Divergence Time Analyses Research Articles

Genomic insights into the evolution of the critically endangered soft-shelled turtle Rafetus swinhoei.

The 2019 death of the female Swinhoes soft-shelled turtle (Rafetus swinhoei) individual in China put this species in a dire conservation state. To avoid the loss of genetic information from the female individual and facilitate the protection and preservation of R. swinhoei, we sequenced and assembled its draft chromosome-level genome by combining BGISEQ short reads, Nanopore long reads, and Hi-C sequencing reads. We characterized its potential ZZ/ZW sex determination system. Phylogeny and divergence time analyses indicated that R. swinhoei has a close relationship with Pelodiscus sinensis, and they shared a common ancestor ~54.4Ma. Population history analyses indicated that R. swinhoei has the lowest heterozygosity among all turtles examined, and its population size has declined dramatically over the past 10million years. Many core genes involved in autophagy and DNA damage response, such as Rab5a and Parp1, were under positive selection and/or evolving rapidly, and these genes may make important contributions to the long lifespan and evolutionary adaptation of R. swinhoei. The loss of several tooth-related genes in turtle genomes explains the genetic basis of their toothless phenotype. This study not only provides a genomic resource for scientists to study the species using the strategy of comparative genomics, but also provides a data basis for us to find more potential R. swinhoei individuals in the wild.

Integrated phylogenomics and fossil data illuminate the evolution of beetles.

Beetles constitute the most biodiverse animal order with over 380 000 described species and possibly several million more yet unnamed. Recent phylogenomic studies have arrived at considerably incongruent topologies and widely varying estimates of divergence dates for major beetle clades. Here, we use a dataset of 68 single-copy nuclear protein-coding (NPC) genes sampling 129 out of the 193 recognized extant families as well as the first comprehensive set of fully justified fossil calibrations to recover a refined timescale of beetle evolution. Using phylogenetic methods that counter the effects of compositional and rate heterogeneity, we recover a topology congruent with morphological studies, which we use, combined with other recent phylogenomic studies, to propose several formal changes in the classification of Coleoptera: Scirtiformia and Scirtoidea sensu nov., Clambiformia ser. nov. and Clamboidea sensu nov., Rhinorhipiformia ser. nov., Byrrhoidea sensu nov., Dryopoidea stat. res., Nosodendriformia ser. nov. and Staphyliniformia sensu nov., and Erotyloidea stat. nov., Nitiduloidea stat. nov. and Cucujoidea sensu nov., alongside changes below the superfamily level. Our divergence time analyses recovered a late Carboniferous origin of Coleoptera, a late Palaeozoic origin of all modern beetle suborders and a Triassic–Jurassic origin of most extant families, while fundamental divergences within beetle phylogeny did not coincide with the hypothesis of a Cretaceous Terrestrial Revolution.

Phylogenetic revision of the lichenized family Gomphillaceae (Ascomycota: Graphidales) suggests post-K–Pg boundary diversification and phylogenetic signal in asexual reproductive structures

