Divergence Time Estimates Research Articles

Phylogeography of Cold Water Soft Coral Alcyonium spp. (Anthozoa, Octocorallia: Alcyonacea) Between South America and the West Antarctic Peninsula.

The Antarctic marine environment has a unique geologic and climatic history that has contributed to the evolution of high species diversity. Given the current trend of environmental warming, understanding the history of Antarctic species is crucial for predicting the impact of climate change on ecosystem function. Soft corals are a group of striking presence in the benthic marine assemblages in the Southern Ocean, which is recognized as a biodiversity hotspot. DNA sequences (Cox1, mtMutS, and 28S rDNA) were utilized for molecular phylogenetic reconstructions, species delimitations, and divergence estimations to investigate the spatial patterns of genetic diversity in Alcyonium species in the southern South American-Antarctic region. Significant genetic divergence was observed between regions, with a clear genetic break between South America and the West Antarctic Peninsula and the identification of four putative species. Divergence time estimates indicated that Alcyonium's diversification began about 41.1 million years ago (Ma), coinciding with the opening of the Drake Passage and the formation of the Antarctic Circumpolar Current (ACC, ~42 Ma). This indicates that Alcyonium has persisted insitu for an extensive period, enduring a wide range of environmental conditions.

Bayesian Selection of Relaxed-clock Models: Distinguishing Between Independent and Autocorrelated Rates.

In Bayesian molecular-clock dating of species divergences, rate models are used to construct the prior on the molecular evolutionary rates for branches in the phylogeny, with independent and autocorrelated rate models being commonly used. The two classes of models, however, can result in markedly different divergence time estimates for the same dataset, and thus selecting the best rate model appears important for obtaining reliable in- ferences of divergence times. However, the properties of Bayesian rate model selection are not well understood, in particular when the number of sequence partitions analysed increases and when age calibrations (such as fossil calibrations) are misspecified. Further- more, Bayesian rate model selection is computationally expensive as it requires calculation of marginal likelihoods by MCMC sampling, and therefore methods that can speed up the model selection procedure without compromising its accuracy are desirable. In this study, we use a combination of computer simulations and real data analysis to investigate the sta- tistical behaviour of Bayesian rate model selection and we also explore approximations of the likelihood to improve computational efficiency in large phylogenomic datasets. Our simulations demonstrate that the posterior probability for the correct rate model converges to one as more molecular sequence partitions are analysed and when no calibrations are used, as expected due to asymptotic Bayesian model selection theory. Furthermore, we also show the model selection procedure is robust to slight misspecification of calibrations, and reliable inference of the correct rate model is possible in this case. However, we show that when calibrations are seriously misspecified, calculated model probabilities are com- pletely wrong and may converge to one for the wrong rate model. Finally, we demonstrate that approximating the phylogenetic likelihood under an arcsine branch-length transform can dramatically reduce the computational cost of rate model selection without compro- mising accuracy. We test the approximate procedure on two large phylogenies of primates (372 species) and flowering plants (644 species), replicating results obtained on smaller datasets using exact likelihood. Our findings and methodology can assist users in selecting the optimal rate model for estimating times and rates along the Tree of Life.

An integrative species delimitation approach uncovers eriophyoid mite Diptilomiopus ligustri species complex (Acariformes: Eriophyoidea)

AbstractEriophyoid mites (Acari: Eriophyoidea) are among the smallest terrestrial arthropods possessing simplified morphological characters, which challenges the traditional morphology‐based species delimitation. The Diptilomiopus spp. exhibit further morphological degeneration (e.g., lack of genus on both legs and some opisthosoma setae). Especially, they possess high similarity in the reticulate prodorsal shield patterns, leading to cryptic species complex and hampering our understanding of species diversity. In this study, we implemented an integrated approach, including genetic distance analysis, phylogenetic analysis, population genetic structure construction, introgression test, and morphometric analysis, to delimitate the Diptilomiopus ligustri complex. We obtained 52 mitochondrial COI gene sequences and 19 whole‐genome sequences across 18 sample sites of this complex. All samples were collected from Ligustrum plants in China, which may cover their main distribution ranges. Our results demonstrate that the D. ligustri complex consists of at least four distinct species (i.e., D. ligustri, D. cf. ligustri sp1., D. cf. ligustri sp2., and D. cf. ligustri sp3.), which are genetically divergent but do not differ morphologically, assessed by principal component analysis of 27 morphological characteristics. No significant gene flow was observed among this complex. Divergence time estimates further showed that most Diptilomiopus species diverged in a short time interval at the Paleogene–Neogene boundary, indicating a rapid radiation. Our results highlight the integrated approaches in eriophyoid mite species complex delimitation.

