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Background: Endemic plants are key to understanding the evolutionary history and enhancing biodiversity within their unique regions, while also offering significant economic potential. The East Asian endemic genus Corchoropsis Siebold & Zucc., classified within the subfamily Dombeyoideae of Malvaceae s.l., comprises three species. Results: This study characterizes the complete plastid genomes (plastomes) of C. crenata var. crenata Siebold & Zucc. and C. crenata var. hupehensis Pamp., which range from 160,093 to 160,724 bp. These genomes contain 78 plastid protein-coding genes, 30 tRNA, and four rRNA, except for one pseudogene, infA. A total of 316 molecular diagnostic characters (MDCs) specific to Corchoropsis were identified. In addition, 91 to 92 simple sequence repeats (SSRs) in C. crenata var. crenata and 75 in C. crenata var. hupehensis were found. Moreover, 49 long repeats were identified in both the Chinese C. crenata var. crenata and C. crenata var. hupehensis, while 52 were found in the South Korean C. crenata var. crenata. Our phylogenetic analyses, based on 78 plastid protein-coding genes, reveal nine subfamilies within the Malvaceae s.l. with high support values and confirm Corchoropsis as a member of Dombeyoideae. Molecular dating suggests that Corchoropsis originated in the Oligocene, and diverged during the Miocene, influenced by the climate shift at the Eocene–Oligocene boundary. Conclusions: The research explores the evolutionary relationships between nine subfamilies within the Malvaceae s.l. family, specifically identifying the position of the Corchoropsis in the Dombeyoideae. Utilizing plastome sequences and fossil data, the study establishes that Corchoropsis first appeared during the Eocene and experienced further evolutionary divergence during the Miocene, paralleling the evolutionary patterns observed in other East Asian endemic species. [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]

Aim Location Time Period Major Taxa Studied Methods Results Main Conclusions To date a vicariant event through the mutualistic relationship of a hylid frog and its bromeliad host found across two isolated mountain ranges as part of an island–continental split and to use this information to calibrate a molecular dating analysis of hylids.South America.Pliocene.Treefrogs, Arboranae.Pliocene tectonic movements sank a portion of a mountain range that connected present‐day Trinidad (island) and northern Venezuela, eventually isolating populations of the golden tree frog Phytotriades auratus and its host bromeliad Glomeropitcairnia erectiflora on both sides of a saltwater barrier. We estimated the submersion rate timing of the vicariant event, then employed ecological niche modelling to establish the distribution of the frog and its host to the Pliocene. We generated nucleotide sequence data for the hylid on each side of the marine barrier and proposed a biogeographic calibration for the split between populations. Using Bayesian phylogenetic analysis, we evaluated the impact of incorporating this biogeographic calibration on estimates of treefrog divergence times.A relatively continuous, high‐elevation mountain range existed before the Pliocene and the opening of the Gulf of Paria (4.45 ± 0.85 Ma). Phytotriades auratus and G. erectiflora would have been distributed across the Paria and Northern Range mountains as a single population since the Pliocene. Divergence times among treefrogs (Arboranae) were older than those inferred using fossil calibrations alone, with mean age estimates for subfamilies and genera being ~2 and ~1.2 million years older, respectively.Our study presents a biogeographic calibration based on a vicariant model that connects the evolution of the populations of a hylid through geology and ecological data. The implementation of this date as a molecular clock calibration reduces the uncertainty in date estimates for the shallower nodes in the phylogeny of Arboranae. [ABSTRACT FROM AUTHOR]

Biotic exchanges between Taiwan and Mainland China have shaped the biodiversity and ecosystems of both regions. Exchanges from Mainland China to Taiwan have received more attention, mainly studied in terrestrial vertebrates, while the reverse direction and invertebrates have largely been overlooked. Here, we explore the dispersal events between these two regions based on the moths of three species groups of Obeidia, including Taiwan taxa and its relatives from mainland. We conducted mixed methods and analysis, including reconstructing a phylogenetic tree, estimating associated divergence times and inferring ancestral areas and source regions, to explore the phylogeographical structure and genetic pattern of three groups based on eight genes. Our results revealed a structure of three clades and every clade included at least one Taiwanese taxa and its closest relatives of mainland of China, and also served Taiwan as an important source region of two mainland taxa. Our study revealed various origin pattern and dispersal models on the basis of three species groups of Obeidia. Bi‐directional biotic exchange via a land bridge were found: four Taiwanese taxa originated from mainland, and two of them migrated back to mainland. Both eastern Himalayas and south China are important origin areas for Taiwan biota, and the dominant source region may need multiple insect cases to confirm. Our study also provided evidences for disjunct distribution from the perspective of insecta molecular phylogeny. [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]

Abstract Background Endemic plants are key to understanding the evolutionary history and enhancing biodiversity within their unique regions, while also offering significant economic potential. The East Asian endemic genus Corchoropsis Siebold & Zucc., classified within the subfamily Dombeyoideae of Malvaceae s.l., comprises three species. Results This study characterizes the complete plastid genomes (plastomes) of C. crenata var. crenata Siebold & Zucc. and C. crenata var. hupehensis Pamp., which range from 160,093 to 160,724 bp. These genomes contain 78 plastid protein-coding genes, 30 tRNA, and four rRNA, except for one pseudogene, infA. A total of 316 molecular diagnostic characters (MDCs) specific to Corchoropsis were identified. In addition, 91 to 92 simple sequence repeats (SSRs) in C. crenata var. crenata and 75 in C. crenata var. hupehensis were found. Moreover, 49 long repeats were identified in both the Chinese C. crenata var. crenata and C. crenata var. hupehensis, while 52 were found in the South Korean C. crenata var. crenata. Our phylogenetic analyses, based on 78 plastid protein-coding genes, reveal nine subfamilies within the Malvaceae s.l. with high support values and confirm Corchoropsis as a member of Dombeyoideae. Molecular dating suggests that Corchoropsis originated in the Oligocene, and diverged during the Miocene, influenced by the climate shift at the Eocene–Oligocene boundary. Conclusions The research explores the evolutionary relationships between nine subfamilies within the Malvaceae s.l. family, specifically identifying the position of the Corchoropsis in the Dombeyoideae. Utilizing plastome sequences and fossil data, the study establishes that Corchoropsis first appeared during the Eocene and experienced further evolutionary divergence during the Miocene, paralleling the evolutionary patterns observed in other East Asian endemic species.

