Divergence Time Analyses Research Articles

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

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

The Indo-Burma biodiversity hotspot for ferns: Updated phylogeny, hidden diversity, and biogeography of the java fern genus Leptochilus (Polypodiaceae)

The Indo-Burma Biodiversity Hotspot is renowned for its rich biodiversity, including that of vascular plants. However, the fern diversity and its endemism in this hotspot have not been well understood and so far, the diversity of very few groups of ferns in this region has been explored using combined molecular and morphological approaches. Here, we updated the plastid phylogeny of the Java fern genus Leptochilus with 226 (115% increase of the latest sampling) samples across the distribution range, specifically those of three phylogenetically significant species, Leptochilus ovatus, L. pedunculatus, and L. pothifolius. We also reconstructed the first nuclear phylogeny of the genus based on pgiC gene data. Based on molecular and morphological evidence, we identified three new major clades and six new subclades, redefined three existing species, discovered a number of cryptic species of the genus, and elucidated the evolution of the three most variable characters. Our divergence time analyses and ancestral area reconstruction showed that Leptochilus originated in the Oligocene and diversified from early Miocene and 15 dispersal events from lower to higher latitudes are identified. The evolution of three most important morphological characters is analyzed in a context of the new phylogeny. Our analysis showed that 30 (59% of total 51) species of Leptochilus occur in Indo-Burma hotspot, 24 (80% of the 30 species) of which are endemic to this hotspot. We argue that the Indo-Burma hotspot should be recognized as a diversity hotspot for ferns.

Complete characterization and comparative analysis of the mitochondrial genome of Indian tasar silkworm Antheraea mylitta (Lepidoptera: Saturniidae) and phylogenetic implications

The Indian tasar silkworm Antheraea mylitta (A. mylitta) is an economically important silkmoth and is native to tropical India. Our current research has deciphered the mitochondrial genome (mitogenome) of A. mylitta by recovering the complete genome sequence from the NCBI-SRA database and comparing it with other mitogenomes from the order Lepidoptera. The mitogenome is a double-stranded circular molecule spanning 15,354 bp with an A + T content of roughly 80.4%. It consists of a total of 37 genes, comprising 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), and two ribosomal RNAs (rRNAs), along with a 337 bp long control region. The arrangement of PCGs is similar to other Lepidoptera mitogenomes, with the exception of Cox1 and Cox2, which have different initiation codons. The control region of A. mylitta contains a conserved five bp ATAGA motif as seen in other Antheraea species. Phylogenetic analysis supports previous morphological hypotheses that Bombycoidea, Noctuoidea, Geometroidea, Papilionoidea, and Torticoidea are monophyletic. The divergence time analysis of 13 protein-coding genes reported that A. mylitta diverged from the last common ancestor ∼ 23 million years ago. As per our knowledge, this is the first documented record of the entire mitogenome of A. mylitta.

The Mitogenomic Landscape of Hexacorallia Corals: Insight into Their Slow Evolution.

The utility of the mitochondrial genomes (mitogenomes) in analyzing the evolutionary history of animals has been proven. Five deep-sea corals (Bathypathes sp.1, Bathypathes sp.2, Schizopathidae 1, Trissopathes sp., and Leiopathes sp.) were collected in the South China Sea (SCS). Initially, the structures and collinearity of the five deep-sea coral mitogenomes were analyzed. The gene arrangements in the five deep-sea coral mitogenomes were similar to those in the order Antipatharia, which evidenced their conservation throughout evolutionary history. Additionally, to elucidate the slow evolutionary rates in Hexacorallia mitogenomes, we conducted comprehensive analyses, including examining phylogenetic relationships, performing average nucleotide identity (ANI) analysis, and assessing GC-skew dissimilarity combining five deep-sea coral mitogenomes and 522 reference Hexacorallia mitogenomes. Phylogenetic analysis using 13 conserved proteins revealed that species clustered together at the order level, and they exhibited interspersed distributions at the family level. The ANI results revealed that species had significant similarities (identity > 85%) within the same order, while species from different orders showed notable differences (identity < 80%). The investigation of the Hexacorallia mitogenomes also highlighted that the GC-skew dissimilarity was highly significant at the order level, but not as pronounced at the family level. These results might be attributed to the slow evolution rate of Hexacorallia mitogenomes and provide evidence of mitogenomic diversity. Furthermore, divergence time analysis revealed older divergence times assessed via mitogenomes compared with nuclear data, shedding light on significant evolutionary events shaping distinct orders within Hexacorallia corals. Those findings provide new insights into understanding the slow evolutionary rates of deep-sea corals in all lineages of Hexacorallia using their mitogenomes.

