Phylogeny and biogeography of the rice tribe (Oryzeae): Evidence from combined analysis of 20 chloroplast fragments

Based on sequences of 20 chloroplast fragments, we generated a fully resolved phylogeny of Oryzeae and estimated divergence times of its major lineages as well as explored the historical biogeography of the tribe. Our results (1) confirmed the monophyly of Oryzeae and two-subtribe subdivision; (2) indicated that Maltebrunia, Potamophila and Prosphytochloa were genetically distinct enough to deserve generic status but Maltebrunia and Prosphytochloa were sister groups in the subtribe Oryzinae while Potamophila was a member in the subtribe Zizaniinae; (3) suggested that the previously unresolved phylogeny of the subtribe Zizaniinae was most likely explained by insufficient data due to rapid radiation; (4) provided the first well-corroborated timescale for the origin and divergence of Oryzeae, with the crown node of Oryzeae and the deepest split of Oryza at ～24 and 15 MYA, respectively; (5) developed a biogeographic history of the tribe and substantiated the important roles of long-distance dispersal in the origin and diversification of the tribe Oryzeae.     

Phylogeny and biogeography of Cedrus (Pinaceae) inferred from sequences of seven paternal chloroplast and maternal mitochondrial DNA regions

BACKGROUND AND AIMS: Cedrus (true cedars) is a very important horticultural plant group. It has a disjunct distribution in the Mediterranean region and western Himalaya. Its evolution and biogeography are of great interest to botanists. This study aims to investigate the phylogeny and biogeography of Cedrus based on sequence analyses of seven cytoplasmic DNA fragments. METHODS: The methods used were PCR amplification and sequencing of seven paternal cpDNA and maternal mtDNA fragments, parsimony and maximum likelihood analyses of the DNA dataset, and molecular clock estimate of divergence times of Cedrus species. KEY RESULTS: Phylogenies of Cedrus constructed from cpDNA, mtDNA and the combined cp- and mt-DNA dataset are identical in topology. It was found that the Himalayan cedar C. deodara diverged first, and then the North African species C. atlantica separated from the common ancestor of C. libani and C. brevifolia, two species from the eastern Mediterranean area. Molecular clock estimates suggest that the divergence between C. atlantica and the eastern Mediterranean clade at 23.49 +/- 3.55 to 18.81 +/- 1.25 Myr and the split between C. libani and C. brevifolia at 7.83 +/- 2.79 to 6.56 +/- 1.20 Myr. CONCLUSIONS: The results, combined with palaeogeographical and palaeoecological information, indicate that Cedrus could have an origin in the high latitude area of Eurasia, and its present distribution might result from vicariance of southerly migrated populations during climatic oscillations in the Tertiary and further fragmentation and dispersal of these populations. It is very likely that Cedrus migrated into North Africa in the very late Tertiary, while its arrival in the Himalayas would not have been before the Miocene, after which the phased or fast uplift of the Tibetan plateau happened.     

Evolutionary trends in leaf morphology and biogeography of Altingiaceae based on fossil evidence

The extant woody family Altingiaceae, consisting of only one genus Liquidambar L. with ca. 15 species, demonstrates a typical disjunctive distribution among East Asia, North America, and the Mediterranean. However, the fossil record throughout the Cenozoic indicates that Altingiaceae was once widespread in the Northern Hemisphere. After studying the abundant Altingiaceae fossil leaf collections, we revised the easily-confused fossil leaves and corrected the misidentifications. Consequently, we proposed an evolutionary history of Altingiaceae leaf morphology in consulting the modern leaf characteristics. It is revealed that the trilobated leaf morphology is the ancestral character state, whereas both the pentalobated and the undivided, pinnate-veined lineages evolved separately. The latter diverged from the trilobated ancestor in South China in Eocene. The lobed and undivided lineages represent the deciduous and evergreen, respectively. An extensive fossil database of Altingiaceae was built to reconstruct its biogeographical history. We reconfirmed that Altingiaceae developed into a temperate and a subtropical-tropical patterns and migrated across both the Bering and North Atlantic land bridges since Cretaceous, independently. It was widespread in the early Neogene of North America and Eurasia, and became extinct in the high latitude triggered by the global cooling and aridification. The modern disjunctive distribution was finally formed, with southeast Asia as its modern diversity center. This study provides new fossil evidence for understanding the morphology and biogeography of the family Altingiaceae.     

