Community assembly and metaphylogeography of soil biodiversity: insights from haplotype-level community DNA metabarcoding within an oceanic island

Most of our understanding of island diversity comes from the study of aboveground systems, while the patterns and processes of diversification and community assembly for belowground biotas remain poorly understood. Here we take advantage of a relatively young and dynamic oceanic island to advance our understanding of eco-evolutionary processes driving community assembly within soil mesofauna. Using whole organism community DNA (wocDNA) metabarcoding and the recently developed metaMATE pipeline, we have generated spatially explicit and reliable haplotype-level DNA sequence data for soil mesofaunal assemblages sampled across the four main habitats within the island of Tenerife. Community ecological and metaphylogeographic analyses have been performed at multiple levels of genetic similarity, from haplotypes to species and supraspecific groupings. Broadly consistent patterns of local-scale species richness across different insular habitats have been found, whereas local insular richness is lower than in continental settings. Our results reveal an important role for niche conservatism as a driver of insular community assembly of soil mesofauna, with only limited evidence for habitat shifts promoting diversification. Furthermore, support is found for a fundamental role of habitat in the assembly of soil mesofauna, where habitat specialism is mainly due to colonisation and the establishment of preadapted species. Hierarchical patterns of distance decay at the community level and metaphylogeographical analyses support a pattern of geographic structuring over limited spatial scales, from the level of haplotypes through to species and lineages, as expected for taxa with strong dispersal limitations. Our results demonstrate the potential for wocDNA metabarcoding to advance our understanding of biodiversity.

Systematic Revision of a New Butterfly Genus, Cisandina Nakahara & Espeland, n. gen., with Descriptions of Three New Taxa (Lepidoptera: Nymphalidae: Satyrinae)

We here establish a new genus in the nymphalid butterfly subtribe Euptychiina, Cisandina Nakahara & Espeland, n. gen. to harbor five species hitherto placed within two polyphyletic genera, namely Magneuptychia Forster, 1964 and Euptychoides Forster, 1964. We compiled data from over 350 specimens in 17 public and private collections, as well as DNA sequence data for all relevant species, to revise the species-level classification of this new genus. According to our multi-locus molecular phylogeny estimated with the maximum likelihood approach, Cisandina lean. comb., Cisandina philippan. comb. & reinst. stat., Cisandina fidan. comb., Cisandina sanmarcosn. comb., and Cisandina trinitensisn. comb. are proposed as new taxonomic combinations, since these species are distantly related to the type species of Magneuptychia and Euptychoides and cannot reasonably be accommodated in any other genus. Lectotypes are designated for Papilio lea Cramer, 1777, Papilio junia Cramer, 1780, Euptychia philippa Butler, 1867, and Eupytchia fida Weymer, 1911. Two new species of Cisandinan. gen. are named and described herein, C. esmeralda Nakahara & Barbosa, n. sp. and C. castanya Lamas & Nakahara, n. sp., increasing the described species diversity of the genus to seven. The immature stages of C. castanyan. sp. and C. philippan. comb. & reinst. stat. are documented along with their natural hostplants, representing the first two species of the genus with known life history information. We describe a new subspecies, Cisandina fida directa Nakahara & Willmott, n. ssp., based on a limited number of specimens from southern Ecuador and central Peru. We were unable to obtain genetic data for the nominate race of C. fidan. comb., and thus, this taxonomic hypothesis is currently based solely on phenotypic characters.

