[Show abstract][Hide abstract] ABSTRACT: 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 and polyploidization. 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 differentiate 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.
Full-text · Article · Oct 2014 · Ecology and Evolution
[Show abstract][Hide abstract] ABSTRACT: 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.
Full-text · Article · Jan 2014 · Proceedings of the Royal Society B: Biological Sciences
[Show abstract][Hide abstract] ABSTRACT: Recent molecular phylogenetic analyses have revealed that Saxifraga sect. Trachyphyllum as currently circumscribed is polyphyletic, with the designated type, S. aspera, falling outside of the more speciose clade. Several other lines of morphological, geographic, and ecological evidence also distinguish the two distantly related groups from one another. In combination, these data necessitate the circumscription of a new section, S. sect. Bronchiales, which is described herein. The section is hypothesized to have arisen in the southern Rocky Mountains of North America, followed by northwestward expansion across Beringia and diversification among refugia.
[Show abstract][Hide abstract] ABSTRACT: 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.
[Show abstract][Hide abstract] ABSTRACT: 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 bryoides L. 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.
[Show abstract][Hide abstract] ABSTRACT: AimSpecies distribution models (SDMs) are commonly used to forecast climate change impacts. These models, however, are subject to important assumptions and limitations. By integrating two independent but complementary methods, ensemble SDMs and statistical phylogeography, we addressed key assumptions and created robust assessments of climate change impacts on species distributions while improving the conservation value of these projections. LocationNorth American cordillera. Methods
This approach was demonstrated using the arctic‐alpine plant Rhodiola integrifolia (Crassulaceae). SDMs were fitted to current and past climates using eight models, two thresholds and one to three climate data sets. These projections were combined to create a map of stable climate (refugia) since the Last Interglacial (124,000 kya). Five biogeographic hypotheses were developed based on the configuration of refugia and tested using statistical phylogeography. Projection of SDMs into the future was contingent on agreement across approaches; future projections (to 2085) used five climate data sets and two greenhouse gas scenarios. ResultsA multiple‐refugia hypothesis was supported by both methods, confirming the assumption of niche conservatism in R. integrifolia and justifying the projection of SDMs onto future climates. Future projections showed substantial loss of climatically suitable habitat. Southern populations had the greatest losses, although the biogeographic scale of modelling may overpredict extinction risks in areas of topographic complexity. Past and future SDMs were assessed for novel values of climate variables; areas of novel climate were flagged as having higher uncertainty. Main conclusionsIntegrating molecular approaches with spatial analyses of species distributions under global change has great potential to improve conservation decision‐making. Molecular tools can support and improve current methods for understanding the vulnerability of species to climate change and provide additional data upon which to base conservation decisions, such as prioritizing the conservation of areas of high genetic diversity to build evolutionary resiliency within populations.
[Show abstract][Hide abstract] ABSTRACT: Background/Question/Methods
Species distribution models (SDMs) are commonly used to forecast climate change impacts on species and ecosystems. These models, however, are subject to important assumptions and limitations. By integrating two independent but complementary methods, ensemble SDMs and statistical phylogeography, we were able to address key assumptions and create robust assessments of climate change impacts on species’ distributions while improving the conservation value of these projections.
This approach was demonstrated using Rhodiola integrifolia, an alpine-arctic plant specialist distributed at high elevations and latitudes throughout the North American cordillera. SDMs for R. integrifolia were fit to current and past climates using eight model algorithms, two threshold methods, and between one and three climate data sets (from general circulation models, GCMs). This ensemble of projections was combined using consensus methods to create a map of stable climate (refugial habitat) since the Last Interglacial (124,000 years before present).
Four biogeographic hypotheses were developed based on the configuration of refugial habitat and tested using a statistical phylogeographic approach. Statistical phylogeography evaluates the probability of alternative models of population history given uncertainty about past population parameters. Agreement between SDM projections and phylogeographic analyses provides support for niche conservatism and the ability of the SDMs to accurately project distributions over time. Disagreement can indicate dispersal barriers, a lack of niche conservatism, or errors in the modeling process.
For R. integrifolia the multiple-refugia hypothesis was supported by both methods, validating the assumption of niche conservatism and justifying the projection of the SDMs onto future climates. SDMs were projected onto two greenhouse gas scenarios (A1B and A2) for 2085 using climate data from five GCMs. Projections at 2085 showed substantial losses of climatically suitability habitat for R. integrifolia across its range. Southern populations had the greatest losses, though the biogeographic scale of modeling may overpredict extinction risks in these areas of topographic complexity. Finally, past and future SDM projections were assessed for novel values of climate variables; projections in areas of novel climate were flagged as having higher uncertainty.
