IF 3.9 2区生物学

Cladistics Pub Date : 2025-06-23 DOI: 10.1111/cla.70001

Kexin Gao, Xing He, Hui Wang, Chong Chen, Xinyu Gu, Qianyan Lai, Maëva Perez, Shigeaki Kojima, Kazutaka Amano, Jin Sun

{"title":"Phylogenomic analyses of Pliocardiinae (Bivalvia: Vesicomyidae) update genus-level taxonomy and shed light on trait evolution.","authors":"Kexin Gao, Xing He, Hui Wang, Chong Chen, Xinyu Gu, Qianyan Lai, Maëva Perez, Shigeaki Kojima, Kazutaka Amano, Jin Sun","doi":"10.1111/cla.70001","DOIUrl":"https://doi.org/10.1111/cla.70001","url":null,"abstract":"Vesicomyid clams in the subfamily Pliocardiinae are chemosymbiotic and specific to deep-sea chemosynthetic ecosystems with wide bathymetric and geographic ranges, making them a suitable model to study molecular adaptation and biogeography. Its phylogeny, however, still remains contentious due to limited molecular markers. Here, we elucidate the evolutionary relationships among pliocardiines based on phylogenomics data. By testing a wide range of matrices with methods including maximum likelihood, maximum parsimony, Bayesian inference, and a coalescent approach, we present a robust phylogenomic tree at the genus level supported by AU-test and GLS analyses. We revise the genus-level taxonomy of pliocardiines updating from Johnson et al. (Syst. Biodivers. 2017, 15, 346) synonymising a number of species in the \"gigas-group\" with Archivesica-also supported by a mitogenome phylogeny. Our fossil-calibrated tree based on the phylogenomic backbone reveals that Pliocardiinae originated earlier than [41.06, 42.00] Ma in the middle Eocene, while its diversification has been concurrent with global climatic cooling events. Ancestral state reconstruction analyses found two independent invasions into the abyssal zone, and a shift from harbouring the Ca. Ruthia symbionts to Ca. Vesicomyosocius symbionts. Our results present a solid backbone for future investigations into molecular adaptation, biogeography and symbiosis in this fascinating group of molluscs.","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144477734","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

The phylogenetic relationships of Bokermann´s treefrogs: species groups, reproductive biology, and biogeography (Anura: Hylidae: Bokermannohyla). Bokermann树蛙的系统发育关系：种群、生殖生物学和生物地理学（无尾目：树蛙科：Bokermannohyla）。

IF 3.9 2区生物学

Cladistics Pub Date : 2025-06-23 DOI: 10.1111/cla.12619

Julian Faivovich, Ana Carolina C Lourenço, Paulo D P Pinheiro, Mariana L Lyra, Délio Baêta, Rafael F Magalhães, Taran Grant, Tiago L Pezzuti, Felipe S F Leite, Katyuscia Araujo-Vieira, Reuber A Brandão, Thiago R Carvalho, Pedro Marinho, Victor G D Orrico, Ariadne F Sabbag, Bianca Berneck, Martín O Pereyra, Ariovaldo A Giaretta, L Felipe Toledo, Paulo C A Garcia, José P Pombal, Ward C Wheeler, Miguel T Rodrigues, Marcelo F Napoli, Célio F B Haddad

