-
Bayesian tip‐dated phylogeny and biogeography of Cissampelideae (Menispermaceae): Mitigating the effects of homoplastic morphological characters Cladistics (IF 3.6) Pub Date : 2024-03-12 Lian Lian, Huan‐Wen Peng, Andrey S. Erst, Rosa del C. Ortiz, Florian Jabbour, Zhi‐Duan Chen, Wei Wang
The integration of morphological and molecular data is essential to understand the affinities of fossil taxa and spatio‐temporal evolutionary processes of organisms. However, homoplastic morphological characters can mislead the placement of fossil taxa and impact downstream analyses. Here, we provide an example of how to mitigate effectively the effect of morphological homoplasy on the placement of
-
-
Multi‐armed bandits, Thomson sampling and unsupervised machine learning in phylogenetic graph search Cladistics (IF 3.6) Pub Date : 2024-02-28 Ward C. Wheeler
A phylogenetic graph search relies on a large number of highly parameterized search procedures (e.g. branch‐swapping, perturbation, simulated annealing, genetic algorithm). These procedures vary in effectiveness over datasets and at alternative points in analytical pipelines. The multi‐armed bandit problem is applied to phylogenetic graph searching to more effectively utilize these procedures. Thompson
-
Wincladtree: Publication‐quality tree‐diagrams with TNT scripts Cladistics (IF 3.6) Pub Date : 2024-02-27 Pablo A. Goloboff
This note describes the implementation and use of wincladtree, a TNT script to plot publication‐quality tree‐diagrams. This is intended to assist analysis of morphological datasets, where displaying the synapomorphies for the different groups in a compact “Hennigian” style is the norm.
-
Nothing to it: a reply to Wheeler's “much ado about nothing” Cladistics (IF 3.6) Pub Date : 2024-02-12 Jan De Laet, Pablo A. Goloboff
Wheeler (Cladistics 2023, 39, 475) recently suggested that the issues with inapplicable characters in phylogenetic analysis can be dealt with directly by treating observed absences of a feature not in a separate absence/presence character but as insertion/deletion events in a complex character that describes the feature in all its variation; and that this dynamic homology view can be achieved by imposing
-
Introgression and incomplete lineage sorting blurred phylogenetic relationships across the genomes of sclerophyllous oaks from southwest China Cladistics (IF 3.6) Pub Date : 2024-01-10 Xiang-Guang Ma, Yue-Bo Ren, Hang Sun
Resolving evolutionary relationships among closely related species with interspecific gene flow is challenging. Genome-scale data provide opportunities to clarify complex evolutionary relationships in closely related species and to observe variations in species relationships across the genomes of such species. The Himalayan–Hengduan subalpine oaks have a nearly completely sympatric distribution in
-
Areas of endemism of Pteridaceae (Polypodiopsida) in Brazil: a first approach Cladistics (IF 3.6) Pub Date : 2023-12-20 Aline Possamai Della, Jefferson Prado
Areas of endemism (AoE) comprise regions host to two or more endemic taxa, whose distributional limits are congruent and not random. These areas are important for two reasons: they comprise the smallest geographic units for biogeographic analyses and they are priority targets for conservation actions. Ferns are a monophyletic group that despite having a wide geographic distribution, concentrates great
-
Systematics and character evolution of capitate hydrozoans Cladistics (IF 3.6) Pub Date : 2023-12-19 Davide Maggioni, Peter Schuchert, Andrew N. Ostrovsky, Andrea Schiavo, Bert W. Hoeksema, Daniela Pica, Stefano Piraino, Roberto Arrigoni, Davide Seveso, Enrico Montalbetti, Paolo Galli, Simone Montano
Capitate hydrozoans are a morphologically and ecologically diverse hydrozoan suborder, currently including about 200 species. Being grouped in two clades, Corynida and Zancleida, these hydrozoans still show a number of taxonomic uncertainties at the species, genus and family levels. Many Capitata species established symbiotic relationships with other benthic organisms, including bryozoans, other cnidarians
-
ONTbarcoder 2.0: rapid species discovery and identification with real-time barcoding facilitated by Oxford Nanopore R10.4 Cladistics (IF 3.6) Pub Date : 2023-12-02 Amrita Srivathsan, Vivian Feng, Daniel Suárez, Brent Emerson, Rudolf Meier
Most arthropod species are undescribed and hidden in specimen-rich samples that are difficult to sort to species using morphological characters. For such samples, sorting to putative species with DNA barcodes is an attractive alternative, but needs cost-effective techniques that are suitable for use in many laboratories around the world. Barcoding using the portable and inexpensive MinION sequencer
