Cladistics最新文献

Homo luzonensis lived during the upper Pleistocene in the northern Philippines, east of the Wallace line. The few specimens attributed to this species show a mosaic of plesiomorphies for the genus Homo and apomorphies found in upper Pleistocene Homo species. Plesiomorphic traits could result from a close phylogenetic relationship with Australopithecus or Homo habilis/rudolfensis or from insular evolution favouring reversals, possibly linked to a relationship with a more recent species like Homo erectus. We conducted a cladistic analysis based on dental and postcranial remains of adult H. luzonensis to test these hypotheses. The trees obtained indicate that both hypotheses are supported by different anatomical elements. The trees suggesting H. luzonensis is close to H. erectus (as a sister-taxon or as a close relative of H. erectus) are supported by dental characters and feature high retention and consistency indices. Moreover, H. luzonensis likely had reduced body size and postural/locomotor modifications, similar to other insular mammals with medium-to-large-sized ancestors. The tropical forest environment of Luzon Island may have favoured the selection of these features. Based on these results and our current knowledge of insular evolution, we suggest that H. luzonensis likely evolved from an Asian H. erectus population in an insular context.

The stalk-eyed flies (Diptera: Schizophora: Diopsidae) are a diverse clade of acalyptrate flies known for their remarkable eye stalks and intriguing courtship behaviours. Despite their striking appearance and significance as subjects for ecological and ethological studies, phylogenetic relationships within Diopsidae have not yet been comprehensively investigated, and the evolutionary history of the family remains inadequately resolved. We here present the first time-calibrated phylogenetic analysis of Diopsidae based on 17 genes (12S, 16S, 18S, 28S, and 13 mitochondrial protein-coding genes, 18 536 bp) from 48 taxa, including all extant subfamilies and ~76% extant genera of the family, thus clarifying a number of outstanding questions about intra-familial relationships and the evolutionary history of the stalk-eyed flies. Our results support the monophyly of Diopsidae and its three subfamilies; Centrioncinae is recovered as sister to the stalk-eyed lineage Sphyracephalinae + Diopsinae; the Teleopsis genus-group as well as several currently recognized genera are non-monophyletic and require further taxonomic review to better resolve their phylogenetic status. Molecular dating and biogeographic analyses indicate an African origin of the crown group of Diopsidae in the middle Eocene, ca. 45 Ma; its early diversification events might have been driven by climatic and ecosystem transformations during the middle Eocene to middle Miocene; available evidence suggests that factors shaping the current distribution of Diopsidae include colonization of Madagascar from Africa via the Mozambique Channel, out-of-Africa dispersals mediated by the Gomphotherium land bridge along with favourable environmental conditions, and colonization of North America via the Bering Land Bridge. This study provides a framework for future investigations into the evolutionary history of the stalk-eyed flies, as well as for ecological and morphological evolutionary research.

Subfamily Microsoroideae represent the third largest subfamily within Polypodiaceae. However, due to insufficient sampling, limited informative sites and considerable morphological diversification, the generic-level classification within Microsoroideae has been contentious. Furthermore, the origin and diversification history of this subfamily remain unclear. With the most extensive sampling to date, we provide a comprehensive and systematic elucidation of the evolutionary history of Microsoroideae. Our key findings include the following: (1) Microsoroideae can be divided into 5 superclades and 17 fully supported clades based on the plastome dataset, while nuclear gene dataset supports the division of Microsoroideae into 6 superclades and 19 monophyletic clades; (2) significant cytonuclear discordance and gene tree conflicts exist within Microsoroideae and can be explained by incomplete lineage sorting-particularly regarding the conflicting phylogenetic positions of Bosmania, and introgressive hybridization; (3) molecular dating consistently indicates that Microsoroideae originated in the early Eocene and began to diversify around the middle Eocene; (4) ancestral area reconstruction supports the Asian continent as both the origin and diversification centres of Microsoroideae; (5) paleoenvironmental changes, geological events and a series of dispersal and vicariance events are the primary drivers of the current distribution of Microsoroideae; (6) diversification rate analyses reveal that abrupt changes in the diversification rate of the maternal lineages of Microsoroideae are associated with the Middle Eocene Climatic Optimum; (7) nuclear gene data show that the diversification rate of the Lecanopteris clade is significantly higher than other clades, which is linked to its unique ant-associated traits; and (8) the diversification rates of Microsoroideae inferred from nuclear gene data exhibit different trends compared with those inferred from plastome data. This discrepancy may arise from frequent hybridization and polyploidization, which buffer environmental pressures. The findings not only have significant implications for the classification of Microsoroideae but also provide insights for the adaptive evolution of ferns.

