Molecular Divergence Time Research Articles

Evolutionary History and Ecology of Andrena (Foveoandrena) androfovea: A New Nearctic Mining Bee (Hymenoptera, Andrenidae) Species and Subgenus.

With about 1700 described species, the mining bee genus Andrena is a rapidly diversifying lineage and one of the most species-rich groups of bees. Recent phylogenomic advances have greatly improved our understanding of the phylogeny of the genus, yet many species still await description, subgeneric assignments that are in line with their evolutionary history, as well as study of their morphology and behavior. Here we provide a comprehensive account of a newly discovered species, Andrena androfovea n. sp. We sequence the genome of the new species and include it in the presently most comprehensive phylogenomic analysis of Andrena using ultraconserved element (UCE) sequence data, comprising 264 samples and 249 species. Given the recovered phylogenetic position of the new species, we establish a new subgenus, Foveoandrena, provide a detailed morphological description, and discuss the antiquity and historical biogeography of the lineage in light of molecular divergence time estimates. Lastly, we study and document the foraging behavior of the new species with photos and video footage, and discuss the species' unusual host plant associations with Chamaesaracha and Quincula, both Solanaceae. Being likely oligolectic on these plants, we present the first documented case of an Andrena species being narrowly associated with members of this plant family. By integrating multiple lines of documentation, our study provides a particularly detailed account of species discovery and description.

Multiple origins of freshwater invasion and parental care reflecting ancient vicariances in the bivalve family Cyrenidae (Mollusca)

Habitat transitions in living organisms are key innovations often coupled with species diversification after their successful adaptation to new environment. The Cyrenidae is among the most well-known heterodont bivalve groups that have successfully invaded freshwater systems from brackish water environments and display diverse lineage-specific developmental modes. Phylogenetic and molecular clock-based divergence time analyses using 12 complete mitochondrial genome sequences suggest that Cyrenidae species independently colonized freshwater habitats during three distinct spatial and geological periods: one from the American continents approximately in the Early Jurassic and the two others from Australasian/East Asian continents in the Early/Middle Cretaceous and the Paleogene-Neogene boundary, respectively. This study provides significant insight into the temporal and spatial patterns of multiple freshwater invasions, aligning with ancient vicariance events inferred from different geological timelines of plate tectonics. Additionally, mitogenome phylogeny confirms the earlier hypothesis of the repeated parallel evolution of parental care system within this bivalve group.

Sampling poorly studied lineages improves resolution in mitogenome-based phylogenies of leafhoppers (Hemiptera: Cicadellidae)

Abstract Cicadellidae (leafhoppers) may be the most diverse and abundant insect herbivores in terrestrial ecosystems worldwide, with more than 23,000 described species in 20 extant subfamilies. Although prior studies have supported the monophyly of most recognized subfamilies, relationships among these groups remain inconsistently resolved and previous molecular phylogenies have failed to support the monophyly of a few subfamilies. To help address this deficiency, we combined 24 new complete mitogenomes representing 6 previously unsequenced subfamilies and 13 tribes with previously available data to create a dataset of 79 cicadellid taxa representing 16 subfamilies for phylogenetic analysis. The new analyses confirm that leafhopper mitochondrial genomes are highly conservative in overall structure, with only a few rare rearrangements of tRNAs. All phylogenetic analyses consistently supported the monophyly of previously recognized cicadellid tribes for which more than 1 representative was included and all of the included subfamilies were also consistently recovered as monophyletic with the exception of Aphrodinae and Eurymelinae. Bayesian inference and Maximum Likelihood analyses with site-homogeneous models are only slightly affected by nucleotide compositional heterogeneity and yield more stable phylogenetic relationships of family-group taxa than analyses with a heterogeneous-site mixture model using PhyloBayes. Molecular divergence time estimates indicate that the main lineages of Cicadellidae, most corresponding to recognized subfamilies, diverged during the Cretaceous period (93–121 Mya).

