Ribosomal RNA genes and deuterostome phylogeny revisited: more cyclostomes, elasmobranchs, reptiles, and a brittle star

This is an expanded study of the relationships among the deuterostome animals based on combined, nearly complete 28S and 18S rRNA genes (>3925 nt.). It adds sequences from 20 more taxa to the approximately 45 sequences used in past studies. Seven of the new taxa were sequenced here (brittle star Ophiomyxa, lizard Anolis, turtle Chrysemys, sixgill shark Hexanchus, electric ray Narcine, Southern Hemisphere lamprey Geotria, and Atlantic hagfish Myxine for 28S), and the other 13 were from GenBank and the literature (from a chicken, dog, rat, human, three lungfishes, and several ray-finned fishes, or Actinopterygii). As before, our alignments were based on secondary structure but did not account for base pairing in the stems of rRNA. The new findings, derived from likelihood-based tree-reconstruction methods and by testing hypotheses with parametric bootstrapping, include: (1) brittle star joins with sea star in the echinoderm clade, Asterozoa; (2) with two hagfishes and two lampreys now available, the cyclostome (jawless) fishes remain monophyletic; (3) Hexanchiform sharks are monophyletic, as Hexanchus groups with the frilled shark, Chlamydoselachus; (4) turtle is the sister taxon of all other amniotes; (5) bird is closer to the lizard than to the mammals; (6) the bichir Polypterus is in a monophyletic Actinopterygii; (7) Zebrafish Danio is the sister taxon of the other two teleosts we examined (trout and perch); (8) the South American and African lungfishes group together to the exclusion of the Australian lungfish. Other findings either upheld those of the previous rRNA-based studies (e.g., echinoderms and hemichordates group as Ambulacraria; orbitostylic sharks; batoids are not derived from any living lineage of sharks) or were obvious (monophyly of mammals, gnathostomes, vertebrates, echinoderms, etc.). Despite all these findings, the rRNA data still fail to resolve the relations among the major groups of deuterostomes (tunicates, Ambulacraria, cephalochordates and vertebrates) and of gnathostomes (chondrichthyans, lungfishes, coelacanth, actinopterygians, amphibians, and amniotes), partly because tunicates and lungfishes are rogue taxa that disrupt the tree. Nonetheless, parametric bootstrapping showed our RNA-gene data are only consistent with these dominant hypotheses: (1) deuterostomes consist of Ambulacraria plus Chordata, with Chordata consisting of tunicates and 'vertebrates plus cephalochordates'; and (2) lungfishes are the closest living relatives of tetrapods.     

Molecular phylogeny and divergence times of drosophilid species

The phylogenetic relationships and divergence times of 39 drosophilid species were studied by using the coding region of the Adh gene. Four genera--Scaptodrosophila, Zaprionus, Drosophila, and Scaptomyza (from Hawaii)--and three Drosophila subgenera--Drosophila, Engiscaptomyza, and Sophophora--were included. After conducting statistical analyses of the nucleotide sequences of the Adh, Adhr (Adh-related gene), and nuclear rRNA genes and a 905-bp segment of mitochondrial DNA, we used Scaptodrosophila as the outgroup. The phylogenetic tree obtained showed that the first major division of drosophilid species occurs between subgenus Sophophora (genus Drosophila) and the group including subgenera Drosophila and Engiscaptomyza plus the genera Zaprionus and Scaptomyza. Subgenus Sophophora is then divided into D. willistoni and the clade of D. obscura and D. melanogaster species groups. In the other major drosophilid group, Zaprionus first separates from the other species, and then D. immigrans leaves the remaining group of species. This remaining group then splits into the D. repleta group and the Hawaiian drosophilid cluster (Hawaiian Drosophila, Engiscaptomyza, and Scaptomyza). Engiscaptomyza and Scaptomyza are tightly clustered. Each of the D. repleta, D. obscura, and D. melanogaster groups is monophyletic. The splitting of subgenera Drosophila and Sophophora apparently occurred about 40 Mya, whereas the D. repleta group and the Hawaiian drosophilid cluster separated about 32 Mya. By contrast, the splitting of Engiscaptomyza and Scaptomyza occurred only about 11 Mya, suggesting that Scaptomyza experienced a rapid morphological evolution. The D. obscura and D. melanogaster groups apparently diverged about 25 Mya. Many of the D. repleta group species studied here have two functional Adh genes (Adh-1 and Adh-2), and these duplicated genes can be explained by two duplication events.      

