Phylogeography of hepatitis B: The role of Portugal in the early dissemination of HBV worldwide

In Portugal, the genetic diversity, origin of HBV, and the Portuguese role in the dissemination of HBV worldwide were never investigated. In this work, we studied the epidemic history and transmission dynamics of HBV genotypes that are endemic in Portugal. HBV pol gene was sequenced from 130 patients followed in Lisbon. HBV genotype A (HBV/A) was the most prevalent (n=54, 41.5%), followed by D [HBV/D; (n=44, 33.8%)], and E [HBV/E; (n=32, 24.6%)]. Spatio-temporal evolutionary dynamics was reconstructed in BEAST using a Bayesian Markov Chain Monte Carlo method, with a GTR nucleotide substitution model, an uncorrelated lognormal relaxed molecular clock model, a Bayesian skyline plot, and a continuous diffusion model. HBV/D4 was the first subgenotype to be introduced in Portugal around 1857 (HPD 95% 1699-1931) followed by HBV/D3 and A2 a few decades later. HBV/E and HBV/A1 were introduced in Portugal later, almost simultaneously. Our results also indicate a very important role of Portugal in the exportation of HBV/D4 and A2 to Brazil and Cape Verde, respectively, at the beginning of the XX century. This work clarifies the epidemiological history of HBV in Portugal and shows that Portugal had an important role in the global spread of this virus.

Lack of Fe(II) transporters in basal Cyanobacteria complicates iron uptake in ferruginous Archean oceans.

Cyanobacteria oxygenated Earth's atmosphere during the Great Oxygenation Event (GOE) through oxygenic photosynthesis. Their high iron requirement was presumed met by high levels of Fe(II) in the anoxic Archean ocean. Here we show that most basal Cyanobacteria cannot synthesize the primary Fe(II) transporter, FeoB. Relaxed molecular clock analyses estimate the arrival of FeoB, as well as the Fe(III) transporters, cFTR1 and FutB, in the Cyanobacteria after the GOE. Furthermore Pseudanabaena sp. PCC7367, a basal marine, benthic strain grown under simulated Archean conditions, constitutively expressed cftr1, even after the addition of Fe(II). By utilizing gene expression studies under a simulated Archean atmosphere, as well as comparative genomics, phylogenetics and molecular clock analyses, this study identified a need to reappraise iron uptake in ancestral Cyanobacteria, as genetic profiling suggests that scavenging of siderophore bound Fe(III), rather than Fe(II), appears to have been the means of iron acquisition prior to the GOE.

Characterization of four mitochondrial genomes of family Neritidae (Gastropoda: Neritimorpha) and insight into its phylogenetic relationships

Neritidae is one of the most diverse families of Neritimorpha and possesses euryhaline properties. Members of this family usually live on tropical and subtropical coasts and are mainly gregarious. The phylogenetic relationships between several subclasses of Gastropoda have been controversial for many years. With an increase in the number of described species of Neritidae, the knowledge of the evolutionary relationships in this family has improved. In the present study, we sequenced four complete mitochondrial genomes from two genera (Clithon and Nerita) and compared them with available complete mitochondrial genomes of Neritidae. Gene order exhibited a highly conserved pattern among three genera in the Neritidae family. Our results improved the phylogenetic resolution within Neritidae, and more comprehensive taxonomic sampling of subclass Neritimorpha was proposed. Furthermore, we reconstructed the divergence among the main lineages of 19 Neritimorpha taxa under an uncorrelated relaxed molecular clock.