Phylogenetic and Comparative Genomics Study of Papilionidae Based on Mitochondrial Genomes.

Most species of Papilionidae are large and beautiful ornamental butterflies. They are recognized as model organisms in ecology, evolutionary biology, genetics, and conservation biology but present numerous unresolved phylogenetic problems. Complete mitochondrial genomes (mitogenomes) have been widely used in phylogenetic studies of butterflies, but mitogenome knowledge within the family Papilionidae is limited, and its phylogeny is far from resolved. In this study, we first report the mitogenome of Byasa confusa from the subfamily Papilioninae of Papilionidae. The mitogenome of B. confusa is 15,135 bp in length and contains 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and an AT-rich control region (CR), closely mirroring the genomic structure observed in related butterfly species. Comparative analysis of 77 Papilionidae mitogenomes shows gene composition and order to be identical to that of an ancestral insect, and the AT bias, Ka/Ks, and relative synonymous codon usage (RSCU) are all consistent with that of other reported butterfly mitogenomes. We conducted phylogenetic analyses using maximum-likelihood (ML) and Bayesian-inference (BI) methods, with 77 Papilionidae species as ingroups and two species of Nymphalidae and Lycaenidae as outgroups. The phylogenetic analysis indicated that B. confusa were clustered within Byasa. The phylogenetic trees show the monophyly of the subfamily Papilioninae and the tribes Leptocircini, Papilionini, and Troidini. The data supported the following relationships in tribe level on Papilioninae: (((Troidini + Papilionini) + Teinopalpini) + Leptocircini). The divergence time analysis suggests that Papilionidae originated in the late Creataceous. Overall, utilizing the largest number of Papilionidae mitogenomes sequenced to date, with the current first exploration in a phylogenetic analysis on Papilionidae (including four subfamilies), this study comprehensively reveals the mitogenome characteristics and mitogenome-based phylogeny, providing information for further studies on the mitogenome, phylogeny, evolution, and taxonomic revision of the Papilionidae family.

The nature of the last universal common ancestor and its impact on the early Earth system

The nature of the last universal common ancestor (LUCA), its age and its impact on the Earth system have been the subject of vigorous debate across diverse disciplines, often based on disparate data and methods. Age estimates for LUCA are usually based on the fossil record, varying with every reinterpretation. The nature of LUCA’s metabolism has proven equally contentious, with some attributing all core metabolisms to LUCA, whereas others reconstruct a simpler life form dependent on geochemistry. Here we infer that LUCA lived ~4.2 Ga (4.09–4.33 Ga) through divergence time analysis of pre-LUCA gene duplicates, calibrated using microbial fossils and isotope records under a new cross-bracing implementation. Phylogenetic reconciliation suggests that LUCA had a genome of at least 2.5 Mb (2.49–2.99 Mb), encoding around 2,600 proteins, comparable to modern prokaryotes. Our results suggest LUCA was a prokaryote-grade anaerobic acetogen that possessed an early immune system. Although LUCA is sometimes perceived as living in isolation, we infer LUCA to have been part of an established ecological system. The metabolism of LUCA would have provided a niche for other microbial community members and hydrogen recycling by atmospheric photochemistry could have supported a modestly productive early ecosystem.