Just a Fragment of Undescribed Diversity: Twenty New Oriental and Palearctic Species of Sciaroidea (Diptera), including DNA Sequence Data and Two New Fossil Genera

The following 17 extant new species of Sciaroidea (Diptera: Bibionomorpha) are described: Bolitophila nikolae Ševčík sp. nov. (Bolitophilidae, Taiwan), Catocha jingfui sp. nov. (Cecidomyiidae, Taiwan), Catocha manmiaoe sp. nov. (Cecidomyiidae, Taiwan), Catocha shengfengi sp. nov. (Cecidomyiidae, Taiwan), Planetella taiwanensis sp. nov. (Cecidomyiidae, Taiwan), Diadocidia pseudospinusola sp. nov. (Diadocidiidae, Taiwan), Asioditomyia bruneicola sp. nov. (Ditomyiidae, Brunei), Asioditomyia lacii sp. nov. (Ditomyiidae, Taiwan), Ditomyia asiatica sp. nov. (Ditomyiidae, Thailand), Chetoneura davidi sp. nov. (Keroplatidae, Brunei), Euceroplatus mantici sp. nov. (Keroplatidae, Thailand), Setostylus fangshuoi sp. nov. (Keroplatidae, Taiwan), Platyceridion yunfui sp. nov. (Keroplatidae, Hainan), Terocelion adami sp. nov. (Keroplatidae, Taiwan), Hadroneura martini sp. nov. (Mycetophilidae, Taiwan), Paratinia furcata sp. nov. (Mycetophilidae, Czech Republic, Slovakia), and Nepaletricha sikorai sp. nov. (Sciaroidea incertae sedis, Thailand). Two new genera are described from the mid-Cretaceous Burmese amber, Burmasymmerus gen. nov. (Ditomyiidae, type species Burmasymmerus korneliae sp. nov., including also B. wieslawi sp. nov.), representing the first record of the family Ditomyiidae from the Mesozoic, and Burmatricha gen. nov. (Sciaroidea incertae sedis, type species Burmatricha mesozoica sp. nov.). Molecular phylogeny of Ditomyiidae, based on two DNA markers (28S, COI), as well as that of Catocha Haliday, 1833, based on the mitochondrial COI and 16S fragments, are also presented.

New species of Nearctic oak gall wasps (Hymenoptera: Cynipidae, Cynipini)

Twenty nine new species of cynipid oak gall wasps from the Nearctic region (America north of Mexico) are described: Andricus archboldi Melika & Abrahamson, sp. nov., A. catalinensis Melika, Nicholls & Stone, sp. nov., A. chapmanii Melika & Abrahamson, sp. nov., A. chiricahuensis Melika, Nicholls & Stone, sp. nov., A. coconinoensis Melika, Nicholls & Stone, sp. nov., A. columbiensis Melika, Nicholls & Stone, sp. nov., A. cooki Melika, Nicholls & Stone, sp. nov., A. fitzpatricki Melika & Abrahamson, sp. nov., A. highlandensis Melika, Nicholls & Stone, sp. nov., A. mellificus Nicholls, Stone & Melika, sp. nov., A. menkei Melika & Abrahamson, sp. nov., A. mogollonensis Melika, Nicholls & Stone, sp. nov., A. nichollsi Melika & Stone, sp. nov., A. schickae Nicholls, Melika & Stone, sp. nov., A. torreyaensis Melika & Abrahamson, sp. nov., A. williami Melika, Nicholls & Stone, sp. nov., Antron lovellae Melika, Nicholls & Stone, sp. nov., A.tomkursari Melika, Nicholls & Stone, sp. nov., Dryocosmus archboldi Melika & Abrahamson, sp. nov., Loxaulus virginianae Melika & Buss, sp. nov., Neuroterus alexandrae Nicholls & Melika, sp. nov., N. aliceae Melika, Nicholls & Stone, sp. nov., N. bussae Melika & Nicholls, sp. nov., N. oblongifoliae Nicholls, Stone & Melika, sp. nov., N. quaili Melika, Nicholls & Stone, sp. nov., N. rosieae Melika, Nicholls & Stone, sp. nov., N. stonei Melika & Nicholls, sp. nov., Zapatella abrahamsoni Melika, sp. nov., Z. brooksvillei Melika & Abrahamson, sp. nov.. Alternate asexual and sexual generations are described for four species, Andricus archboldi Melika & Abrahamson, sp. nov., A. fitzpatricki Melika & Abrahamson, sp. nov., A. schickae Nicholls, Melika & Stone, sp. nov., Neuroterus aliceae Melika, Nicholls & Stone, sp. nov.. Descriptions, diagnoses, plus information on biology and host associations are given for all new species. All taxa are supported by morphological data; matching of generations is established using DNA sequence data. We also demonstrate that Neuroterus niger var. alimas Kinsey should be considered as a nomen dubium.