-
Farewell to the requirement for character independence: phylogenetic methods to incorporate different types of dependence between characters Cladistics (IF 3.6) Pub Date : 2023-11-28 Pablo A. Goloboff, Jan De Laet
This paper discusses methods to take into account interactions between characters, in the context of parsimony analysis. These interactions can be in the form of some characters becoming inapplicable given certain states of other, primary characters; in the form of only certain states being allowed in some characters when a given state or set of states occurs for other characters; or in the form of
-
Species delimitation in Amana (Liliaceae): transcriptomes battle with evolutionary complexity Cladistics (IF 3.6) Pub Date : 2023-11-20 Mei-Zhen Wang, Jing Wu, Sheng-Lu Zhang, Li-Mi Mao, Tetsuo Ohi-Toma, Atsuko Takano, Yong-Hua Zhang, Kenneth M. Cameron, Pan Li
Species delimitation has long been a subject of controversy, and there are many alternative concepts and approaches used to define species in plants. The genus Amana (Liliaceae), known as ”East Asian tulips” has a number of cryptic species and a huge genome size (1C = 21.48–57.35 pg). It also is intriguing how such a spring ephemeral genus thrives in subtropical areas. However, phylogenetic relationships
-
The Chalcidoidea bush of life: evolutionary history of a massive radiation of minute wasps Cladistics (IF 3.6) Pub Date : 2023-11-02 Astrid Cruaud, Jean-Yves Rasplus, Junxia Zhang, Roger Burks, Gérard Delvare, Lucian Fusu, Alex Gumovsky, John T. Huber, Petr Janšta, Mircea-Dan Mitroiu, John S. Noyes, Simon van Noort, Austin Baker, Julie Böhmová, Hannes Baur, Bonnie B. Blaimer, Seán G. Brady, Kristýna Bubeníková, Marguerite Chartois, Robert S. Copeland, Natalie Dale-Skey Papilloud, Ana Dal Molin, Chrysalyn Dominguez, Marco Gebiola
Chalcidoidea are mostly parasitoid wasps that include as many as 500 000 estimated species. Capturing phylogenetic signal from such a massive radiation can be daunting. Chalcidoidea is an excellent example of a hyperdiverse group that has remained recalcitrant to phylogenetic resolution. We combined 1007 exons obtained with Anchored Hybrid Enrichment with 1048 ultra-conserved elements (UCEs) for 433
-
PhylogeneticGraph (PhyG) a new phylogenetic graph search and optimization program Cladistics (IF 3.6) Pub Date : 2023-10-19 Ward C. Wheeler, Alexander Washburn, Louise M. Crowley
We present Phylogenetic Graph (PhyG), an open-source, phylogenetic search tool for diverse data types and graphs, including softwired and hardwired networks, in addition to trees. This allows for analysis of horizontal transfer and hybridization scenarios, as well as the necessary vertical inheritance of trees. PhyG is the successor to POY5 in performing combined data tree-alignment with enhancements
-
Phylogenomic analysis of Tachinidae (Diptera: Calyptratae: Oestroidea): a transcriptomic approach to understanding the subfamily relationships Cladistics (IF 3.6) Pub Date : 2023-10-13 Letícia Chiara Baldassio de Paula, Rodrigo de Vilhena Perez Dios, Filipe Macedo Gudin, Marcelo Domingos de Santis, Deivys Moises Alvarez-Garcia, Manuel Antunes Júnior, Beatriz Vieira Freire, Fernando Portella de Luna Marques, Daniel José Galafasse Lahr, Silvio Shigueo Nihei
Tachinidae is the second most species-rich family of Diptera. It comprises four subfamilies, and all of its members have parasitoid habits. We present the first phylogenomic analysis of Tachinidae using transcriptomic data, based on 30 species. We constructed four datasets: three using translated data at the amino acid level (100% coverage, with 106 single-copy protein-coding genes; 75% coverage, with
-
Toward transparent taxonomy: an interactive web-tool for evaluating competing taxonomic arrangements Cladistics (IF 3.6) Pub Date : 2023-10-12 Oksana V. Vernygora, Felix A. H. Sperling, Julian R. Dupuis
Informative and consistent taxonomy above the species level is essential to communication about evolution, biodiversity and conservation, and yet the practice of taxonomy is considered opaque and subjective by non-taxonomist scientists and the public alike. While various proposals have tried to make the basis for the ranking and inclusiveness of taxa more transparent and objective, widespread adoption
-
Advances in the reconstruction of the spider tree of life: A roadmap for spider systematics and comparative studies Cladistics (IF 3.6) Pub Date : 2023-10-03 Siddharth Kulkarni, Hannah M. Wood, Gustavo Hormiga
In the last decade and a half, advances in genetic sequencing technologies have revolutionized systematics, transforming the field from studying morphological characters or a few genetic markers, to genomic datasets in the phylogenomic era. A plethora of molecular phylogenetic studies on many taxonomic groups have come about, converging on, or refuting prevailing morphology or legacy-marker-based hypotheses