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]

Water crickets of the subfamily Haloveliinae are semi‐aquatic bugs occurring in freshwater and marine habitats throughout the Indo‐Australian region, presently including six genera with more than 80 extant species. Whether lineage diversification in Haloveliinae is associated with the utilization of new ecological niches caused by transition events between freshwater and marine habitats remains poorly understood. We investigate the evolutionary history of Haloveliinae using large‐scale phylogenomic datasets and a set of novel redefined morphological characters based on 24 ingroup taxa representing all recognized genera. Our phylogenetic results based on the novel datasets definitively indicate that the freshwater genus Strongylovelia Esaki as currently defined is paraphyletic and supports the establishment of a new genus: Metavelia gen. nov., including three congeneric species: Metavelia patiooni comb. nov. (type species), Metavelia priori comb. nov. and Metavelia albicolli comb. nov. Reconstruction of ancestral habitats suggests a freshwater origin for the Haloveliinae. Divergence time estimations reveal that the origin of the monophyletic marine clade occurred at around 83 Ma (95% highest posterior density: 71–98 Ma) in the Late Cretaceous, involving a single transition event from freshwater to marine habitats. This time coincides with the period of high global sea levels in the Late Cretaceous. During this period, the marine incursions caused by the massive sea level rise flooded the continental margins, especially in Southeast Asia, where ancestral Haloveliinae were probably distributed. The appearance of new marine habitats after the marine incursions (e.g., intertidal, mangroves and estuarine) probably led to a subsequent establishment and diversification of the marine lineages. [ABSTRACT FROM AUTHOR]

Sengis (order Macroscelidea) are small mammals endemic to Africa. The taxonomy and phylogeny of sengis has been difficult to resolve due to a lack of clear morphological apomorphies. Molecular phylogenies have already significantly revised sengi systematics, but until now no molecular phylogeny has included all 20 extant species. In addition, the age of origin of the sengi crown clade and the divergence age of its two extant families remain unclear. Two recently published studies based on different datasets and age-calibration parameters (DNA type, outgroup selection, fossil calibration points) proposed highly different divergent age estimates and evolutionary scenarios. We obtained nuclear and mitochondrial DNA from mainly museum specimens using target enrichment of single-stranded DNA libraries to generate the first phylogeny of all extant macroscelidean species. We then explored the effects of different parameters (type of DNA, ratio of ingroup to outgroup sampling, number and type of fossil calibration points) and their resulting impacts on age estimates for the origin and initial diversification of Macroscelidea. We show that, even after correcting for substitution saturation, both using mitochondrial DNA in conjunction with nuclear DNA or alone results in much older ages and different branch lengths than when using nuclear DNA alone. We further show that the former effect can be attributed to insufficient amounts of nuclear data. If multiple calibration points are included, the age of the sengi crown group fossil prior has minimal impact on the estimated time frame of sengi evolution. In contrast, the inclusion or exclusion of outgroup fossil priors has a major effect on the resulting node ages. We also find that a reduced sampling of ingroup species does not significantly affect overall age estimates and that terminal specific substitution rates can serve as a means to evaluate the biological likeliness of the produced temporal estimates. Our study demonstrates how commonly varied parameters in temporal calibration of phylogenies affect age estimates. Dated phylogenies should therefore always be seen in the context of the dataset which was used to produce them.

In the present study, we have characterized the complete chloroplast (Cp) genome of Meconopsis torquata Prain (family Papaveraceae), revealing the plastome size of 153,290 bp, and a GC content of 38.72 %. The cp genome features the typical circular quadripartite structure found in flowering plants, including a pair of inverted repeat regions (25,816 bp), isolated by a small single-copy region (17,740 bp) and a large single-copy (83,918 bp). Genome annotation revealed 132 genes: 87 protein-coding genes, 37 tRNAs and eight rRNAs. This comparative study demonstrated that the genome structure, gene number and GC ratio are consistent with several other cp genomes of Meconopsis and Papaver genera. A total of 120 SSRs were detected in the plastome, the majority (111) of which were mononucleotide repeats. Among the longer repeats, palindromic sequences were most common, followed by forward, reverse, and complement repeats. The whole genome alignment revealed the conserved nature of the inverted repeat region over single-copy zones. Nucleotide diversity unveiled hypervariable sites (ycf1, rps16, accD, atpB and psbD) in both the small and large single-copy regions, which could be useful for designing molecular markers for taxonomic identification. Phylogenetic analysis revealed a close alliance of M. torquata with other Meconopsis species, such as M. pinnatifolia and M. paniculata, with strong bootstrap support. Molecular dating suggests that M. torquata originated during the Tortonian age of the Miocene epoch of the Cenozoic era. These findings provide valuable insights for biological research, especially in understanding the genetic and evolutionary divergence within the Papaveraceae family.

Lepidoziaceae are the third‐largest family of liverworts, with about 860 species distributed on all continents. The evolutionary history of this family has not been satisfactorily resolved, with taxa such as Micropterygioideae yet to be included in phylogenetic analyses. We inferred a dated phylogeny of Lepidoziaceae using a data set consisting of 13 genetic markers, sampled from 147 species. Based on our phylogenetic estimate, we used statistical dispersal‐vicariance analysis to reconstruct the biogeographic history of the family. We inferred a crown age of 197 Ma (95% credible interval 157–240 Ma) for the family in the Australian region, with most major lineages also originating in the same region. Micropterygioideae are placed as the sister group to Lembidioideae, with these two lineages diverging from each other about 132 Ma in the South American–Australian region. With South America and Australia being connected through Antarctica at the time, our results suggest a circum‐Antarctic link between Micropterygioideae and the rest of the family. Crown Micropterygioideae were inferred to have arisen 45 Ma in South America before the continent separated from Antarctica. Extinction from southern temperate regions might explain the present‐day restriction of Micropterygioideae to the Neotropics. Our study reveals the influence of past geological events, such as continental drift, on the evolution and distribution of a widespread and diverse family of liverworts. [ABSTRACT FROM AUTHOR]

Increasingly sophisticated molecular techniques and research tools have greatly advanced the understanding of species diversity and phylogenetic relationships in freshwater mussels. However, malacologists have been puzzled by the taxonomic position and species validity of certain species, particularly those described solely based on conchological characteristics. The genus Lepidodesma is one such group. Here, we integrate shell morphology, soft-body anatomy, and molecular phylogeny to delimit the species validity of Lepidodesma aligera (Heude in Conchyliologie Fluviatile de la Provoince de Nanking 3:17–24, 1877) and Lepidodesma languilati (Heude in Journal De Conchyliologie 22:112–118, 1874). Comparative morphology reveals that L. aligera can be distinguished from L. languilati by its higher post-dorsal wing covered with scattered nodules, as well as differences in the incurrent aperture, excurrent aperture, and gill. Additionally, the average genetic distance based on DNA barcodes (COI) between both species is 4.0%. Integrative taxonomy supports the distinct species of L. aligera, rather than synonymy for L. languilati. Mitochondrial phylogenomic analyses confirm four monophyletic groups (Ambleminae + (Gonideinae + (Unioninae + Parreysiinae))) within the family Unionidae. L. aligera and L. languilati have a well-supported sister-group relationship and form a basal clade splitting from the rest of Unioninae. Therefore, the genus Lepidodesma should be classified as Lepidodesmini in Unioninae. The molecular clock with fossil calibration indicates that Lepidodesma originated in the Early Cretaceous (~121.30 Mya, 95% HPD = 90.37–156.54 Mya) and diverged in the Middle Neogene (~12.94 Mya, 95% HPD = 6.72–22.13 Mya). This study firstly provides anatomical features and molecular data for L. aligera and demonstrates the species validity and the systematic position of Lepidodesma taxa, which enrich our understanding of this rare group and facilitate its management and conservation. [ABSTRACT FROM AUTHOR]

