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Analysis of alternative homologies with parsimony and step-matrix recoding. 具有简约性和步进矩阵重编码的备选同调分析。
IF 6.2 2区 生物学
Cladistics Pub Date : 2026-03-19 DOI: 10.1111/cla.70033
Pablo A Goloboff
{"title":"Analysis of alternative homologies with parsimony and step-matrix recoding.","authors":"Pablo A Goloboff","doi":"10.1111/cla.70033","DOIUrl":"https://doi.org/10.1111/cla.70033","url":null,"abstract":"<p><p>This paper describes how prior uncertainty of the homology of different parts of organisms, and therefore of the characters contained in those parts, can be analysed by recoding the set of characters into a complex character. In this complex character, states represent combinations of states and homologies among the original characters, and transformation costs between states are set to values that maximize (weighted) homology. This allows a proper treatment of both the alternative homologies and the inapplicability of the characters contained in parts that can be absent or present. All the methods described are implemented in the program TNT, with a relatively simple syntax. This facilitates the treatment of characters in body parts of uncertain homology, including parts that can appear or disappear making their characters inapplicable. The analyses can also be combined with definitions of other types of dependences (e.g. morphofunctional constraints, inapplicabilities determined from characters outside of the parts of ambiguous homology). Although recoding into combinations of states and homologies allows handling relatively low numbers of characters per part (because of computation time and RAM requirements), TNT also implements options that facilitate creating alternative static alignments, allowing approximate analysis of larger number of characters.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147488209","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}
引用次数: 0
Phylogenetic relationships of the Neotropical genera of Hylobiina (Coleoptera: Curculionidae: Molytinae: Molytini): seventy years after Kuschel's proposal. 新热带海参属的系统发育关系(鞘翅目:Curculionidae: Molytinae: Molytini):在Kuschel提出70年后。
IF 6.2 2区 生物学
Cladistics Pub Date : 2026-03-15 DOI: 10.1111/cla.70032
Julian Alexander Mendivil-Nieto, Juan J Morrone
{"title":"Phylogenetic relationships of the Neotropical genera of Hylobiina (Coleoptera: Curculionidae: Molytinae: Molytini): seventy years after Kuschel's proposal.","authors":"Julian Alexander Mendivil-Nieto, Juan J Morrone","doi":"10.1111/cla.70032","DOIUrl":"https://doi.org/10.1111/cla.70032","url":null,"abstract":"<p><p>This study presents the first phylogenetic analysis focused on the Neotropical genera of the subtribe Hylobiina, including species of 28 out of the 29 currently recognized genera. A morphological data matrix comprising 131 terminal taxa and 162 characters was analysed under maximum parsimony using a heuristic search with extended implied weighting, resulting in a single most parsimonious tree. The analysis recovered Myrtacebius as unrelated to the remaining genera of the group. The genera Arniticus, Byzes, Calvertius, Centor, Cyriaspis, Haplogenus, Heilipus, Heilus, Hilipinus, Iphipus, Ischiomastus, Lymanchonus, Marshallius, Neseilipus, Nothofagius, Ozoctenus, Placeilipus, Plethes, Polymicrus, Pseudanchonus, Syphorbus, Tartarisus and Typacrus were recovered as monophyletic, whereas Epistrophus, Heilipodus, Parabyzes and Rhineilipus were found to be non-monophyletic. Based on these results, Whiteheadlobius gen. nov. is proposed, supported by the presence of a ventrite-femoral stridulatory system of type 2. This genus includes the following species, formerly placed in Heilipodus: Whiteheadlobius argentinicus, comb. nov., W. bajulus, comb. nov., W. biplagiatus, comb. nov., W. cinctipennis, comb. nov., W. clavipes, comb. nov., W. destructor, comb. nov., W. naevulus, comb. nov., and W. unifasciatus, comb. nov. In addition, Rhineilipus is redefined to include Parabyzes, now considered a junior synonym, and several species formerly assigned to Heilipodus are transferred to Rhineilipus: R. austerus, comb. nov., R. caliginosus, comb. nov., R. callosus, comb. nov., R. cynicus, comb. nov., R. decussatus, comb. nov., R. jocosus, comb. nov., R. lutosus, comb. nov., R. quadrinodosus, comb. nov., and R. suspensus. An updated identification key to the Neotropical genera of Hylobiina is also provided.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147464015","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}
引用次数: 0
On a recent phylogenetic reanalysis of Sphaenorhynchini (Anura: Hylidae: Hylinae): Does it all come down to the method? 最近对海蛛(无尾目:海蛛科:海蛛科)的系统发育再分析:这一切都归结为方法吗?
