UNLABELLED: • PREMISE OF THE STUDY: We investigated the origins of 252 Southern Appalachian woody species representing 158 clades to analyze larger patterns of biogeographic connectivity around the northern hemisphere. We tested biogeographic hypotheses regarding the timing of species disjunctions to eastern Asia and among areas of North America. • METHODS: We delimited species into biogeographically informative clades, compiled sister-area data, and generated graphic representations of area connections across clades. We calculated taxon diversity within clades and plotted divergence times. • KEY RESULTS: Of the total taxon diversity, 45% were distributed among 25 North American endemic clades. Sister taxa within eastern North America and eastern Asia were proportionally equal in frequency, accounting for over 50% of the sister-area connections. At increasing phylogenetic depth, connections to the Old World dominated. Divergence times for 65 clades with intercontinental disjunctions were continuous, whereas 11 intracontinental disjunctions to western North America and nine to eastern Mexico were temporally congruent. • CONCLUSIONS: Over one third of the clades have likely undergone speciation within the region of eastern North America. The biogeographic pattern for the region is asymmetric, consisting of mostly mixed-aged, low-diversity clades connecting to the Old World, and a minority of New World clades. Divergence time data suggest that climate change in the Late Miocene to Early Pliocene generated disjunct patterns within North America. Continuous splitting times during the last 45 million years support the hypothesis that widespread distributions formed repeatedly during favorable periods, with serial cooling trends producing pseudocongruent area disjunctions between eastern North America and eastern Asia.
Previous phylogenetic studies in oaks (Quercus, Fagaceae) have failed to resolve the backbone topology of the genus with strong support. Here, we utilize next-generation sequencing of restriction-site associated DNA (RAD-Seq) to resolve a framework phylogeny of a predominantly American clade of oaks whose crown age is estimated at 23-33 million years old. Using a recently developed analytical pipeline for RAD-Seq phylogenetics, we created a concatenated matrix of 1.40 E06 aligned nucleotides, constituting 27,727 sequence clusters. RAD-Seq data were readily combined across runs, with no difference in phylogenetic placement between technical replicates, which overlapped by only 43-64% in locus coverage. 17% (4,715) of the loci we analyzed could be mapped with high confidence to one or more expressed sequence tags in NCBI Genbank. A concatenated matrix of the loci that BLAST to at least one EST sequence provides approximately half as many variable or parsimony-informative characters as equal-sized datasets from the non-EST loci. The EST-associated matrix is more complete (fewer missing loci) and has slightly lower homoplasy than non-EST subsampled matrices of the same size, but there is no difference in phylogenetic support or relative attribution of base substitutions to internal versus terminal branches of the phylogeny. We introduce a partitioned RAD visualization method (implemented in the R package RADami; http://cran.r-project.org/web/packages/RADami) to investigate the possibility that suboptimal topologies supported by large numbers of loci--due, for example, to reticulate evolution or lineage sorting--are masked by the globally optimal tree. We find no evidence for strongly-supported alternative topologies in our study, suggesting that the phylogeny we recover is a robust estimate of large-scale phylogenetic patterns in the American oak clade. Our study is one of the first to demonstrate the utility of RAD-Seq data for inferring phylogeny in a 23-33 million year-old clade.
UNLABELLED: • PREMISE OF THE STUDY: Hybridization is thought to have played an important role in diversification of the speciose shrub genus Ceanothus; putative hybrid species have been described, and data suggest that intrinsic barriers may not exist among closely related species. However, the extent to which hybridization occurs in the wild is not known, and little is understood about how extrinsic factors such as soil chemistry may influence the process. The present research focuses on the gabbro-endemic C. roderickii and the closely related soil-generalist C. cuneatus. Though the species occur peripatrically, they remain distinct across an edaphic disjunction. • METHODS: AFLP was used to quantify hybridization and introgression. Biological data and experiments were used to test for prezygotic isolation. Growth trials were used to test for local adaptation and selection against hybrids. • KEY RESULTS: Ceanothus cuneatus and C. roderickii were strongly differentiated morphologically and genetically, despite a lack of evidence for prezygotic barriers. Hybrids and back-crosses were present but infrequent. Finally, there was selection against hybrids in nonnative soil. • CONCLUSIONS: There is little genetic exchange between the focal species across an edaphic disjunction, despite the absence of prezygotic barriers. This result implies that soil conditions, as well as other extrinsic factors, should be considered as forces that may restrict hybridization and gene flow in Ceanothus, influencing local adaptation and speciation. Findings presented here are significant because they imply that exchange of genetic material between plants may be limited directly by the abiotic environment, rather than by the biology of the plants.
An overview of recent achievements and development of genomic resources in the Fagaceae is provided, with major emphasis on the genera Castanea and Quercus. The Fagaceae is a large plant family comprising more than 900 species belonging to 8-10 genera. Using a wide range of molecular markers, population genetics and gene diversity surveys were the focus of many studies during the past 20 years. This work set the stage for investigations in genomics beginning in the early 1990s and facilitated the application of genetic and quantitative trait loci mapping approaches. Transferability of markers across species and comparative mapping have indicated tight macrosynteny between Quercus and Castanea. Omic technologies were more recently developed and the corresponding resources are accessible via electronic and physical repositories (expressed sequence tag sequences, single-nucleotide polymorphisms, candidate genes, cDNA clones, bacterial artificial chromosome (BAC) libraries) that have been installed in North America and Europe. BAC libraries and physical maps were also constructed in Castanea and Quercus and provide the necessary resources for full nuclear genome sequencing projects that are currently under way in Castanea mollissima (Chinese chestnut) and Quercus robur (pedunculate oak). © 2012 The Author(s).
High diversity and endemism in the California Floristic Province (CFP) are an alleged response to the late Cenozoic advent of Mediterranean-type climate in this region. Ceanothus comprises two divergent subgenera with centers of diversity in the CFP. We reconstruct the evolution of Ceanothus by using DNA sequence data from the nuclear gene nitrate reductase. We find that the timing of diversification events is related to geological and climatic history. In both subgenera, diversification is characterized by recent divergence of extant taxa and geographically structured phylogenetic relationships. A strong north-south divergence of subgenus Cerastes across the Transverse Ranges indicates that phylogenetic relationships may be structured by climatically divergent regions of the CFP. Divergence-time estimation suggests that the age of extant diversification in both subgenera is;6 Ma. This agrees with the fossil record but predates the hypothesized Quaternary (2-Ma) origin of Mediterranean-type climate in the region. © 2011 by The University of Chicago. All rights reserved.