-
Large-scale genomic data reveal the phylogeny and evolution of owlet moths (Noctuoidea) Cladistics (IF 3.6) Pub Date : 2023-10-03 Xuankun Li, Jesse W. Breinholt, Jose I. Martinez, Kevin Keegan, Emily A. Ellis, Nicholas T. Homziak, Andreas Zwick, Caroline G. Storer, Duane McKenna, Akito Y. Kawahara
The owlet moths (Noctuoidea; ~43–45K described species) are one of the most ecologically diverse and speciose superfamilies of animals. Moreover, they comprise some of the world's most notorious pests of agriculture and forestry. Despite their contributions to terrestrial biodiversity and impacts on ecosystems and economies, the evolutionary history of Noctuoidea remains unclear because the superfamily
-
Fifth mass extinction event triggered the diversification of the largest family of freshwater gastropods (Caenogastropoda: Truncatelloidea: Hydrobiidae) Cladistics (IF 3.6) Pub Date : 2023-09-15 Diana Delicado, Torsten Hauffe, Thomas Wilke
The fifth mass extinction event (MEE) at the Cretaceous–Palaeogene (K–Pg) boundary 66 million years ago (Ma) led to massive species loss but also triggered the diversification of higher taxa. Five models have been proposed depending on whether this diversification occurred before, during or after the K–Pg boundary and the rate of species accumulation. While the effects of the K–Pg MEE on vertebrate
-
Wing pattern diversity in Eunica butterflies (Nymphalidae: Biblidinae): phylogenetic analysis implies decoupled adaptive trends in dorsal sexual dimorphism and ventral eyespot evolution Cladistics (IF 3.6) Pub Date : 2023-09-15 Ivonne J. Garzón-Orduña, Karina Lucas Silva-Brandão, Keith Willmott, André V. L. Freitas, Niklas Wahlberg, Andrew V. Z. Brower
Butterfly eyespots are wing patterns reminiscent of vertebrate eyes, formed by concentric rings of contrastingly coloured scales. Eyespots are usually located close to the wing margin and often regarded as the single most conspicuous pattern element of butterfly wing colour displays. Recent efforts to understand the processes involved in the formation of eyespots have been driven mainly by evo-devo
-
Untangling the evolution of soldier beetles (Coleoptera: Cantharidae) and the evaluation of the morphological phylogenetic signal in a soft-bodied elateroid lineage Cladistics (IF 3.6) Pub Date : 2023-08-30 Michal Motyka, Dominik Kusy, Gabriel Biffi, Michael Geiser, Sergey V. Kazantsev, Renata Bilkova, Eva Jahodarova, Alfried P. Vogler, Ladislav Bocak
This study addresses the long-standing uncertainty about the internal classification of soldier beetles (Elateroidea: Cantharidae). Four datasets were compiled and analysed: 66 genes for 14 terminals, 15 mtDNA genes for 79 terminals, one mtDNA and two rRNA genes for 217 terminals, and barcodes for 576 terminals. Based on congruent topologies, Chauliognathinae is proposed as a sister to the remaining
-
What else is dentition telling us? A new specimen-level phylogeny of Mesotheriidae (Mammalia, Notoungulata) Cladistics (IF 3.6) Pub Date : 2023-07-25 Matías Alberto Armella, Facundo Deforel
Mesotheriidae (Panperissodactyla, Notoungulata) are an extinct clade (early Oligocene–Pleistocene) of small to medium-sized herbivorous mammals that were widely distributed in South America. Although two subfamilies traditionally have been recognized (Trachytheriinae and Mesotheriinae), recent cladistic analyses based on discrete characters have indicated that “Trachytheriinae” is a paraphyletic assemblage
-
Much ado about nothing: inapplicable data as insertion–deletion events Cladistics (IF 3.6) Pub Date : 2023-07-19 Ward C. Wheeler
The treatment of inapplicable characters has proved especially vexing to systematists. Investigators have wrestled with alternative coding scenarios to capture both the presence and absence of a feature, and its variation when present, in a reasonable manner. Three basic issues have presented themselves: (i) impossible states at internal nodes; (ii) action at a distance among disparate parts of the
-
Parsimony optimization of phylogenetic networks Cladistics (IF 3.6) Pub Date : 2023-07-19 Ward C. Wheeler, Alexander J. Washburn
An algorithm is described for the optimization of character data (e.g. qualitative, nucleic acid sequence) on softwired phylogenetic networks. The algorithm presented here is an extension of those developed for trees under the parsimony criterion and can form the basis for phylogenetic network search procedures. Although the problem is (in general) an NP-Hard optimization, the resolution-based algorithm
-