Mitochondrial phylogenomics supports a Carboniferous origin of Xenonomia

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

Comparative analyses of complete mitochondrial genomes of four sillaginids fish (Perciformes: Sillaginidae) and phylogenetic implications

Sillago muktijoddhai, S. mengjialensis, S. sihama and Sillaginops macrolepis (Perciformes, Sillaginidae) are common coastal sand borers. The first three species are found in the Northeastern Indian Ocean, and the fourth one is located in the Western Central Pacific Ocean only. Molecular data applying in the prior investigations on systematics and phylogenetic relationships were not only incomplete but also uncertain for these fishes. This study sequenced their complete mitochondrial genomes using Sanger Dideoxy DNA sequencing for the first time. Their complete mitochondrial genome was a circular molecule of 17,022, 16,624, 16,825 and 16,502bp in length for S. muktijoddhai, S. mengjialensis, S. sihama and Sillaginops macrolepis, respectively. Most protein-coding genes (PCGs) were initiated with the typical ATG codon and terminated with the TAA or TAG codon and the incomplete termination codon T/TA could be detected in the four species. The majority of AT-skew and GC-skew values of the entire mitogenomes among the four species were negative. The Ka/Ks ratio analyses indicated 13 PCGs were suffering strong purifying selection. In the phylogenetic analysis, S. muktijoddhai, S. mengjialensis, and S. sihama were placed with relative species of the genus Sillago supporting morphological phylogeny. However, S. macrolepis was situated in the clade of genus Sillago that contrasted to morphological phylogeny. Divergence time analysis showed that Sillaginidae species diverged around 61 million years ago. Bangladesh J. Sci. Ind. Res. 59(2), 87-104, 2024

Morphological observation, molecular identification and evolutionary analysis of Hydatigera kamiyai found in Neodon fuscus from the Qinghai-Tibetan plateau

Hydatigera kamiyai (H. kamiyai) is a new species within Hydatigera that has recently been resurrected. Voles and cats are hosts of H. kamiyai and have a certain impact on its health and economy. Moreover, the Qinghai-Tibetan plateau (QTP) is a research hotspot representing Earth's biodiversity, as its unique geographical environment and climatic conditions support the growth of a variety of mammals and provide favorable conditions for various parasites to complete their life history. The aim of this study was to reveal the phylogenetic relationships and divergence times of H. kamiyai strains isolated from Neodon fuscus on the QTP using morphological and molecular methods. In this study, we morphologically observed H. kamiyai and sequenced the whole mitochondrial genome. Then, we constructed phylogenetic trees with the maximum likelihood (ML) and Bayesian inference (BI) methods. The GTR alternative model was selected for divergence time analysis. These data demonstrated that the results were consistent with the general morphological characteristics of Hydatigera. The whole genome of H. kamiyai was 13,822 bp in size, and the A + T content (73%) was greater than the G + C content (27%). The Ka/Ks values were all <1, indicating that all 13 protein-coding genes (13 PCGs) underwent purifying selection during the process of evolution. The phylogenetic tree generated based on the 13 PCGs, cytochrom oxidase subunit I (COI), 18S rRNA and 28S rRNA revealed close phylogenetic relationships between H. kamiyai and Hydatigera, with high node support for the relationship. The divergence time based on 13 PCGs indicated that H. kamiyai diverged approximately 11.3 million years ago (Mya) in the Miocene. Interestingly, it diverged later than the period of rapid uplift in the QTP. We also speculated that H. kamiyai differentiation was caused by host differentiation due to the favorable living conditions brought about by the uplift of the QTP. As there have been relatively few investigations on the mitochondrial genome of H. kamiyai, our study could provide factual support for further studies of H. kamiyai on the QTP. We also emphasized the importance of further studies of its hosts, Neodon fuscus and cats, which will be important for further understanding the life cycle of H. kamiyai.

Comparative mitogenome research revealed the phylogenetics and evolution of the superfamily Tenebrionoidea (Coleoptera: Polyphage).