First Miocene fossils of Vivianiaceae shed new light on phylogeny,divergence times,and historical biogeography of Geraniales

The origin of Geraniales (approximately 900 species in three families: Geraniaceae, Melianthaceae, and Vivianiaceae) is traced back to the Cretaceous of Gondwana, yet their geotemporal history is largely unknown because of a limited fossil record and incomplete phylogenies. In the present study, we provide the first fossil record of Vivianiaceae and a highly resolved molecular phylogeny for all extant Geraniales genera. Our results support the hypothesis that five (instead of three) families should be recognized in the order Geraniales: Francoaceae A. Juss. (Francoa, Greyia, Tetilla), Geraniaceae Juss. (Erodium, Geranium, Monsonia, Pelargonium), Hypseocharitaceae Wedd. (monogeneric), Melianthaceae Horan. (Bersama, Melianthus), and Vivianiaceae Klotzsch (Balbisia, Rhynchotheca, Viviania). The four major lineages (i.e. Geraniaceae, Francoaceae + Melianthaceae, Hypseocharitaceae, Vivianiaceae) all originated within a narrow time frame during the Eocene (36.9–49.9 Mya) based on the five fossil calibration points. The divergence of most of the extant genera occurred much later, from the Miocene onwards. The South American–South African disjunction in Francoaceae apparently goes back to long distance dispersal with an estimated divergence time of the lineages in the Middle Miocene [11.2 (5.9–17.7) Mya]. Diversification in Melianthus appears to be much more recent than previously assumed [starting approximately 3.4 (1.9–5.2) Mya rather than approximately 8–20 Mya]. However, divergence of the Andean Hypseocharis lineage [36.9 (31.9–42.8) Mya] significantly predates the main Andean uplift: Current distributions likely go back to northward migrations and subsequent extinctions in Patagonia. Similarly, Rhynchotheca, Balbisia, and Viviania have a current southern distribution limit > 10°N of the fossil finds, indicating a massive northward displacement. The present evidence suggests that niche conservatism likely played a major role in the historical biogeography of Geraniales. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ?? , ??–??.     

Primate phylogeny, evolutionary rate variations, and divergence times: a contribution from the nuclear gene IRBP

The first third (ca. 1200 bp) of exon 1 of the nuclear gene encoding the interstitial retinoid-binding protein (IRBP) has been sequenced for 12 representative primates belonging to Lemuriformes, Lorisiformes, Tarsiiformes, Platyrrhini, and Catarrhini, and combined with available data (13 other primates, 11 nonprimate placentals, and 2 marsupials). Phylogenetic analyses using maximum likelihood on nucleotides and amino acids robustly support the monophyly of primates, Strepsirrhini, Lemuriformes, Lorisiformes, Anthropoidea, Catarrhini, and Platyrrhini. It is interesting to note that 1) Tarsiidae grouped with Anthropoidea, and the support for this node depends on the molecular characters considered; 2) Cheirogaleidae grouped within Lemuriformes; and 3) Daubentonia was the sister group of all other Lemuriformes. Study of the IRBP evolutionary rate shows a high heterogeneity within placentals and also within primates. Maximum likelihood local molecular clocks were assigned to three clades displaying significantly contrasted evolutionary rates. Paenungulata were shown to evolve 2.5-3 times faster than Perissodactyla and Lemuriformes. Six independent calibration points were used to estimate splitting ages of the main primate clades, and their compatibility was evaluated. Divergence ages were obtained for the following crown groups: 13.8-14.2 MY for Lorisiformes, 26.5-27.2 MY for Lemuroidea, 39.6-40.7 MY for Lemuriformes, 45.4-46.7 MY for Strepsirrhini, and 56.7-58.4 MY for Haplorrhini. The incompatibility between some paleontological and molecular estimates may reflect the incompleteness of the placental fossil record, and/or indicate that the variable IRBP evolutionary rates are not fully accommodated by local molecular clocks.     

