Why Georeferencing Matters: Introducing a Practical Protocol to Prepare Species Occurrence Records for Spatial Analysis

Species Distribution Models (SDMs) are widely used to understand environmental controls on species’ ranges and to forecast species range shifts in response to climatic changes. The quality of input data is crucial determinant of the model’s accuracy. While museum records can be useful sources of presence data for many species, they do not always include accurate geographic coordinates. Therefore, actual locations must be verified through the process of georeferencing. We present a practical, standardized manual georeferencing method (the Spatial Analysis Georeferencing Accuracy (SAGA) protocol) to classify the spatial resolution of museum records specifically for building improved SDMs. We used the high-elevation plant Saxifraga austromontana Wiegand (Saxifragaceae) as a case study to test the effect of using this protocol when developing an SDM. In MAXENT, we generated and compared SDMs using a comprehensive occurrence dataset that had undergone three different levels of georeferencing: (1) trained using all publicly available herbarium records of the species, minus outliers (2) trained using herbarium records claimed to be previously georeferenced, and (3) trained using herbarium records that we have manually georeferenced to a ≤ 1-km resolution using the SAGA protocol. Model predictions of suitable habitat for S. austromontana differed greatly depending on georeferencing level. The SDMs fitted with presence locations georeferenced using SAGA outperformed all others. Differences among models were exacerbated for future distribution predictions. Under rapid climate change, accurately forecasting the response of species becomes increasingly important. Failure to georeference location data and cull inaccurate samples leads to erroneous model output, limiting the utility of spatial analyses. We present a simple, standardized georeferencing method to be adopted by curators, ecologists, and modelers to improve the geographic accuracy of museum records and SDM predictions

Integrating Environmental, Molecular, and Morphological Data to Unravel an Ice-age Radiation of Arctic-alpine Campanula in Western North America

Many arctic-alpine plant genera have undergone speciation during the Quaternary. The bases for these radiations have been ascribed to geographic isolation,abiotic and biotic differences between populations, and/or hybridization andpolyploidization. The Cordilleran Campanula L. (Campanulaceae Juss.), a monophyletic clade of mostly endemic arctic-alpine taxa from western North America, experienced a recent and rapid radiation. We set out to unravel the factors that likely influenced speciation in this group. To do so, we integrated environmental, genetic, and morphological datasets, tested biogeographic hypotheses, and analyzed the potential consequences of the various factors on the evolutionary history of the clade. We created paleodistribution models to identify potential Pleistocene refugia for the clade and estimated niche space for individual taxa using geographic and climatic data. Using 11 nuclear loci, we reconstructed a species tree and tested biogeographic hypotheses derived from the paleodistribution models. Finally, we tested 28 morphological characters, including floral, vegetative, and seed characteristics, for their capacity to differ- entiate taxa. Our results show that the combined effect of Quaternary climatic variation, isolation among differing environments in the mountains in western North America, and biotic factors influencing floral morphology contributed to speciation in this group during the mid-Pleistocene. Furthermore, our biogeographic analyses uncovered asynchronous consequences of interglacial and glacial periods for the timing of refugial isolation within the southern and northwestern mountains, respectively. These findings have broad implications for understanding the processes promoting speciation in arctic-alpine plants and the rise of numerous endemic taxa across the region

Deep Genetic Divergence between Disjunct Refugia in the Arctic-Alpine King’s Crown, Rhodiola integrifolia (Crassulaceae)

Despite the strength of climatic variability at high latitudes and upper elevations, we still do not fully understand how plants in North America that are distributed between Arctic and alpine areas responded to the environmental changes of the Quaternary. To address this question, we set out to resolve the evolutionary history of the King’s Crown, Rhodiola integrifolia using multi-locus population genetic and phylogenetic analyses in combination with ecological niche modeling. Our population genetic analyses of multiple anonymous nuclear loci revealed two major clades within R. integrifolia that diverged from each other ~ 700 kya: one occurring in Beringia to the north (including members of subspecies leedyi and part of subspecies integrifolia), and the other restricted to the Southern Rocky Mountain refugium in the south (including individuals of subspecies neomexicana and part of subspecies integrifolia). Ecological niche models corroborate our hypothesized locations of refugial areas inferred from our phylogeographic analyses and revealed some environmental differences between the regions inhabited by its two subclades. Our study underscores the role of geographic isolation in promoting genetic divergence and the evolution of endemic subspecies in R. integrifolia. Furthermore, our phylogenetic analyses of the plastid spacer region trnL-F demonstrate that among the native North American species, R. integrifolia and R. rhodantha are more closely related to one another than either is to R. rosea. An understanding of these historic processes lies at the heart of making informed management decisions regarding this and other Arctic-alpine species of concern in this increasingly threatened biome