{"title":"The phylogenetic relationships of Bokermann´s treefrogs: species groups, reproductive biology, and biogeography (Anura: Hylidae: Bokermannohyla).","authors":"Julian Faivovich, Ana Carolina C Lourenço, Paulo D P Pinheiro, Mariana L Lyra, Délio Baêta, Rafael F Magalhães, Taran Grant, Tiago L Pezzuti, Felipe S F Leite, Katyuscia Araujo-Vieira, Reuber A Brandão, Thiago R Carvalho, Pedro Marinho, Victor G D Orrico, Ariadne F Sabbag, Bianca Berneck, Martín O Pereyra, Ariovaldo A Giaretta, L Felipe Toledo, Paulo C A Garcia, José P Pombal, Ward C Wheeler, Miguel T Rodrigues, Marcelo F Napoli, Célio F B Haddad","doi":"10.1111/cla.12619","DOIUrl":"https://doi.org/10.1111/cla.12619","url":null,"abstract":"The hylid genus Bokermannohyla comprises 31 species distributed across the Atlantic Forest, Caatinga and Cerrado domains, and their transition zones in Brazil. These species are currently included in three species groups (the B. circumdata, B. martinsi and B. pseudopseudis groups). In this paper, we present the results of a molecular phylogenetic analysis that includes 30 of the 31 species of the genus. Our results indicate that the currently recognized species groups are polyphyletic. To remedy this, we recognize four well-supported species groups-the B. astartea, B. izecksohni, B. nanuzae and B. oxente groups-and leave B. alvarengai, B. saxicola, B. ibitiguara and B. sazimai unassigned to any group. The new phylogenetic hypothesis allowed us to examine the evolution of oviposition sites, revealing that oviposition in water retained in restricted aquatic spaces (rock crevices, natural or male-modified basins or male-excavated tunnels) evolved from oviposition in streams during the evolutionary history of Bokermannohyla. Finally, our results support the hypothesis that this genus initially diversified in the Campos Rupestres (highland rocky fields) of the Serra do Espinhaço, with a subsequent, major diversification in the Atlantic Forest.","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144477735","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

Establishing new grid-size-dependent attributes to rank areas of endemism for conservation priorities. 建立新的与网格大小相关的属性，对特有区域进行优先保护排序。

IF 3.9 2区生物学

Cladistics Pub Date : 2025-06-19 DOI: 10.1111/cla.70002

Augusto Frota, Weferson Júnio da Graça

{"title":"Establishing new grid-size-dependent attributes to rank areas of endemism for conservation priorities.","authors":"Augusto Frota, Weferson Júnio da Graça","doi":"10.1111/cla.70002","DOIUrl":"10.1111/cla.70002","url":null,"abstract":"Delineating Areas of Endemism (AEs) is crucial for identifying priority areas for biodiversity conservation in a spatial planning framework. Endemicity Analysis in the NDM/VNDM software is one of the primary methodologies for its delineation. Larger grid sizes have been employed to yield higher endemicity scores for AEs, recovering more endemic species and enhancing their conservation appeal. Compiling a robust geographic distribution dataset for 399 freshwater fish species from Southern Brazil, we identified AEs by conducting endemicity analyses with three different grid sizes. We also developed a spatial conservation Priority Index incorporating three grid-size-dependent attributes. We identified 153 AEs, each varying in endemicity scores, species richness, and threatened species. These variations were influenced by the analysed grid size and spatial overlap with specific freshwater ecoregions. The recovered AEs show freshwater fish distribution patterns corroborating significant vicariance events and faunal exchanges between river basins in distinct bordering ecoregions. We found an almost 50% reduction in spatial area when ranking Endemicity and Priority Index scores. This finding demonstrates the effectiveness of the Priority Index in highlighting similar sets of endemic, sympatric, and threatened species within smaller areas. This approach can effectively reconcile attributes easily extracted from the NDM/VNDM program when prioritizing spatial conservation.","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144334382","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 reconstruction and species delimitation in Stipeae with special reference to Stipa (Poaceae, Pooideae) using mitochondrial genomes. 利用线粒体基因组重建棘针虫科棘针虫科的系统发育与种界。

IF 3.9 2区生物学

Cladistics Pub Date : 2025-05-28 DOI: 10.1111/cla.12618

Katarzyna Krawczyk, Mateusz Maździarz, Łukasz Paukszto, Marcin Nobis, Jakub Sawicki