To survive changes in climate, successful species shift their geographic ranges to remain in suitable habitats. For parasites and other highly specialized species, distributional changes not only are dictated by climate but can also be engineered by their hosts. The extent of host control on parasite range expansion is revealed through comparisons of host and parasite migration and demographic histories. However, understanding the codistributional history of entire forest communities is complicated by challenges in synthesizing datasets from multiple interacting species of differing datatypes. Here we integrate genetic and fossil pollen datasets from a host-parasite pair; specifically, the population structure of the parasitic plant (Epifagus virginiana) was compared with both its host (Fagus grandifolia) genetic patterns and abundance data from the paleopollen record of the last 21,000 y. Through tests of phylogeographic structure and spatial linear regression models we find, surprisingly, host range changes had little effect on the parasite's range expansion and instead host density is the main driver of parasite spread. Unlike other symbionts that have been used as proxies to track their host's movements, this parasite's migration routes are incongruent with the host and instead reflect the greater importance of host density in this community's assembly. Furthermore, these results confirm predictions of disease ecological models regarding the role of host density in the spread of pathogens. Due to host density constraints, highly specialized species may have low migration capacities and long lag times before colonization of new areas.
The tree genus Juglans (nogal, walnut) is generally thought of as a north temperate group, but most of the 16 species of black walnuts (Juglans sect. Rhysocaryon) occur in subtropical areas of the New World, spanning Central America, Andean South America, and the Greater Antilles. The two species native to Central America (J. olanchana var. olanchana and J. steyermarkii) and two closely related Mexican taxa (J. olanchana var. standleyi and J. pyriformis) have not been studied thoroughly from a comparative systematic perspective, so here we provide a detailed investigation of their morphology and natural history as a first step towards a broad-based synthesis of J. sect. Rhysocaryon. Fieldwork in Guatemala and Mexico provided the material for germination studies, morphological analyses, and phylogenetic reconstruction using DNA sequences. Juglans steyermarkii was rediscovered in its type locality in Guatemala, and new populations were located during the course of fieldwork. SEM analysis of trichome diversity and density, along with leaflet shape, provided characters to differentiate among five taxa of Juglans in the accompanying key. Staminate flowers and pollen examined for the first time in J. steyermarkii showed close morphological similarities to those of other species of black walnuts. Variation in the pattern of nut-wall sculpture appears to be a promising source of variation; however, adequate capture and quantification of this variation will likely require three-dimensional scanning techniques. There was high variability in percent seed germination of the two Central American species and no observed advantage to leaching, scarification, or a prolonged stratification period. DNA studies included in the exploration of three promising sources of nuclear sequence variation: the ETS and ITS (external and internal transcribed spacer of ribosomal DNA), and the second intron of the LEAFY gene. Combined phylogenetic analysis of these sequences provided a moderately resolved topology containing two major groups of black walnuts and a general correlation between phylogeny and geography. The analyses supported a division between taxa from northern Mexico and the USA, and those from southern Mexico, Guatemala, the West Indies (Greater Antilles), and South America. Observations on the geographic range of Juglans in Mexico and Guatemala indicated a frequent association with coffee plantations, suggesting similar climatic requirements. Our studies of the dispersed and most likely fragmented populations indicate that Juglans may still be found in native plant communities as a canopy tree, although it is much more common to observe populations in cleared areas where the trees were retained as shade for coffee. We are not aware of any major efforts to conserve the native nogal in Central America, though they are sometimes left and/or planted as shade trees in coffee fincas. A study conducted in Mexico suggests that Juglans might be useful in agroforestry efforts to rehabilitate degraded sites. © Torrey Botanical Club.
Pollination systems frequently reflect adaptations to particular groups of pollinators. Such systems are indicative of evolutionary specialization and have been important in angiosperm diversification. We studied the evolution of pollination systems in the large genus Ruellia. Phylogenetic analyses, morphological ordinations, ancestral state reconstructions, and a character mapping simulation were conducted to reveal key patterns in the direction and lability of floral characters associated with pollination. We found significant floral morphological differences among species that were generally associated with different groups of floral visitors. Floral evolution has been highly labile and also directional. Some specialized systems such as hawkmoth or bat pollination are likely evolutionary dead-ends. In contrast, specialized pollination by hummingbirds is clearly not a dead-end. We found evidence for multiple reverse transitions from presumed ancestral hummingbird pollination to more derived bee or insect pollination. These repeated origins of insect pollination from hummingbird-pollinated ancestors have not evolved without historical baggage. Flowers of insect-pollinated species derived from hummingbird-pollinated ancestors are morphologically more similar to hummingbird flowers than they are to other more distantly related insect-pollinated flowers. Finally, some pollinator switches were concomitant with changes in floral morphology that are associated with those pollinators. These observations are consistent with the hypothesis that some transitions have been adaptive in the evolution of Ruellia.
In the conifer genus Juniperus (Cupressaceae), many species are increasing rapidly in distribution, abundance, and dominance in arid and semiarid regions. To help understand the success of junipers in drier habitats, we studied hydraulic traits associated with their water stress resistance, including vulnerability to xylem cavitation, specific conductivity (K(S)), tracheid diameter, conduit reinforcement, and wood density in stems and roots, as well as specific leaf area (SLA) of 14 species from the United States and the Caribbean. A new phylogeny based on DNA sequences tested the relationships between vulnerability to cavitation and other traits using both traditional cross-species correlations and independent contrast correlations. All species were moderately to highly resistant to water-stress-induced cavitation in both roots and shoots. We found strong phylogenetic support for two clades previously based on leaf margin serration (serrate and smooth). Species in the serrate clade were 34-39% more resistant to xylem cavitation in stems and roots than were species in the smooth clade and had ∼35% lower K(S) and 39% lower SLA. Root and stem resistance to cavitation and SLA were all highly conserved traits. A high degree of conservation within clades suggests that hydraulic traits of Juniperus species strongly reflect phylogenetic history. The high resistance to cavitation observed may help explain the survival of junipers during recent extreme droughts in the southwestern United States and their expansion into arid habitats across the western and central United States.
