More Miocene Dispersal Between Africa and Asia—the Case of Bridelia (Phyllanthaceae)

Several hundred angiosperm genera range from Africa to Asia and Australia, among them Bridelia (Phyllanthaceae), with ca. 40 species, including commercially important timber trees. We here use nuclear and chloroplast DNA sequences from herbarium material, plus new collections from China, to test the monophyly of Bridelia and to infer the geologic times when it acquired its disjunct range. For the Southeast Asian mainland, within-species sampling, including material collected close to the type localities, allowed testing current species concepts. Based on a sample of 114 chloroplast matK sequences of Phyllanthaceae, Bridelia is monophyletic and sister to an Asian clade which requires resurrecting an older generic name to make the African Cleistanthus monophyletic. Within Bridelia, gene trees from the combined data (3,177 aligned nucleotides from 25 species of Bridelia plus outgroups) agree with most morphological species boundaries. Exceptions are that B. tomentosa must include B. harmandii and B. curtisii to become monophyletic and that B. fordii is distinct from B. retusa. The topology, together with relaxed clock divergence times, implies that Bridelia dispersed from tropical Asia to Africa once or twice between 10 and 1.85 million years ago (Ma). Australia was reached, probably from New Guinea, at least twice, both times ca. 2 Ma. Together with earlier studies, there are now at least eight cases of Neogene long distance dispersal between Africa and Asia (followed by speciation), with no directional bias apparent so far.

Download Full-text

Evolutionary Insights from DNA Sequences from Chaetanthera Ruiz & Pav. and Oriastrum Poepp. & Endl. (Asteraceae; Mutisieae). I. Of Molecules and Systematics

10.32942/osf.io/ak68m ◽

2021 ◽

Author(s):

Mark Hershkovitz

Keyword(s):

Dna Sequences ◽

Phylogenetic Reconstruction ◽

Intergenic Spacer ◽

Nominal Species ◽

Gene Trees ◽

Species Trees ◽

Phylogenetic Resolution ◽

Extraterrestrial Origin ◽

Epistemological Framework ◽

Combined Data

Phylogenetic analysis of combined ribosomal DNA internal transcribed spacer (ITS) and chloroplast DNA rpl32-trnL intergenic spacer sequences greatly improves phylogenetic resolution of Chaetanthera Ruiz & Pav. and Oriastrum Poepp. & Endl. (Asteraceae; Mutisieae) over a previously published phylogeny based on ITS alone. The results support segregation of Chaetanthera subg. Liniphyllum Less. from C. subg. Chaetanthera. One sample with peculiar ITS and rpl32-trnL sequences may be of extraterrestrial origin. Fifteen of 16 nominal species sampled more than once for both loci were polymorphic for at least one of them, and only half of the polymorphic samples were demonstrably monophyletic in the combined data analysis. An additional five species sampled only for ITS all were polymorphic. These results underscore the ontological difference between gene trees and species trees and further discredit the notion of “species barcodes.” The gene trees for both loci manifest departures from all evolutionary models implemented for phylogenetic reconstruction. This result is explained as a consequence of evolutionary idiosyncraticity, in turn a function of the determinacy of biological organisms and processes consequent to autopoiesis. This determinacy implicates a chaotic evolutionary function that theoretically cannot be reconstructed or predicted by stochastic models. However, because phylogenetic history and clades are materially tangible entities, their reconstruction is within the realm of scientific inquiry. I discuss the phylogeny of Chaetanthera/Oriastrum in this epistemological framework.

Download Full-text

Systematics, Biogeography, and Morphological Character Evolution of the Hemiepiphytic Subfamily Monsteroideae (Araceae)

Annals of the Missouri Botanical Garden ◽

10.3417/2018269 ◽

2019 ◽

Vol 104 (1) ◽

pp. 33-48 ◽

Cited By ~ 4

Author(s):

Alejandro Zuluaga ◽

Martin Llano ◽

Ken Cameron

Keyword(s):

