Divergence Time Estimates Research Articles

Towards a global perspective for Salvia L.: Phylogeny, diversification and floral evolution.

Salvia is the most species-rich genus in Lamiaceae, encompassing approximately 1000 species distributed all over the world. We sought a new evolutionary perspective for Salvia by employing macroevolutionary analyses to address the tempo and mode of diversification. To study the association of floral traits with speciation and extinction, we modelled and explored the evolution of corolla length and the lever-mechanism pollination system across our Salvia phylogeny. We reconstructed a multigene phylogeny for 366 species of Salvia in the broad sense including all major recognized lineages and 50 species from Iran, a region previously overlooked in studies of the genus. Our comprehensive sampling of Iranian species of Salvia provides higher phylogenetic resolution for southwestern Asian species than obtained in previous studies. Our phylogenetic data in combination with divergence time estimates were used to examine the evolution of corolla length, woody versus herbaceous habit, and presence versus absence of a lever mechanism. We investigated the timing and dependence of Salvia diversification related to corolla length evolution through a disparity test and BAMM analysis. A HiSSE model was used to evaluate the dependency of diversification on the lever-mechanism pollination system in Salvia. A medium corolla length (15-18 mm) was reconstructed as the ancestral state for Salvia with multiple shifts to shorter and longer corollas. Macroevolutionary model analyses indicate that corolla length disparity is high throughout Salvia evolution, significantly different from expectations under a Brownian motion model during the last 28 million years of evolution. Our analyses show evidence of a higher diversification rate of corolla length for some Andean species of Salvia compared to other members of the genus. Based on our tests of diversification models, we reject the hypothesis of a direct effect of the lever mechanism on Salvia diversification. Therefore, we suggest caution in considering the lever-mechanism pollination system as one of the main drivers of speciation in Salvia.

Role of paleoclimatic and paleohydrological processes in lineage divergence in freshwater organisms: A snippet from lentic genus Pila

The Indian subcontinent is extremely diverse in terms of its flora and fauna. However, only a handful of studies have aimed to understand the diversity of freshwater invertebrates using multiple lines of evidence in recent times. Here we aimed to estimate the cryptic diversity of two widespread freshwater snail species within the genus Pila (Röding, 1798) and uncover the processes behind lineage diversification in these species. We sequenced mitochondrial and nuclear markers from a comprehensive sampling of specimens from different river basins in India. We implemented an integrative taxonomy approach to delimit the lineages in these groups, employing phylogenetic, geometric morphometric and niche modelling-based methods. Then, we investigated the drivers of lineage divergence in these species using population genetic tools in conjunction with divergence time estimation. We found that both species consist of several genetically and ecologically distinct lineages. The genetic data showed that several of these lineages are restricted to a single or a few river basins. The divergence time estimation analyses indicated that the time frame of divergence within the species coincided with paleohydrological and paleoclimatic events in the Miocene. The diversification was primarily driven by allopatric isolation into different river basins. To conclude, the study sheds light on the complex interaction between the habitat preference of the species and the environment in shaping the diversification patterns in this group.

Re-Evaluating Botryosphaeriales: Ancestral State Reconstructions of Selected Characters and Evolution of Nutritional Modes.