Grapevine Pinot gris virus (GPGV) isolates were obtained from German vineyards to investigate their diversity. Phylogenetic and dating analyses of these and GPGV genes and genomes available in GenBank showed that the virus probably diverged from grapevine berry inner necrosis virus (GINV) in wild and cultivated Vitis species, notably Vitis coignetiae, growing in North‐east Asia around 3500 years ago. GPGV probably infected the Eurasian grape (Vitis vinifera subsp. vinifera) when those cultivars were first taken to China during the Han Dynasty (226 BCE–220 CE). GPGV then spread to Europe around 1800 CE, probably via the dissemination of infected plants, and from there, eventually spread worldwide. German isolates were only found in all parts of the post‐1800 CE phylogeny. The German isolates were genetically more diverse, for both MP and CP genes, than those of other European populations, suggesting that the initial stages of the GPGV invasion of Europe were in Germany, not Italy. We discuss the likely North‐east Asian origin of both GPGV and GINV, and the possible coincidences of phylogenetic date estimates with changes to European and world viticulture practices. [ABSTRACT FROM AUTHOR]

Within-host HIV populations continually diversify during untreated infection, and this diversity persists within infected cell reservoirs during antiretroviral therapy (ART). Achieving a better understanding of on-ART proviral evolutionary dynamics, and a better appreciation of how the overall persisting pool of (largely genetically defective) proviruses differs from the much smaller replication-competent HIV reservoir, is critical to HIV cure efforts. We reconstructed within-host HIV evolutionary histories in blood from seven participants of the Women’s Interagency HIV Study who experienced HIV seroconversion, and used these data to characterize the diversity, lineage origins, and ages of proviral env-gp120 sequences sampled longitudinally up to 12 years on ART. We also studied HIV sequences emerging from the reservoir in two participants. We observed that proviral clonality generally increased over time on ART, with clones frequently persisting long term. While on-ART proviral integration dates generally spanned the duration of untreated infection, HIV emerging in plasma was exclusively younger (i.e., dated to the years immediately pre-ART). The genetic and age distributions of distinct proviral sequences remained stable during ART in all but one participant, in whom there was evidence that younger proviruses had been preferentially eliminated after 12 years on ART. Analysis of the gag region in three participants corroborated our env-gp120-based observations, indicating that our observations are not influenced by the HIV region studied. Our results underscore the remarkable genetic stability of the distinct proviral sequences that persist in blood during ART. Our results also suggest that the replication-competent HIV reservoir is a genetically restricted, younger subset of this overall proviral pool. IMPORTANCE Characterizing the genetically diverse HIV sequences that persist in the reservoir despite antiretroviral therapy (ART) is critical to cure efforts. Our observations confirm that proviruses persisting in blood on ART, which are largely genetically defective, broadly reflect the extent of within-host HIV evolution pre-ART. Moreover, on-ART clonal expansion is not appreciably accompanied by the loss of distinct proviral lineages. In fact, on-ART proviral genetic composition remained stable in all but one participant, in whom, after 12 years on ART, proviruses dating to around near ART initiation had been preferentially eliminated. We also identified recombinant proviruses between parental sequence fragments of different ages. Though rare, such sequences suggest that reservoir cells can be superinfected with HIV from another infection era. Overall, our finding that the replication-competent reservoir in blood is a genetically restricted, younger subset of all persisting proviruses suggests that HIV cure strategies will need to eliminate a reservoir that differs in key respects from the overall proviral pool. [ABSTRACT FROM AUTHOR]

Orf virus (ORFV) belongs to the genus Parapoxvirus (Poxviridae family). It is the causative agent of contagious ecthyma (CE) that is an economically detrimental disease affecting small ruminants globally. Contagious ecthyma outbreaks are usually reported in intensive breeding of sheep and goats but they have also been reported in wildlife species. Notably, ORFV can infect humans, leading to a zoonotic disease. This study aims to elucidate the global evolutionary history of ORFV genomes in sheep and goats, including the first genomes from Central America in the analyses. In comparison to the last study on ORFV whole genomes, the database now includes 11 more sheep and goat genomes, representing an increase of 42%. The analysis of such a broader database made it possible to obtain a fine molecular dating of the coalescent time for ORFV S and G genomes, further highlighting the genetic structuring between sheep and goat genomes and corroborating their emergence in the latter half of 20th century. [ABSTRACT FROM AUTHOR]

Simple Summary: Pinna nobilis, a species of marine shellfish living in the Mediterranean Sea, is at a high risk of extinction due to a not-entirely-known disease that started affecting its populations in 2016. In this paper, we reported the main traits of its evolutionary history to understand how this species evolved over time and space from the moment its ancestor entered the Mediterranean. To achieve this goal, we analysed a total of 469 sequences from all over the Mediterranean Sea. Our research showed that P. nobilis evolved from its ancestor about 2.5 million years ago, following a rapid and catastrophic entry of waters from the Atlantic Ocean that pushed the P. nobilis ancestor into the Mediterranean around 5.3 million years ago. Our results also suggest that the central part of the western Mediterranean was the first marine area where this species settled and, later on, it spread to the Adriatic and the eastern part of the basin. This information is of twofold importance, as it helps us to understand how this species adapted to the Mediterranean over time and may be the basis of present and future restocking plans which want to take into consideration the reconstruction of pre-existing genetic variability. Pinna nobilis, commonly known as the noble pen shell, is a marine bivalve endemic to the Mediterranean Sea. Unfortunately, due to a multifactorial disease that began affecting its populations in 2016, the species is currently facing the threat of extinction. To gain insights into the evolutionary history of P. nobilis before the mass mortality event (MME), and to obtain a comprehensive understanding of how evolutionary processes led to the adaptation of the species into the Mediterranean Sea, phylogenetic and phylogeographic analyses were carried out. The dataset analysed includes 469 sequences of COI gene fragment both from GenBank and the present study (100). The analysis performed evidenced that P. nobilis diverged about 2.5 mya, after the entrance of its ancestor into the Mediterranean Sea following the Zanclean flood (5.33 mya). Moreover, our results suggest that the starting point of colonisation was the central part of the western Mediterranean basin, with the eastern basin being populated subsequently. From a conservational viewpoint, these results provide important hints for present and future restocking plans, helping to reconstruct the pre-existing genetic variability in sites where the species became extinct. [ABSTRACT FROM AUTHOR]

