Barn swallows before barns: population histories and intercontinental colonization

The barn swallow (Hirundo rustica) is one of most widely distributed swallows, owing in part to its recent switch from natural nest sites to human structures. We conducted phylogenetic analysis of mitochondrial (mt) and nuclear DNA to explore the recent evolutionary history of this species. Strongly supported mtDNA clades corresponded to Europe, Asia and North America plus the Baikal region of Asia. Analysis of sequence data from a sex-linked nuclear gene was unable to recover the phylogenetic splits in the mtDNA tree, confirming that the main clades evolved recently. The phylogenetic pattern suggests that the ancestral area of the barn swallow was the holarctic; most divergence events are consistent with vicariance. Most unexpectedly, analyses show that barn swallows from North America colonized the Baikal region in the recent past (one fixed substitution). This dispersal direction is opposite of that for most nearctic-palearctic taxon exchanges. Although this invasion was envisioned to coincide with the appearance of new types of human dwelling in the Baikal region, calibration of molecular divergence suggests an older dispersal event. A recent history of gene flow within the main palearctic clades is consistent with range and population expansion owing to new nesting opportunities provided by human settlements. Contrary to expectation, populations in North America appear historically larger and more stable than those in the palearctic. The Baikal population apparently has not increased greatly since colonization.     

A fossil-calibrated relaxed clock for Ephedra indicates an Oligocene age for the divergence of Asian and New World clades and Miocene dispersal into South America

Ephedra comprises approximately 50 species, which are roughly equally distributed between the Old and New World deserts, but not in the intervening regions （amphitropical range）. Great heterogeneity in the substitution rates of Gnetales （Ephedra, Gnetum, and Welwitschia） has made it difficult to infer the ages of the major divergence events in Ephedra, such as the timing of the Beringian disjunction in the genus and the entry into South America. Here, we use data from as many Gnetales species and genes as available from GenBank and from a recent study to investigate the timing of the major divergence events. Because of the tradeoff between the amount of missing data and taxon/gene sampling, we reduced the initial matrix of 265 accessions and 12 loci to 95 accessions and 10 loci, and further to 42 species （and 7736 aligned nucleotides） to achieve stationary distributions in the Bayesian molecular clock runs. Results from a relaxed clock with an uncorrelated rates model and fossil-based calibration reveal that New World species are monophyletic and diverged from their mostly Asian sister clade some 30 mya, fitting with many other Beringian disjunctions. The split between the single North American and the single South American clade occurred approximately 25 mya, well before the closure of the Panamanian Isthmus. Overall, the biogeographic history of Ephedra appears dominated by long-distance dispersal, but finer-scale studies are needed to test this hypothesis.     

Global historical biogeography of hadrosaurid dinosaurs

Hadrosaurids were the most derived ornithopods and amongst the most diverse herbivore dinosaurs during the Late Cretaceous of Europe, Asia, and the two Americas. Here, their biogeographical history is reconstructed using dispersal‐vicariance analysis (DIVA). The results showed that Hadrosauridae originated in North America and soon after dispersed to Asia no later than the Late Santonian. The most recent common ancestor of Saurolophidae (= Saurolophinae + Lambeosaurinae) is inferred to have been widespread in North America and Asia. The split between saurolophines and lambeosaurines occurred in response to vicariance no later than the Late Santonian: the former clade originated in North America, whereas the latter did so in Asia. Saurolophine biogeographical history included a minimum of five dispersal events followed by vicariance. Four of these dispersals were inferred to have occurred from North America to Asia during the Campanian and Early Maastrichtian, whereas a fifth event represented a southward dispersal from North to South America no later than the Late Campanian. The historical biogeography of lambeosaurines was characterized by an early evolution in Asia, with a Campanian dispersal to the European archipelago followed by vicariance. Reconstruction of the ancestral areas for the deepest nodes uniting the more derived lambeosaurines clades (‘hypacrosaurs’, ‘corythosaurs’, and ‘parasaurolophs’) is ambiguous. The split between North American and Asian clades of ‘hypacrosaurs’ and ‘parasaurolophs’ occurred in response to vicariance during the Campanian. The evolutionary history of North American ‘hypacrosaurs’ and ‘parasaurolophs’ was characterized by duplication events. The latter also characterized the Late Campanian ‘corythosaurs’, which remained restricted to North America. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 159 , 503–525.     