We present the first broad molecular-phylogenetic revision of the lichenized family Gomphillaceae, based on 408 newly generated sequences of the mitochondrial SSU rDNA and nuclear LSU rDNA, representing 342 OTUs. The phylogenetic analysis of 20 out of the 28 currently accepted genera resulted in 48 clades. Twelve genera were resolved as monophyletic: Actinoplaca, Arthotheliopsis, Bullatina, Caleniopsis, Corticifraga, Gomphillus, Gyalectidium, Gyalidea, Jamesiella, Rolueckia, Rubrotricha, and Taitaia. Two genera resulted paraphyletic, namely Aulaxina (including Caleniopsis) and Asterothyrium (including Linhartia). Six genera were in part highly polyphyletic: Aderkomyces, Calenia, Echinoplaca, Gyalideopsis, Psorotheciopsis, and Tricharia. While ascoma morphology and anatomy has traditionally been considered as main character complex to distinguish genera, our study supported the notion that the characteristic asexual anamorph of Gomphillaceae, the so-called hyphophores, are diagnostic for most of the newly recognized clades. As a result, we recognize 26 new genus-level clades, three of which have names available (Microxyphiomyces, Psathyromyces, Spinomyces) and 23 that will require formal description as new genera. We also tested monophyly for 53 species-level names for which two or more specimens were sequenced: 27 were supported as monophyletic and representing a single species, 13 as monophyletic but with an internal topology suggesting cryptic speciation, four as paraphyletic, and nine as polyphyletic. These data suggest that species richness in the family is higher than indicated by the number of accepted names (currently 425); they also confirm that recently refined species concepts reflect species richness better than the broad concepts applied in Santesson's monograph. A divergence time analysis revealed that foliicolous Gomphillaceae diversified after the K–Pg-boundary and largely during the Miocene, a notion supported by limited data available for other common foliicolous lineages such as Chroodiscus (Graphidaceae), Pilocarpaceae, and Porinaceae. This contradicts recent studies suggesting that only macrofoliose Lecanoromycetes exhibit increased diversification rates in the Cenozoic.

The Complete Mitochondrial Genome of One Breeding Strain of Asian Swamp Eel (Monopterus albus, Zuiew 1793) Using PacBio and Illumina Sequencing Technologies and Phylogenetic Analysis in Synbranchiformes.

Asian swamp eel (Monopterus albus, Zuiew 1793) is a commercially important fish due to its nutritional value in Eastern and Southeastern Asia. One local strain of M. albus distributed in the Jianghan Plain of China has been subjected to a selection breeding program because of its preferred body color and superiority of growth and fecundity. Some members of the genus Monopterus have been reclassified into other genera recently. These classifications require further phylogenetic analyses. In this study, the complete mitochondrial genomes of the breeds of M. albus were decoded using both PacBio and Illumina sequencing technologies, then phylogenetic analyses were carried out, including sampling of M. albus at five different sites and 14 species of Synbranchiformes with complete mitochondrial genomes. The total length of the mitogenome is 16,621 bp, which is one nucleotide shorter than that of four mitogenomes of M. albus sampled from four provinces in China, as well as one with an unknown sampling site. The gene content, gene order, and overall base compositions are almost identical to the five reported ones. The results of maximum likelihood (ML) and Bayesian inference analyses of the complete mitochondrial genome and 13 protein-coding genes (PCGs) were consistent. The phylogenetic trees indicated that the selecting breed formed the deepest branch in the clade of all Asian swamp eels, confirmed the phylogenetic relationships of four genera of the family Synbranchidae, also providing systematic phylogenetic relationships for the order Synbranchiformes. The divergence time analyses showed that all Asian swamp eels diverged about 0.49 million years ago (MYA) and their common ancestor split from other species about 45.96 MYA in the middle of the Miocene epoch. Altogether, the complete mitogenome of this breed of M. albus would serve as an important dataset for germplasm identification and breeding programs for this species, in addition to providing great help in identifying the phylogenetic relationships of the order Synbranchiformes.

Comparative and Phylogenetic Analysis of the Complete Chloroplast Genome of Santalum (Santalaceae)