Deep Genetic Divergence Between Disjunct Refugia in the Arctic-Alpine King\u27s Crown, Rhodiola integrifolia (Crassulaceae)

Despite the strength of climatic variability at high latitudes and upper elevations, we still do not fully understand how plants in North America that are distributed between Arctic and alpine areas responded to the environmental changes of the Quaternary. To address this question, we set out to resolve the evolutionary history of the King’s Crown, Rhodiola integrifolia using multi-locus population genetic and phylogenetic analyses in combination with ecological niche modeling. Our population genetic analyses of multiple anonymous nuclear loci revealed two major clades within R. integrifolia that diverged from each other ~ 700 kya: one occurring in Beringia to the north (including members of subspecies leedyi and part of subspecies integrifolia), and the other restricted to the Southern Rocky Mountain refugium in the south (including individuals of subspecies neomexicana and part of subspecies integrifolia). Ecological niche models corroborate our hypothesized locations of refugial areas inferred from our phylogeographic analyses and revealed some environmental differences between the regions inhabited by its two subclades. Our study underscores the role of geographic isolation in promoting genetic divergence and the evolution of endemic subspecies in R. integrifolia. Furthermore, our phylogenetic analyses of the plastid spacer region trnL-F demonstrate that among the native North American species, R. integrifolia and R. rhodantha are more closely related to one another than either is to R. rosea. An understanding of these historic processes lies at the heart of making informed management decisions regarding this and other Arctic-alpine species of concern in this increasingly threatened biome

On the Evolutionary and Biogeographic History of Saxifraga Sect. Trachyphyllum (Gaud.) Koch (Saxifragaceae Juss.)

Arctic-alpine plants in the genus Saxifraga L. (Saxifragaceae Juss.) provide an excellent system for investigating the process of diversification in northern regions. Yet, sect.Trachyphyllum (Gaud.) Koch, which is comprised of about 8 to 26 species, has still not been explored by molecular systematists even though taxonomists concur that the section needs to be thoroughly re-examined. Our goals were to use chloroplast trnL-F and nuclear ITS DNA sequence data to circumscribe the section phylogenetically, test models of geographically-based population divergence, and assess the utility of morphological characters in estimating evolutionary relationships. To do so, we sequenced both genetic markers for 19 taxa within the section. The phylogenetic inferences of sect. Trachyphyllum using maximum likelihood and Bayesian analyses showed that the section is polyphyletic, with S. aspera L. and S bryoidesL. falling outside the main clade. In addition, the analyses supported several taxonomic re-classifications to prior names. We used two approaches to test biogeographic hypotheses: i) a coalescent approach in Mesquite to test the fit of our reconstructed gene trees to geographically-based models of population divergence and ii) a maximum likelihood inference in Lagrange. These tests uncovered strong support for an origin of the clade in the Southern Rocky Mountains of North America followed by dispersal and divergence episodes across refugia. Finally we adopted a stochastic character mapping approach in SIMMAP to investigate the utility of morphological characters in estimating evolutionary relationships among taxa. We found that few morphological characters were phylogenetically informative and many were misleading. Our molecular analyses provide a foundation for the diversity and evolutionary relationships within sect. Trachyphyllum and hypotheses for better understanding the patterns and processes of divergence in this section, other saxifrages, and plants inhabiting the North Pacific Rim

Why Georeferencing Matters: Introducing a Practical Protocol to Prepare Species Occurrence Records for Spatial Analysis

Species Distribution Models (SDMs) are widely used to understand environmental controls on species’ ranges and to forecast species range shifts in response to climatic changes. The quality of input data is crucial determinant of the model’s accuracy. While museum records can be useful sources of presence data for many species, they do not always include accurate geographic coordinates. Therefore, actual locations must be verified through the process of georeferencing. We present a practical, standardized manual georeferencing method (the Spatial Analysis Georeferencing Accuracy (SAGA) protocol) to classify the spatial resolution of museum records specifically for building improved SDMs. We used the high-elevation plant Saxifraga austromontana Wiegand (Saxifragaceae) as a case study to test the effect of using this protocol when developing an SDM. In MAXENT, we generated and compared SDMs using a comprehensive occurrence dataset that had undergone three different levels of georeferencing: (1) trained using all publicly available herbarium records of the species, minus outliers (2) trained using herbarium records claimed to be previously georeferenced, and (3) trained using herbarium records that we have manually georeferenced to a ≤ 1-km resolution using the SAGA protocol. Model predictions of suitable habitat for S. austromontana differed greatly depending on georeferencing level. The SDMs fitted with presence locations georeferenced using SAGA outperformed all others. Differences among models were exacerbated for future distribution predictions. Under rapid climate change, accurately forecasting the response of species becomes increasingly important. Failure to georeference location data and cull inaccurate samples leads to erroneous model output, limiting the utility of spatial analyses. We present a simple, standardized georeferencing method to be adopted by curators, ecologists, and modelers to improve the geographic accuracy of museum records and SDM predictions