As a reference mitogenome, the complete mitochondrial genome of the white-breasted hedgehog, Erinaceus concolor , was firstly presented in this study by employing Long-Range PCR and Next-Generation Sequencing. The total lengths of the mitogenomes were 17.451 bp and 17.455 bp. A total of 37 genes, namely two ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs), 13 protein-coding genes (PCGs), and a non-coding D-loop were encoded in the mitogenome, compatible with the previously reported mitogenomes belonging to representatives of the family Erinaceidae (Mammalia: Eulipotyphla). Maximum Likelihood and Bayesian Inference phylogenetic analyses of Eulipotyphla and Erinaceidae based on the complete mitogenomes revealed a conventional relationship for the relevant organism's groups. Divergence time analyses based on complete mitogenome data revealed that evolutionary divergence events within Erinaceidae began about 58.87 Myr ago corresponding to the early Eocene, and the basal split of Erinaceus dates back to approximately 11.01 Myr ago in the late Miocene. Single cytochrome b -based analyses can be considered weaker, as they produce phylogenies that are relatively inconsistent with the natural classification of Eulipotyphla and put the onset of evolutionary divergence events earlier. The genetic information obtained as a result of this study can be used as a genetic resource for conservation biology studies; it will also undoubtedly contribute to the understanding of molecular evolution of E. concolor and closely related taxa. [ABSTRACT FROM AUTHOR]

Mantodea is a predatory insect group, its members occupying a diverse array of widely distributed habitats. Praying mantis species utilize hunting strategies including remarkable mimicry and unique camouflage for hiding from natural enemies while catching their prey. The emergence of a "cyclopean ear" in mantises is thought to be a morphological innovation of the group, and an "arms race" with echolocating bats is one of the hypotheses put forward to account for the emergence of the mantis ear from a coevolutionary perspective. However, this hypothesis has not been rigorously tested because of a lack of robust higher‐level phylogeny and a detailed chronogram of Mantodea. Previous phylogenetic studies found an incongruence between traditional classification and molecular phylogenetics due to the convergent evolution of various ecomorphic strategies of the lineage. Here, we performed a comprehensive phylogenetic analysis of Mantodea based on data from 61 mitogenomes. Our analyses showed that the monophyly of Acanthopidae, Haaniidae, Nanomantidae, Miomantidae and Mantidea was supported. The newly updated Gonypetidae were paraphyletic, whereas Eremiaphilidae, Deroplatyidae and Toxoderidae were polyphyletic. Our molecular dating analyses inferred that Spinomantodea originated at ca. 149 Ma (Late Jurassic), whereas the origin of hearing mantises (Cernomantodea) was inferred as Early Cretaceous (119 Ma, 95% CI: 110–129 Ma). The molecular dating results indicated that the hearing organ in mantises did not arise in response to bat predation. Our study provides a robust framework for further evolutionary comparative studies of mantises. [ABSTRACT FROM AUTHOR]

Abstract Lepidoziaceae are the third‐largest family of liverworts, with about 860 species distributed on all continents. The evolutionary history of this family has not been satisfactorily resolved, with taxa such as Micropterygioideae yet to be included in phylogenetic analyses. We inferred a dated phylogeny of Lepidoziaceae using a data set consisting of 13 genetic markers, sampled from 147 species. Based on our phylogenetic estimate, we used statistical dispersal‐vicariance analysis to reconstruct the biogeographic history of the family. We inferred a crown age of 197 Ma (95% credible interval 157–240 Ma) for the family in the Australian region, with most major lineages also originating in the same region. Micropterygioideae are placed as the sister group to Lembidioideae, with these two lineages diverging from each other about 132 Ma in the South American–Australian region. With South America and Australia being connected through Antarctica at the time, our results suggest a circum‐Antarctic link between Micropterygioideae and the rest of the family. Crown Micropterygioideae were inferred to have arisen 45 Ma in South America before the continent separated from Antarctica. Extinction from southern temperate regions might explain the present‐day restriction of Micropterygioideae to the Neotropics. Our study reveals the influence of past geological events, such as continental drift, on the evolution and distribution of a widespread and diverse family of liverworts.

Lagerstroemia L. (Lythraceae) is a widely distributed genus of trees and shrubs native to tropical and subtropical environments from Southeast Asia to Australia, with numerous species highly valued as ornamentals. Although the plastomes of many species in this genus have been sequenced, the rates of functional gene evolution and their effect on phylogenetic analyses have not been thoroughly examined. We compared three plastome sequence matrices to elucidate how differences in these datasets affected phylogenetic analyses. Robust phylogenetic relationships for Lagerstroemia species were reconstructed based on different plastome sequence partitions and multiple phylogenetic methods. Identification of single-nucleotide variants within different genes also provides basic data on the patterns of functional gene evolution in Lagerstroemia and may provide insights into how those mutations affect protein structure and potentially drive divergence via cytonuclear incompatibility. These results as well as analyses of non-synonymous and synonymous mutations, indicate that heterotachic modes of evolution are present in functional plastome genes and should be accounted for in the analyses of molecular evolution. In addition, divergence events within the Lagerstroemia were dated for the first time. Several of the divergence estimates corresponded to well-known Earth history events, such as the reduction in global temperatures at the Eocene/Oligocene boundary. Our analyses conducted in Lagerstroemia here dissects the various patterns in the divergence of Lagerstroemia and may provide a useful guide to help plant breeders, as well as the necessity of using plastomic data and as possible as to combine evidence from morphological characteristics to investigate the complicated interspecies relationship and the evolutionary dynamics of species.

ABSTRACTIn order to cure human immunodeficiency virus (HIV), we need to better understand the within-host evolutionary origins of the small reservoir of genome-intact proviruses that persist within infected cells during antiretroviral therapy (ART). Most prior studies on reservoir evolutionary dynamics, however, did not discriminate genome-intact proviruses from the vast background of defective ones. We reconstructed within-host pre-ART HIV evolutionary histories in six individuals and leveraged this information to infer the ages of intact and defective proviruses sampled after an average of >9 years on ART, along with the ages of rebound and low-level/isolated viremia occurring during this time. We observed that the longest-lived proviruses persisting on ART were exclusively defective, usually due to large deletions. In contrast, intact proviruses and rebound HIV exclusively dated to the years immediately preceding ART. These observations are consistent with genome-intact proviruses having shorter lifespans, likely due to the cumulative risk of elimination following viral reactivation and protein production. Consistent with this, intact proviruses (and those with packaging signal defects) were three times more likely to be genetically identical compared to other proviral types, highlighting clonal expansion as particularly important in ensuring their survival. By contrast, low-level/isolated viremia sequences were heterogeneous in terms of age, with some potentially originating from defective proviruses. Results reveal that the HIV reservoir is dominated by clonally enriched and genetically younger sequences that date to the period of untreated infection when viral populations had been under within-host selection pressures for the longest duration. Knowledge of these qualities may help focus strategies for reservoir elimination.IMPORTANCECharacterizing the human immunodeficiency virus (HIV) reservoir that endures despite antiretroviral therapy (ART) is critical to cure efforts. We observed that the oldest proviruses persisting during ART were exclusively defective, while intact proviruses (and rebound HIV) dated to nearer ART initiation. This helps explain why studies that sampled sub-genomic proviruses on-ART (which are largely defective) routinely found sequences dating to early infection, whereas those that sampled replication-competent HIV found almost none. Together with our findings that intact proviruses were more likely to be clonal, and that on-ART low-level/isolated viremia originated from proviruses of varying ages (including possibly defective ones), our observations indicate that (i) on-ART and rebound viremia can have distinct within-host origins, (ii) intact proviruses have shorter lifespans than grossly defective ones and thus depend more heavily on clonal expansion for persistence, and (iii) an HIV reservoir predominantly “dating” to near ART initiation will be substantially adapted to within-host pressures, complicating immune-based cure strategies.