Botryosphaeriales (Dothideomycetes, Ascomycota) occur in a wide range of habitats as endophytes, saprobes, and pathogens. The order Botryosphaeriales has not been subjected to evaluation since 2019 by Phillips and co-authors using phylogenetic and evolutionary analyses. Subsequently, many studies introduced novel taxa into the order and revised several families separately. In addition, no ancestral character studies have been conducted for this order. Therefore, in this study, we re-evaluated the character evolution and taxonomic placements of Botryosphaeriales species based on ancestral character evolution, divergence time estimation, and phylogenetic relationships, including all the novel taxa that have been introduced so far. Maximum likelihood, maximum parsimony, and Bayesian inference analyses were conducted on a combined LSU and ITS sequence alignment. Ancestral state reconstruction was carried out for conidial colour, septation, and nutritional mode. Divergence times estimates revealed that Botryosphaeriales originated around 109 Mya in the early epoch of the Cretaceous period. All six families in Botryosphaeriales evolved in the late epoch of the Cretaceous period (66-100 Mya), during which Angiosperms also appeared, rapidly diversified and became dominant on land. Families of Botryosphaeriales diversified during the Paleogene and Neogene periods in the Cenozoic era. The order comprises the families Aplosporellaceae, Botryosphaeriaceae, Melanopsaceae, Phyllostictaceae, Planistromellaceae and Saccharataceae. Furthermore, current study assessed two hypotheses; the first one being "All Botryosphaeriales species originated as endophytes and then switched into saprobes when their hosts died or into pathogens when their hosts were under stress"; the second hypothesis states that "There is a link between the conidial colour and nutritional mode in botryosphaerialean taxa". Ancestral state reconstruction and nutritional mode analyses revealed a pathogenic/saprobic nutritional mode as the ancestral character. However, we could not provide strong evidence for the first hypothesis mainly due to the significantly low number of studies reporting the endophytic botryosphaerialean taxa. Results also showed that hyaline and aseptate conidia were ancestral characters in Botryosphaeriales and supported the relationship between conidial pigmentation and the pathogenicity of Botryosphaeriales species.

The extant moss genus Leucobryum (Bryopsida: Leucobryaceae) from Miocene Zhangpu amber

The fossil record of bryophytes from worldwide amber deposits substantially increased within the past decade. Inclusions of mosses have now been described from 15 Cretaceous and Cenozoic amber localities. These fossils stand out by their excellent preservation and are therefore very valuable for divergence time estimates as well as for the reconstruction of the evolution of morphological traits through time. The amber inclusions are three-dimensional and show diminutive details which are crucial for classification of bryophytes. Many moss fossils preserved in amber were convincingly assigned to extant genera and, in the case of Miocene taxa, sometimes even to living species. Here, we describe a fossil Leucobryum from Zhangpu amber of southeastern China. The extant genus Leucobryum comprises between 35 and 83 mainly tropical species and is characterized by a highly modified costa consisting of one layer of small chlorocysts between two layers of large, empty leucocysts. Some leaves of the fossil specimens are broken and show the arrangement of cells typical for extant species. We provide a thorough comparison to extant representatives, however, as several characters necessary for assignment at species level are not accessible in the fossil, it is uncertain whether it represents an extinct or extant species.

Genome Assembly of a Relict Arabian Species of Daphnia O. F. Müller (Crustacea: Cladocera) Adapted to the Desert Life

The water flea Daphnia O.F. Müller 1776 (Crustacea: Cladocera) is an important model of recent evolutionary biology. Here, we report a complete genome of Daphnia (Ctenodaphnia) arabica (Crustacea: Cladocera), recently described species endemic to deserts of the United Arab Emirates. In this study, genome analysis of D. arabica was carried out to investigate its genomic differences, complexity as well as its historical origins within the subgenus Daphnia (Ctenodaphnia). Hybrid genome assembly of D. arabica resulted in ~116 Mb of the assembled genome, with an N50 of ~1.13 Mb (BUSCO score of 99.2%). From the assembled genome, in total protein coding, 5374 tRNA and 643 rRNA genes were annotated. We found that the D. arabica complete genome differed from those of other Daphnia species deposited in the NCBI database but was close to that of D. cf. similoides. However, its divergence time estimate sets D. arabica in the Mesozoic, and our demographic analysis showed a great reduction in its genetic diversity compared to other Daphnia species. Interestingly, the population expansion in its diversity occurred during the megadrought climate around 100 Ka ago, reflecting the adaptive feature of the species to arid and drought-affected environments. Moreover, the PFAM comparative analysis highlights the presence of the important domain SOSS complex subunit C in D. arabica, which is missing in all other studied species of Daphnia. This complex consists of a few subunits (A, B, C) working together to maintain the genome stability (i.e., promoting the reparation of DNA under stress). We propose that this domain could play a role in maintaining the fitness and survival of this species in the desert environment. The present study will pave the way for future research to identify the genes that were gained or lost in this species and identify which of these were key factors to its adaptation to the harsh desert environment.

