Estimated Divergence Times Research Articles

Comparative Study of Phytolacca Species Through Morphological, Chloroplast Genome, and Phylogenetic Analysis

Phytolacca acinosa Roxb. and P. americana L. are recognized as the primary sources of Phytolaccae Radix, which is traditionally utilized for various medicinal purposes. However, because of their potent toxicity, it is essential to distinguish these species. This study has aimed to clarify the classification of Phytolacca species based on their morphology and genetic differences. The chloroplast genome of P. acinosa was sequenced and comparative analyses were conducted to identify the regions of variation and nucleotide diversity among the species. The results revealed that P. acinosa shares more sequence similarity with other Phytolacca species than with P. americana. Additionally, the dN/dS analysis showed that the ndhH gene of P. americana had a value of 1.0871, indicating positive selection. The phylogenetic tree, supported by strong bootstrap values and posterior probabilities, confirmed that P. acinosa and P. americana formed distinct clusters. Furthermore, the estimated divergence time between P. acinosa and P. americana was approximately 15.07 million years ago, indicating that they diverged earlier than P. insularis, P. polyandra, P. japonica, and P. latbenia. These findings indicated that P. acinosa and P. americana are phylogenetically distinct species, highlighting the need for accurate species identification and taxonomic reassessment to ensure the safe use of these toxic medicinal plants.

High genetic variation, low differentiation, and Pleistocene expansions of the migratory and endangered long-nosed tequila bat, Leptonycteris nivalis, inferred using both maternal and paternal genetic markers.

Tequila bats (genus Leptonycteris) have gained attention for their critical role in pollinating different plant species, especially Agave spp. and columnar cacti. Leptonycteris nivalis is the largest nectar-feeding bat in the Americas, and the females exhibit migratory behavior during the breeding season. Due to its relatively small and seemingly declining population sizes, this species is protected by government agencies in the United States and Mexico. We conducted population genetics and phylogeographic analyses to elucidate the genetic structure and demographic history of the species using two mitochondrial markers and a Y chromosome-associated gene, to describe both maternal and paternal lineages. We estimated high haplotypic diversity measures for the different markers (Dloop-Hd = 0.775; Cyt-b-Hd = 0.937; DBY -Hd = 0.946). We found that geographic genetic differentiation is very low, and there is high connectivity among localities. The estimated divergence time between L. nivalis and L. yerbabuenae, the other species in the genus found in Mexico, aligns with previous estimates for the genus (6.91-9.43 mya). A demographic expansion was detected approximately at 600 ka-700 ka (thousands of years ago). The historical demographic changes observed in L. nivalis appear to be associated with environmental shifts during the Pleistocene, which likely impacted the distribution range of the plants that these bats feed on, such as Agave species.

High-quality genome of Firmiana hainanensis provides insights into the evolution of Malvaceae subfamilies and the mechanism of their wood density formation.

The Malvaceae family, the most diverse family in the order Malvales, consists of nine subfamilies. Within the Firmiana genus of the Sterculioideae subfamily, most species are considered globally vulnerable, yet their genomes remain unexplored. Here, we present a chromosome-level genome assembly for a representative Firmiana species, F. hainanensis, 2n = 40, totaling 1536 Mb. Phylogenomic analysis shows that F. hainanensis and Durio zibethinus have the closest evolutionary relationship, with an estimated divergence time of approximately 21 MYA and distinct polyploidization events in their histories. Evolutionary trajectory analyses indicate that fissions and fusions may play a crucial role in chromosome number variation (2n = 14 to 2n = 96). Analysis of repetitive elements among Malvaceae reveals that the Tekay subfamily (belonging to the Gypsy group) contributes to variation in genome size (ranging from 324 Mb to 1620 Mb). Additionally, genes associated with P450, peroxidase, and microtubules, and thereby related to cell wall biosynthesis, are significantly contracted in F. hainanensis, potentially leading to its lower wood density relative to Hopea hainanensis. Overall, our study provides insights into the evolution of chromosome number, genome size, and the genetic basis of cell wall biosynthesis in Malvaceae species.

Phylogeny, antiquity, and niche occupancy of Trinomia (Hymenoptera: Halictidae), an Afrotropical endemic genus of Nomiinae.