Microbial plankton play a central role in marine biogeochemical cycles, but the timing in which abundant lineages diversified into ocean environments remains unclear. Here, we reconstructed the timeline in which major clades of bacteria and archaea colonized the ocean using a high-resolution benchmarked phylogenetic tree that allows for simultaneous and direct comparison of the ages of multiple divergent lineages. Our findings show that the diversification of the most prevalent marine clades spans throughout a period of 2.2 Ga, with most clades colonizing the ocean during the last 800 million years. The oldest clades – SAR202, SAR324, Ca. Marinimicrobia, and Marine Group II – diversified around the time of the Great Oxidation Event, during which oxygen concentration increased but remained at microaerophilic levels throughout the Mid-Proterozoic, consistent with the prevalence of some clades within these groups in oxygen minimum zones today. We found the diversification of the prevalent heterotrophic marine clades SAR11, SAR116, SAR92, SAR86, and Roseobacter as well as the Marine Group I to occur near to the Neoproterozoic Oxygenation Event (0.8–0.4 Ga). The diversification of these clades is concomitant with an overall increase of oxygen and nutrients in the ocean at this time, as well as the diversification of eukaryotic algae, consistent with the previous hypothesis that the diversification of heterotrophic bacteria is linked to the emergence of large eukaryotic phytoplankton. The youngest clades correspond to the widespread phototrophic clades Prochlorococcus, Synechococcus, and Crocosphaera, whose diversification happened after the Phanerozoic Oxidation Event (0.45–0.4 Ga), in which oxygen concentrations had already reached their modern levels in the atmosphere and the ocean. Our work clarifies the timing at which abundant lineages of bacteria and archaea colonized the ocean, thereby providing key insights into the evolutionary history of lineages that comprise the majority of prokaryotic biomass in the modern ocean.

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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]

The first recombinant SARS-CoV-2 variants were identified in 2022, causing public health concerns. The importance of recombinant variants has increased especially since the WHO designated the recombinant variant XBB and its lineages as subvariants that require monitoring on 20 November 2022. In this study, we provide the first insights into the new SARS-CoV-2 variant named XAN, a recombinant composed of Omicron sub-lineages BA.2 and BA.5. To our knowledge, this is the first report on the recombinant SARS-CoV-2 XAN variant identified in Bulgaria. [ABSTRACT FROM AUTHOR]

A molecular phylogenetic investigation was undertaken for 30 species belonging to 15 genera of the palm family Arecaceae in Bangladesh to infer evolutionary relationships and molecular dating utilizing plastid-based matK and rbcL genes through multifacetedalgorithm driven approaches with Neighbor-Joining, Maximum-Likelihood, and Bayesian Inference methods. The study revealed that matK has better species discrimination efficiency than rbcL gene due to its highly variable nature. Transition/transversion bias test corroborated this finding as matK showed higher bias (2.632) than rbcL (2.235). Nucleotide substitution patterns were visualized via HYPERMUT program, which unveiled higher variability in matK and lower variability in rbcL alignment. Phylogenetic trees constructed with matK revealed monophyletic nature of origin for all the three subfamilies, viz. Arecoideae, Coryphoideae and Calamoideae, while rbcL trees exhibited polyphyly for Coryphoideae and monophyly for Arecoideae and Calamoideae. All the nine tribes belonging to three subfamilies demonstrated monophyletic nature in matK trees. Bootstrap support and Bayesian posterior probability were found to be higher in matK topologies than that of rbcL. The molecular clock test unraveled an equal evolutionary rate for matK and unequal rate for rbcL sequences. Molecular dating approach unveiled Calamoideae to be the most ancient subfamily (65.75 MYA) among the three subfamilies that originated during the Late Cretaceous period in the Mesozoic era, whereas Coryphoideae and Arecoideae were found to have originated in the Cenozoic era. [ABSTRACT FROM AUTHOR]

In the present study, we reconstruct phylogenetic relationships within the chromosomally variable Sorex araneus species group based on 20 nuclear loci and the mitochondrial cyt b gene. In the species tree, Nearctic S. arcticus represents the earliest offshoot of the group followed by Holarctic S. tundrensis and Siberian S. daphaenodon. Five other species distributed mostly in Europe form a well‐supported clade. Coding regions showed stronger phylogenetic signal than introns. The results suggest a high incidence of reticulation in the evolution of the group. The authentic mitochondrial lineage of the Iberian shrew S. granarius was found to be close phylogenetically to S. coronatus, which confirms that some populations of the Iberian shrew S. granarius were introgressed from S. araneus. Footprints of deeper reticulations are revealed for the first time, indicating the potential hybrid origin of the S. arcticus and S. coronatus lineages. Ancient hybridisations are hypothesised to be the source of discordance between molecular‐ and karyotype‐based phylogenetic reconstructions. [ABSTRACT FROM AUTHOR]

We identified an emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant by viral whole-genome sequencing of 2,172 nasal/nasopharyngeal swab samples from 44 counties in California, a state in the western United States. Named B.1.427/B.1.429 to denote its two lineages, the variant emerged in May 2020 and increased from 0% to >50% of sequenced cases from September 2020 to January 2021, showing 18.6%-24% increased transmissibility relative to wild-type circulating strains. The variant carries three mutations in the spike protein, including an L452R substitution. We found 2-fold increased B.1.427/B.1.429 viral shedding in vivo and increased L452R pseudovirus infection of cell cultures and lung organoids, albeit decreased relative to pseudoviruses carrying the N501Y mutation common to variants B.1.1.7, B.1.351, and P.1. Antibody neutralization assays revealed 4.0- to 6.7-fold and 2.0-fold decreases in neutralizing titers from convalescent patients and vaccine recipients, respectively. The increased prevalence of a more transmissible variant in California exhibiting decreased antibody neutralization warrants further investigation.

