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Relaxing the molecular clock using models of how substitution rates change across lineages has become essential for addressing evolutionary problems. The diversity of rate evolution models and their implementations are substantial, and studies have demonstrated their impact on divergence time estimates can be as significant as that of calibration information. In this review, we trace the development of rate evolution models from the proposal of the molecular clock concept to the development of sophisticated Bayesian and non-Bayesian methods that handle rate variation in phylogenies. We discuss the various approaches to modeling rate evolution, provide a comprehensive list of available software, and examine the challenges and advancements of the prevalent Bayesian framework, contrasting them to faster non-Bayesian methods. Lastly, we offer insights into potential advancements in the field in the era of big data. [ABSTRACT FROM AUTHOR]

Besleria , a genus of perennial herbs, shrubs, or small trees growing in the understorey of rainforests, is one of the largest genera of neotropical Gesneriaceae, with over 165 species. Despite the ecological importance and ubiquity of Besleria in rainforest ecosystems, taxonomic and evolutionary studies of Besleria are limited. Here, we generated a phylogenetic analysis of Besleria using four nuclear and chloroplast DNA regions (ITS, mat K, rps 16, and trn L- trn F) covering more than 50% of the recognized species, along with two secondary calibration points to infer divergence times. Our results support the monophyly of Besleria and allowed us to revise the infrageneric classification and biogeographical history of the genus. We identified five major clades that do not correspond to sections or subsections in previous classifications. These clades are well circumscribed geographically but remain difficult to characterize using previously hypothesized morphological characters. Biogeographical reconstructions indicate an origin in the northern Andes during the Middle Miocene (ca. 15 Mya). The current distribution patterns of this plant group have been significantly shaped by geological and climatic events, particularly Andean uplift and the formation of the Panama Isthmus. [ABSTRACT FROM AUTHOR]

Estimating how traits evolved and impacted diversification across the tree of life represents a critical topic in ecology and evolution. Although there has been considerable research in comparative biology, large parts of the tree of life remain underexplored. Sharks are an iconic clade of marine vertebrates, and key components of marine ecosystems since the early Mesozoic. However, few studies have addressed how traits evolved or whether they impacted their extant diversity patterns. Our study aimed to fill this gap by reconstructing the largest time-calibrated species-level phylogeny of sharks and compiling an exhaustive database for ecological (diet, habitat) and biological (reproduction, maximum body length) traits. Using state-of-the-art models of evolution and diversification, we outlined the major character shifts and modes of trait evolution across shark species. We found support for sequential models of trait evolution and estimated a small to medium-sized lecithotrophic and coastal-dwelling most recent common ancestor for extant sharks. However, our exhaustive hidden traits analyses do not support trait-dependent diversification for any examined traits, challenging previous works. This suggests that the role of traits in shaping sharks' diversification dynamics might have been previously overestimated and should motivate future macroevolutionary studies to investigate other drivers of diversification in this clade. [ABSTRACT FROM AUTHOR]

Background and Aims The geographical origin and evolutionary mechanisms underpinning the rich and distinctive New Caledonian flora remain poorly understood. This is attributable to the complex geological past of the island and to the scarcity of well-resolved species-level phylogenies. Here, we infer phylogenetic relationships and divergence times of New Caledonian palms, which comprise 40 species. We use this framework to elucidate the biogeography of New Caledonian palm lineages and to explore how extant species might have formed. Methods A phylogenetic tree including 37 New Caledonian palm species and 77 relatives from tribe Areceae was inferred from 151 nuclear genes obtained by targeted sequencing. Fossil-calibrated divergence times were estimated and ancestral ranges inferred. Ancestral and extant ecological preferences in terms of elevation, precipitation and substrate were compared between New Caledonian sister species to explore their possible roles as drivers of speciation. Key Results New Caledonian palms form four well-supported clades, inside which relationships are well resolved. Our results support the current classification but suggest that Veillonia and Campecarpus should be resurrected and fail to clarify whether Rhopalostylidinae is sister to or nested in Basseliniinae. New Caledonian palm lineages are derived from New Guinean and Australian ancestors, which reached the island through at least three independent dispersal events between the Eocene and Miocene. Palms then dispersed out of New Caledonia at least five times, mainly towards Pacific islands. Geographical and ecological transitions associated with speciation events differed across time and genera. Substrate transitions were more frequently associated with older events than with younger ones. Conclusions Neighbouring areas and a mosaic of local habitats shaped the palm flora of New Caledonia, and the island played a significant role in generating palm diversity across the Pacific region. This new spatio-temporal framework will enable population-level ecological and genetic studies to unpick the mechanisms underpinning New Caledonian palm endemism. [ABSTRACT FROM AUTHOR]

Asymmetrical rates of cladogenesis and extinction abound in the tree of life, resulting in numerous minute clades that are dwarfed by larger sister groups. Such taxa are commonly regarded as phylogenetic relicts or "living fossils" when they exhibit an ancient first appearance in the fossil record and prolonged external morphological stasis, particularly in comparison to their more diversified sister groups. Due to their special status, various phylogenetic relicts tend to be well-studied and prioritized for conservation. A notable exception to this trend is found within Amblypygi ("whip spiders"), a visually striking order of functionally hexapodous arachnids that are notable for their antenniform first walking leg pair (the eponymous "whips"). Paleoamblypygi, the putative sister group to the remaining Amblypygi, is known from Late Carboniferous and Eocene deposits but is survived by a single living species, Paracharon caecus Hansen (1921) , that was last collected in 1899. Due to the absence of genomic sequence-grade tissue for this vital taxon, there is no global molecular phylogeny for Amblypygi to date, nor a fossil-calibrated estimation of divergences within the group. Here, we report a previously unknown species of Paleoamblypygi from a cave site in Colombia. Capitalizing upon this discovery, we generated the first molecular phylogeny of Amblypygi, integrating ultraconserved element sequencing with legacy Sanger datasets and including described extant genera. To quantify the impact of sampling Paleoamblypygi on divergence time estimation, we performed in silico experiments with pruning of Paracharon. We demonstrate that the omission of relicts has a significant impact on the accuracy of node dating approaches that outweighs the impact of excluding ingroup fossils, which bears upon the ancestral range reconstruction for the group. Our results underscore the imperative for biodiversity discovery efforts in elucidating the phylogenetic relationships of "dark taxa," and especially phylogenetic relicts in tropical and subtropical habitats. The lack of reciprocal monophyly for Charontidae and Charinidae leads us to subsume them into one family, Charontidae, new synonymy. [ABSTRACT FROM AUTHOR]

Rates of nucleotide substitution vary substantially across the Tree of Life, with potentially confounding effects on phylogenetic and evolutionary analyses. A large acceleration in mitochondrial substitution rate occurs in the cockroach family Nocticolidae, which predominantly inhabit subterranean environments. To evaluate the impacts of this among-lineage rate heterogeneity on estimates of phylogenetic relationships and evolutionary timescales, we analyzed nuclear ultraconserved elements (UCEs) and mitochondrial genomes from nocticolids and other cockroaches. Substitution rates were substantially elevated in nocticolid lineages compared with other cockroaches, especially in mitochondrial protein-coding genes. This disparity in evolutionary rates is likely to have led to different evolutionary relationships being supported by phylogenetic analyses of mitochondrial genomes and UCE loci. Furthermore, Bayesian dating analyses using relaxed-clock models inferred much deeper divergence times compared with a flexible local clock. Our phylogenetic analysis of UCEs, which is the first genome-scale study to include all 13 major cockroach families, unites Corydiidae and Nocticolidae and places Anaplectidae as the sister lineage to the rest of Blattoidea. We uncover an extraordinary level of genetic divergence in Nocticolidae, including two highly distinct clades that separated ~115 million years ago despite both containing representatives of the genus Nocticola. The results of our study highlight the potential impacts of high among-lineage rate variation on estimates of phylogenetic relationships and evolutionary timescales. [ABSTRACT FROM AUTHOR]