Multilocus phylogeography of a holarctic duck: colonization of north america from eurasia by gadwall (Anas strepera)

More than 100 species of birds have Holarctic distributions extending across Eurasia and North America, and many of them likely achieved these distributions by recently colonizing one continent from the other. Mitochondrial DNA (mtDNA) and five nuclear introns were sequenced to test the direction and timing of colonization for a Holarctic duck, the gadwall (Anas strepera). Three lines of evidence suggest gadwalls colonized North America from Eurasia. First, New World (NW) gadwalls had fewer alleles at every locus and 61% of the allelic richness found in Old World (OW) gadwalls. Second, NW gadwalls had lower mtDNA allelic richness than other NW ducks. Third, coalescent analysis suggested that less than 5% of the ancestral population contributed to NW gadwalls at the time of divergence. Gadwalls likely colonized North America during the Late Pleistocene (approximately 81,000 years ago), but the confidence interval on that estimate was large (8500-450,000 years ago). Intercontinental gene flow and selection also likely contributed to genetic diversity in gadwalls. This study illustrates the use of multiple loci and coalescent analyses for critically testing a priori hypotheses regarding dispersal and colonization and provides an independent datapoint supporting an OW to NW bias in the direction of colonization.     

The Phylogeny and Biogeographic History of Ashes (Fraxinus,Oleaceae) Highlight the Roles of Migration and Vicariance in the Diversification of Temperate Trees

The cosmopolitan genus Fraxinus, which comprises about 40 species of temperate trees and shrubs occupying various habitats in the Northern Hemisphere, represents a useful model to study speciation in long-lived angiosperms. We used nuclear external transcribed spacers (nETS), phantastica gene sequences, and two chloroplast loci (trnH-psbA and rpl32-trnL) in combination with previously published and newly obtained nITS sequences to produce a time-calibrated multi-locus phylogeny of the genus. We then inferred the biogeographic history and evolution of floral morphology. An early dispersal event could be inferred from North America to Asia during the Oligocene, leading to the diversification of the section Melioides sensus lato. Another intercontinental dispersal originating from the Eurasian section of Fraxinus could be dated from the Miocene and resulted in the speciation of F. nigra in North America. In addition, vicariance was inferred to account for the distribution of the other Old World species (sections Sciadanthus, Fraxinus and Ornus). Geographic speciation likely involving dispersal and vicariance could also be inferred from the phylogenetic grouping of geographically close taxa. Molecular dating suggested that the initial divergence of the taxonomical sections occurred during the middle and late Eocene and Oligocene periods, whereas diversification within sections occurred mostly during the late Oligocene and Miocene, which is consistent with the climate warming and accompanying large distributional changes observed during these periods. These various results underline the importance of dispersal and vicariance in promoting geographic speciation and diversification in Fraxinus. Similarities in life history, reproductive and demographic attributes as well as geographical distribution patterns suggest that many other temperate trees should exhibit similar speciation patterns. On the other hand, the observed parallel evolution and reversions in floral morphology would imply a major influence of environmental pressure. The phylogeny obtained and its biogeographical implications should facilitate future studies on the evolution of complex adaptive characters, such as habitat preference, and their possible roles in promoting divergent evolution in trees.     