Phylogeny of Malpighiaceae: evidence from chloroplast ndhF and trnl-F nucleotide sequences

The Malpighiaceae are a family of ～1250 species of predominantly New World tropical flowering plants. Infrafamilial classification has long been based on fruit characters. Phylogenetic analyses of chloroplast DNA nucleotide sequences were analyzed to help resolve the phylogeny of Malpighiaceae. A total of 79 species, representing 58 of the 65 currently recognized genera, were studied. The 3' region of the gene ndhF was sequenced for 77 species and the noncoding intergenic spacer region trnL-F was sequenced for 65 species; both sequences were obtained for the outgroup, Humiria (Humiriaceae). Phylogenetic relationships inferred from these data sets are largely congruent with one another and with results from combined analyses. The family is divided into two major clades, recognized here as the subfamilies Byrsonimoideae (New World only) and Malpighioideae (New World and Old World). Niedenzu's tribes are all polyphyletic, suggesting extensive convergence on similar fruit types; only de Jussieu's tribe Gaudichaudieae and Anderson's tribes Acmanthereae and Galphimieae are monophyletic. Fleshy fruits evolved three times in the family and bristly fruits at least three times. Among the wing-fruited vines, which constitute more than half the diversity in the family, genera with dorsal-winged samaras are fairly well resolved, while the resolution of taxa with lateral-winged samaras is poor. The trees suggest a shift from radially symmetrical pollen arrangement to globally symmetrical pollen at the base of one of the clades within the Malpighioideae. The Old World taxa fall into at least six and as many as nine clades.     

蹄盖蕨科的系统发育: 叶绿体DNA trnL-F区序列证据

蹄盖蕨科Athyriaceae是蕨类植物中一个复杂的大科,由于属间关系不甚清楚,该科分类系统还有一些问题,比如新蹄盖蕨、拟鳞毛蕨属、假冷蕨属、肠蕨属、短肠蕨属和菜蕨属的系统位置常有争议。根据蹄盖蕨科34种植物和3种外类群植物的叶绿体DNA trnL-F区序列建立了系统发育树,结果显示:1.trnL_F区序列分析的结果与rbcL基因序列分析的结果几乎一致。2.新蹄盖蕨属Neoathyrium Ching&Z.R.Wang不应成立,该属应与角蕨属Cornopteris Nakai合并。3.假冷蕨属Pseudo     

Phylogeny and biogeography of the genus Lycium (Solanaceae): inferences from chloroplast DNA sequences

Lycium comprises approximately 70 species and is disjunctly distributed in temperate to subtropical regions in South America, North America, southern Africa, Eurasia, and Australia. Among them, only Lycium sandwicense A. Gray sporadically occurs widely on oceanic islands in the Pacific Ocean. To investigate phylogenetic and biogeographic relationships of the genus with emphasis on L. sandwicense, the coding region of matK, the two intergenic spacers trnT (UGU)-trnL (UAA) and trnL (UAA)-trnF (GAA), and the trnL (UAA) intron of chloroplast DNA (cpDNA) were sequenced. A strict consensus tree resulting from the phylogenetic analysis indicates the following: (1) New World species comprise a potentially paraphyletic assemblage; (2) southern African, Australian, and Eurasian species together are monophyletic; (3) southern African species are a paraphyletic assemblage; and (4) L. sandwicense is in a clade with certain New World species. The estimated biogeographic events based on the cpDNA analysis indicate that (1) Lycium originated in the New World, (2) all southern African, Australian, and Eurasian species have a common ancestor from the New World, (3) Australian and Eurasian species originated once from a southern African progenitor, and (4) L. sandwicense differentiated from the New World species.     