IF 6.2 2区 生物学
Cladistics Pub Date : 2026-03-11 Epub Date: 2025-11-16 DOI: 10.1111/cla.70018
Katyuscia Araujo-Vieira, Pedro Henrique dos Santos Dias, Martín O. Pereyra, Boris L. Blotto, Ulisses Caramaschi, Célio F.B. Haddad, Julián Faivovich, Taran Grant
{"title":"On a recent phylogenetic reanalysis of Sphaenorhynchini (Anura: Hylidae: Hylinae): Does it all come down to the method?","authors":"Katyuscia Araujo-Vieira,&nbsp;Pedro Henrique dos Santos Dias,&nbsp;Martín O. Pereyra,&nbsp;Boris L. Blotto,&nbsp;Ulisses Caramaschi,&nbsp;Célio F.B. Haddad,&nbsp;Julián Faivovich,&nbsp;Taran Grant","doi":"10.1111/cla.70018","DOIUrl":"10.1111/cla.70018","url":null,"abstract":"<p>Sphaenorhynchini comprises 15 species of small, greenish treefrogs from <i>cis</i>-Andean South America. Araujo-Vieira et al. (2019, A total evidence analysis of the phylogeny of hatch-faced treefrogs [Anura: Hylidae: <i>Sphaenorhynchus</i>], <i>Cladistics</i> 35, 469–486) conducted a total evidence parsimony analysis of DNA sequences and phenotypic data, corroborating the monophyly of <i>Sphaenorhynchus</i>, identifying three species groups, and placing the unusual species <i>S</i>. <i>pauloalvini</i> as sister to all other species. On this basis and numerous phenotypic differences, Araujo-Vieira et al. (2020, A new genus of lime treefrogs [Anura: Hylidae: Sphaenorhynchini], <i>Zool. Anz.</i> 286, 81–89) erected the genus <i>Gabohyla</i> for <i>S</i>. <i>pauloalvini</i>. Subsequently, Pereira et al. (2022, The dispersal between Amazonia and Atlantic Forest during the Early Neogene revealed by the biogeography of the treefrog tribe Sphaenorhynchini [Anura, Hylidae], <i>Ecol. Evol.</i> 12, e8754) performed a Bayesian analysis of a subset of Araujo-Vieira et al.'s (2019) molecular data and found <i>G</i>. <i>pauloalvini</i> to be nested within <i>Sphaenorhynchus</i>, which they attributed exclusively to choice of analytical method. To test this claim, we performed parsimony and Bayesian analyses of the total evidence dataset and the complete and partial molecular datasets with either the entire outgroup sample or a single terminal. The topology from the Bayesian analysis of the complete dataset is almost identical to that of Araujo-Vieira et al. (2019), with <i>G. pauloalvini</i> sister to <i>Sphaenorhynchus</i>, thereby refuting Pereira et al.'s claim. Moreover, the monophyly of <i>Sphaenorhynchus</i> sensu stricto was remarkably robust, being recovered in all analyses except the Bayesian analysis of the partial molecular dataset with a single outgroup terminal (i.e., the analysis performed by Pereira et al.). In addition to supporting the continued recognition of <i>Gabohyla</i>, our results underscore the importance of considering not only the choice of analytical method, but also character and taxon sampling—including outgroup sampling—before rejecting prior findings.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"42 2","pages":"206-218"},"PeriodicalIF":6.2,"publicationDate":"2026-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145535058","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}
引用次数: 0
Revealing patterns of endemism in the transatlantic family Chelodesmidae (Polydesmida: Diplopoda) 揭示跨大西洋龟科的特有模式(多足目:双足目)。
IF 6.2 2区 生物学
Cladistics Pub Date : 2026-03-11 Epub Date: 2025-12-30 DOI: 10.1111/cla.70022
Rodrigo Salvador Bouzan, Jackson Means, Kaloyan Ivanov, Antonio Domingos Brescovit, Luiz Felipe Moretti Iniesta