Santalum (Santalaceae, sandalwood) is a hemiparasitic genus that includes approximately 15 extant species. It is known for its aromatic heartwood oil, which is used in incense and perfume. Demand for sandalwood-based products has led to drastic over-harvesting, and wild Santalum populations are now threatened. Knowledge of phylogenetic relationships will be critical for the conservation and proper management of this genus. Here, we sequenced the chloroplast genome of 11 Santalum species. The data were then used to investigate chloroplast genome evolutionary dynamics and relationships and divergence time within Santalum and related species. The Santalum chloroplast genome contains typical quadripartite structures, ranging from 143,291 to 144,263 bp. The chloroplast genome contains 110 unique genes. The whole set of ndh genes and the infA gene were found to lose their functions. The P-distance among the Santalum species was 0.0003 to 0.00828. Three mutation hotspot regions, 14 small inversions, and 460 indels events were discovered in the Santalum chloroplast genome. Branch-model-based selection analyses showed that the Santalum species were under widespread purifying selection. Our phylogenomic assessment provides an improved resolution to the phylogenetic relationships of Santalum compared to the past analyses. Our divergence time analysis showed that the crown age of Santalum was 8.46 Mya (million years ago), the first divergence occurred around 6.97 Mya, and diversification was completed approximately 1 Mya. By sequencing the 11 Santalum species chloroplast genomes, we identified the variations in the Santalum chloroplast genomes. Using the chloroplast genome sequences, phylogeny and divergence time analyses discovered that the Santalum species were likely to originate due to radiation evolution, and most speciation events occurred less than 1 Mya.

The chloroplast genome of Amygdalus L. (Rosaceae) reveals the phylogenetic relationship and divergence time

BackgroundLimited access to genetic information has greatly hindered our understanding of the molecular evolution, phylogeny, and differentiation time of subg. Amygdalus. This study reported complete chloroplast (cp) genome sequences of subg. Amygdalus, which further enriched the available valuable resources of complete cp genomes of higher plants and deepened our understanding of the divergence time and phylogenetic relationships of subg. Amygdalus.ResultsThe results showed that subg. Amygdalus species exhibited a tetrad structure with sizes ranging from 157,736 bp (P. kansuensis) to 158,971 bp (P. davidiana), a pair of inverted repeat regions (IRa/IRb) that ranged from 26,137–26,467 bp, a large single-copy region that ranged from 85,757–86,608 bp, and a small single-copy region that ranged from 19,020–19,133 bp. The average GC content of the complete cp genomes in the 12 species was 36.80%. We found that the structure of the subg. Amygdalus complete cp genomes was highly conserved, and the 12 subg. Amygdalus species had an rps19 pseudogene. There was not rearrangement of the complete cp genome in the 12 subg. Amygdalus species. All 12 subg. Amygdalus species clustered into one clade based on both Bayesian inference and maximum likelihood. The divergence time analyses based on the complete cp genome sequences showed that subg. Amygdalus species diverged approximately 15.65 Mya.ConclusionOur results provide data on the genomic structure of subg. Amygdalus and elucidates their phylogenetic relationships and divergence time.

Fossilization processes have little impact on tip‐calibrated divergence time analyses

AbstractThe importance of palaeontological data in divergence time estimation has increased with the introduction of Bayesian total‐evidence dating methods, which use fossil taxa directly for calibration, facilitated by the joint analysis of morphological and molecular data. Fossil taxa are invariably incompletely known as a consequence of taphonomic processes, resulting in the decidedly non‐random distribution of missing data. The impact of non‐random missing data on the accuracy and precision of clade age estimation is unknown. In an attempt to constrain the impact of taphonomy on tip‐calibrated dating analyses, we compared clade ages estimated from a very complete morphological matrix to ages estimated from the same matrix permuted to simulate the progressive loss of anatomical information resulting from taphonomic processes. We demonstrate that systematically distributed missing data negatively influence clade age estimates, but that successive stages within the taphonomic process introduce greater differences in age estimates, when compared to estimates obtained from untreated data. Despite these effects, the general influence of missing data is weak, presumably due to the compensatory effect of extensive morphological data from extant taxa. We suggest that, in the absence of models that can explicitly account for taphonomic processes, morphological datasets should be constructed to minimize the impact of taphonomy on divergence time estimation.

A New Pipeline for Removing Paralogs in Target Enrichment Data.