A second species of Stenasellus Dollfus, 1897 (Isopoda, Stenasellidae) from sulfidic groundwater of Iran described using morphological and molecular methods

We report on a new species of Stenasellus Dollfus, 1897 (Isopoda, Stenasellidae) from groundwater of Iran. Stenasellus stygopersicus Jugovic, Malek-Hosseini & Issartel sp. nov. inhabits the Chah Kabootari Cave that is adjacent to the Tashan Cave, the type locality of the first recorded species of Stenasellidae from Iran, Stenasellus tashanicus Khalaji-Pirbalouty, Fatemi, Malek-Hosseini & Kuntner, 2018. Both caves are fed by sulfidic groundwater and belong to the Tashan-Chah Kabootari species-rich aquifer on the Zagros Mountains. Both species are characterized by a large body size (≥ 20 mm), a female-biased sexual size dimorphism, and a distinct black-pigmented Bellonci’s organ. Stenasellus stygopersicus differs from S. tashanicus by a short and wide protopodite of pleopod I, setae set essentially along the apical margin of pleopod I exopodite, the subequal length and width of the male pleopod II protopodite, and deeply bilobed endopodites of pleopods III–V. Molecular evidence suggests that while Stenasellus stygopersicus is sister to S. tashanicus, the species are genetically distinguishable, with divergence time estimates ranging from 23 to 39.8 Ma.

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.

Phylogenomic insights into species relationships, reticulate evolution, and biogeographic diversification of the ginseng genus Panax (Araliaceae), with an emphasis on the diversification in the Himalayan‐Hengduan Mountains

AbstractPanax (Araliaceae) is a small genus containing several well known medicinally important species. It has a disjunct distribution between Eastern Asia and Eastern North America, with most species from eastern Asia, especially the Himalayan‐Hengduan Mountains (HHM). This study used the genomic target enrichment method to obtain 358 nuclear ortholog loci and complete plastome sequences from 59 accessions representing all 18 species of the genus. Divergence time estimation and biogeographic analyses suggest that Panax was probably widely distributed from North America to Asia during the middle Eocene. During the late Eocene to Oligocene Panax may have experienced extensive extinctions during global climate cooling. It survived and diverged early in the mountains of Southwest China and tropical Indochina, where some taxa migrated northwestward to the HHM, eastward to central and eastern China, and then onward toward Japan and North America. Gene flow is identified as the main contributor to phylogenetic discordance (33.46%) within Panax. We hypothesize that the common ancestors of the medicinally important P. ginseng + P. japonicus + P. quinquefolius clade had experienced allopolyploidization, which increased adaptability to cooler and drier environments. During the middle to late Miocene, several dispersals occurred from the region of the HHM to contiguous areas, suggesting that HHM acted as a refugium and also served as a secondary diversification center for Panax. Our findings highlight that the interplay of orographic uplift and climatic changes in the HHM greatly contributed to the species diversity of Panax.

Comparative analysis of chloroplast genomes and phylogenetic relationships in the endemic Chinese bamboo Gelidocalamus (Bambusoideae).