{"title":"Revealing patterns of endemism in the transatlantic family Chelodesmidae (Polydesmida: Diplopoda)","authors":"Rodrigo Salvador Bouzan,&nbsp;Jackson Means,&nbsp;Kaloyan Ivanov,&nbsp;Antonio Domingos Brescovit,&nbsp;Luiz Felipe Moretti Iniesta","doi":"10.1111/cla.70022","DOIUrl":"10.1111/cla.70022","url":null,"abstract":"<p>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.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"42 2","pages":"159-171"},"PeriodicalIF":6.2,"publicationDate":"2026-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12977946/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145858939","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Complex evolutionary dynamics of Sichuana, an endemic katydid genus in the Hengduan Mountains illuminated by mitochondrial phylogenomics and morphological evidence 线粒体系统基因组学和形态学证据揭示了横断山区特有蝈蝈属四川蝈蝈的复杂进化动力学。
IF 6.2 2区 生物学
Cladistics Pub Date : 2026-03-11 Epub Date: 2025-12-05 DOI: 10.1111/cla.70020
Chengjie Zheng, Yi Zhou, Wei Yuan, Shilv Fan, Wu Dai, Yanli Yue, Jun-Jie Gu
{"title":"Complex evolutionary dynamics of Sichuana, an endemic katydid genus in the Hengduan Mountains illuminated by mitochondrial phylogenomics and morphological evidence","authors":"Chengjie Zheng,&nbsp;Yi Zhou,&nbsp;Wei Yuan,&nbsp;Shilv Fan,&nbsp;Wu Dai,&nbsp;Yanli Yue,&nbsp;Jun-Jie Gu","doi":"10.1111/cla.70020","DOIUrl":"10.1111/cla.70020","url":null,"abstract":"<p>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 <i>Sichuana</i>, endemic to the HDM, integrating mitochondrial genomics, morphology and biogeography. We sequenced complete mitochondrial genomes of all known geographic populations of <i>Sichuana</i>, 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 (<i>S. brevicerca</i> sp. nov., <i>S. fortidens</i> sp. nov., <i>S. qiuzhi</i> sp. nov., <i>S. luqiaoensis</i> sp. nov. and <i>S. pseudomagna</i> sp. nov.) and two subspecies (<i>S. pseudomagna pseudomagna</i> subsp. nov. and <i>S. pseudomagna borealis</i> 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.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"42 2","pages":"128-158"},"PeriodicalIF":6.2,"publicationDate":"2026-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145679357","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}
引用次数: 0
A new Chinese dicynodont and the frequent dispersal of tetrapods between Northern and Southern Pangaea during the late Permian 一种新的中国双齿兽和晚二叠纪南北盘古之间四足动物的频繁分布。
IF 6.2 2区 生物学
Cladistics Pub Date : 2026-03-11 Epub Date: 2025-12-15 DOI: 10.1111/cla.70019
Yu-Tai Shi, Jun Liu
{"title":"A new Chinese dicynodont and the frequent dispersal of tetrapods between Northern and Southern Pangaea during the late Permian","authors":"Yu-Tai Shi,&nbsp;Jun Liu","doi":"10.1111/cla.70019","DOIUrl":"10.1111/cla.70019","url":null,"abstract":"<p>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 <i>Dinanomodon</i>, a genus formerly only known from South Africa, although it represents a new species—<i>D. guoi</i>. 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.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"42 2","pages":"172-192"},"PeriodicalIF":6.2,"publicationDate":"2026-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145757773","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}
引用次数: 0
Phylogenomics reveals the reticulate evolution and biogeographic history of New World cypresses, Hesperocyparis (Cupressaceae) 系统基因组学揭示了新世界柏树(柏科)的网状进化和生物地理历史。
IF 6.2 2区 生物学
Cladistics Pub Date : 2026-03-11 Epub Date: 2025-12-22 DOI: 10.1111/cla.70021
Jialiang Li, Shiyu Jia, Dayu Wu, Wenjing Tao, Markus Ruhsam, Kangshan Mao