The Afrotropical region is home to many endemic bee groups, yet almost none have been studied from an integrated, holistic perspective. Among them, the halictid subfamily Nomiinae contains exceptional African diversity with variable distributions and life histories. Here, we combine phylogenomics, molecular dating, and distributional modelling to explore the evolutionary ecology of the genus Trinomia. We analyzed a matrix of 59 species of Nomiinae using ultraconserved element (UCE) and whole genome data, including all six species of Trinomia, and estimated divergence times for the subfamily. We then generated distribution models for all six species of Trinomia using Maximum Entropy models (MaxEnt) and 671 spatial data points. From these methods, we discovered a monophyletic Trinomia with an unexpected sister group relationship to the Asian-endemic genus Gnathonomia, as well as a recent origin of Trinomia in the late Miocene (∼5.8 million years ago). From our results, we found hints of phylogenetic conservatism in distribution among sister-groups of Trinomia, however, our results also highlight the need for additional efforts inventorying, identifying, and sharing data on African bees. This study represents an exemplary first step into studying bee spatial phylogenomics of African endemic bees.

Patterns of Genomic Heterogeneity in a Classic Field Cricket Mosaic Hybrid Zone

ABSTRACTBarriers to gene exchange can be semi‐permeable; some genes are expected to freely flow across species boundaries whereas others, under divergent selection or responsible for reproductive isolation, might not. Genome scans in recently diverged species have identified divergent genomic regions, a pattern that has often been interpreted as islands of restricted introgression in a background of relatively free gene exchange (“genomic islands of speciation”). Areas of high differentiation, most located in the X chromosome (females XX, males X0), have been identified in the hybridizing field crickets Gryllus firmus and Gryllus pennsylvanicus. These species were assumed to follow an islands of speciation model, with highly differentiated areas interpreted as areas of reduced introgression. We sequenced the G. firmus genome to localize previously studied SNPs and sample a larger area around them in 8 allopatric populations (4 of each species). We use these data to test expectations for the islands model, in which non‐introgressing areas should have both high absolute and relative differentiation. We find that in the allopatric populations, the areas with high relative differentiation (mostly X‐linked), previously interpreted as non‐introgressing, do not have high absolute differentiation as would be expected under the “islands model.” We also show that the estimated divergence time based on nuclear DNA is about 4× older than that estimated based on mtDNA (800 K vs. 200 K years ago). We discuss the implications of our results for introgression into allopatric populations.

Phylogenetics, biogeography, and life history evolution in the broadly distributed treefrog genus Dendropsophus (Anura: Hylidae: Hylinae).

Dendropsophusis one of the most species-rich genera of hylid treefrogs. Recent studies integrating Sanger-generated mitochondrial and nuclear loci with phenomic characters (SP) have advanced understanding of this clade, but questions about its internal relationships and biogeographic history persist. To address these questions, we used anchored hybrid enrichment (AHE) to combine 432 nuclear loci for 78 taxa (72% of species) with published data. Quantitatively, the impact of the AHE data was modest, with compositional differences in only three recognized clades and more than 80% of the clades in the AHE + SP analyses also supported in the SP-only analyses. Nevertheless, the impact of AHE was crucial for resolving and increasing support for multiple nodes. We transferred one species of the formerD. ruschiigroup to theD. decipiensgroup and redefined theD. leucophyllatusgroup to avoid paraphyly. We estimated divergence times to reconstruct the clade's biogeographic history. We also examined evolution of oviposition sites and assessed its effect on lineage accumulation. Dendropsophuslikely originated∼57mya, predating the Andean uplift, with some taxa showing dispersal patterns less constrained by ecological changes than previously thought.

Chilling Out: Cooler Climates Triggered Divergence of Sabal (Arecaceae: Coryphoideae: Sabaleae) at the End of the Mid-Miocene Climatic Optimum