Aim: This study aims to assess the role of long-distance seed dispersal and topographic barriers in the post-glacial colonization of red maple (Acer rubrum L.) using chloroplast DNA (cpDNA) variation, and to understand whether this explains the relatively higher northern diversity found in eastern North American tree species compared with that in Europe. Location: North-eastern United States. Methods: The distribution of intraspecific cpDNA variation in temperate tree populations has been used to identify aspects of post-glacial population spread, including topographic barriers to population expansion and spread by long-distance seed dispersal. We sequenced c. 370 cpDNA base pairs from 221 individuals in 100 populations throughout the north-eastern United States, and analysed spatial patterns of diversity and differentiation. Results: Red maple has high genetic diversity near its northern range limit, but this diversity is not partitioned by topographic barriers, suggesting that the northern Appalachian Mountains were not a barrier to the colonization of red maple. We also found no evidence of the patchy genetic structure that has been associated with spread by rare long-distance seed dispersal in previous studies. Main conclusions: Constraints on post-glacial colonization in eastern North America seem to have been less stringent than those in northern Europe, where bottlenecks arising from long-distance colonization and topographic barriers appear to have strongly reduced genetic diversity. In eastern North America, high northern genetic diversity may have been maintained by a combination of frequent long-distance dispersal, minor topographic obstacles and diffuse northern refugia near the ice sheet. © 2008 The Authors.
Fagaceae include nine genera and ca. 900 species, making it one of the largest and economically important groups within Fagales. Phylogenetic relationships remain unresolved despite a long history of systematic study. We used CRABS CLAW, a single-copy nuclear gene, to generate over 2,900 base pairs of new sequence data, and combined it with previously collected molecular data to examine morphological evolution in the Fagaceae. We clarified the relationships of Chrysolepis, Lithocarpus and Quercus, and in this improved phylogenetic context we inferred morphological transformations of the cupule. Phylogenetic analyses supported an origin for Quercus from a castaneoid ancestor and a novel sister group relationship for Asian Lithocarpus and Chrysolepis; however the monophyly of both Lithocarpus and subfamily Castaneoideae was rejected. Our data suggest that North American Lithocarpus densiflorus is distantly related to Asian Lithocarpus and more closely related to Quercus, supporting the hypothesis that the uniflorous cupules of L. densiflorus and Quercus are derived from dichasium cupules via loss of lateral flowers. The sister group relationship of Asian Lithocarpus and Chrysolepis is supported by the morphological synapomorphy that each fruit is surrounded by a cupule. A new hypothesis is proposed to explain the evolution of the unusual cupules of Asian Lithocarpus and Chrysolepis. In this model, every flower represents a reduced dichasium, and we interpret the cupules of these taxa to be compound in nature, formed by multiple single-flowered cupules.
It is widely acknowledged that integrating fossils into data sets of extant taxa is imperative for proper placement of fossils, resolution of relationships, and a better understanding of character evolution. The importance of this process has been further magnified because of the crucial role of fossils in dating divergence times. Outstanding issues remain, including appropriate methods to place fossils in phylogenetic trees, the importance of molecules versus morphology in these analyses, as well as the impact of potentially large amounts of missing data for fossil taxa. In this study we used the angiosperm clade Juglandaceae as a model for investigating methods of integrating fossils into a phylogenetic framework of extant taxa. The clade has a rich fossil record relative to low extant diversity, as well as a robust molecular phylogeny and morphological database for extant taxa. After combining fossil organ genera into composite and terminal taxa, our objectives were to (1) compare multiple methods for the integration of the fossils and extant taxa (including total evidence, molecular scaffolds, and molecular matrix representation with parsimony [MRP]); (2) explore the impact of missing data (incomplete taxa and characters) and the evidence for placing fossils on the topology; (3) simulate the phylogenetic effect of missing data by creating "artificial fossils"; and (4) place fossils and compare the impact of single and multiple fossil constraints in estimating the age of clades. Despite large and variable amounts of missing data, each of the methods provided reasonable placement of both fossils and simulated "artificial fossils" in the phylogeny previously inferred only from extant taxa. Our results clearly show that the amount of missing data in any given taxon is not by itself an operational guideline for excluding fossils from analysis. Three fossil taxa (Cruciptera simsonii, Paleoplatycarya wingii, and Platycarya americana) were placed within crown clades containing living taxa for which relationships previously had been suggested based on morphology, whereas Polyptera manningii, a mosaic taxon with equivocal affinities, was placed firmly as sister to two modern crown clades. The position of Paleooreomunnea stoneana was ambiguous with total evidence but conclusive with DNA scaffolds and MRP. There was less disturbance of relationships among extant taxa using a total evidence approach, and the DNA scaffold approach did not provide improved resolution or internal support for clades compared to total evidence, whereas weighted MRP retained comparable levels of support but lost crown clade resolution. Multiple internal minimum age constraints generally provided reasonable age estimates, but the use of single constraints provided by extinct genera tended to underestimate clade ages.
Regional phylogeographical studies involving co-distributed animal and plant species have been conducted for several areas, most notably for Europe and the Pacific Northwest of North America. Until recently, phylogeographical studies in unglaciated eastern North America have been largely limited to animals. As more studies emerge for diverse lineages (including plants), it seems timely to assess the phylogeography across this region: (i) comparing and contrasting the patterns seen in plants and animals; (ii) assessing the extent of pseudocongruence; and (iii) discussing the potential applications of regional phylogeography to issues in ecology, such as response to climatic change. Unglaciated eastern North America is a large, geologically and topographically complex area with the species examined having diverse distributions. Nonetheless, some recurrent patterns emerge: (i) maritime - Atlantic vs. Gulf Coast; (ii) Apalachicola River discontinuity; (iii) Tombigbee River discontinuity; (iv) the Appalachian Mountain discontinuity; (v) the Mississippi River discontinuity; and (vi) the Apalachicola River and Mississippi River discontinuities. Although initially documented in animals, most of these patterns are also apparent in plants, providing support for phylogeographical generalizations. These patterns may generally be attributable to isolation and differentiation during Pleistocene glaciation, but in some cases may be older (Pliocene). Molecular studies sometimes agree with longstanding hypotheses of glacial refugia, but also suggest additional possible refugia, such as the southern Appalachian Mountains and areas close to the Laurentide Ice Sheet. Many species exhibit distinct patterns that reflect the unique, rather than the shared, aspects of species' phylogeographical histories. Furthermore, similar modern phylogeographical patterns can result from different underlying causal factors operating at different times (i.e. pseudocongruence). One underemphasized component of pseudocongruence may result from the efforts of researchers to categorize patterns visually - similar patterns may, in fact, not fully coincide, and inferring agreement may obscure the actual patterns and lead to erroneous conclusions. Our modelling analyses indicate no clear spatial patterning and support the hypothesis that phylogeographical structure in diverse temperate taxa is complex and was not shaped by just a few barriers. © 2006 The Authors.