Two new Cypridopsinae Kaufmann, 1900 (Crustacea, Ostracoda) from southern Africa

Two new Cypridopsinae ostracods, Potamocypris meissnerisp. nov. and Sarscypridopsis harundinetisp. nov. are described. Both were found only as asexual (all-female) populations in temporary waters of southern Africa. Potamocypris meissneri was collected from a small pan in the North-West Province of South Africa. It is approximately 0.5 mm long and belongs to the species group with long swimming setae on the second antennae. However, the species has a somewhat isolated position in the genus owing to the conspicuously reticulated carapace, which is furthermore densely covered by prominent conuli with normal pores carrying long sensilla, as well as to the wide anterior and posterior flanges on the left valve. To allow identification of the new species in relation to its closest congeners, a key to the species of the genus Potamocypris Brady, 1870 from southern Africa is provided. The genus Sarscypridopsis McKenzie, 1977 mostly has an Afrotropical distribution with only few species occurring in other regions. Sarscypridopsis harundineti was collected from floodplains of the outskirts of the Okavango Delta in Botswana. It is approximately 0.4 mm long and can be distinguished from congeners mainly by the smaller and more oval-shaped valves. We conclude that southern African Cypridopsinae urgently need integrated taxonomic revision, by means of both morphological characters and DNA-sequence data.

FUSARIUM-ID v.3.0: An updated, downloadable resource for Fusarium species identification

Species within Fusarium are of global agricultural, medical, and food/feed safety concern and have been extensively characterized. However, accurate identification of species is challenging and usually requires DNA sequence data. FUSARIUM-ID (http://isolate.fusariumdb.org/) is a publicly available database designed to support the identification of Fusarium species using sequences of multiple phylogenetically informative loci, especially the highly informative ~680 bp 5' portion of the translation elongation factor 1-alpha (TEF1) gene that has been adopted as the primary barcoding locus in the genus. However, FUSARIUM-ID v.1.0 and 2.0 had several limitations, including inconsistent metadata annotation for the archived sequences and poor representation of some species complexes and marker loci. Here, we present FUSARIUM-ID v.3.0, which provides the following improvements: (i) additional and updated annotation of metadata for isolates associated with each sequence, (ii) expanded taxon representation in the TEF1 sequence database, (iii) availability of the sequence database as a downloadable file to enable local BLAST queries, and (iv) a tutorial file for users to perform local BLAST searches using either freely-available software, such as SequenceServer, BLAST+ executable in the command line, and Galaxy, or the proprietary Geneious software. FUSARIUM-ID will be updated on a regular basis by archiving sequences of TEF1 and other loci from newly identified species and greater in-depth sampling of currently recognized species.

Biogeographic evidence supports the Old Amazon hypothesis for the formation of the Amazon fluvial system