{"title":"Phylogenetic reconstruction and species delimitation in Stipeae with special reference to Stipa (Poaceae, Pooideae) using mitochondrial genomes.","authors":"Katarzyna Krawczyk, Mateusz Maździarz, Łukasz Paukszto, Marcin Nobis, Jakub Sawicki","doi":"10.1111/cla.12618","DOIUrl":"https://doi.org/10.1111/cla.12618","url":null,"abstract":"Compared to plastid genomes, plant mitochondrial genomes have been less frequently used for species discrimination and phylogenetic studies due to assembly challenges, lower substitution rates and rapid structural evolution. However, this study demonstrates that mitochondrial genome fragments can be valuable for both molecular species identification and phylogenetic analysis in grasses of the tribe Stipeae. To explore this potential, we first assembled the complete mitochondrial genome of Nassella tenuissima-the first fully described mitogenome in Stipeae-which served as a reference for selecting 29 aligned mitochondrial genome fragments totalling 139 680 bp. These fragments were then analysed across 49 representatives of the tribe, including 43 Stipa species and six other taxa. The mitochondrial fragments achieved a species discrimination efficiency of 75%, slightly exceeding the 71% efficiency observed for plastid super-barcodes. Additionally, comparative phylogenetic analyses using plastid and mitochondrial genomes underscored the utility of mitochondrial data in resolving phylogenetic relationships within Stipeae. Our findings provide a valuable resource for future research in transcriptomics, comparative genomics, phylogenomics and phylogeography of grasses.","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144175528","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

Areas of endemism of semiaquatic bugs (Hemiptera: Gerromorpha): an approach to the biogeographic regionalization of Colombia. 半水生昆虫（半翅目：Gerromorpha）的特有区：哥伦比亚生物地理区划的一种方法。

IF 3.9 2区生物学

Cladistics Pub Date : 2025-05-22 DOI: 10.1111/cla.12616

Irina Morales, Patricia Mondragón-F, Ximena A Galindo-Malagón, Jorge D Mercado-Gómez

{"title":"Areas of endemism of semiaquatic bugs (Hemiptera: Gerromorpha): an approach to the biogeographic regionalization of Colombia.","authors":"Irina Morales, Patricia Mondragón-F, Ximena A Galindo-Malagón, Jorge D Mercado-Gómez","doi":"10.1111/cla.12616","DOIUrl":"https://doi.org/10.1111/cla.12616","url":null,"abstract":"Areas of endemism, defined by the congruence of the distribution of two or more taxa that are only found in that specific area, are considered an important input for biogeographic regionalization and determining priority areas for conservation. Herein we inferred the areas of endemism of Gerromorpha and their representation within the current protected areas system of Colombia. We analyzed 480 records of 69 species of semiaquatic bugs (Hemiptera - Gerromorpha) using the NDM/VNDM and three different grid sizes. We identified eight areas of endemism and 15 endemic species belonging to the genera Altavelia, Hydrometra, Oiovelia, Microvelia, Platygerris, Potamobates, Rhagovelia, Rheumatobates, Stridulivelia, Telmatometropsis and Veloidea. We identified five consensus areas. The endemism patterns of Gerromorpha from smaller units within the biogeographic provinces proposed by Morrone (Zootaxa 2014, 3782, 1-110). Rather, they form smaller units within provinces, similar to those found in vertebrates, suggesting the existence of biogeographic districts and therefore the need for a new classification. Only six of the 15 endemic species are protected under the current protected areas system. Defining Gerromorpha AEs constitutes a first step to infer the biogeographic history and the evolutionary processes that influence the distribution of semiaquatic bugs in Colombia and guide actions for their conservation.","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144121408","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

The limits of phylogenetic analysis: identifying analytical hallucinations. 系统发育分析的局限性：分析性幻觉的识别。

IF 3.9 2区生物学

Cladistics Pub Date : 2025-05-12 DOI: 10.1111/cla.12617

Ward C Wheeler

引用次数: 0

Morphological data, phylogenomics and recalcitrant nodes. 形态数据，系统基因组学和顽固性节点。

IF 3.9 2区生物学

Cladistics Pub Date : 2025-04-22 DOI: 10.1111/cla.12615

Rob DeSalle, Michael Tessler

引用次数: 0

On the effect of measures for comparing trees on the representation of treespace. 比较树的度量对树空间表示的影响。

IF 3.9 2区生物学

Cladistics Pub Date : 2025-04-05 DOI: 10.1111/cla.12614

Pablo A Goloboff, Martín E Morales

引用次数: 0

A new morphological phylogeny of Malacostraca comparing the application of character dependencies and implied weighting 一种新的马甲形态系统发育——比较性状依赖和隐含加权的应用。

