Molecular evidence for phylogenetic relationships among buntings and American sparrows (Emberizidae)

To help clarify controversial phylogenetic relationships within the family Emberizidae, we sequenced 1238 bp of mitochondrial DNA from the cytochrome b gene and a flanking portion of ND5. Although the longspurs ( Calcarius ) and the snow buntings ( Plectrophenax ) have been grouped with the Old World buntings ( Emberiza ) in traditional classifications, our molecular phylogenies constructed with maximum likelihood and maximum parsimony place these genera basal to a clade in which the Old World buntings and North American sparrows are sister groups. Contrary to the hypothesis that the radiation within Emberiza is recent following a westward expansion of emberizid stock into Eurasia from North America, we found that the level of genetic divergence among Old World buntings approximates those among different genera in North American sparrows. Thus the radiation of the Emberizidae seems to have occurred at roughly the same time in the Palaearctic and Nearctic. Our results are consistent with earlier analyses of allozymes, but sequences from multiple genes and new morphological analyses are required to fully resolve phylogenetic relationships within the Emberizidae.     

Paleobiogeographic relationships of angiosperms from the Cretaceous and early Tertiary of the North American area

The biogeographic affinities of the Cretaceous and early Tertiary angiosperm floras of the North American area (which includes Meso-America, and the Greater Antilles) have been the subject of considerable interest. Although recent treatments of isolated taxa have shown affinities between North American, European, east Asian and Neotropic floras, the relationships have not been quantified. This study compiles the records of fossils whose familial relationships seem secure. This provides a carefully culled, and uniformly presented review of the Cretaceous and Paleogene record from 1950 to 1989 and supplements LaMotte (1950). A subset of these records, which showed compelling evidence of subfamilial relationships, was analyzed to quantify the relationships of the Cretaceous, Paleocene, Eocene and Oligocene floras to other regions. The analysis suggests that for the entire period 24% of the fossil species had affinities with extant taxa from the Northern Hemisphere; 10% with taxa from the Northern Hemisphere that have a few species in South America; 17% with taxa from Eurasia; 3% with taxa with a disjunct Eurasian-South American pattern; 19% with taxa from South America and/or Africa; 8% with taxa from South America and/or Africa that have an important sister group in southeast Asia; 5% with taxa from the Old World; and 13% with taxa having other distribution patterns. Those fossils with affinities to Laurasian taxa are mostly found in the northern and western portions of the North American area. The fossils with affinities to South American and/or African taxa are found in the southern portions of North America, Meso-America, and the Greater Antilles. The taxa with disjunct distributions show both patterns. These patterns suggest that during this time there were wide-spread temperate elements, found throughout Laurasia; Boreotropical flora elements, distributed in North America, Europe and along the Tethys seaway to southeast Asia; and West Gondwana elements which show dispersion from South America across the proto-Caribbean. The paleobotanical data are compatible with current geological, paleontological and biogeographical studies.     

Melastomeae come full circle: biogeographic reconstruction and molecular clock dating

Rhexia, with 11 species in the Coastal Plain province of North America, is the only temperate zone endemic of the tropical eudicot family Melastomataceae. It is a member of the only pantropical tribe of that family, Melastomeae. Based on the chloroplast gene ndhF, we use a fossil-calibrated molecular clock to address the question of the geographic origin and age of Rhexia. Sequences from 37 species in 21 genera representing the tribe's geographical range were analyzed together with five outgroups. To obtain better clade support, another chloroplast region, the rpl16 intron, was added for 24 of the species. Parsimony analysis of the combined data and maximum-likelihood analysis of ndhF alone indicate that the deepest split is between Rhexia plus its sister group, a small Central American genus, and all other Melastomeae. Old World Melastomeae are monophyletic and nested within New World Melastomeae. Although likelihood-ratio tests of clock and nonclock substitution models for the full or moderately pruned datasets rejected the clock, these models yielded identical topologies (for 30 taxa) with few significantly different branch lengths as assessed by a Student's t-test. Age estimates obtained were 22 million years ago (Mya) for the divergence of Rhexia from its sister group, 12 Mya for the dispersal of Melastomeae from the New World to West Africa, and 1 Mya for the diversification of Melastoma in Southeast Asia. The only other genus of Melastomeae to have reached Southeast Asia from Africa or Madagascar is Osbeckia. The age and geographic distribution of fossils, which come from Miocene sites throughout Eurasia, suggest that Melastomeae once ranged from Eurasia across Beringia to North America from whence they reached South America and subsequently Africa and Southeast Asia. Climate deterioration led to their extinction in the Northern Hemisphere, with Rhexia possibly surviving in Coastal Plain refugia.     

