Cladistics最新文献

{"title":"Molecular phylogenetics reveals Eocene origin and out-of-Africa dispersals of the stalk-eyed flies (Diptera: Schizophora: Diopsidae).","authors":"Jiale Zhou, Neal L Evenhuis, Ding Yang","doi":"10.1111/cla.70026","DOIUrl":"10.1111/cla.70026","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":" ","pages":"221-235"},"PeriodicalIF":6.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145913815","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phylogenomics, reticulate evolution and spatiotemporal diversification in Anthocoris (Hemiptera: Anthociridae): impacts of repeated uplifts of the Qinghai-Tibetan Plateau across Eurasia.","authors":"Ze-Chen Tang, Xue Dong, Kazutaka Yamada, Xiu-Xiu Zhu, Kai-Bing Wang, Dan-Li Zhang, Si-Ying Fu, Mu Qiao, Ying Wang, Jia-Yue Zhou, Zhen Ye, Wen-Jun Bu","doi":"10.1111/cla.70025","DOIUrl":"10.1111/cla.70025","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":" ","pages":"264-285"},"PeriodicalIF":6.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145890423","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Corrigendum.","authors":"","doi":"10.1111/cla.70031","DOIUrl":"10.1111/cla.70031","url":null,"abstract":"","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":" ","pages":"317"},"PeriodicalIF":6.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146221936","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phylogeny and evolutionary history of subfamily Microsoroideae (Polypodiaceae): new insights from plastome and nuclear gene data.","authors":"Jing Zhao, Jia-Guan Wang, Hong-Bin Niu, Wei-Hao Pan, Chuan-Jie Huang, Zhen-Long Liang, Zhao-Rong He, Li-Ju Jiang, Xin-Mao Zhou","doi":"10.1111/cla.70024","DOIUrl":"10.1111/cla.70024","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":" ","pages":"236-263"},"PeriodicalIF":6.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145890494","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Homo luzonensis and the role of homoplasy in the morphology of hominin insular species.","authors":"Pierre Gousset, Jérémie Bardin, Isabelle Rouget, Armand S Mijares, Florent Détroit","doi":"10.1111/cla.70027","DOIUrl":"10.1111/cla.70027","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":" ","pages":"286-316"},"PeriodicalIF":6.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146042193","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Reconstructing the global radiation of Turdidae (Aves: Passeriformes) using explicit geographic ranges under two different palaeogeographic scenarios.","authors":"Ana Gabriela Dantur, Sara Bertelli, Francisca Cunha Almeida, J Salvador Arias","doi":"10.1111/cla.70040","DOIUrl":"https://doi.org/10.1111/cla.70040","url":null,"abstract":"<p><p>The family Turdidae (Aves, Passeriformes) is a diverse clade of passerine birds that presents a global distribution across a wide range of environments. While numerous studies have addressed the biogeography of specific genera, the family's origins remain largely unresolved. To reconstruct this taxon's biogeographic history, we compiled genetic and geographic range data from public sources. This information was used to build a time-calibrated phylogeny based on a concatenated dataset of mitochondrial and nuclear genes for 155 species across 16 genera. Ancestral area reconstructions were performed using PhyGeo, a geographically explicit, diffusion-based method that integrates species distributions with a dynamic palaeogeographic model applied to a pixelated spherical model of the Earth. Our analysis produced contrasting results depending on model assumptions. Under the Global Model, which treats all land features as equally habitable, Turdidae likely originated in West Antarctica-South America, with later colonization of Africa, Australia, and Asia via an Antarctic route. In contrast, the Restricted Model, which excludes unglaciated Antarctic land, shifted the inferred origin to northern North America, placing ancestral ranges closer to extant distributions and more consistent with current evidence. These results underscore the importance of considering multiple lines of evidence and spatially explicit approaches when reconstructing biogeographic histories.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147845626","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"From Southeast Asia to global: phylogeny, biogeography and character evolution of the thread-legged bug tribe Leistarchini (Hemiptera: Reduviidae: Emesinae).","authors":"Zhuo Chen, Hu Li, Wanzhi Cai","doi":"10.1111/cla.70038","DOIUrl":"https://doi.org/10.1111/cla.70038","url":null,"abstract":"<p><p>The thread-legged bug tribe Leistarchini (Hemiptera: Reduviidae: Emesinae) is a cosmopolitan and diverse group characterized by a highly disproportionate spatial distribution across zoogeographic regions. Due to a historical lack of phylogenetic focus, the internal relationships and evolutionary history of the tribe remain poorly understood. In this study, we provide the first robust phylogenetic framework for Leistarchini by integrating molecular data from mitochondrial genomes and nuclear rDNA (88 taxa, 19 937 bp) with universal single-copy orthologs (24 taxa, 667 loci). Our results support the monophyly of Leistarchini and identify five major clades, including a newly described genus Calliemesa gen. n. Our findings further reveal that the five most species-rich genera (Nesita, Orthunga, Pleias, Ploiaria and Tinna) are either paraphyletic or polyphyletic as currently circumscribed. Molecular dating and biogeographic reconstructions suggest a Southeast Asian origin for the Leistarchini crown group during the late Palaeocene (ca. 57 Ma). Early diversification appears to have been driven by Paleogene geological and climatic shifts in Southeast Asia, while multiple intercontinental dispersals since the middle Eocene into the Afrotropics, Madagascar and the New World shaped the current global distribution. Ancestral state reconstructions indicate that the Leistarchini ancestor possessed a well-developed posterior pronotal lobe and a three-segmented protarsus. Subsequent evolutionary trajectories involved four independent transitions toward a shortened posterior pronotal lobe, and four separate reductions in protarsal segmentation.