Extensive characterization of 28 complete chloroplast genomes of Hydrangea species: A perspective view of their organization and phylogenetic and evolutionary relationships

The tribe Hydrangeeae displays a unique, distinctive disjunct distribution encompassing East Asia, North America and Hawaii. Despite its complex trait variations and polyphyletic nature, comprehensive phylogenomic and biogeographical studies on this tribe have been lacking. To address this gap, we sequenced and characterized 28 plastomes of Hydrangeeae. Our study highlights the highly conserved nature of Hydrangeaceae chloroplast (cp) genomes in terms of gene content and arrangement. Notably, synapomorphic characteristics of tandem repeats in the conserved domain of accD were observed in the Macrophyllae, Chinenses, and Dichroa sections within the Hydrangeeae tribe. Additionally, we found lower expression of accD in these sections using structure prediction and quantitative real-time PCR analysis. Phylogenomic analyses revealed the subdivision of the Hydrangeeae tribe into two clades with robust support values. Consistent with polyphyletic relationships, sect. Broussaisia was identified as the basal group in the tribe Hydrangeeae. Our study also provides insights into the phylogenetic relationships of Hydrangea petiolaris in the Jeju and Ulleung Island populations, suggesting the need for further studies with more samples and molecular data. Divergence time estimation and biogeographical analyses suggested that the common ancestors of the tribe Hydrangeeae likely originated from North America and East Asia during the Paleocene period via the Bering Land Bridge, potentially facilitating migration within the tribe between these regions. In conclusion, this study enhances our understanding of the evolutionary history and biogeography of the tribe Hydrangeeae, shedding light on the dispersal patterns and origins of this intriguing plant group with its unique disjunct distribution.

Phylogenetics of the Paleartic model grass Brachypodium sylvaticum uncovers two divergent oriental and occidental micro-taxa lineages

Brachypodium sylvaticum has been selected as a model for perennial grasses, and considerable genomic resources have been generated and a reference genome and several resequenced pangenome accessions are available for this species. Despite these genomic advances, the evolution and systematics of diploid B. sylvaticum s. l. is almost unknown. The B. sylvaticum complex is formed by up to seven taxonomically close micro-taxa which differentiate from typical B. sylvaticum s. s. based on a few morphological features. Moreover, some of them show some largely disjunct geographic distributions on both sides of their native Palearctic region. In this study, we used a phylogenomic approach including representative populations from the oriental and occidental distribution range of B. sylvaticum micro-taxa to elucidate their evolutionary relationships and assess the systematic value of the morphological features that separate them. A combined plastome and nuclear phylogenetic tree supports an early split and high divergence of the oriental lineage, showing the close relationship of the Himalayan B. sylvaticum var. breviglume lineages to the Pacific B. miserum / B. kurilense clade, and the contrasting large homogeneity and low divergence of the occidental European, N African and SW and C Asian lineage, with several B. sylvaticum s. s., B. spryginii, and B. glaucovirens samples showing identical or similar sequences. Divergence time estimate analysis suggests that the oriental lineage diverged from the common ancestor in the early Pleistocene (2.0 Ma), followed by subsequent colonization and isolations in the Himalayas (2.0 – 1.7 Ma) and the Far East (0.36 Ma) in more recent times, while the occidental lineage split in the Mid-Late Pleistocene (0.97 Ma), followed by rapid radiation and postglacial spread in the western Paleartic during the last thousand years.

Origin, evolution and systematics of the genusPoecilimon(Orthoptera: Tettigoniidae)—An outburst of diversification in the Aegean area