ITS sequence data support a single origin for North American Astereae (Asteraceae) and reflect deep geographic divisions in Aster s.l

The Astereae is the largest tribe of Asteraceae in North America. Morphological diversity suggests that the North American assemblage is polyphyletic as 12 endemic genera, as well as lineages of the genus Erigeron and Conyza (Conyzinae), have been hypothesized to represent at least five separate invasions of North America from Africa, Australia, Eurasia, and South America. This hypothesis was tested with a phylogenetic analysis of nucleotide sequence data from the internal transcribed spacers (ITS) of nuclear ribosomal DNA. Sequences for 62 taxa represent seven outgroup taxa and all major Northern and Southern Hemisphere groups of Astereae, including broad taxonomic and geographic sampling of Conyzinae and Aster s.l. (sensu lato). Parsimony analyses indicate that all North American Astereae are members of a strongly supported clade, and that a diverse group of predominantly woody taxa from Africa, Australia, and South America, are basal Astereae. Furthermore, Aster s.l. is deeply polyphyletic as Eurasian taxa, including Aster s.s. (sensu stricto), appear more closely related to Southern Hemisphere taxa than to North American Aster segregates. There is only low to moderate agreement between proposed higher level Astereae relationships based on ITS and those based either on morphology or chloroplast restriction site data.     

Interactions within and between clades shaped the diversification of terrestrial carnivores

A longstanding debate in evolutionary biology and paleontology is whether ecological interactions such as competition impose diversity dependence on speciation and extinction rates. Here, we analyze the fossil record of terrestrial mammalian carnivores in North America and Eurasia using a Bayesian framework to assess whether their diversity dynamics were affected by diversity dependence within and between families (12 in Eurasia, 10 in North America). We found eight instances of within‐clade diversity dependence suppressing speciation rates and detected between‐clade effects increasing extinction rates in six instances. Diversity dependence often involved lineages that migrated between continents and we found that speciation was more responsive to diversity changes within the clade, whereas extinction responded to diversity of taxa in other clades. The analysis of the fossil record of Carnivora suggests that interactions within and between clades are associated with different speciation and extinction regimes, opening room for a broader theory of diversity dependence.     

Phylogeny and biogeography of the flowering plant genus Styrax (Styracaceae) based on chloroplast DNA restriction sites and DNA sequences of the internal transcribed spacer region

Phylogenetic relationships within the flowering plant genus Styrax were investigated with DNA sequence data from the internal transcribed spacer (ITS) region of nuclear ribosomal DNA (nrDNA) and with chloroplast DNA restriction site data from the genes trnK, rpoC1, and rpoC2. The data sets from each genome were analyzed separately and in combination with parsimony methods. The results strongly support the monophyly of each of the four series of the genus but provide little phylogenetic resolution among them. Reticulate evolution may at least partly explain discordance between the molecular phylogenetic estimates and a prior morphological estimate within series Cyrta. The historical biogeography of the genus was inferred with unweighted parsimony character optimization of trees recovered from a combined ITS and morphological data set, after a series of combinability tests for data set congruence was conducted. The results are consistent with the fossil record in supporting a Eurasian origin of Styrax. The nested phylogenetic position of the South American members of the genus within those from southern North America and Eurasia suggests that the boreotropics hypothesis best explains the amphi-Pacific tropical disjunct distribution occurring within section Valvatae. The pattern of relationship recovered among the species of section Styrax ((western North America + western Eurasia) (eastern North America + eastern Eurasia)) is rare among north-temperate Tertiary forest relicts. The monophyly of the group of species from western North America and western Eurasia provides qualified support for the Madrean-Tethyan hypothesis, which posits a Tertiary floristic connection among the semiarid regions in which these taxa occur. A single vicariance event between eastern Asia and eastern North America accounts for the pattern of relationship among intercontinental disjuncts in series Cyrta.     