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147822141","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Description languages as modelling decisions: A comment on Wheeler and Varón (2025).","authors":"Jan De Laet","doi":"10.1111/cla.70037","DOIUrl":"https://doi.org/10.1111/cla.70037","url":null,"abstract":"<p><p>Wheeler and Varón (2025) proposed phylogenetic minimum description length (PMDL) as a phylogenetic optimality criterion grounded in algorithmic (Kolmogorov) complexity. PMDL applies the minimum description length (MDL) principle to phylogenetic inference, but its claim that its graph complexity penalties arise 'naturally' and are 'not externally specified' merits careful interpretation. In MDL, description lengths are defined relative to a fixed description language, which can be interpreted as encoding domain-specific background assumptions that function analogously to implicit priors over hypotheses. In PMDL, this can be illustrated by the large graph complexity penalties assigned to phylogenetic networks, particularly the sharp increase when moving from a tree to a minimal network. These penalties reflect modelling assumptions rather than consequences determined by algorithmic complexity alone. Accordingly, PMDL's graph penalties are natural only in the conditional sense that they are not externally specified once a description language for phylogenetic graphs is fixed. The choice of that language, however, remains a substantive external modelling decision. While graph complexity provides the clearest illustration, the principle that description languages encode substantive modelling decisions also applies to PMDL's model complexity. Making this explicit clarifies the interpretation of PMDL within the MDL framework and renders its background assumptions open to evaluation.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147700115","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phylogenomic evidence provides insights into the phylogeny and speciation patterns in the subgenus Caloscordum (Allium, Amaryllidaceae).","authors":"Rui-Yu Cheng, Xin-Yue Zhang, Jin-Bo Tan, Jia-Hui Sun, Song-Dong Zhou, Xing-Jin He, Deng-Feng Xie","doi":"10.1111/cla.70035","DOIUrl":"https://doi.org/10.1111/cla.70035","url":null,"abstract":"<p><p>Phylogenomics with abundant informative sites offers a powerful means for elucidating complex diversification history. Here, we collected 22 samples from 18 populations representing all species of subgenus Caloscordum (Allium). Using transcriptome and whole-genome resequencing data, we generated 1755 low-copy nuclear genes and 81 plastid genes. By integrating morphological and phylogenomic evidence, we clarified the subgenus's complex evolutionary histories and speciation patterns. A total of 18 morphological characteristics were analysed, with a taxonomic framework established. Our analyses resolved robust species relationships despite detecting extensive phylogenetic discordances, which were attributed to incomplete lineage sorting (ILS) and hybridization. Specifically, our results suggest that A. inutile originated via rapid budding speciation from the widespread A. tubiflorum. This process likely coincided with mid-Pleistocene glacial-interglacial cycles and may have been reinforced by geographic isolation and ecological adaptation. In contrast, the sole tetraploid species, A. peikingense, was confirmed to be of hybrid origin, derived from A. neriniflorum and A. tubiflorum. This allopolyploidization event appears to have been facilitated by secondary contact between the parent species, which was likely associated with climatic oscillations within the 35° N-45° N arid belt. Overall, our findings elucidate the intricate speciation patterns within Caloscordum and highlight how the interplay of polyploidization, ecological isolation, and tectonic uplift-driven aridification has shaped plant diversity in East Asia.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147634901","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A new combined-evidence phylogeny of Toxodontidae (Mammalia, Notoungulata): exploring the radiation and reconstructing hypothetical ancestors.","authors":"Matías Alberto Armella, Facundo Deforel","doi":"10.1111/cla.70036","DOIUrl":"https://doi.org/10.1111/cla.70036","url":null,"abstract":"<p><p>Toxodontidae represents a major extinct radiation of South American native ungulates, but persistent polytomies in morphological phylogenies have masked its evolutionary history. To address this, we perform a new combined-evidence phylogenetic analysis. We integrate a revised and dependency-coded matrix of 54 discrete characters with 42 morphogeometric and 5 continuous characters, across a comprehensive sample of 37 taxa. This approach overcomes key logical limitations of previous discrete datasets and quantitatively captures shape variation. The analysis yields a fully resolved and well-supported topology for Toxodontidae, with Adinotherium, Proadinotherium and Nesodon forming a paraphyletic assemblage. We identify five major clades, several of which are strongly supported and formally define them based on their sister-group relationships: Xotodontinae is sister of Altiplaniinae, both are sister to a clade comprising Haplodontheriinae and Mixodontinae + Toxodontinae. Branch length decomposition shows the initial divergence and key internal nodes were dominated by discrete character change, while later radiations were driven by morphogeometric change, indicating diversification through shape reorganization. Ancestral reconstructions reveal a shift from a generalized morphotype to specialized forms with euhypsodonty, incisor hypertrophy and larger dental dimensions. This robust phylogenetic framework resolves the long-standing impasse within Toxodontidae phylogeny and provides a foundation for testing evolutionary and biogeographic hypotheses.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147595959","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}