The Qinghai-Tibetan Plateau, the core of the Eurasian mountain belt, has repeatedly reshaped the formation and pattern of biodiversity through episodic uplift and associated geoclimatic changes. Despite its central role in shaping biotic evolution across Eurasia, genus-level studies that jointly evaluate the effects of orogeny, hybridization and ecological adaptation remain scarce. Here, we integrate multilocus phylogenomics (nuclear and mitochondrial), network-based reticulation inference, divergence dating, macroevolutionary modelling and codon-based molecular adaptation tests (branch-site dN/dS on protein-coding genes) to reconstruct the spatiotemporal diversification of the predatory insect genus Anthocoris across Eurasia. We identified two episodes of rapid lineage diversification: a basal radiation (BR; late Oligocene-Miocene, ~25-15 Ma) and a terminal radiation (TR; mid-Miocene to Pleistocene), supported by independent evidence from diversification rate shifts (e.g., ClaDS, CoMET) and dense clusters of short branches, with the strongest signals in high-elevation lineages. Genome-scale phylogenomic discordance points to incomplete lineage sorting and ancient introgression as joint drivers of these patterns, gauged by the extent of deep gene-tree conflict and independent genome-wide tests (quartet analyses and D-statistics), with network inference corroborating reticulation. The timing and geography of BR and TR align with major geoclimatic episodes: the formation of the modern Qinghai-Tibetan Plateau (~25-15 Ma), the subsequent formation of the Himalayas-Hengduan Mountains (~15 Ma onward), the closure of the Tethys Sea, Central Asian aridification and the Miocene cooling. Ancestral-range reconstructions place the origin of Anthocoris in northern Eurasia, and coupled with retention and sorting of ancestral polymorphism under niche conservatism, likely facilitated repeated high-elevation adaptation. This study provides new evidence and a theoretical framework showing that the repeated uplift of the Qinghai-Tibetan Plateau-acting with continent-wide geographic and climatic shifts and ancestral gene flow-jointly drove diversification and generated complex spatiotemporal patterns within genera across Eurasia.

With fossil records dating back to the Silurian/Late Ordovician, millipedes stand out as one of the earliest terrestrial animal groups. Their limited vagility and high endemism make them valuable tools for formulating and testing biogeographic hypotheses, including those related to macro-vicariance events. Among the order Polydesmida, the family Chelodesmidae displays an intriguing transatlantic distribution, suggesting a Gondwanan origin. Despite this, the evolutionary relationships and biogeography of the family remain largely unknown. In this study, we explore areas of endemism (AEs) for Chelodesmidae using endemicity analysis (NDM/VNDM), utilising a data set of 1512 records for 725 species. NDM/VNDM analyses identified 135 areas of endemism, which were consolidated into 10 generalised areas. These overlapping patterns revealed common areas of endemism, including Central Africa, Western-Central Africa, Western Africa, West Indies, Northern Amazon, Northern Andes, Guiana Shield, Southern Amazon, America Platina and the Southeastern Mountain Range. This study represents the first explicit assessment of endemism patterns in the family using a quantitative methodology and underscores its significance for further research on Gondwanan distribution patterns.

Deciphering the evolutionary history of lineages shaped by rapid radiation, hybridization and incomplete lineage sorting (ILS) remains a major challenge in phylogenetics. Previous studies of Hesperocyparis (Cupressaceae) relied on limited markers and yielded inconsistent results. Here, we applied target enrichment sequencing across multiple individuals per species to generate comprehensive genomic datasets, including 2628 nuclear single-copy genes and nearly complete plastid genomes. We reconstructed robust phylogenies, assessed gene flow and reticulation and inferred the spatiotemporal and ecological niche evolution of Hesperocyparis. Our analyses resolved the genus into three clades-Macrocarpa, Arizonica and the basal H. bakeri-and strongly supported its monophyly within the HCX clade (Hesperocyparis, Callitropsis, Xanthocyparis). However, significant cytonuclear discordance was observed, reflecting the influence of ancient hybridization and ILS. Molecular dating placed the origin of Hesperocyparis in the late Eocene (~39.2 Ma), with most diversification occurring during the Oligocene and Miocene. Ancestral range and state reconstructions support a northwestern North American origin, followed by complex southward and eastward dispersal patterns likely driven by climatic shifts towards increased aridity. This study highlights the utility of genome-scale data in resolving complex evolutionary relationships and underscores hybridization, climate-driven dispersal and ecological adaptation as key drivers of diversification in Hesperocyparis.