Abstract— In this study we explore the biogeographic patterns and processes underlying the diversification of Sabal, a genus of palm with a range that expands from the tropical rainforests of northern South America into the deciduous subtropical forests of the southeastern United States. We estimate divergence times among species of Sabal using two dated fossils as calibration points to inform ancestral reconstructions of the historical distribution of Sabal, and then use floral volatile composition data in select species of Sabal to integrate plant ecological interactions into our discussion of species distributions. Our results suggest extant Sabal originated within the last 21 million years with a divergence event ∼14 million years ago that effectively split the most recent common ancestor of all southeastern United States and West Indian species from the ancestor of a clade of species with their current distribution in Mexico. This divergence event corresponds with the end of the mid-Miocene climatic optimum, which resulted in cooler climates across southeastern North America where extant cold-tolerant taxa S. minor and S. palmetto are currently distributed. Floral volatile data indicate a generalist pollination strategy involving day foraging insects. Among sampled species, floral scent profiles can mostly be characterized by quantitative differences in five main compounds: benzaldehyde, benzyl alcohol, 2-phenylethanol, (E)-β-ocimene, and hexanal. These profiles align with major clades recovered in our phylogenetic analysis of Sabal and are indicative of evolutionary trends in pollination ecology and reproductive isolation within the genus.

Phylogenetic relationships of Neogene hamsters (Mammalia, Rodentia, Cricetinae) revealed under Bayesian inference and maximum parsimony.

There is an ongoing debate about the internal systematics of today's group of hamsters (Cricetinae), following new insights that are gained based on molecular data. Regarding the closely related fossil cricetids, however, most studies deal with only a limited number of genera and statements about their possible relationships are rare. In this study, 41 fossil species from the Late Miocene to the Pliocene, belonging to seven extinct cricetine genera, Collimys, Rotundomys, Neocricetodon, Pseudocricetus, Cricetulodon, Apocricetus and Hattomys are analysed in a phylogenetic framework using traditional maximum parsimony and Bayesian inference approaches. Following thorough model testing, a relaxed-clock Bayesian inference analysis is performed under tip-dating to estimate divergence times simultaneously. Furthermore, so-called 'rogue' taxa are identified and excluded from the final trees to improve the informative value of the shown relationships. Based on these resulting trees, the fit of the topologies to the stratigraphy is assessed and the ancestral states of the characters are reconstructed under a parsimonious approach and stochastic character mapping. The overall topologies resulting from Bayesian and parsimonious approaches are largely congruent to each other and confirm the monophyly of most of the genera. Additionally, synapomorphies can be identified for each of these genera based on the ancestral state reconstructions. Only Cricetulodon turns out to be paraphyletic, while 'Cricetulodon' complicidens is a member of Neocricetodon. Lastly, this work makes a contribution to a debate that went on for decades, as the genus Kowalskia can be confirmed as junior synonym of Neocricetodon.

Robustness of Divergence Time Estimation Despite Gene Tree Estimation Error: A Case Study of Fireflies (Coleoptera: Lampyridae).

Genomic data has become ubiquitous in phylogenomic studies, including divergence time estimation, but provide new challenges. These challenges include, amongst others, biological gene tree discordance, methodological gene tree estimation error, and computational limitations on performing full Bayesian inference under complex models. In this study, we use a recently published firefly (Coleoptera: Lampyridae) anchored hybrid enrichment dataset (AHE; 436 loci for 88 Lampyridae species and 10 outgroup species) as a case study to explore gene tree estimation error and the robustness of divergence time estimation. First, we explored the amount of model violation using posterior predictive simulations because model violations are likely to bias phylogenetic inferences and produce gene tree estimation error. We specifically focused on missing data (either uniformly distributed or systematically) and the distribution of highly variable and conserved sites (either uniformly distributed or clustered). Our assessment of model adequacy showed that standard phylogenetic substitution models are not adequate for any of the 436 AHE loci. We tested if the model violations and alignment errors resulted indeed in gene tree estimation error by comparing the observed gene tree discordance to simulated gene tree discordance under the multispecies coalescent model. Thus, we show that the inferred gene tree discordance is not only due to biological mechanism but primarily due to inference errors. Lastly, we explored if divergence time estimation is robust despite the observed gene tree estimation error. We selected four subsets of the full AHE dataset, concatenated each subset and performed a Bayesian relaxed clock divergence estimation in RevBayes. The estimated divergence times overlapped for all nodes that are shared between the topologies. Thus, divergence time estimation is robust using any well selected data subset as long as the topology inference is robust.

