High‐quality genomes reveal significant genetic divergence and cryptic speciation in the model organism Folsomia candida (Collembola)

The collembolan Folsomia candida Willem, 1902, is an important representative soil arthropod that is widely distributed throughout the world and has been frequently used as a test organism in soil ecology and ecotoxicology studies. However, it is questioned as an ideal “standard” because of differences in reproductive modes and cryptic genetic diversity between strains from various geographical origins. In this study, we present two high-quality chromosome-level genomes of F. candida, for the parthenogenetic Danish strain (FCDK, 219.08 Mb, N50 of 38.47 Mb, 25,139 protein-coding genes) and the sexual Shanghai strain (FCSH, 153.09 Mb, N50 of 25.75 Mb, 21,609 protein-coding genes). The seven chromosomes of FCDK are each 25–54% larger than the corresponding chromosomes of FCSH, showing obvious repetitive element expansions and large-scale inversions and translocations but no whole-genome duplication. The strain-specific genes, expanded gene families and genes in nonsyntenic chromosomal regions identified in FCDK are highly related to its broader environmental adaptation. In addition, the overall sequence identity of the two mitogenomes is only 78.2%, and FCDK has fewer strain-specific microRNAs than FCSH. In conclusion, FCDK and FCSH have accumulated independent genetic changes and evolved into distinct species since diverging 10 Mya. Our work shows that F. candida represents a good model of rapidly cryptic speciation. Moreover, it provides important genomic resources for studying the mechanisms of species differentiation, soil arthropod adaptation to soil ecosystems, and Wolbachia-induced parthenogenesis as well as the evolution of Collembola, a pivotal phylogenetic clade between Crustacea and Insecta.

Twelve New Species Reveal Cryptic Diversification in Foliicolous Lichens of Strigula s.lat. (Strigulales, Ascomycota)

We employed a molecular phylogenetic approach using five markers (ITS, nuSSU, nuLSU, TEF1-α, and RPB2) to assess potential cryptic speciation in foliicolous members of Strigula s.lat. (Strigulaceae), including the recently segregated genera Phylloporis, Puiggariella, Raciborskiella, Racoplaca, and Serusiauxiella, from tropical areas in Asia, with selected materials from the Neotropics as reference. On the basis of combined molecular and phenotypic datasets, two new species of Racoplaca and 10 new species of Strigula s.str. are described: Racoplaca macrospora sp. nov., R. maculatoides sp. nov., Strigula guangdongensis sp. nov., S. intermedia sp. nov., S. laevis sp. nov., S. microcarpa sp. nov., S. pseudoantillarum sp. nov., S. pseudosubtilissima sp. nov., S. pycnoradians sp. nov., S. sinoconcreta sp. nov., S. stenoloba sp. nov., and S. subtilissimoides sp. nov. In addition, we propose the new combination Phylloporis palmae comb. nov. (≡ =Manaustrum palmae) and we validate the earlier combination Racoplaca melanobapha comb. nov. (≡ Verrucaria melanobapha; Strigula melanobapha). Our data clearly indicate a considerable degree of cryptic diversification in foliicolous representatives of Strigula s.lat., particularly in the presumably widespread taxa Strigula antillarum, S. concreta, S. nitidula, and S. smaragdula. Given that these phylogenetic revisions are thus far limited to few regions, we predict that our findings only represent the proverbial tip of the iceberg in this group of lichenized fungi.

Trends in Taxonomy of Chagas Disease Vectors (Hemiptera, Reduviidae, Triatominae): From Linnaean to Integrative Taxonomy

Chagas disease is a neglected tropical disease caused by the protozoan Trypanosoma cruzi and transmitted mainly by members of the subfamily Triatominae. There are currently 157 species, grouped into 18 genera and five tribes. Most descriptions of triatomine species are based on classical taxonomy. Facing evolutionary (cryptic speciation and phenotypic plasticity) and taxonomic (more than 190 synonymizations) problems, it is evident that integrative taxonomy studies are an important and necessary trend for this group of vectors. Almost two-and-a-half centuries after the description of the first species, we present for the first time the state-of-the-art taxonomy of the whole subfamily, covering from the initial classic studies to the use of integrative taxonomy.

Phylogeography and Diversity Among Populations of the Toxigenic Benthic Dinoflagellate Prorocentrum From Coastal Reef Systems in Mexico

The marine dinoflagellate genus Prorocentrum Ehrenberg comprises many species occupying primarily benthic or epiphytic habitats, particularly in tropical and sub-tropical waters. Despite concerted efforts to establish phylogenetic associations, there remain unresolved issues in defining morphospecies and membership in species complexes. The study described herein addressed the inter- and infraspecific relationships of members of the Prorocentrum lima and Prorocentrum hoffmannianum species complexes (PLSC and PHSC, respectively) by applying multivariate approaches in morphotaxonomy, molecular phylogenetics and chemodiversity to establish affinities among multiple clonal isolates. Morphotaxonomic analysis showed consistency with classical morphospecies descriptors, and high variability in cell size and dimensions, but did not challenge current species complex concepts. Phylogenetic analysis of ITS/5.8S rDNA sequences from isolates from the Gulf of California, Caribbean Sea, and Gulf of Mexico coasts compared with archived global GenBank sequences served to define five consistent clades with separation of the PLSC and PHSC. Secondary structure modeling of ITS2 rRNA variation based on compensatory base changes (CBC) was effective in resolving details of the respective species complexes and even indicated putative incipient or cryptic speciation due to potential hybridization barriers. This study represents the largest (n = 67 isolates) chemodiversity analysis of polyketide-derived toxins associated with diarrheic shellfish poisoning (DSP) from a benthic dinoflagellate genus. Relative composition of some analogs (OA, OA-D8, DTX1, DTX1a, and DTX1a-D8), including two new undescribed isomers, distinguished P. lima from P. hoffmannianum sensu lato, but without clear associations with substrate type or geographical origin. Although all P. lima and most (one exception) P. hoffmannianum were toxigenic, the total cell toxin content could not be linked at the species level. This research demonstrates that clonal chemodiversity in toxin composition cannot yet be effectively applied to define ecological niches or species interactions within local assemblages. Phylogenetic analysis of the ITS/5.8 rDNA, particularly when combined with secondary structure modeling, rather than only a comparison of LSU rDNA sequences, is a more powerful approach to identify cryptic speciation and to resolve species complexes within benthic dinoflagellate groups.