{"title":"Phylogenomics reveals the reticulate evolution and biogeographic history of New World cypresses, Hesperocyparis (Cupressaceae)","authors":"Jialiang Li,&nbsp;Shiyu Jia,&nbsp;Dayu Wu,&nbsp;Wenjing Tao,&nbsp;Markus Ruhsam,&nbsp;Kangshan Mao","doi":"10.1111/cla.70021","DOIUrl":"10.1111/cla.70021","url":null,"abstract":"<p>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 <i>Hesperocyparis</i> (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 <i>Hesperocyparis</i>. Our analyses resolved the genus into three clades—Macrocarpa, Arizonica and the basal <i>H. bakeri</i>—and strongly supported its monophyly within the HCX clade (<i>Hesperocyparis</i>, <i>Callitropsis</i>, <i>Xanthocyparis</i>). However, significant cytonuclear discordance was observed, reflecting the influence of ancient hybridization and ILS. Molecular dating placed the origin of <i>Hesperocyparis</i> 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 <i>Hesperocyparis</i>.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"42 2","pages":"109-127"},"PeriodicalIF":6.2,"publicationDate":"2026-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145806223","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}
引用次数: 0
UITOTO: a software for generating molecular diagnoses for species descriptions UITOTO:为物种描述生成分子诊断的软件。
IF 6.2 2区 生物学
Cladistics Pub Date : 2026-03-11 Epub Date: 2025-12-20 DOI: 10.1111/cla.70023
Ambrosio Torres, Leshon Lee, Amrita Srivathsan, Rudolf Meier
{"title":"UITOTO: a software for generating molecular diagnoses for species descriptions","authors":"Ambrosio Torres,&nbsp;Leshon Lee,&nbsp;Amrita Srivathsan,&nbsp;Rudolf Meier","doi":"10.1111/cla.70023","DOIUrl":"10.1111/cla.70023","url":null,"abstract":"<p>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 <span>UITOTO,</span> 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, <span>UITOTO</span> derives a majority-consensus DMC. To verify whether the generated DMCs are contrastive, <span>UITOTO</span> includes a validation module that tests DMCs against databases, efficiently handling thousands of aligned or unaligned sequences. We here, not only propose <span>UITOTO</span>, but also assess its performance relative to other software that can derive DMCs (e.g. <span>MOLD</span>). For this purpose, we analyse three large empirical datasets: (i) <i>Megaselia</i> (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), <span>UITOTO</span>'s DMCs outcompete DMCs from other software. We furthermore provide guidelines for generating molecular diagnoses and a user-friendly <span>Shiny</span> 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.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"42 2","pages":"193-205"},"PeriodicalIF":6.2,"publicationDate":"2026-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12977935/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145794558","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Rethinking areas of endemism and barriers: perspectives for a causal historical biogeography and a critique of Schultz and Cracraft (2024). 重新思考地方性和障碍的领域:因果历史生物地理学的视角和对舒尔茨和克拉夫特的批评(2024)。
IF 6.2 2区 生物学
Cladistics Pub Date : 2026-03-06 DOI: 10.1111/cla.70030
Augusto Ferrari
{"title":"Rethinking areas of endemism and barriers: perspectives for a causal historical biogeography and a critique of Schultz and Cracraft (2024).","authors":"Augusto Ferrari","doi":"10.1111/cla.70030","DOIUrl":"https://doi.org/10.1111/cla.70030","url":null,"abstract":"<p><p>Historical biogeography faces a persistent conceptual and methodological dilemma concerning the nature of its central analytical units. Using the recent proposal by Schultz and Cracraft (Cladistics 40, 653) as a catalyst, this article critiques the argument that causal inference necessitates the replacement of areas of endemism with barriers, contending that such a forced dichotomy is both artificial and reductionist. It is postulated that modern methodological advances allow areas of endemism to be rigorously treated as dynamic and quantitatively testable hypotheses, thereby overcoming long-standing objections that classify them as mere descriptive constructs. Conversely, an exclusive focus on barriers fundamentally underestimates the multifactorial nature of diversification, neglecting the structural role of dispersal and the complex spatiotemporal dynamism of isolating forces. Effective inference in historical biogeography demands an explicitly pluralistic and process-agnostic perspective, recognizing areas and barriers as complementary, intersecting elements. This integrative approach is essential for accurately capturing the emergent complexity of biogeographic patterns, moving the discipline beyond the limitations of unifocal causal models.