Molecular phylogeny and divergence times of Hormaphidinae (Hemiptera: Aphididae) indicate Late Cretaceous tribal diversification

The aphid subfamily Hormaphidinae is a good candidate for the study of the evolution of insect – plant relationships. Most hormaphidine species depend on woody primary host plants and woody or herbaceous secondary host plants, and represent high host specificity, especially to their primary hosts. No detailed molecular phylogeny of Hormaphidinae has been reported, and the taxonomic positions of some taxa in this group remain unclear. To reconstruct major phylogenetic relationships and to understand the evolution of host association patterns for major lineages, we present the first detailed molecular phylogeny of Hormaphidinae, as inferred from nuclear and mitochondrial DNA sequences, using maximum parsimony, maximum likelihood, and Bayesian methods. The monophyly of Hormaphidinae and its three traditional tribes was supported, and a sister relationship between Hormaphidini and Nipponaphidini was suggested. Most inner relationships within tribes were also supported, and some novel relationships were revealed. Two subtribes of Cerataphidini are proposed. Divergence times estimated using a Bayesian approach indicate that tribal diversifications occurred during the Late Cretaceous and were coincident with the appearance of their primary host plants. The current pattern of secondary host association for the three tribes may have evolved in different time ranges. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 165 , 73–87.     

The colonization of land by animals: molecular phylogeny and divergence times among arthropods

Background  

The earliest fossil evidence of terrestrial animal activity is from the Ordovician, ~450 million years ago (Ma). However, there are earlier animal fossils, and most molecular clocks suggest a deep origin of animal phyla in the Precambrian, leaving open the possibility that animals colonized land much earlier than the Ordovician. To further investigate the time of colonization of land by animals, we sequenced two nuclear genes, glyceraldehyde-3-phosphate dehydrogenase and enolase, in representative arthropods and conducted phylogenetic and molecular clock analyses of those and other available DNA and protein sequence data. To assess the robustness of animal molecular clocks, we estimated the deuterostome-arthropod divergence using the arthropod fossil record for calibration and tunicate instead of vertebrate sequences to represent Deuterostomia. Nine nuclear and 15 mitochondrial genes were used in phylogenetic analyses and 61 genes were used in molecular clock analyses.     

Testing the molecular clock: molecular and paleontological estimates of divergence times in the Echinoidea (Echinodermata)

The phylogenetic relationships of 46 echinoids, with representatives from 13 of the 14 ordinal-level clades and about 70% of extant families commonly recognized, have been established from 3 genes (3,226 alignable bases) and 119 morphological characters. Morphological and molecular estimates are similar enough to be considered suboptimal estimates of one another, and the combined data provide a tree that, when calibrated against the fossil record, provides paleontological estimates of divergence times and completeness of their fossil record. The order of branching on the cladogram largely agrees with the stratigraphic order of first occurrences and implies that their fossil record is more than 85% complete at family level and at a resolution of 5-Myr time intervals. Molecular estimates of divergence times derived from applying both molecular clock and relaxed molecular clock models are concordant with estimates based on the fossil record in up to 70% of cases, with most concordant results obtained using Sanderson's semiparametric penalized likelihood method and a logarithmic-penalty function. There are 3 regions of the tree where molecular and fossil estimates of divergence time consistently disagree. Comparison with results obtained when molecular divergence dates are estimated from the combined (morphology + gene) tree suggests that errors in phylogenetic reconstruction explain only one of these. In another region the error most likely lies with the paleontological estimates because taxa in this region are demonstrated to have a very poor fossil record. In the third case, morphological and paleontological evidence is much stronger, and the topology for this part of the molecular tree differs from that derived from the combined data. Here the cause of the mismatch is unclear but could be methodological, arising from marked inequality of molecular rates. Overall, the level of agreement reached between these different data and methodological approaches leads us to believe that careful application of likelihood and Bayesian methods to molecular data provides realistic divergence time estimates in the majority of cases (almost 80% in this specific example), thus providing a remarkably well-calibrated phylogeny of a character-rich clade of ubiquitous marine benthic invertebrates.     