Origin and evolution of the northern hemisphere disjunction in the moss genus Homalothecium (Brachytheciaceae)

Competing hypotheses that rely either on a stepping-stone dispersal via the North Atlantic or the Bering land bridges, or more recent transoceanic dispersal, have been proposed to explain the disjunct distribution of Mediterranean flora in southern Europe and western North America. These hypotheses were tested with molecular dating using a phylogeny of the moss genus Homalothecium based on ITS, atpB-rbcL, and rpl16 sequence data. The monophyly of two main lineages in Western Palearctic (Europe, central Asia and north Africa) and North America is consistent with the ancient vicariance hypothesis. The monophyly of Madeiran H. sericeum accessions supports the recognition of the Macaronesian endemic H. mandonii. A range of absolute rates of molecular evolution documented in land plants was used as probabilistic calibration prior by a Bayesian inference implementing a relaxed-clock model to derive ages for the nodes of interest. Our age estimates for the divergence of the American and Western Palearctic Homalothecium clade (5.7 Ma, IC 3.52-8.26) and the origin of H. mandonii (2.52 Myr IC 0.86-8.25) are not compatible with the ancient vicariance hypothesis. Age estimates suggests that species distributions result from rare instances of dispersal and subsequent sympatric diversification. The calibrated phylogeny indicates that Homalothecium has undergone a fast radiation during the last 4 Myr, which is consistent with the low levels of morphological divergence among sibling species.     

A fossil‐calibrated relaxed clock for Ephedra indicates an Oligocene age for the divergence of Asian and New World clades and Miocene dispersal into South America

Abstract Ephedra comprises approximately 50 species, which are roughly equally distributed between the Old and New World deserts, but not in the intervening regions (amphitropical range). Great heterogeneity in the substitution rates of Gnetales (Ephedra, Gnetum, and Welwitschia) has made it difficult to infer the ages of the major divergence events in Ephedra, such as the timing of the Beringian disjunction in the genus and the entry into South America. Here, we use data from as many Gnetales species and genes as available from GenBank and from a recent study to investigate the timing of the major divergence events. Because of the tradeoff between the amount of missing data and taxon/gene sampling, we reduced the initial matrix of 265 accessions and 12 loci to 95 accessions and 10 loci, and further to 42 species (and 7736 aligned nucleotides) to achieve stationary distributions in the Bayesian molecular clock runs. Results from a relaxed clock with an uncorrelated rates model and fossil‐based calibration reveal that New World species are monophyletic and diverged from their mostly Asian sister clade some 30 mya, fitting with many other Beringian disjunctions. The split between the single North American and the single South American clade occurred approximately 25 mya, well before the closure of the Panamanian Isthmus. Overall, the biogeographic history of Ephedra appears dominated by long‐distance dispersal, but finer‐scale studies are needed to test this hypothesis.     

Phylogeny, divergence times and species limits of spiny lizards (Sceloporus magister species group) in western North American deserts and Baja California

The broad distribution of the Sceloporus magister species group (squamata: phrynosomatidae) throughout western North America provides an appropriate model for testing biogeographical hypotheses explaining the timing and origins of diversity across mainland deserts and the Baja California Peninsula. We inferred concordant phylogenetic trees describing the higher-level relationships within the magister group using 1.6 kb of mitochondrial DNA (mtDNA) and 1.7 kb of nuclear DNA data. These data provide strong support for the parallel divergence of lineages endemic to the Baja California Peninsula (S. zosteromus and the orcutti complex) in the form of two sequential divergence events at the base of the magister group phylogeny. A relaxed phylogenetic analysis of the mtDNA data using one fossil and one biogeographical constraint provides a chronology of these divergence events and evidence that further diversification within the Baja California clades occurred simultaneously, although patterns of geographical variation and speciation between clades differ. We resolved four major phylogeographical clades within S. magister that (i) provide a novel phylogenetic placement of the Chihuahuan Desert populations sister to the Mojave Desert; (ii) illustrate a mixed history for the Colorado Plateau that includes Mojave and Sonoran Desert components; and (iii) identify an area of overlap between the Mojave and Sonoran Desert clades near Yuma, Arizona. Estimates of bidirectional migration rates among populations of S. magister using four nuclear loci support strong asymmetries in gene flow among the major mtDNA clades. Based on the nonexclusivity of mtDNA haplotypes, nuclear gene flow among populations and wide zones of phenotypic intergradation, S. magister appears to represent a single geographically variable and widespread species.     

