Cladistics

Charbonnier, Sylvain; Audo, Denis; Barriel, Véronique; Garassino, Alessandro; Schweigert, Günter; Simpson, Martin

doi: 10.1111/cla.12088pmid: 34772264

A phylogenetic analysis of a total of 31 species: 27 fossil species from seven families (Glypheidae, Litogastridae, Mecochiridae, Pemphicidae, Erymidae, Clytiopsidae, Chimaerastacidae), and four extant species from three families (Glypheidae, Nephropidae, Stenopodidae) is proposed. Most of the genera considered are coded exclusively based upon their type species and, as much as possible, based upon the type specimens. The cladistic analysis demonstrates that the glypheidean lobsters (infraorder Glypheidea) form a monophyletic group including two superfamilies: Glypheoidea and Pemphicoidea new status. Glypheoidea includes three families: Glypheidae, Mecochiridae and Litogastridae. Litogastridae is the sister group of the clade Glypheidae + Mecochiridae. Pemphicoidea includes a single family: Pemphicidae. A new classification of Glypheidea is proposed and currently known genera are rearranged based upon the phylogenetic analysis.

Martínez, Alejandro; Di Domenico, Maikon; Rouse, Greg W.; Worsaae, Katrine

doi: 10.1111/cla.12089pmid: 34772269

Protodrilidae is a group of small, superficially simple‐looking annelids, lacking chaetae and appendages, except for two prostomial palps. Originally considered to be one of the primitive “archiannelid” families, its affinity within Annelida is still highly debated. Protodrilids are found worldwide in the interstices of intertidal and subtidal marine sediments. Despite their simple appearance they constitute one of the most species‐rich interstitial families, with 36 described species in two genera, Protodrilus and the gutless Astomus. Here we present the first phylogenetic study of Protodrilidae employing five gene fragments, 55 morphological characters and 73 terminals (including seven outgroups) analysed under direct optimization and parsimony as well as model‐based methods. The large data set includes all 36 described species of Protodrilidae (17 of which are represented only by the morphological partition) as well as 30 undescribed or uncertain species (represented by both morphology and molecules). This comprehensive, inclusive and combined analysis revealed a new perspective on the phylogeny of Protodrilidae: the family is shown to contain six cosmopolitan subclades, each supported by several morphological apomorphies, and with the genus Astomus consistently nested among the other five clades rather than next to these. Consequently, the diagnosis of Protodrilus is emended, Astomus remains unchanged and the four remaining lineages are diagnosed and named Megadrilus n. gen, Meiodrilus gen. nov., Claudrilus n. gen and Lindrilus gen. nov. Character transformations showed that large size and presence of pigmentation, oviducts and eyes are plesiomorphies of the family, retained in Protodrilus, Megadrilus gen. nov. and Lindrilus gen. nov. These features are secondarily lost in the gutless Astomus with epidermal uptake of nutrients, as well as in Meiodrilus gen. nov. and some species of Claudrilus n. gen, with smaller size correlated to life in interstices of finer sediments.

Groh, Selina; Giribet, Gonzalo

doi: 10.1111/cla.12087pmid: 34772266

Among the least studied harvestmen are the members of the family Caddidae sensu Shear, , a group of Opiliones with massive eyes and the putative sister group of the remaining Eupnoi. Caddids were originally described as two families, Caddidae and Acropsopilionidae, but these are currently treated as subfamilies of Caddidae. These minute arachnids are rarely collected and present some interesting biogeographical patterns, including a disjunct distribution between East Asia and eastern North America, and some of the few cases of trans‐Pacific genera in southern hemisphere Opiliones. We therefore obtained samples from most of the landmasses inhabited by Caddidae and undertook a phylogenetic study using nuclear and mitochondrial genes for as many samples as possible. Our results, based on a broad taxonomic sampling, surprisingly showed polyphyly of Caddidae, with the genus Caddo forming the sister group of the remaining Eupnoi, whereas the southern hemisphere genera, many of which were originally placed in Acropsopilionidae, within Dyspnoi, formed the sister clade of the remaining Dyspnoi. In addition, the more recently described genus Hesperopilio, from Western Australia and Chile, was unrelated to either Caddidae or Acropsopilionidae, despite having the supposedly diagnostic large ocularium, and instead appeared deeply nested within the Eupnoi superfamily Phalangioidea. Our results are robust to analytical treatment and to homology scheme (dynamic vs. static notions of homology), resulting in a new phylogenetic proposal for Eupnoi and Dyspnoi. Ancestral state reconstruction suggests that the ancestral Palpatores was probably a tiny harvestman with an enlarged ocularium and glandular palpal setae in its enlarged and armed palps. We take the following taxonomic actions: Acropsopilionidae is removed from synonymy under Caddidae and its family status and membership in Dyspnoi are restored. Hesperopilio Shear, is removed from Caddoidea/Caddidae and transferred to Phalangioidea, but it is not assigned to any family.