Physalis (75+ species, Solanaceae) is most diverse in Mexico, with only the type, P. alkekengi, native to the Old World. Interspecific relationships are poorly known, and despite the distinctive inflated fruiting calyces, generic limits remain uncertain. Sequence data from part of the nuclear gene waxy (622 bp) and the internal transcribed spacer of the nrDNA (652 bp) were used to generate a phylogeny of subtribe Physalinae. Thirty-five species of Physalis and eight physaloid genera were sequenced. Data analysis included Bayesian and maximum parsimony methods. The Physalinae was monophyletic, but while the morphologically typical Physalis species formed a strongly supported clade, the morphologically atypical species made the genus paraphyletic. A grade of physaloid genera (Quincula, Oryctes, and Chamaesaracha) and Physalis subgenus Physalodendron separate P. alkekengi, P. carpenteri, and P. microphysa from other Physalis species. The Physalis clade consists of Margaranthus and species with solitary yellow flowers and highly inflated calyces. Most sections of Physalis do not appear to be monophyletic. Leucophysalis viscosa and the Central American physaloid genera Brachistus, Tzeltalia, and Witheringia formed a clade at the base of the Physalinae. © Copyright 2005 by the American Society of Plant Taxonomists.
Recent models and analyses of paleoecological records suggest that tree populations are capable of rapid migration when climate warms. Fossil pollen is commonly interpreted as suggesting that the range of many temperate tree species expanded at rates of 100-1000 m/yr during the early Holocene. We used chloroplast DNA surveys to show that the geography of postglacial range expansion in two eastern North American tree species differs from that expected from pollen-based reconstructions and from patterns emerging from European molecular studies. Molecular evidence suggests that American beech (Fagus grandifolia) and red maple (Acer rubrum) persisted during the late glaciation as low-density populations, perhaps within 500 km of the Laurentide Ice Sheet. Because populations were closer to modern range limits than previously thought, postglacial migration rates may have been slower than those inferred from fossil pollen. Our estimated rates of <100 m/yr are consistent with model predictions based on life history and dispersal data, and suggest that past migration rates were substantially slower than the rates that will be needed to track 21st-century warming. © 2005 by the Ecological Society of America.
Sequences of both internal and external transcribed spacers of nuclear ribosomal DNA were sequenced for four species belonging to the Dactylorhiza maculata group or "spotted marsh-Orchids". These four species are D. fuchsii, D. saccifera, D. foliosa, and D. maculata. Extensive nuclear ribosomal DNA polymorphism was uncovered within the diploid D. fuchsii and the putative autotetraploid D. maculata. Within the phylogenetic trees reconstructed using parsimony and Bayesian analyses, four main lineages (A, B, C, and D) were well supported. While D. saccifera, D. maculata, and D. foliosa were confined to clades B, C, and D, respectively, D. fuchsii accessions were spread over three clades (A, B, and C). Lineage C, which included accessions of the diploid D. fuchsii and the tetraploid D. maculata, was closely related to the lineage of D. foliosa (lineage D), an endemic diploid species from Madeira. Moreover, intra-individual polymorphism was found within accessions of D. maculata, D. fuchsii, and D. saccifera. It is shown that in some instances two lineages, contributed to the observed intra-individual polymorphism (C and A in D. maculata, A and B in D. fuchsii and D. saccifera). Evolutionary scenarios leading to this extensive nuclear ribosomal DNA polymorphism are discussed in the light of results from maternally inherited chloroplast DNA markers and an autopolyploid origin of D. maculata from a D. foliosa-like ancestor is postulated. © 2005 Elsevier Inc. All rights reserved.
Phylogenetic analyses of DNA sequences of six species of Platanus were conducted to estimate species relationships and analyze biogeographic history. On the basis of a broader analysis of the third exon of the nuclear gene LEAFY, the root node for the genus was confirmed to fall between subg. Castaneophyllum (P. kerrii) and the species of subg. Platanus. Separate phylogenetic analyses of the nuclear ribosomal ITS region, the 3′ region of the second intron of LEAFY, and the chloroplast region trnT-trnL intergenic spacer provided various levels of resolution, and the combined data yielded a fully resolved set of relationships within subg. Platanus. Two major clades were identified: one with species from Europe (EUR) and western North America (WNA) (P. orientalis, P. racemosa s.l.), the other with species from eastern North America (ENA; US and Canada) and eastern Mexico (EMEX) (P. mexicana, P. occidentalis, and P. rzedowskii). Within subg. Platanus, six subclades corresponded to previously recognized taxa, and one accession may be of hybrid origin. The historical biogeography of Platanus was interpreted using phylogenetic pattern, estimates of divergence times, the fossil record, and climate reconstructions. The pattern of relationships was consistent with a hypothesis of vicariance and the oldest divergence between taxa within the set of area relationships of ((WNA + EUR), (ENA + MEX)) suggested an initial barrier affecting taxa that are now mostly confined to North America. The second oldest divergence within subg. Platanus involves the intercontinental disjunction of semi-arid species from WNA + EUR, which diverged by at least 15 MYBP, consistent with the Madrean-Tethyan hypothesis. Calibrated phylogenies were used to estimate divergence times for five more recent intracontinental disjunctions. These times correlated with the timing of geological events in southwestern North America and northern Latin America. © Copyright 2005 by the American Society of Plant Taxonomists.