Millions of species remain undescribed, and each eventually will require a species description with a diagnosis. Yet, we lack software that can derive state-specific and contrastive molecular diagnoses and allows the user to validate them based on all available sequences for the taxon under study. Here we introduce UITOTO, which addresses this shortcoming by facilitating the identification, testing, and visualization of diagnostic molecular combinations (DMCs). The software uses a weighted random sampling algorithm based on the Jaccard Index for building candidate DMCs. It then selects DMCs with the highest specificity stability, meeting user-defined thresholds for exclusive character states. If multiple optimal DMCs are identified, UITOTO derives a majority-consensus DMC. To verify whether the generated DMCs are contrastive, UITOTO includes a validation module that tests DMCs against databases, efficiently handling thousands of aligned or unaligned sequences. We here, not only propose UITOTO, but also assess its performance relative to other software that can derive DMCs (e.g. MOLD). For this purpose, we analyse three large empirical datasets: (i) Megaselia (Diptera: Phoridae: 69 species, 2229 training and 30 289 testing barcodes); (ii) Mycetophilidae (Diptera: 118 species, 1456 training, 60 349 testing barcodes); and (iii) European Lepidoptera (49 species, 591 training, 21 483 testing barcodes). Based on classification metrics (e.g. F1 Score), UITOTO's DMCs outcompete DMCs from other software. We furthermore provide guidelines for generating molecular diagnoses and a user-friendly Shiny App-GUI that includes a module for obtaining publication-quality DMC visualizations. Overall, our study confirms that the biggest challenge for generating molecular and morphological diagnoses is similar: balancing specificity and length; short diagnoses often lack specificity, while excessively long DMCs are often so specific that they do not accommodate intraspecific variation.

Advances in Macrodasyida (Gastrotricha) phylogenetics, fuelled by new species discoveries and molecular data, are reshaping taxonomic classifications. Molecular analyses suggest polyphyly in Cephalodasyidae and Macrodasyidae, yet insufficient sampling continues to obscure precise relationships. Our study seeks to enhance the resolution of Macrodasyida's internal phylogeny through expanded taxonomic and molecular sampling. We obtained 63 new sequences from 21 Macrodasyidan species, integrating them with published data. Our dataset includes representatives from nine Macrodasyida families and 21 genera, alongside two chaetonotidans. We analysed the concatenated sequences of three genes (18S, 28S rRNA, COI mtDNA) from 51 terminals using Maximum Parsimony, Maximum Likelihood and Bayesian Inference. Our findings confirm the polyphyly of Cephalodasyidae. Dolichodasys and Paradasys cluster with Redudasyidae, while Cephalodasys and Mesodasys form unrelated lineages. Cephalodasys mahoae is nested within Paradasys rather than Cephalodasys, suggesting an original misidentification. The phylogenetic placement of Pleurodasys remains uncertain. Macrodasyidae is non-monophyletic, with Urodasys forming an independent lineage. The first molecular data ever obtained for Dendrodasys hint that the family Dactylopodolidae is likely polyphyletic as well. We propose an updated classification of Macrodasyida, introducing Mesodasyidae fam. nov., Urodasyidae fam. nov. and Paraurodasys gen. nov. Furthermore, we reassign Dolichodasys and Paradasys to Redudasyidae and Cephalodasys mahoe to Paradasys.

The dispersal pattern of tetrapods across Pangaea is a crucial problem for understanding Permian terrestrial ecosystems. This study describes a rare cross-equatorial record of a dicynodont genus. New fossil material from China can be referred to Dinanomodon, a genus formerly only known from South Africa, although it represents a new species-D. guoi. To investigate the divergence of Bidentalia, a newly assembled dataset was employed to perform maximum parsimony analysis, Bayesian inference and the first tip-dating analysis within the anomodonts. Considering other tetrapod occurrences, we suggest that frequent cross-equatorial dispersal of tetrapods occurred during the Lopingian (late Permian). Based on tetrapod distribution and paleoclimate data, precipitation, rather than temperature, probably represents the major ecological factor influencing corridors for dispersal along the eastern margin of Pangaea.

The Hengduan Mountains (HDM), a biodiversity hotspot in Southwest China, harbour numerous endemic taxa whose diversification has been driven by the complex geological history of this region. This study investigates the diversification of the katydid genus Sichuana, endemic to the HDM, integrating mitochondrial genomics, morphology and biogeography. We sequenced complete mitochondrial genomes of all known geographic populations of Sichuana, revealing four major clades diverging during the Late Miocene (5.06-8.37 Ma). Orogeny-driven vicariance fragmented ancestral populations, while unstable barriers may facilitate mitochondrial introgression, as evidenced by paraphyletic lineages contrasting with distinct morphologies. We describe five new species (S. brevicerca sp. nov., S. fortidens sp. nov., S. qiuzhi sp. nov., S. luqiaoensis sp. nov. and S. pseudomagna sp. nov.) and two subspecies (S. pseudomagna pseudomagna subsp. nov. and S. pseudomagna borealis subsp. nov.), highlighting the taxonomic challenges posed by discordance between mitochondrial DNA-based phylogenies and morphological classifications. This study demonstrates that orogeny-driven vicariance dominates speciation in low-dispersal insects, but transient gene flow complicates species delimitation. Our findings advocate for integrative taxonomy in biodiversity hotspots and highlight the HDM as a model system for studying biogeographic complexity.