Phylogeographic analyses of a circumarctic coastal and a boreal lacustrine mysid crustacean, and evidence of fast postglacial mtDNA rates

Phylogeographic structures of two weakly dispersing Mysis sibling species, one with a circumarctic coastal, the other with a boreal lacustrine-Baltic distribution, were studied from mitochondrial cytochrome c oxidase subunit I (COI) gene sequences. Mysis segerstralei showed high overall diversity and little phylogeographic structure across the Arctic, indicating late-glacial dispersal among coastal and lake populations from Alaska, Siberia and the north of Europe. A strongly divergent refugial lineage was however identified in Beringia. The boreal 'glacial relict'Mysis salemaai in turn displayed clear structuring among postglacially isolated Scandinavian lake populations. The inferred pattern of intralake mitochondrial DNA (mtDNA) monophyly in Scandinavia suggested relatively small population sizes and a remarkably fast postglacial mtDNA divergence rate (0.27% per 10 000 years). Nevertheless, the broader phylogeographic pattern did not support distinct eastern and western glacial refugia in Northern Europe, unlike in some other aquatic taxa. In all, the two species comprised three equidistant mitochondrial lineages (approximately 2% divergence), corresponding to M. salemaai, to the bulk of M. segerstralei, and to the Beringian M. segerstralei lineage. The lack of reciprocal monophyly of the two species in respect to their mitochondrial genealogy could indicate postspeciation mitochondrial introgression, also exemplified by an evidently more recent capture of M. segerstralei mitochondria in a Karelian population of M. salemaai. Overall, the data suggest that the continental boreal M. salemaai has a relatively recent ancestry in arctic coastal waters, whereas two other boreal 'glacial relict'Mysis sibling species in Europe (Mysis relicta) and North America (Mysis diluviana) have colonized inland waters much earlier (approximately 8% COI divergence).     

Genetic diversity of North American populations of Cristatella mucedo, inferred from microsatellite and mitochondrial DNA

Research over the past 20 years has shown, with the help of molecular markers, that the population genetics and distribution patterns of freshwater invertebrates in North America are often more complex than was previously believed. Here we extend this research to an, as yet, unstudied but widespread and common group, the freshwater bryozoans. Colonies of the bryozoan Cristatella mucedo were collected from a number of lakes across central North America, and were characterized genetically by analysis of microsatellite loci and mitochondrial DNA (mtDNA) cytochrome b sequences. The microsatellites illustrate a pattern of generally diverse and highly differentiated populations that contain little evidence of recent gene flow. The mtDNA sequences yielded highly variable levels of divergence, ranging from 0.0 to 8.8% within populations, and 0.0 to 9.8% among populations. The multiple divergent mtDNA lineages within populations provide evidence for repeated colonization events. The lack of clustering of haplotypes by site suggests that there has been widespread dispersal of multiple genetic lineages since the last ice age. While some of the haplotype lineages may have evolved in disjunct glacial refugia, the maximum levels of divergence predate the time since the last glacial-interglacial cycles. It is likely that multiple factors including vicariance events, patterns of dispersal, localized extinction, and an unusual life history, explain the unique phylogeographic patterns evident today in populations of C. mucedo.     

Multiple intercontinental dispersals shaped the distribution area of Hordeum (Poaceae)

The grass genus Hordeum (Poaceae, Triticeae), comprising 31 species distributed in temperate and dry regions of the world, was analysed to determine the relative contributions of vicariance and long-distance dispersal to the extant distribution pattern of the genus. Sequences from three nuclear regions (DMC1, EF-G and ITS) were combined and analysed phylogenetically for all diploid (20 species) and two tetraploid Hordeum species and the outgroup Psathyrostachys. Ages of clades within Hordeum were estimated using a penalized likelihood analysis of sequence divergence. The sequence data resulted in an almost fully resolved phylogenetic tree that allowed the reconstruction of intrageneric migration routes. Hordeum evolved c. 12 million years ago in South-west Asia and spread into Europe and Central Asia. The colonization of the New World and South Africa involved at least six intercontinental exchanges during the last 4 million years (twice Eurasia-North America, North America-South America, twice South America-North America and Europe-South Africa). Repeated long-distance dispersal between the northern and southern hemisphere were important colonization mechanisms in Hordeum.     