On the four complementary aspects of hierarchical character relationships and their bearing on scoring constraints, expressed in a new syntax for character dependencies Cladistics (IF 3.6) Pub Date : 2023-07-10 Markus Grams, Stefan Richter
Morphological matrices, including the conceptualization of characters and character states and scoring thereof, still are a valuable and necessary tool for phylogenetic analyses. Although they are often seen only as numerically simplified summaries of observations for the purpose of cladistic analyses, they also hold value as collections of ideas, concepts and the current state of knowledge, conveying
-
Congruence between ultraconserved element-based matrices and phylotranscriptomic datasets in the scorpion Tree of Life Cladistics (IF 3.6) Pub Date : 2023-07-04 Carlos E. Santibáñez-López, Andrés A. Ojanguren-Affilastro, Matthew R. Graham, Prashant P. Sharma
Scorpions are ancient and historically renowned for their potent venom. Traditionally, the systematics of this group of arthropods was supported by morphological characters, until recent phylogenomic analyses (using RNAseq data) revealed most of the higher-level taxa to be non-monophyletic. While these phylogenomic hypotheses are stable for almost all lineages, some nodes have been hard to resolve
-
Biogeographic–tectonic calibration of 14 nodes in a butterfly timetree Cladistics (IF 3.6) Pub Date : 2023-06-06 Michael Heads, John R. Grehan, John Nielsen, Brian Patrick
The butterfly subtribe Coenonymphina (Nymphalidae: Satyrinae) comprises four main clades found, respectively, in (1) the Solomon Islands, (2) Australasia, (3) NW South America and (4) Laurasia, with a phylogeny: 1 (2 (3 + 4)). In assessing biogeographic evolution in the group we rejected the conversion of fossil-calibrated clade ages to likely maximum clade ages by the imposition of arbitrary priors
-
Molecular phylogeny, divergence time, biogeography and trends in host plant usage in the agriculturally important tortricid tribe Grapholitini (Lepidoptera: Tortricidae: Olethreutinae) Cladistics (IF 3.6) Pub Date : 2023-05-20 Gui-Lin Hu, John Brown, Maria Heikkilä, Leif Aarvik, Marko Mutanen
The leaf-roller moth tribe Grapholitini comprises about 1200 described species and contains numerous notorious pests of fruits and seeds. The phylogeny of the tribe has been little studied using contemporary methods, and the monophyly of several genera remains questionable. In order to provide a more robust phylogenetic framework for the group, we conducted a multiple-gene phylogenetic analysis of
-
Himalayan upliftment and Shiwalik succession act as a cradle for divergence in Bengal monitor lizard Varanus bengalensis (Reptilia: Varanidae) in India Cladistics (IF 3.6) Pub Date : 2023-05-18 Kumudani Bala Gautam, Ajit Kumar, Abhijit Das, Sandeep Kumar Gupta
The Himalayan foothills and associated environment are well-known for driving the rapid diversification of many species and the formation of biodiversity hotspots. The effects of environmental change since the Miocene have accelerated species diversification, and hence are useful for studying population genetic structure, and evolutionary relationships via genetic approaches. To date, the effects of
-
A unified view of homology Cladistics (IF 3.6) Pub Date : 2023-04-25 Igor Ballego-Campos, Stéphani K. V. Bonifácio, Leandro C. S. Assis
As it spread through time and into distinct areas of science—from comparative anatomy to evolutionary biology, cladistics, developmental and molecular biology—the homology concept has changed considerably, presenting various meanings. Despite many attempts at developing a comprehensive understanding of the concept, this context-sensitive notion of homology has been a subject of an ongoing debate. Inspired
-
Quantification of congruence among gene trees with polytomies using overall success of resolution for phylogenomic coalescent analyses Cladistics (IF 3.6) Pub Date : 2023-04-25 Mark P. Simmons, Pablo A. Goloboff, Ben C. Stöver, Mark S. Springer, John Gatesy
Gene-tree-inference error can cause species-tree-inference artefacts in summary phylogenomic coalescent analyses. Here we integrate two ways of accommodating these inference errors: collapsing arbitrarily or dubiously resolved gene-tree branches, and subsampling gene trees based on their pairwise congruence. We tested the effect of collapsing gene-tree branches with 0% approximate-likelihood-ratio-test
-
Splitting one species into 22: an unusual tripling of molecular, morphological, and geographical differentiation in the fern family Didymochlaenaceae (Polypodiales) Cladistics (IF 3.6) Pub Date : 2023-04-21 Hui Shang, Zhi-Qing Xue, Zhen-Long Liang, Michael Kessler, Rossarin Pollawatn, Ngan Thi Lu, Yu-Feng Gu, Xue-Ping Fan, Yun-Hong Tan, Liang Zhang, Xin-Mao Zhou, Xia Wan, Li-Bing Zhang