Given the Indian block’s ancient association with Gondwana and subsequent separation from Africa, then Madagascar, then the Seychelles, vicariance has often been invoked to explain the distribution of some of India’s extant biota that might have had Gondwanan origins. Here I review phylogenetic studies and fossil data of Indian tetrapods to ascertain the contribution of dispersal and vicariance in shaping the assemblage. Paleogene dispersal into India accounts for almost all of the tetrapod clades in India. Vicariance is invoked for three groups, all fossorial; the caecilians, the frog family Nasikabatrachidae and the blindsnake family Gerrhopilidae. This review concludes that practically all of India’s Late Cretaceous tetrapod fauna (of Gondwanan origin) was extirpated during the Cretaceous-Paleogene mass extinction, which may have been exacerbated by the coeval volcanism associated with the emplacement of the Deccan Trap large igneous province. Subsequently, the tetrapod fauna was built up by incoming elements as India advanced towards Asia, docking with the continent in the Paleogene.

Orf virus (ORFV) belongs to the genus Parapoxvirus (Poxviridae family). It is the causative agent of contagious ecthyma (CE) that is an economically detrimental disease affecting small ruminants globally. Contagious ecthyma outbreaks are usually reported in intensive breeding of sheep and goats but they have also been reported in wildlife species. Notably, ORFV can infect humans, leading to a zoonotic disease. This study aims to elucidate the global evolutionary history of ORFV genomes in sheep and goats, including the first genomes from Central America in the analyses. In comparison to the last study on ORFV whole genomes, the database now includes 11 more sheep and goat genomes, representing an increase of 42%. The analysis of such a broader database made it possible to obtain a fine molecular dating of the coalescent time for ORFV S and G genomes, further highlighting the genetic structuring between sheep and goat genomes and corroborating their emergence in the latter half of 20th century.

Two species of large cats found at the Tanzanian Pliocene australopithecine locality of Laetoli have been controversial since their first description in 1987. A lion-sized form was referred to Panthera onca gombaszoegensis, P. palaeosinensis, P. shawi, P. leo or to a related form, and most recently compared to P. onca. A leopard-sized species was attributed to P. pardus or to Puma pardoides. Accepting the leopard-like form as the oldest evidence of the genus Panthera to calibrate molecular dating, this site started to play an important role in understanding felid evolution. A new discussion of the extremely scanty material now revises the earlier classifications and shows that the Laetoli "lion" is not a lion and the Laetoli "leopard" is not a leopard. There seems to be no doubt that the lion-sized cat is a species of its own, representing an early stage of Panthera intrageneric evolution, the metapopulation around the first node as defined by molecular phylogenetics. Taxonomically it is introduced as Panthera principialis sp. nov. The Early Pleistocene lion-sized cat from the South African sites Bolt's Farm, Swartkrans and Kromdraai is here attributed species rank, P. shawi, and understood to represent the metapopulation around the lion-leopard evolutionary node. The leopard-sized Laetoli cat qualifies as an early African member of the genus Puma, but it is not the same as the later Early Pleistocene Swartkrans form. The latter, originally described as Panthera pardus incurva, is proposed here to have arisen by introgressive hybridization of an African puma with an early Panthera species and named Puma incurva. The results of this review give definite support for one of competing sets of molecular dating. [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]

The islands of Southeast Asia comprise one of the most geologically and biogeographically complex areas in the world and are a centre of exceptional floristic diversity, harbouring 45,000 species of flowering plants. Cyrtandra, with over 800 species of herbs and shrubs, is the largest genus in the family Gesneriaceae and is one of the most emblematic and species-rich genera of the Malesian rainforest understorey. The high number of species and tendency to narrow endemism make Cyrtandra an ideal genus for examining biogeographic patterns. We sampled 128 Cyrtandra taxa from key localities across Southeast Asia to evaluate the geo-temporal patterns and evolutionary dynamics of this clade. One nuclear and four chloroplast regions were used for phylogenetic reconstruction, molecular dating, and ancestral range estimation. Results from the dating analysis suggest that the great diversity of Cyrtandra seen in the Malesian region results from a recent radiation, with most speciation taking place in the last five million years. Borneo was recovered as the most likely ancestral range of the genus, with the current distribution of species resulting from a west to east migration across Malesia that corresponds with island emergence and mountain building. Lastly, our investigation into the biogeographic history of the genus indicates high levels of floristic exchange between the islands on the Sunda shelf and the important role of the Philippines as a stepping stone to Wallacea and New Guinea. These patterns underlie much of the plant diversity in the region and form an emerging paradigm in Southeast Asian plant biogeography.

Abstract Background Betulaceae is a relatively small but morphologically diverse family, with many species having important economic and ecological values. Although plastome structure of Betulaceae has been reported sporadically, a comprehensive exploration for plastome evolution is still lacking. Besides, previous phylogenies had been constructed based on limited gene fragments, generating unrobust phylogenetic framework and hindering further studies on divergence ages, biogeography and character evolution. Here, 109 plastomes (sixteen newly assembled and 93 previously published) were subject to comparative genomic and phylogenomic analyses to reconstruct a robust phylogeny and trace the diversification history of Betulaceae. Results All Betulaceae plastomes were highly conserved in genome size, gene order, and structure, although specific variations such as gene loss and IR boundary shifts were revealed. Ten divergent hotspots, including five coding regions (P i > 0.02) and five noncoding regions (P i > 0.035), were identified as candidate DNA barcodes for phylogenetic analysis and species delimitation. Phylogenomic analyses yielded high-resolution topology that supported reciprocal monophyly between Betula and Alnus within Betuloideae, and successive divergence of Corylus, Ostryopsis, and Carpinus-Ostrya within Coryloideae. Incomplete lineage sorting and hybridization may be responsible for the mutual paraphyly between Ostrya and Carpinus. Betulaceae ancestors originated from East Asia during the upper Cretaceous; dispersals and subsequent vicariance accompanied by historical environment changes contributed to its diversification and intercontinental disjunction. Ancestral state reconstruction indicated the acquisition of many taxonomic characters was actually the results of parallel or reversal evolution. Conclusions Our research represents the most comprehensive taxon-sampled and plastome-level phylogenetic inference for Betulaceae to date. The results clearly document global patterns of plastome structural evolution, and established a well-supported phylogeny of Betulaceae. The robust phylogenetic framework not only provides new insights into the intergeneric relationships, but also contributes to a perspective on the diversification history and evolution of the family.