Timing the eastern Asian-eastern North American floristic disjunction: molecular clock corroborates paleontological estimates

Sequence data of the chloroplast gene rbcL were used to estimate the time of the well-known eastern Asian-eastern North American floristic disjunction. Sequence divergence of rbcL was examined for 22 species of 11 genera (Campsis, Caulophyllum, Cornus, Decumaria, Liriodendron, Menispermum, Mitchella, Pachysandra, Penthorum, Podophyllum, and Phryma) representing a diverse array of flowering plants occurring disjunctly in eastern Asia and eastern North America. Divergence times of putative disjunct species pairs were estimated from synonymous substitutions, using rbcL molecular clocks calibrated for Cornus. Relative rate tests were performed to assess rate constancy of rbcL evolution among lineages. Corrections of estimates of divergence times for each species pair were made based on rate differences of rbcL between Cornus and other species pairs. Results of these analyses indicate that the time of divergence of species pairs examined ranges from 12.56 +/- 4.30 million years to recent (<0.31 million years), with most within the last 10 million years (in the late Miocene and Pliocene). These results suggest that the isolation of most morphologically similar disjunct species in eastern Asia and eastern North America occurred during the global climatic cooling period that took place throughout the late Tertiary and Quaternary. This estimate is closely correlated with paleontological evidence and in agreement with the hypothesis that considers the eastern Asian-eastern North American floristic disjunction to be the result of the range restriction of a once more or less continuously distributed mixed mesophytic forest of the Northern Hemisphere that occurred during the late Tertiary and Quaternary. This implies that in most taxa the disjunction may have resulted from vicariance events. However, long-distance dispersal may explain the disjunct distribution of taxa with low divergence, such as Menispermum.     

Inferences on the phylogeography of the fungal pathogen Heterobasidion annosum, including evidence of interspecific horizontal genetic transfer and of human-mediated, long-range dispersal

Fungi in the basidiomycete species complex Heterobasidion annosum are significant root-rot pathogens of conifers throughout the northern hemisphere. We utilize a multilocus phylogenetic approach to examine hypotheses regarding the evolution and divergence of two Heterobasidion taxa associated with pines: the Eurasian H. annosum sensu stricto and the North American H. annosum P intersterility group (ISG). Using DNA sequence information from portions of two nuclear and two mitochondrial loci, we infer phylogenetic relationships via parsimony, Bayesian and median-joining network analysis. Analysis of isolates representative of the entire known geographic range of the two taxa results in monophyletic sister Eurasian and North American lineages, with North America further subdivided into eastern and western clades. Genetically anomalous isolates from the Italian presidential estate of Castelporziano are always part of a North American clade and group with eastern North America, upholding the hypothesis of recent, anthropogenically mediated dispersal. P ISG isolates from Mexico have phylogenetic affinity with both eastern and western North America. Results for an insertion in the mitochondrial rDNA suggest this molecule was obtained from the Heterobasidion S ISG, a taxon sympatric with the P ISG in western North America. These data are compatible with an eastern Eurasian origin of the species, followed by dispersal of two sister taxa into western Eurasia and into eastern North America over a Beringean land bridge, a pattern echoed in the phylogeography of other conifer-associated basidiomycetes.     

Molecular claims of Gondwanan age for Australian agamid lizards are untenable

A recent mtDNA study proposes a surprisingly deep (approximately 150 MYA) divergence between SE Asian and Australasian agamid lizards, consistent with ancient Gondwanan vicariance rather than dispersal across the Indonesian Archipelago. However, the analysis contains a fundamental error: use of rates of molecular evolution inferred from uncorrected sequence divergence to put a time frame on a tree with branch lengths greatly elongated by complex likelihood and rate-smoothing models. Furthermore, this date implies that basal splits within agamids occurred implausibly early, at least 300 MYA (100 Myr before the first fossil lizards and coincident with the earliest fossil reptiles). Analyses of the mtDNA data using more appropriate methods and new information from nuclear (c-mos) sequences suggest a much more recent divergence between SE Asian and Australian agamids (around 30 MYA). Using two fossil boundary dates, bootstrapping the c-mos data gives a 95% confidence interval for this divergence time that is sufficiently recent (14-41 MYA) to exclude an ancient Gondwanan vicariance and is more consistent with Miocene over-water dispersal. As with the mtDNA, the c-mos data implies implausibly old basal divergences among agamids if a Gondwanan age is assumed for the Australasian clade. The analyses also highlight how methods for creating ultrametric trees (especially nonparametric rate smoothing) can greatly modify branch lengths and, thus, always require internal calibrations. The errors associated with inferred dates in the previous study (inferred through parametric bootstrapping) were also unjustifiably low, as this method only considers stochasticity in the substitution model and ignores much larger sources of uncertainty, such as variation in character sampling, tree topology, and calibration accuracy.     