Inferring Evolutionary Timescales without Independent Timing Information: An Assessment of “Universal” Insect Rates to Calibrate a Collembola (Hexapoda) Molecular Clock

Previous estimates of nucleotide substitution rates are routinely applied as secondary or “universal” molecular clock calibrations for estimating evolutionary timescales in groups that lack independent timing information. A major limitation of this approach is that rates can vary considerably among taxonomic groups, but the assumption of rate constancy is rarely evaluated prior to using secondary rate calibrations. Here I evaluate whether an insect mitochondrial DNA clock is appropriate for estimating timescales in Collembola—a group of insect-like arthropods characterized by high levels of cryptic diversity. Relative rates of substitution in cytochrome oxidase subunit 1 (COI) were inferred via Bayesian analysis across a topologically constrained Hexapod phylogeny using a relaxed molecular clock model. Rates for Collembola did not differ significantly from the average rate or from the rates estimated for most other groups (25 of 30), suggesting that (1) their apparent cryptic diversity cannot be explained by accelerated rates of molecular evolution and (2) clocks calibrated using “universal” insect rates may be appropriate for estimating evolutionary timescales in this group. However, of the 31 groups investigated, 10 had rates that deviated significantly from the average (6 higher, 4 lower), underscoring the need for caution and careful consideration when applying secondary insect rate calibrations. Lastly, this study exemplifies a relatively simple approach for evaluating rate constancy within a taxonomic group to determine whether the use of secondary rates are appropriate for molecular clock calibrations.

Nucleotide substitutions during speciation may explain substitution rate variation

ABSTRACTAlthough molecular mechanisms associated with the generation of mutations are highly conserved across taxa, there is widespread variation in mutation rates between evolutionary lineages. When phylogenies are reconstructed based on nucleotide sequences, such variation is typically accounted for by the assumption of a relaxed molecular clock, which, however, is just a statistical distribution of mutation rates without any underlying biological mechanism. Here, we propose that variation in accumulated mutations may be partly explained by an elevated mutation rate during speciation. Using simulations, we show how shifting mutations from branches to speciation events impacts inference of branching times in phylogenetic reconstruction. Furthermore, the resulting nucleotide alignments are better described by a relaxed than by a strict molecular clock. Thus, elevated mutation rates during speciation potentially explain part of the variation in substitution rates that is observed across the tree of life.

Phylogenetic placement and the timing of diversification in Australia’s endemic Vachellia (Caesalpinioideae, Mimosoid Clade, Fabaceae) species

The genus Vachellia Wight & Arn. has a pantropical distribution, with species being distributed through Africa, the Americas, Asia and Australia. The relationships among the lineages from Africa and America are well understood, but the phylogenetic placement and evolutionary origins of the Australian species of Vachellia are not known. We, therefore, sequenced four plastid genes from representatives of each of the nine Australian species of Vachellia, and used Bayesian inference to assess the phylogenetic placement of these lineages, and a relaxed molecular clock to assess the timing of diversification. The Australian species of Vachellia form a well-supported monophyletic clade, with molecular-dating analysis suggesting a single dispersal into Australia 6.5 million years ago (95% range 13.9–2.7 million years ago). Diversification of the Australian clade commenced more recently, c. 3.1 million years ago (95% range 9.2–1.2 million years ago), perhaps driven by the increased aridification of Australia at this time. The closest relatives to the Australian Vachellia were not from the Malesian bioregion, suggesting either a long-distance dispersal from Africa, or two separate migrations through Asia. These results not only improve our understanding of the biogeography of Vachellia species, but also have significant implications for the biological control of invasive Vachellia species in Australia.

Australasian orchid diversification in time and space: molecular phylogenetic insights from the beard orchids (Calochilus, Diurideae)

Phylogenetic relationships in Calochilus (~30 species) were inferred based on a supermatrix of 81 loci including 22 species. To examine the spatio-temporal evolution of Calochilus, divergence-time estimations were conducted within a Bayesian framework using an uncorrelated relaxed molecular-clock model, followed by maximum-likelihood ancestral-range reconstructions comparing four biogeographic models. To trace the evolution of key floral and vegetative characters, maximum-likelihood ancestral-character reconstructions were carried out. The stem age of Calochilus was dated to ~12.0 million years ago in the mid-Miocene. Divergence of Calochilus into a tropical and a temperate clade was inferred to have occurred ~7.6 million years ago in the late Miocene. Northern Australia was reconstructed as the ancestral area of the tropical clade and the Euronotian region for the temperate clade. Range expansions from Australia to other Australasian regions, such as New Zealand and New Guinea, were inferred to have occurred only in recent geological times, commencing in the Pleistocene. The infrageneric classification for Calochilus was revised, erecting two subgenera, subgenus Calochilus and subgenus Tropichilus subgen. nov. Section Calochilus Szlach. was recircumscribed, and sect. Abrochilus sect. nov., and section Placochilus sect. nov. were erected. Identification keys to subgenera and sections and a taxonomic synopsis of the genus are provided.

