Taxonomy and molecular phylogeny of the Neotropical genusAtlantoscia(Oniscidea, Philosciidae): DNA barcoding and description of two new species

Intra-island patterns of cryptic diversity within an oceanic island: Insights from the differentiation of Schizidium Verhoeff, 1901 (Oniscidea, Armadillidiidae) within Cyprus, with descriptions of two new species

Cyprus is a Mediterranean island of volcanic origin isolated for at least 5.3 Myr from surrounding continental areas. The present study focuses on the diversification of the isopod genus Schizidium within the island, including also specimens from surrounding continental areas. The genus Schizidium sensu lato is probably non monophyletic, comprising 26 species distributed from Greece to Iran. Up to date the only representative of the genus reported from Cyprus was Schizidium fissum. Aiming to investigate the patterns of genetic diversity within the focal island, to evaluate the morphology-based taxonomy of the species in the genus, and at the same time to explore phylogenetic relationships with mainland populations, we applied genome-wide ddRADseq as well as Sanger sequencing targeting three mitochondrial (16S, COI and 12S) and the nuclear NaK loci. Results of phylogenetic analyses support the existence of two distinct epigean Schizidium clades with well-defined geographic boundaries that conform to the known paleogeography of Cyprus, plus one endogean clade with restricted distribution within the island. Genetic data and morphology corroborate the assignment of this latter endogean clade to a new species, Schizidium myrrae n. sp. The two epigean clades are also considered as distinct species, one corresponding to the known S. fissum at the eastern part of the island (Pentadaktylos massif) and the other to the newly described S. christosi n. sp. distributed along the western part of the island (Troodos massif). Even though detailed examination of many specimens could not retrieve any morphological differences among representatives of these two clades, clado-chronological analysis indicates a long isolation between them, estimated at ∼ 9 Mya, as well as the sharing of a common ancestor with S. tiberianum from Israel at ∼ 15 Mya. Hence, we can consider these epigean Schizidium species as one more case of cryptic diversity on Cyprus, exhibiting similar patterns with the recently described case in the genus Armadillo.

The genus Armadillo Latreille, 1802 (Oniscidea, Armadillidae) from Cyprus, with descriptions of two new species

The present work aims to morphologically characterize the species of Armadillo from Cyprus. Moreover, two new species of the genus are described, A. konstantinoui sp. nov. from several places along the island, and A. karametae sp. nov. from Pafos region. The circum-Mediterranean species A. officinalis is also redescribed.

The efficiency of the COI gene as a DNA barcode and an overview of Orthoptera (Caelifera and Ensifera) sequences in the BOLD System

Orthoptera, among the oldest and most numerous insect lineages, is an excellent model for evolutionary studies but has numerous taxonomic problems. To mitigate these issues, the cytochrome c oxidase subunit I (COI), standardized with the DNA barcode for Metazoa, is increasingly used for specimen identification and species delimitation. We tested the performance of COI as a DNA barcode in Orthoptera, using two analyses based on intra- and interspecific distances, barcode gap and Probability of Correct Identification (PCI); and estimated species richness through Automatic Barcode Gap Discovery (ABGD) and Assemble Species by Automatic Partitioning (ASAP). We filtered all sequences of Orthoptera available in Barcode of Life Data System (BOLD) and used 11,605 COI sequences, covering 1,132 species, 226 genera, and 18 families. The overall average PCI was 73.86%. For 82.2% of genera the barcode gap boxplots were classified as good or intermediate, indicating that COI can be effective as a DNA barcode in Orthoptera, although with varying efficiency depending on the need for more information. ABGD and ASAP inferred species richness similar to labels informed by BOLD for the suborders Caelifera and Ensifera. The representation of Orthoptera in the BOLD database and the results of these analyses are discussed.

Diversification within an oceanic Mediterranean island: Insights from a terrestrial isopod