Mitochondrial phylogenomics supports a Carboniferous origin of Xenonomia

Polyneoptera includes some of the best-known insect species, such as grasshoppers and cockroaches. While the evolutionary history of many Polyneoptera orders has been thoroughly explored, others have been partially overlooked. This is the case with Xenonomia, a clade consisting of two species-poor insect orders with a relatively recent taxonomic history: Mantophasmatodea and Grylloblattodea. Here, we provide a temporal framework for their evolution, leveraging a mitochondrial phylogenomics approach encompassing all Polyneoptera orders. To strengthen the confidence in our divergence times estimation, we specifically focused on the possible impact of phylogenetic biases, such as long branch attraction, the influence of specific fossil priors, the use of nucleotide or amino acid alignments, and different clock models. Our results consistently support the origin of Xenonomia during the Carboniferous, and the divergence between the two orders is inferred to have happened before the Permian. While Grylloblattodea diversification is inferred to have occurred earlier than that of Mantophasmatodea, extant species of both orders most likely diversified after the Permian/Triassic and Triassic/Jurassic mass extinctions. Our molecular divergence time analyses complement the fossil record and support the ancient relict status of these two polyneopteran orders.

Exploring the mitogenomes of Batracomorphus (Hemiptera: Cicadellidae: Iassinae): new insights from structural diversity and phylogenomic analyses

Abstract Comparisons of mitogenomes are widely used for species identification and to explore the phylogenetic relationship among insect taxa. Batracomorphus is the third most diverse and widely distributed genus in the Cicadellidae (Hemiptera). However, there have been no analyses of genome structure and phylogenetic relationships within the genus. To compensate for the paucity of genomic information in this genus, we sequenced novel complete mitochondrial genomes of 11 Batracomorphus species and combined these with 23 previously sequenced mitochondrial genomes to perform structural comparisons and phylogenomic studies. Our results reveal generally conserved mitogenome organization, with one case of tRNA gene rearrangement, with trnI-trnQ reversed to trnQ-trnI when compared with the ancestral arrangement. Analysis of the ratio of nonsynonymous (Ka) to synonymous substitutions (Ks) showed ATP8 is the fastest and COI is the slowest evolving gene. ND2 and ND6 have highly variable nucleotide diversity, whereas COI and ND1 exhibit the lowest diversity. Phylogenetic analysis of nucleotide sequences grouped Batracomorphus species into a clade within the subfamily Iassinae. Within Batracomorphus, 3 clades were reconstructed consistent with the observed gene rearrangement, indicating that such rearrangements can serve as reliable molecular markers supporting phylogenetic hypotheses. These clades also correspond to clusters of species recovered by morphometric analysis of aedeagal shape, suggesting that characters of the male genitalia traditionally used for species delimitation are phylogenetically informative. Molecular divergence time estimates indicate that most speciation events within Batracomorphus occurred between the Paleogene and Neogene. This study provides insight into the population genetics, molecular biology, phylogeny, and morphological evolution of the leafhopper subfamily Iassinae and its largest genus, Batracomorphus.

Structure, gene composition, divergence time and phylogeny analysis of the woody desert species Neltuma alba, Neltuma chilensis and Strombocarpa strombulifera

Neltuma alba (Algarrobo blanco), Neltuma chilensis (Algarrobo Chileno) and Strombocarpa strombulifera (Fortuna) are some of the few drought resistant trees and shrubs found in small highly fragmented populations, throughout the Atacama Desert. We reconstructed their plastid genomes using de novo assembly of paired-end reads from total genomic DNA. We found that the complete plastid genomes of N. alba and N. chilensis are larger in size compared to species of the Strombocarpa genus. The Strombocarpa species presented slightly more GC content than the Neltuma species. Therefore, we assume that Strombocarpa species have been exposed to stronger natural selection than Neltuma species. We observed high variation values in the number of cpSSRs (chloroplast simple sequence repeats) and repeated elements among Neltuma and Strombocarpa species. The p-distance results showed a low evolutionary divergence within the genus Neltuma, whereas a high evolutionary divergence was observed between Strombocarpa species. The molecular divergence time found in Neltuma and Strombocarpa show that these genera diverged in the late Oligocene. With this study we provide valuable information about tree species that provide important ecosystem services in hostile environments which can be used to determine these species in the geographically isolated communities, and keep the highly fragmented populations genetically healthy.