Phylogenetic relationships in Disa based on non-coding trnL-trnF chloroplast sequences: evidence of numerous repeat regions

Sequence data from the intron and spacer of the trnL-F chloroplast region elucidate the phylogenetic relationships of the tribe Diseae (Orchidoideae: Orchidaceae). Within Diseae, 41 species of Disa, two of Brownleea, three of Satyrium, and two of Corycium were included, with five species of Habenaria sensu lato (Orchideae) and one epidendroid as outgroups. The sequences revealed substitutions and considerable length variation, due mainly to the presence of repeat motifs. Phylogenetic analysis using parsimony revealed five distinct clades. The branching order of the five weakly supported the paraphyly of Diseae, with the successive divergence of Brownleea, Corycium, Habenaria, Satyrium, and Disa. Within the monophyletic Disa, three main groupings appeared, two strongly supported clades representing sect. Racemosae and sect. Coryphaea and the third grouping containing several clades currently grouped into sections based on morphological phylogenies. Some discrepancies between the molecular phylogeny and the phylogeny based on morphological characters may require reevaluation of some of the morphological characters. The presence of different numbers of repeat motifs, both among different taxa and within taxa, indicates that these characters may be phylogenetically informative at the population level.     

Phylogeny of sipunculan worms: A combined analysis of four gene regions and morphology

The intra-phyletic relationships of sipunculan worms were analyzed based on DNA sequence data from four gene regions and 58 morphological characters. Initially we analyzed the data under direct optimization using parsimony as optimality criterion. An implied alignment resulting from the direct optimization analysis was subsequently utilized to perform a Bayesian analysis with mixed models for the different data partitions. For this we applied a doublet model for the stem regions of the 18S rRNA. Both analyses support monophyly of Sipuncula and most of the same clades within the phylum. The analyses differ with respect to the relationships among the major groups but whereas the deep nodes in the direct optimization analysis generally show low jackknife support, they are supported by 100% posterior probability in the Bayesian analysis. Direct optimization has been useful for handling sequences of unequal length and generating conservative phylogenetic hypotheses whereas the Bayesian analysis under mixed models provided high resolution in the basal nodes of the tree.     

Phylogeny and biogeography of Crinum L. (Amaryllidaceae) inferred from nuclear and limited plastid non-coding DNA sequences

The genus Crinum L. is the only pantropical genus of the Amaryllidaceae. Phylogenetic and biogeographical analyses of nrDNA ITS and plastid trnL-F sequences for all continental groups of the genus Crinum and related African genera are presented, with the genus Amaryllis used as outgroup. ITS indicates that C. baumii is more closely related to Ammocharis and Cybistetes than to Crinum sensu stricto . Three clades are resolved in Crinum s.s. One unites a monophyletic American group with tropical and North African species. The second includes all southern African species and the Australian endemic C. flaccidum . The third includes monophyletic Madagascar, Australasian and Sino-Himalayan clades, with southern African species. The trnL-F phylogeny resolves an American and an Asian/Madagscar clade, and confirms the relationship of C. flaccidum with species endemic to southern Africa. The salverform, actinomorphic perianths of subg. Crinum appear to have evolved several times in the genus from ancestors with zygomorphic perianths (subg. Codonocrinum ), thus neither subgenus is monophyletic. Biogeographical analyses place the origin of Crinum in southern Africa, as the region is optimized at all ancestral nodes in the tree topology, and in basal interior nodes of all but one of the major clades. The genus underwent three major waves of radiation corresponding to the three main clades resolved in our trees. Two entries into Australia for the genus are indicated, as are separate Sino-Himalayan and Australasian dispersal events.  © 2003 The Linnean Society of London, Botanical Journal of the Linnean Society , 2003, 141 , 349–363.     

