databases, Climate change, Expert knowledge, GBIF, IUCN, Species distribution modelling
Fournier A, Sullivan A, Bump J, Perkins M, Shieldcastle M, King S (2016)
Combining citizen science species distribution models and stable isotopes reveals migratory connectivity in the secretive Virginia rail
Journal of Applied Ecology.
1.Stable hydrogen isotope (δD) methods for tracking animal movement are widely used yet often produce low resolution assignments. Incorporating prior knowledge of abundance, distribution, or movement patterns can ameliorate this limitation but data are lacking for most species. We demonstrate how observations reported by citizen scientists can be used to develop robust estimates of species distributions and to constrain δD assignments. 2.We developed a Bayesian framework to refine isotopic estimates of migrant animal origins conditional on species distribution models constructed from citizen scientist observations. To illustrate this approach, we analysed the migratory connectivity of the Virginia rail Rallus limicola, a secretive and declining migratory game bird in North America. 3.Citizen science observations enabled both estimation of sampling bias and construction of bias-corrected species distribution models. Conditioning δD assignments on these species distribution models yielded comparably high-resolution assignments. 4.Most Virginia rails wintering across five Gulf Coast sites spent the previous summer near the Great Lakes, although a considerable minority originated from the Chesapeake Bay watershed or Prairie Pothole region of North Dakota. Conversely, the majority of migrating Virginia rails from a site in the Great Lakes most likely spent the previous winter on the Gulf Coast between Texas and Louisiana. 5.Synthesis and applications. In this analysis Virginia rail migratory connectivity does not fully correspond to the administrative flyways used to manage migratory birds. This example demonstrates that with the increasing availability of citizen science data to create species distribution models, our framework can produce high-resolution estimates of migratory connectivity for many animals, including cryptic species. Empirical evidence of links between seasonal habitats will help enable effective habitat management, hunting quotas, and population monitoring and also highlight critical knowledge gaps.
Keywords: Bayesian, Virginia rail Rallus limicola, citizen science, eBird, feathers, hydrogen isotopes, migration, migratory connectivity, species distribution model (SDM), δD animal origins
Frishkoff L, Karp D, Flanders J, Zook J, Hadly E, Daily G et al. (2016)
Ecology Letters 19(9) 1081-1090.
Land-use change and climate change are driving a global biodiversity crisis. Yet, how species' responses to climate change are correlated with their responses to land-use change is poorly understood. Here, we assess the linkages between climate and land-use change on birds in Neotropical forest and agriculture. Across > 300 species, we show that affiliation with drier climates is associated with an ability to persist in and colonise agriculture. Further, species shift their habitat use along a precipitation gradient: species prefer forest in drier regions, but use agriculture more in wetter zones. Finally, forest-dependent species that avoid agriculture are most likely to experience decreases in habitable range size if current drying trends in the Neotropics continue as predicted. This linkage suggests a synergy between the primary drivers of biodiversity loss. Because they favour the same species, climate and land-use change will likely homogenise biodiversity more severely than otherwise anticipated.
Keywords: Anthropocene, bird, climate niche, countryside biogeography, deforestation, habitat conversion, homogenisation.
González J, Rodríguez-Cortés F, Cronie O, Mateu J (2016)
Spatial Statistics 18 505-544.
Spatio-temporal point process data have been analysed quite a bit in specialised fields, with the aim of better understanding the inherent mechanisms that govern the temporal evolution of events placed in a planar region. In particular, in the last decade there has been an acceleration of methodological developments, accompanied by a broad collection of applications as spatio-temporally indexed data have become more widely available in many scientific fields. We present a self-contained review describing statistical models and methods that can be used to analyse patterns of points in space and time when the questions of scientific interest concern both their spatial and their temporal behaviour. We revisit moment characteristics that define summary statistics, as well as conditional intensities which uniquely characterise certain spatio-temporal point processes. We make use of these concepts to describe models and associated methods of inference for spatio-temporal point process data. Three new motivating real-data examples are described and analysed throughout the paper to illustrate the most relevant techniques, discussing the pros and cons of the different considered approaches.
Keywords: Edge-correction, Empirical models, Intensity function, Mechanistic models, Second-order properties, Separability
Hantemirova E, Heinze B, Knyazeva S, Musaev A, Lascoux M, Semerikov V (2016)
A new Eurasian phylogeographical paradigm? Limited contribution of southern populations to the recolonization of high latitude populations in Juniperus communis L. (Cupressaceae)
Journal of Biogeography.
Aim The aims of this population genetics study of the common juniper across Eurasia were to (1) assess the contribution of southern mountain ranges to the post-glacial recolonization of high latitudes and (2) test whether recent expansion or high gene flow could explain the low genetic differentiation in Northern Eurasia. Location Northern Eurasia and mountain regions of Central Europe and Asia. Methods Six hundred and twenty-two individuals were sampled in 42 populations. Two chloroplast DNA (cpDNA) fragments were investigated (trnT-trnL and 16S-trnA). Analyses of the distribution of haplotypes across the continent included a suite of phylogeographical and phylogenetic tests. Putative geographical distribution in the past was reconstructed using environmental niche modelling. Results Eighty-four haplotypes clustered into four main clades (GL1-GL4). The largest clade, GL3, corresponds to populations from the Alps, northern Europe, Western Caucasus and Siberia. These populations were moderately differentiated (28%) compared to the total range (76%) and Fu's Fs statistic was negative, indicating a population expansion. Some haplotypes within GL3 form subclades with a restricted geographical distribution, suggesting a local origin of the mutation and limited dispersal. In line with these findings, modelling of ecological niches found no significant reduction in the expected range during the LGM. Remarkably, populations from the eastern part of North Caucasus, the Himalayas, Tien Shan and south Siberia were distinctly different from populations in the rest of the range. Main conclusions As in Siberian larch species, the pattern of genetic diversity at cpDNA across the natural range of J. communis suggests that colonization of northern Europe and Siberia started from a limited area and predated the last glaciation. It is likely that juniper survived the subsequent glacial epoch at high latitudes in cryptic refugia serving as secondary centres of recolonization. Southern mountain refugia contribution to the recolonization of high latitudes was, at best, limited.