Comparison of the chloroplast genomics of nine endangered Habenaria species and phylogenetic analysis

BackgroundHabenaria, a genus in the family Orchidaceae, are the nearly cosmopolitan orchids, and most species have significant medicinal and ornamental values. Despite the morphological and molecular data that have been studied in recent years, the phylogenetic relationship is still unclear.ResultsWe sequenced, assembled, and annotated the chloroplast (cp) genomes of two species (Habenaria aitchisonii Rchb.f. and Habenaria tibetica Schltr.ex Limpricht) of Habenaria grown on the Qinghai-Tibetan Plateau (QTP), and compared them with seven previously published cp genomes which may aid in the genomic profiling of these species. The two genomes ranged from 155,259–155,269 bp in length and both included 132 genes, encoding 86 proteins, 38 tRNAs and 8 rRNAs. In the cp genomes, the tandem repeats (797), SSRs (2195) and diverse loci (3214) were identified. Comparative analyses of codon usage, amino frequency, microsatellite, oligo repeats and transition and transversion substitutions revealed similarities between the species. Moreover, we identified 16 highly polymorphic regions with a nucleotide diversity above 0.02, which may be suitable for robust authentic barcoding and inferring in the phylogeny of Habenaria species. Among the polymorphic regions, positive selection was significantly exerted on several genes, such as cemA, petA, and ycf1. This finding may suggest an important adaptation strategy for the two Habenaria species on the QTP. The phylogenetic relationship revealed that H. aitchisonii and H. tibetica were more closely related to each other than to the other species, and the other seven species were clustered in three groups. In addition, the estimated divergence time suggested that the two species separated from the others approximately 0.39 Mya in the Neogene period. Our findings also suggest that Habenaria can be divided into different sections.ConclusionsThe results of this study enriched the genomics resources of Habenaria, and SSR marker may aid in the conservation management of two endangered species.

The complete mitochondrial genome of Dimorphopterus japonicus (Hidaka, 1959) (Hemiptera, Lygaeoidea) and phylogenetic relationships within the Lygaeoidea superfamily

Dimorphopterus japonicus is a kind of pest which seriously harms sorghum and millet. In this study, we sequenced the mitochondrial whole genome of D. japonicus (Hidaka, 1959), and characterized and analyzed the mitogenome. The D. japonicus genome length is 15,473 bp, and it exhibits a typical high A + T content (77.6%). The mitogenomic structure of D. japonicus is highly conservative and there are no gene rearrangements. The evolutionary rates of the PCGs are in the order of atp8 > nad3 > nad6 > nad2 > nad5 > atp6 > nad4 > nad4L > cox2 > nad1 > cytb > cox3 > cox1. By using the Bayesian inference and maximum likelihood methods, we inferred the phylogenetic relationships within Lygaeoidea and estimated their divergence times based on concatenated mitogenome genes. The stable clades of (Oxycarenidae + Piesmatidae), (Malcidae + Colobathristidae), (Meschiidae + Berytidae), and (Blissidae+(Cymidae + Ninidae)) were consistently recovered in all analyses. Estimated divergence times revealed that the divergence time of the Lygaeoidea was 99.4 Ma (95% HPD: 83.4-124.8 Ma), and most lygaeoid families diverged during the early Cretaceous to late Paleogene. Berytidae is the latest differentiation in the lygaeoid families, and the genus Dimorphopterus was differentiated in 45.9 Ma (95% HPD: 39.8–47.7 Ma). This study is of great significance for reconstructing the phylogeny of Lygaeoidea and providing insights into its evolutionary history.

Spatial and Temporal Variation of Precipitation Drives the Genome Size Variation in Scolopendra in Chinese Mainland.

Genome size is an adaptive trait, and its variations influence the organismal phenotype and fitness. In this study, we propose a hypothesis linking variations in genome size within Scolopendra to ecological factors. To test this hypothesis, we employed flow cytometry to estimate genome size in seven Scolopendra species from Chinese mainland. Subsequently, we reconstructed the phylogenetic relationship of these species using the cytochrome c oxidase subunit 1 gene and conducted phylogenetic comparative analysis to assess the relationships between genome size and niche breadth or 19 bioclimatic variables. Our findings indicate the following: (1) genome size in Scolopendra can be categorized into three groups, similar to the phylogenetic clades; (2) there is a negative correlation between genome size in Scolopendra species and the precipitation niche breadth of species; (3) the estimated divergence time of Scolopendra dates back 153 Mya, during the Jurassic period. We assume that consistent aridity geological periods may promote the evolution of Scolopendra species with a large genome size, whereas rapidly fluctuating humidity geological periods may have the opposite effect.