Human immunodeficiency virus 1 (HIV) proviruses archived in the persistent reservoir currently pose the greatest obstacle to HIV cure due to their evasion of combined antiretroviral therapy and ability to reseed HIV infection. Understanding the dynamics of the HIV persistent reservoir is imperative for discovering a durable HIV cure. Here, we explore Bayesian methods using the software BEAST2 to estimate HIV proviral integration dates. We started with within-host longitudinal HIV sequences collected prior to therapy, along with sequences collected from the persistent reservoir during suppressive therapy. We built a BEAST2 model to estimate integration dates of proviral sequences collected during suppressive therapy, implementing a tip date random walker to adjust the sequence tip dates and a latency-specific prior to inform the dates. To validate our method, we implemented it on both simulated and empirical data sets. Consistent with previous studies, we found that proviral integration dates were spread throughout active infection. Path sampling to select an alternative prior for date estimation in place of the latency-specific prior produced unrealistic results in one empirical data set, whereas on another data set, the latency-specific prior was selected as best fitting. Our Bayesian method outperforms current date estimation techniques with a root mean squared error of 0.89 years on simulated data relative to 1.23–1.89 years with previously developed methods. Bayesian methods offer an adaptable framework for inferring proviral integration dates. [ABSTRACT FROM AUTHOR]

Hybridization and polyploidy are key evolutionary forces in plant diversification, and their co-occurrence in the context of allopolyploid speciation is often associated with increased ability to colonize new environments and invasiveness. In the genus Ulex (Fabaceae), the European gorse (Ulex europaeus subsp. europaeus) is the only invasive and the only polyploid that has recently spread in different eco-geographical regions across the world. Understanding what confers such ecological advantages to this species, compared to its diploid and polyploid congeners, first requires clarification of the ecogeographical and evolutionary context of its formation. To achieve this, the geographical distributions of all Ulex spp. were estimated from species occurrence records, and phylogenetic analyses including all Ulex spp. were performed based on four nuclear (ITS and ETS nrDNA) and plastid (rps12 intron and trnK - matK) regions. The resulting trees were dated using a secondary calibration. Patterns of DNA sequence variation and dated phylogenetic trees were then interpreted in light of previous knowledge of chromosome numbers in Ulex to infer past events of polyploid speciation in the genus. We show that: (1) most current Ulex spp. radiated in the Iberian Peninsula during the past 1–2 Myr; (2) the history of Ulex was punctuated by multiple whole-genome duplication events; and (3) U. europaeus subsp. europaeus is the only gorse taxon that was formed by hybridization of two well-differentiated lineages (which separated c. 5 Mya) with wide climatic ranges (currently represented by Ulex minor and Ulex europaeus subsp. latebracteatus), possibly contributing to the invasive nature and wider climatic range of U. europaeus subsp. europaeus. These findings provide a much-needed evolutionary framework in which to explore the adaptive consequences of genome mergers and duplication in Ulex. [ABSTRACT FROM AUTHOR]

Background Monkeypox is an emerging zoonosis endemic to Central and West Africa. Monkeypox virus (MPXV) is genetically structured in 2 major clades (clades 1 and 2/3), but its evolution is poorly explored. Methods We retrieved MPXV genomes from public repositories and we analyzed geographic patterns using STRUCTURE. Molecular dating was performed using a using a Bayesian approach. Results We show that the population transmitted in West Africa (clades 2/3) experienced limited drift. Conversely, clade 1 (transmitted in the Congo Basin) possibly underwent a bottleneck or founder effect. Depending on the model used, we estimated that the 2 clades separated ∼560–860 (highest posterior density: 450–960) years ago, a period characterized by expansions and contractions of rainforest areas, possibly creating the ecological conditions for the MPXV reservoir(s) to migrate. In the Congo Basin, MPXV diversity is characterized by 4 subpopulations that show no geographic structuring. Conversely, clades 2/3 are spatially structured with 2 populations located West and East of the Dahomey Gap. Conclusions The distinct histories of the 2 clades may derive from differences in MPXV ecology in West and Central Africa. [ABSTRACT FROM AUTHOR]

Background and Aims The most species-rich and ecologically diverse plant radiation on the Canary Islands is the Aeonium alliance (Crassulaceae). In island radiations like this, speciation can take place either within islands or following dispersal between islands. Aiming at quantifying intra- and inter-island speciation events in the evolution of Aeonium , and exploring their consequences, we hypothesized that (1) intra-island diversification resulted in stronger ecological divergence of sister lineages, and that (2) taxa on islands with a longer history of habitation by Aeonium show stronger ecological differentiation and produce fewer natural hybrids. Methods We studied the biogeographical and ecological setting of diversification processes in Aeonium with a fully sampled and dated phylogeny inferred using a ddRADseq approach. Ancestral areas and biogeographical events were reconstructed in BioGeoBEARS. Eleven morphological characters and three habitat characteristics were taken into account to quantify the morphological and ecological divergence between sister lineages. A co-occurrence matrix of all Aeonium taxa is presented to assess the spatial separation of taxa on each island. Key Results We found intra- and inter-island diversification events in almost equal numbers. In lineages that diversified within single islands, morphological and ecological divergence was more pronounced than in lineages derived from inter-island diversification, but only the difference in morphological divergence was significant. Those islands with the longest history of habitation by Aeonium had the lowest percentages of co-occurring and hybridizing taxon pairs compared with islands where Aeonium arrived later. Conclusions Our findings illustrate the importance of both inter- and intra-island speciation, the latter of which is potentially sympatric speciation. Speciation on the same island entailed significantly higher levels of morphological divergence compared with inter-island speciation, but ecological divergence was not significantly different. Longer periods of shared island habitation resulted in the evolution of a higher degree of spatial separation and stronger reproductive barriers. [ABSTRACT FROM AUTHOR]

The prolonged interplay between orographic and climatic changes creates biogeographic barriers, resulting in the allopatric differentiation of plants in the Himalaya–Hengduan Mountains. Such consequences have led us to investigate the long-term Neogene–Quaternary geo-climatic history of the Eastern Himalaya–Hengduan Mountains. Narrowly distributed populations of Koenigia forrestii were sampled (ten populations, 97 individuals) and analysed for their genetic architecture, including phylogenetic reconstruction (based on plastome and plastid DNA/nuclear regions), molecular dating and demography, in combination with niche dynamics. We estimated that K. forrestii (stem age: 11.39 Mya) diverged into three non-overlapping distributed lineages during the Neogene–Quaternary periods (5.84–2.57 Mya), with Eastern Himalaya (EHa) being the first and most diverse lineage. 'Isolation by environment' revealed the existence of genetic structures that were significantly affected by the disparate environment. The presence of demographic events is well supported by the Bayesian skyline plot, indicating recent demographic expansion. Hence, lineage divergence and differentiation were mainly triggered by the heterogeneous environment associated with the biogeographic barriers due to the Tsangpo-Brahmaputra Grand Canyon, Mekong-Salween Divide and local mountain systems. Nevertheless, niche shift and local adaptation are the keys to determining the genetic architecture, demographic dynamics and diversification history of K. forrestii. [ABSTRACT FROM AUTHOR]

Mites of the genus Analges (Acariformes: Analgidae) inhabit the down feathers of passeriform birds. The evolutionary history of Analges and the co-phylogentic relationships between these mites and their hosts are unknown. Our phylogenetic analysis supported the monophyly of the genus, but it did not support previous taxonomic hypotheses subdividing the genus into the subgenera Analges and Analgopsis or arranging some species into the A. chelopus and A. passerinus species groups. Molecular data reveal seven new species inhabiting Eurasian passerines and support the existence of several multi-host species. According to molecular dating, the origin of the Analges (c. 41 Mya) coincided with the Eocene diversification of Passerida into Sylvioidea and Muscicapoidea–Passeroidea. The initial diversification of Analges took place on the Muscicapoidea clade, while remaining passerine superfamilies appear to have been colonized because of host-switching. Co-speciation appears to be relatively common among Analges species and their hosts, but the most striking pattern in the co-phylogenetic scenario involves numerous complete host-switches, spreads and several failures to speciate. The mechanism of long-term gene-flow among different populations of multi-host Analges species is enigmatic and difficult to resolve. Probably, in some cases mites could be transferred between birds via feathers used as nest material. [ABSTRACT FROM AUTHOR]