Evolution of the Madrean-Tethyan disjunctions and the North and South American amphitropical disjunctions in plants

The present paper reviews advances in the study of two major intercontinental disjunct biogeographic patterns： （i） between Eurasian and western North American deserts with the Mediterranean climate （the Madrean- Tethyan disjunctions）; and （ii） between the temperate regions of North and South America （the amphitropical disjunctions）. Both disjunct patterns have multiple times of origin. The amphitropical disjunctions have largely resulted from long-distance dispersal, primarily from the Miocene to the Holocene, with available data indicating that most lineages dispersed from North to South America. Results of recent studies on the Mediterranean disjuncts between the deserts of Eurasia and western North America support the multiple modes of origin and are mostly consistent with hypotheses of long-distance dispersal and the North Atlantic migration. Axelrod＇s Madrean-Tethyan hypothesis, which implies vicariance between the two regions in the early Tertiary, has been favored by a few studies. The Beringian migration corridor for semiarid taxa is also supported in some cases.     

Molecular phylogenetics and the historical biogeography of dippers (Cinclus)

I used combined sequences of mitochondrial cytochrome  b and ND2 genes to determine the molecular phylogenetic relationships of all five extant species of dipper ( Cinclus ), as well as the relationships of Cinclidae to postulated nearest relatives. All methods of analysis resulted in a single best tree of dipper relationships, uniting the two South American taxa (as sisters) with the single North American exemplar, and the two Eurasian taxa forming a sister clade to the New World taxa. Further, each tree identified thrushes (Turdidae) as the closest relative to Cinclidae. Based on relationships within Cinclus , a Eurasian ancestral area is proposed, with subsequent movement into the New World. Dating of species divergences suggest that dippers arose approximately 4 mya, and achieved their present continental distributions soon after.     

The genus Artemisia (Asteraceae: Anthemideae) at a continental crossroads: molecular insights into migrations, disjunctions, and reticulations among Old and New World species from a Beringian perspective

Artemisia is the largest genus (ca. 350-500+ spp.) in the tribe Anthemideae and is composed of ecologically, morphologically, and chemically diverse species that are found primarily throughout the Northern Hemisphere. Two major centers of diversity for the genus are located in Eurasia and western North America, but phytogeographic links connecting these two regions are observed all across the North Pacific Rim and adjacent areas in the Arctic, including many islands and archipelagos. Previous phylogenetic studies have helped to clarify major lineages and identify likely sister relationships, but many questions remain unanswered regarding the relationships and migration history of New and Old World species. Here we investigate the phylogenetics of Artemisia within a biogeographic context centered in the Beringian Region and offer new hypotheses concerning species relationships, migration history, and the likely role of reticulate evolution in the genus. Our sampling included many new taxa and emphasized multiple accessions of widespread species, species from proposed refugia, and species with disjunct/vicariant distributions. The ITS phylogeny contained 173 accessions (94 new and 79 from GenBank) and indicated that Artemisia is paraphyletic by the exclusion of several small Asian genera and the North American genus Sphaeromeria. Following a survey of thirteen chloroplast loci, phylogenies based on two plastid markers (psbA-trnH and rpl32-trnL spacers) were constructed with a reduced data set, and though largely consistent with the ITS topology, revealed several cases of possible introgression among New World and Beringian species. Our analysis reveals that North American Artemisia species have multiple origins, and that western North America has served as a source for some colonizing elements in eastern Asia and South America.     

Evolution of the Madrean–Tethyan disjunctions and the North and South American amphitropical disjunctions in plants

Abstract The present paper reviews advances in the study of two major intercontinental disjunct biogeographic patterns: (i) between Eurasian and western North American deserts with the Mediterranean climate (the Madrean–Tethyan disjunctions); and (ii) between the temperate regions of North and South America (the amphitropical disjunctions). Both disjunct patterns have multiple times of origin. The amphitropical disjunctions have largely resulted from long‐distance dispersal, primarily from the Miocene to the Holocene, with available data indicating that most lineages dispersed from North to South America. Results of recent studies on the Mediterranean disjuncts between the deserts of Eurasia and western North America support the multiple modes of origin and are mostly consistent with hypotheses of long‐distance dispersal and the North Atlantic migration. Axelrod's Madrean–Tethyan hypothesis, which implies vicariance between the two regions in the early Tertiary, has been favored by a few studies. The Beringian migration corridor for semiarid taxa is also supported in some cases.     