Reconstructing host plant repertoire and timing of evolution of phyline plant bugs (Hemiptera, Miridae)

AbstractThe diversity of phytophagous insects is often attributed to the success of land plants in the framework of ecological speciation. Several hypotheses have been proposed to explain host plant driven insect diversification in a phylogenetic context and have mostly been explored using Lepidoptera. We posit that Miridae are a great system to examine these hypotheses because they are one of the largest primarily phytophagous insect families and include many species with narrow host repertoire. Focusing on the species‐rich Phylinae (>2700 spp.), we generate the most taxon‐rich phylogeny published to date and for the first time estimate divergence times and trace the evolution of host plant associations across the group. Focusing on two clades of oak‐associated phylines, we further examine if diversification in these insects and their hosts coincided or if the insects tracked their hosts. We find that Phylinae diverged from their orthotyline sister group before the end of the Cretaceous, tribal‐level taxa diversified throughout the Paleogene, and diversification within genera mostly occurred in the Neogene. Host plant repertoire reconstructions at the family level show transitions from stenophagy to polyphagy are more common than the reverse. We reconstructed the ancestral phyline host as ambiguous, followed by Asterales throughout most of the deep splits. Species‐level divergences in the two oak‐associated clades coincide with those in oaks, a pattern is that is consistent with the hypothesis that these plant bugs may have cospeciated with their hosts. Our study shows that Phylinae are a suitable system to further test hypotheses on ecological speciation of plants and insects but will require more robust phylogenetic hypotheses of the group.

Museum specimens shedding light on the evolutionary history and cryptic diversity of the hedgehog family Erinaceidae.

The family Erinaceidae encompasses 27 extant species in two subfamilies: Erinaceinae, which includes spiny hedgehogs, and Galericinae, which comprises silky-furred gymnures and moonrats. Although they are commonly recognized by the general public, their phylogenetic history remains incompletely understood, and several species have never been included in any molecular analyses. Additionally, previous research suggested that the species diversity of Erinaceidae might be underestimated. In this study, we sequenced the mitochondrial genomes of 29 individuals representing 18 erinaceid species using 18 freshly collected tissue and 11 historical museum specimens. We also integrated previously published data for a concatenated analysis. We aimed to elucidate the evolutionary relationships within Erinaceidae, estimate divergence times, and uncover potential underestimated species diversity. Our data finely resolved intergeneric and interspecific relationships and presented the first molecular evidence for the phylogenetic position of Mesechinus wangi, Paraechinus micropus, and P. nudiventris. Our results revealed a sister relationship between Neotetracus and Neohylomys gymnures, as well as a sister relationship between Hemiechinus and Mesechinus, supporting previous hypotheses. Additionally, our findings provided a novel phylogenetic position for Paraechinus aethiopicus, placing it in a basal position within the genus. Furthermore, our study uncovered cryptic species diversity within Hylomys suillus as well as in Neotetracus sinensis, Atelerix albiventris, P. aethiopicus, and Hemiechinus auratus, most of which have been previously overlooked.

Mitogenomic Architecture of Atlantic Emperor Lethrinus atlanticus (Actinopterygii: Spariformes): Insights into the Lineage Diversification in Atlantic Ocean.

The evolutionary history of emperors, particularly in the Atlantic and Indo-West Pacific Oceans, remains largely unmapped. This study explores the maternal lineage evolution of Lethrinids by examining the complete mitogenome of Lethrinus atlanticus, which is endemic to the Eastern Atlantic Ocean. Utilizing advanced next-generation sequencing, we found that the mitogenome spans 16,789 base pairs and encompasses 37 genes, including 13 protein-coding genes (PCGs), two ribosomal RNAs, 22 transfer RNAs, and an AT-rich control region (CR). Our analysis indicates a preference for AT base pairs in the L. atlanticus mitogenome (53.10%). Most PCGs begin with the ATG codon, except for COI, which starts with GTG. Relative synonymous codon usage reveals high frequencies for alanine, leucine, proline, serine, and threonine. The ratio of nonsynonymous to synonymous substitutions suggests strong negative selection across all PCGs in Lethrinus species. Most transfer RNAs exhibit typical cloverleaf structures, with the exception of tRNA-serine (GCT), which lacks a dihydrouracil stem. Comparative analysis of conserved sequence blocks across the CRs of three Lethrinus species shows notable differences in length and nucleotide composition. Phylogenetic analysis using concatenated PCGs clearly distinguishes all Lethrinus species, including L. atlanticus, and sheds light on the evolutionary relationships among Spariformes species. The estimated divergence time of approximately 20.67 million years between L. atlanticus and its Indo-West Pacific relatives provides insights into their historical separation and colonization during the late Oligocene. The distribution of Lethrinids may be influenced by ocean currents and ecological factors, potentially leading to their speciation across the Eastern Atlantic and Indo-West Pacific. This study enhances our understanding of the genetic diversity and phylogenetic relationships within Lethrinus species. Further exploration of other emperor fish mitogenomes and comprehensive genomic data could provide vital insights into their genetic makeup, evolutionary history, and environmental adaptability in marine ecosystems globally.