Saccharomycotina yeasts belong to diverse clades within the kingdom of fungi and are important to human everyday life. This work investigates the evolutionary relationships among these yeasts from a mitochondrial (mt) genomic perspective. A comparative study of 155 yeast mt genomes representing all major phylogenetic lineages of Saccharomycotina was performed, including genome size and content variability, intron and intergenic regions' diversity, genetic code alterations, and syntenic variation. Findings from this study suggest that mt genome size diversity is the result of a ceaseless random process, mainly based on genetic recombination and intron mobility. Gene order analysis revealed conserved syntenic units and many occurring rearrangements, which can be correlated with major evolutionary events as shown by the phylogenetic analysis of the concatenated mt protein matrix. For the first time, molecular dating indicated a slower mt genome divergence rate in the early stages of yeast evolution, in contrast with a faster rate in the late evolutionary stages, compared to their nuclear time divergence. Genetic code reassignments of mt genomes are a perpetual process happening in many different parallel evolutionary steps throughout the evolution of Saccharomycotina. Overall, this work shows that phylogenetic studies based on the mt genome of yeasts highlight major evolutionary events. [ABSTRACT FROM AUTHOR]

The Neotropical tinamous are of particular interest in our efforts to understand the evolution of modern birds. They inhabit both forested and open environments and, although volant, have limited flight capabilities. Numerous studies have recognized the monophyly of tinamous and their relationships either as sister to the flightless ratites (ostriches, emus and their relatives) or within the ratites themselves. Despite the numerous bird phylogenies published recently, modern investigations of relationships within the tinamous themselves have been limited. Here, we present the first detailed phylogenetic analysis and divergence-date estimation including a significant number of tinamou species, both extant and fossil. The monophyly of most currently recognized polytypic genera is recovered with high support, with the exception of the paraphyletic Nothura and Nothoprocta. The traditional subdivision between those tinamous inhabiting open areas (Nothurinae) and forest environments (Tinaminae) is also confirmed. A temporal calibration of the resultant phylogeny estimates that the basal divergence of crown Tinamidae took place between 31 and 40 Mya. [ABSTRACT FROM AUTHOR]

Background and Aims Theaceae, with three tribes, nine genera and more than 200 species, are of great economic and ecological importance. Recent phylogenetic analyses based on plastomic data resolved the relationships among the three tribes and the intergeneric relationships within two of those tribes. However, generic-level relationships within the largest tribe, Theeae, were not fully resolved. The role of putative whole-genome duplication (WGD) events in the family and possible hybridization events among genera within Theeae also remain to be tested further. Methods Transcriptomes or low-depth whole-genome sequencing of 57 species of Theaceae, as well as additional plastome sequence data, were generated. Using a dataset of low-copy nuclear genes, we reconstructed phylogenetic relationships using concatenated, species tree and phylogenetic network approaches. We further conducted molecular dating analyses and inferred possible WGD events by examining the distribution of the number of synonymous substitutions per synonymous site (Ks) for paralogues in each species. For plastid protein-coding sequences , phylogenies were reconstructed for comparison with the results obtained from analysis of the nuclear dataset. Results Based on the 610 low-copy nuclear genes (858 606 bp in length) investigated, Stewartieae was resolved as sister to the other two tribes. Within Theeae, the Apterosperma – Laplacea clade grouped with Pyrenaria , leaving Camellia and Polyspora as sister. The estimated ages within Theaceae were largely consistent with previous studies based mainly on plastome data. Two reticulation events within Camellia and one between the common ancestor of Gordonia and Schima were found. All members of the tea family shared two WGD events, an older At-γ and a recent Ad-β; both events were also shared with the outgroups (Diapensiaceae, Pentaphylacaceae, Styracaceae and Symplocaceae). Conclusions Our analyses using low-copy nuclear genes improved understanding of phylogenetic relationships at the tribal and generic levels previously proposed based on plastome data, but the phylogenetic position of the Apterosperma–Laplacea clade needs more attention. There is no evidence for extensive intergeneric hybridization within Theeae or for a Theaceae-specific WGD event. Land bridges (e.g. the Bering land bridge) during the Late Oligocene may have permitted the intercontinental plant movements that facilitated the putative ancient introgression between the common ancestor of Gordonia and Schima. [ABSTRACT FROM AUTHOR]

Despite the importance of natural selection in species' evolutionary history, phylogenetic methods that take into account population-level processes typically ignore selection. The assumption of neutrality is often based on the idea that selection occurs at a minority of loci in the genome and is unlikely to compromise phylogenetic inferences significantly. However, genome-wide processes like GC-bias and some variation segregating at the coding regions are known to evolve in the nearly neutral range. As we are now using genome-wide data to estimate species trees, it is natural to ask whether weak but pervasive selection is likely to blur species tree inferences. We developed a polymorphism-aware phylogenetic model tailored for measuring signatures of nucleotide usage biases to test the impact of selection in the species tree. Our analyses indicate that although the inferred relationships among species are not significantly compromised, the genetic distances are systematically underestimated in a node-height-dependent manner: that is, the deeper nodes tend to be more underestimated than the shallow ones. Such biases have implications for molecular dating. We dated the evolutionary history of 30 worldwide fruit fly populations, and we found signatures of GC-bias considerably affecting the estimated divergence times (up to 23%) in the neutral model. Our findings call for the need to account for selection when quantifying divergence or dating species evolution. [ABSTRACT FROM AUTHOR]

Four coronaviruses (HCoV-OC43, HCoV-HKU1, HCoV-NL63, and HCoV-229E) are endemic in human populations. All these viruses are seasonal and generate short-term immunity. Like the highly pathogenic coronaviruses, the endemic coronaviruses have zoonotic origins. Thus, understanding the evolutionary dynamics of these human viruses might provide insight into the future trajectories of SARS-CoV-2 evolution. Because the zoonotic sources of HCoV-OC43 and HCoV-229E are known, we applied a population genetics–phylogenetic approach to investigate which selective events accompanied the divergence of these viruses from the animal ones. Results indicated that positive selection drove the evolution of some accessory proteins, as well as of the membrane proteins. However, the spike proteins of both viruses and the hemagglutinin-esterase (HE) of HCoV-OC43 represented the major selection targets. Specifically, for both viruses, most positively selected sites map to the receptor-binding domains (RBDs) and are polymorphic. Molecular dating for the HCoV-229E spike protein indicated that RBD Classes I, II, III, and IV emerged 3–9 years apart. However, since the appearance of Class V (with much higher binding affinity), around 25 years ago, limited genetic diversity accumulated in the RBD. These different time intervals are not fully consistent with the hypothesis that HCoV-229E spike evolution was driven by antigenic drift. An alternative, not mutually exclusive possibility is that strains with higher affinity for the cellular receptor have out-competed strains with lower affinity. The evolution of the HCoV-OC43 spike protein was also suggested to undergo antigenic drift. However, we also found abundant signals of positive selection in HE. Whereas such signals might result from antigenic drift, as well, previous data showing co-evolution of the spike protein with HE suggest that optimization for human cell infection also drove the evolution of this virus. These data provide insight into the possible trajectories of SARS-CoV-2 evolution, especially in case the virus should become endemic. [ABSTRACT FROM AUTHOR]

A new classification for the freshwater crabs of the Americas, the superfamily Pseudothelphusoidea¸ is presented based on a multigene phylogeny complemented by morphological analyses. We propose that the superfamily Pseudothelphusoidea be composed of two families, the Epiloboceridae and the Pseudothelphusidae, with the subsequent reorganization of the latter into eight subfamilies, of which five (Hypolobocerinae, Kingsleyinae, Potamocarcininae, Pseudothelphusinae, Strengerianinae) represent previously recognized tribes. We erect three new subfamilies: Guinotiinae, Ptychophallinae and Raddausinae, to reflect relationships that have become clear with the new analyses. The new classification scheme has a high level of congruence with the geographical distribution of species and genera. A divergence time estimate suggests that the Pseudothelphusoidea originated in the late Cretaceous around 68 Mya. Subsequent divergence events can be correlated with emergent landmasses throughout the range of the superfamily. There is high concordance among several elements of our proposal: (1) the main morphological types of male gonopods correspond to well defined clades obtained with molecular analyses; (2) the geographic distribution of the subfamilies has a structured pattern; and (3) the estimated times of divergence of each group can be associated to the geological history of each region. The combination of these elements results in a robust new classification scheme. [ABSTRACT FROM AUTHOR]