AbstractOur study focuses on the origin, dispersal patterns, evolutionary strategies and systematics ofPoecilimon, the largest bush‐cricket genus in the Palaearctic with over 150 taxa described. We employ phylogenetic and divergence time estimation analyses based on multilocus sequence data (ND2 + COI + 12 S + 16 S + ITS+28 S), perform ancestral area reconstruction, and track the evolution of behavioural (evolution of sound communication) and morpho‐physiological traits (body size and shape, and spermatophore size) in this genus. Based on our results, we propose a revised systematics ofPoecilimon, including description of a new species,P. nivalissp. n., and hypothesize three stages in the evolution ofPoecilimon. (1) In the early evolution of the genus in Tortonian, when open dry habitats appeared in the Eastern Mediterranean, diversification rates were low and speciation was possibly induced by vicariance and habitat fragmentation; physiology and morphology during this period retained their ancestral states but the evolution of main lineages may have been accompanied by behavioural specializations. (2) Climate cooling and aridification during the Messinian induced dispersals and adaptation to new habitats, followed by physiological and behavioural adaptations; major clades formed or started diversifying. (3) Starting at the end of Messinian and continuing through the Plio‐ and Pleistocene, a few dispersal events from Anatolia to the Balkans took place and climatic oscillations were followed by allo‐ and parapatric divergence of habitat specialists, while ecological adaptations enhanced song diversity and led to morpho‐physiological changes.

One in, one out: Generic circumscription within subtribe Manilkarinae (Sapotaceae)

AbstractPrevious phylogenetic studies have demonstrated that the Manilkarinae are a monophyletic subtribe if Northia is excluded. The subtribe consists of four genera: Faucherea, Labourdonnaisia, Labramia and Manilkara. However, the same phylogenetic studies also raised taxonomic issues concerning unclear generic delimitations and unresolved relationships. The current study's aims are: to resolve these taxonomic issues using a molecular phylogeny based on hundreds of nuclear markers sequenced from a representative sampling of taxa across the four genera; to find relevant morphological characters allowing the distinction of the clades retrieved with the phylogeny; and finally to understand the evolutionary history of the subtribe by conducting a divergence time estimation and ancestral state reconstructions. Our phylogeny shows a well‐resolved backbone with four main lineages: the Labramia clade, the main clade of Manilkara, a clade in which all species of Labourdonnaisia and Faucherea are mixed, and a clade of three Pacific Manilkara species. The main clade of Manilkara is retrieved as sister to Labramia, and the Labourdonnaisia‐Faucherea clade is clearly assessed as sister to the three Pacific Manilkara species. As a consequence, Faucherea is synonymized with Labourdonnaisia, and the three Pacific Manilkara are considered to be a separate genus, for which the name Abebaia is resurrected. We provide emended descriptions for Labourdonnaisia and Abebaia as well as the necessary new combinations. The ancestral state reconstruction of flower characters shows that ancestral Manilkarinae were characterized by a hexamerous corolla, well‐developed dorsal appendages and staminodes, and a pubescent ovary. These character states have been retained in the main Manilkara clade, but surprisingly also in Abebaia, which appears as a cryptic genus. The lack of dorsal appendages and the reduction of staminodes observed in Labourdonnaisia appeared after the split from Abebaia. The increase in corolla merism observed mainly in the Mascarene Labourdonnaisia, which was used to separate it from Faucherea, appears to be a derived state, which evolved separately in a few species during the radiation of Labourdonnaisia on Madagascar and the Mascarenes. The glabrous ovary state observed in Labramia also constitutes a derived synapomorphic state in the genus.

Molecular and morphological evidence support the recognition of three genera within Radulaceae (Porellales: Marchantiophyta)

The discovery of new fossil bryophytes allows refined estimates of divergence times when the fossils have unambiguous synapomorphies enabling their confident assignment to nodes within molecular phylogenies. We use two fossil Radula species from Cretaceous age Burmese amber to estimate divergence times for Radula. One of these fossils, R. cretacea which has synapomorphies of subg. Odontoradula, has been used previously; the other, with relative synapomorphies of subg. Amentuloradula, has not. In combination these two fossils, when used to constrain the crown node age of their respective subgenera, result in median age estimates for the Radula crown node of 263 million years, under our preferred time-calibration scenario where subgeneric crown-node fossil assignments are coupled with a secondary maximum age constraint on the Porellales crown node. We explore other time-calibration scenarios, including deeper fossil assignments, and conclude that, under all, Radula as currently circumscribed is an outlier among land plant genera on the basis of its age. While this violates no established norms regarding how old genera should be, the absolute age, the relative ages of other families within Porellales, and the morphological distinctiveness of the two serial sister lineages, subg. Cladoradula, with seven species, and subg. Dactyloradula with one species, motivates our proposal to elevate these two subgenera to generic rank, resulting in three genera within the family Radulaceae. We provide diagnoses for genera, new combinations for species, and an emended circumscription for Radula, that reflect this change.