Exploring Deep-Sea Biodiversity in the Porcupine Bank (NE Atlantic) through Fish Integrative Taxonomy

This study combined morphological and molecular approaches to the species assignment of several rare or poorly known deep-water fishes caught between 549 and 1371 m depth during a Spanish bottom trawl survey in the Porcupine Bank, west of Ireland. The following fish species were identified: Nessorhamphus ingolfianus (Schmidt, 1912), Borostomias antarcticus (Lönnberg 1905), Scopelosaurus lepidus (Krefft and Maul 1955), Bathypterois dubius Vaillant, 1888, Evermannella balbo (Risso, 1820), Antimora rostrata (Günther, 1878), Melanonus zugmayeri Norman, 1930, Lyconus brachycolus Holt and Byrne, 1906; Paraliparis hystrix Merrett, 1983, Neocyttus helgae (Holt and Byrne, 1908); Platyberyx opalescens Zugmayer, 1911; Howella atlantica Post and Quéro, 1991, Lycodes terraenovae Collett, 1896 and Pseudoscopelus altipinnis Parr, 1933. The presence of L. brachycolus, P. opalescens and P. altipinnis is reported for the first time in the Bank. The DNA barcoding results were largely consistent with morphological identification in 10 species but four did not fit the current taxonomy, indicating cases of potential cryptic speciation, misidentification, synonymy or recent diversification. Among them, the results strongly suggest that P. garmani and P. hystrix are conspecific, making P. hystrix a junior synonym of P. garmani.

Intraspecific and Interspecific Phenotypic Differences Confirm the Absence of Cryptic Speciation in Triatoma sordida (Hemiptera, Triatominae)

Triatoma sordida is an endemic Chagas disease vector in South America, distributed in Brazil, Bolivia, Paraguay, and Uruguay. Chromosomal, molecular, isoenzimatic, and cuticular hydrocarbon pattern studies indicate cryptic speciation in T. sordida. Recently, T. rosai was described from specimens from Argentina initially characterized as T. sordida. Although several authors assume that the speciation process that supports this differentiation in T. sordida is the result of cryptic speciation, further morphological and/or morphometric studies are necessary to prove the application of this evolutionary event, because the only morphological intraspecific comparison performed in T. sordida is based on geometric morphometry and the only interspecific comparison made is between T. rosai and T. sordida from Brazil that evaluated morphological and morphometric differences. Based on this, morphological analyses of thorax and abdomen using Scanning Electron Microscopy and morphometric analyses of the head, thorax, and abdomen among T. sordida from Brazil, Bolivia, and Paraguay, as well as T. rosai, were performed to assess whether the evolutionary process responsible for variations is the cryptic speciation phenomenon. Morphological differences in the thorax and female external genitalia, as well as morphometric differences in the head, thorax, abdomen, pronotum, and scutellum structures, were observed. Based on this, the evolutionary process that supports, so far, these divergences observed for T. sordida populations/T. sordida subcomplex is not cryptic speciation. Moreover, we draw attention to the necessity for morphological/morphometric studies to correctly apply the cryptic species/speciation terms in triatomines.

DNA Barcoding for Scorpion Species from New Valley Governorate in Egypt Reveals Different Degrees of Cryptic Speciation and Species Misnaming

(1) Background: Scorpions (Arthropoda: Arachnida) represent a diverse group of invertebrates, accounting for a significant proportion of earth’s predators and ecosystems’ modulators. Surviving mostly in hardly reachable nests, and representing key hazards to human health, they attracted major interest for characterizing their eco-, morpho-, and genotypes. (2) Methods: Four scorpion species were collected from the New Valley governorate in Upper Egypt, where a high level of scorpionism and related neurological symptoms are found, that were Leiurus quinquestriatus, Androctonus amoreuxi, Orthochirus innesi, Buthacus leptochelys. They were DNA barcoded, genetically and phylogenetically analyzed through PCR amplification and sequencing of the mitochondrial cytochrome oxidase subunit 1 (COI) gene hypervariable 5′ region. (3) Results: New, morphologically authenticated scorpion barcodes could be added to the barcoding databases. However, several discrepancies and barcode database inadequacies could be revealed. Moreover, taxon-specific patterns for nitrogenous bases’ distribution could be identified, resulting in a significantly high percentage of COI barcode guanine in scorpionids, in comparison to araneids and opilions. (4) Conclusions: For a group of animals where both cryptic speciation and a high risk of human envenomation are evident, the findings of the current study strongly recommend continuous and comprehensive research efforts dealing with morphogenetic authentication for different species of scorpions.