Gelidocalamus Wen is a small yet taxonomically challenging genus within the Arundinarieae tribe. Recent molecular studies have suggested it may not be monophyletic. However, limited species sampling and insufficient molecular marker information have resulted in poorly resolved phylogenetic relationships within this genus. The complete chloroplast genomes covering all 16 species and one variant of Gelidocalamus were sequenced, and comparative analyses were conducted. Phylogenetic analyses were performed using different molecular markers, including chloroplast data, the nuclear ribosomal DNA (nrDNA) repeats region, and 29 mitochondrial protein-coding genes. Additionally, the divergence times of Gelidocalamus were estimated to reveal their evolutionary history. The plastomes of Gelidocalamus ranged in size from 139,500 bp to 139,801 bp, with a total of 137 identified genes, including 90 protein-coding genes, 39 tRNA genes, and 8 rRNA genes. The size of the nrDNA repeats ranged from 5,802 bp to 5,804 bp. Phylogenetic analysis based on chloroplast data revealed that Gelidocalamus is polyphyletic, with different subclades distributed within the IV and V clades. However, phylogenetic analysis based on nrDNA and mitochondrial genes did not effectively resolve the relationships within the genus. Comparative analysis of chloroplast genomes indicated that Gelidocalamus shares a high degree of similarity with closely related genera in terms of chloroplast genome collinearity, codon usage bias, and repetitive sequences. Divergence time estimation suggests that it is a relatively young group, with all members appearing successively over the past four million years. The complex phylogenetic patterns may arise from the rapid radiation of Arundinarieae. This study provides a preliminary foundation for further in-depth research on the phylogeny, genomic structural features, and divergence times of this genus.

Plio/Pleistocene-induced climatic oscillations drive cladogenesis in a high-altitude freshwater crab, Potamonautes mariepskoppie (Decapoda: Potamonautidae), in South Africa

Abstract In this study, we explored the phylogeographical history of the mountain-dwelling freshwater crab Potamonautes mariepskoppie to understand evolutionary processes and identify possible hidden lineages. DNA sequence data from mitochondrial loci (COI, 12S rRNA, and 16S rRNA) and a nuclear locus (histone 3) were analysed using both maximum likelihood and Bayesian inference. Species delimitation was tested with four methods: ASAP, bPTP, bGMYC, and STACEY. Divergence time estimation and ecological niche modelling with ENMEval and Maxent were used to study species distribution and elucidate abiotic factors affecting evolution. Phylogenetic analyses showed three distinct clades, corresponding to geographical regions: Limpopo, Mpumalanga, and Mount Sheba. These clades had no shared haplotypes and exhibited moderate genetic differentiation. Divergence time estimates indicated that these clades diverged during the Plio/Pleistocene, a period of significant climatic shifts in southern Africa. All four species delimitation methods consistently supported the recognition of these clades as distinct species; however, discriminant function analyses of carapace characteristics showed significant overlap between the three clades. Ecological niche modelling indicated that rainfall is a key factor in the species distribution. The present study highlights the need for further investigation of the high-elevation plateaus throughout Limpopo and Mpumalanga, because fine-scale sampling might unmask considerable hitherto-undocumented biodiversity.

Sperm as a speciation phenotype in promiscuous songbirds.

Sperm morphology varies considerably among species. Sperm traits may contribute to speciation if they diverge fast in allopatry and cause conspecific sperm precedence upon secondary contact. However, their role in driving prezygotic isolation has been poorly investigated. Here we test the hypothesis that, early in the speciation process, female promiscuity promotes a reduction in overlap in sperm length distributions among songbird populations. We assembled a data set of 20 pairs of populations with known sperm length distributions, a published estimate of divergence time, and an index of female promiscuity derived from extrapair paternity rates or relative testis size. We found that sperm length distributions diverged more rapidly in more promiscuous species. Faster divergence between sperm length distributions was caused by the lower variance in the trait in more promiscuous species, and not by faster divergence of the mean sperm lengths. The reduced variance is presumably due to stronger stabilizing selection on sperm length mediated by sperm competition. If divergent sperm length optima in allopatry causes conspecific sperm precedence in sympatry, which remains to be shown empirically, female promiscuity may promote prezygotic isolation and rapid speciation in songbirds.

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.

Phylogenetic analysis of Syrphidae (Insecta, Diptera) based on low-coverage whole genomes

Abstract The hoverflies are one of the most abundant families in Diptera and an important category of resource insects. They can provide important ecosystem services such as pollination and beneficial biological control agents. In the four-subfamily classification system of the Syrphidae, the monophyly of the Eristalinae within Syrphidae has not been recovered. In this study, we performed new sequencing and analysis of low-coverage whole genomes for 25 species of Syrphidae. Phylogenetic reconstructions were conducted based on different datasets and analytical strategies. Across all our analyses, the monophyly of the Syrphinae is supported but we do not recover the monophyly of the Eristalinae, consistent with previous research findings. Additionally, employing fossil calibrations for divergence time estimation, our results indicate that the origin of the Syrphidae occurred between the Albian and Aptian stages, approximately between 120.5 and 109.3 million years ago, the origin of the subfamily Syrphinae was dated in the Early Eocene, about 50.8–47.8 million years ago, in accordance with the diversification of their prey. This study will help us understand the higher-level phylogenetic and evolutionary relationships within Syrphidae.