Phylogeny and biogeography of Caltha (Ranunculaceae) based on chloroplast and nuclear DNA sequences

The genus Caltha (Ranunculaceae) consists of 10 species of low-growing, perennial herbs distributed throughout the moist temperate and cold regions of both the Northern and Southern Hemispheres. Traditionally, the species have been divided into two sections: section Psychrophila in the Southern Hemisphere with diplophyllous leaves and section Caltha in the Northern Hemisphere with leaves lacking inflexed appendages. This study uses chloroplast and nuclear DNA sequences to determine the relationships among the 10 species, test the monophyly of sections Psychrophila and Caltha, trace the evolutionary history of diplophylly, and explore biogeographical hypotheses for the genus. Analysis of these data resulted in a well-resolved and well-supported phylogeny. Section Psychrophila (C. sagittata, C. appendiculata, C. dionaeifolia, C. obtusa, C. introloba, and C. novae-zelandiae) was resolved as monophyletic, indicating a single origin of diplophylly. The species of section Caltha (C. natans, C. scaposa, C. palustris, and C. leptosepala) formed a paraphyletic grade. The resulting phylogeny strongly supports a Northern Hemisphere origin for Caltha, followed by dispersal to the Southern Hemisphere (Gondwanaland). A vicariance model is invoked to explain present-day distributions in South America, Australia, and New Zealand.     

Universal primers for amplification of three non-coding regions of chloroplast DNA

Six primers for the amplification of three non-coding regions of chloroplast DNA via the polymerase chain reaction (PCR) have been designed. In order to find out whether these primers were universal, we used them in an attempt to amplify DNA from various plant species. The primers worked for most species tested including algae, bryophytes, pteridophytes, gymnosperms and angiosperms. The fact that they amplify chloroplast DNA non-coding regions over a wide taxonomic range means that these primers may be used to study the population biology (in supplying markers) and evolution (inter- and probably intraspecific phylogenies) of plants.     

Phylogeny of the basal angiosperm genus Pseuduvaria (Annonaceae) inferred from five chloroplast DNA regions, with interpretation of morphological character evolution

Phylogenetic relationships within the magnoliid basal angiosperm genus Pseuduvaria (Annonaceae) are investigated using chloroplast DNA sequences from five regions: psbA-trnH spacer, trnL-F, matK, rbcL, and atpB-rbcL spacer. Over 4000 nucleotides from 51 species (of the total 53) were sequenced. The five cpDNA datasets were analyzed separately and in combination using maximum parsimony (MP), maximum likelihood (ML), and Bayesian methods. The phylogenetic trees constructed using all three phylogenetic methods, based on the combined data, strongly support the monophyly of Pseuduvaria following the inclusion of Craibella phuyensis. The trees generated using MP were less well resolved, but relationships are similar to those obtained using the other methods. ML and Bayesian analyses recovered trees with short branch lengths, showing five main clades. This study highlights the evolutionary changes in seven selected morphological characters (floral sex, stamen and carpel numbers, inner petal color, presence of inner petal glands, flowering peduncle length, and monocarp size). Although floral unisexuality is ancestral within the genus, several evolutionary lineages reveal reversal to bisexuality. Other phylogenetic transitions include the evolution of sapromyophily, and fruit-bat frugivory and seed dispersal, thus allowing a wide range of adaptations for species survival.     

Phylogeny and biogeography of Caribbean mammals

Vicariance and dispersal hypotheses have been proposed over the last two hundred years to explain the distribution, diversity, and faunal composition of the Caribbean biota. Despite great advances in understanding the geological history of the region, recent biogeographical reviews have not used historical biogeographical methods. In this paper I review the taxonomy, distribution and phylogeny of all Cenozoic Caribbean non‐volant mammals and four bat lineages, and present reconciled trees for available phylogenies. Dates available from the fossil record and hypotheses of divergence based on molecular phylogenetic studies are also included in general assessments of fit between proposed geological models and Caribbean mammal diversification. The evidence posited in mammalian phylogenies does not add to the argument of dispersal vs. vicariance. One previously unidentified temporal pattern, the colonization of the Caribbean by South American mammals between the Palaeocene and the Middle Miocene, accounts for the distribution and phylogeny of the majority of lineages studied. Choloepodine and megalocnine sloths, hystricognath rodents, and primates all arrived during this window of colonization. Of these, megalocnine sloths, hystricognath rodents, Brachyphylla and allied bats, Stenodermatina bats, and primates fit the pattern of divergence from the mainland implied by the Gaarlandia hypothesis. Sloths, rodents and primates also roughly fit the timing of arrival to the Caribbean implied by Gaarlandia. The remaining taxa show contradictory dates of divergence according to molecular clock estimates, and no taxa fit the predicted timing and pattern of divergence among Antillean landmasses under the Gaarlandia model. Choloepodine sloths, murid rodents, insectivorans, mormoopids, and natalids show patterns of divergence from the mainland that are inconsistent with the Gaarlandia hypothesis and seem to require taxon‐specific biogeographical explanations. © 2004 The Linnean Society of London, Biological Journal of the Linnean Society, 2004, 81 , 373–394.     