Out of South America? Additional evidence for a southern origin of melanopline grasshoppers

Molecular phylogenetic methods provide a useful tool for critically evaluating competing biogeographic hypotheses. This paper focuses on conjectures at the intercontinental level. An earlier phylogeographic study of the grasshopper subfamily Melanoplinae examined relationships among taxa occupying the Americas and Eurasia. The objective was to test which of three scenarios best described the subfamily's origins and patterns of intercontinental movement. It was tentatively proposed that the melanopline grasshoppers evolved somewhere in the Americas and spread to the Old World. The present article, by including additional Neotropical species, not only upholds that conjecture, but is able to identify South America as the site of origin. Phylogenetic analysis indicates a direction of dispersal: South America-->North America-->Eurasia, that is opposite to what was previously believed. This study also provides, for the first time, a preliminary molecular phylogeny of selected South American melanopline genera.     

The Central American land bridge as an engine of diversification in New World doves

Aim The closure of the Central American land‐bridge connection between North and South America 3.5 million years ago was a major biogeographic event that allowed considerable interchange of the previously isolated faunas of these continents. However, the role that this connection may have had in diversification of North and South American faunas is less well understood. The goal of this study was to evaluate the potential role of the formation of this land connection in generating diversity, through repeated rare dispersal events followed by isolation. Location North and South America. Methods We evaluated the role of the Central American land‐bridge connection in avian diversification using a molecular phylogeny based on four gene regions for mid‐sized New World doves. Diversification events were dated using a Bayesian relaxed clock analysis and internal calibration points for endemic island taxa with known island ages. Results The reconstructed phylogenetic tree was well supported and recovered monophyly of the genera Leptotila and Zenaida, but the quail‐doves (Geotrygon) were paraphyletic, falling into three separate lineages. The phylogeny indicated at least nine dispersal‐driven divergence events between North and South America. There were also five dispersal events in the recent past that have not yet led to differentiation of taxa (polymorphic taxa). Main conclusions Most of these dispersal‐driven diversification events occurred at the time of or after the formation of the Central American land bridge, indicating that this land connection played a role in facilitating divergence via dispersal of doves between continents.     

Molecular phylogenetics and biogeography of Lepus in Eastern Asia based on mitochondrial DNA sequences

In spite of several classification attempts among taxa of the genus Lepus, phylogenetic relationships still remain poorly understood. Here, we present molecular genetic evidence that may resolve some of the current incongruities in the phylogeny of the leporids. The complete mitochondrial cytb, 12S genes, and parts of ND4 and control region fragments were sequenced to examine phylogenetic relationships among Chinese hare taxa and other leporids throughout the World using maximum parsimony, maximum likelihood, and Bayesian phylogenetic reconstruction approaches. Using reconstructed phylogenies, we observed that the Chinese hare is not a single monophyletic group as originally thought. Instead, the data infers that the genus Lepus is monophyletic with three unique species groups: North American, Eurasian, and African. Ancestral area analysis indicated that ancestral Lepus arose in North America and then dispersed into Eurasia via the Bering Land Bridge eventually extending to Africa. Brooks Parsimony analysis showed that dispersal events followed by subsequent speciation have occurred in other geographic areas as well and resulted in the rapid radiation and speciation of Lepus. A Bayesian relaxed molecular clock approach based on the continuous autocorrelation of evolutionary rates along branches estimated the divergence time between the three major groups within Lepus. The genus appears to have arisen approximately 10.76 MYA (+/-0.86 MYA), with most speciation events occurring during the Pliocene epoch (5.65+/-1.15 MYA approximately 1.12 +/- 0.47 MYA).     

WEEDY ADAPTATION IN SETARIA SPP. I. ISOZYME ANALYSIS OF GENETIC DIVERSITY AND POPULATION GENETIC STRUCTURE IN SETARIA VIRIDIS

Setaria viridis is an important self-pollinating, cosmopolitan weed of temperate regions worldwide. Allozyme markers were used to investigate genetic diversity and structure in 168 accessions (including four S. italica) collected mainly from North America and Eurasia. Genetic diversity in green foxtail, and its population genetic structure, provided important clues about this weed's evolutionary history. Genetic diversity was low, with marked population differentiation: the percentage of polymorphic loci was 25% (0.95 criterion); mean number of alleles per locus was 1.86; mean panmictic heterozygosity was 0.07; and the coefficient of population genetic differentiation was 0.65. A common genotype occurred in 25 accessions distributed in six countries from both the Old World and New World, in a wide variety of ecological situations. Relatively little genetic divergence occurred between Eurasia and North America, with Nei's unbiased genetic identity between the two regions equaling 1.0. Populations from these two continents also had equivalent genetic diversity. Within North America, regional differentiation was indicated by northern and southern groups separated at 43.5° N latitude. No geographic pattern in genetic diversity was found within Eurasia. The size of the geographic range from which populations were sampled was not an accurate indicator of the extent of genetic diversity found among populations from that region. These results suggest that present patterning among green foxtail populations in North America is the consequence of multiple introductions into the New World followed by local adaptation and regional differentiation. Finally, S. italica and several green foxtail varieties did not differ isozymatically from typical forms of green foxtail. This supports the view that S. italica and S. viridis are conspecific, that the former (foxtail millet) is a domesticated form of the latter, and also questions the taxonomic validity of formally recognizing morphological varieties within green foxtail.     