The pantropical fern genus Didymochlaena (Didymochlaenaceae) has long been considered to contain one species only. Recent studies have resolved this genus/family as either sister to the rest of eupolypods I or as the second branching lineage of eupolypods I, and have shown that this genus is not monospecific, but the exact species diversity is unknown. In this study, a new phylogeny is reconstructed
-
New Cretaceous empidoids and the Mesozoic dance fly revolution (Diptera: Empidoidea) Cladistics (IF 3.6) Pub Date : 2023-04-20 Davide Badano, Bradley J. Sinclair, Qingqing Zhang, Francesca Palermo, Nicola Pieroni, Laura Maugeri, Michela Fratini, Pierfilippo Cerretti
Dance flies and relatives (Empidoidea) are a diverse and ecologically important group of Diptera in nearly all modern terrestrial ecosystems. Their fossil record, despite being scattered, attests to a long evolutionary history dating back to the early Mesozoic. Here, we describe seven new species of Empidoidea from Cretaceous Kachin amber inclusions, assigning them to the new genus Electrochoreutes
-
Systematics and biogeography of the Old World fern genus Antrophyum Cladistics (IF 3.6) Pub Date : 2023-04-20 Cheng-Wei Chen, Stuart Lindsay, Joel Nitta, Germinal Rouhan, Michael Sundue, Leon R. Perrie, Yao-Moan Huang, Wen-Liang Chiou, Kuo-Fang Chung
Antrophyum is one of the largest genera of vittarioid ferns (Pteridaceae) and is most diverse in tropical Asia and the Pacific Islands, but also occurs in temperate Asia, Australia, tropical Africa and the Malagasy region. The only monographic study of Antrophyum was published more than a century ago and a modern assessment of its diversity is lacking. Here, we reconstructed a comprehensively sampled
-
Phylogenetic analysis of Blaberoidea reveals non-monophyly of taxa and supports the creation of multiple new subfamilies Cladistics (IF 3.6) Pub Date : 2023-04-17 Yi-Shu Wang, Jia-Wei Zhang, Nathan Lo, Thomas Bourguignon, Lin Guo, Bian-Lun Li, Yan-Li Che, Zong-Qing Wang
The superfamily Blaberoidea is a highly species-rich group of cockroaches. High-level blaberoidean phylogenetics are still under debate owing to variable taxon sampling and incongruence between mitochondrial and nuclear evolution, as well as different methods used in various phylogenetic studies. We here present a phylogenetic analysis of Blaberoidea based on a dataset combining the mitochondrial genome
-
Behavioural evolution of Neotropical social wasps (Vespidae: Polistinae): the queen selection process Cladistics (IF 3.6) Pub Date : 2023-03-04 Laura Chavarría-Pizarro, Marjorie da Silva, Danilo C. Ament, Eduardo A. B. Almeida, Fernando Barbosa Noll
All Epiponini wasps are polygynic, with multiple queens alternating over the colony cycle. There are several potential queens in the early stages of this cycle, but as it progresses, the number of queens is reduced. Because most individuals remain reproductively totipotent, there is great potential for conflicts over reproduction. Workers could have an advantage in controlling queen production because
-
Morphology and phylogenetic significance of the pelvic articular region in elasmobranchs (Chondrichthyes) Cladistics (IF 3.6) Pub Date : 2023-03-01 João Paulo C. B. da Silva, Diego F. B. Vaz
The morphology of paired fins is commonly overlooked in morphological studies, particularly the pelvic girdle and fins. Consequently, previous phylogenetic studies incorporating morphological data used few skeletal characters from this complex. In this paper, the phylogenetic significance of pelvic articular characters for elasmobranchs is discussed in light of the morphological variation observed
-
Hierarchies, classifications, cladograms and phylogeny Cladistics (IF 3.6) Pub Date : 2023-02-14 Andrew V. Z. Brower
Figure 18 of Hennig's Phylogenetic Systematics (University of Illinois Press, Urbana, IL, 1966) shows a phylogenetic tree (a generative hierarchy) and what appear to be nested sets (an inclusive hierarchy) that he stated were two representations of the same pattern of relationships. This essay questions whether this is correct or not, explores the meanings of different hierarchical patterns, reviews
-
Homologues and homology and their related terms in phylogenetic systematics Cladistics (IF 3.6) Pub Date : 2023-02-04 Torben Göpel, Stefan Richter
In the field of phylogenetic systematics, the terms homology and homologue and their relationship to cladistic terms such as character, character state, synapomorphy and symplesiomorphy, as well as their relationships to each other, have been and are still discussed frequently. A recent re-emergence of concepts of homology/homologue free of any reference to explanatory hypotheses prompted us to explore
-