Model-based multi-locus estimation of decapod phylogeny and divergence times

Phylogenetic relationships among all of the major decapod infraorders have never been estimated using molecular data, while morphological studies produce conflicting results. In the present study, the phylogenetic relationships among the decapod basal suborder Dendrobranchiata and all of the currently recognized decapod infraorders within the suborder Pleocyemata (Caridea, Stenopodidea, Achelata, Astacidea, Thalassinidea, Anomala, and Brachyura) were inferred using 16S mtDNA, 18S and 28S rRNA, and the histone H3 gene. Phylogenies were reconstructed using the model-based methods of maximum likelihood and Bayesian methods coupled with Markov Chain Monte Carlo inference. The phylogenies revealed that the seven infraorders are monophyletic, with high clade support values (bp>70; pP>0.95) under both methods. The two suborders also were recovered as monophyletic, but with weaker support (bp=70; pP=0.74). Although the nodal support values for infraordinal relationships were low (bp<50; pP<0.77) the Anomala and Brachyura were basal to the rest of the 'Reptantia' in both reconstructions and using Bayesian tree topology tests alternate morphology-based hypotheses were rejected (P<0.01). Newly developed multi-locus Bayesian and likelihood heuristic rate-smoothing methods to estimate divergence times were compared using eight fossil and geological calibrations. Estimated times revealed that the Decapoda originated earlier than 437MYA and that the radiation within the group occurred rapidly, with all of the major lineages present by 325MYA. Node time estimation under both approaches is severely affected by the number and phylogenetic distribution of the fossil calibrations chosen. For analyses incorporating fossils as fixed ages, more consistent results were obtained by using both shallow and deep or clade-related calibration points. Divergence time estimation using fossils as lower and upper limits performed well with as few as one upper limit and a single deep fossil lower limit calibration.     

Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds

We implement a Bayesian Markov chain Monte Carlo algorithm for estimating species divergence times that uses heterogeneous data from multiple gene loci and accommodates multiple fossil calibration nodes. A birth-death process with species sampling is used to specify a prior for divergence times, which allows easy assessment of the effects of that prior on posterior time estimates. We propose a new approach for specifying calibration points on the phylogeny, which allows the use of arbitrary and flexible statistical distributions to describe uncertainties in fossil dates. In particular, we use soft bounds, so that the probability that the true divergence time is outside the bounds is small but nonzero. A strict molecular clock is assumed in the current implementation, although this assumption may be relaxed. We apply our new algorithm to two data sets concerning divergences of several primate species, to examine the effects of the substitution model and of the prior for divergence times on Bayesian time estimation. We also conduct computer simulation to examine the differences between soft and hard bounds. We demonstrate that divergence time estimation is intrinsically hampered by uncertainties in fossil calibrations, and the error in Bayesian time estimates will not go to zero with increased amounts of sequence data. Our analyses of both real and simulated data demonstrate potentially large differences between divergence time estimates obtained using soft versus hard bounds and a general superiority of soft bounds. Our main findings are as follows. (1) When the fossils are consistent with each other and with the molecular data, and the posterior time estimates are well within the prior bounds, soft and hard bounds produce similar results. (2) When the fossils are in conflict with each other or with the molecules, soft and hard bounds behave very differently; soft bounds allow sequence data to correct poor calibrations, while poor hard bounds are impossible to overcome by any amount of data. (3) Soft bounds eliminate the need for "safe" but unrealistically high upper bounds, which may bias posterior time estimates. (4) Soft bounds allow more reliable assessment of estimation errors, while hard bounds generate misleadingly high precisions when fossils and molecules are in conflict.     