Molecular phylogenetic analysis of Leibnitzia Cass. (Asteraceae: Mutisieae: Gerbera-complex), an Asian-North American disjunct genus

Leibnitzia comprises six species of perennial herbs that are adapted to high elevation conditions and is one of only two Asteraceae genera known to have an exclusively disjunct distribution spanning central to eastern Asia and North America. Molecular phylogenetic analysis of Leibnitzia and other Gerbera-complex members indicates that Leibnitzia is monophyletic, which is in contrast with our expectation that the American Leibnitzia species L. Lyrata and L. Occimadremis would be more closely related to another American member of the Gerbera-complex, namely Chaptalia. Ancestral area reconstructions show that the historical biogeography of the Gerbera-complex mirrors that of the entire Asteraceae, with early diverging lineages located in South America that were followed by transfers to Africa and Eurasia and, most recently, to North America. Intercontinental transfer of Leibnitzia appears to have been directed from Asia to North America. Independent calibrations of nuclear (ribosomal DNA internal transcribed spacer region) and chloroplast (trnL-rpl32 intron) DNA sequence data using relaxed clock methods and either mean rate or fossil-based priors unanimously support Miocene and younger divergence times for Gerbera-complex taxa. The ages are not consistent with most Gondwanan vicariance episodes and, thus, the global distribution of Gerbera-complex members must be explained in large part by long-distance dispersal. American species of Leibnitzia are estimated to have diverged from then- Asian ancestor during the Quaternary (ca. 2 mya) and either migrated overland to North America via Beringia and retreated southwards along high elevation corridors to their- present location in southwestern North America or were dispersed long distance.     

Phylogenomics,biogeography, and evolution of the blue‐ or white‐fruited dogwoods (Cornus)—Insights into morphological and ecological niche divergence following intercontinental geographic isolation