A novel probe set for the phylogenomics and evolution of RTA spiders Cladistics (IF 3.6) Pub Date : 2023-01-31 Junxia Zhang, Zhaoyi Li, Jiaxing Lai, Zhisheng Zhang, Feng Zhang
Spiders are important models for evolutionary studies of web building, sexual selection and adaptive radiation. The recent development of probes for UCE (ultra-conserved element)-based phylogenomic studies has shed light on the phylogeny and evolution of spiders. However, the two available UCE probe sets for spider phylogenomics (Spider and Arachnida probe sets) have relatively low capture efficiency
-
Total-evidence phylogeny and evolutionary morphology of New World pitvipers (Serpentes: Viperidae: Crotalinae) Cladistics (IF 3.6) Pub Date : 2023-01-26 Paola A. Carrasco, Claudia Koch, Felipe G. Grazziotin, Pablo J. Venegas, Juan C. Chaparro, Gustavo J. Scrocchi, David Salazar-Valenzuela, Gerardo C. Leynaud, Camilo I. Mattoni
Crotalines (pitvipers) in the Americas are distributed from southern Canada to southern Argentina, and are represented by 13 genera and 163 species that constitute a monophyletic group. Their phylogenetic relationships have been assessed mostly based on DNA sequences, while morphological data have scarcely been used for phylogenetic inquiry. We present a total-evidence phylogeny of New World pitvipers
-
TNT version 1.6, with a graphical interface for MacOS and Linux, including new routines in parallel Cladistics (IF 3.6) Pub Date : 2023-01-22 Pablo A. Goloboff, Martín E. Morales
A new graphical user interface (GUI) for the parsimony program TNT is presented that works under the Linux and Mac operating systems, as well as the Cygwin environment (which runs under Windows). The new interface is based on the GIMP Tool Kit, GTK (version 3). Formerly, only Windows versions of TNT had a GUI. The new interface improves upon the existing Windows GUI in several respects. These changes
-
Phylogenomics and systematics of Entomobryoidea (Collembola): marker design, phylogeny and classification Cladistics (IF 3.6) Pub Date : 2022-12-30 Nerivania Nunes Godeiro, Yinhuan Ding, Nikolas Gioia Cipola, Sopark Jantarit, Bruno Cavalcante Bellini, Feng Zhang
Entomobryoidea has been the focus of phylogenetic studies in recent years owing to a divergence between morphological and genetic data. Recent phylogenies have converged on the sister relationship of Orchesellidae with the remaining Entomobryoidea, and on the non-monophyly of the traditional Paronellidae and Entomobryidae, but still lack resolution. Known molecular phylogenies of the superfamily differ
-
Morphology, nuclear SNPs and mate selection reveal that COI barcoding overestimates species diversity in a Mediterranean freshwater amphipod by an order of magnitude Cladistics (IF 3.6) Pub Date : 2022-12-28 Kamil Hupało, Denis Copilaș-Ciocianu, Florian Leese, Martina Weiss
DNA sequence information has revealed many morphologically cryptic species worldwide. For animals, DNA-based assessments of species diversity usually rely on the mitochondrial cytochrome c oxidase subunit I (COI) gene. However, a growing amount of evidence indicate that mitochondrial markers alone can lead to misleading species diversity estimates due to mito-nuclear discordance. Therefore, reports
-
The oldest Gondwanan fossil of Leiinae (Diptera, Mycetophilidae): Phylogenetic and evolutionary implications Cladistics (IF 3.6) Pub Date : 2022-12-08 Dalton de Souza Amorim, Sarah Siqueira Oliveira, Daniel Dias Dornelas do Carmo, Guilherme Cunha Ribeiro
A fossil Mycetophilidae from the Aptian Crato Formation—Cretomanota gondwanica gen. nov., sp. nov.—is described, which is the first mycetophilid from the Crato Formation and corresponds to the oldest known fossil leiine and only the second Gondwanan fossil mycetophilid described so far. Cretomanota gondwanica and both species of Alavamanota Blagoderov and Arillo were added as terminals to the data
-
When phylogenetics met biogeography: Willi Hennig, Lars Brundin and the roots of phylogenetic and cladistic biogeography Cladistics (IF 3.6) Pub Date : 2022-10-19 Juan J. Morrone
Willi Hennig's (Beitr. Ent. 1960, 10, 15) Die Dipteren-Fauna von Neuseeland als systematisches und tiergeographisches Problem applied a phylogenetic approach to examine the distributional patterns exhibited by the Diptera of New Zealand. Hennig showed how phylogenetic trees may be used to infer dispersal, based on the progression and deviation rules, and also discussed the existence of vicariance patterns
-
Molecular phylogeny of the tropical wandering spiders (Araneae, Ctenidae) and the evolution of eye conformation in the RTA clade Cladistics (IF 3.6) Pub Date : 2022-10-06 Nicolas A. Hazzi, Gustavo Hormiga