Pronounced Mitochondrial DNA Population Genetic Structure in a Brooding Coastal Marine Invertebrate

Analyses of phylogeographic and population genetic structure of marine species with large population sizes, low fecundity, larval brooding, and limited dispersal such as the New Zealand flat oyster, Ostrea chilensis Küster, 1844, permit testing of the effects of historical and contemporary processes affecting patterns of coastal genetic differentiation and diversity. Analyses of DNA sequences from two mitochondrial DNA regions (COI, Cyt-b) compiled from O. chilensis individuals from 14 localities revealed a pronounced structure with three genetic clusters [Hauraki Gulf (HG); North; South] being resolved. These results suggest that historical processes have contributed to patterns of regional separation that have in turn contributed to regional genetic differences that are still observable today. Divergence time estimates of HG from North+South (1.97 Ma) and of North from South (0.36 Ma) indicate that O. chilensis from these regions represent evolutionarily significant units that evolved separately and rapidly in the early to middle Pleistocene. Analyses revealed no obvious periods of population expansion within any of the regions. These results contribute to a better understanding of how historical factors can result in pronounced mitochondrial DNA patterns of contemporary genetic structure and show how key life-history characteristics, e.g., larval brooding, can contribute to phylogeographic structure in coastal marine invertebrates.

Integrative taxonomy of the stalk‐eyed bug genus Chauliops (Heteroptera: Malcidae: Chauliopinae) reveals orogeny‐driven speciation

AbstractEconomically significant bean pests of the genus Chauliops are species rich in the areas surrounding the Qinghai–Tibet Plateau and provide an excellent system for speciation studies. Here, an integrative taxonomic approach, employing morphological analyses, population genetic methods, and multiple molecular species delimitation methods, was used to clarify the taxonomy of Chauliops in East and Southeast Asia. Four new species (Chauliops parahorizontalis Li & Bu, sp. nov., Chauliops albida Li & Bu, sp. nov., Chauliops bicoloripes Li & Bu, sp. nov., and Chauliops paraconica Li & Bu, sp. nov.) were described, which increases the number of Chauliops species in this area from six to 10; a key for Chauliops species is also provided. Phylogenetic analysis and divergence time estimation revealed that Chauliops was divided into four clades: Clade A (Chauliops bisontula + [Chauliops horizontalis + C. parahorizontalis sp. nov.]), Clade B (C. albida sp. nov. and C. bicoloripes sp. nov.), Clade C (Chauliops quaternaria and Chauliops zhengi), and Clade D (Chauliops fallax + [Chauliops conica + C. paraconica sp. nov.]). Two species diversification events of Chauliops estimated to have occurred 7–1 million years ago (Ma) and 25–13 Ma were detected. These speciation events were consistent with the two historical uplift events of the Qinghai–Tibet Plateau, suggesting that orogeny might have provided opportunities for the diversification of Chauliops species on the southeastern margin of the Qinghai–Tibet Plateau. Our findings show that population genetic analyses can be used to delimit related species and that orogeny is a key driver of species diversification on the southeastern margin of the Qinghai–Tibet Plateau.

Insights into the evolutionary history and taxonomic status of Sinopteris (Pteridaceae)