Dna Sequences ◽

Pacific Islands ◽

R Package ◽

Morphological Characters ◽

Ancestral State ◽

Seed Shape ◽

Long Distance ◽

The Pacific ◽

And Migration ◽

The Tropics

The subfamily Monsteroideae (Araceae) is the third richest clade in the family, with ca. 369 described species and ca. 700 estimated. It comprises mostly hemiepiphytic or epiphytic plants restricted to the tropics, with three intercontinental disjunctions. Using a dataset representing all 12 genera in Monsteroideae (126 taxa), and five plastid and two nuclear markers, we studied the systematics and historical biogeography of the group. We found high support for the monophyly of the three major clades (Spathiphylleae sister to Heteropsis Kunth and Rhaphidophora Hassk. clades), and for six of the genera within Monsteroideae. However, we found low rates of variation in the DNA sequences used and a lack of molecular markers suitable for species-level phylogenies in the group. We also performed ancestral state reconstruction of some morphological characters traditionally used for genera delimitation. Only seed shape and size, number of seeds, number of locules, and presence of endosperm showed utility in the classification of genera in Monsteroideae. We estimated ancestral ranges using a dispersal-extinction-cladogenesis model as implemented in the R package BioGeoBEARS and found evidence for a Gondwanan origin of the clade. One tropical disjunction (Monstera Adans. sister to Amydrium Schott–Epipremnum Schott) was found to be the product of a previous Boreotropical distribution. Two other disjunctions are more recent and likely due to long-distance dispersal: Spathiphyllum Schott (with Holochlamys Engl. nested within) represents a dispersal from South America to the Pacific Islands in Southeast Asia, and Rhaphidophora represents a dispersal from Asia to Africa. Future studies based on stronger phylogenetic reconstructions and complete morphological datasets are needed to explore the details of speciation and migration within and among areas in Asia.

Download Full-text

Bayes Estimation of Species Divergence Times and Ancestral Population Sizes Using DNA Sequences From Multiple Loci

Genetics ◽

10.1093/genetics/164.4.1645 ◽

2003 ◽

Vol 164 (4) ◽

pp. 1645-1656 ◽

Cited By ~ 3

Author(s):

Bruce Rannala ◽

Ziheng Yang

Keyword(s):

Dna Sequences ◽

Gene Tree ◽

Species Tree ◽

Bayes Estimation ◽

Ancestral Population ◽

Divergence Times ◽

Gene Trees ◽

Species Divergence ◽

Multiple Loci ◽

Population Sizes

Abstract The effective population sizes of ancestral as well as modern species are important parameters in models of population genetics and human evolution. The commonly used method for estimating ancestral population sizes, based on counting mismatches between the species tree and the inferred gene trees, is highly biased as it ignores uncertainties in gene tree reconstruction. In this article, we develop a Bayes method for simultaneous estimation of the species divergence times and current and ancestral population sizes. The method uses DNA sequence data from multiple loci and extracts information about conflicts among gene tree topologies and coalescent times to estimate ancestral population sizes. The topology of the species tree is assumed known. A Markov chain Monte Carlo algorithm is implemented to integrate over uncertain gene trees and branch lengths (or coalescence times) at each locus as well as species divergence times. The method can handle any species tree and allows different numbers of sequences at different loci. We apply the method to published noncoding DNA sequences from the human and the great apes. There are strong correlations between posterior estimates of speciation times and ancestral population sizes. With the use of an informative prior for the human-chimpanzee divergence date, the population size of the common ancestor of the two species is estimated to be ∼20,000, with a 95% credibility interval (8000, 40,000). Our estimates, however, are affected by model assumptions as well as data quality. We suggest that reliable estimates have yet to await more data and more realistic models.

Download Full-text

Relationships of North American members of Rhodiola (Crassulaceae)

Botany ◽

10.1139/cjb-2014-0009 ◽

2014 ◽

Vol 92 (12) ◽

pp. 901-910 ◽

Cited By ~ 3

Author(s):

Joel P. Olfelt ◽

William A. Freyman

Keyword(s):

Dna Sequences ◽

North American ◽

Phylogenetic Analyses ◽

Black Hills ◽

Trnl Intron ◽

The North ◽

Alpine Habitats ◽

Rare And Endangered ◽

Chloroplast Dna Sequences ◽

Rhodiola Integrifolia

Taxa of Rhodiola L. (Crassulaceae) generally grow in arctic or alpine habitats. Some Rhodiola species are used medicinally, one taxon, Rhodiola integrifolia Raf. subsp. leedyi (Rosend. & J.W.Moore) Moran, (Leedy’s roseroot), is rare and endangered, and the group’s biogeography in North America is intriguing because of distributional disjunctions and the possibility that Rhodiola rhodantha (A.Gray) H.Jacobsen (2n = 7II) and Rhodiola rosea L. (2n = 11II) hybridized to form Rhodiola integrifolia Raf. (2n = 18II). Recent studies of the North American Rhodiola suggest that the group’s current taxonomy is misleading. We analyzed nuclear and chloroplast DNA sequences (internal transcribed spacer (ITS), trnL intron, trnL–trnF spacer, trnS–trnG spacer) from the North American Rhodiola taxa. We combined our data with GenBank sequences from Asian Rhodiola species, performed parsimony, maximum likelihood (ML), and Bayesian phylogenetic analyses, and applied a Bayesian clock model to the ITS data. Our analyses reveal two major Rhodiola clades, suggest that hybridization between R. rhodantha and R. rosea lineages was possible, show two distinct clades within R. integrifolia, and demonstrate that a Black Hills, South Dakota, Rhodiola population should be reclassified as Leedy’s roseroot. We recommend that R. integrifolia be revised, and that the Black Hills Leedy’s roseroot population be managed as part of that rare and endangered taxon.

Download Full-text