Tropical wandering spiders (Ctenidae) are a diverse group of cursorial predators with its greatest species richness in the tropics. Traditionally, Ctenidae are diagnosed based on the presence of eight eyes arranged in three rows (a 2–4–2 pattern). We present a molecular phylogeny of Ctenidae, including for the first time representatives of all of its subfamilies. The molecular phylogeny was inferred
-
Relative performance of Bayesian morphological clock and parsimony methods for phylogenetic reconstructions: Insights from the case of Myomiminae and Dryomyinae glirid rodents Cladistics (IF 3.6) Pub Date : 2022-08-31 Andrea Dalmasso, Pablo Peláez-Campomanes, Raquel López-Antoñanzas
Extinct organisms provide crucial information about the origin and time of origination of extant groups. The importance of morphological phylogenetics for rigorously dating the tree of life is now widely recognized and has been revitalized by methodological developments such as the application of tip-dating Bayesian approaches. Traditionally, molecular clocks have been node calibrated. However, node
-
Multi-gene phylogeny of North American clear-winged moths (Lepidoptera: Sesiidae): a foundation for future evolutionary study of a speciose mimicry complex Cladistics (IF 3.6) Pub Date : 2022-08-09 Anthony I. Cognato, William Taft, Rachel K. Osborn, Daniel Rubinoff
Sesiids are a diverse group of predominantly diurnal moths, many of which are Batesian mimics of Hymenoptera. However, their diversity and relationships are poorly understood. A multi-gene phylogenetic analysis of 48 North American sesiid species confirmed the traditional taxonomic tribal ranks, demonstrated the paraphyly of Carmenta and Synanthedon with respect to several other genera and ultimately
-
The stepwise Indian–Eurasian collision and uplift of the Himalayan-Tibetan plateau drove the diversification of high-elevation Scytodes spiders Cladistics (IF 3.6) Pub Date : 2022-07-08 Yufa Luo, Shuqiang Li
The Cenozoic Indian–Eurasian collision and uplift of the Himalayan-Tibetan Plateau (HTP) are among the most important geological events in the world. They have affected the diversification of regional biota of many taxonomic groups on and around the HTP. However, the exact timing and model of the collision and uplift events and speciation on and around the HTP are still in debate. The Himalayas group
-
Intersubjective Corroboration Cladistics (IF 3.6) Pub Date : 2022-07-04 Andrew V. Z. Brower
Conflicts of interest The author declares no conflicts of interest. The opinions expressed in this review do not necessarily represent the policies or views of the United States government or the U.S. Department of Agriculture.
-
Female terminalia morphology and cladistic relations among Tok-Tok beetles (Tenebrionidae: Sepidiini) Cladistics (IF 3.6) Pub Date : 2022-07-04 Marcin J. Kamiński, Olivia M. Gearner, Marcin Raś, Elliot T. Hunsinger, Amelia L. Smith, Paloma Mas-Peinado, Jennifer C. Girón, Aleksandra G. Bilska, Werner P. Strümpher, Christopher C. Wirth, Kojun Kanda, Kali Swichtenberg, Dariusz Iwan, Aaron D. Smith
Tok-tokkies are one of the most iconic lineages within Tenebrionidae. In addition to containing some of the largest darkling beetles, this tribe is recognized for its remarkable form of sexual communication known as substrate tapping. Nevertheless, the phylogenetic relationships within the group remain poorly understood. This study investigates the usefulness of female terminalia morphology for delimiting
-
New insights into the phylogeny of the complex thalloid liverworts (Marchantiopsida) based on chloroplast genomes Cladistics (IF 3.6) Pub Date : 2022-07-02 You-Liang Xiang, Xin-Jie Jin, Chao Shen, Xia-Fang Cheng, Lei Shu, Rui-Liang Zhu
Marchantiopsida (complex thalloid liverworts) are one of the earliest lineages of embryophytes (land plants), and well-known for their air pores and chambers, pegged rhizoids, and absence of organellular RNA editing sites. Despite their importance to an understanding of early embryophyte evolution, many key nodes within this class remain poorly resolved, owing to the paucity of genetic loci previously
-
Hyb-Seq provides new insights into the phylogeny and evolution of the Chrysanthemum zawadskii species complex in China Cladistics (IF 3.6) Pub Date : 2022-06-29 Wen-Xun Lu, Xue-Ying Hu, Zi-Zhao Wang, Guang-Yuan Rao
A species complex is an assemblage of closely related species with blurred boundaries, and from which species could arise from different speciation processes and/or a speciation continuum. Such a complex can provide an opportunity to investigate evolutionary mechanisms acting on speciation. The Chrysanthemum zawadskii species complex in China, a monophyletic group of Chrysanthemum, consists of seven
-