Understanding intra-island patterns of evolutionary divergence, including cases of cryptic diversity, is a crucial step towards deciphering speciation processes. Cyprus is an oceanic island isolated for at least 5.3 Mya from surrounding continental regions, while it remains unclear whether it was ever connected to the mainland, even during the Messinian Salinity Crisis. The terrestrial isopod species Armadillo officinalis, that is widespread across the Mediterranean, offers the opportunity to explore intra-island divergence patterns that might exhibit geographical structure related also to the region's known paleogeography. Genome-wide ddRADseq, as well as Sanger sequencing for four mitochondrial and three nuclear loci data were generated for this purpose. In total, 71 populations from Cyprus, neighbouring continental sites, i.e., Israel, Lebanon and Turkey, and other Mediterranean regions, i.e. Greece, Italy, and Tunisia, were included in the analysis. Phylogenetic reconstructions and population structure analyses support the existence of at least six genetically discrete groups across the study area. Five of these distinct genetic clades occur on Cyprus, four of which are endemic to the island and one is widely distributed along the circum-Mediterranean countries. The sixth clade is distributed in Israel. The closest evolutionary relationship of endemic Cypriot populations is with those from Israel, while the evolutionary clade that is present in countries all around the Mediterranean is very shallow. Cladochronological analyses date the origin of the species on the island at ∼6 Mya. Estimated f4 and D statistics as well as F_ST values indicate the genetic isolation between the populations sampled from Cyprus and surrounding continental areas, while there is evident gene flow among populations within the island. Species delimitation and population genetic metrics support the existence of three distinct taxonomic units across the study area, two of which occur on the island and correspond to the endemic clade and the widespread circum-Mediterranean one, respectively, while the third corresponds to Israel's clade. The islands' paleogeographic history and recent human activities seem to have shaped current patterns of genetic diversity in this group of species.

Surprisingly high genetic divergence of the mitochondrial DNA barcode fragment (COI) within Central European woodlice species (Crustacea, Isopoda, Oniscidea)

DNA barcoding has become the most popular approach for species identification in recent years. As part of the German Barcode of Life project, the first DNA barcode library for terrestrial and freshwater isopods from Germany is presented. The analyzed barcode library included 38 terrestrial (78% of the documented species of Germany) and five freshwater (63%) species. A total of 513 new barcodes was generated and 518 DNA barcodes were analyzed. This analysis revealed surprisingly high intraspecific genetic distances for numerous species, with a maximum of 29.4% for Platyarthrus hoffmannseggii Brandt, 1833. The number of BINs per species ranged from one (32 species, 68%) to a maximum of six for Trachelipus rathkii (Brandt, 1833). In spite of such high intraspecific variability, interspecific distances with values between 12.6% and 29.8% allowed a valid species assignment of all analyzed isopods. The observed high intraspecific distances presumably result from phylogeographic events, Wolbachia infections, atypical mitochondrial DNAs, heteroplasmy, or various combinations of these factors. Our study represents the first step in generating an extensive reference library of DNA barcodes for terrestrial and freshwater isopods for future molecular biodiversity assessment studies.

Barcoding a can of worms: testing cox1 performance as a DNA barcode of Nematoda

Accurate taxonomic identifications and species delimitations are a fundamental problem in biology. The complex taxonomy of Nematoda is primarily based on morphology, which is often dubious. DNA barcoding emerged as a handy tool to identify specimens and assess diversity, but its applications in Nematoda are incipient. We evaluated cytochrome c oxidase subunit I (cox1) efficiency as a DNA barcode for nematodes scrutinising 5241 sequences retrieved from BOLD and GenBank. The samples included genera with medical, agricultural, or ecological relevance: Anguillicola, Caenorhabditis, Heterodera, Meloidogyne, Onchocerca, Strongyloides, and Trichinella. We assessed cox1 performance through barcode gap and Probability of Correct Identification (PCI) analyses, and estimated species richness through Automatic Barcode Gap Discovery (ABGD). Each genus presented distinct gap ranges, mirroring the evolutionary diversity within Nematoda. Thus, to survey the diversity of the phylum, a careful definition of thresholds for lower taxonomic levels should be considered. PCIs were around 70% for both databases, highlighting operational biases and challenges in nematode taxonomy. ABGD inferred higher richness than the taxonomic labels informed by databases. The prevalence of specimen misidentifications and dubious species delimitations emphasise the value of integrative approaches to nematode taxonomy and systematics. Overall, cox1 is a relevant tool for integrative taxonomy of nematodes.