Phylogenetic relationships and divergence times of Charadriiformes genera: multigene evidence for the Cretaceous origin of at least 14 clades of shorebirds

Comparative study of character evolution in the shorebirds is presently limited because the phylogenetic placement of some enigmatic genera remains unclear. We therefore used Bayesian methods to obtain a well-supported phylogeny of 90 recognized genera using 5 kb of mitochondrial and nuclear sequences. The tree comprised three major clades: Lari (gulls, auks and allies plus buttonquails) as sister to Scolopaci (sandpipers, jacanas and allies), and in turn sister to Charadrii (plovers, oystercatchers and allies), as in previous molecular studies. Plovers and noddies were not recovered as monophyletic assemblages, and the Egyptian plover Pluvianus is apparently not a plover. Molecular dating using multiple fossil constraints suggests that the three suborders originated in the late Cretaceous between 79 and 102 Mya, and at least 14 lineages of modern shorebirds survived the mass extinction at the K/T boundary. Previous difficulties in determining the phylogenetic relationships of enigmatic taxa reflect the fact that they are well-differentiated relicts of old, genus-poor lineages. We refrain from suggesting systematic revisions for shorebirds at this time because gene trees may fail to recover the species tree when long branches are connected to deep, shorter branches, as is the case for some of the enigmatic taxa.     

Molecular phylogeny and radiation time of Erysiphales inferred from the nuclear ribosomal DNA sequences

Phylogenetic relationships of Erysiphales within Ascomycota were inferred from the newly determined sequences of the 18S rDNA and partial sequences of the 28S rDNA including the D1 and D2 regions of 10 Erysiphales taxa. Phylogenetic analyses revealed that the Erysiphales form a distinct clade among ascomycetous fungi suggesting that the Erysiphales diverged from a single ancestral taxon. The Myxotrichaceae of the Onygenales was distantly related to the other onygenalean families and was the sister group to the Erysiphales calde, with which it combined to form a clade. The Erysiphales/Myxotrichaceae clade was also closely related to some discomycetous fungi (Leotiales, Cyttariales and Thelebolaceae) including taxa that form cleistothecial ascomata. The present molecular analyses as well as previously reported morphological observations suggest the possible existence of a novel evolutionary pathway from cleistothecial discomycetous fungi to Erysiphales and Myxotrichaceae. However, since most of these fungi, except for the Erysiphales, are saprophytic on dung and/or plant materials, the questions of how and why an obligate biotroph like the Erysiphales radiated from the saprophytic fungi remain to be addressed. We also estimated the radiation time of the Erysiphales using the 18S rDNA sequences and the two molecular clockes that have been previously reported. The calculation showed that the Erysiphales split from the Myxotrichaceae 190–127 myr ago. Since the radiation time of the Erysiphales does not exceed 230 myr ago, even when allowance is made for the uncertainty of the molecular clocks, it is possible to consider that the Erysiphales evolved after the radiation of angiosperms. The results of our calculation also showed that the first radiation within the Erysiphales (138–92 myr ago) coincided with the date of a major diversification of angiosperms (130–90 myr ago). These results may support our early assumption that the radiation of the Erysiphales coincided with the evolution of angiosperm plants. Contribution No. 152 from the Laboratory of Plant Pathology, Mie University     

Joint reconstruction of divergence times and life-history evolution in placental mammals using a phylogenetic covariance model

Violation of the molecular clock has been amply documented, and is now routinely taken into account by molecular dating methods. Comparative analyses have revealed a systematic component in rate variation, relating it to the evolution of life-history traits, such as body size or generation time. Life-history evolution can be reconstructed using Brownian models. However, the resulting estimates are typically uncertain, and potentially sensitive to the underlying assumptions. As a way of obtaining more accurate ancestral trait and divergence time reconstructions, correlations between life-history traits and substitution rates could be used as an additional source of information. In this direction, a Bayesian framework for jointly reconstructing rates, traits, and dates was previously introduced. Here, we apply this model to a 17 protein-coding gene alignment for 73 placental taxa. Our analysis indicates that the coupling between molecules and life history can lead to a reevaluation of ancestral life-history profiles, in particular for groups displaying convergent evolution in body size. However, reconstructions are sensitive to fossil calibrations and to the Brownian assumption. Altogether, our analysis suggests that further integrating inference of rates and traits might be particularly useful for neontological macroevolutionary comparative studies.     