The Amazon has high biodiversity, which has been attributed to different geological events such as the formation of rivers. The Old and Young Amazon hypotheses have been proposed regarding the date of the formation of the Amazon basin. Different studies of historical biogeography support the Young Amazon model, however, most studies use secondary calibrations or are performed at the population level, preventing evaluation of a possible older formation of the Amazon basin. Here, we evaluated the fit of molecular phylogenetic and biogeographic data to previous models regarding the age of formation of the Amazon fluvial system. We reconstructed time-calibrated molecular phylogenies through Bayesian inference for six taxa belonging to Amphibia, Aves, Insecta and Mammalia, using both, nuclear and mitochondrial DNA sequence data and fossils as calibration points, and explored priors for both data sources. We detected the most plausible vicariant barriers for each phylogeny and performed an ancestral reconstruction analysis using areas bounded by major Amazonian rivers, and therefore, evaluated the effect of different dispersal rates over time based on geological and biogeographical information. The majority of the genes analyzed fit a relaxed clock model. The log normal distribution fits better and leads to more precise age estimations than the exponential distribution. The data suggested that the first dispersals to the Amazon basin occurred to Western Amazonia from 16.2–10.4 Ma, and the taxa covered most of the areas of the Amazon basin between 12.2–6.2 Ma. Additionally, regardless of the method, we obtained evidence for two rivers: Tocantins and Madeira, acting as vicariant barriers. Given the molecular and biogeographical analyses, we found that some taxa were fitted to the “Old Amazon” model.

trioPhaser: using Mendelian inheritance logic to improve genomic phasing of trios

Background When analyzing DNA sequence data of an individual, knowing which nucleotide was inherited from each parent can be beneficial when trying to identify certain types of DNA variants. Mendelian inheritance logic can be used to accurately phase (haplotype) the majority (67–83%) of an individual's heterozygous nucleotide positions when genotypes are available for both parents (trio). However, when all members of a trio are heterozygous at a position, Mendelian inheritance logic cannot be used to phase. For such positions, a computational phasing algorithm can be used. Existing phasing algorithms use a haplotype reference panel, sequencing reads, and/or parental genotypes to phase an individual; however, they are limited in that they can only phase certain types of variants, require a specific genotype build, require large amounts of storage capacity, and/or require long run times. We created trioPhaser to address these challenges. Results trioPhaser uses gVCF files from an individual and their parents as initial input, and then outputs a phased VCF file. Input trio data are first phased using Mendelian inheritance logic. Then, the positions that cannot be phased using inheritance information alone are phased by the SHAPEIT4 phasing algorithm. Using whole-genome sequencing data of 52 trios, we show that trioPhaser, on average, increases the total number of phased positions by 21.0% and 10.5%, respectively, when compared to the number of positions that SHAPEIT4 or Mendelian inheritance logic can phase when either is used alone. In addition, we show that the accuracy of the phased calls output by trioPhaser are similar to linked-read and read-backed phasing. Conclusion trioPhaser is a containerized software tool that uses both Mendelian inheritance logic and SHAPEIT4 to phase trios when gVCF files are available. By implementing both phasing methods, more variant positions are phased compared to what either method is able to phase alone.

Deep phylogeographic splits but no taxonomic structure in the disjointly distributed Draba pacheri (Brassicaceae), a subendemic of the Eastern Alps

Draba (Brassicaeae), a model group for diversification and evolution in Arctic and mountain habitats, is taxonomically challenging and many of its species are insufficiently investigated. One such species is D. pacheri, an endemic of the eastern European Alps and the western Carpathians (here presumably extinct). Several hypotheses exist with respect to the phylogenetic position and the taxonomy of this species, but none of these has ever been tested using molecular data. In this article we examine (i) DNA sequence data to assess the phylogenetic position of D. pacheri within the genus and (ii) AFLP fingerprint data as well as morphometric data to address whether this species can be divided taxonomically into species or subspecies. DNA sequence data firmly place D. pacheri within the Core Draba Group III, whose internal relationships are, however, insufficiently resolved to precisely identify the closest relative of D. pacheri. AFLP data identify several genetically divergent lineages corresponding to geographically distinct regions. Although these lineages are congruent with hypotheses distinguishing either two species (D. pacheri s. str., D. norica) or one species with several subspecies, the lack of clear morphological separation, both with respect to the entire set of traits and single presumably diagnostic characters such as trichome morphology, renders recognition of a single species D. pacheri, as suggested previously, the best taxonomic solution. The deep and geographically strongly structured splits of D. pacheri likely are the result of isolation in several Pleistocene refugia and warrant that conservation efforts should involve populations from each of the main geographic subgroups.