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147369295","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}
引用次数: 0
Multi-angle, cross-domain fusion strategy enhances automated insect identification and hierarchical categorization: a case study on assassin bugs (Hemiptera: Reduviidae). 多角度、跨域融合策略增强了昆虫自动识别和分层分类——以半翅目:猎蝽科为例
IF 6.2 2区 生物学
Cladistics Pub Date : 2026-02-11 DOI: 10.1111/cla.70029
Xinkai Wang, Huaiyu Liu, Zhuo Chen, Yisheng Zhao, Yingqi Liu, Haoyang Xiong, Yuange Duan, Fang Song, Wanzhi Cai, Xuankun Li, Hu Li
{"title":"Multi-angle, cross-domain fusion strategy enhances automated insect identification and hierarchical categorization: a case study on assassin bugs (Hemiptera: Reduviidae).","authors":"Xinkai Wang, Huaiyu Liu, Zhuo Chen, Yisheng Zhao, Yingqi Liu, Haoyang Xiong, Yuange Duan, Fang Song, Wanzhi Cai, Xuankun Li, Hu Li","doi":"10.1111/cla.70029","DOIUrl":"10.1111/cla.70029","url":null,"abstract":"<p><p>Automated insect identification systems hold significant value for biodiversity monitoring, pest management, citizen science initiatives and systematic studies, particularly in an era of declining expertise in insect taxonomy. However, current deep learning approaches often rely on standardized specimen photos from limited-angles and simplified backgrounds, limiting their generalization and effectiveness in diverse practical scenarios. Here, we address this limitation using assassin bugs (Hemiptera: Reduviidae) as a model system-a highly diverse group with complex morphological variation. We developed a comprehensive, high-quality dataset of 11 915 expert-validated images from 92 species across 48 genera and six subfamilies, integrating three image types: standard, turntable-captured and ecological. Using ConvNeXt-B architecture, we systematically evaluated the performance of classification and hierarchical categorization to higher taxonomic ranks across different training and testing scenarios. Multi-angle fusion increased species recognition accuracy by 5.72% and F1-score by 0.061 and increased the hierarchical categorization of unseen species to correct genera by 13.53% and the F1-score by 0.129. Incorporating ecological images further enhanced model performance by 13% for both tasks. Grad-CAM visualization revealed that multi-angle, cross-domain fusion guides the model to focus on taxonomically diagnostic traits, yielding hierarchical feature representations aligned with classical taxonomy across lab and wild environments. Our results demonstrate that integrating diverse viewing angles and ecological contexts substantially improves model cross-domain adaptation, providing a practical framework for developing reliable automated insect identification tools for diverse practical scenarios. Furthermore, our model's ability to accurately categorize unseen taxa into higher taxonomic ranks holds significant potential for future applications in systematics, including facilitate specimen sorting and generating testable phylogenetic hypotheses.</p>","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146167770","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}
引用次数: 0
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