Despite the worldwide distribution and rich diversity of the superfamily Tenebrionoidea, the knowledge of the mitochondrial genomes (mtgenome) characteristics of the superfamily is still very limited, and its phylogenetics and evolution remain unresolved. In the present study, we newly sequenced mtgenomes from 19 species belonging to Tenebrionoidea, and a total of 90 mitochondrial genomes from 16 families of Tenebrionoidea were used for phylogenetic analysis. There exist 37 genes for all 82 species of complete mtgenomes of 16 families investigated, and their characteristics are identical as reported mtgenomes of other Tenebrionoids. The Ka/Ks analysis suggests that all 13 PCGs have undergone a strong purifying selection. The phylogenetic analysis suggests the monophyly of Mordellidae, Meloidae, Oedemeridae, Pyrochroidae, Salpingidae, Scraptiidae, Lagriidae, and Tenebrionidae, and the Mordellidae is close to the Ripiphoridae. The "Tenebrionidae clade" and "Meloidae clade" are monophyletic, and both of them are sister groups. In the "Meloidae clade," Meloidae is close to Anthicidae. In the "Tenebrionidae clade," the family Lagriidae and Tenebrionidae are sister groups. The divergence time analysis suggests that Tenebrionoidea originated in the late Jurassic, Meloidae Mordellidae, Lagriidae, and Tenebrionidae in the Cretaceous, Oedemeridae in Paleogene. The work lays a base for the study of mtgenome, phylogenetics, and evolution of the superfamily Tenebrionoidea.

Phylogeny and biogeography of harmochirine jumping spiders (Araneae: Salticidae)

We use ultraconserved elements (UCE) and Sanger data to study the phylogeny, age, and biogeographical history of harmochirine jumping spiders, a group that includes the species-rich genus Habronattus, whose remarkable courtship has made it the focus of studies of behaviour, sexual selection, and diversification. We recovered 1947 UCE loci from 43 harmochirine taxa and 4 outgroups, yielding a core dataset of 193 UCEs with at least 50 % occupancy. Concatenated likelihood and ASTRAL analyses confirmed the separation of harmochirines into two major clades, here designated the infratribes Harmochirita and Pellenita. Most are African or Eurasian with the notable exception of a clade of pellenites containing Habronattus and Pellenattus of the Americas and Havaika and Hivanua of the Pacific Islands. Biogeographical analysis using the DEC model favours a dispersal of the clade’s ancestor from Eurasia to the Americas, from which Havaika’s ancestor dispersed to Hawaii and Hivanua’s ancestor to the Marquesas Islands. Divergence time analysis on 32 loci with 85 % occupancy, calibrated by fossils and island age, dates the dispersal to the Americas at approximately 4 to 6 million years ago. The explosive radiation of Habronattus perhaps began only about 4 mya. The phylogeny clarifies both the evolution of sexual traits (e.g., the terminal apophyses was enlarged in Pellenes and not subsequently lost) and the taxonomy. Habronattus is confirmed as monophyletic. Pellenattus is raised to the status of genus, and 13 species moved into it as new combinations. Bianor stepposus Logunov, 1991 is transferred to Sibianor, and Pellenes bulawayoensis Wesołowska, 1999 is transferred to Neaetha. A molecular clock rate estimate for spider UCEs is presented and its utility to inform prior distributions is discussed.

Phylogenetic, phylogeographic and divergence time analysis of Anopheles subpictus species complex using ITS2 and COI sequences

Objective: To address the phylogenetic and phylogeographic relationship between different lineages of Anopheles (An.) subpictus species complex in most parts of the Asian continent by maximum utilization of Internal Transcriber Spacer 2 (ITS2) and cytochrome C oxidase I (COI) sequences deposited at the GenBank. Methods: Seventy-five ITS2, 210 COI and 26 concatenated sequences available in the NCBI database were used. Phylogenetic analysis was performed using Bayesian likelihood trees, whereas median-joining haplotype networks and time-scale divergence trees were generated for phylogeographic analysis. Genetic diversity indices and genetic differentiation were also calculated. Results: Two genetically divergent molecular forms of An. subpictus species complex corresponding to sibling species A and B are established. Species A evolved around 37-82 million years ago in Sri Lanka, India, and the Netherlands, and species B evolved around 22-79 million years ago in Sri Lanka, India, and Myanmar. Vietnam, Thailand, and Cambodia have two molecular forms: one is phylogenetically similar to species B. Other forms differ from species A and B and evolved recently in the above mentioned countries, Indonesia and the Philippines. Genetic subdivision among Sri Lanka, India, and the Netherlands is almost absent. A substantial genetic differentiation was obtained for some populations due to isolation by large geographical distances. Genetic diversity indices reveal the presence of a long-established stable mosquito population, at mutation-drift equilibrium, regardless of population fluctuations. Conclusions: An. subpictus species complex consists of more than two genetically divergent molecular forms. Species A is highly divergent from the rest. Sri Lanka and India contain only species A and B.