Background and Aims Cephalotaxus is a paleo-endemic genus in East Asia that consists of about 7–9 conifer species. Despite its great economic and ecological importance, the relationships between Cephalotaxus and related genera, as well as the interspecific relationships within Cephalotaxus , have long been controversial, resulting in contrasting taxonomic proposals in delimitation of Cephalotaxaceae and Taxaceae. Based on plastome data, this study aims to reconstruct a robust phylogeny to infer the systematic placement and the evolutionary history of Cephalotaxus. Methods A total of 11 plastomes, representing all species currently recognized in Cephalotaxus and two Torreya species, were sequenced and assembled. Combining these with previously published plastomes, we reconstructed a phylogeny of Cephalotaxaceae and Taxaceae with nearly full taxonomic sampling. Under a phylogenetic framework and molecular dating, the diversification history of Cephalotaxus and allied genera was explored. Key Results Phylogenetic analyses of 81 plastid protein-coding genes recovered robust relationships between Cephalotaxus and related genera, as well as providing a well-supported resolution of interspecific relationships within Cephalotaxus , Taxus , Torreya and Amentotaxus. Divergence time estimation indicated that most extant species of these genera are relatively young, although fossil and other molecular evidence consistently show that these genera are ancient plant lineages. Conclusions Our results justify the taxonomic proposal that recognizes Cephalotaxaceae as a monotypic family, and contribute to a clear-cut delineation between Cephalotaxaceae and Taxaceae. Given that extant species of Cephalotaxus are derived from recent divergence events associated with the establishment of monsoonal climates in East Asia and Pleistocene climatic fluctuations, they are not evolutionary relics. [ABSTRACT FROM AUTHOR]

Phylogenetic trees inferred from sequence data often have branch lengths measured in the expected number of substitutions and therefore, do not have divergence times estimated. These trees give an incomplete view of evolutionary histories since many applications of phylogenies require time trees. Many methods have been developed to convert the inferred branch lengths from substitution unit to time unit using calibration points, but none is universally accepted as they are challenged in both scalability and accuracy under complex models. Here, we introduce a new method that formulates dating as a nonconvex optimization problem where the variance of log-transformed rate multipliers is minimized across the tree. On simulated and real data, we show that our method, wLogDate, is often more accurate than alternatives and is more robust to various model assumptions. [ABSTRACT FROM AUTHOR]

Evolution sometimes proceeds by loss, especially when structures and genes become dispensable after an environmental shift relaxes functional constraints. Subterranean vertebrates are outstanding models to analyze this process, and gene decay can serve as a readout. We sought to understand some general principles on the extent and tempo of the decay of genes involved in vision, circadian clock, and pigmentation in cavefishes. The analysis of the genomes of two Cuban species belonging to the genus Lucifuga provided evidence for the largest loss of eye-specific genes and nonvisual opsin genes reported so far in cavefishes. Comparisons with a recently evolved cave population of Astyanax mexicanus and three species belonging to the Chinese tetraploid genus Sinocyclocheilus revealed the combined effects of the level of eye regression, time, and genome ploidy on eye-specific gene pseudogenization. The limited extent of gene decay in all these cavefishes and the very small number of loss-of-function mutations per pseudogene suggest that their eye degeneration may not be very ancient, ranging from early to late Pleistocene. This is in sharp contrast with the identification of several vision genes carrying many loss-of-function mutations in ancient fossorial mammals, further suggesting that blind fishes cannot thrive more than a few million years in cave ecosystems. [ABSTRACT FROM AUTHOR]

We studied the evolutionary history of Chrysobalanaceae with phylogenetic analyses of complete plastid genomes from 156 species to assess the tempo of diversification in the Neotropics and help to unravel the causes of Amazonian plant diversification. These plastid genomes had a mean length of 162 204 base pairs, and the nearly complete DNA sequence matrix, with reliable fossils, was used to estimate a phylogenetic tree. Chrysobalanaceae diversified from 38.9 Mya (95% highest posterior density, 95% HPD: 34.2–43.9 Mya). A single clade containing almost all Neotropical species arose after a single dispersal event from the Palaeotropics into the Amazonian biome c. 29.1 Mya (95% HPD: 25.5–32.6 Mya), with subsequent dispersals into other Neotropical biomes. All Neotropical genera diversified from 10 to 14 Mya, lending clear support to the role of Andean orogeny as a major cause of diversification in Chrysobalanaceae. In particular, the understory genus Hirtella diversified extremely rapidly, producing > 100 species in the last 6 Myr (95% HPD: 4.9–7.4 Myr). Our study suggests that a large fraction of the Amazonian tree flora has been assembled in situ in the last 15 Myr. [ABSTRACT FROM AUTHOR]

The Mediterranean Basin can be considered as a natural laboratory with which to study the effects of sea currents in the dispersal of coastal plant species that use hydrochory. Pancratium maritimum is a perennial geophyte, with a wide distribution along Mediterranean coasts. We aim to provide a timeframe for the origin of the diversification of this plant, to clarify its phylogeographical structure and to investigate the role of currents in the Mediterranean Sea in influencing spatial patterns of its genetic distribution. The phylogeographic history was analysed using 50 populations. A genetic structure analysis and divergence time estimation was performed using plastid sequences. Five haplotypes were detected, of which two were the most abundant; a third was observed in the central Mediterranean, and two rare haplotypes were present in the eastern Mediterranean. The genetic breaks were concordant with the direction of the major Mediterranean currents. The divergence time estimation for the origin of P. maritimum was located at the end of the Neogene (mid Pliocene to mid Pleistocene). We showed the importance of sea currents in the Mediterranean in acting both as a means of dispersal and as a barrier to the distribution and evolution of P. maritimum due to the special adaptations of its seeds. [ABSTRACT FROM AUTHOR]

Background and Aims Afromontane forests host a unique biodiversity distributed in isolated high-elevation habitats within a matrix of rain forests or savannahs, yet they share a remarkable flora that raises questions about past connectivity between currently isolated forests. Here, we focused on the Podocarpus latifolius–P. milanjianus complex (Podocarpaceae), the most widely distributed conifers throughout sub-Saharan African highlands, to infer its demographic history from genetic data. Methods We sequenced the whole plastid genome, mitochondrial DNA regions and nuclear ribosomal DNA of 88 samples from Cameroon to Angola in western Central Africa and from Kenya to the Cape region in eastern and southern Africa to reconstruct time-calibrated phylogenies and perform demographic inferences. Key Results We show that P. latifolius and P. milanjianus form a single species, whose lineages diverged during the Pleistocene, mostly between approx, 200 000 and 300 000 years BP, after which they underwent a wide range expansion leading to their current distributions. Confronting phylogenomic and palaeoecological data, we argue that the species originated in East Africa and reached the highlands of the Atlantic side of Africa through two probable latitudinal migration corridors: a northern one towards the Cameroon volcanic line, and a southern one towards Angola. Although the species is now rare in large parts of its range, no demographic decline was detected, probably because it occurred too recently to have left a genetic signature in our DNA sequences. Conclusions Despite the ancient and highly fluctuating history of podocarps in Africa revealed by palaeobotanical records, the extended distribution of current P. latifolius/milanjianus lineages is shown to result from a more recent history, mostly during the mid-late Pleistocene, when Afromontane forests were once far more widespread and continuous. [ABSTRACT FROM AUTHOR]