First De Novo genome assembly and characterization of Gaultheria prostrata.

Gaultheria Kalm ex L. (Ericaceae), a type of evergreen shrub, known as a natural source of methyl salicylate, possesses rich germplasm resources, strong habitat adaptability, significant ornamental value, and noteworthy pharmacological activities. However, due to the paucity of whole genomic information, genetically deep research in these areas remains limited. Consequently, we intend to obtain genome data through high-throughput sequencing, gene annotation, flow cytometry, transcription factors prediction and genetic marker analysis for a representative species of this genus, with Gaultheria prostrata selected for our study. In this study, we preliminarily obtained the genome of G. prostrata through next-generation sequencing methods. Utilizing 47.94 Gb of high-quality sequence data (108.95× coverage), assembled into 114,436 scaffolds, with an N50 length of 33,667 bp. The genome size assembled by SOAPdenovo, approximately 417 Mb, corresponded closely to predictions by flow cytometry (440 Mb) and k-mer analysis (447 Mb). The genome integrity was evaluated using BUSCO with 91%. The heterozygosity ratio was 0.159%, the GC content was 38.85%, and the repetitive regions encompassed over 34.6% of the genome. A total of 26,497 protein-coding genes have been predicted and annotated across Nr, Swissprot, GO, KEGG, and Pfam databases. Among these, 14,377 and 2,387 genes received functional annotation in Nr and Swissprot, respectively; 21,895, 24,424, and 22,330 genes were similarly annotated in GO, KEGG, and Pfam. Moreover, A total of 279,785 SSRs were identified and 345,270 primers for these SSRs were designed. Within the various nucleotide types of SSRs, AG/CT and AAG/CTT constituted the predominant dinucleotide and trinucleotide repeat types in G. prostrata. In addition, 1,395 transcription factors (TFs) from 75 TF families, 462 transcription regulators (TRs) from 33 TR families and 840 protein kinase (PKs) from 118 PK families were identified in this genome. We also performed phylogenetic analyses of G. prostrata and related species, including estimation of divergence times and expansion and contraction analyses, followed by positive selection analyses of orthologous gene pairs of G. prostrata and its close relative Vaccinium corymbosum. These results provide a reference for in-depth study of genus Gaultheria, contributing to future functional and comparative genomics analyses and providing supporting data for the development of molecular markers.

Phylogenetic and divergence analysis of Pentatomidae, with a comparison of the mitochondrial genomes of two related species (Hemiptera, Pentatomidae).

Pentatomidae, the most diverse family of Pentatomoidea, is found worldwide. Currently, the phylogenetic relationships among Pentatomidae tribes remain unstable, and subfamily divergence has not been estimated. Here, we sequenced and analyzed the complete mitochondrial genomes of two species of Lelia, and studied the phylogenetic relationships among Pentatominae tribes. We also selected three available fossil as the calibration points in the family, and preliminarily discussed the divergence time of Pentatomidae. Trees of Pentatomidae were reconstructed using the Bayesian inference method. Divergence times of Pentatominae were estimated based on the nucleotide sequences of protein-coding genes with a relaxed clock log-normal model in BEASTv.1.8.2. The results showed that the gene arrangements, nucleotide composition, and codon preferences were highly conserved in Lelia. Further, a phylogenetic analysis recovered Eysarcorini, Strachiini, Phyllocephalini, and Menidini as monophyletic with strong support, however, the monophyly of Antestiini, Nezarini, Carpocorini, Pentatomini and Cappaeini were rejected. Moreover, Pentatominae diverged from Pentatomidae soon after the origin of the Cretaceous Period, at approximately 110.38 Ma. This study enriches the mitochondrial genome database of Pentatomidae and provides a reference for further phylogenetic studies, and provides a more accurate estimate of divergence time.