Molecular and taxonomic analyses in troglobiotic Alpioniscus (Illyrionethes) species from the Dinaric Karst (Isopoda: Trichoniscidae)

Species richness of terrestrial isopods is high in caves of the Dinaric Karst, which hosts ~10% of the world’s nominal oniscidean troglobionts. The most widespread taxon is the southern European genus Alpioniscus, which consists of two subgenera: Alpioniscus s.s. and Illyrionethes. Before this study, 14 nominal troglobiotic Illyrionethes taxa were recorded from the Dinaric Karst. Our molecular analyses using two mitochnodrial DNA (16S rRNA and COI) fragments and a nuclear gene (H3) fragment on all known Dinaric taxa identified three distinct lineages: strasseri-, heroldi- and magnus-lineage. Our results confirmed the validity of most nominal species. The exceptions are Alpioniscus balthasari, which consists of two different species including Alpioniscus iapodicus, and Alpioniscus heroldi, which is paraphyletic with respect to Alpioniscus bosniensis. The strasseri-lineage was highly supported by all phylogenetic methods used; therefore, we performed a detailed morphological analysis to distinguish and characterize the species of this group. New morphological characters, such as body part ratios, are proposed for future species identification. In addition, we redescribe three known species (Alpioniscus strasseri, Alpioniscus christiani and Alpioniscus balthasari) and describe two new ones (Alpioniscus hirci sp. nov. and Alpioniscus velebiticus sp. nov.). As a result, 15 nominal species of Illyrionethes are currently known from the Dinaric Karst.

How coexistence may influence life history: the reproductive strategies of sympatric congeneric terrestrial isopods (Crustacea, Oniscidea)

Patterns of allocation between reproduction, survival, and maintenance are what we call life history. By investigating the life-history strategy of sympatric species, we may understand how they are able to coexist, as different strategies are expected to evolve in species that occupy similar niche space. Terrestrial isopods are a group in which multiple species frequently inhabit the same area. Notably, they are usually infected by Wolbachia Hertig, 1936, a notorious manipulator of the hosts’ reproductive processes. Thus, the aim of this study was to analyze the investment in reproduction in three sympatric and closely related species of terrestrial isopods: Atlantoscia floridana (Van Name, 1940), Atlantoscia inflata Campos-Filho and Araujo, 2015, and Atlantoscia petronioi Campos-Filho, Contreira and Lopes-Leitzke, 2012, only the latter being infected with Wolbachia. We showed that the presence of the bacteria seems not to affect the fitness of A. petronioi, because there was no clear difference in the reproductive output of infected and noninfected individuals. On the other hand, we observed that the three species possess alternative life-history strategies; that is, they differ in how much they invest in maintenance (body size) and reproductive effort. Such differences probably facilitate the species coexistence, reducing the competition among them.

Integrative taxonomy reveals a new genus and new species of Philosciidae (Crustacea: Isopoda: Oniscidea) from the Neotropical region

Although new methods and data are conquering space in the field of taxonomy, such as integrative taxonomy, most terrestrial isopod species are still described based only on morphology. Species of the genus Atlantoscia Ferrara and Taiti, 1981 were the first and are the unique terrestrial isopods from the Neotropics for which a molecular phylogeny was already conducted. Previous results indicated that this genus could be paraphyletic, and a more detailed analysis would be required. Our aim was to reconstruct the phylogeny of Atlantoscia using mitochondrial and nuclear markers and test its monophyly by integrating molecular and morphological data. We observed that, indeed, Atlantoscia is paraphyletic. Atlantoscia ituberasensis Campos-Filho, Lisboa and Araujo, 2013 and Atlantoscia rubromarginata Araujo and Leistikow, 1999 were placed in a new genus of terrestrial isopods, Paratlantoscia gen. nov., together with a new species described in the present study, Paratlantoscia robusta sp. nov. The new genus is defined by the presence of specialized respiratory areas in the pleopod exopods and its validity is highly corroborated by molecular analyses and by biogeographic information. This study highlights the importance of multiple and complementary perspectives as a way to improve the quality of species hypothesis and associated descriptions.

New species and new records of terrestrial isopods (Crustacea, Isopoda, Oniscidea) from Brazil

ABSTRACT. A large collection of terrestrial isopods from different Brazilian regions was examined. Two new species of Amazoniscus Lemos de Castro, 1967 (Scleropactidae) are described: A. zimmeri Campos-Filho, Montesanto & Araujo sp. nov. from the state of Pará and A. schmidti Campos-Filho, Montesanto & Taiti sp. nov. from the state of Minas Gerais. Pseudotyphloscia alba (Dollfus, 1898) (Philosciidae) is firstly recorded from Brazil. The systematic position of Venezillo tuberosus (Budde-Lund, 1904) is discussed and transferred to Ctenorillo Verhoeff, 1942. Androdeloscia lejeunei (Lemos de Castro & Souza, 1986) and Diploexochus echinatus Brandt, 1833 from the state of Pará, are redescribed.