Phylogeny and historical biogeography of the leafhopper subfamily Coelidiinae (Hemiptera: Cicadellidae) based on morphological and molecular data

AbstractThe phylogenetic relationships among major lineages of the globally distributed leafhopper subfamily Coelidiinae were reconstructed by analysis of 2903 nucleotide positions from two mitochondrial genes (COI and 16S), four nuclear genes (28S, H3, H2A and Wingless) and 102 discrete morphological characters, compiled for 86 species representing 52 genera within 9 coelidiine tribes broadly representative of the world fauna in addition to 12 outgroup taxa. Maximum likelihood and Bayesian analyses yielded well‐resolved phylogenetic estimates that were highly congruent with most branches receiving strong support. The results indicate Coelidiinae sensu stricto (=Coelidiinae sensu lato without Equeefini and Macroceratogoniini), Thagriini, Tharrini, Tinobregmini and Equeefini are monophyletic. However, the two largest tribes, Coelidiini and Teruliini, are paraphyletic, as well as Youngolidiini and most genera of Oriental Coelidiini. Fossil‐calibrated molecular divergence time analysis indicates that the Coelidiinae sensu stricto originated ca. 149 Ma, prior to the complete separation of the Gondwanan continents, and the tribe‐level lineages diverged between the Lower and Upper Cretaceous (92.77–138.03 Ma). The major lineages of Coelidiinae arose in the Oriental and Neotropical regions, and Oriental Coelidiini arose as a result of dispersal and colonisation from the Afrotropical region.

Completing a molecular timetree of apes and monkeys.

The primate infraorder Simiiformes, comprising Old and New World monkeys and apes, includes the most well-studied species on earth. Their most comprehensive molecular timetree, assembled from thousands of published studies, is found in the TimeTree database and contains 268 simiiform species. It is, however, missing 38 out of 306 named species in the NCBI taxonomy for which at least one molecular sequence exists in the NCBI GenBank. We developed a three-pronged approach to expanding the timetree of Simiiformes to contain 306 species. First, molecular divergence times were searched and found for 21 missing species in timetrees published across 15 studies. Second, untimed molecular phylogenies were searched and scaled to time using relaxed clocks to add four more species. Third, we reconstructed ten new timetrees from genetic data in GenBank, allowing us to incorporate 13 more species. Finally, we assembled the most comprehensive molecular timetree of Simiiformes containing all 306 species for which any molecular data exists. We compared the species divergence times with those previously imputed using statistical approaches in the absence of molecular data. The latter data-less imputed times were not significantly correlated with those derived from the molecular data. Also, using phylogenies containing imputed times produced different trends of evolutionary distinctiveness and speciation rates over time than those produced using the molecular timetree. These results demonstrate that more complete clade-specific timetrees can be produced by analyzing existing information, which we hope will encourage future efforts to fill in the missing taxa in the global timetree of life.

A new species of Kana Distant representing the first record of Evacanthinae (Hemiptera: Cicadellidae) from Madagascar.

Kana ranomafanensis sp. n. is described and illustrated based on specimens from montane rainforests in eastern Madagascar. This is the first record of the diverse and widely distributed leafhopper subfamily Evacanthinae from Madagascar. A revised diagnosis of Kana Distant is provided and the new species is compared to species from the Indomalayan and Afrotropical regions. Evidence from previous molecular divergence time analyses suggests that ancestors of the new species arrived in Madagascar via transoceanic dispersal. The ovipositor of the genus and the male genitalia of Kana decora (Melichar), previously known only from the female holotype from Sri Lanka, are illustrated for the first time.

Phylogenomic resolution of Imparidentia (Mollusca: Bivalvia) diversification through mitochondrial genomes.

The online version contains supplementary material available at 10.1007/s42995-023-00178-x.