A Bayesian phylogenetic analysis of 36 Ipomoea species using sequence data from the internal transcribed spacer region was compared with classification schemes based on traditional methods and a previously published cpDNA restriction fragment length polymorphism (RFLP) study. These molecular studies support a diversity of groups that were circumscribed on the basis of phenetic principles and agree generally with the results from cpDNA RFLP analyses. The congruence between the phylogenetic hypotheses based on new molecular data and the understanding of relationships developed in earlier studies indicate that these classifications may reflect evolutionary history. Two large clades of species, with one including sections Tricolores, Calonyction, and Pharbitis and the other including sections Mina and Leptocallis, were identified. Furthermore, morphologically distinct groups of Ipomoea species received support from the DNA sequence data. Indices of convergence for the Markov chain Monte Carlo (MCMC) in the Bayesian phylogenetic analysis were evaluated. A limited range of posterior probabilities for each node in the trees from a set of five MCMC samples provides a useful index of convergence. Bayesian node support values were generally higher than bootstrap values from a maximum parsimony analysis. This is consistent with the notion that these measures of support estimate different qualities of the data.
The perianthless members of the Piperales are unique among the basal lineages of angiosperms because they are mainly herbaceous plants with over 2000 species possessing highly reduced flowers. There have been several attempts to address the evolution of the flower morphology in the group, but no previous study has included a DNA-based estimate of phylogeny. Here we present a robust reconstruction of the phylogenetic relationships of the genera in the perianthless Piperales using DNA sequence data from three genes (rbcL, atpB, and 18S) and two genomes (nuclear and chloroplast). We estimated the likelihood values of ancestral character states of mature floral structures. Developmental sequences also were analyzed using step matrices under specific models of character state change to examine the origin of meristic differences of the androecium and gynoecium. Developmental lability is the general theme in the evolution of floral merosity in the perianthless Piperales, with different developmental processes giving rise to morphologically identical mature stages. Our findings confirm this notion based on several distinct patterns: (1) nonidentical ontogenies give rise to homoplasious, six-staminate androecia of Saururaceae and some Piperaceae most likely through terminal addition; (2) identical ontogenies produce the homoplasious two-staminate flowers in Peperomia and Piper umbellatum through deletion; and (3) nearly identical ontogenies produce homplasious tricarpellate gynoecia of Piper and Anemopsis + Houttuynia clade, and the apocarpous gynoecium of Saururus may be secondarily derived, both end products occurring through deletion. We note that changes in organ number and the degree of carpel fusion have been important during the evolutionary history of the perianthless Piperales as well as the basal angiosperms in general and should be studied more extensively. Overall we emphasize the lability of developmental pathways, especially in the flower, and endorse the methodological utility of developmental sequences for directing future investigations of floral evolution.
Nucleotide sequences of six regions from three plant genomes - trnL-F, matK, rbcL, atpB (plastid), matR (mtDNA), and 18S rDNA (nuclear) - were used to analyze inter- and infrafamilial relationships of Fagales. All 31 extant genera representing eight families of the order were sampled. Congruence among data sets was assessed using the partition homogeneity test, and five different combined data sets were analyzed using maximum parsimony and the Bayesian approach. At the familial level, the same phylogenetic relationships were inferred from five different analyses of these data. Nothofagus, followed by Fagaceae, are subsequent sisters to the rest of the order. Fagaceae are then sister to the core "higher" hamamelids, which consist of two main subclades, one being Myricaceae (Rhoipteleaceae (Juglandaceae)) and the other Casuarinaceae (Ticodendraceae (Betulaceae)). The combined data sets provide the best-supported estimate of evolutionary relationships within Fagales. Our results suggest that the combination of different sequences from several species within the same genus representing a terminal taxon has little influence on phylogenetic accuracy. Inclusion of taxa with some missing data in combined data sets also does not have a major impact on the topology.
Exostema (Rubiaceae) comprises 25 neotropical woody species, ranging from western South America and Mesoamerica to the West Indies, with 19 species occurring in Cuba and Hispaniola. Biogeographical hypotheses based upon a phylogenetic analysis of morphological data depict a South American origin for the group, with species radiations in the Greater Antilles. Molecular phylogenetic analyses were conducted using ITS and rbcL sequence data for a sample of 14 species of Exostema and nine species from eight closely related genera. Results indicate that Exostema is paraphyletic with respect to Coutarea, Erithalis, and Chiococca. Hypotheses invoking independent South American origins for subclades of Exostema are not supported. Coutarea and the South American Exostema species form a clade sister to the Caribbean Exostema species with terminal inflorescences. Relationships among axillary flowered Exostema species are not well resolved. Distribution, ecology, and seed traits indicate over-water dispersal is important for wide-spread species (e.g., E. caribaeum). Sister species relationships between the Cuban and Hispaniolan endemics E. salicifolium and E. acuminatum are strongly supported. Disjunctions between various regions of Cuba and Hispaniola are consistent with geohistorical connections between these composite islands. Biogeographical patterns found in Exostema are similar to those reported for other Caribbean plant groups, with vicariance detected in certain cases, and dispersal often indicated by distribution, ecology and phylogeny for many taxa.