Integrating genetic approaches with spatial analyses of species distributions under global change has great potential to improve conservation decision-making. Genetic tools can support and improve current methods for understanding species vulnerability to climate change, and provide additional data upon which to base conservation decisions, such as prioritizing the conservation of areas of high genetic diversity in order to build evolutionary resiliency within populations.
[Show abstract][Hide abstract] ABSTRACT: 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.
[Show abstract][Hide abstract] ABSTRACT: Species and sequence data used for phylogenetic analysis of the Campanulaceae. For each species we list the major clade in which it falls, herbarium voucher number (only for newly sequenced species/individuals from this study), Genbank numbers for available sequence data, and citations for previously published data (see reference list following table). Species names marked with an asterisk (*) have been updated from the names originally listed on the Genbank accessions to be consistent with the classification scheme of Lammers (2007). Similarly, Asyneuma comosiforme has been changed to Campanula comosiformis based on the findings of Frajman and Schneeweiss (2009). A cross (†) next to a species name indicates ambiguity in the placement of the species within major clades due to incongruent results from different individuals or genetic markers. Uncertainty in clade assignments due to poor phylogenetic resolution is denoted by a question mark (?) in the “Clade” column.
[Show abstract][Hide abstract] ABSTRACT: Best maximum likelihood phylogeny for the Campanulaceae based on all available rbcL DNA sequences. Outgroups have been removed for clarity. Numbers after species names are Genbank accession numbers for sequences used to build the tree. Pie graphs on branches indicate relationships that are well supported under one or more of the three tree-building methods that were employed. Black-filled segments of the graphs indicate maximum parsimony (upper left) or maximum likelihood (upper right) bootstrap values >75, or Bayesian posterior probabilities >0.95 (bottom). Black arrow marks Campanula rapunculoides (Genbank # FJ587271), which some Bayesian analyses placed in an alternative position in the tree (grey text and arrow). The topology shown here is consistent with the most commonly retrieved Bayesian tree.
[Show abstract][Hide abstract] ABSTRACT: Best maximum likelihood phylogeny for the Campanulaceae based on all available atpB DNA sequences. Outgroups have been removed for clarity. Numbers after species names are Genbank accession numbers for sequences used to build the tree. Pie graphs on branches indicate relationships that are well supported under one or more of the three tree-building methods that were employed. Black-filled segments of the graphs indicate maximum parsimony (upper left) or maximum likelihood (upper right) bootstrap values >75, or Bayesian posterior probabilities >0.95 (bottom).
[Show abstract][Hide abstract] ABSTRACT: Best maximum likelihood phylogeny for the Rapunculus clade based on all available trnL-F DNA sequences. Outgroups have been removed for clarity. Numbers after species names are Genbank accession numbers for sequences used to build the tree. Pie graphs on branches indicate relationships that are well supported under one or more of the three tree-building methods that were employed. Black-filled segments of the graphs indicate maximum parsimony (upper left) or maximum likelihood (upper right) bootstrap values >75, or Bayesian posterior probabilities >0.95 (bottom).
[Show abstract][Hide abstract] ABSTRACT: Best maximum likelihood phylogeny for the Campanulaceae based on all available matK DNA sequences. Outgroups have been removed for clarity. Numbers after species names are Genbank accession numbers for sequences used to build the tree. Pie graphs on branches indicate relationships that are well supported under one or more of the three tree-building methods that were employed. Black-filled segments of the graphs indicate maximum parsimony (upper left) or maximum likelihood (upper right) bootstrap values >75, or Bayesian posterior probabilities >0.95 (bottom).
[Show abstract][Hide abstract] ABSTRACT: To assess effects of historical climate change on northern species, we quantified the population history of the arctic ground squirrel (Spermophilus parryii), an arctic-adapted rodent that evolved in Beringia and was strongly influenced by climatic oscillations of the Quaternary. Competing hypotheses for the species' population history were derived from patterns of mitochondrial (mtDNA) structure and a bioclimatic envelope model (BEM). Hypotheses invoked (1) sequential isolation of regional populations beginning with the Arctic, (2) deep isolation only across central Alaska, and (3) widespread panmixia, and were tested using coalescent methods applied to eight nuclear (nDNA) loci. The data rejected strict interpretations of all three hypotheses, but perspectives underlying each encompassed aspects of the species' history. Concordance between mtDNA and nDNA geographic structure revealed three semi-independently evolving phylogroups, whereas signatures of gene flow at nDNA loci were consistent with a historical contact between certain populations as inferred by the BEM. Demographic growth was inferred for all regions despite expectations of postglacial habitat contraction for parts of Beringia. Our results highlight the complementary perspectives on species' histories that multiple lines of evidence provide, and underscore the utility of multilocus data for resolving complex population histories relevant to understanding effects of climate change.