Molecular systematics of chinchilla rats and taxonomic assessment of the Abrocoma cinerea species complex

Abstract Chinchilla rats (family Abrocomidae) are hystricomorph rodents primarily inhabiting the central Andes in South America with 8 species in the genus Abrocoma and 2 in Cuscomys. The systematics of this family—relying only on morphological differences—has faced several controversies, particularly in arid-adapted species of Abrocoma (the A. cinerea species complex, or ACC). By using partial DNA sequences of 1 mitochondrial (Cytochrome b) and 2 nuclear genes (GHR and RAG1), we: (i) inferred phylogenetic relationships between 5 species of Abrocoma and 1 of Cuscomys; (ii) performed molecular species-delimitation analyses in 4 species of the ACC (A. cinerea, A. famatina, A. schistacea, and A. uspallata); and (iii) estimated divergence times using stratigraphic ages of extinct taxa. Our phylogenetic analyses recovered 3 main clades: A. bennettii (basal); C. ashaninka; and the ACC. Striking differences in habitat use, morphology, and genetics suggest that each of these main clades might represent a distinct genus. In species-delimitation analyses in the ACC, only 2 species were recognized, and we thus suggest the synonymy of A. famatina with A. cinerea and of A. uspallata with A. schistacea. The origin of extant abrocomids was estimated at the late Miocene (~5.6 million years ago, Ma) with the subsequent origin of arboreal species during the early Pliocene (~4.3 Ma) and the ACC during the late Pliocene (~3.3 Ma). We hypothesize that topographic uplift of the central Andes and associated climatic and ecological changes were the main drivers of diversification in this family.

Positive Selection of Mitochondrial cytochrome b Gene in the Marine Bivalve Keenocardium buelowi (Bivalvia, Cardiidae)

The mitochondrial genome provides valuable data for phylogenetic analysis and evolutionary research. In this study, we sequenced, assembled, and annotated the mitochondrial genome of Keenocardium buelowi using the Illumina platform. The genome spanned 16,967 bp and included 13 protein-coding genes (PCGs), two ribosomal RNAs, and 22 transfer RNAs. All PCGs utilized standard ATN start codons and TAN stop codons. The phylogenetic tree based on maximum likelihood and Bayesian inference analyses revealed Clinocardiinae as the sister group to Trachycardiinae, with the estimated divergence time being 44.5 million years ago (MYA) between K. buelowi and Vasticardium flavum. Notably, the cytochrome b gene (cob) exhibited a positive selection signal. Our findings provide valuable insights into the evolutionary history and molecular phylogeny of K. buelowi.

Phylogenomic Analysis of Target Enrichment and Transcriptome Data Uncovers Rapid Radiation and Extensive Hybridization in Slipper Orchid Genus Cypripedium L.

