Perspectives in Earthworm Molecular Phylogeny: Recent Advances in Lumbricoidea and Standing Questions

Earthworm systematics have been limited by the small number of taxonomically informative morphological characters and high levels of homoplasy in this group. However, molecular phylogenetic techniques have yielded significant improvements in earthworm taxonomy in the last 15 years. Several different approaches based on the use of different molecular markers, sequencing techniques, and compromises between specimen/taxon coverage and phylogenetic information have recently emerged (DNA barcoding, multigene phylogenetics, mitochondrial genome analysis, transcriptome analysis, targeted enrichment methods, and reduced representation techniques), providing solutions to different evolutionary questions regarding European earthworms. Molecular phylogenetics have led to significant advances being made in Lumbricidae systematics, such as the redefinition or discovery of new genera (Galiciandrilus, Compostelandrilus, Vindoboscolex, Castellodrilus), delimitation and revision of previously existing genera (Kritodrilus, Eophila, Zophoscolex, Bimastos), and changes to the status of subspecific taxa (such as the Allolobophorachaetophora complex). These approaches have enabled the identification of problems that can be resolved by molecular phylogenetics, including the revision of Aporrectodea, Allolobophora, Helodrilus, and Dendrobaena, as well as the examination of small taxa such as Perelia, Eumenescolex, and Iberoscolex. Similar advances have been made with the family Hormogastridae, in which integrative systematics have contributed to the description of several new species, including the delimitation of (formerly) cryptic species. At the family level, integrative systematics have provided a new genus system that better reflects the diversity and biogeography of these earthworms, and phylogenetic comparative methods provide insight into earthworm macroevolution. Despite these achievements, further research should be performed on the Tyrrhenian cryptic complexes, which are of special eco-evolutionary interest. These examples highlight the potential value of applying molecular phylogenetic techniques to other earthworm families, which are very diverse and occupy different terrestrial habitats across the world. The systematic implementation of such approaches should be encouraged among the different expert groups worldwide, with emphasis on collaboration and cooperation.

Discovery of the freshwater sponge genus Corvospongilla Annandale (Porifera: Spongillida) in Australia with the description of a new species and phylogeographic implications

A recent discovery of freshwater sponges in an unexplored hydrographic basin in north-western Australia provided the opportunity to investigate the genus Corvospongilla Annandale (Spongillida: Spongillidae) using integrative systematics. Emendation of the genus diagnosis is provided. A comparative analysis of a Corvospongilla global dataset of morphological traits together with biogeographic patterns disclosed a new Australasian Corvospongilla species and along with molecular analyses provided the basis for a phylogenetic and phylogeographic tree for some Asian, Afrotropical and Australasian lineages.

Integrative systematics reveals the new land-snail genus Taphrenalla (Eupulmonata: Ariophantidae) with a description of nine new species from Thailand

The endemic terrestrial Crown Snail from Southern Thailand formerly in Macrochlamys Gray, 1847 is now described as Taphrenalla Pholyotha & Panha gen. nov., based on comparative morphology and molecular data. Overall, eleven Taphrenalla species are now recognized, including two nominal species: T. asamurai and T. diadema. A total of nine new species are proposed: T. alba sp. nov., T. conformis sp. nov., T. corona sp. nov., T. dalli sp. nov., T. incilis sp. nov., T. macrosulcata sp. nov., T. parversa sp. nov., T. pygmaea sp. nov. and T. zemia sp. nov. The molecular phylogeny constructed from the mitochondrial cytochrome oxidase c subunit I (COI) and 16S rRNA gene fragments plus the nuclear 28S rDNA gene fragments revealed that Taphrenalla gen. nov. is monophyletic with a well-supported clade. The diagnostic characters of Taphrenalla gen. nov. are the shell sculpture with several radial grooves, body with well-developed colourful stripes running from the head to tail, and genitalia similar to Macrochamys but with an un-coiling epiphallic caecum. The spermatophore has one or two spines near the sperm sac and a spineless tail.

Multilocus, phenotypic, behavioral, and ecological niche analyses provide evidence for two species within Euphonia affinis (Aves, Fringillidae)