Phylogenomics, evolution of trophic traits and divergence times of hemiodontid fishes (Ostariophysi: Characiformes)

The South American characiform family Hemiodontidae comprises five genera and 34 species. The family lacks comprehensive phylogenetic hypotheses resolving its species relationships. The studies that addressed these questions exhibited a narrow taxon sampling or used single-locus markers. Herein we surveyed hundreds of ultraconserved elements (UCEs) loci to provide the first molecular phylogenetic hypothesis and divergence time estimates for hemiodontids encompassing all its genera and most species (27 of the 34 valid species). We also tracked the history of the protractile upper jaw in the genera Argonectes and Bivibranchia across the recovered phylogenies through ancestral state reconstruction. Our results corroborate the monophyly of Hemiodontidae and the genera Argonectes and Bivibranchia in all phylogenetic methods with maximum clade support. The genera Anodus and Hemiodus were not monophyletic because Anodus elongatus was sister to the monotypic Micromischodus instead of A. orinocensis, and H. immaculatus did not form a clade with its other congeners, but instead was sister to the clade including Anodus and Micromischodus. All remaining species of Hemiodus were placed together into a monophyletic group, where they were arranged into four major subclades. The relationship in the family is summarised as: (Bivibranchia, (Argonectes, ((H. immaculatus, (Anodus, Micromischodus)), Hemiodus clade))), in discordance with the morphological phylogeny that placed all genera monophyletic and resolved the family as: ((Anodus, Micromischodus), (Hemiodus, (Argonectes, Bivibranchia))). The origin of Hemiodontidae was estimated from the Late Cretaceous to the Middle Paleogene, with the mean age in the Paleocene, while the origin of most hemiodontid genera except Bivibranchia occurred in the Miocene. Unordered parsimony and likelihood reconstruction indicates that Argonectes and Bivibranchia developed their protractile upper jaw independently.

Molecular phylogeny, divergence time, biogeography and trends in host plant usage in the agriculturally important tortricid tribe Grapholitini (Lepidoptera: Tortricidae: Olethreutinae).

The leaf-roller moth tribe Grapholitini comprises about 1200 described species and contains numerous notorious pests of fruits and seeds. The phylogeny of the tribe has been little studied using contemporary methods, and the monophyly of several genera remains questionable. In order to provide a more robust phylogenetic framework for the group, we conducted a multiple-gene phylogenetic analysis of 104 species representing 27 genera of Grapholitini and 29 outgroup species. Divergence time, ancestral area, and host plant usage were also inferred to explore evolutionary trends in the tribe. Our analyses indicate that Larisa and Corticivora, traditionally assigned to Grapholitini, are best excluded from the tribe. After removal of these two genera, the tribe is found to be monophyletic, represented by two major lineages-a Dichrorampha clade and a Cydia clade, the latter of which can be divided into seven generic groups. The genus Grapholita was found to be polyphyletic, comprising three different clades, and we propose three genera to accommodate these groups: Grapholita (sensu stricto), Aspila (formerly a subgenus of Grapholita) and Ephippiphora (formerly considered a synonym of Grapholita). We summarize each generic group, including related genera not included in our analysis, providing morphological, pheromone and food plant characters that support particular branches within the molecular hypotheses. Biogeographical analyses indicate that Grapholitini probably originated in the Nearctic, Afrotropical and Neotropical regions in the Lutetian of the middle Eocene (ca. 44.3 Ma). Our results also indicate that most groups in Grapholitini originated from Fabaceae-feeding monophagous or oligophagous ancestors, and that host plant shifts probably promoted species diversification within the tribe.

Cretaceous pollen cone with three-dimensional preservation sheds light on the morphological evolution of cycads in deep time.

The Cycadales are an ancient and charismatic group of seed plants. However, their morphological evolution in deep time is poorly understood. While molecular divergence time analyses estimate a Cretaceous origin for most major living cycad clades, much of the extant diversity is inferred to be a result of Neogene diversifications. This leads to long branches throughout the cycadalean phylogeny that, with few exceptions, have yet to be rectified by unequivocal fossil cycads. We report a permineralized pollen cone from the Campanian Holz Shale located in Silverado Canyon, CA, USA (c. 80 million yr ago). This fossil was studied via serial sectioning, SEM, 3D reconstruction and phylogenetic analyses. Microsporophyll and pollen morphology indicate this cone is assignable to Skyttegaardia, a recently described genus based on disarticulated lignitized microsporophylls from the Early Cretaceous of Denmark. Data from this new species, including a simple cone architecture, anatomical details and vasculature organization, indicate cycadalean affinities for Skyttegaardia. Phylogenetic analyses support this assignment and recover Skyttegaardia as crown-group Cycadales, nested within Zamiaceae. Our findings support a Cretaceous diversification for crown-group Zamiaceae, which included the evolution of morphological divergent extinct taxa with unique traits that have yet to be widely identified in the fossil record.