Integrating Multiple Lines of Evidence into Historical Biogeography Hypothesis Testing: A Bison bison Case Study

One of the grand goals of historical biogeography is to understand how and why species’ population sizes and distributions change over time. Multiple types of data drawn from disparate fields, combined into a single modelling framework, are necessary to document changes in a species’s demography and distribution, and to determine the drivers responsible for change. Yet truly integrated approaches are challenging and rarely performed. Here, we discuss a modelling framework that integrates spatio-temporal fossil data, ancient DNA, palaeoclimatological reconstructions, bioclimatic envelope modelling and coalescence models in order to statistically test alternative hypotheses of demographic and potential distributional changes for the iconic American bison (Bison bison). Using different assumptions about the evolution of the bioclimatic niche, we generate hypothetical distributional and demographic histories of the species. We then test these demographic models by comparing the genetic signature predicted by serial coalescence against sequence data derived from subfossils and modern populations. Our results supported demographic models that include both climate and human-associated drivers of population declines. This synthetic approach, integrating palaeoclimatology, bioclimatic envelopes, serial coalescence, spatio-temporal fossil data and heterochronous DNA sequences, improves understanding of species’ historical biogeography by allowing consideration of both abiotic and biotic interactions at the population level

Resolving the Evolutionary History of Campanula (Campanulaceae) in Western North America

Recent phylogenetic works have begun to address long-standing questions regarding the systematics of Campanula (Campanulaceae). Yet, aspects of the evolutionary history, particularly in northwestern North America, remain unresolved. Thus, our primary goal in this study was to infer the phylogenetic positions of northwestern Campanula species within the greater Campanuloideae tree. We combined new sequence data from 5 markers (atpB, rbcL, matK, and trnL-F regions of the chloroplast and the nuclear ITS) representing 12 species of Campanula with previously published datasets for worldwide campanuloids, allowing us to include approximately 75% of North American Campanuleae in a phylogenetic analysis of the Campanuloideae. Because all but one of North American Campanula species are nested within a single campanuloid subclade (the Rapunculus clade), we conducted a separate set of analyses focused specifically on this group. Our findings show that i) the campanuloids have colonized North America at least 6 times, 4 of which led to radiations, ii) all but one North American campanuloid are nested within the Rapunculus clade, iii) in northwestern North America, a C. piperi – C. lasiocarpa ancestor gave rise to a monophyletic Cordilleran clade that is sister to a clade containing C. rotundifolia, iv) within the Cordilleran clade, C. parryi var. parryi and C. parryi var. idahoensis exhibit a deep, species-level genetic divergence, and v) C. rotundifolia is genetically diverse across its range and polyphyletic. Potential causes of diversification and endemism in northwestern North America are discussed

Off-axis symbiosis found: characterization and biogeography of bacterial symbionts of Bathymodiolus mussels from Lost City hydrothermal vents

Organisms at hydrothermal vents inhabit discontinuous chemical ‘islands’ along mid-ocean ridges, a scenario that may promote genetic divergence among populations. The 2003 discovery of mussels at the Lost City Hydrothermal Field provided a means of evaluating factors that govern the biogeography of symbiotic bacteria in the deep sea. The unusual chemical composition of vent fluids, the remote location, and paucity of characteristic vent macrofauna at the site, raised the question of whether microbial symbioses existed at the extraordinary Lost City. If so, how did symbiotic bacteria therein relate to those hosted by invertebrates at the closest known hydrothermal vents along the Mid-Atlantic Ridge (MAR)? To answer these questions, we performed microscopic and molecular analyses on the bacteria found within the gill tissue of Bathymodiolus mussels (Mytilidae, Bathymodiolinae) that were discovered at the Lost City. Here we show that Lost City mussels harbour chemoautotrophic and methanotrophic endosymbionts simultaneously. Furthermore, populations of the chemoautotrophic symbionts from the Lost City and two sites along the MAR are genetically distinct from each other, which suggests spatial isolation of bacteria in the deep sea. These findings provide new insights into the processes that drive diversification of bacteria and evolution of symbioses at hydrothermal vents.Organismic and Evolutionary Biolog