IF 3.9 2区生物学

Cladistics Pub Date : 2025-04-04 DOI: 10.1111/cla.12611

Markus Grams, Ambrosio Torres, Christian S. Wirkner, Stefan Richter

{"title":"A new morphological phylogeny of Malacostraca comparing the application of character dependencies and implied weighting","authors":"Markus Grams, Ambrosio Torres, Christian S. Wirkner, Stefan Richter","doi":"10.1111/cla.12611","DOIUrl":"10.1111/cla.12611","url":null,"abstract":"Using a new character matrix composed of revised matrices of previous analyses and new morphological findings, the phylogeny of Malacostraca (Pancrustacea) is analysed anew with 207 characters for 35 terminal taxa across all recognized orders. Particular emphasis was placed on methodological versatility, including different degrees of implied weighting and one of the first applications of methods recently developed in TNT (with the xlinks-command) for considering character dependencies. With >67% of ontological dependencies our character matrix offers a perfect opportunity for putting this new methodology to the test. In particular, we can demonstrate the significant impact of character dependencies and conclusively argue the usefulness of “xlinks” (or the consideration of character dependencies in general). Furthermore, the multimethod framework also enables a comparative evaluation of established and new approaches, and the resulting cladograms thereof. Although our various results leave many questions about the phylogeny of Malacostraca unanswered, clear support is emerging for some monophyla, whereas some surprising findings give reason for methodological reflection. Also, the necessity for an increased attention in terms of taxon sampling and additional character examinations in certain groups becomes obvious. We herein provide (i) an R-function for automatically translating the character dependency syntax proposed by Grams and Richter (Cladistics, 2023, 39, 437) into xlinks-commands for TNT; and (ii) a TNT-script for analysing a character matrix successively under various k-values for implied weighting.","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"41 3","pages":"283-303"},"PeriodicalIF":3.9,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/cla.12611","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143781771","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

Phylogenetic analysis and biogeography of Scolia (Hymenoptera, Scoliidae, Scoliinae): implications for the classification and origin of Scoliini 翅虫（膜翅目，翅虫科，翅虫科）的系统发育分析和生物地理学：对翅虫分类和起源的启示。

IF 3.9 2区生物学

Cladistics Pub Date : 2025-03-25 DOI: 10.1111/cla.12612

Ivan Fernandes Golfetti, Marjorie da Silva, Eduardo Fernando Dos Santos, Fernando Barbosa Noll

{"title":"Phylogenetic analysis and biogeography of Scolia (Hymenoptera, Scoliidae, Scoliinae): implications for the classification and origin of Scoliini","authors":"Ivan Fernandes Golfetti, Marjorie da Silva, Eduardo Fernando Dos Santos, Fernando Barbosa Noll","doi":"10.1111/cla.12612","DOIUrl":"10.1111/cla.12612","url":null,"abstract":"Scoliidae is a commonly found cosmopolitan family and currently one of the most neglected taxa within Hymenoptera. As expected, information on the members of this group is scarce and extremely outdated, especially when it comes to their phylogenetic relationships. The genus Scolia Fabricius, 1755 includes species that do not present diagnostic characters used to identify the other genera of Scoliini, and so it can be considered a “dumping ground group”. Seeking to better understand the evolutionary history and, consequently, the morphological variation in “New World” Scolia species, the phylogenetic relationships among all species from the Neotropical and Nearctic Regions and their biogeography are analysed for the first time. For this, 104 morphological characters are proposed from males and females of 45 species. The phylogenetic analysis points to the monophyly of the “New World” species, and the biogeographical analysis indicates that the “New World” species originated from a Palaearctic ancestor, through a dispersal event to the Nearctic Region. Considering the taxonomic history and phylogenetic relationships obtained, aiming to initially resolve a part of the chaotic taxonomic situation of Scolia and its subgenera, here we proposed that the subgenus Discolia should be restricted exclusively to the “New World” and the species from the “Old World” should no longer be treated as Discolia, being considered as members of Scolia s.s. Additionally, Hesperoscolia should be considered a junior synonym of Discolia. Furthermore, the phylogenetic analysis confirms the monophyly of most Scoliini genera included in it.","PeriodicalId":50688,"journal":{"name":"Cladistics","volume":"41 3","pages":"304-320"},"PeriodicalIF":3.9,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143711929","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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