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]

Camellia contains tea, oil camellia, and camellias which benefit people globally. Its infrageneric classification is, however, controversial and unstable, and former phylogenetic analyses failed to yield robust and consistent trees. Here, we aimed to reconstruct a robust phylogenetic tree, date all clades and discuss the evolutionary history of Camellia. Emphasizing the taxonomically comprehensive sampling rather than more DNA data, orthologous nuclear RPB2 introns 11–15 and 23, and waxy were sequenced for 99 taxa of Camellia to reconstruct its phylogenetic history. Ten clades are identified in Camellia: Camellia II, Camelliopsis, Corallina, Furfuracea, Heterogenea, Paracamellia, Piquetia, Stereocarpus, Thea and Yellow camellias II. Camellia grijsii and C. shensiensis are not closely related with other oil camellias that form the clade Paracamellia. Sections Camelliopsis and Theopsis together form the clade Camelliopsis, while clade Furfuracea consists of sect. Furfuracea and C. hongkongensis. Camellia connata is separated from C. lanceolata but nested in the clade Heterogenea, and C. longissima is nested in the clade Thea, suggesting a new germplasm for tea breeding. Molecular dating using four fossil calibration points suggests that the crown age of Camellia is 39.5 Ma with clade Corallina probably the earliest infrageneric clade to diversify and the most widespread clade, Paracamellia, the latest. Our findings provide new insights into the phylogenetic relationships, systematics and evolutionary history of Camellia. [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]

Nemognathinae is the most widespread subfamily of Meloidae, with ~600 species, and includes the only blister beetles distributed in Australia and on islands of the western Pacific. Four tribes are recognised based on morphology: Stenoderini, Palaestrini, Horiini and Nemognathini. Using two mitochondrial (16S , COI) and three nuclear markers (CAD , 28S , ITS2), and both maximum likelihood and Bayesian approaches, this study describes the evolutionary history of Nemognathinae based on molecular data for the first time. We provided a fossil-calibrated phylogeny that unravels the phylogenetic relationships among the tribes and among most of the genera, and a reconstruction of the biogeographic history using a parametric approach. Our results recognised the four tribes that were described previously based on morphology and revealed the presence of another well-differentiated clade corresponding to the genus Zoltanzonitis. Phylogenetic relationships among the tribes are well supported, with Stenoderini as the most ancient lineage, followed by Zoltanzonitini, Palaestrini, Horiini and Nemognathini. A few long-standing genera within Nemognathini (Nemognatha , Zonitis , Stenoria) and the nominate subgenus Stenodera (Stenodera) were recovered as polyphyletic. In addition, biogeographic analyses revealed the origin of the subfamily in the Old World during the Eocene, and the associated diversification into the five tribes astride the Eocene and Oligocene between 46 and 30 Ma. Based on these results we propose the new tribe Zoltanzonitini, and the elevation of the subgenus Pronemognatha to genus level, new status. In addition, Zonitoschema breveapicalis new comb. , Z. curticeps new comb. and Z. pulchella new status are proposed. ZooBank: urn:lsid:zoobank.org:pub:72EECC6D-36A6-4DD7-B4DB-D0692034E775. Nemognathinae is the most widespread Meloidae subfamily, with ~600 species, among which are the only blister beetle species that occur in Oceania. A comprehensive molecular phylogeny for the group is lacking. We investigated the history of this subfamily with a fossil-calibrated molecular approach, revealing the presence of a new tribe, the polyphyly of a few genera and an Eocene origin in the Old World. This work represents the first molecular phylogeny of Nemognathinae and contributes to revealing the evolutionary history of the Meloidae. [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]

The current distribution patterns of many Mediterranean species are often a consequence of large and impactful past geoclimatic events, such as the Messinian Salinity Crisis (MSC) and the Quaternary glacial cycles. Cicadas are flying insects with poor dispersal ability, which have experienced intense local differentiation in the Mediterranean, where the genus Tettigettalna has surfaced as a biogeographic model. The genus includes 10 species with species‐specific calling songs but identical morphology. All Tettigettalna species are restricted to Southern Iberia, with the exception of T. estrellae (northwest Iberia), the widespread T. argentata (mainly Iberia, France and Italy), and T. afroamissa (Morocco). With an expanded genetic dataset involving nuclear (EF1α) and mitochondrial (5′ and 3′ COI and ATP) loci, we reconstructed the phylogeny of the genus and estimated divergence dates for Tettigettalna species under a Bayesian framework. Phylogeny with the new mitochondrial dataset was in agreement with previous studies, whereas the nuclear EF1α supported T. josei and T. afroamissa as monophyletic clades but lacked resolution to resolve the remaining taxa. Some sister taxa share mitochondrial haplotypes, hinting for incomplete lineage sorting. Estimates of divergence time settled T. josei as the earliest diverging lineage, likely as a pre‐ or early‐MSC event. As for the origin of T. afroamissa in Morocco, though time estimates could not entirely rule out post‐MSC dispersal, the most likely scenario points to isolation of African Tettigettalna after the reopening of the strait of Gibraltar. The Pleistocene glaciations that followed likely impacted on the diversification of the remaining species of the genus in southern Iberia refugia. [ABSTRACT FROM AUTHOR]

Encompassing ca. 200 species distributed in paleotropical Africa and Asia, Amorphophallus is one of the largest genera of Araceae. In spite of the great economic interest in its glucomannan production, only a few studies have attempted to grasp the evolutionary history of this genus. In the current state of knowledge, four main clades, mostly linked to biogeographical delineation, have been identified from phylogenies based on a few genes. However, relationships among and within these clades still remain unclear, due to the rapid radiation that occurred during the early evolutionary history of the genus. Here, we generated genome skimming libraries for 43 specimens from 36 species distributed across the 4 clades, which allowed us to produce a phylogenetic matrix for a set of 71 plastid genes. Our phylogenies confirm the monophyly of these clades but show a new and well‐resolved arrangement among these clades. Our analyses therefore provide a new scenario and timeline for the evolution of the main Amorphophallus clades, consistent with the morphological characteristics of the clades. The inferred scenario is also in agreement with climate dynamics and the onset of long‐distance dispersal by the earliest migratory birds near the Oligocene/Miocene transition around 23 million years ago. Our study provides an up‐to‐date baseline to understand biogeographic and ecological processes that shaped the current diversity and distribution of Amorphophallus, paving the way for larger‐scale phylogenomic studies based on plastid and nuclear genomes. [ABSTRACT FROM AUTHOR]

Pinna nobilis, commonly known as the noble pen shell, is a marine bivalve endemic to the Mediterranean Sea. Unfortunately, due to a multifactorial disease that began affecting its populations in 2016, the species is currently facing the threat of extinction. To gain insights into the evolutionary history of P. nobilis before the mass mortality event (MME), and to obtain a comprehensive understanding of how evolutionary processes led to the adaptation of the species into the Mediterranean Sea, phylogenetic and phylogeographic analyses were carried out. The dataset analysed includes 469 sequences of COI gene fragment both from GenBank and the present study (100). The analysis performed evidenced that P. nobilis diverged about 2.5 mya, after the entrance of its ancestor into the Mediterranean Sea following the Zanclean flood (5.33 mya). Moreover, our results suggest that the starting point of colonisation was the central part of the western Mediterranean basin, with the eastern basin being populated subsequently. From a conservational viewpoint, these results provide important hints for present and future restocking plans, helping to reconstruct the pre-existing genetic variability in sites where the species became extinct.