Chloroplast genome analysis and evolutionary insights in the versatile medicinal plant Calendula officinalis L.

Calendula officinalis L.is a versatile medicinal plant with numerous applications in various fields. However, its chloroplast genome structure, features, phylogeny, and patterns of evolution and mutation remain largely unexplored. This study examines the chloroplast genome, phylogeny, codon usage bias, and divergence time of C. officinalis, enhancing our understanding of its evolution and adaptation. The chloroplast genome of C. officinalis is a 150,465 bp circular molecule with a G + C content of 37.75% and comprises 131 genes. Phylogenetic analysis revealed a close relationship between C. officinalis, C. arvensis, and Osteospermum ecklonis. A key finding is the similarity in codon usage bias among these species, which, coupled with the divergence time analysis, supports their close phylogenetic proximity. This similarity in codon preference and divergence times underscores a parallel evolutionary adaptation journey for these species, highlighting the intricate interplay between genetic evolution and environmental adaptation in the Asteraceae family. Moreover unique evolutionary features in C. officinalis, possibly associated with certain genes were identified, laying a foundation for future research into the genetic diversity and medicinal value of C. officinalis.

Complex evolution in thin air: Investigating female flightlessness and diel behaviour in geometrid moths (Lepidoptera)

AbstractMany unique high‐altitude mountain ecosystems have been declining due to climate change, posing a threat to flora and fauna that have adapted to these ecosystems. This study explores the evolution of high‐altitude adaptations, focusing on female flightlessness and diel activity, in geometrid moths (Lepidoptera: Ennominae, Gnophini) within the European Alps. We constructed a phylogeny of Gnophini moths using a dataset of 157 taxa, with up to seven genetic markers and traced the evolutionary history of diel activity and wing length reduction in females. Analysis of divergence times suggested that female flightlessness has evolved at least three times independently between the early and late Miocene. The evolution of wing length reduction is likely correlated with elevation, indicating adaptations to cold and windy conditions in high altitude. The evolutionary events leading to shifts in adult diel activity, from ancestral nocturnality to diurnality, have occurred independently at least three times and may also be a consequence of adaptations at high elevations. Strikingly, among diurnal Sciadia, two species have evolved further to become nocturnal like their ancestors. Our findings highlight how phylogenies can provide new insights into evolutionary patterns in moths. We provided a robust basis for resolving taxonomic ambiguities in Alpine Gnophini, leading us to propose 10 changes to the current classification: Scrupodes Lee &amp; Sihvonen gen. n., Elophos Boisduval (type species Geometra operaria Hübner) is considered a junior synonym of Sciadia Hübner syn. n., Yezognophos dilucidaria (Denis &amp; Schiffermüller) and Y. sproengertsi (Püngeler) are transferred to Parietaria Leraut comb. n., Yezognophos serotinaria (Denis &amp; Schiffermüller) is transferred to Scrupeus Lee &amp; Sihvonen comb. n., Elophos caelibaria (Heydenreich), E. zirbitzensis (Pieszcek), E. operaria (Hübner) and E. andereggaria (De La Harpe) are transferred to Sciadia Hübner comb. n. and Dichrognophos Wehrli (type species Gnophos orthogonia Wehrli) is transferred from Ennominae: Cassymini to Ennominae: Gnophini.