Do morphometric data improve phylogenetic reconstruction? A systematic review and assessment

BackgroundIsolating phylogenetic signal from morphological data is crucial for accurately merging fossils into the tree of life and for calibrating molecular dating. However, subjective character definition is a major limitation which can introduce biases that mislead phylogenetic inferences and divergence time estimation. The use of quantitative data, e.g., geometric morphometric (GMM; shape) data can allow for more objective integration of morphological data into phylogenetic inference. This systematic review describes the current state of the field in using continuous morphometric data (e.g., GMM data) for phylogenetic reconstruction and assesses the efficacy of these data compared to discrete characters using the PRISMA-EcoEvo v1.0. reporting guideline, and offers some pathways for approaching this task with GMM data. A comprehensive search string yielded 11,123 phylogenetic studies published in English up to Oct 2023 in the Web of Science database. Title and abstract screening removed 10,975 articles, and full-text screening was performed for 132 articles. Of these, a total of twelve articles met final inclusion criteria and were used for downstream analyses.ResultsPhylogenetic performance was compared between approaches that employed continuous morphometric and discrete morphological data. Overall, the reconstructed phylogenies did not show increased resolution or accuracy (i.e., benchmarked against molecular phylogenies) as continuous data alone or combined with discrete morphological datasets.ConclusionsAn exhaustive search of the literature for existing empirical continuous data resulted in a total of twelve articles for final inclusion following title/abstract, and full-text screening. Our study was performed under a rigorous framework for systematic reviews, which showed that the lack of available comparisons between discrete and continuous data hinders our understanding of the performance of continuous data. Our study demonstrates the problem surrounding the efficacy of continuous data as remaining relatively intractable despite an exhaustive search, due in part to the difficulty in obtaining relevant comparisons from the literature. Thus, we implore researchers to address this issue with studies that collect discrete and continuous data sets with directly comparable properties (i.e., describing shape, or size).

A new exceptionally preserved sawfly fossil (Hymenoptera: Pergidae) and an evaluation of its utility for divergence time estimation and biogeography

A new exceptionally preserved sawfly fossil (Hymenoptera: Pergidae) and an evaluation of its utility for divergence time estimation and biogeography

Sequence comparison of the mitochondrial genomes of five caridean shrimps of the infraorder Caridea: phylogenetic implications and divergence time estimation

BackgroundThe Caridea, affiliated with Malacostraca, Decapoda, and Pleocyemata, constitute one of the most significant shrimp groups. They are widely distributed across diverse aquatic habitats worldwide, enriching their evolutionary history. In recent years, considerable attention has been focused on the classification and systematic evolution of Caridea, yet controversies still exist regarding the phylogenetic relationships among families.MethodsHere, the complete mitochondrial genome (mitogenome) sequences of five caridean species, namely Heterocarpus sibogae, Procletes levicarina, Macrobrachium sp., Latreutes anoplonyx, and Atya gabonensis, were determined using second-generation high-throughput sequencing technology. The basic structural characteristics, nucleotide composition, amino acid content, and codon usage bias of their mitogenomes were analyzed. Selection pressure values of protein-coding genes (PCGs) in species within the families Pandalidae, Palaemonidae, and Atyidae were also computed. Phylogenetic trees based on the nucleotide and amino acid sequences of 13 PCGs from 103 caridean species were constructed, and divergence times for various families within Caridea were estimated.ResultsThe mitogenome of these five caridean species vary in length from 15,782 to 16,420 base pairs, encoding a total of 37 or 38 genes, including 13 PCGs, 2 rRNA genes, and 22 or 23 tRNA genes. Specifically, L. anoplonyx encodes an additional tRNA gene, bringing its total gene count to 38. The base composition of the mitogenomes of these five species exhibited a higher proportion of adenine-thymine (AT) bases. Six start codons and four stop codons were identified across the five species. Analysis of amino acid content and codon usage revealed variations among the five species. Analysis of selective pressure in Pandalidae, Palaemonidae, and Atyidae showed that the Ka/Ks values of PCGs in all three families were less than 1, indicating that purifying selection is influencing on their evolution. Phylogenetic analysis revealed that each family within Caridea is monophyletic. The results of gene rearrangement and phylogenetic analysis demonstrated correlations between these two aspects. Divergence time estimation, supported by fossil records, indicated that the divergence of Caridea species occurred in the Triassic period of the Mesozoic era, with subsequent differentiation into two major lineages during the Jurassic period.ConclusionsThis study explored the fundamental characteristics and phylogenetic relationships of mitogenomes within the infraorder Caridea, providing valuable insights into their classification, interspecific evolutionary patterns, and the evolutionary status of various Caridea families. The findings provide essential references for identifying shrimp species and detecting significant gene rearrangements within the Caridea infraorder.