Phylogeny of basal eudicots: Insights from non-coding and rapidly evolving DNA

Sequence data of the trnL group I intron, the petD group II intron, the trnL-F and petB-D spacers, and the rapidly evolving matK gene were analysed from all families of the basal eudicot grade and from representatives of 19 core eudicot orders. The dataset comprised 5654 positions of aligned sequence plus a matrix of 1087 binary indel characters. Mutational hotspots correspond in number and extension to hotspots already known from basal angiosperms and, with respect to secondary structure, are generally located in terminal parts of stem-loop regions. Parsimony, Bayesian, and likelihood analyses depict Ranunculales as sister to all remaining eudicots with maximum support. The branching order in the basal eudicot grade is further resolved as Sabiales, Proteales, Trochodendrales, and Buxales. Nearly all of the backbone nodes gain high confidence, except for the node showing Proteales diverging before Trochodendrales, which is only moderately supported (83% JK). In Ranunculales, the woody Eupteleaceae are first-branching, with Papaveraceae plus Fumariaceae coming next. Within Proteales, Nelumbo is clearly resolved as sister to a Platanaceae–Proteaceae clade. Gunnerales are found as the first branch in core eudicots, with maximum support in the combined analysis. This node is also resolved with matK alone, but unsupported. It appears that the combined analysis of sequence data from rapidly evolving and non-coding genomic regions leads to significantly improved statistical support values in comparison to earlier studies of basal eudicots using multiple conserved genes.See also Electronic Supplement at doi:10.1016/j.ode.2006.08.001     

Phylogeny of Henicopidae (Chilopoda: Lithobiomorpha): a combined analysis of morphology and five molecular loci

Abstract. Relationships in Henicopidae, the dominant southern temperate clade of Lithobiomorpha, are appraised based on parsimony analysis of forty-nine morphological characters and sequence data from five loci (nuclear ribosomal RNAs 18S and 28S, mitochondrial ribosomal RNAs 12S and 16S, protein-coding mitochondrial cytochrome c oxidase I). A combined analysis of these data used direct character optimization, and tested stability of hypotheses through parameter-sensitivity analysis. The morphology dataset highlighted the mandibles as a source of new characters. Morphology, as well as the most congruent parameters for the sequence data and combined analysis, resolved Zygethobiini within Henicopini. Groups retrieved by combined analysis of the sequences and combination with morphology for all parameters include Anopsobiinae/Henicopinae, Lamyctes + Lamyctinus + Henicops , Paralamyctes ( Paralamyctes ), and a clade that groups the southeastern Australian/New Zealand Paralamyctes ( Haasiella ) and P . ( Thingathinga ). Paralamyctes (including Haasiella ) is a Gondwanan clade in the most congruent cladograms based on all molecular data and combination with morphological data. Biogeographic analysis of subtrees for Paralamyctes resolved the interrelationships of Gondwana as (Patagonia ((New South Wales + southeastern Queensland) ((Tasmania) (southern Africa + India) (New Zealand + north Queensland)))).     

Phylogeny of South American Bufo (Anura: Bufonidae) inferred from combined evidence