Target enrichment (such as Hyb-Seq) is a well-established high throughput sequencing method that has been increasingly used for phylogenomic studies. Unfortunately, current widely used pipelines for analysis of target enrichment data do not have a vigorous procedure to remove paralogs in target enrichment data. In this study, we develop a pipeline we call Putative Paralogs Detection (PPD) to better address putative paralogs from enrichment data. The new pipeline is an add-on to the existing HybPiper pipeline, and the entire pipeline applies criteria in both sequence similarity and heterozygous sites at each locus in the identification of paralogs. Users may adjust the thresholds of sequence identity and heterozygous sites to identify and remove paralogs according to the level of phylogenetic divergence of their group of interest. The new pipeline also removes highly polymorphic sites attributed to errors in sequence assembly and gappy regions in the alignment. We demonstrated the value of the new pipeline using empirical data generated from Hyb-Seq and the Angiosperms353 kit for two woody genera Castanea (Fagaceae, Fagales) and Hamamelis (Hamamelidaceae, Saxifragales). Comparisons of data sets showed that the PPD identified many more putative paralogs than the popular method HybPiper. Comparisons of tree topologies and divergence times showed evident differences between data from HybPiper and data from our new PPD pipeline. We further evaluated the accuracy and error rates of PPD by BLAST mapping of putative paralogous and orthologous sequences to a reference genome sequence of Castanea mollissima. Compared to HybPiper alone, PPD identified substantially more paralogous gene sequences that mapped to multiple regions of the reference genome (31 genes for PPD compared with 4 genes for HybPiper alone). In conjunction with HybPiper, paralogous genes identified by both pipelines can be removed resulting in the construction of more robust orthologous gene data sets for phylogenomic and divergence time analyses. Our study demonstrates the value of Hyb-Seq with data derived from the Angiosperms353 probe set for elucidating species relationships within a genus, and argues for the importance of additional steps to filter paralogous genes and poorly aligned regions (e.g., as occur through assembly errors), such as our new PPD pipeline described in this study. [Angiosperms353; Castanea; divergence time; Hamamelis; Hyb-Seq, paralogs, phylogenomics.]

Comparative study: nonsynonymous and synonymous substitution of SARS-CoV-2, SARS-CoV, and MERS-CoV genome.

The direction of evolution can estimate based on the variation among nonsynonymous to synonymous substitution. The simulative study investigated the nucleotide sequence of closely related strains of respiratory syndrome viruses, codon-by-codon with maximum likelihood analysis, z selection, and the divergence time. The simulated results, dN/dS > 1 signify that an entire substitution model tends towards the hypothesis's positive evolution. The effect of transition/transversion proportion, Z-test of selection, and the evolution associated with these respiratory syndromes, are also analyzed. Z-test of selection for neutral and positive evolution indicates lower to positive values of dN-dS (0.012, 0.019) due to multiple substitutions in a short span. Modified Nei-Gojobori (P) statistical technique results also favor multiple substitutions with the transition/transversion rate from 1 to 7. The divergence time analysis also supports the result of dN/dS and imparts substantiating proof of evolution. Results conclude that a positive evolution model, higher dN-dS, and transition/transversion ratio significantly analyzes the evolution trend of severe acute respiratory syndrome coronavirus 2, severe acute respiratory syndrome coronavirus, and Middle East respiratory syndrome coronavirus.

Plastid genome data provide new insights into the phylogeny and evolution of the genus Epimedium

IntroductionEpimedium L., the largest herbaceous genus of Berberidaceae, is one of the most taxonomically difficult representatives. The classification and phylogenetic relationships within Epimedium are controversial and unresolved. ObjectivesFor the first time, we systematically studied the phylogeny and evolution of Epimedium based on plastid genome (plastome) data for better understanding this enigmatic genus. MethodsWe explored the molecular phylogeny, assessed the infrageneric classification, estimated the divergence times, and inferred the ancestral states for flower traits of Epimedium based on 45 plastomes from 32 species. ResultsThe Epimedium plastome length ranged from 156,635 bp to 159,956 bp. Four types of plastome organization with different inverted repeat boundary changes were identified. Phylogenetic analysis revealed a strong support for the sister relationship of sect. Macroceras and sect. Diphyllon but did not provide a distinct route for petal evolution in sect. Diphyllon. Disharmony between phylogenetic relationships and traditional classification of sect. Diphyllon was observed. Results from divergence time analysis showed that Epimedium diverged in the early Pleistocene (~2.11 Ma, 95% HPD = 1.88–2.35 Ma). Ancestral character state reconstructions indicated transitions from long spur (large-flowered group) to other petal types (small-flowered group) in Epimedium. ConclusionThese findings provide new insights into the relationships among Epimedium species and pave the way for better elucidation of the classification and evolution of this genus.