The conventional wisdom in molecular evolution is to apply parameter-rich models of nucleotide and amino acid substitutions for estimating divergence times. However, the actual extent of the difference between time estimates produced by highly complex models compared with those from simple models is yet to be quantified for contemporary data sets that frequently contain sequences from many species and genes. In a reanalysis of many large multispecies alignments from diverse groups of taxa, we found that the use of the simplest models can produce divergence time estimates and credibility intervals similar to those obtained from the complex models applied in the original studies. This result is surprising because the use of simple models underestimates sequence divergence for all the data sets analyzed. We found three fundamental reasons for the observed robustness of time estimates to model complexity in many practical data sets. First, the estimates of branch lengths and node-to-tip distances under the simplest model show an approximately linear relationship with those produced by using the most complex models applied on data sets with many sequences. Second, relaxed clock methods automatically adjust rates on branches that experience considerable underestimation of sequence divergences, resulting in time estimates that are similar to those from complex models. And, third, the inclusion of even a few good calibrations in an analysis can reduce the difference in time estimates from simple and complex models. The robustness of time estimates to model complexity in these empirical data analyses is encouraging, because all phylogenomics studies use statistical models that are oversimplified descriptions of actual evolutionary substitution processes. [ABSTRACT FROM AUTHOR]

Herpes simplex virus types 1 and 2 (HSV-1 and HSV-2) are ubiquitous human pathogens. Both viruses evolved from simplex viruses infecting African primates and they are thus thought to have left Africa during early human migrations. We analyzed the population structure of HSV-1 and HSV-2 circulating strains. Results indicated that HSV-1 populations have limited geographic structure and the most evident clustering by geography is likely due to recent bottlenecks. For HSV-2, the only level of population structure is accounted for by the so-called "worldwide" and "African" lineages. Analysis of ancestry components and nucleotide diversity, however, did not support the view that the worldwide lineage followed early humans during out-of-Africa dispersal. Although phylogeographic analysis confirmed an African origin for both viruses, molecular dating with a method that corrects for the time-dependent rate phenomenon indicated that HSV-1 and HSV-2 migrated from Africa in relatively recent times. In particular, we estimated that the HSV-2 worldwide lineage left the continent in the 18th century, which corresponds to the height of the transatlantic slave trade, possibly explaining the high prevalence of HSV-2 in the Americas (second highest after Africa). The limited geographic clustering of HSV-1 makes it difficult to date its exit from Africa. The split between the basal clade, containing mostly African sequences, and all other strains was dated at ∼5,000 years ago. Our data do not imply that herpes simplex viruses did not infect early humans but show that the worldwide distribution of circulating strains is the result of relatively recent events. [ABSTRACT FROM AUTHOR]

The biota of the Indian subcontinent was assembled through multiple associations with various landmasses during a period spanning the Late Cretaceous to the present. It consists of Gondwanan elements that subsequently dispersed 'out-of-India' and biota that dispersed 'into-India' after the subcontinent collided with Asia. However, the relative contribution of these connections to the current biotic assembly of the subcontinent has been under-explored. Our aim here was to understand the relative importance of these various routes of biotic assembly in India by studying the historical biogeography of the tropical Old World freshwater snail genus Pila. We reconstructed a near-complete phylogeny, based on nuclear and mitochondrial markers, of Ampullariidae including all the described Pila species from India and Ampullariids worldwide. Thereafter, molecular dating and ancestral range estimation analyses were carried out to ascertain the time frame and route of colonization of India by Pila. The results showed that Pila dispersed into India as well as other parts of tropical Asia from Africa after both India and Africa collided with Eurasia. Furthermore, multiple dispersals took place between Southeast Asia and India. These findings corroborate increasing evidence that much of the current Indian assemblage of biota actually dispersed 'into-India' after it collided with Asia. [ABSTRACT FROM AUTHOR]

JC polyomavirus (JCPyV) is one of the most prevalent human viruses. Findings based on the geographic distribution of viral subtypes suggested that JCPyV codiverged with human populations. This view was however challenged by data reporting a much more recent origin and expansion of JCPyV. We collected information on ∼1,100 worldwide strains and we show that their geographic distribution roughly corresponds to major human migratory routes. Bayesian phylogeographic analysis inferred a Subsaharan origin for JCPyV, although with low posterior probability. High confidence inference at internal nodes provided strong support for a long-standing association between the virus and human populations. In line with these data, pairwise F ST values for JCPyV and human mtDNA sampled from the same areas showed a positive and significant correlation. Likewise, very strong relationships were found when node ages in the JCPyV phylogeny were correlated with human population genetic distances (nuclear-marker based F ST). Reconciliation analysis detected a significant cophylogenetic signal for the human population and JCPyV trees. Notably, JCPyV also traced some relatively recent migration events such as the expansion of people from the Philippines/Taiwan area into Remote Oceania, the gene flow between North-Eastern Siberian and Ainus, and the Koryak contribution to Circum-Arctic Americans. Finally, different molecular dating approaches dated the origin of JCPyV in a time frame that precedes human out-of-Africa migration. Thus, JCPyV infected early human populations and accompanied our species during worldwide dispersal. JCPyV typing can provide reliable geographic information and the virus most likely adapted to the genetic background of human populations. [ABSTRACT FROM AUTHOR]

Establishing an accurate evolutionary timescale for green plants (Viridiplantae) is essential to understanding their interaction and coevolution with the Earth's climate and the many organisms that rely on green plants. Despite being the focus of numerous studies, the timing of the origin of green plants and the divergence of major clades within this group remain highly controversial. Here, we infer the evolutionary timescale of green plants by analyzing 81 protein-coding genes from 99 chloroplast genomes, using a core set of 21 fossil calibrations. We test the sensitivity of our divergence-time estimates to various components of Bayesian molecular dating, including the tree topology, clock models, clock-partitioning schemes, rate priors, and fossil calibrations. We find that the choice of clock model affects date estimation and that the independent-rates model provides a better fit to the data than the autocorrelated-rates model. Varying the rate prior and tree topology had little impact on age estimates, with far greater differences observed among calibration choices and clock-partitioning schemes. Our analyses yield date estimates ranging from the Paleoproterozoic to Mesoproterozoic for crown-group green plants, and from the Ediacaran to Middle Ordovician for crown-group land plants. We present divergence-time estimates of the major groups of green plants that take into account various sources of uncertainty. Our proposed timeline lays the foundation for further investigations into how green plants shaped the global climate and ecosystems, and how embryophytes became dominant in terrestrial environments. [ABSTRACT FROM AUTHOR]

Members of the Orchidaceae, one of the largest families of flowering plants, evolved the crassulacean acid metabolism (CAM) photosynthesis strategy. It is thought that CAM triggers adaptive radiation into new niche spaces, yet very little is known about its origin and diversification on different continents. Here, we assess the prevalence of CAM in Dendrobium , which is one of the largest genera of flowering plants and found in a wide range of environments, from the high altitudes of the Himalayas to relatively arid habitats in Australia. Based on phylogenetic time trees, we estimated that CAM, as determined by δ 13C values less negative than –20.0‰, evolved independently at least eight times in Dendrobium. The oldest lineage appeared in the Asian clade during the middle Miocene, indicating the origin of CAM was associated with a pronounced climatic cooling that followed a period of aridity. Divergence of the four CAM lineages in the Asian clade appeared to be earlier than divergence of those in the Australasian clade. However, CAM species in the Asian clade are much less diverse (25.6%) than those in the Australasian clade (57.9%). These findings shed new light on CAM evolutionary history and the aridity levels of the paleoclimate on different continents. [ABSTRACT FROM AUTHOR]