Molecular phylogeny and divergence time estimates for native giant clams (Cardiidae: Tridacninae) in the Asia-Pacific: Evidence from mitochondrial genomes and nuclear 18S rRNA genes

Giant clams are conspicuous bivalves that inhabit in coral reefs. Among the giant clams, eight species of subfamily Tridacninae are the most common in the Asia-Pacific. However, very little is known about their evolutionary history. Here, we determined the complete mitochondria genome of Hippopus porcellanus, which was 29,434 bp in size and contained 13 protein-coding genes, 2 rRNAs and 23 tRNAs. The A+T composition of protein-coding regions was 57.99%, and the AT composition of the 3rd codon position was 59.33%, of which in agreement with the invertebrate bias favoring codons ending in A or T. Analysis of phylogenetic relationships according to the concatenated nucleotide data set containing 18S rRNA gene and 13 protein-coding genes, the phylogenetic relationship was analyzed by Maximum likelihood and Bayesian inference methods. The results showed that T. maxima was placed with the clade comprising T. noae, T. squamosa, and T. crocea, in which T. squamosa was highly similar to T. crocea and is consistent with the results of the previous studies using15 mitochondrial markers and nuclear 18S rRNA. Moreover, the inferred divergence time of Tridacnidae species is generally consistent with the fossil record of Tridacnidae. The divergence time of H. porcellanus and H. hippopus was about 10.64 Mya, this result is in agreement with the speculation that H. porcellanus also originated in Miocene. The availability of molecular phylogeny and divergence time estimation provides information genetic relationship of Tridacninae, which could be helpful to the ecological research and conservation of giant clams.

Sexual Signals Persist over Deep Time: Ancient Co-option of Bioluminescence for Courtship Displays in Cypridinid Ostracods.

Although the diversity, beauty, and intricacy of sexually selected courtship displays command the attention of evolutionists, the longevity of these traits in deep time is poorly understood. Population-based theory suggests sexual selection could either lower or raise extinction risk, resulting in high or low persistence of lineages with sexually selected traits. Furthermore, empirical studies that directly estimate the longevity of sexually selected traits are uncommon. Sexually selected signals-including bioluminescent courtship-originated multiple times during evolution, allowing the empirical study of their longevity after careful phylogenetic and divergence time analyses. Here, we estimate the first transcriptome-based molecular phylogeny and divergence times of Cypridinidae. We report extreme longevity of bioluminescent courtship, a trait important in mate choice and probably under sexual selection. Our relaxed-clock estimates of divergence times coupled with stochastic character mapping show luminous courtship evolved only once in Cypridinidae-in a Sub-Tribe, we name Luxorina-at least 151 millions of years ago from cypridinid ancestors that used bioluminescence only in antipredator displays, defining a Tribe we name Luminini. This time-calibrated molecular phylogeny of cypridinids will serve as a foundation for integrative and comparative studies on the biochemistry, molecular evolution, courtship, diversification, and ecology of cypridinid bioluminescence. The persistence of luminous courtship for hundreds of millions of years suggests that sexual selection did not cause a rapid loss of associated traits, and that rates of speciation within the group exceeded extinction risk, which may contribute to the persistence of a diverse clade of signaling species. [Ancestral state reconstruction; Biodiversity; co-option; divergence time estimates; macroevolution; Ostracoda; phylogenomics; sexual selection.].