Abstract Background An accurate timescale of evolutionary history is essential to testing hypotheses about the influence of historical events and processes, and the timescale for evolution is increasingly derived from analysis of DNA sequences. But variation in the rate of molecular evolution complicates the inference of time from DNA. Evidence is growing for numerous factors, such as life history and habitat, that are linked both to the molecular processes of mutation and fixation and to rates of macroevolutionary diversification. However, the most widely used methods rely on idealised models of rate variation, such as the uncorrelated and autocorrelated clocks, and molecular dating methods are rarely tested against complex models of rate change. One relationship that is not accounted for in molecular dating is the potential for interaction between molecular substitution rates and speciation, a relationship that has been supported by empirical studies in a growing number of taxa. If these relationships are as widespread as current evidence suggests, they may have a significant influence on molecular dates. Results We simulate phylogenies and molecular sequences under three different realistic rate variation models—one in which speciation rates and substitution rates both vary but are unlinked, one in which they covary continuously and one punctuated model in which molecular change is concentrated in speciation events, using empirical case studies to parameterise realistic simulations. We test three commonly used “relaxed clock” molecular dating methods against these realistic simulations to explore the degree of error in molecular dates under each model. We find average divergence time inference errors ranging from 12% of node age for the unlinked model when reconstructed under an uncorrelated rate prior using BEAST 2, to up to 91% when sequences evolved under the punctuated model are reconstructed under an autocorrelated prior using PAML. Conclusions We demonstrate the potential for substantial errors in molecular dates when both speciation rates and substitution rates vary between lineages. This study highlights the need for tests of molecular dating methods against realistic models of rate variation generated from empirical parameters and known relationships.

Background: Betulaceae is a relatively small but morphologically diverse family, with many species having important economic and ecological values. Although plastome structure of Betulaceae has been reported sporadically, a comprehensive exploration for plastome evolution is still lacking. Besides, previous phylogenies had been constructed based on limited gene fragments, generating unrobust phylogenetic framework and hindering further studies on divergence ages, biogeography and character evolution. Here, 109 plastomes (sixteen newly assembled and 93 previously published) were subject to comparative genomic and phylogenomic analyses to reconstruct a robust phylogeny and trace the diversification history of Betulaceae. Results: All Betulaceae plastomes were highly conserved in genome size, gene order, and structure, although specific variations such as gene loss and IR boundary shifts were revealed. Ten divergent hotspots, including five coding regions (Pi > 0.02) and five noncoding regions (Pi > 0.035), were identified as candidate DNA barcodes for phylogenetic analysis and species delimitation. Phylogenomic analyses yielded high-resolution topology that supported reciprocal monophyly between Betula and Alnus within Betuloideae, and successive divergence of Corylus, Ostryopsis, and Carpinus-Ostrya within Coryloideae. Incomplete lineage sorting and hybridization may be responsible for the mutual paraphyly between Ostrya and Carpinus. Betulaceae ancestors originated from East Asia during the upper Cretaceous; dispersals and subsequent vicariance accompanied by historical environment changes contributed to its diversification and intercontinental disjunction. Ancestral state reconstruction indicated the acquisition of many taxonomic characters was actually the results of parallel or reversal evolution. Conclusions: Our research represents the most comprehensive taxon-sampled and plastome-level phylogenetic inference for Betulaceae to date. The results clearly document global patterns of plastome structural evolution, and established a well-supported phylogeny of Betulaceae. The robust phylogenetic framework not only provides new insights into the intergeneric relationships, but also contributes to a perspective on the diversification history and evolution of the family. [ABSTRACT FROM AUTHOR]

Major aridification events in Australia during the Pliocene may have had significant impact on the distribution and structure of widespread species. To explore the potential impact of Pliocene and Pleistocene climate oscillations, we estimated the timing of population fragmentation and past connectivity of the currently isolated but morphologically similar subspecies of the widespread brushtail possum (Trichosurus vulpecula). We use ecological niche modeling (ENM) with the current fragmented distribution of brushtail possums to estimate the environmental envelope of this marsupial. We projected the ENM on models of past climatic conditions in Australia to infer the potential distribution of brushtail possums over 6 million years. D‐loop haplotypes were used to describe population structure. From shotgun sequencing, we assembled whole mitochondrial DNA genomes and estimated the timing of intraspecific divergence. Our projections of ENMs suggest current possum populations were unlikely to have been in contact during the Pleistocene. Although lowered sea level during glacial periods enabled connection with habitat in Tasmania, climate fluctuation during this time would not have facilitated gene flow over much of Australia. The most recent common ancestor of sampled intraspecific diversity dates to the early Pliocene when continental aridification caused significant changes to Australian ecology and Trichosurus vulpecula distribution was likely fragmented. Phylogenetic analysis revealed that the subspecies T. v. hypoleucus (koomal; southwest), T. v. arnhemensis (langkurr; north), and T. v. vulpecula (bilda; southeast) correspond to distinct mitochondrial lineages. Despite little phenotypic differentiation, Trichosurus vulpecula populations probably experienced little gene flow with one another since the Pliocene, supporting the recognition of several subspecies and explaining their adaptations to the regional plant assemblages on which they feed. [ABSTRACT FROM AUTHOR]

Consisting of approximately 320 species, Macrocheles is the most widely distributed genus in the family Macrochelidae. Though some studies have focused on the description of Macrochelidae using molecular techniques (e.g., RAPD) and sequencing of some genes, the interspecies relationships within Macrocheles still remain uncertain. As such, in the present study, we examine all publicly available data in GenBank to explore the evolutionary relationships, divergence times, and amino acid variations within Macrocheles. Exploring the patterns of variation in the secondary protein structure shows high levels of conservation in the second and last helices, emphasizing their involvement in the energy metabolism function of the cytochrome oxidase subunit I enzyme. According to our phylogenetic analysis, all available Macrocheles species are clustered in a monophyletic group. However, in the reconstructed trees, we subdivided M. merdarius and M. willowae into two well‐supported intraspecific clades that are driven by geographic separation and host specificity. We also estimate the divergence time of selected species using calibration evidence from available fossils and previous studies. Thus, we estimate that the age of the Parasitiformes is 320.4 (273.3–384.3) Mya (Permian), and the Mesostigmata is 285.1 (270.8–286.4) Mya (Carboniferous), both with likely origins in the Paleozoic era. We also estimate that Macrocheles diverged from other Mesostigmata mites during the Mesozoic, approximately 222.9 Mya. [ABSTRACT FROM AUTHOR]