Despite the considerable research that has focused on the evolutionary relationships and biogeography of the genus Bufo, an evolutionary synthesis of the entire group has not yet emerged. In the present study, almost 4 kb of DNA sequence data from mitochondrial (12S, tRNA^Val, and 16S) and nuclear (POMC; Rag-1) genes, and 83 characters from morphology were analysed to infer a phylogeny of South American toads. Phylogenies were reconstructed with parsimony and maximum likelihood and Bayesian model-based methods. The results of the analysis of morphological data support the hypothesis that within Bufo , some skull characters (e.g. frontoparietal width), correlated with the amount of cranial ossification, are prone to homoplasy. Unique and unreversed morphological synapomorphies are presented that can be used to diagnose recognized species groups of South American toads. The results of all phylogenetic analyses support the monophyly of most species groups of South American Bufo . In most DNA-only and combined analyses, the South American (minus the B. guttatus and part of the ' B. spinulosus ' groups), North American, Central American, and African lineages form generally well-supported clades: ((((((((South America) (North America + Central America)) Eurasia) Africa) Eurasia) South America) West Indies) South America). This result confirms and extends prior studies recovering South American Bufo as polyphyletic. The biogeographical results indicate that: (1) The origin of Bufo predates the fragmentation of Gondwana; (2) Central and North American species compose the sister group to a large, 'derived' clade of South American Bufo ; and (3) Eurasian species form the sister group to the New World clade.  © 2006 The Linnean Society of London, Zoological Journal of the Linnean Society , 2006, 146 , 407–452.     

Crocodyliform biogeography during the Cretaceous: evidence of Gondwanan vicariance from biogeographical analysis

Explanations of the distributions of terrestrial vertebrates during the Mesozoic are currently vigorously contested and debated in palaeobiogeography. Recent studies focusing on dinosaurs yield conflicting hypotheses. Dispersal, coupled with regional extinction or vicariance driven by continental break-up, have been cited as the main causal factors behind dinosaur distributions in the Mesozoic. To expand the scope of the debate and test for vicariance within another terrestrial group, I herein apply a cladistic biogeographical method to a large sample of Cretaceous crocodyliform taxa. A time-slicing methodology is employed and a refinement made to account for the divergence times of the analysed clades. The results provide statistically significant evidence that Gondwana fragmentation affected crocodyliform diversification during the Mid-Late Cretaceous. Detection of a vicariant pattern within crocodyliforms is important as it helps corroborate vicariance hypotheses in other fossil and extant groups as well as furthers the move towards more taxonomically diverse approaches to palaeobiogeographical research.     

Takhtajan's floristic regions and foliicolous lichen biogeography: a compatibility analysis

Abstract:Takhtajan's floristic regions of the world, based on vascular plant distribution, were used for a comparative analysis of foliicolous lichen biogeography. Of the 35 regions distinguished by that author, 23 feature foliicolous lichens. The South-East African, Fijian, Polynesian and Hawaiian regions lack sufficient information and were excluded from further analysis. Using multi-dimensional scaling and cluster and cladistic analyses, the remaining 19 regions were grouped into six lichenogeographical regions: (1) Neotropics, (2) African Paleotropics (including Madagascar, Réunion and Seychelles), (3) Eastern Paleotropics (including North-East Australia and New Caledonia), (4) Valdivian region (temperate rainforest in southern South America), (5) Tethyan region (subtropical areas of Macaronesia, Mediterranean, and Western Irano-Turanian) and (6) Neozealandic-Tasmanian region (temperate rainforests of New Zealand and Tasmania). Affinities between these six large scale regions, with 57–77% shared species, are still stronger than those between the 35 smaller scale regions defined by Takhtajan [(20–)40–60(–75)% shared species]. Based on presence/absence within each of the six regions, 22 potential distribution patterns were defined for foliicolous lichens. Many species are widely distributed; 21% are cosmopolitan or pantropical, while 19% are disjunct on at least two continents, and only 60% are restricted to one of the three major tropical areas (nearly 100% in vascular plants). Most of the latter are found in the Neotropics, while the African Paleotropics are poor in endemics. Most genera deviate significantly from overall distribution patterns; for example, Strigula and Calopadia have higher proportions of widely distributed species, while Porina displays a concentration of Eastern Paleotropical endemics. Species diversity and composition of the six regions indicate that the three extra-tropical foliicolous lichen biotas (Valdivian, Tethyan, Neozealandic-Tasmanian) are the result of partly separate evolutionary histories. On the other hand, there is a strong affinity between the Neotropics and the African Paleotropics, suggesting a shared Western Gondwanan element in the foliicolous lichen biotas of these two regions.