Aim: To describe current geographical patterns of genetic diversity and infer the historical population dynamics of the stone oaks (Lithocarpus) in Southeast Asia. Location: We sampled three populations in Indochina: (1) Yunnan province, China; (2) Pyin Oo Lwin area, Myanmar and (3) north-western Vietnam; two in western Borneo: (1) South-western Sarawak and (2) West Kalimantan, Indonesia; two in central Borneo: (1) north coastal Sarawak and (2) north-eastern Sarawak, Malaysia; and two in northern Borneo: (1) Central Sabah and (2) Northern Sabah, Malaysia. Methods: A phylogenetic reconstruction of chloroplast DNA sequence variation from numerous individuals of multiple species was used to determine geographical distribution of genetic diversity. A resampling scheme was used to determine the significance of these patterns at different hierarchical levels of the phylogeny. Results were compared with a previously published set of nuclear DNA sequence data. Results: A high level of chloroplast sequence variation was found, which was divided equally between two major clades separated by four non-homoplasious changes. One clade was confined to the island of Borneo, while the other was widespread. Strong geographical structure was observed in the chloroplast sequence variation. The Indochinese populations were much more closely related than expected, comparable with the highly endemic and isolated population on the western coast of Borneo. Conversely, individuals from the Kelabit Highlands were found to be more distantly related than expected. The highest levels of genetic endemism were observed in western Borneo. More geographical structure was observed in the Bornean clade than in the Widespread clade, because of limited genetic diversity in the Widespread clade. Relatively weak geographical structure was found in the nuclear sequence variation: only populations in southern China and central Sabah were significantly related. Conclusions: The high levels of chloroplast genetic diversity and the persistence of an ancestral haplotype that is a single step away from a haplotype found in Castanopsis indicates the continuous presence of tropical rain forest in Southeast Asia throughout the evolutionary history of the genus (c. 40 Myr). This conclusion is supported by the high frequency of numerous endemic types observed in every population and the relatively few number of 'missing' haplotypes. This situation suggests both limited migration and limited extinction. In contrast, the nuclear genetic diversity contained less geographical structure, indicating that our taxonomic sampling among populations was unbiased and that gene flow mediated through pollen is less geographically restricted and contains less geographical structure than purely seed-mediated (chloroplast) gene flow. The most likely scenario suggested by the evidence involves four major patterns: (1) the widespread presence of an ancestral haplotype; (2) the large degree of separation (four non-homoplasious base pairs) between the types found in the two major clades; (3) the concentration of derived types from both major clades found in central and northern Borneo; and (4) the molecular endemism found in each location. These patterns suggest four primary things about the population dynamics of Lithocarpus since the late Eocene: (1) populations have either spanned the entire region throughout much of the evolutionary history of the genus or substantial populations have persisted in both Indochina and Borneo with limited migration between them; (2) significant fragmentation has occurred subsequently between the Asian mainland and the Melasian island archipelago, leading to independent genetic diversification in both regions; (3) several locations possessing significant independent histories, have experienced little migration and have never gone completely extinct; and (4) that the central highlands of Borneo have been re-invaded from the north and the west. The timing of these events is difficult to ascertain but probably predate the Quaternary Period, suggesting that although the recent ice ages might have affected the overall distribution of rain forest in Southeast Asia, it managed to persist in most regions even through the most dramatic drying events.
With ∼1000 species distributed pantropically, the genus Piper is one of the most diverse lineages among basal angiosperms. To rigorously address the evolution of Piper we use a phylogenetic analysis of sequences of the internal transcribed spacers (ITS) of nuclear ribosomal DNA based on a worldwide sample. Sequences from a total of 51 species of Piper were aligned to yield 257 phylogenetically informative sites. A single unrooted parsimony network suggested that taxa representing major geographic areas could potentially form three monophyletic groups: Asia, the South Pacific, and the Neotropics. The position of Pothomorphe was well supported among groups of New World taxa. Simultaneous phylogenetic analysis of an expanded alignment including outgroups suggested that taxa from the South Pacific and Asia formed a monophyletic group, provisionally supporting a single origin of dioecy. Within the Neotropical sister clade, resolution was high and strong bootstrap support confirmed the monophyly of several traditionally recognized infrageneric groups (e.g., Enckea [including Arctottonia], Ottonia, Radula, Macrostachys). In contrast, some of the species representing the highly polytypic subgroup Steffensia formed a clade corresponding to the previously recognized taxon Schilleria, while others were strongly associated with several of the more specialized groups of taxa. The distribution of putatively derived inflorescence and floral character states suggested that both umbellate and solitary axillary inflorescences have multiple origins. Reduction in anther number appears to be associated with highly packaged inflorescences or with larger anther primordia per flower, trends that are consistent with the suppression of later stages of androecial development.
The family Fagaceae includes nine currently recognized genera and ca. 1000 species, making it one of the largest and most economically important groups within the order Fagales. In addition to wide variation in cupule and fruit morphology, polymorphism in pollination syndrome (wind vs. generalistic insect) also contributes to the uniqueness of the family. Phylogenetic relationships were examined using 179 accessions spanning the taxonomic breadth of the family, emphasizing tropical, subtropical, and relictual taxa. Nuclear ribosomal DNA sequences encoding the 5.8S rRNA gene and two flanking internal transcribed spacers (ITS) were used to evaluate phylogenetic hypotheses based on previous morphological cladistic analysis and intuitive schemes. Parsimony analyses rooted with Fagus supported two clades within the family, Trigonobalanus sensu lato and a large clade comprising Quercus and the castaneoid genera (Castanea+Castanopsis, Chrysolepis, Lithocarpus). Three DNA sequence data sets, 179-taxon ITS, 60-taxon ITS, and a 14-taxon combined nuclear and chloroplast (matK), were used to test a priori hypotheses of reproductive character state evolution. We used Templeton's (1983) test to assess alternative scenarios of single and multiple origins of derived and seemingly irreversible traits such as wind pollination, hypogeal cotyledons, and flower cupules. On the basis of previous exemplar-based and current in-depth analyses of Fagaceae, we suggest that wind pollination evolved at least three times and hypogeal cotyledons once. Although we could not reject the hypothesis that the acorn fruit type of Quercus is derived from a dichasium cupule, combined analysis provided some evidence for a relationship of Quercus to Lithocarpus and Chrysolepis, taxa with dichasially arranged pistillate flowers, where each flower is surrounded by cupular tissue. This indicates that a more broadly defined flower cupule, in which individual pistillate flowers seated within a separate cupule, may have a single origin.
We tested the phylogenetic hypothesis that the circumscription of the genus Ipomoea comprises all members of Hallier's historical taxon, subfamily "Echinoconiae", including Argyreia, Astripomoea, Lepistemon, Rivea, Stictocardia, and Turbina. Support for the paraphyly of Ipomoea was found based on phylogenetic analysis of 45 taxa using DNA sequences (the ITS region and three exons and two introns of the 3′ end of the nuclear gene waxy) in combination with morphological data. Two major clades within Ipomoea s. 1. were resolved in the strict consensus of 16 most parsimonious trees. One clade included most of the smaller segregate genera interspersed with species of Ipomoea, whereas the other was formed by Ipomoea s.s. and Astripomoea. Our results also indicated the genus Turbina is polyphyletic and Rivea is nested within Argyreia. Together, these results suggest new phylogenetic interpretations and point towards a revised view of the nature of morphological evolution among these taxa. We used both our current understanding of morning glory systematics and the distribution of character state variation in seven taxonomically important characters to demonstrate that: 1) the common Ipomoea form is widely distributed, 2) the common form has given rise to specialized forms exhibiting a diversity of character state combinations, and 3) many of the specialized forms have arisen repeatedly. On the basis of these observations, we forward a general model of mosaic evolution that emphasizes extreme evolutionary lability in morphology among morning glory species.