Phylogenomics of flavobacterial insect nutritional endosymbionts with implications for Auchenorrhyncha phylogeny.

"Candidatus Sulcia muelleri" (Sulcia) is a diverse lineage of intracellular nutritional endosymbiotic bacteria strictly associated with auchenorrhynchous hemipteran insects. Sulcia has undergone long-term codiversification with its insect hosts but the phylogeny of these endosymbionts, their relationships to other bacteria, and the extent of their occurrence within various groups of Auchenorrhyncha remain inadequately explored. Comprehensive phylogenetic analyses of Sulcia and related bacteria were performed to elucidate its position relative to other members of Phylum Bacteroidetes and the degree of congruence to the phylogeny of its auchenorrhynchous hosts. Maximum likelihood (ML) and maximum parsimony (MP) analyses of Flavobacteriales based on genomic data from 182 bacterial strains recover a monophyletic Sulcia within a larger clade of flavobacterial insect endosymbionts, closely related to Weeksellaceae. Molecular divergence time analysis of Sulcia dates the origin of Sulcia at approximately 339.95 million years ago (Myr) and the initial divergence within Sulcia at approximately 256.91 Myr but these are considered underestimates due to the tendency for endosymbionts to evolve at higher rates compared to their free-living relatives. Screening of 96 recently sequenced hemipteran transcriptomes revealed that 73 of these species, all Auchenorrhyncha, harbored Sulcia. Phylogenetic analysis of 131 orthologous genes plus 16S rRNA for 101 Sulcia strains, representing six fulgoroid families and all the families of Cicadomorpha except Tettigarctidae, recover largely congruent phylogenies between Sulcia and Auchenorrhyncha. The phylogeny of Sulcia strongly supports the superfamily relationships Fulgoroidea + (Cicadoidea + (Cercopoidea + Membracoidea)). Relationships within individual superfamilies are also largely concordant, with the few areas of apparent incongruence between Sulcia and insect genes attributable to low branch support in one or both datasets. These results suggest that analysis of Sulcia phylogeny may contribute to resolution of contentious aspects of Auchenorrhyncha phylogeny.

Astacus multicavatus Bell, 1863 is a marine lobster (Decapoda: Erymoidea: Erymidae), not a freshwater crayfish

Abstract Crayfishes comprise a large and diverse group of freshwater lobster-like crustaceans. Despite being abundant in the recent, they are extremely rare in the fossil record. We revise a putative occurrence of Astacus multicavatusBell, 1863 from the marine Hauterivian of Speeton Clay (Speeton, United Kingdom), which was used a few years ago as a calibration fossil representing AstacusFabricius, 1775 for divergence time analyses. This species is actually a senior synonym to Eryma sulcatumHarbort, 1905. It so appears that Eryma multicavatum (Bell, 1863) comb. nov. is not a freshwater crayfish but a marine representative of Erymidae. Two co-occurring isolated chelae, also from the Speeton Clay, may correspond to larger, older specimens of E. multicavatum comb. nov.