[Show abstract][Hide abstract] ABSTRACT: The Bering Land Bridge has been a major highway for Asian plants into North America, but also a barrier to some and a filter for others. Additionally, there are widely separated and highly local occurrences of Asiatic species in Alaska and adjacent Yukon that are thought by some to be relicts of late-glacial steppe-tundra. Molecular sequence data successful-ly clarify historical dispersal and vicariance events and will help resolve the role that Beringia played in facilitating and/ or inhibiting plant migrations. Furthermore, hypothesis testing through coalescence-based analyses of molecular se-quence data provides a powerful means of investigating the region's floristic history.
[Show abstract][Hide abstract] ABSTRACT: Background: Evidence strongly suggests that Beringia was a refugium for tundra taxa throughout the Quaternary (the last 2 million years). However, the genetic consequences of the repeated formation and flooding of the Bering Land Bridge remain uncertain.Aims: The goal of this paper was to determine the role that the unique environmental history of Beringia played in the diversification of tundra flora.Methods: I adopted a comparative coalescent approach to test models of divergence for arctic flora within Beringia. The literature was surveyed for phylogeographic studies that sampled broadly across the region and incorporated molecular markers appropriate for coalescent analyses. Of the 13 possible taxa, only two fit these criteria: Saxifraga oppositifolia (Saxifragaceae) and Vaccinium uliginosum (Ericaceae). Observed gene trees were compared with a distribution of trees simulated under neutral coalescence to test models of population divergence. Population models fell within two major categories reflecting the importance of either the Bering Land Bridge or the Bering Sea dispersal barrier on the distribution of genetic diversity in the species.Results: Both species fit ‘bridge’ models, but S. oppositifolia supported a model of eastward migration while V. uliginosum fits a unified Beringia refugium model. The evolutionary implications of these findings are discussed.Conclusions: The limited number of studies emphasises the need for more sequence-based research in the region. This will help resolve the history of the Beringia tundra ecosystem, which has important implications for the diversification of tundra flora, the history of Beringia, and the potential consequences of climate change on the distribution of biological diversity.
[Show abstract][Hide abstract] ABSTRACT: Recent evidence suggests that deep-sea vestimentiferan tube worms acquire their endosymbiotic bacteria from the environment
each generation; thus, free-living symbionts should exist. Here, free-living tube worm symbiont phylotypes were detected in
vent seawater and in biofilms at multiple deep-sea vent habitats by PCR amplification, DNA sequence analysis, and fluorescence
in situ hybridization. These findings support environmental transmission as a means of symbiont acquisition for deep-sea tube
[Show abstract][Hide abstract] ABSTRACT: 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.
Full-text · Article · Dec 2006 · Environmental Microbiology
[Show abstract][Hide abstract] ABSTRACT: Bathymodiolus azoricus and Bathymodiolus puteoserpentis are symbiont-bearing mussels that dominate hydrothermal vent sites along the northern Mid-Atlantic Ridge (MAR). Both species live in symbiosis with two physiologically and phylogenetically distinct Gammaproteobacteria: a sulfur-oxidizing chemoautotroph and a methane-oxidizer. A detailed analysis of mussels collected from four MAR vent sites (Menez Gwen, Lucky Strike, Rainbow, and Logatchev) using comparative 16S rRNA sequence analysis and fluorescence in situ hybridization (FISH) showed that the two mussel species share highly similar to identical symbiont phylotypes. FISH observations of symbiont distribution and relative abundances showed no obvious differences between the two host species. In contrast, distinct differences in relative symbiont abundances were observed between mussels from different sites, indicating that vent chemistry may influence the relative abundance of thiotrophs and methanotrophs in these dual symbioses.
[Show abstract][Hide abstract] ABSTRACT: The Quaternary climate cycles forced species to repeatedly migrate across a continually changing landscape. How these shifts in distribution impacted the evolution of unrelated but ecologically associated taxa has remained elusive due to the stochastic nature of the evolutionary process and variation in species-specific biological characteristics and environmental constraints. To account for the uncertainty in genealogical estimates, we adopted a coalescent approach for testing hypotheses of population divergence in coevolving taxa. We compared genealogies of a specialized herbivorous insect, Parnassius smintheus (Papilionidae), and its host plant, Sedum lanceolatum (Crassulaceae), from the alpine tundra of the Rocky Mountains to null distributions from coalescent simulations to test whether tightly associated taxa shared a common response to the paleoclimatic cycles. Explicit phylogeographic models were generated from geologic and biogeographic data and evaluated over a wide range of divergence times given calibrated mutation rates for both species. Our analyses suggest that the insect and its host plant responded similarly but independently to the climate cycles. By promoting habitat expansion and mixing among alpine populations, glacial periods repeatedly reset the distributions of genetic variation in each species and inhibited continual codivergence among pairs of interacting species.