As an endemic Chinese genus, Sinopteris C. Chr. & Ching was once considered an early diverged taxon of cheilanthoid ferns, and its taxonomic status has long been controversial. In this study, eight datasets spanning the complete chloroplast genomes and three nuclear genes were used to reconstruct the phylogeny of Sinopteris and its relatives. In addition, combining morphological analyses, divergence time estimation, and ancestral trait reconstruction, the origin and evolutionary history of Sinopteris were comprehensively discussed. Based on the complete chloroplast genome dataset, our analyses yielded a phylogram with all clades strongly supported (ML-BS = 100, BI-PP = 1.0), and the topology was almost identical to that based on the concatenated sequences of nrDNA, CRY2, and IBR3. Two species of Sinopteris were united and sister to Aleuritopteris niphobola (C. Chr.) Ching. They constituted a stable monophyletic group embedded in Aleuritopteris Fée. This was also consistent with the results of morphological analyses. Divergence time estimation indicated that the clade of Aleuritopteris and Sinopteris originated in the early Miocene (ca. 16.80 Ma) and experienced two rapid diversifications, which could coincide with environmental heterogeneity caused by the progressive uplift of the Himalayas and the intense uplift of the Hengduan Mountains. Sinopteris originated in the late Miocene (ca. 6.96 Ma), accompanied by the sharp intensifications of Asian Monsoon, and began to diversify at 2.34 Ma, following the intense uplift of the Hengduan Mountains. Ancestral character reconstruction showed that monangial sori and subsessile sporangia were clearly late derived states rather than early diverged states. Both the molecular phylogenetic and morphological analyses support the inclusion of Sinopteris in Aleuritopteris.

Diversification of Amazonian spiny tree rats in genus Makalata (Rodentia, Echimyidae): Cryptic diversity, geographic structure and drivers of speciation.

Amazonian mammal diversity is exceptionally high, yet new taxonomic discoveries continue to be made and many questions remain for understanding its diversification through time and space. Here we investigate the diversification of spiny rats in the genus Makalata, whose species are strongly associated with seasonally flooded forests, watercourses and flooded islands. We use a biogeographical approach based on a mitochondrial cytochrome b gene through divergence time estimation and reconstruction of ancestral areas and events. Our findings indicate an ancient origin of Makalata for the Guiana Shield and Eastern Amazonia as ancestral area. A first cladogenetic event led to a phylogeographic break into two broader clades of Makalata through dispersal, implying a pattern of western/Eastern Amazonian clades coinciding with the Purus Arch (middle Miocene). Most of subclades we infer originated between the late Pliocene to the early Pleistocene, with few recent exceptions in the early Pliocene through dispersal and vicariant events. The hypothesis of rivers as dispersal barriers is not corroborated for Makalata, as expected for mammalian species associated with seasonally flooded environments. We identify two key events for the expansion and diversification of Makalata species: the presence of geologically stable areas in the Guiana and Brazilian shields and the transition from lacustrine conditions in western Amazonia (Acre system) to a river system, with the establishment of the Amazon River transcontinental system and its tributaries. Our results are congruent with older geological scenarios for the Amazon basin formation (Miocene), but we do not discard the influence of recent dynamics on some speciation events and, mainly, on phylogeographic structuring processes.

A reappraisal of the phylogeny and historical biogeography of Sparganium (Typhaceae) using complete chloroplast genomes

BackgroundSparganium (Typhaceae) is a widespread temperate genus of ecologically important aquatic plants. Previous reconstructions of the phylogenetic relationships among Sparganium species are incompletely resolved partly because they were based on molecular markers comprising < 7,000 bp. Here, we sequenced and assembled the complete chloroplast genomes from 19 Sparganium samples representing 15 putative species and three putative subspecies in order to explore chloroplast genome evolution in this genus, clarify taxonomic lineages, estimate the divergence times of Sparganium species, and reconstruct aspects of the biogeographic history of the genus.ResultsThe 19 chloroplast genomes shared a conserved genome structure, gene content, and gene order. Our phylogenomic analysis presented a well-resolved phylogeny with robust support for most clades. Non-monophyly was revealed in three species: S. erectum, S. eurycarpum, and S. stoloniferum. Divergence time estimates suggest that the two subgenera of Sparganium split from each other ca. 30.67 Ma in the middle Oligocene. The subgenus Xanthosparganium diversified in the late Oligocene and Miocene, while the subgenus Sparganium diversified in the late Pliocene and Pleistocene. Ancestral area reconstruction suggested that the two subgenera may have originated in East Eurasia and North America.ConclusionThe non-monophyletic nature of three putative species underscores the necessity of taxonomic revision for Sparganium: S. stoloniferum subsp. choui may be more appropriately identified as S. choui, and subspecies of S. erectum may be in fact distinct species. The estimated diversification times of the two subgenera correspond to their species and nucleotide diversities. The likely ancestral area for most of subgenus Xanthosparganium was East Eurasia and North America from where it dispersed into West Eurasia and Australia. Most of subgenus Sparganium likely originated in North America and then dispersed into Eurasia. Our study demonstrates some of the ways in which complete chloroplast genome sequences can provide new insights into the evolution, phylogeny, and biogeography of the genus Sparganium.