Three species of Bryopsis have commonly been reported from the western North Atlantic, but continuous morphological variation has often confounded specimen identification. This study evaluates the utility of the coding and non-coding sequences of the psbB gene cluster of Bryopsis, compared to morphological characters, as a means of distinguishing Bryopsis species. The sequences examined include a group II intron within the psbT gene, the 3′ exon of this gene, the spacer separating psbT and psbH, as well as the 5′ part of the latter gene. Sequences of 616 bp of Bryopsis from 28 collections from the study area were aligned with those for eight collections from elsewhere in the Atlantic and Pacific, in order to test the monophyly of Atlantic Bryopsis. The phylogenies were rooted using Lambia as an outgroup. Parsimony analysis resolved the sequences into five clades, with strong bootstrap support. Three of the clades had wide distributions, two including individuals from both the western and eastern North Atlantic and the Pacific and one including plants from the Caribbean and the Pacific. The other two clades were more restricted: one clade was found only in the warm temperate western North Atlantic, and the other derived from the central California coast. Three methods of cluster analysis were applied to the morphological data but failed to find robust higher level structure; they neither supported nor refuted the molecular data. The four clades from the western North Atlantic and Caribbean appear to be either seasonally or geographically disjunct throughout this region. The molecular data support the current recognition of multiple species of Bryopsis along the western North Atlantic, some with worldwide distributions, but the morphological data do not correlate with this.
A comprehensive systematic investigation was conducted on the extant Juglandaceae based on 25 species representing a broad sample of generic and infrageneric diversity. A total of 206 phylogenetically informative characters derived from morphological, chemical, chromosomal, and sequence-based studies formed the basis for comparative studies. Phylogenetic analysis was used to infer relationships and examine patterns of convergence in key biochemical and morphological traits associated with dispersal biology. Separate and combined parsimony analyses of three previously unpublished data sets (ITS, chloroplast DNA, morphology/chemistry) supported two major clades, Juglandoideae and Engelhardioideae, in agreement with a recent subfamilial classification. Within Engelhardioideae, the genus Engelhardia was found to be paraphyletic, as E. roxburghiana of the monotypic section Psilocarpeae was resolved as sister taxon to a New World subclade composed of Oreomunnea + Alfaroa. Within Juglandoideae, two tribes are recognized: Platycaryeae and Juglandeae. The monotypic genus Platycarya formed the sister group to Juglandeae, which was resolved fully (Carya-(Juglans-(Cyclocarya + Pterocarya))). Two new subtribes, Juglandinae and Caryinae, are described based on the cladistic pattern. Unique morphological apomorphies were detected for all genera, including the previously little-studied Cyclocarya, which was also determined to possess a novel base chromosome number for the family (N = 28). The nested position of Annamocarya sinensis within Old World Carya, combined with its lack of unique apomorphies suggested sectional recognition within Carya might be more appropriate for this taxon. Phylogenetic context was used to interpret patterns of morphological and chemical variation associated with the evolution of seed dispersal and the tropical versus temperate habitat. Although the syndrome of wind dispersal appears to be ancestral within the family, four novel origins of wing tissue are represented by Engelhardia/Oreomunnea, Platycarya, Pterocarya, and Cyclocarya. The convergence on animal dispersal has been achieved through three different developmental pathways in the production of a husk in Alfaroa, Carya, and Juglans. In general, wind-dispersed seeds have epigeal germination and those that are animal-dispersed are hypogeous, but Oreomunnea and Cyclocarya are exceptions in their respective clades by having wind-dispersed seeds with hypogeal germination. The seed-energy reserves are also revealing. With the exception of Oreommunea, wind-dispersed seeds have relatively high concentrations of the unsaturated linolenic (C) and linoleic (B) fatty acids (CB pattern), whereas all animal-dispersed fruits (viz., Alfaroa, Carya, and Juglans), and Oreomunnea, have relatively high concentrations of the unsaturated oleic (A) and linoleic (B) fatty acids (BA or AB pattern). Tropical genera, whether wind- or animal-dispersed (viz., Oreomunnea, Alfaroa, Annamocarya), have relatively high concentrations of the saturated palmitic fatty acid. Conversely, wind- and animal-dispersed fruits of temperate genera (viz., Carya, Juglans, Cyclocarya, Pterocarya, and Platycarya) have relatively low percentages of palmitic acid. The explanation here is based on the fact that seed fats must be fluid at the temperature of the living plant, thus selecting for saturated fats in warm tropical climates and unsaturated lipids in cool temperate climates.
The Bornean species of Lithocarpus Bl. section Synaedrys (Lindl.) Barnett (Fagaceae) are discussed in terms of their unifying characteristics, and keys to the species are provided. A novel morphological feature present in the genus, where the seed in the mature fruit is enclosed by a lignified and thickened receptacle, is illustrated. A new species, L. palungensis Cannon and Manos, is described. It can be distinguished from L. pulcher (King) Markgr. by its submontane distribution, prominent reflexed cupular spines, present at all stages, and broadly oblong leaves with scattered open fasciculate trichomes on the abaxial surface. Foliar trichome types present within the section are also described. Distinctiveness of fruit wall and receptacle shape, as described by two-dimensional elliptic Fourier transformation, is demonstrated by principal components analysis. (C) 2000 The Linnean Society of London.