Co-estimation of phylogeny and divergence times of Argonautoidea using relaxed phylogenetics

This is the first study to investigate molecular phylogenetic relationships among all four genera of the superfamily Argonautoidea, a clade of diverse pelagic cephalopods with extraordinary characters such as ovoviviparity, dwarf males and secondary “shell” development. Phylogenetic relationships and divergence times within the superfamily were co-estimated using relaxed phylogenetic techniques. A sister-taxon relationship was recovered between Argonauta and Ocythoe and between Tremoctopus and Haliphron. The most recent common ancestor of Argonautoidea was estimated to date from the early Tertiary under the scenario that a lack of a “shell” in the ocythoid lineage is a primary characteristic. In contrast, a later Tertiary most recent common ancestor was estimated under the scenario that a “shell” was present in the early ocythoid lineage and was subsequently lost.     

Molecular phylogeny and phylogeography of the Greek populations of the genus Orthometopon (Isopoda, Oniscidea) based on mitochondrial DNA sequences

We infer phylogenetic relationships among isopod species of the genus Orthometopon distributed in the Greek area, comparing partial mitochondrial DNA sequences for cytochrome oxidase I (COI). All phylogenetic analyses produced topologically identical trees that revealed a well-resolved phylogeny. These trees support the monophyly of the genus Orthometopon , and suggest two clades that correspond to separate geographical regions (west and east of the mid-Aegean trench). However, the phylogenetic relationships among Greek populations of Orthometopon spp. are different from the presumed pattern on the basis of morphological evidence. The distinct geographical distribution of the major clades of the phylogenetic tree and its topology suggest a spatial and temporal sequence of phylogenetic separations, which coincide with some major palaeogeographical separations during the geological history of the Aegean Sea. The results stress the need for a reconsideration of the evolutionary history of Orthometopon species, which will help overcome difficulties encountered in classical taxonomy at the species level. © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society , 2008, 152 , 707–715.     

Molecular phylogeny and divergence times of Malagasy tenrecs: Influence of data partitioning and taxon sampling on dating analyses

Background  

Malagasy tenrecs belong to the Afrotherian clade of placental mammals and comprise three subfamilies divided in eight genera (Tenrecinae: Tenrec, Echinops, Setifer and Hemicentetes; Oryzorictinae: Oryzorictes, Limnogale and Microgale; Geogalinae: Geogale). The diversity of their morphology and incomplete taxon sampling made it difficult until now to resolve phylogenies based on either morphology or molecular data for this group. Therefore, in order to delineate the evolutionary history of this family, phylogenetic and dating analyses were performed on a four nuclear genes dataset (ADRA2B, AR, GHR and vWF) including all Malagasy tenrec genera. Moreover, the influence of both taxon sampling and data partitioning on the accuracy of the estimated ages were assessed.     

Estimating the phylogeny and divergence times of primates using a supermatrix approach

Background  

The primates are among the most broadly studied mammalian orders, with the published literature containing extensive analyses of their behavior, physiology, genetics and ecology. The importance of this group in medical and biological research is well appreciated, and explains the numerous molecular phylogenies that have been proposed for most primate families and genera. Composite estimates for the entire order have been infrequently attempted, with the last phylogenetic reconstruction spanning the full range of primate evolutionary relationships having been conducted over a decade ago.     