Extensive reorganization of the chloroplast genome of Corydalis platycarpa: A comparative analysis of their organization and evolution with other Corydalis plastomes.

The chloroplast (cp) is an autonomous plant organelle with an individual genome that encodes essential cellular functions. The genome architecture and gene content of the cp is highly conserved in angiosperms. The plastome of Corydalis belongs to the Papaveraceae family, and the genome is comprised of unusual rearrangements and gene content. Thus far, no extensive comparative studies have been carried out to understand the evolution of Corydalis chloroplast genomes. Therefore, the Corydalis platycarpa cp genome was sequenced, and wide-scale comparative studies were conducted using publicly available twenty Corydalis plastomes. Comparative analyses showed that an extensive genome rearrangement and IR expansion occurred, and these events evolved independently in the Corydalis species. By contrast, the plastomes of its closely related subfamily Papaveroideae and other Ranunculales taxa are highly conserved. On the other hand, the synapomorphy characteristics of both accD and the ndh gene loss events happened in the common ancestor of the Corydalis and sub-clade of the Corydalis lineage, respectively. The Corydalis-sub clade species (ndh lost) are distributed predominantly in the Qinghai-Tibetan plateau (QTP) region. The phylogenetic analysis and divergence time estimation were also employed for the Corydalis species. The divergence time of the ndh gene in the Corydalis sub-clade species (44.31 - 15.71 mya) coincides very well with the uplift of the Qinghai-Tibet Plateau in Oligocene and Miocene periods, and maybe during this period, it has probably triggered the radiation of the Corydalis species. To the best of the authors' knowledge, this is the first large-scale comparative study of Corydalis plastomes and their evolution. The present study may provide insights into the plastome architecture and the molecular evolution of Corydalis species.

Plastid phylogenomics sheds light on divergence time and ecological adaptations of the tribe Persicarieae (Polygonaceae).

Southwestern China, adjacent to the Qinghai-Tibetan Plateau (QTP), is known as a hotspot for plant diversity and endemism, and it is the origin and diversification center of Persicarieae. As one of the major lineages in Polygonaceae, Persicarieae represents a diverse adaptation to various habitats. As a result of morphological plasticity and poorly resolving molecular markers, phylogenetic relationships and infrageneric classification within Persicarieae have long been controversial. In addition, neither plastome phylogenomic studies nor divergence time estimates on a larger sample of Persicarieae species have been made thus far. We sequenced and assembled 74 complete plastomes, including all of the recognized genera within Persicarieae and their relatives. We conducted a comprehensive phylogenetic study of the major clades within Persicarieae and, based on the thus obtained robust phylogeny, also estimated divergence time and the evolution of diagnostic morphological traits. Major relationships found in previous phylogenetic studies were confirmed, including those of the backbone of the tree, which had been a major problem in previous phylogenies of the tribe. Phylogenetic analysis revealed strong support for Koenigia as sister to Bistorta, and together they were sister to the robustly supported Persicaria. Based on the phylogenetic and morphological evidence, we recognize five sections in Persicaria: Persicaria, Amphibia, Tovara, Echinocaulon, and Cephalophilon. It is estimated that the divergence of the Persicarieae began around the late Paleocene, with diversification concentrated in the Eocene and Miocene. In addition, it is suggested that the increasing westerly and monsoon winds in conjunction with the uplift of the QTP may be the driving force for origin and diversification of Persicarieae species. These results provide a valuable evolutionary framework for the study of adaptation in Polygonaceae and insights into plant diversification on the QTP and adjacent areas.

Phylogenetic risk assessment is robust for forecasting the impact of European insects on North American conifers.