Cretaceous lophocoronids with short proboscis and retractable female genitalia provide the earliest evidence for their feeding and oviposition habits Cladistics (IF 3.6) Pub Date : 2022-06-27 Weiting Zhang, Chungkun Shih, Michael S. Engel, Dong Ren
We describe two new species of Lophocoronidae: Acanthocorona hedida Zhang, Shih and Engel sp. n. and Acanthocorona venulosa Zhang, Shih and Engel sp. n., and an undetermined specimen from mid-Cretaceous Kachin amber. Phylogenetic analysis of basal lepidopteran lineages, including three extinct families, was undertaken. The analysis supported monophyly of Glossata although internal relationships remain
-
Benefits of alignment quality-control processing steps and an Angiosperms353 phylogenomics pipeline applied to the Celastrales Cladistics (IF 3.6) Pub Date : 2022-05-15 Mark P. Simmons, Olivier Maurin, Paul Bailey, Grace E. Brewer, Shyamali Roy, Julio A. Lombardi, Félix Forest, William J. Baker
We examined the impact of successive alignment quality-control steps on downstream phylogenomic analyses. We applied a recently published phylogenomics pipeline that was developed for the Angiosperms353 target-sequence-capture probe set to the flowering plant order Celastrales. Our final dataset consists of 158 species, including at least one exemplar from all 109 currently recognized Celastrales genera
-
Benefits of alignment quality-control processing steps and an Angiosperms353 phylogenomics pipeline applied to the Celastrales. Cladistics (IF 3.6) Pub Date : 2022-05-15 Mark P Simmons,Olivier Maurin,Paul Bailey,Grace E Brewer,Shyamali Roy,Julio A Lombardi,Félix Forest,William J Baker
We examined the impact of successive alignment quality-control steps on downstream phylogenomic analyses. We applied a recently published phylogenomics pipeline that was developed for the Angiosperms353 target-sequence-capture probe set to the flowering plant order Celastrales. Our final dataset consists of 158 species, including at least one exemplar from all 109 currently recognized Celastrales genera
-
Somewhere I belong: phylogeny and morphological evolution in a species-rich lineage of ectoparasitic flatworms infecting cichlid fishes Cladistics (IF 3.6) Pub Date : 2022-04-30 Armando J. Cruz-Laufer, Antoine Pariselle, Michiel W. P. Jorissen, Fidel Muterezi Bukinga, Anwar Al Assadi, Maarten Van Steenberge, Stephan Koblmüller, Christian Sturmbauer, Karen Smeets, Tine Huyse, Tom Artois, Maarten P. M. Vanhove
A substantial portion of biodiversity has evolved through adaptive radiation. However, the effects of explosive speciation on species interactions remain poorly understood. Metazoan parasites infecting radiating host lineages could improve our knowledge because of their intimate host relationships. Yet limited molecular, phenotypic and ecological data discourage multivariate analyses of evolutionary
-
Phylogeny and biogeography of the ancient spider family Filistatidae (Araneae) is consistent both with long-distance dispersal and vicariance following continental drift Cladistics (IF 3.6) Pub Date : 2022-04-27 Ivan L. F. Magalhaes, Martín J. Ramírez
Filistatids, the crevice weavers, are an ancient family of cribellate spiders without extant close relatives. As one of the first lineages of araneomorph spiders, they present a complicated mixture of primitive and derived characters that make them a key taxon to elucidate the phylogeny of spiders, as well as the evolution of phenotypic characters in this group. Their moderate diversity (187 species
-
Phylogeny and biogeography of the ancient spider family Filistatidae (Araneae) is consistent both with long-distance dispersal and vicariance following continental drift. Cladistics (IF 3.6) Pub Date : 2022-04-27 Ivan L F Magalhaes,Martín J Ramírez
Filistatids, the crevice weavers, are an ancient family of cribellate spiders without extant close relatives. As one of the first lineages of araneomorph spiders, they present a complicated mixture of primitive and derived characters that make them a key taxon to elucidate the phylogeny of spiders, as well as the evolution of phenotypic characters in this group. Their moderate diversity (187 species
-
Phylogeny and biogeography of the northern temperate genus Dracocephalum s.l. (Lamiaceae) Cladistics (IF 3.6) Pub Date : 2022-03-31 Ya-Ping Chen, Turginov Orzimat Turdimatovich, Maxim S. Nuraliev, Predrag Lazarević, Bryan T. Drew, Chun-Lei Xiang
The northern temperate genus Dracocephalum consists of approximately 70 species mainly distributed in the steppe-desert biomes of Central and West Asia and the alpine region of the Qinghai-Tibetan Plateau (QTP). Previous work has shown that Dracocephalum is not monophyletic and might include Hyssopus and Lallemantia. This study attempts to clarify the phylogenetic relationships, diversification patterns