Dated phylogeny and ancestral range estimation of sand scorpions (Buthidae: Buthacus) reveal Early Miocene divergence across land bridges connecting Africa and Asia

Sand scorpions of the genus Buthacus Birula, 1908 (Buthidae C.L. Koch, 1837) are widespread in the sandy deserts of the Palearctic region, occurring from the Atlantic coast of West Africa across the Sahara, and throughout the Middle East to Central Asia. The limits of Buthacus, its two species groups, and many of its species remain unclear, and in need of revision using modern systematic methods. The study presented here set out to investigate the phylogeny and biogeography of the Buthacus species occurring in the Levant, last studied in 1980. A phylogenetic analysis was performed on 104 terminals, including six species collected from more than thirty localities in Israel and other countries in the region. Three mitochondrial and two nuclear gene loci were sequenced for a total of 2218 aligned base-pairs. Morphological datasets comprising 22 qualitative and 48 quantitative morphological characters were compiled. Molecular and morphological datasets were analyzed separately and simultaneously with Bayesian Inference, Maximum Likelihood, and parsimony. Divergence time and ancestral range estimation analyses were performed, to understand dispersal and diversification. The results support a revised classification of Levantine Buthacus, and invalidate the traditional species groups of Buthacus, instead recovering two geographically-delimited clades, an African clade and an Asian clade, approximately separated by the Jordan Valley (the Jordan Rift Valley or Syro-African Depression), the northernmost part of the Great Rift Valley. The divergence between these clades occurred in the Early Miocene (ca. 19 Ma) in the Levant, coinciding temporally with the existence of two land bridges, which allowed faunal exchange between Africa and Asia.

Mitochondrial substitution rates estimation for divergence time analyses in modern birds based on full mitochondrial genomes

Mitochondrial DNA (mtDNA) is a popular resource used for the study of evolutionary processes in birds, especially to infer divergence times between lineages. In many cases, due to the scarcity of fossils with which to constrain the age of nodes on a phylogenetic topology, dating relies on mtDNA substitution rates that, ideally, are specific to the taxa being studied. As such values are often unavailable, many studies use fixed‐rate values from other studies, such as the ‘standard molecular clock’. The validity of this universal rate across all bird lineages and for the different mtDNA loci has been questioned by multiple authors. We here performed the most comprehensive calibration of the mtDNA molecular clock in birds, with the inclusion of complete mitochondrial genomes for 622 bird species and 25 reliable fossil calibrations. The results show variation in the rates among lineages and among markers, confirming the lack of universality of the standard molecular clock. Moreover, we provide specific rates for every mtDNA marker (except D‐loop) in each of the sampled avian orders, a valuable tool for molecular clock analyses in the absence of fossil calibrations.

Origin and diversification of flax and their relationship with heterostyly across the range

AbstractAimUnderstanding plant diversity and how different traits have shaped the current biodiversity setting across the world is one of the major challenges for evolutionary biology. In this sense, genus Linum have been broadly studied as a model of species showing heterostyly, but no studies have attempted to investigate possible correlations between heterostyly and diversification. Thus, in this study we aim to explore the origin and diversification of the genus Linum and to determine its centre of diversity and potential source for the colonisation of other areas. Also, we aim to study how heterostyly may have shaped diversification rates and colonisation patterns in the genus.LocationWorldwide (focused on the Western Palearctic).TaxonGenus Linum L. (Linaceae).MethodsWe analysed nuclear ITS and plastid ndhF, matK and trnL‐F DNA regions in a total of 103 samples of 93 different species of the genus Linum, as well as seven samples from other Linaceae. We performed divergence time analysis in BEAST2 under a birth‐death tree model, then used the resulting tree for an ancestral area reconstruction using the R package “BioGeoBEARS.” Finally, we estimated diversification rates using BAMM and examined the correlation between diversification rates and geographic ranges and heterostyly.ResultsLinum s.l. diverged during the late Eocene to mid Oligocene (27.2–38.29 Ma at 95% highest posterior density interval) in the Western Palearctic, where most species diversified. Within‐area speciation is the main mechanism of diversification in the genus. Most dispersal events occurred from the Western Palearctic to other regions, probably through long‐distance dispersal (LDD). No changes were found regarding diversification rates in specific clades or in relation with reproductive system (heterostyly) or geographic areas. Colonisation of new areas was achieved mostly by monomorphic lineages, whereas heterostylous species mostly remained in the ancestral Western Paleartic area.Main conclusionsThe Western Palearctic acted as a source of dispersal in seven out of nine total dispersal events but never as a sink. All species or lineages that colonised new areas after LDD were monomorphic for style length, as predicted by the theory on reproductive traits of colonising species. Thus, heterostyly is shown to affect establishment success in a new area. Neither biogeographic changes nor analysed trait changes can explain speciation nor extinction rates in Linum. Our results confirm that the evolution of heterostyly is related to the paleogeographic history and are not consistent with the idea that a key innovation or “dispersification” has shaped the diversification patterns in Linum.