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

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

Phylogenomics of Puya (Bromeliaceae): Evolution in the Andean slopes and sky island ecosystems

AbstractPhylogenomics enhances our understanding of plant radiations in the biodiverse Andes. Our study focuses on Puya, primarily Andean and a part of the Bromeliaceae family. Using a phylogenomic framework based on the Angiosperms353 probe set for 80 species, we explored Puya′s phenotypic evolution and biogeography. Divergence time analyses and ancestral area estimations suggested that Puya originated in Central Coastal Chile around 9 million years ago (Ma). Subsequently, it dispersed to the dry valleys of the Central Andes and Puna regions between 5–8 Ma, leading to the emergence of major lineages. Key events in the last 2–4 million years include the recolonization of Chilean lowlands and dispersal to the northern Andes via Peru's Jalcas, facilitating passage through the Huancabamba depression. This event gave rise to the high‐elevation Northern Andes clade. Using phylogenetic comparative methods, we tested the hypothesis that adaptation to the Andes' island‐like high‐elevation ecosystems was facilitated by unique leaf and floral traits, life history, and inflorescence morphology. Our findings suggest correlations between inflorescence axis compression, protective bract overlap, and high‐elevation living, potentially preventing reproductive structure freezing. Semelparity evolved exclusively at high elevations, although its precise adaptive value remains uncertain. Our framework offers insights into Andean evolution, highlighting that lineages adapted to life in dry ecosystems can easily transition to high‐elevation biomes. It also underscores how the island‐like nature of high‐elevation ecosystems influences phenotypic evolution rates. Moreover, it opens avenues to explore genetic mechanisms underlying adaptation to extreme mountain conditions.

Tectonically driven climate change and the spread of temperate biomes: Insights from dragon pseudoscorpions (Pseudotyrannochthoniidae), a globally distributed arachnid lineage

AbstractAimUnderstanding the historical biogeography of the Earth's oldest terrestrial lineages provides insights into lineage diversification in relation to plate tectonics, climate change and biome shifts at maximum timescales. We investigate the biogeography of an ancient arachnid family, dragon pseudoscorpions, which are found today in mesic (mostly temperate) forests on all continents except Antarctica and Europe, have potential origins on Pangea and comprise species with extremely limited dispersal capacities. We evaluate the respective role of continental vicariance (abiotic) and biome shifts (biotic) deep in time and unravel the evolutionary history of this ancient group.LocationGlobal.TaxonPseudotyrannochthoniidae (Arachnida: Pseudoscorpiones).MethodsFive loci were sequenced for 75 Pseudotyrannochthoniidae samples collected across the globe. A matrix was compiled comprising 106 terminals and ~8800 bp, and phylogenetic analyses were performed to uncover relationships. Divergence time and ancestral range estimation analyses were used to reconstruct historical biogeography.ResultsPseudotyrannochthoniidae was monophyletic with high support but relationships among genera did not reflect current taxonomy and instead showed geographical structuring. Pseudotyrannochthoniidae originated in East Asia during the Middle Triassic and began diversifying in the Early Cretaceous.Main ConclusionsDiversity and distributional patterns of dragon pseudoscorpions can be explained by the interplay of continental vicariance through Pangaean breakup, and biome shifts via the spread of temperate habitats in the Cretaceous and their ongoing distributional fluctuations. Pseudotyrannochthoniidae diversification began in the Early Cretaceous as they dispersed with temperate forests across the Northern Hemisphere. Cretaceous vicariance, followed by widespread Holarctic extinction in the Late Tertiary–Quaternary, created their disjunct distribution at northern latitudes. Northern and Southern Hemisphere lineages diverged as Gondwana and Laurasia rifted, and Gondwanan breakup resulted in Afrotropical/Indomalayan and Austral clades. Austral lineages spread with temperate forests, however, cooling caused their disappearance from Antarctica and led to disjunct distributions at low latitudes.

Comparative and phylogenetic analysis of chloroplast genomes from ten species in Quercus section Cyclobalanopsis.