Cypripedium is the most widespread and morphologically diverse genus of slipper orchids. Despite several published phylogenies, the topology and monophyly of its infrageneric taxa remained uncertain. Here, we aimed to reconstruct a robust section-level phylogeny of Cypripedium and explore its evolutionary history using target capture data for the first time. We used the orchid-specific bait set Orchidaceae963 in combination with transcriptomic data to reconstruct the phylogeny of Cypripedium based on 913 nuclear loci, covering all 13 sections. Subsequently, we investigated discordance among nuclear and chloroplast trees, estimated divergence times and ancestral ranges, searched for anomaly zones, polytomies, and diversification rate shifts, and identified potential gene (genome) duplication and hybridization events. All sections were recovered as monophyletic, contrary to the two subsections within sect. Cypripedium. The two subclades within this section did not correspond to its subsections but matched the geographic distribution of their species. Additionally, we discovered high levels of discordance in the short backbone branches of the genus and within sect. Cypripedium, which can be attributed to hybridization events detected based on phylogenetic network analyses, and incomplete lineage sorting caused by rapid radiation. Our biogeographic analysis suggested a Neotropical origin of the genus during the Oligocene (~30 Ma), with a lineage of potentially hybrid origin spreading to the Old World in the Early Miocene (~22 Ma). The rapid radiation at the backbone likely occurred in Southeast Asia around the Middle Miocene Climatic Transition (~15-13 Ma), followed by several independent dispersals back to the New World. Moreover, the Pliocene-Quaternary glacial cycles may have contributed to further speciation and reticulate evolution within Cypripedium. Our study provided novel insights into the evolutionary history of Cypripedium based on high-throughput molecular data, shedding light on the dynamics of its distribution and diversity patterns from its origin to the present.

Differences between phytophagous and predatory species in Pentatomidae based on the mitochondrial genome.

Pentatomidae includes many species of significant economic value as plant pests and biological control agents. The feeding habits of Pentatomidae are closely related to their energy metabolism and ecological adaptations. In this study, we sequenced the mitochondrial genomes of 12 Asopinae species using the next-generation sequencing to explore the effect of dietary changes on mitochondrial genome evolution. Notably, all sequences were double-stranded circular DNA molecules containing 37 genes and one control region. We then compared and analyzed the mitochondrial genome characteristics of phytophagous and predatory bugs. Notably, no significant difference was observed in the length of the mitochondrial genomes between the predatory and phytophagous bugs. However, the AT content was higher in the mitochondrial genomes of phytophagous bugs than that of predatory bugs. Moreover, phytophagous bugs prefer codon usage patterns ending in A/T compared with predatory bugs. The evolution rate of predatory bugs was lower than that of phytophagous bugs. The phylogenetic relationships across phytophagous bugs' lineages were largely consistent at depth nodes based on different datasets and tree-reconstructing methods, and strongly supported the monophyly of predatory bugs. Additionally, the estimated divergence times indicated that Pentatomidae explosively radiated in the Early Cretaceous. Subsequently, the subfamily Asopinae and the genus Menida diverged in the Late Cretaceous. Our research results provide data supporting for the evolutionary patterns and classification of Pentatomidae.

Adaptive radiation of the Callicarpa genus in the Bonin Islands revealed through double-digest restriction site-associated DNA sequencing analysis.

The Bonin Islands, comprised of the Mukojima, Chichijima, and Hahajima Islands, are known for their isolated and distinctive habitats, hosting a diverse array of endemic flora and fauna. In these islands, adaptive radiation has played a remarkable role in speciation, particularly evident in the Callicarpa genus that is represented by three species: Callicarpa parvifolia and C. glabra exclusive to the Chichijima Islands, and Callicarpa subpubescens, distributed across the entire Bonin Islands. Notably, C. subpubescens exhibits multiple ecotypes, differing in leaf hair density, flowering time, and tree size. In this study, we aimed to investigate species and ecotype diversification patterns, estimate divergence times, and explore cryptic species within Callicarpa in the Bonin Islands using phenotypic and genetic data (double-digest restriction site-associated DNA sequencing). Genetic analysis revealed that C. parvifolia and C. glabra both formed single, distinct genetic groups. Conversely, C. subpubescens consisted of six genetic groups corresponding to different ecotypes and regions, and a hybrid group resulting from the hybridization between two of these genetic groups. Population demography analysis focusing on six Chichijima and Hahajima Islands-based species/ecotypes indicated that all species and ecotypes except one ecotype diverged simultaneously around 73-77 kya. The star-shaped neighbor-net tree also suggests the simultaneous divergence of species and ecotypes. The species and ecotypes that simultaneously diverged adapted to dry environments and understory forests, suggesting that aridification may have contributed to this process of adaptive radiation. Moreover, leaf morphology, flowering time, and genetic analyses suggested the presence of two cryptic species and one hybrid species within C. subpubescens.