Historical biogeography of New World passalid beetles (Coleoptera, Passalidae) reveals Mesoamerican tropical forests as a centre of origin and taxonomic diversification

AbstractAimThe fauna of Mesoamerica is extraordinarily species rich and exhibits a high degree of local, regional and high‐elevation endemism. Traditionally, this area has been seen as a transition zone between the Nearctic and Neotropical regions; in contrast, new data suggest that Mesoamerica is a centre of origin and taxonomic diversification. For example, the diversity of species and genera of Passalidae in Mesoamerica is concentrated in montane environments and there are many locally endemic taxa; thus, Mesoamerica has been suggested as a centre of origin and taxonomic diversification for the group. However, this hypothesis has not been formally tested.LocationNew World tropics, with an emphasis on Mesoamerica.TaxonColeoptera, Passalidae (tribes Passalini and Proculini)MethodsWe studied timing and geographic patterns in the taxonomic diversification of Neotropical Passalidae. We used DNA sequence data from 3 genes (CAD, Wingless, 28S) for 93 species of Passalidae, along with information from the fossil record, to generate a time‐calibrated phylogeny for the group. Additionally, we performed Ancestral Area Estimation and Ancestral State Reconstruction of the altitudinal distribution niche.ResultsThe divergence time analyses recovered a much older estimated timing of origin and diversification events in Passalidae than previously proposed. We recovered the origins of the New World Passalidae in the late Jurassic and the split between Passalini and Proculini during the mid‐Cretaceous. Moreover, we observed congruence between timing and patterns of clade diversification and major paleogeographical events; for example, the origin and crown diversification of montane genera during the uplift and emergence of Mesoamerica from the sea.Main conclusionsOrogenic events throughout the Paleogene and Neogene played a major role in the diversification of New World Passalidae. Moreover, Nuclear and Southern Mesoamerica are centres of origin and taxonomic diversification for Proculini.

Molecular Evolution of Infectious Pancreatic Necrosis Virus in China.

Passive virus surveillance was performed in twenty-nine salmon and trout farms from seven provinces and districts in China during the period 2017–2020. A total of 25 infectious pancreatic necrosis virus (IPNV) isolates were obtained, mainly from rainbow trout (Oncorhynchus mykiss). The molecular evolution of these Chinese IPNV isolates and the previously reported Chinese IPNV strains ChRtm213 and WZ2016 was analyzed, based on their VP2 gene coding region sequences (CDS). All 27 Chinese IPNV isolates clustered within genogroups I and V, with 24 of the IPNV isolates belonging to genogroup I (including ChRtm213 and WZ2016), and only three isolates clustering in genogroup V. The Chinese genogroup I IPNV isolates lacked diversity, composing six haplotypes with 41 polymorphic sites, and the identity of nucleotide and amino acid sequences among the entire VP2 gene CDS from these isolates was 97.44%–100% and 98.19%–100%, respectively. Divergence time analyses revealed that the Chinese genogroup I IPNV isolates likely diverged from Japanese IPNV isolates in 1985 (95% highest posterior density (HPD), 1965–1997), and diverged again in 2006 (95% HPD, 1996–2013) in China. Each of the three Chinese genogroup V IPNV isolates has a unique VP2 gene CDS, with a total of 21 polymorphic sites; the identity of nucleotide and amino acid sequences among all VP2 gene CDS from these isolates was 98.5%–99.5% and 98.6%–99.0%, respectively. The data demonstrate that genogroups I and V are more likely the currently prevalent Chinese IPNV genotypes.