The genus Quercus L. is widely acknowledged as a significant assemblage within East Asia tropical and subtropical broadleaf evergreen forests, possessing considerable economic importance. Nevertheless, the differentiation of Quercus species is deemed arduous, and the interrelations among these species remain enigmatic. Leveraging Illumina sequencing, we undertook the sequencing and assembly of the chloroplast (cp) genomes of seven species belonging to Quercus section Cyclobalanopsis (Quercus argyrotricha, Q. augustinii, Q. bambusifolia, Q. bella, Q. edithiae, Q. jenseniana, and Q. poilanei). Furthermore, we collated three previously published cp genome sequences of Cyclobalanopsis species (Q. litseoides, Q. obovatifolia, and Q. saravanensis). Our primary objective was to conduct comparative genomics and phylogenetic analyses of the complete cp genomes of ten species from Quercus section Cyclobalanopsis. This investigation unveiled that Quercus species feature a characteristic circular tetrad structure, with genome sizes ranging from 160,707 to 160,999 base pairs. The genomic configuration, GC content, and boundaries of inverted repeats/single copy regions exhibited marked conservation. Notably, four highly variable hotspots were identified in the comparative analysis, namely trnK-rps16, psbC-trnS, rbcL-accD, and ycf1. Furthermore, three genes (atpF, rpoC1, and ycf2) displayed signals of positive selection pressure. Phylogenetic scrutiny revealed that the four sections of Cyclobalanopsis clustered together as sister taxa. The branch support values ranged from moderate to high, with most nodes garnering 100% support, underscoring the utility of cp genomic data in elucidating the relationships within the genus. Divergence time analysis revealed that Section Cyclobalanopsis represents the earliest type of Quercus genus. The outcomes of this investigation establish a foundation for forthcoming research endeavors in taxonomy and phylogenetics.

Population Structure and Genetic Diversity Analyses Provide New Insight into the Endemic Species Aster spathulifolius Maxim. and Its Evolutionary History.

Aster spathulifolius, an ecologically significant plant species native to the coastal regions of Korea and Japan, remains understudied in terms of its genetic structure and evolutionary history. In this study, we employed four chloroplast markers and the nuclear ITS region from 15 populations of A. spathulifolius from both Korea and Japan, including their islands, to unravel the spatial genetic structure, differentiation, gene flow, phylogenetic, and biogeographical relationships. Analysis based on multiple methods identified a low level of genetic diversity, genetic differentiation and gene flow among A. spathulifolius populations. Network analysis and principal coordinates analysis showed that 15 populations could be divided into two groups: mainland and island. Furthermore, UPGMA, neighbor-net, maximum-likelihood and Bayesian inference-based phylogenetic tree confirmed that these populations formed two distinct clades. Therefore, the island populations might be treated as A. spathulifolius populations rather than A. oharai populations. Divergence time analysis estimated the divergence of A. spathulifolius lineages approximately 23.09 million years ago, while ancestral area reconstruction analysis suggested Korea as the potential origin, conflicting with alternative scenarios. These findings contribute to a comprehensive understanding of the evolutionary history, genetic structure, and adaptive strategies of A. spathulifolius in coastal environments. Our study challenges previous assumptions and underscores the necessity for further population studies to elucidate the intricate dynamics of this distinctive plant species.

The Grasshopper Paradigm in damselflies: evidence for phalanx-like postglacial recolonization of Europe from a Balkan refugium in Platycnemis pennipes Pallas (Odonata: Zygoptera: Platycnemidae)

We explore haplotype diversity, phylogeography and phylogenetic relationships of the damselfly Platycnemis pennipes in Europe based on 618 bp DNA from the mitochondrial gene COI. A haplotype network analysis shows that the species is divided into two haplotype groups. One is restricted to the Italian Peninsula, while the other is found from the Black Sea region across eastern and central Europe to Scandinavia, England, and southwestern France. This pattern is recovered in a Bayesian phylogenetic analysis. Genetic distance (K2P) between the two groups is approximately 1.5%, while within-group variation is an order of magnitude lower. An analysis of the molecular variance (AMOVA) shows that variation between the two groups account for more than 96% of the total variation within the dataset, adding to the evidence that they have been isolated for a considerable amount of time. The pattern we find is similar to the so-called Grasshopper Paradigm in European phylogeography, where a species has recolonized Europe after the last glaciation from a glacial refugium in the southeast, while other refugial populations in the Iberian and Italian peninsulas have remained isolated to this day. In P. pennipes there is only an isolated refugial population in Italy as the species does not have current populations in the Iberian Peninsula. By comparing the genetic distance between the two groups to a previously published divergence time analysis of European Odonata we estimate that they have likely been isolated since the onset of the Saale Glaciation ca 400 ky ago.