Quercus is one of the most abundant and economically important genera of woody plants in the Northern Hemisphere. To infer phylogenetic relationships within Quercus subgenus Quercus, chloroplast DNA (cpDNA) restriction sites and nucleotide sequences of the internal transcribed spacers (ITS) and the 5.8S coding region of the nuclear ribosomal DNA repeat were obtained for 44 individuals, including 25 species, intraspecific samples, and three outgroups. Separate parsimony analyses of each data set showed that individual gene trees were congruent and often complementary in supporting clades that generally corresponded to previously recognized taxonomic groups. Only one instance of strongly supported gene tree incongruence was detected and this anomalous pattern was explained best by ancient introgression of cpDNA across sectional boundaries. Simultaneous parsimony analysis of the pruned data sets supported the recognition of the strictly Eurasian section Cerris and resolved a novel hypothesis for the major infrageneric groups (Cerris- (Lobatae- (Protobalanus + Quercus sensu stricto))). The biogeographic hypothesis that all major oak lineages evolved locally at middle latitudes within the general distribution of their fossil ancestors was fully supported. This set of relationships also suggested a New World origin for the widespread white oaks of the Northern Hemisphere (section Quercus s. s.). For both data sets, inter- and intraspecific sampling within section Protobalanus showed little correspondence to morphological species. Greater cladistic structure among the samples was obtained by cpDNA restriction sites and two well-delimited plastomes types comprising a total of 15 distinct haplotypes were resolved. Haplotypes of 2 of the peripheral species in this species complex occupy terminal portions of one of the plastome clades, suggesting a more recent origin relative to those of more widespread species. The phylogeography of the two divergent plastome types suggested a north-south pattern, consistent with a Late Tertiary disjunction in the ancestral distribution of section Protobalanus.
Ipomoea is a large and complex genus containing over 600 species of vines and shrubs widely distributed throughout the tropics and subtropics. The phylogeny of 40 species representing the three currently recognized subgenera and nine sections within the genus was analyzed using sequences of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA and sequences for three exons and two introns of the 3' end of the nuclear gene waxy. Nucleotide data from each gene or region were analyzed singly and in combination using parsimony. Exon and intron sequences from the relatively unexplored waxy gene provided appreciable levels of site mutations, and intron sequences revealed several phylogenetically informative deletions. ITS provided greater resolution and was largely congruent with waxy. Combined analyses using Merremia and Operculina as outgroups showed strong support for two major clades, including a novel assemblage of four Old World species and a larger clade composed of the remaining sample. Within the larger clade were numerous well-supported subclades, several of which corresponded to previously recognized taxonomic groups. Higher level hierarchical relationships within the two clades and the among the subclades did not support the most recent classification scheme, which divides Ipomoea into three subgenera, Ipomoea, Quamoclit, and Eriospermum. A striking result from this study was identifying a close relationship between species of section Pharbitis (subgenus Ipomoea) and species of subgenus Quamoclit. This clade is comprised of taxa with a broad range of morphological diversity, implying both floral and vegetative morphology may have been evolutionarily labile within the genus. The composition of three clades consisting largely of species of subg. Eriospermum suggests a novel set of relationships between New World and Australian species. Several clades identified in this study are prime candidates for future studies of character evolution, including several putative cases of independent pigment transformations of red and white flowers from purple flowers.
Phylogenetic relationships were examined within the southern beech family Nothofagaceae using 22 species representing the four currently recognized subgenera and related outgroups. Nuclear ribosomal DNA sequences encoding the 5.8s rRNA and two flanking internal transcribed spacers (ITS) provided 95 phylogenetically informative nucleotide sites from a single alignment of ~ 588 bases per species. Parsimony analysis of this variation produced two equally parsimonious trees supporting four monophyletic groups, which correspond to groups designated by pollen type. These topologies were compared to trees from reanalyses of previously reported rbcL sequences and a modified morphological data set. Results from parsimony analysis of the three data sets were highly congruent, with topological differences restricted to the placement of a few terminal taxa. Combined analysis of molecular and morphological data produced six equally parsimonious trees. The consensus of these trees suggests two basal clades within Nothofagus. Within the larger of the two clades, tropical Nothofagus (subgenus Brassospora) of New Guinea and New Caledonia are strongly supported as sister to cool-temperate species of South America (subgenus Nothofagus). Most of the morphological apomorphies of the cupule, frail and pollen of Nothofagus are distributed within this larger clade. An area cladogram based on the consensus of combined data supports three trans-Antarctic relationships, two within pollen groups and one between pollen groups. Fossil data support continuous ancestral distributions for all four pollen groups prior to continental drift; therefore, vicariance adequately explains two of these disjunctions. Extinction of trans-Antarctic sister taxa within formerly widespread pollen groups explains the third disjunction; this results in a biogeographic pattern indicative of phylogenetic relationship not vicariance. For the biogeographically informative vicariant clades, area relationships based on total evidence support the recently advanced hypothesis that New Zealand and Australia share a unique common ancestry. Contrary to previous thought, the distribution of extant Nothofagus is informative on the area relationships of the Southern Hemisphere, once precise phylogenetic relationships are placed in the context of fossil data.
Phylogenetic relationships were examined within the 'higher' Hamamelididae using 21 species representing eight families and related outgroups. Chloroplast DNA sequences encoding the matK gene (~ 1 kilobase) provided 258 informative nucleotide sites. Phylogenetic analysis of this variation produced one most parsimonious tree supporting three monophyletic groups. In this tree. Nothofagus was basal to a well supported clade of remaining 'higher' hamamelids, in which Fagaceae, including Fagus, were sister to a clade of core 'higher' hamamelids that share wind-pollination, bicarpellate flowers, granular pollen walls, and reduced pollen apertures. Within the core 'higher' hamamelids three subclades were resolved, Myricaceae, (Casuarina-(Ticodendron-(Betulaceae))), and (Rhoiptelea-Juglandaceae). Each subclade was well supported but relationships among them were not. The basal position of Nothofagus within the matK tree is consistent with the fossil record of 'higher' hamamelids in which Nothofagus pollen appears earlier than microfossils with affinities to other modern 'higher' hamamelids. This placement supports the exclusion of Nothofagus from Fagaceae and suggests two hypotheses for the origin of the cupule. The cupule may be ancestral within 'higher' hamamelids and subsequently lost in core members of the clade or there may have been two independent origins. It is suggested that the three clades (1) Nothofagaceae, (2) Fagaceae, and (3) Juglandaceae, Rhoiptelea, Myricaceae, Casuarina, Ticodendron, and Betulaceae be considered at the ordinal level and that traditional orders, such as Fagales sensu Cronquist (Fagaceae, Nothofagaceae, and Betulaceae) be abandoned. Comparative analyses of matK sequences with previously published rbcL sequences demonstrate that for the taxa considered here matK sequences produced trees with greater phylogenetic resolution and a higher consistency index.