Lewis, Delano S.; Sperling, Felix A. H.; Nakahara, Shinichi; Cotton, Adam M.; Kawahara, Akito Y.; Condamine, Fabien L.

doi: 10.1111/cla.12092pmid: 34772262

Numerous hypotheses on the evolution of Neotropical biodiversity have stimulated research to provide a better understanding of diversity dynamics and distribution patterns of the region. However, few studies integrate molecular and morphological data with complete sampling of a Neotropical group, and so there has been little synthesis of the multiple processes governing biodiversity through space and time. Here, a total‐evidence phylogenetic approach is used to reconstruct the evolutionary history of the butterfly subgenus Heraclides. We used DNA sequences for two mitochondrial genes and one nuclear gene and coded 133 morphological characters of larvae and adults. A robust and well‐resolved phylogeny was obtained using several analytical approaches, while molecular dating and biogeographical analyses indicated an early Miocene origin (22 Mya) in the Caribbean Islands. We inferred six independent dispersal events from the Caribbean to the mainland, and three from the mainland to the Caribbean, and we suggest that cooling climates with decreasing sea levels may have contributed to these events. The time‐calibrated tree is best explained by a museum model of diversity in which both speciation and extinction rates remained constant through time. By assessing both continental and fine‐scale biodiversity patterns, this study provides new findings, for instance that islands may act as source of diversity rather than as a sink, to explain spatio‐temporal macroevolutionary processes within the Neotropical region.

Assis, Leandro C. S.

doi: 10.1111/cla.12085pmid: 34772265

The present paper is mainly concerned with homology assessment through phylogenetic analyses. It raises a fundamental question: What are the epistemological differences between modern parsimony and model‐based analyses in relation to homology assessment and phylogenetic inference? Although these methods usually achieve concordant topological results, they may generate discordant inferences of character evolution from the same datasets. This indicates that method selection has serious implications for evolutionary scenarios and classificatory arrangements. Notwithstanding that parsimony and model‐based approaches use the Hennigian concepts of monophyly and synapomorphy, they employ different epistemological ways of dealing with the monophyly/synapomorphy relationship. Independently of their differences, these analyses should take into account all relevant evidence in support of the phylogenetic inferences. A focus on morphological homologues means that they must be included in data matrices, evaluated as part of the phylogenetic analysis, and cannot be ignored in calculation of the tree(s) length (parsimony), maximum‐likelihood (maximum‐likelihood), and posterior probabilities (Bayes).

Antunes Carvalho, Fernanda; Filer, Denis; Renner, Susanne S.

doi: 10.1111/cla.12095pmid: 34772277

The need for taxonomists to take full advantage of biodiversity informatics has been clear for at least 10 years. Significant progress has been made in providing access to taxonomic resources online, including images of specimens (especially types), original species descriptions, and georeferenced collection data. However, in spite of persuasive calls for e‐monography, there are few, if any, completed project, even though monographic research is the only mechanism for reducing synonymous names, which are estimated to comprise 50% of all published names. Caricaceae is an economically important family of flowering plants from Africa and the Neotropics, best known for the fruit crop papaya. There is a large amount of information on the family, especially on chemistry, crop improvement, genomics, and the sex chromosomes of papaya, but up‐to‐date information on the 230 names and which species they might belong to was not available. A dynamically updated e‐monograph of the Caricaceae now brings together all information on this family, including keys, species descriptions, and specimen data relating the 230 names to 34 species and one hybrid. This may be the first taxonomic monograph of a plant family completely published online. The curated information will be continuously updated to improve the monograph's comprehensiveness and utility.

Farris, James S.

doi: 10.1111/cla.12090pmid: N/A

Brower, Andrew V. Z.

doi: 10.1111/cla.12086pmid: N/A