Uncorrelated Lognormal Relaxed Clock Research Articles

Geographic range and habitat reconstructions shed light on palaeotropical intercontinental disjunction and regional diversification patterns in Artabotrys (Annonaceae)

AbstractAimThe biogeographical and habitat history of the species‐rich angiosperm genus Artabotrys is reconstructed to assess hypotheses relating to processes that underlie palaeotropical intercontinental disjunction (PID) and regional diversification patterns.LocationPalaeotropics.TaxonArtabotrys (Annonaceae).MethodsPhylogenetic relationships were estimated based on 53 Artabotrys species, using four chloroplast and 10 nuclear markers (c. 15.7 kb). Divergence times were estimated using two fossil calibrations and an uncorrelated lognormal relaxed clock model. Ancestral range estimation was performed under a dispersal–extinction–cladogenesis model while ancestral habitat reconstruction was conducted using the BAYAREALIKE model.ResultsArtabotrys is unequivocally monophyletic, with a species‐rich main Artabotrys clade (MAC) comprising distinct African and Asian sister clades, and an early divergent grade (EDG) comprising two African species. An ancestral range in Africa is inferred, with a single dispersal to Asia. The PID at the MAC crown occurred in the Miocene. A broad habitat tolerance spanning rain forests and seasonally dry forests/savannas was inferred at the MAC stem and crown nodes. Several shifts from rain forests to seasonally dry habitats were inferred, but there is no indication of a reverse transition.Main conclusionsThe most plausible explanation for the PID involves overland migration across Arabia in the Miocene, prior to subsequent climate deterioration. Long‐standing differences in climatic niche may have resulted in a significant yet porous biogeographical divide at the Isthmus of Kra, but Wallace's line does not reflect differences in climatic niches. Niche conservatism is an underlying pattern in Artabotrys, with local niche shifts occurring rather recently.

Data partitioning and correction for ascertainment bias reduce the uncertainty of placental mammal divergence times inferred from the morphological clock.

Bayesian estimates of divergence times based on the molecular clock yield uncertainty of parameter estimates measured by the width of posterior distributions of node ages. For the relaxed molecular clock, previous works have reported that some of the uncertainty inherent to the variation of rates among lineages may be reduced by partitioning data. Here we test this effect for the purely morphological clock, using placental mammals as a case study. We applied the uncorrelated lognormal relaxed clock to morphological data of 40 extant mammalian taxa and 4,533 characters, taken from the largest published matrix of discrete phenotypic characters. The morphologically derived timescale was compared to divergence times inferred from molecular and combined data. We show that partitioning data into anatomical units significantly reduced the uncertainty of divergence time estimates for morphological data. For the first time, we demonstrate that ascertainment bias has an impact on the precision of morphological clock estimates. While analyses including molecular data suggested most divergences between placental orders occurred near the K‐Pg boundary, the partitioned morphological clock recovered older interordinal splits and some younger intraordinal ones, including significantly later dates for the radiation of bats and rodents, which accord to the short‐fuse hypothesis.

Multiple shifts to open habitats in Melastomateae (Melastomataceae) congruent with the increase of African Neogene climatic aridity

AbstractAimAfrican Melastomateae (Melastomataceae) comprise c. 185 species occurring in closed or open habitats throughout sub‐Saharan Africa. We sought to reconstruct biogeographical and habitat history, and shifts in diversification rates of African Melastomateae using a well‐sampled, dated molecular phylogeny.LocationAmericas, sub‐Saharan Africa, Madagascar, SE Asia.TaxonAngiosperms, Melastomataceae, African Melastomateae.MethodsPhylogenetic relationships were estimated based on an extensive sampling of New and Old World Melastomateae, using two nuclear and three plastid markers. Divergence times were estimated in BEAST based on three calibration priors under Bayesian uncorrelated lognormal relaxed clock and birth–death speciation process. The dated phylogeny was used to infer the biogeographical history under a dispersal–extinction–cladogenesis model in “BioGeoBEARS”. The ancestral habitat of African Melastomateae was estimated using maximum likelihood and stochastic character mapping in “Phytools” and “ape” respectively. Finally, shifts in diversification rates were tested using BAMM.ResultsMelastomateae dispersed from South America to Africa during the Oligocene with subsequent dispersals to Madagascar and SE Asia during the Middle Miocene. Ancestral African Melastomateae were adapted to closed habitats with at least 12 shifts to open habitats occurring during the Middle Miocene or Pliocene. Speciation rates steadily increased since the Neogene, and none of the habitat shifts led to a significant increase in diversification rates.Main conclusionsLong‐distance dispersal from South America during the Early Miocene explains the origin of African Melastomateae. The inferred adaptation to open habitats from an ancestrally closed habitat is congruent with the Neogene increase of aridity across Africa. The adaptation to open habitats during the Neogene is an important driver of African plant diversity, but is not always followed by increased diversification rates.