A time-calibrated phylogeny of the diversification of Holoadeninae frogs.

The phylogeny of the major lineages of Amphibia has received significant attention in recent years, although evolutionary relationships within families remain largely neglected. One such overlooked group is the subfamily Holoadeninae, comprising 73 species across nine genera and characterized by a disjunct geographical distribution. The lack of a fossil record for this subfamily hampers the formulation of a comprehensive evolutionary hypothesis for their diversification. Aiming to fill this gap, we inferred the phylogenetic relationships and divergence times for Holoadeninae using molecular data and calibration information derived from the fossil record of Neobatrachia. Our inferred phylogeny confirmed most genus-level associations, and molecular dating analysis placed the origin of Holoadeninae in the Eocene, with subsequent splits also occurring during this period. The climatic and geological events that occurred during the Oligocene-Miocene transition were crucial to the dynamic biogeographical history of the subfamily. However, the wide highest posterior density intervals in our divergence time estimates are primarily attributed to the absence of Holoadeninae fossil information and, secondarily, to the limited number of sampled nucleotide sites.

Genetic Structure of Monochamus alternatus (Hope) in Qinling-Daba Mountains and Expansion Trend: Implications for Pest Prevention and Management.

Pine wilt disease (PWD), caused by Bursaphelenchus xylophilus, severely threatens global pine forests. Monochamus alternatus is the primary vector of B. xylophilus in East Asia. Understanding the population structure and evolutionary forces of vector insects is critical for establishing effective PWD management strategies. The present work explores the genetic structure and phylogenetic relationships of 20 populations of M. alternatus from the Qinling-Daba Mountains (QDM) in China using the mitochondria DNA dataset, supplemented by ecological niche modeling (ENM). All M. alternatus populations were categorized into three phylogeographic clusters (Clade A, Clade B, and Clade C), with Clade A and Clade B corresponding to the western and eastern QDM, respectively. The results of divergence time estimation concur with environmental changes induced by Quaternary glacial climate oscillations in QDM of China. M. alternatus populations exhibited significant genetic differentiation, with expansion in their population size. Ecological niche modeling (ENM) demonstrated that precipitation and temperature significantly influence the distribution of M. alternatus and the species is anticipated to grow into higher latitude and higher altitude regions in the future. In a nutshell, exploring the genetic structure and evolutionary dynamics of M. alternatus can provide valuable insights into the prevention and occurrence of B. xylophilus. These findings also serve as a reference for research on population differentiation and phylogeography of other species in QDM and adjacent areas.

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).

Phylogenomic analysis of brachyuran crabs using transcriptome data reveals possible sources of conflicting phylogenetic relationships within the group

Despite extensive morphological and molecular studies, the phylogenetic interrelationships within the infraorder Brachyura and the phylogenetic positions of many taxa remain uncertain. Studies that used a limited number of molecular markers have often failed to provide sufficient resolution, and may be susceptible to stochastic errors and incomplete lineage sorting (ILS). Here we reconstructed the phylogenetic relationships within the Brachyura using transcriptome data of 56 brachyuran species, including 14 newly sequenced taxa. Five supermatrices were constructed in order to exclude different sources of systematic error. The results of the phylogenetic analyses indicate that Heterotremata is non-monophyletic, and that the two Old World primary freshwater crabs (Potamidae and Gecarcinucidae) and the Hymenosomatoidea form a clade that is sister to the Thoracotremata, and outside the Heterotremata. We also found that ILS is the main cause of the gene-tree discordance of these freshwater crabs. Divergence time estimations indicate that the Brachyura has an ancient origin, probably either in the Triassic or Jurassic, and that the majority of extant families and superfamilies first appeared during the Cretaceous, with a constant increase of diversity in Post-Cretaceous-Palaeogene times. The results support the hypothesis that the two Old World freshwater crab families included in this study (Potamidae and Gecarcinucidae) diverged from their marine ancestors around 120 Ma, in the Cretaceous. In addition, this work provides new insights that may aid in the reclassification of some of the more problematic brachyuran groups.