Keywords: Cupressaceae, Eurasia, chloroplast DNA, common juniper, glacial cycles, phylogeography
Hof A, Rodríguez-Castañeda G, Allen A, Jansson R, Nilsson C (2016)
Recent research predicts that future climate change will result in substantial biodiversity loss associated with loss of habitat for species. However, the magnitude of the anticipated biodiversity impacts are less well known. Studies of species vulnerability to climate change through species distribution models are often limited to assessing the extent of species’ exposure to the consequences of climate change to their local environment, neglecting species sensitivity to global change. The likelihood that species or populations will decline or go extinct due to climate change also depends on the general sensitivity and adaptive capacity of species. Hence, analyses should also obtain more accurate assessments of their vulnerability. We addressed this by constructing a vulnerability matrix for 180 bird species currently breeding in subarctic and arctic Europe that integrates a climatic exposure-based vulnerability index and a natural-history trait-based vulnerability index. Species that may need extra conservation attention based on our matrix include the great snipe (Gallinago media), the rough-legged buzzard (Buteo lagopus), the red-throated pipit (Anthus cervinus), the common swift (Apus apus), the horned lark (Eremophila alpestris), and the bar-tailed godwit (Limosa lapponica). Our vulnerability matrix stresses the importance of looking beyond exposure to climate change when species conservation is the aim. For the species that scored high in our matrix the future in the region looks grim and targeted conservation actions, incorporating macro-ecological and global perspectives, may be needed to alleviate severe population declines. We further demonstrate that climate change is predicted to significantly reduce the current breeding range of species adapted to cold climates in subarctic and arctic Europe. The number of incubation days and whether the species was a habitat specialist or not were also amongst the variables most strongly related to predicted contraction or expansion of species’ breeding ranges. This approach may aid the identification of vulnerable bird species worldwide.
Keywords: arctic region, biodiversity, birds, climate change, natural history traits, specialists, species distribution modeling, subarctic region
Jia S, Zhang M, Raab-Straube E, Thulin M (2016)
Evolutionary history of Gymnocarpos (Caryophyllaceae) in the arid regions from North Africa to Central Asia
Biological Journal of the Linnean Society.
Gymnocarpos has only about ten species distributed in the arid regions of Asia and Africa, but it exhibits a geographical disjunction between eastern Central Asia and western North Africa and Minor Asia. We sampled eight species of the genus and sequenced two chloroplast regions (rps16 and psbB–psbH), and the nuclear rDNA (ITS) to study the phylogeny and biogeography. The results of the phylogenetic analyses corroborated that Gymnocarpos is monophyletic, in the phylogenetic tree two well supported clades are recognized: clade 1 includes Gymnocarpos sclerocephalus and G. decandrus, mainly the North African group, whereas clade 2 comprises the remaining species, mainly in the Southern Arabian Peninsula. Molecular dating analysis revealed that the divergence age of Gymnocarpos was c. 31.33 Mya near the Eocene and Oligocene transition boundary, the initial diversification within Gymnocarpos dated to c. 6.69 Mya in the late Miocene, and the intraspecific diversification mostly occurred during the Quaternary climate oscillations. Ancestral area reconstruction suggested that the Southern Arabian Peninsula was the ancestral area for Gymnocarpos. Our conclusions revealed that the aridification since mid-late Miocene significantly affected the diversification of the genus in these areas.
Keywords: 2016, CN, China, DE, GBIF_used, Germany, SE, Sweden, phylogenetic analysis, phylogenetics
Lagomarsino L, Condamine F, Antonelli A, Mulch A, Davis C (2016)
The New phytologist.
The tropical Andes of South America, the world's richest biodiversity hotspot, are home to many rapid radiations. While geological, climatic, and ecological processes collectively explain such radiations, their relative contributions are seldom examined within a single clade. We explore the contribution of these factors by applying a series of diversification models that incorporate mountain building, climate change, and trait evolution to the first dated phylogeny of Andean bellflowers (Campanulaceae: Lobelioideae). Our framework is novel for its direct incorporation of geological data on Andean uplift into a macroevolutionary model. We show that speciation and extinction are differentially influenced by abiotic factors: speciation rates rose concurrently with Andean elevation, while extinction rates decreased during global cooling. Pollination syndrome and fruit type, both biotic traits known to facilitate mutualisms, played an additional role in driving diversification. These abiotic and biotic factors resulted in one of the fastest radiations reported to date: the centropogonids, whose 550 species arose in the last 5 million yr. Our study represents a significant advance in our understanding of plant evolution in Andean cloud forests. It further highlights the power of combining phylogenetic and Earth science models to explore the interplay of geology, climate, and ecology in generating the world's biodiversity.
Keywords: Andes, Lobelioideae, Neotropics, biodiversity hotspot, climate change, diversification, pollination syndromes, rapid radiation