A new Annonaceae genus, Wuodendron, provides support for a post–boreotropical origin of the Asian–Neotropical disjunction in the tribe Miliuseae

AbstractRecent molecular and morphological studies have clarified generic circumscriptions in Annonaceae tribe Miliuseae and resulted in the segregation of disparate elements from the previously highly polyphyletic genus Polyalthia s.l. Several names in Polyalthia nevertheless remain unresolved, awaiting assignment to specific genera, including Polyalthia litseifolia. Phylogenetic analyses of seven chloroplast regions (atpB–rbcL, matK, ndhF, psbA–trnH, rbcL, trnL–F, ycf1; ca. 8.3 kb, 116 accessions, including representatives of all currently accepted genera in subfamily Malmeoideae) unambiguously placed Polyalthia litseifolia in a clade with three accessions from Thailand, which have previously been shown to represent an undescribed genus sister to the Neotropical clade (Desmopsis, Sapranthus, Stenanona, Tridimeris) in the predominantly Asian tribe Miliuseae. The collective clade is sister to Meiogyne. Polyalthia litseifolia shares several diagnostic characters with most species in the Neotropical genera and Meiogyne, including: petals that are similar in shape and size in both whorls; multiple ovules per ovary in one or two rows; and lamelliform endosperm ruminations. It is distinct in being deciduous, bearing subpetiolar buds and having inflorescences growing from the leaf scar of the dropped leaves. Morphological comparisons and phylogenetic analyses corroborate its recognition as a new genus, which is formally described and illustrated here as Wuodendron. Polyalthia litseifolia is furthermore found to be conspecific with Desmos praecox, and the latter name is used as the basis for the name of the type. Molecular divergence time estimates under an uncorrelated lognormal relaxed clock place the Wuodendron–Neotropical clade split within the Miocene (ca. 14–12 Ma), highlighting the importance of post–boreotropical dispersal and vicariance in shaping intercontinental tropical disjunctions in Annonaceae.

Historical biogeography of Goniothalamus and Annonaceae tribe Annoneae: dispersal–vicariance patterns in tropical Asia and intercontinental tropical disjunctions revisited

AbstractAimThe historical biogeography of the species‐rich flowering plant genus Goniothalamus (c. 130 species) and the wider Annonaceae tribe Annoneae is investigated to evaluate hypotheses regarding the processes underlying tropical intercontinental disjunctions (‘long‐distance dispersal [LDD]’ versus ‘boreotropics’) and floristic exchange between biodiversity hotspots in tropical Asia.LocationTropics, tropical Asia.MethodsDivergence time estimation was based on plastid DNA sequence data (c. 10 kb; 164 Annonaceae accessions, including 65 Goniothalamus species) using an uncorrelated lognormal relaxed clock model and two fossil calibrations. Likelihood ancestral range estimation was performed using dispersal‐extinction‐cladogenesis models with and without time‐stratified dispersal constraints.ResultsThe boreotropics model incorporating high chances for intercontinental dispersal during 68–34 Ma fitted the data significantly better than LDD models enforcing low intercontinental dispersal rates. Multiple vicariance events were identified in Annoneae including at the Annoneae crown node (57–49 Ma, Africa/S+N America), and the Disepalum‐Asimina split (27–24 Ma, Asia/N America). A wide ancestral range in continental SE Asia, W and E Malesia was inferred at the Goniothalamus crown node (24–21 Ma). Several dispersal events from continental SE Asia/W Malesia were identified in the Miocene: two north‐eastwards to the Philippines, one eastwards to the Sahul Shelf and two westwards to India.Main conclusionsThe boreotropics hypothesis provides a well‐supported, plausible explanation for the disjunctions and dispersal–vicariance patterns in tribe Annoneae. The wide distribution inferred at the Goniothalamus crown node indicates that its ancestors already bridged the marine gap between the Sunda and Sahul Shelves by LDD or rafting on tectonic plate microfragments. Dispersal across long‐standing water bodies in Malesia occurred multiple times from the early Miocene as marine gaps decreased following tectonic plate convergence and land emergence. Substantially older crown group divergence estimates compared with previous studies indicate that hypotheses of rapid recent radiation in Goniothalamus must be rejected.