A new agamid lizard in mid-Cretaceous amber from northern Myanmar

The first amber-embedded fossil representing the lizard family Agamidae, Protodraco monocoli gen. et sp. nov., is described in burmite of the lowermost Cenomanian (ca. 99 Ma; mid-Cretaceous) from northern Myanmar. It is among both the oldest known amber lizards and the oldest fossils of the family. The fossil is a well preserved left hind foot with shank, morphologically similar to basal taxa of modern Southeast Asian agamids. Because of the sparse Cretaceous fossil record it could provide a calibration point for divergence-time analyses and contradicts views that agamids colonized SE Asia during the Paleogene.

Iguanian lizards from the Split Rock Formation, Wyoming: exploring the modernization of the North American lizard fauna

Terrestrial ecosystems in North America changed substantially during the Neogene. Previous authors have documented changes in plants and mammals but squamates have received comparatively little attention. Several Miocene lizard fossils were described previously from the Split Rock Formation (Wyoming), which was deposited just before or during the mid-Miocene Climatic Optimum (c. 18–14 Ma). I re-evaluate the identifications of some of the previously published fossil lizards from the Split Rock Formation and describe several new fossil lizards. I focus on the iguanians and revise the biogeographical and temporal context for the evolution of several clades. I establish a minimum age for crown Phrynosomatidae and describe the oldest known occurrence of Crotaphytidae. The fossils provide evidence of a relatively modern lizard fauna in central North America by ∼17.5 Ma and support a substantial turnover from the Eocene to the middle Miocene. I also describe a new taxon, Caeruleodentatus lovei, with a distinctive dentary morphology. The revised iguanian lizard fauna is more diverse than previously described. I discuss difficulties and considerations with using apomorphies to identify fossils, biogeographical biases that affect fossil identifications, and the previous and future use of fossils from the Split Rock Formation in divergence time analyses. I recommend that comparative samples used for identifying fossils should not be intentionally limited by biogeography or stratigraphy, and underscore the importance of topology selection when constructing an apomorphy-based diagnosis. While apomorphy-based diagnoses may decrease taxonomic resolution of fossil identifications, they do not necessarily decrease our capacity to interpret the phylogenetic, biogeographical or ecological significance of fossils. http://zoobank.org/urn:lsid:zoobank.org:pub:F15984C6-144C-4110-A317-6714C6EEE295

Phylogenomic analyses based on genome-skimming data reveal cyto-nuclear discordance in the evolutionary history of Cotoneaster (Rosaceae)

As a consequence of hybridization, polyploidization, and apomixis, the genus Cotoneaster (Rosaceae) represents one of the most complicated and controversial lineages in Rosaceae, with ca. 370 species which have been classified into two subgenera and several sections, and is notorious for its taxonomic difficulty. The infrageneric relationships and taxonomy of Cotoneaster have remained poorly understood. Previous studies have focused mainly on natural hybridization involving only several species, and phylogeny based on very limited markers. In the present study, the sequences of complete chloroplast genomes and 204 low-copy nuclear genes of 72 accessions, representing 69 species as ingroups, were used to conduct the most comprehensive phylogenetic analysis so far for Cotoneaster. Based on the sequences of complete chloroplast genomes and many nuclear genes, our analyses yield two robust phylogenetic trees respectively. Chloroplast genome and nuclear data confidently resolved relationships of this genus into two major clades which largely supported current classification based on morphological evidence. However, conflicts between the chloroplast genome and low-copy nuclear phylogenies were observed in both the species level and clade level. Cyto-nuclear discordance in the phylogeny could be caused by frequent hybridization events and incomplete sorting lineage (ILS). In addition, our divergence-time analysis revealed an evolutionary radiation of the genus from late Miocene to date.