Some introduced species cause severe damage, although the majority have little impact. Robust predictions of which species are most likely to cause substantial impacts could focus efforts to mitigate those impacts or prevent certain invasions entirely. Introduced herbivorous insects can reduce crop yield, fundamentally alter natural and managed forest ecosystems, and are unique among invasive species in that they require certain host plants to succeed. Recent studies have demonstrated that understanding the evolutionary history of introduced herbivores and their host plants can provide robust predictions of impact. Specifically, divergence times between hosts in the native and introduced ranges of a nonnative insect can be used to predict the potential impact of the insect should it establish in a novel ecosystem. However, divergence time estimates vary among published phylogenetic datasets, making it crucial to understand if and how the choice of phylogeny affects prediction of impact. Here, we tested the robustness of impact prediction to variation in host phylogeny by using insects that feed on conifers and predicting the likelihood of high impact using four different published phylogenies. Our analyses ranked 62 insects that are not established in North America and 47 North American conifer species according to overall risk and vulnerability, respectively. We found that results were robust to the choice of phylogeny. Although published vascular plant phylogenies continue to be refined, our analysis indicates that those differences are not substantial enough to alter the predictions of invader impact. Our results can assist in focusing biosecurity programs for conifer pests and can be more generally applied to nonnative insects and their potential hosts by prioritizing surveillance for those insects most likely to be damaging invaders.

Revealing the non-overlapping characteristics between original centers and genetic diversity of Purpureocillium lilacinum

Purpureocillium lilacinum is a free-living, multitrophic, cosmopolitan fungus. This study estimated the genetic diversity of P. lilacinum and its geographic distribution pattern based on a global ITS dataset. At the intercontinental levels, the highest genetic diversity was in Asia. Divergence time estimation indicated that Hap 5, Hap 9, Hap 31, and Hap 32 from the Hainan, Guangdong, Jiangxi, and Fujian regions of China in Asia were the earliest divergence haplotypes. The neutrality test indicated that P. lilacinum is undergoing population expansion. These results support that the southeastern coastal region of China is the original center of P. lilacinum, while the East Asian region adjacent to this origin is the center of the genetic diversity of P. lilacinum. The geographical distribution pattern of P. lilacinum showed that only one haplotype (Hap 1) was globally distributed and that most haplotypes were distributed in Asia, while the few remaining haplotypes were scattered on other continents. The results provide valuable information to elucidate the origin, genetic diversity, and evolution of fungi.

A draft genome assembly of ectoparasitic mite Pyemotes zhonghuajia Yu, Zhang &amp;amp; He (Prostigmata: Pyemotidae)

Pyemotes zhonghuajia Yu, Zhang &amp; He (Prostigmata: Pyemotidae) is an ectoparasitic mite species with a variety of insects-specific protein toxins, which are harmless to mammals and human. This mite can cause the death of many agricultural and forestry pests which can be 680,000 times greater than its own body weight (Tian et al., 2020; Chen et al., 2021). Exploring its genome will help us understand its parasitic mechanism. PacBio technology was used to sequence the genome of P. zhonghuajia. The genome size of P. zhonghuajia was estimated to be 71.943 Mb, which captured 90.6% of the Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness (Song et al., 2022). A total of 11,183 protein coding genes were annotated with 91.2% BUSCO completeness. Maximum Likelihood phylogenetic tree was constructed using 473 single-copy genes of 12 species including two species of spiders, two species of scorpions and 10 species of mites, of which spiders and scorpions were outgroups. The result shows that Pyemotes zhonghuajia is sister to Tetranychus urticae. An estimate of species divergence time showed that P. zhonghuajia and T. urticae emerged during Triassic (223.43~247.66 Mya). In P. zhonghuajia, there were 621 gene families (containing 1,224 genes) expanded, and 3664 gene families (containing 3,927 genes) contracted. Most importantly, we found that P. zhonghuajia contained three types of toxin proteins, which were neurotoxins, dermonecrotic toxins and agatoxins. Neurotoxin and dermonecrotic toxin-related genes are significantly expanded. The toxin-related gene expression level of one-day-old mites was higher than that of seven-day-pregnant mites, which might explain why one one-day-old mite had such strongly toxin (Chen et al., 2021). We also verified the function of the toxin proteins and explored its effect on insect cells to lay a theoretical foundation for the study and development of biopesticides with multi-target insecticidal toxins (Song et al., 2022).&#x0D;