Oceanic islands originate from volcanism or tectonic activity without connections to continental landmasses, are colonized by organisms, and eventually vanish due to erosion and subsidence. Colonization of oceanic islands occurs through long-distance dispersals (LDDs) or metapopulation vicariance, the latter resulting in lineages being older than the islands they inhabit. If metapopulation vicariance is valid, island ages cannot be reliably used to provide maximum age constraints for molecular dating. We explore the relationships between the ages of members of a widespread plant genus (Planchonella , Sapotaceae) and their host islands across the Pacific to test various assumptions of dispersal and metapopulation vicariance. We sampled three nuclear DNA markers from 156 accessions representing some 100 Sapotaceae taxa, and analyzed these in BEAST with a relaxed clock to estimate divergence times and with a phylogeographic diffusion model to estimate range expansions over time. The phylogeny was calibrated with a secondary point (the root) and fossils from New Zealand. The dated phylogeny reveals that the ages of Planchonella species are, in most cases, consistent with the ages of the islands they inhabit. Planchonella is inferred to have originated in the Sahul Shelf region, to which it back-dispersed multiple times. Fiji has been an important source for range expansion in the Pacific for the past 23 myr. Our analyses reject metapopulation vicariance in all cases tested, including between oceanic islands, evolution of an endemic Fiji–Vanuatu flora, and westward rollback vicariance between Vanuatu and the Loyalty Islands. Repeated dispersal is the only mechanism able to explain the empirical data. The longest (8900 km) identified dispersal is between Palau in the Pacific and the Seychelles in the Indian Ocean, estimated at 2.2 Ma (0.4–4.8 Ma). The first split in a Hawaiian lineage (P. sandwicensis) matches the age of Necker Island (11.0 Ma), when its ancestor diverged into two species that are distinguished by purple and yellow fruits. Subsequent establishment across the Hawaiian archipelago supports, in part, progression rule colonization. In summary, we found no explanatory power in metapopulation vicariance and conclude that Planchonella has expanded its range across the Pacific by LDD. We contend that this will be seen in many other groups when analyzed in detail. [ABSTRACT FROM AUTHOR]

Molecular dating offers a tool for inferring the time of divergence between two lineages. In this study, we discuss how dated molecular reconstructions are informative of two different, albeit often intermingled, time estimates with regard to a fundamental process in island biogeography: the time of island colonization (TIC). We illustrate how stem age estimates provide information on the divergence between the extant island lineage and their closest relatives (i.e. the onset of lineage differentiation). Such estimates, however, are typically poor TIC predictors, as they are strongly affected by spatial and temporal uncertainty, particularly in cases of deep stem ages. Crown ages of endemic island lineages, in contrast, provide information on the temporal onset of island in situ diversification, and may represent a better proxy for TIC when the associated uncertainty is taken into account. Thus, the geographic and temporal distance separating the island and mainland lineages in phylogenetic/phylogeographic reconstructions are key factors for determining the reliability of these two estimates as proxies of TIC. We show how divergence times can be used to investigate the biogeographic patterns of two well-studied oceanic archipelagos: Hawaii and the Canary Islands. A compilation of molecular age estimates for nearly one-third of the endemic plant lineages in each archipelago reveals that Canarian plant lineages exhibit significantly younger mean crown ages (2.1 ± 2.4 Myr) than Hawaiian lineages (3.5 ± 2.9 Myr), despite island substrates being much older in the Canarian archipelago. We postulate that this pattern suggests: (1) a more important role of submerged islands during plant colonization in Hawaii, and (2) higher taxon turnover in the Canaries, mediated by relatively young (Mediterranean) lineages, and probably facilitated by the combination of the high incidence of extinction for the last 5 Myr and the close proximity of mainland source areas as compared to Hawaii. [ABSTRACT FROM AUTHOR]

Drilini are soft-bodied predatory click-beetles (Elateridae: Agrypninae) with incompletely metamorphosed females. Due to divergent morphology, their classification has been contentious. We present the first densely sampled molecular phylogeny of Drilini based on nuclear and mitochondrial markers. Altogether, 44 species, representing all genera, were analysed using maximum likelihood and the Bayesian approach. Molecular analyses recovered five major clades that were also well supported by morphology. Afrotropical lineages mark deep splits. Most Palearctic species belong to a terminal clade. A few species of the predominantly Afrotropical Selasia are distributed from Arabia up to the Himalayas and Thailand. The origin of Drilini is dated to the Late Eocene (~35.5 Mya) and rapid radiation is identified from the Eocene/Oligocene to the Middle Miocene. We describe the gradual transformation of male morphological traits, e.g. the level of sclerotization, structure of mouthparts, loss of the thoracic interlocking mechanism, shortened elytra and expanded larviform abdomen. Five new genera, Austroselasia , Habeshaselasia , Illubaboria , Malacodrilus and Mashaselasia are proposed. Latoselasia , previously a subgenus of Wittmerselasia , is elevated to the genus rank. Five new species, Habeshaselasia nekemtensis , H. illubaborensis , Illubaboria bicolor , Malacodrilus hajeki and Mashaselasia aethiopica are described. [ABSTRACT FROM AUTHOR]

Factors shaping biotic assembly of an island compared with the mainland are of considerable interest in biogeography, and the island of Sri Lanka and mainland India provide an interesting setting in which to study this process. We tested two contrasting hypotheses, faunal exchange vs. in situ diversification, to explain how the biota of Sri Lanka might have assembled. We studied the radiation of Hemidactylus geckos, endemic to India and Sri Lanka, to understand the biogeographical processes underlying the faunal assembly of Sri Lanka. We performed molecular phylogenetic analysis, divergence data estimation and ancestral area reconstruction. Diversification in this radiation began ~34.5 Mya in India, followed by seven independent dispersal events from India to Sri Lanka. Two dispersal events occurred in the Early to Middle Miocene, leading to two endemic Sri Lankan species. Marine transgression events separating the two landmasses are likely to have led to vicariant speciation in these cases. The other five dispersal events led to range expansion in species largely restricted to open semi-arid habitats and were likely to be more recent. These results indicate that the biotic exchange model better explains the assembly of Sri Lankan Hemidactylus geckos. [ABSTRACT FROM AUTHOR]

We explored the effects of Quaternary climate changes on the campos rupestre sky island ecosystem in central and eastern Brazil studying the phylogeography of Richterago discoidea (Asteraceae) to better understand the effect of historical biogeographic processes on species diversification in this region. DNA sequences of nuclear (ITS) and plastid (psbA - trnH, rpl32 - trnL UAG , trnK UUU - rps16 and ycf3 - trnS) markers and 83 AFLP loci were used to genotype up to 90 individuals from 19 populations of R. discoidea. We investigated intraspecific genetic structure, demographic history and spatiotemporal diversification. Also, ecological niche modelling was used to infer palaeodistribution. Three lineages (without strong geographical structure) were identified in the Bayesian genetic structure analysis of 25 haplotypes, whereas AFLPs revealed two lineages with considerable levels of admixture. The origin of diversification of R. discoidea is on the Diamantina Plateau (Espinhaço Meridional, Minas Gerais), from where lineages expanded to the central highlands of Brazil during glacial periods in the Mid-Pleistocene. The current disjunct distribution is a relict of an ancient wide distribution, resulting from retraction during interglacial periods, confining populations to mountain-top sky islands that acted as refugia (Espinhaço Range and Goiás highlands). Expansion within refugium sites during the LGM blurred deeper genetic structure, and pressure of selection in ecological outliers favoured high genetic diversity outside refugia. © 2018 The Linnean Society of London, Biological Journal of the Linnean Society, 2018, YY, 000–000 [ABSTRACT FROM AUTHOR]

Phylogeographical study of the small five-toed jerboa (Scarturus elater) and examination of the phylogenetic position of S. vinogradovi were performed using the mitochondrial cytochrome b (cytb) gene and fragments of the BRCA1 and IRBP nuclear genes. Phylogenetic analysis of the cytb data including 115 specimens of S. elater from 47 localities across the species range revealed the existence of three highly divergent (10–11.3%) genetic clades: North (N), South (S) and South-West (SW). The N and S clades are well supported by nuclear genes and occur in sympatry across a large part of the range south of the Aral Sea. We found no trace of admixture between these clades, which suggests their reproductive isolation. We detected no morphological differences in the skull or glans penis between these two lineages, which we consider to represent an intriguing example of cryptic species. Given the reciprocal monophyly and deep genetic divergence, the SW lineage also deserves full species rank. The data indicate that S. vinogradovi is not a close relative of S. elater. It is placed as a separate deep branch in a clade also containing S. elater s.l. and S. williamsi + S. euphratica. [ABSTRACT FROM AUTHOR]