The integration of genetic, morphological, behavioral, and ecological information in the analysis of species boundaries has increased, allowing integrative systematics that better reflect the evolutionary history of biological groups. In this context, the goal of this study was to recognize independent evolutionary lineages within Euphonia affinis at the genetic, morphological, and ecological levels. Three subspecies have been described: E. affinis godmani, distributed in the Pacific slope from southern Sonora to Guerrero; E. affinis affinis, from Oaxaca, Chiapas and the Yucatan Peninsula to Costa Rica; and E. affinis olmecorum from Tamaulipas and San Luis Potosi east to northern Chiapas (not recognized by some authors). A multilocus analysis was performed using mitochondrial and nuclear genes. These analyses suggest two genetic lineages: E. godmani and E. affinis, which diverged between 1.34 and 4.3 My, a period in which the ice ages and global cooling fragmented the tropical forests throughout the Neotropics. To analyze morphometric variations, six morphometric measurements were taken, and the Wilcoxon Test was applied to look for sexual dimorphism and differences between the lineages. Behavioral information was included, by performing vocalization analysis which showed significant differences in the temporal characteristics of calls. Finally, Ecological Niche Models were estimated with MaxEnt, and then compared using the method of Broennimann. These analyses showed that the lineage distributed in western Mexico (E. godmani) has a more restricted niche than the eastern lineage (E. affinis) and thus we rejected the hypotheses of niche equivalence and similarity. Based on the combined evidence from genetic, morphological, behavioral, and ecological data, it is concluded that E. affinis (with E. olmecorum as its synonym) and E. godmani represent two independent evolutionary lineages.

Integrative systematics untangles the evolutionary history of Stenochrus (Schizomida: Hubbardiidae), a neglected junkyard genus of North American short-tailed whipscorpions

Until recently, the Nearctic short-tailed whipscorpion genus, StenochrusChamberlin, 1922, included 27 species distributed primarily in Mexico, the USA and Central America. Morphological disparity among its species, associated with their adaptation to diverse habitats, raised the question as to whether Stenochrus was monophyletic. The phylogenetic relationships among short-tailed whipscorpions have only recently begun to be explored, and the monophyly of Stenochrus had never been tested. The present contribution provides the first phylogeny of Stenochrus and related genera, based on 61 morphological characters and 2991 aligned DNA nucleotides from two nuclear and two mitochondrial gene markers, for 73 terminal taxa. Separate and simultaneous analyses of the morphological and molecular data sets were conducted with Bayesian Inference, Maximum Likelihood, and parsimony with equal and implied weighting. Terminals represented only by morphological data (‘orphans’) were included in some analyses for evaluation of their phylogenetic positions. As previously defined, Stenochrus sensuReddell & Cokendolpher (1991, 1995) was consistently polyphyletic and comprised eight monophyletic clades, justifying its reclassification into eight genera including Heteroschizomus Rowland, 1973, revalidated from synonymy with Stenochrus by Monjaraz-Ruedas et al. (2019). Rowland & Reddell’s (1980)mexicanus and pecki species groups were consistently paraphyletic. Orphans grouped with the most morphologically similar taxa.

Integrative systematics unveils the controversial identity of Engraulidae fishing stocks in a Neotropical estuary, northeast Brazil

ABSTRACT In Brazil, the use and diversity of the common names of fish species, coupled with taxonomic uncertainties, hinder the reliability of fishing statistical data. In this scenario, there are the so-called pilombetas of the São Francisco River, an important fishing resource in region. Despite its importance, the real diversity of species identified in the area remains obscure. In order to properly identify and delimit the species popularly known as pilombetas, an integrative approach involving traditional taxonomy, geometric morphometrics and molecular systematics was applied. Results from geometric morphometrics and molecular analyses were consistent with the results of the traditional morphological analysis, also indicating the delimitation of six taxa belonging to Engraulidae in the lower São Francisco River. In addition, species delimitation methods revealed an intrapopulation genetic divergence of 1.7% for Lycengraulis grossidens. The results revealed that the currently known richness species of Engraulidae in the studied area has been underestimated. Thus, an updated taxonomic key is herein proposed for the Engraulidae species from the lower São Francisco River and estuary. The integrative analysis approach revealed to be effective to address taxonomic questions and help the management of stocks, ensuring the maintenance of local diversity of fishes in the Neotropical region.

Integrative systematics and ecology of a new deep-sea family of tanaidacean crustaceans

A new family of paratanaoidean Tanaidacea – Paranarthrurellidae fam. nov. – is erected to accommodate two genera without family classification (Paratanaoidea incertae sedis), namely Armatognathia Kudinova-Pasternak, 1987 and Paranarthrurella Lang, 1971. Seven new species of Paranarthrurella and two of Armatognathia are described from material taken in different deep-sea areas of the Atlantic and Pacific oceans. The type species of Paranarthrurella — P. caudata (Kudinova-Pasternak, 1965) — is redescribed based on the paratype. The genus Cheliasetosatanais Larsen and Araújo-Silva, 2014 originally classified within Colletteidae is synonymised with Paranarthrurella, and Arthrura shiinoi Kudinova-Pasternak, 1973 is transferred to Armatognathia. Amended diagnoses of Armatognathia and Paranarthrurella genera are given. Choosing characters for distinguishing and defining both genera was supported by Principal Component Analysis. Designation of the new family is supported by molecular phylogenetic analysis of COI and 18S datasets. The distribution of all species currently included in the new family was visualised and their bathymetric distribution analysed.