Fossil record of stem groups employed in evaluating the chronogram of insects (Arthropoda: Hexapoda).

Insecta s. str. (=Ectognatha), comprise the largest and most diversified group of living organisms, accounting for roughly half of the biodiversity on Earth. Understanding insect relationships and the specific time intervals for their episodes of radiation and extinction are critical to any comprehensive perspective on evolutionary events. Although some deeper nodes have been resolved congruently, the complete evolution of insects has remained obscure due to the lack of direct fossil evidence. Besides, various evolutionary phases of insects and the corresponding driving forces of diversification remain to be recognized. In this study, a comprehensive sample of all insect orders was used to reconstruct their phylogenetic relationships and estimate deep divergences. The phylogenetic relationships of insect orders were congruently recovered by Bayesian inference and maximum likelihood analyses. A complete timescale of divergences based on an uncorrelated log-normal relaxed clock model was established among all lineages of winged insects. The inferred timescale for various nodes are congruent with major historical events including the increase of atmospheric oxygen in the Late Silurian and earliest Devonian, the radiation of vascular plants in the Devonian, and with the available fossil record of the stem groups to various insect lineages in the Devonian and Carboniferous.

Estimating Divergence Times and Substitution Rates in Rhizobia.

Accurate estimation of divergence times of soil bacteria that form nitrogen-fixing associations with most leguminous plants is challenging because of a limited fossil record and complexities associated with molecular clocks and phylogenetic diversity of root nodule bacteria, collectively called rhizobia. To overcome the lack of fossil record in bacteria, divergence times of host legumes were used to calibrate molecular clocks and perform phylogenetic analyses in rhizobia. The 16S rRNA gene and intergenic spacer region remain among the favored molecular markers to reconstruct the timescale of rhizobia. We evaluate the performance of the random local clock model and the classical uncorrelated lognormal relaxed clock model, in combination with four tree models (coalescent constant size, birth–death, birth–death incomplete sampling, and Yule processes) on rhizobial divergence time estimates. Bayes factor tests based on the marginal likelihoods estimated from the stepping-stone sampling analyses strongly favored the random local clock model in combination with Yule process. Our results on the divergence time estimation from 16S rRNA gene and intergenic spacer region sequences are compatible with age estimates based on the conserved core genes but significantly older than those obtained from symbiotic genes, such as nodIJ genes. This difference may be due to the accelerated evolutionary rates of symbiotic genes compared to those of other genomic regions not directly implicated in nodulation processes.

Phylogenetic Analysis of HIV-1 CRF65_CPX Reveals Yunnan Province Is Still a Source Contributing to the Spread of HIV-1 in China

Phylogenetic Analysis of HIV-1 CRF65_CPX Reveals Yunnan Province Is Still a Source Contributing to the Spread of HIV-1 in China

Molecular phylogeny of the ‘Cape snow’ genus Syncarpha (Asteraceae: Gnaphalieae) reveals a need for generic re-delimitation

A phylogenetic hypothesis is presented for the charismatic but taxonomically poorly-known Cape daisy genus Syncarpha, based on near-complete ingroup sampling and good coverage of outgroup taxa. A combination of nuclear ribosomal and chloroplast spacer DNA sequence data gives a well-resolved phyogenetic hypothesis, the robustness of which is assessed via both parsimony bootstrap and Bayesian posterior probabilities based on the uncorrelated lognormal relaxed clock model. Syncarpha species fall into two well-supported and distantly-related clades that last shared a common ancestor in the mid-Miocene. The larger Syncarpha 1 grouping contains the type species and corresponds to African ‘Helipterum’; this clade is sister to Edmondia and belongs in a larger clade which also includes the Australian Gnaphalieae. The Syncarpha 2 clade contains the taxa associated with Syncarpha paniculata (formerly Helichrysum paniculatum) and is more closely related to Plecostachys and some species of Gnaphalium. Formal assessment of monophyly lays the groundwork for future revisionary taxonomic work.