Ontogenetic changes in citrate synthase and lactate dehydrogenase activity in the jumping muscle of the American locust (Schistocerca americana)

Intraspecific studies have repeatedly shown that muscle-specific oxidative enzyme activities scale negatively with body mass while muscle-specific glycolytic enzyme activities scale positively. However, most of these studies have not included juveniles. In this study, we examined how citrate synthase (CS, EC 2.3.3.1) and lactate dehydrogenase (LDH; EC 1.1.1.27) activity in the jumping muscle of Schistocerca americana grasshoppers varied with ontogeny across a 40-fold increase in body size. In contrast to the pattern observed when adult conspecifics are compared, we show that jumping muscle CS activity increased more than 2-fold from 2nd instars to adults, while jumping muscle LDH activity increased more than 5-fold. The increased LDH activity in older grasshoppers supports previous data that older grasshoppers have a reduced jumping endurance. The increased CS activity with age may help older grasshoppers efficiently produce aerobic ATP to bend cuticular springs for energy storage before a jump or alternatively recover from anaerobic metabolism after jumping. Metabolic changes in S. americana jumping muscle are similar to other developing taxa and highlight the importance of including juveniles within intraspecific studies. When compared to adults, juvenile locomotion may have increased selection pressure because of both greater energetic demands during growth and higher predation rates.     

Higher-level phylogeny of new world vireos (aves: vireonidae) based on sequences of multiple mitochondrial DNA genes.

Interfamilial relationships of the New World songbird family Vireonidae are uncertain. Thus, we sequenced 3069 bp of four mitochondrial genes (cyt b, ND2, ND3, COI) from 19 taxa in five families and two outgroups, to examine higher-level alliances with proposed relatives. We also sequenced cyt b and ND2 from an additional five vireonids to examine intergeneric relationships within the Vireonidae and incorporated 14 sequences of cyt b from GenBank to test the effects of taxon sampling on gene tree resolution. Families appeared monophyletic in all analyses, and the affinity of vireonids to Old World corvoids was corroborated. However, relationships among the Vireonidae and other families were not resolved. Sequences of vireonids revealed high levels of divergence within and between genera, with either Cyclarhis or Vireolanius positioned basally, depending on the analysis. On the basis of mitochondrial DNA and biogeographic evidence, vireonids represent a deep lineage derived from an Old World ancestor that colonized the New World, most likely via Beringia, with subsequent radiation in the Middle American tropics. We hypothesize postcolonization dispersal of the ancestor into Middle America, followed by extinction of the ancestor in North America. This extinction event left the North Temperate Zone unoccupied by any vireonid until northward reinvasion by some species of Vireo. Although the closest living relative of vireonids remains unidentified, broad-scale sequencing of additional extant corvoids with multiple molecular markers should further elucidate Old World alliances.     

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.     

Phylogenetic relationships in Nuphar (Nymphaeaceae): evidence from morphology,chloroplast DNA,and nuclear ribosomal DNA

The genus Nuphar consists of yellow-flowered waterlilies and is widely distributed in north-temperate bodies of water. Despite regular taxonomic evaluation of these plants, no explicit phylogenetic hypotheses have been proposed for the genus. We investigated phylogenetic relationships in Nuphar using morphology and sequences of the chloroplast gene matK and of the internal transcribed spacer (ITS) regions of nuclear ribosomal DNA. Two major lineages within Nuphar are consistently resolved with the morphological and molecular data sets. One lineage comprises New World taxa and the other represents a primarily Old World lineage. Relationships within the major lineages were poorly resolved by morphology and ITS, yet certain relationships were elucidated by all analyses. Most notable is the strong support for a monophyletic lineage of dwarf taxa and the alliance of the North American N. microphylla with the Eurasian taxa. Minor discordance between the independent cladograms is accounted for by hybridization. The common taxonomic practice of uniting all North American and Eurasian taxa under one species is not supported phylogenetically.