Background and Aims Although dioecy, which characterizes only 6 % of angiosperm species, has been considered an evolutionary dead end, recent studies have demonstrated that this is not necessarily the case. Moraceae (40 genera, 1100 spp. including Ficus, 750 spp.) are particularly diverse in breeding systems (including monoecy, gynodioecy, androdioecy and dioecy) and thus represent a model clade to study macroevolution of dioecy. Methods Ancestral breeding systems of Ficus and Moraceae were inferred. To do so, a new dated phylogenetic tree of Ficus and Moraceae was first reconstructed by combining a revised 12-fossil calibration set and a densely sampled molecular data set of eight markers and 320 species. Breeding system evolution was then reconstructed using both parsimony and model-based (maximum likelihood and Bayesian) approaches with this new time scale. Key Results The crown group ages of Ficus and Moraceae were estimated in the Eocene (40.6–55.9 Ma) and Late Cretaceous (73.2–84.7 Ma), respectively. Strong support was found for ancestral dioecy in Moraceae. Although the ancestral state of Ficus remained particularly sensitive to model selection, the results show that monoecy and gynodioecy evolved from dioecy in Moraceae, and suggest that gynodioecy probably evolved from monoecy in Ficus. Conclusions Dioecy was found not to be an evolutionary dead end in Moraceae. This study provides a new time scale for the phylogeny and a new framework of breeding system evolution in Ficus and Moraceae. [ABSTRACT FROM AUTHOR]

The eastern Australian temperate biota harbours many plants with fragmented geographic ranges distributed over 1000s of kilometres, yet the spatial genetic structure of their populations remains largely unstudied. In this study, we investigated genetic variation of the nuclear internal transcribed spacer (ITS) and chloroplast DNA sequences to disentangle the phylogeography of two widely distributed but highly fragmented eastern Australian fire-sensitive temperate conifers: Callitris oblonga (12 populations and 121 individuals) and C. rhomboidea (22 populations and 263 individuals). The three highly disjunct populations of C. oblonga all had unique chloroplast and ITS haplotypes consistent with the classification of these three populations as distinct subspecies. Molecular dating indicates that divergences of these populations occurred pre- to mid- Pleistocene (2.66 to 1.08 mya). Callitris rhomboidea showed greater diversity of chloroplast haplotypes which was strongly phylogeographically structured (Gst = 0.972), with haplotypes unique to specific geographic regions. ITS haplotype diversity was far higher than in C. oblonga with 38 haplotypes displaying high geographic structuring (Gst = 0.387) with many population-specific haplotypes. A phylogeographic break was identified between populations north and south of eastern Victoria dated at 0.43–0.47 mya. In both species, the strong genetic structuring of both chloroplast and ITS haplotypes provides evidence that their widespread ranges have resulted from long term persistence in low fire frequency refugia combined with poor dispersal. Any loss of populations due to increasing fire frequency or habitat loss is likely to result in a reduction of genetic diversity. [ABSTRACT FROM AUTHOR]

The yam genus Dioscorea comprises c. 650 species of tropical vines with starch-rich tubers, useful as an energy source and often containing secondary metabolites. The Neotropical region holds the highest diversity of species and morphology of yams. We generated a time calibrated tree for Dioscorea using, for the first time, a dense sampling of Neotropical species (64 species, 20% of all Neotropical species and 22 sections) to trace the biogeography of these plants in this region. Four origins of Dioscorea in the Neotropics have been estimated since the Eocene. The two most diverse lineages originated between the Eocene and Oligocene, respectively, in the Southern Andes and in a large and disconnected group of areas including Central America, northern Andes and Atlantic forest. Both lineages occupied the South American 'Dry Diagonal' after the Miocene, but New World II clade remained associated with forest habitats. Several exchanges between Dry Diagonal and adjacent forested biomes occurred, corroborating the interchange between these vegetation types. Dispersals to Central America occurred before the closure of the Isthmus of Panama. We highlight two important events of long-distance dispersal, the colonization of Central American before the closure of the Isthmus of Panama and the dispersal of the D. antaly lineage to Madagascar. In addition, our phylogenetic tree reveals the unnatural nature of the classical infrageneric classification of Dioscorea. The taxonomic implications of our results are discussed. © 2018 The Linnean Society of London, Biological Journal of the Linnean Society, 2018, YY, 000–000. [ABSTRACT FROM AUTHOR]

The ‘out of Australia’ hypothesis describes taxa with ancestors present on the Australian continent before the contact of the Australian plate with Southeast Asia and the subsequent biological interchange between these regions across Wallacea. Our study supports the ‘out of Australia’ hypothesis for the tropical tree genus Alphitonia and its closest relatives. A common ancestor of the entire clade inhabited Australia in the Miocene, and westward dispersal into Wallacea, the Philippines and the Asian continent was reconstructed to be of Quaternary origin. Furthermore, our study supports the currently applied taxonomy in Alphitonia and related genera, although it highlights potentially underestimated diversity. Finally, our study highlights the need for further investigations in Alphitonia and related genera and for including fossil-rich related taxa. The need for these investigations also arises from a potential human-mediated dispersal of Alphitonia spp. in Polynesia, which cannot be clearly proven by our approach. [ABSTRACT FROM AUTHOR]

Ascaridoids are among the commonest groups of zooparasitic nematodes (roundworms) and occur in the alimentary canal of all major vertebrate groups, including humans. They have an extremely high diversity and are of major socio-economic importance. However, their evolutionary history remains poorly known. Herein, we performed a comprehensive phylogenetic analysis of the Ascaridoidea. Our results divided the Ascaridoidea into six monophyletic major clades, i.e. the Heterocheilidae, Acanthocheilidae, Anisakidae, Ascarididae, Toxocaridae, and Raphidascarididae, among which the Heterocheilidae, rather than the Acanthocheilidae, represents the sister clade to the remaining ascaridoids. The phylogeny was calibrated using an approach that involves time priors from fossils of the co-evolving hosts, and dates the common ancestor of the Ascaridoidea back to the Early Carboniferous (approximately 360.47–325.27 Ma). The divergence dates and ancestral host types indicated by our study suggest that members of the Ascaridoidea first parasitized terrestrial tetrapods, and subsequently, extended their host range to elasmobranchs and teleosts. We also propose that the fundamental terrestrial-aquatic switches of these nematodes were affected by changes in sea-level during the Triassic to the Early Cretaceous. [ABSTRACT FROM AUTHOR]

The main outcome of molecular dating, the timetree, provides crucial information for understanding the evolutionary history of lineages and is a requirement of several evolutionary analyses. Although essential, the estimation of divergence times from molecular data is frequently regarded as a complicated task. However, establishing biological timescales can be performed in a straightforward manner, even with large, genome-wide data sets. This protocol presents all the necessary steps to estimate a timetree in the program MEGA X. It also illustrates how the TimeTree resource can be a useful tool to obtain chronological information based on previous studies, therefore yielding calibration boundaries. [ABSTRACT FROM AUTHOR]

Liliaceae sensu APG IV include c. 600 species, and have been circumscribed into three subfamilies, Lilioideae, Calochortoideae and Streptopoideae. Molecular phylogenetic approaches to this family have produced dynamic changes in the generic circumscriptions. We conducted molecular phylogenetic analyses, time estimations and biogeographical analyses to confirm generic relationships, discuss their circumscription for classification and clarify the evolutionary history of the family. A phylogenetic analysis is presented as a combined data set of c. 6.1 kb from four plastid coding gene sequences for 142 taxa representing all the genera of Liliaceae. Medeoloideae were newly defined as an independent subfamily from Lilioideae. Tricyrtis of Calochortoideae is embedded in Streptopoideae, despite its unique characteristics. The crown age of Liliaceae was calculated at c. 85 Mya, and Liliaceae are considered to have originated in temperate Asia in the late Cretaceous and to have expanded their distribution via dispersal with the occurrence of repetitive vicariance events during their evolution. [ABSTRACT FROM AUTHOR]