The eastern Asian (EA)–eastern North American (ENA) floristic disjunction represents a major pattern of phytogeography of the Northern Hemisphere. Despite 20 years of studies dedicated to identification of taxa that display this disjunct pattern, its origin and evolution remain an open question, especially regarding post‐isolation evolution. The blue‐ or white‐fruited dogwoods (BW) are the most species‐rich among the four major clades of Cornus L., consisting of ~35 species divided into three subgenera (subg. Yinquania, subg. Mesomora, and subg. Kraniopsis). The BW group provides an excellent example of the EA–ENA floristic disjunction for biogeographic study due to its diversity distribution centered in eastern Asia and eastern North America, yet its species relationships and delineation have remained poorly understood. In this study, we combined genome‐wide markers from RAD‐seq, morphology, fossils, and climate data to understand species relationships, biogeographic history, and ecological niche and morphological evolution. Our phylogenomic analyses with RAxML and MrBayes recovered a strongly supported and well‐resolved phylogeny of the BW group with three intercontinental disjunct clades in EA and ENA or Eurasia and North America, of which two are newly identified within subg. Kraniopsis. These analyses also recovered a potential new species but failed to resolve relationships within the C. hemsleyi–C. schindleri complex. In an effort to develop an approach to reduce computation time, analysis of different nodal age settings in treePL suggests setting a node's minimum age constraint to the lower bound of a fossil's age range to obtain similar ages to that of BEAST. Divergence time analyses with BEAST and treePL dated the BW stem back to the very Late Cretaceous and the divergence of the three subgenera in the Paleogene. By integrating fossil ages and morphology, a total evidence‐based dating approach was used in conjunction with time‐slice probabilities of dispersal under a DEC model to resolve ancestral ranges of each disjunct in the Miocene: Eurasia and ENA (disjunct 1), EA and western North America (disjunct 2), and EA (disjunct 3). The dated biogeographic history supports dispersal via the North Atlantic Land Bridge in the late Paleogene in disjunct 1 and dispersal via the Bering Land Bridge in the Miocene for disjuncts 2 and 3. Character mapping with a stochastic model in phytools and comparison of ecological niche, morphospace, and rate of evolution indicated differential divergence patterns in morphology, ecological niche, and molecules between disjunct sisters. Although morphological stasis was observed in most of the characters, evolutionary changes in growth habit and some features of leaf, flower, and fruit morphology occurred in one or both sister clades. A significant differentiation of ecological habitats in temperature, precipitation, and elevation between disjunct sisters was observed, suggesting a role of niche divergence in morphological evolution post‐isolation. The patterns of evolutionary rate between morphology and molecules varied among disjunct clades and were not always congruent between morphology and molecules, suggesting cases of non‐neutral morphological evolution driven by ecological selection. Our phylogenetic evidence and comparisons of evolutionary rate among disjunct lineages lend new insights into the formation of the diversity anomaly between EA and ENA, with particular support of an early diversification in EA. These findings, in conjunction with previous studies, again suggest that the EA–ENA disjunct floras are an assembly of lineages descended from the Mesophytic Forests that evolved from the early Paleogene “boreotropical flora” through varied evolutionary pathways across lineages.     

Phylogeography and lineage‐specific patterns of genetic diversity and molecular evolution in a group of North American skinks

Geography influences the evolutionary trajectory of species by mediating opportunities for hybridization, gene flow, demographic shifts and adaptation. We sought to understand how geography and introgression can generate species‐specific patterns of genetic diversity by examining phylogeographical relationships in the North American skink species Plestiodon multivirgatus and P. tetragrammus (Squamata: Scincidae). Using a multilocus dataset (three mitochondrial genes, four nuclear genes; a total of 3455 bp) we discovered mito‐nuclear discordance, consistent with mtDNA introgression. We further tested for evidence of species‐wide mtDNA introgression by using comparisons of genetic diversity, selection tests and extended Bayesian skyline analyses. Our findings suggest that P. multivirgatus acquired its mitochondrial genome from P. tetragrammus after their initial divergence. This putative species‐wide mitochondrial capture was further evidenced by statistically indistinguishable substitution rates between mtDNA and nDNA in P. multivirgatus. This rate discrepancy was observed in P. multivirgatus but not P. tetragrammus, which has important implications for studies that combine mtDNA and nDNA sequences when inferring time since divergence between taxa. Our findings suggest that by facilitating opportunities for interspecific introgression, geography can alter the course of molecular evolution between recently diverged lineages.     

Phylogeography and the origins of range disjunctions in a north temperate fish,the pygmy whitefish (Prosopium coulterii), inferred from mitochondrial and nuclear DNA sequence analysis

Aim To investigate the degree of phylogeographical divergence within pygmy whitefish (Prosopium coulterii) and to test hypotheses concerning the origin of disjunct populations within North America. Location North America from western Alaska to Lake Superior. Methods Mitochondrial (ATPase subunit VI) and nuclear (ITS‐1, ITS‐2) DNA sequence variation was assessed across the species’ North American range to test for the existence of distinct phylogeographical groupings of pygmy whitefish associated with known glacial refugia. Coalescent simulations of the mitochondrial DNA (mtDNA) data were used to test hypotheses of population structure. Results This species is composed of two monophyletic mitochondrial clades across its North American range. The two mtDNA clades differed by an average 3.3% nucleotide sequence divergence. These clades were also distinguished by ITS‐2, but the relationships among lineages were not resolved by the ITS‐1 analysis. Coalescent analyses rejected the null hypothesis of the current disjunct distributions being a result of fragmentation of a single widespread ancestral lineage across a variety of effective population sizes and divergence times. Main conclusions The current range disjunctions of pygmy whitefish in North America probably resulted from isolation, genetic divergence, and selective dispersal from at least two major Pleistocene glacial refugia: Beringia and Cascadia. More recent isolation and dispersal from an upper Mississippi refugium is suggested by relationships within one of the clades and by distributional evidence from co‐distributed species. The Beringian and Cascadian refugia have played major roles in the zoogeography of Nearctic temperate aquatics, but the roles of smaller refugia appear more variable among other species.     