Molecular phylogenetic analysis of bats in the family Vespertilionidae in Mongolia

Bat species in Mongolia have received a relatively low conservation priority compared to avian and other mammalian species. This might partially result from their understudied ecologies, distributions, and population sizes in Mongolia. Additionally, Mongolia hosts a relatively small assembly of bat species. In this study, we investigated the genetic characteristics of 14 species of bats ( n = 61) from six genera ( Myotis, Vespertilio, Eptesicus, Hypsugo , Plecotus , and Murina ) using a 598 bp long mitochondrial DNA cytochrome c oxidase subunit 1 gene. We reconstructed Maximum likelihood and Bayesian-inference trees, together with estimated molecular divergence times on nodes of interest using an HKY substitution model. Our findings clearly showed four distinct clades (I–IV). Through the partial fragment mitochondrial DNA cytochrome c oxidase subunit 1 gene, 26 haplotypes ( H d = 0.94 ± 0.0001) were identified overall from 61 individuals. We estimated a divergence time of 31.71–55.84 mya (95% highest posterior density (HPD)) on the node of clade I (genus Myotis ) and the other three clades (other genera). Interestingly, in clade II, we no longer considered animals in haplotype 2 (H2) of Hypsugo alaschanicus as H. alaschanicus. Instead, this haplotype was recently described as H. stubbei. Additional molecular genetic studies are required to clarify intraspecific divergences of some vesper bats in Mongolia, particularly, M. ikonnikovi, M. davidii, H. alaschanicus, and P. ognevi .

Integrative Phylogenetics: Tools for Palaeontologists to Explore the Tree of Life.

Simple SummaryAll life is derived from a single common ancestor, whose descendants coevolved with the planet, shaping the structure of biodiversity and the physical processes that operate on Earth. This complex history cannot be inferred solely by studying the genomes of living organisms, nor through analysis of the fossil remains of their extinct relatives. Only a unified approach integrating living and extinct species and drawing from both genomic and anatomical evidence can achieve this aim. In this review, we highlight recent advances, challenges, and opportunities in this endeavour. These include the development of models for analysis of anatomical data; methods for combined analysis of fossil and living species, as well as anatomical and genomic data; and the combined estimation of evolutionary relationships, geographic range, and evolutionary rates. However, the application of such methods is limited by a shortage of expertise in taxonomy and comparative anatomy, which are skills required for the compilation of anatomical datasets. Whereas there is a common concern for the incompleteness of the fossil record, knowledge with respect to the comparative anatomy of living species is equally incomplete. We anticipate that the increased demand for an integrative phylogenetic approach to reconstruct the tree of life and evolutionary patterns and processes will encourage researchers to overcome these challenges with the aim of elucidating the complexities behind organismal evolution across broad taxonomic and time scales.The modern era of analytical and quantitative palaeobiology has only just begun, integrating methods such as morphological and molecular phylogenetics and divergence time estimation, as well as phenotypic and molecular rates of evolution. Calibrating the tree of life to geological time is at the nexus of many disparate disciplines, from palaeontology to molecular systematics and from geochronology to comparative genomics. Creating an evolutionary time scale of the major events that shaped biodiversity is key to all of these fields and draws from each of them. Different methodological approaches and data employed in various disciplines have traditionally made collaborative research efforts difficult among these disciplines. However, the development of new methods is bridging the historical gap between fields, providing a holistic perspective on organismal evolutionary history, integrating all of the available evidence from living and fossil species. Because phylogenies with only extant taxa do not contain enough information to either calibrate the tree of life or fully infer macroevolutionary dynamics, phylogenies should preferably include both extant and extinct taxa, which can only be achieved through the inclusion of phenotypic data. This integrative phylogenetic approach provides ample and novel opportunities for evolutionary biologists to benefit from palaeontological data to help establish an evolutionary time scale and to test core macroevolutionary hypotheses about the drivers of biological diversification across various dimensions of organisms.

Revisiting R.H. Tschudy’s fern-spore spike concept 40 years later: connecting Tschudy’s ‘disaster taxon’ concept with paleopolyploidization in Stenochlaena J. Sm