Clock model makes a large difference to age estimates of long-stemmed clades with no internal calibration: a test using Australian grasstrees.

BackgroundEstimating divergence times in phylogenies using a molecular clock depends on accurate modeling of nucleotide substitution rates in DNA sequences. Rate heterogeneity among lineages is likely to affect estimates, especially in lineages with long stems and short crowns (“broom” clades) and no internal calibration. We evaluate the performance of the random local clocks model (RLC) and the more routinely employed uncorrelated lognormal relaxed clock model (UCLN) in situations in which a significant rate shift occurs on the stem branch of a broom clade. We compare the results of simulations to empirical results from analyses of a real rate-heterogeneous taxon – Australian grass trees (Xanthorrhoea) – whose substitution rate is slower than in its sister groups, as determined by relative rate tests.ResultsIn the simulated datasets, the RLC model performed much better than UCLN: RLC correctly estimated the age of the crown node of slow-rate broom clades, whereas UCLN estimates were consistently too young. Similarly, in the Xanthorrhoea dataset, UCLN returned significantly younger crown ages than RLC (mean estimates respectively 3–6 Ma versus 25–35 Ma). In both real and simulated datasets, Bayes Factor tests strongly favored the RLC model over the UCLN model.ConclusionsThe choice of an unsuitable molecular clock model can strongly bias divergence time estimates. In particular, for data predicted to have more rate variation among than within clades, dating with RLC is much more likely to be accurate than with UCLN. The choice of clocks should be informed by the biology of the study group (e.g., life-form) or assessed with relative rate tests and post-hoc model comparisons.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-014-0263-3) contains supplementary material, which is available to authorized users.

Origin and Outbreak of HIV-1 CRF55_01B Among MSM in Shenzhen, China

Origin and Outbreak of HIV-1 CRF55_01B Among MSM in Shenzhen, China

Rapid Expansion of a HIV-1 Subtype F Cluster of Recent Origin Among Men Who Have Sex With Men in Galicia, Spain

Rapid Expansion of a HIV-1 Subtype F Cluster of Recent Origin Among Men Who Have Sex With Men in Galicia, Spain

Cryptic variation in an ecological indicator organism: mitochondrial and nuclear DNA sequence data confirm distinct lineages of Baetis harrisoni Barnard (Ephemeroptera: Baetidae) in southern Africa.

BackgroundBaetis harrisoni Barnard is a mayfly frequently encountered in river studies across Africa, but the external morphological features used for identifying nymphs have been observed to vary subtly between different geographic locations. It has been associated with a wide range of ecological conditions, including pH extremes of pH 2.9–10.0 in polluted waters. We present a molecular study of the genetic variation within B. harrisoni across 21 rivers in its distribution range in southern Africa.ResultsFour gene regions were examined, two mitochondrial (cytochrome c oxidase subunit I [COI] and small subunit ribosomal 16S rDNA [16S]) and two nuclear (elongation factor 1 alpha [EF1α] and phosphoenolpyruvate carboxykinase [PEPCK]). Bayesian and parsimony approaches to phylogeny reconstruction resulted in five well-supported major lineages, which were confirmed using a general mixed Yule-coalescent (GMYC) model. Results from the EF1α gene were significantly incongruent with both mitochondrial and nuclear (PEPCK) results, possibly due to incomplete lineage sorting of the EF1α gene. Mean between-clade distance estimated using the COI and PEPCK data was found to be an order of magnitude greater than the within-clade distance and comparable to that previously reported for other recognised Baetis species. Analysis of the Isolation by Distance (IBD) between all samples showed a small but significant effect of IBD. Within each lineage the contribution of IBD was minimal. Tentative dating analyses using an uncorrelated log-normal relaxed clock and two published estimates of COI mutation rates suggest that diversification within the group occurred throughout the Pliocene and mid-Miocene (~2.4–11.5 mya).ConclusionsThe distinct lineages of B. harrisoni correspond to categorical environmental variation, with two lineages comprising samples from streams that flow through acidic Table Mountain Sandstone and three lineages with samples from neutral-to-alkaline streams found within eastern South Africa, Malawi and Zambia. The results of this study suggest that B. harrisoni as it is currently recognised is not a single species with a wide geographic range and pH-tolerance, but may comprise up to five species under the phylogenetic species concept, each with limited pH-tolerances, and that the B. harrisoni species group is thus in need of taxonomic review.