Are diversification rates and chromosome evolution in the temperate grasses (Pooideae) associated with major environmental changes in the Oligocene-Miocene?

The Pooideae are a highly diverse C3 grass subfamily that includes some of the most economically important crops, nested within the highly speciose core-pooid clade. Here, we build and explore the phylogeny of the Pooideae within a temporal framework, assessing its patterns of diversification and its chromosomal evolutionary changes in the light of past environmental transformations. We sequenced five plastid DNA loci, two coding (ndhF,matk) and three non-coding (trnH-psbA,trnT-LandtrnL-F), in 163 Poaceae taxa, including representatives for all subfamilies of the grasses and all but four ingroup Pooideae tribes. Parsimony and Bayesian phylogenetic analyses were conducted and divergence times were inferred in BEAST using a relaxed molecular clock. Diversification rates were assessed using the MEDUSA approach, and chromosome evolution was analyzed using the chromEvol software. Diversification of the Pooideae started in the Late-Eocene and was especially intense during the Oligocene-Miocene. The background diversification rate increased significantly at the time of the origin of the Poodae + Triticodae clade. This shift in diversification occurred in a context of falling temperatures that potentially increased ecological opportunities for grasses adapted to open areas around the world. The base haploid chromosome numbern = 7 has remained stable throughout the phylogenetic history of the core pooids and we found no link between chromosome transitions and major diversification events in the Pooideae.

Estimation of phylogenetic divergence times in Panagrolaimidae and other nematodes using relaxed molecular clocks calibrated with insect and crustacean fossils

This study presents the use of relaxed molecular clock methods to infer the dates of divergence between Panagrolaimus species. Autocorrelated relaxed tree methods, combined with well characterised fossil calibration dates, yield estimates of nematode divergence dates in accordance with the palaeontological age of fossil ascarid eggs and with the previously estimated date of 18 Ma (range 11.6 to 29.9 Ma) for the divergence of the Caenorhabditis lineage. Our data indicate that Panagrolaimus davidi from Antarctica separated ca 21.98 Ma from its currently known, most closely related strain. Thus, P. davidi may have existed in Antarctica prior to the Last Glacial Maximum, although this seems unlikely as it shares physiological and life history traits with closely related nematodes from temperate climates. These traits may have facilitated colonisation of Antarctica by P. davidi after the quaternary glaciation, analogous to the colonisation of Surtsey Island, Iceland, by P. superbus after its volcanic formation. This study demonstrates that autocorrelated relaxed tree methods combined with well characterised fossil calibration dates may be used as a method to estimate the divergence dates within nematodes in order to gain insight into their evolutionary history.

Grouping substitution types into different relaxed molecular clocks

Different types of nucleotide substitutions experience different patterns of rate change over time. We propose clustering context-dependent (or context-independent) nucleotide substitution types according to how their rates change and then using the grouping for divergence time estimation. With our models, relative rates among types that are in the same group are fixed, whereas absolute rates of the types within a group change over time according to a shared relaxed molecular clock. We illustrate our procedure by analysing a 0.15 Mb intergenic region to infer divergence times relating eight primates. The different groupings of substitution types that we explore have little effect on the posterior means of divergence times, but the widths of the credibility intervals decrease as the number of groups increases. This article is part of the themed issue ‘Dating species divergences using rocks and clocks’.