Less Pollen-Mediated Gene Flow for More Signatures of Glacial Lineages: Congruent Evidence from Balsam Fir cpDNA and mtDNA for Multiple Refugia in Eastern and Central North America

The phylogeographic structure and postglacial history of balsam fir (Abies balsamea), a transcontinental North American boreal conifer, was inferred using mitochondrial DNA (mtDNA) and chloroplast DNA (cpDNA) markers. Genetic structure among 107 populations (mtDNA data) and 75 populations (cpDNA data) was analyzed using Bayesian and genetic distance approaches. Population differentiation was high for mtDNA (dispersed by seeds only), but also for cpDNA (dispersed by seeds and pollen), indicating that pollen gene flow is more restricted in balsam fir than in other boreal conifers. Low cpDNA gene flow in balsam fir may relate to low pollen production due to the inherent biology of the species and populations being decimated by recurrent spruce budworm epidemics, and/or to low dispersal of pollen grains due to their peculiar structural properties. Accordingly, a phylogeographic structure was detected using both mtDNA and cpDNA markers and population structure analyses supported the existence of at least five genetically distinct glacial lineages in central and eastern North America. Four of these would originate from glacial refugia located south of the Laurentide ice sheet, while the last one would have persisted in the northern Labrador region. As expected due to reduced pollen-mediated gene flow, congruence between the geographic distribution of mtDNA and cpDNA lineages was higher than in other North American conifers. However, concordance was not complete, reflecting that restricted but nonetheless detectable cpDNA gene flow among glacial lineages occurred during the Holocene. As a result, new cpDNA and mtDNA genome combinations indicative of cytoplasmic genome capture were observed.     

Phylogeny and infrageneric classification of Symplocos (Symplocaceae) inferred from DNA sequence data

Symplocos comprises ～300 species of woody flowering plants with a disjunct distribution between the warm-temperate to tropical regions of eastern Asia and the Americas. Phylogenetic analyses of 111 species of Symplocos based on the nuclear ribosomal internal transcribed spacer (ITS) region and the chloroplast genes rpl16, matK, and trnL-trnF yielded topologies in which only one of the four traditionally recognized subgenera (Epigenia; Neotropics) is monophyletic. Section Cordyloblaste (subgenus Symplocos; eastern Asia) is monophyletic and sister to a group comprising all other samples of Symplocos. Section Palura (subgenus Hopea; eastern Asia) is sister to a group comprising all other samples of Symplocos except those of section Cordyloblaste. Symplocos wikstroemiifolia (eastern Asia) and S. tinctoria (southeastern United States), both of subgenus Hopea, form a clade that groups with S. longipes (tropical North America) and the species of subgenus Epigenia. The remaining samples of subgenus Hopea (eastern Asia) form a clade. Section Neosymplocos (subgenus Microsymplocos; Neotropics) is well nested within a clade otherwise comprising the samples of section Symplocastrum (subgenus Symplocos; Neotropics). Section Urbaniocharis (subgenus Microsymplocos; Antilles) groups as sister to the clade comprising Symplocastrum and Neosymplocos. The data support the independent evolution of deciduousness among section Palura and S. tinctoria. The early initial divergence of sections Cordyloblaste and Palura from the main group warrants their recognition at taxonomic levels higher than those at which they are currently placed. An inferred eastern Asian origin for Symplocos with subsequent dispersal to the Americas is consistent with patterns from other phylogenetic studies of eastern Asian-American disjunct plant groups but contrary to a North American origin inferred from the earliest fossil occurrences of the genus.