Plant domestication genetics has been of interest not only for evolutionary biologists but also for anthropologists and breeders, because of its past and present role in human cultural evolution. Capsicum baccatum, which grows in the Seasonally Dry Tropical Forests of South America (SDTF), was domesticated by native peoples and used as a spice. The centre of domestication has been discussed, and vast territories of Peru and Bolivia have been proposed. The aims of this research were to elucidate the geographical origin of cultivated C. baccatum and to infer geological and climate events that have influenced the distribution of its genetic variability. Samples were collected from 25 localities across the entire range of wild C. baccatum and analysed using DNA sequences and phylogeographical approaches; they were then compared with 20 samples of cultivated forms obtained from different South American markets. We found a main centre of C. baccatum domestication spanning Bolivian Amazonia and the inter-Andean valleys. We also inferred an ancient cultivation site between Bolivia and Argentina. Finally, we found two lineages of wild populations distributed in nuclei of SDTFs which have been fragmented during glacial periods, when aridity increased and expansion of Chaco vegetation fragmented the region. [ABSTRACT FROM AUTHOR]

This study introduces a newBayesian technique formolecular dating that explicitly accommodates for uncertainty in the phylogenetic position of calibrated nodes derived from the analysis of fossil data. The proposed approach thus defines an adequate framework for incorporating expert knowledge and/or prior information about the way fossils were collected in the inference of node ages. Although it belongs to the class of "node-dating" approaches, this method shares interesting properties with "tip-dating" techniques. Yet, it alleviates some of the computational and modeling difficulties that hamper tip-dating approaches. The influence of fossil data on the probabilistic distribution of trees is the crux of the matter considered here. More specifically, among all the phylogenies that a treemodel (e.g., the birth--death process) generates, only a fraction of them "agree" with the fossil data. Bayesian inference under the new model requires taking this fraction into account. However, evaluating this quantity is difficult in practice. A generic solution to this issue is presented here. The proposed approach relies on a recent statistical technique, the so-called exchange algorithm, dedicated to drawing samples from "doubly intractable" distributions. A small example illustrates the problem of interest and the impact of uncertainty in the placement of calibration constraints in the phylogeny given fossil data. An analysis of land plant sequences and multiple fossils further highlights the pertinence of the proposed approach. [ABSTRACT FROM AUTHOR]

Primates have long been a test case for the development of phylogenetic methods for divergence time estimation. Despite a large number of studies, however, the timing of origination of crown Primates relative to the Cretaceous--Paleogene (K--Pg) boundary and the timing of diversification of the main crown groups remain controversial. Here, we analysed a data set of 372 taxa (367 Primates and 5 outgroups, 3.4 million aligned base pairs) that includes nine primate genomes.We systematically explore the effect of different interpretations of fossil calibrations and molecular clock models on primate divergence time estimates.We find that even small differences in the construction of fossil calibrations can have a noticeable impact on estimated divergence times, especially for the oldest nodes in the tree. Notably, choice of molecular rate model (autocorrelated or independently distributed rates) has an especially strong effect on estimated times, with the independent rates model producing considerably more ancient age estimates for the deeper nodes in the phylogeny. We implement thermodynamic integration, combined with Gaussian quadrature, in the program MCMCTree, and use it to calculate Bayes factors for clock models. Bayesian model selection indicates that the autocorrelated rates model fits the primate data substantially better, and we conclude that time estimates under this model should be preferred.We show that for eight core nodes in the phylogeny, uncertainty in time estimates is close to the theoretical limit imposed by fossil uncertainties. Thus, these estimates are unlikely to be improved by collecting additional molecular sequence data. All analyses place the origin of Primates close to the K--Pg boundary, either in the Cretaceous or straddling the boundary into the Palaeogene. [ABSTRACT FROM AUTHOR]

The systematics and the phylogenetic position of the Caribbean representatives of Phaenonotum Sharp (Coleoptera: Hydrophilidae) are investigated to understand the composition of the Caribbean fauna and its origin. Phylogenetic analysis based on mitochondrial and nuclear genes has revealed the Caribbean species to be situated in three deeply nested clades, inferring multiple colonization of Caribbean islands from the continent. Time-tree analysis and BioGeoBEARS analyses of ancestral ranges estimated the oldest clade, consisting of wingless single-island endemics of Cuba (P. delgadoi), Jamaica (P. ondreji sp. nov.) and Hispaniola (P. laterale sp. nov.), to have diverged c. 46.6 Mya from the South American ancestor and subsequently colonizing the Caribbean most likely via the GAARlandia land bridge connecting South America with the Greater Antilles. The remaining three Caribbean species, including the Puerto Rican endemic, P. borinquenum sp. nov., are of more recent (Miocene to Pliocene) origin and colonized the Greater Antilles by over-water dispersal. All the Caribbean species are illustrated and diagnosed, and three new species are described. The genus Phaenonotum, excluding P. caribense Archangelsky, is confirmed as a monophylum. We demonstrate that species-level taxonomy of Phaenonotum is difficult to solve by morphology alone and ideally requires the combination of morphology and molecular markers. [ABSTRACT FROM AUTHOR]

Phyllomys is the most species-rich genus among spiny tree rats of the family Echimyidae and includes members widely distributed throughout the Atlantic Forest of South America. Among recognized species recovered in previous studies, 4 lineages are unnamed and their taxonomic distinctness needs further investigation. Biogeographic analyses recovered an Amazonian ancestor of the basal lineage leading to living Phyllomys, suggesting ancient connections between the 2 largest South American rainforests, and presence of rainforest corridors within the central Brazilian dry biomes. Based on exhaustive taxonomic sampling of Phyllomys, applying multigene phylogenetic methods, and morphological and karyological data, we described a new species of Phyllomys from central Brazil. Geographical records from the center of the Cerrado biome of central Brazil indicate an unexpected location for the distribution of the genus, given the contrast between the physical and biological characteristics of the Cerrado and Atlantic Forest habitats. Contrary to previous studies, the analysis of the ancestral geographic range performed here suggests a Cerrado ancestral distribution for Phyllomys during the late Miocene. This result favors the hypothesis of a past link between the Amazon and Atlantic Forest in central Brazil, through the region occupied today by the dry Cerrado, and that forest expansions and contractions may have occurred in Brazilian dry biomes over the course of the Tertiary. [ABSTRACT FROM AUTHOR]

The Mammarenavirus genus includes several pathogenic species of rodent-borne viruses. Old World (OW) mammarenaviruses infect rodents in the Murinae subfamily and are mainly transmitted in Africa and Asia; New World (NW) mammarenaviruses are found in rodents of the Cricetidae subfamily in the Americas. We applied a selection-informed method to estimate that OW and NW mammarenaviruses diverged less than ~45,000 years ago (ya). By incorporating phylogeographic inference, we show that NW mammarenaviruses emerged in the Latin America-Caribbean region ~41,400-3,300 ya, whereas OW mammarenaviruses originated ~23,100-1,880 ya, most likely in Southern Africa. Cophylogenetic analysis indicated that cospeciation did not contribute significantly to mammarenavirus-host associations. Finally, we show that extremely strong selective pressure on the viral polymerase accompanied the speciation of NW viruses. These data suggest that the evolutionary history of mammarenaviruses was not driven by codivergence with their hosts. The viral polymerase should be regarded as a major determinant of mammarenavirus adaptation. [ABSTRACT FROM AUTHOR]

A phylogeographical study of the northern three-toed jerboa, Dipus sagitta, which has one of the largest geographical ranges among Palaearctic desert rodents, was performed using complete mitochondrial cytochrome b (Cytb) and fragments of two nuclear genes. Phylogenetic analysis of the Cytb data, including 222 specimens from 69 localities revealed, six allopatric lineages divergent at 7.4-10.1%. In some lineages the Cytb data are supported by nuclear data, thus confirming a high level of cryptic diversity within D. sagitta. The recovered pattern of genetic differentiation was reviewed from a taxonomic perspective. In general, the mitochondrial lineages show relatively good correlation with morphological subspecies. Both mitochondrial and nuclear data support the isolated position of the Qaidam lineage, which diverged from the rest in the Early Pleistocene (~1.5 Myr) according to our molecular clock results. Therefore, we propose to recognize this lineage as a separate species, Dipus deasyi; the taxonomic status of other lineages remains to be clarified. The results are consistent with the hypothesis that the centre of the origin of the D. sagitta complex is located in the eastern part of the range. The geographical structure of genetic variation in D. sagitta is compared to those in other desert rodents. [ABSTRACT FROM AUTHOR]