The Cretaceous/Paleogene (K/Pg) boundary fern-spore spike concept was first introduced by R.H. Tschudy 40 years ago and established the precept that ferns are so-called ‘disaster taxa’ that flourish after natural disasters because of the high colonization potential of their wind-blown spores. Among the least understood topics at the crux of contemporary K/Pg boundary fern-spike studies is whether Stenochlaena-like or other stem blechnaceous ferns were among those that flourished after the K/Pg event, contributing to the Laevigatosporites-dominated phase of the fern-spore spike. For instance, dispersed Stenochlaena-like spores – e.g. Polypodiisporites usmensis (van der Hammen) Khan & Martin – first appear in the upper Eocene stratigraphic record of South America, whereas megafossils of Stenochlaena-like ferns are first known from the upper Paleocene strata of this same region. Beyond this traditional focus on taphonomic and taxonomic uncertainty regarding the identity of dispersed spore producers, however, there is further discordance between contemporary paleobotanical and molecular phylogenetic perspectives on the timing of diversification of stem lineages of blechnaceous ferns in relation to the K/Pg boundary. This investigation reconciles these two perspectives by constraining molecular clock divergence time estimates using contemporary fossil data. If this reconciliation is correct, then paleopolyploidization (whole genome duplication or WGD) associated with the origin of the genus Stenochlaena J. Sm. predated evolution of polocytic stomata, a heavily ornamented exospore, and a hemi-epiphytic to epiphytic habit observed in the crown lineage. Critically, this novel perspective elicits a merger of the K/Pg boundary fern spike and K/Pg boundary-WGD concepts, suggesting a link between polyploidy and the ‘disaster taxon’ concept.

Gene arrangement, phylogeny and divergence time estimation of mitogenomes in Thrips.

The metazoan mitogenomes usually display conserved gene arrangement while thrips are known for their extensive gene rearrangement, and duplication of the control region. We sequenced complete mitogenomes of eight species of thrips to determine the gene arrangement, phylogeny and divergence time estimation. All contain 37 genes and one control region, (CR) except four species with two CRs. Duplicated tRNAs were detected in Mycterothrips nilgiriensis and Thrips florum. nad4-nad4L were not found adjacent to each other in Phibalothrips peringueyi and Plicothrips apicalis. Both Bayesian and likelihood phylogenetic analyses of thrips mitogenomes supported the monophyly of two suborders (Terebrantia and Tubulifera) and the two largest families (Phlaeothripidae and Thripidae). Out of seven earlier proposed ancestral gene blocks, six are conserved in Panchaetothripinae, three in Thripinae and two in Phlaeothripidae. Additionally, eight Thrips Gene Blocks were identified, of which, three conserved in Tubulifera, four in Terebrantia, and one only in Aeolothripidae. Forty-two gene boundaries (15 from previous study + 27 new) were identified. The molecular divergence time is estimated for the order Thysanoptera and suggested that these insects may have been diversified from hemipterans in the late Permian period. The most recent ancestors belong to family Thripidae and Phlaeothripidae, which were diversified in upper Cretaceous period and showed higher rates of rearrangement from the ancestral gene order. The current study is the first largest effort to provide the new insights into the mitogenomic features, gene arrangement, phylogeny and divergence time estimation of thrips belonging to the order Thysanoptera.

Recent Zoonotic Spillover and Tropism Shift of a Canine Coronavirus Is Associated with Relaxed Selection and Putative Loss of Function in NTD Subdomain of Spike Protein.

A canine coronavirus (CCoV) has now been reported from two independent human samples from Malaysia (respiratory, collected in 2017–2018; CCoV-HuPn-2018) and Haiti (urine, collected in 2017); these two viruses were nearly genetically identical. In an effort to identify any novel adaptations associated with this apparent shift in tropism we carried out detailed evolutionary analyses of the spike gene of this virus in the context of related Alphacoronavirus 1 species. The spike 0-domain retains homology to CCoV2b (enteric infections) and Transmissible Gastroenteritis Virus (TGEV; enteric and respiratory). This domain is subject to relaxed selection pressure and an increased rate of molecular evolution. It contains unique amino acid substitutions, including within a region important for sialic acid binding and pathogenesis in TGEV. Overall, the spike gene is extensively recombinant, with a feline coronavirus type II strain serving a prominent role in the recombinant history of the virus. Molecular divergence time for a segment of the gene where temporal signal could be determined, was estimated at around 60 years ago. We hypothesize that the virus had an enteric origin, but that it may be losing that particular tropism, possibly because of mutations in the sialic acid binding region of the spike 0-domain.