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

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

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

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 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

Phylogeny for <i>Saxifraga</i> sect. <i>Trachyphyllum</i>, based on the entire ITS1, 5.8S, and ITS2 locus data generated in this study.

<p>Pie graphs on branches indicate relationships that are well-supported under Bayesian (upper; black >0.95, gray 0.90–0.94) and maximum likelihood (lower; black >70, gray 60–69) tree-building methods. Sub-clades referred to in the text are numbered (1–21). Locations are given for members of sect. <i>Trachyphyllum</i>, where CA = Canada, EU = Europe, RU = Russia, USA = United States, Is. = Island, and ONP = Olympic National Park. Clade T1, including both <i>S. aspera</i> and <i>S. bryoides</i>, is shaded in gray to emphasize the position relative to the main clade of sect. <i>Trachyphyllum</i>, Clade T2. For members of the genus <i>Saxifraga</i>, only the specific or subspecific epithet is used to label each taxon on the tree.</p

Most likely reconstruction of geographic range evolution in the SRM model for sect. <i>Trachyphyllum</i>, inferred through Lagrange.

<p>Colors correspond to areas shown on the map in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0069814#pone-0069814-g001" target="_blank">Fig. 1</a> (blue = North America Interior [NAI]; green = North America Coast [NAC]; yellow = Beringia [BER]; orange = Central Asia & Siberia [CAS]; red = Japan [JAP]). On the phylogeny, white bars represent interglacial periods and gray bars denote glacials. Dispersal matrices for interglacial periods are shown above for each model, with ‘>’ representing directional dispersal and ‘-’ meaning no dispersal. Dispersal was not permitted during glacial periods. The models are as follows: SRM - origin in North America Interior followed by westward dispersal across Beringia and into Asia; BER - dispersal out of Beringia onto both continents; CAS - origin in Central Asia with eastward dispersal across Beringia and into North America; JAP - origin in Japan with eastward dispersal across Beringia and into North America; REF - isolation in each refugium with no dispersal possible until 10 - 0 kya. Time is shown in thousands of years along the bottom of the figure.</p

Geographic models of population divergence.

<p>Models of population divergence based on the location of potential glacial refugia and possible origins and migration routes are shown as follows: A) Refugia - fragmentation of an ancestral population among all refugia, B) Southern Rocky Mountain (SRM) - an origin in the southern Rocky Mountains of North America followed by westward dispersal, C) and D) Japan I and II - origin in Japan with northern and eastward dispersal, and E) and F) Central Asia I and II - an Asian origin with southern and eastward dispersal. NAI = North America Interior, NAC = North America Cascadia, BER = Beringia, CAS = Central Asia & Siberia, JAP = Japan. Observed DC values and P-values for each model are shown. The coalescent simulations produced a distribution of DC values with mean = 8.18 and st. dev. = 2.34. The Refugia (A) and the SRM (B) models were supported at α<0.05. All others were rejected.</p