Molecular phylogeny of the tribe Bovini (Mammalia: Artiodactyla): alternative placement of the Anoa

Noncoding regions from the genes encoding aromatase cytochrome P450 and lactoferrin have been sequenced in ten bovine and one cervid species for an investigation of the evolutionary relationships within the tribe Bovini. The evolutionary rate of DNA-nucleotide alterations along the ancestral bovine lineage amounts to 0.38% per million years, as estimated from this combined 0.478-kb-single copy nuclear (scn) DNA sequence data set. Whereas rate homogenity is apparent within the Bovini, the relative rate test suggests that the boselaphine lineage (as represented by Boselaphus) has evolved at only about one third of the rate found within the Bovini. Consistent with other results, the scnDNA data provide evidence for (i) a monophyletic origin of the Bovini, (ii) a sister group position of the Boselaphini, and (iii) two different clades within the Bovini, the buffaloes (Bubalus and Syncerus) and the cattle (Bos/Bibos and Bison). Surprisingly, the results indicate very clearly that the enigmatic dwarf buffalo of Sulawesi Island (Anoa depressicornis) is most closely related to Boselaphus and that the divergence from the true Bovini occurred close to the base of bovine cladogenesis in the Middle Miocene (≈ 14—12 million years ago).     

Molecular phylogeny and timing of radiation in Lessonia (Phaeophyceae,Laminariales)

The genus Lessonia Bory de Saint‐Vincent is distributed solely in the Southern Hemisphere, with four species found in South America and five in Australasia. Our goal was to determine the evolutionary relationships between the Lessonia species of the two disjunct areas and hypothesize dispersal patterns and timing of radiation. We combined mitochondria, plastid and nuclear markers in a comprehensive dataset from multiple individuals per known species. Furthermore, for some species we added samples from multiple populations to take account of their widespread distribution over known bioregions. In all analyses the Australasian Lessonia formed a monophyletic group and in most analyses the South American species form a paraphyletic grade. Delimitations of the accepted species are highly supported except for L. variegata J. Agardh and L. nigrescens Bory de Saint‐Vincent. We showed for the first time four lineages for the New Zealand endemic Lessonia variegata with an unexpected high level of genetic differentiation. Our analysis cannot resolve whether the dispersal of the common ancestor of this genus was from the Americas to Australasia or vice versa. Molecular clock analysis suggested that a sudden radiation took place in Australasia c. 3.5 Mya when almost all Australasian species diverged within a time frame of only 35 000 years.     

Molecular dating of phylogenetic trees: A brief review of current methods that estimate divergence times

This article reviews the most common methods used today for estimating divergence times and rates of molecular evolution. The methods are grouped into three main classes: (1) methods that use a molecular clock and one global rate of substitution, (2) methods that correct for rate heterogeneity, and (3) methods that try to incorporate rate heterogeneity. Additionally, links to the most important literature on molecular dating are given, including articles comparing the performance of different methods, papers that investigate problems related to taxon, gene and partition sampling, and literature discussing highly debated issues like calibration strategies and uncertainties, dating precision and the calculation of error estimates.     

Approximate likelihood calculation on a phylogeny for Bayesian estimation of divergence times

The molecular clock provides a powerful way to estimate species divergence times. If information on some species divergence times is available from the fossil or geological record, it can be used to calibrate a phylogeny and estimate divergence times for all nodes in the tree. The Bayesian method provides a natural framework to incorporate different sources of information concerning divergence times, such as information in the fossil and molecular data. Current models of sequence evolution are intractable in a Bayesian setting, and Markov chain Monte Carlo (MCMC) is used to generate the posterior distribution of divergence times and evolutionary rates. This method is computationally expensive, as it involves the repeated calculation of the likelihood function. Here, we explore the use of Taylor expansion to approximate the likelihood during MCMC iteration. The approximation is much faster than conventional likelihood calculation. However, the approximation is expected to be poor when the proposed parameters are far from the likelihood peak. We explore the use of parameter transforms (square root, logarithm, and arcsine) to improve the approximation to the likelihood curve. We found that the new methods, particularly the arcsine-based transform, provided very good approximations under relaxed clock models and also under the global clock model when the global clock is not seriously violated. The approximation is poorer for analysis under the global clock when the global clock is seriously wrong and should thus not be used. The results suggest that the approximate method may be useful for Bayesian dating analysis using large data sets.