Metazoa-level USCOs as markers in species delimitation and classification.

Metazoa-level universal single-copy orthologs (mzl-USCOs) are universally applicable markers for DNA taxonomy in animals that can replace or supplement single-gene barcodes. Previously, mzl-USCOs from target enrichment data were shown to reliably distinguish species. Here, we tested whether USCOs are an evenly distributed, representative sample of a given metazoan genome and therefore able to cope with past hybridization events and incomplete lineage sorting. This is relevant for coalescent-based species delimitation approaches, which critically depend on the assumption that the investigated loci do not exhibit autocorrelation due to physical linkage. Based on 239 chromosome-level assembled genomes, we confirmed that mzl-USCOs are genetically unlinked for practical purposes and a representative sample of a genome in terms of reciprocal distances between USCOs on a chromosome and of distribution across chromosomes. We tested the suitability of mzl-USCOs extracted from genomes for species delimitation and phylogeny in four case studies: Anopheles mosquitos, Drosophila fruit flies, Heliconius butterflies and Darwin's finches. In almost all instances, USCOs allowed delineating species and yielded phylogenies that corresponded to those generated from whole genome data. Our phylogenetic analyses demonstrate that USCOs may complement single-gene DNA barcodes and provide more accurate taxonomic inferences. Combining USCOs from sources that used different versions of ortholog reference libraries to infer marker orthology may be challenging and, at times, impact taxonomic conclusions. However, we expect this problem to become less severe as the rapidly growing number of reference genomes provides a better representation of the number and diversity of organismal lineages.

Combining morphological and genomic evidence to resolve species diversity and study speciation processes of the Pallenopsis patagonica (Pycnogonida) species complex.

BACKGROUND: Pallenopsis patagonica (Hoek, 1881) is a morphologically and genetically variable sea spider species whose taxonomic classification is challenging. Currently, it is considered as a species complex including several genetic lineages, many of which have not been formally described as species. Members of this species complex occur on the Patagonian and Antarctic continental shelves as well as around sub-Antarctic islands. These habitats have been strongly influenced by historical large-scale glaciations and previous studies suggested that communities were limited to very few refugia during glacial maxima. Therefore, allopatric speciation in these independent refugia is regarded as a common mechanism leading to high biodiversity of marine benthic taxa in the high-latitude Southern Hemisphere. However, other mechanisms such as ecological speciation have rarely been considered or tested. Therefore, we conducted an integrative morphological and genetic study on the P. patagonica species complex to i) resolve species diversity using a target hybrid enrichment approach to obtain multiple genomic markers, ii) find morphological characters and analyze morphometric measurements to distinguish species, and iii) investigate the speciation processes that led to multiple lineages within the species complex. RESULTS: Phylogenomic results support most of the previously reported lineages within the P. patagonica species complex and morphological data show that several lineages are distinct species with diagnostic characters. Two lineages are proposed as new species, P. aulaeturcarum sp. nov. Dömel & Melzer, 2019 and P. obstaculumsuperavit sp. nov. Dömel, 2019, respectively. However, not all lineages could be distinguished morphologically and thus likely represent cryptic species that can only be identified with genetic tools. Further, morphometric data of 135 measurements showed a high amount of variability within and between species without clear support of adaptive divergence in sympatry. CONCLUSIONS: We generated an unprecedented molecular data set for members of the P. patagonica sea spider species complex with a target hybrid enrichment approach, which we combined with extensive morphological and morphometric analyses to investigate the taxonomy, phylogeny and biogeography of this group. The extensive data set enabled us to delineate species boundaries, on the basis of which we formally described two new species. No consistent evidence for positive selection was found, rendering speciation in allopatric glacial refugia as the most likely model of speciation.

Phylogenomics of the longitarsal Colossendeidae: The evolutionary history of an Antarctic sea spider radiation.

Sea spiders (Pycnogonida) constitute a group of marine benthic arthropods that has a particularly high species diversity in the Southern Ocean. The "longitarsal" group of the sea spider family Colossendeidae is especially abundant in this region. However, this group also includes some representatives from other oceans, which raises the question where the group originates from. Therefore, we here investigated the phylogeny of the group with a hybrid enrichment approach that yielded a dataset of 1607 genes and over one million base pairs. We obtained a well-resolved phylogeny of the group, which is mostly consistent with morphological data. The data support an Antarctic origin of the longitarsal Colossendeidae and multiple dispersal events to other regions, which occurred at different timescales. This scenario is consistent with evidence found in other groups of marine invertebrates and highlights the role of the Southern Ocean as a source for non-Antarctic biota, especially of the deep sea. Our results suggest an initially slow rate of diversification followed by a more rapid radiation possibly correlated with the mid-Miocene cooling of Antarctica, similar to what is found in other taxa.

Feeding ecology in sea spiders (Arthropoda: Pycnogonida): what do we know?

Sea spiders (Pycnogonida) are a widespread and phylogenetically important group of marine arthropods. However, their biology remains understudied, and detailed information about their feeding ecology is difficult to find. Observations on pycnogonid feeding are scattered in the literature, often in older sources written in various languages, and have never been comprehensively summarized. Here we provide an overview of all information on feeding in pycnogonids that we have been able to find and review what is known on feeding specializations and preferences in the various pycnogonid taxa. We deduce general findings where possible and outline future steps necessary to gain a better understanding of the feeding ecology of one of the world's most bizarre animal taxa.

The mitochondrial genomes of the caddisflies Sericostoma personatum and Thremma gallicum (Insecta: Trichoptera).

The mitochondrial genomes of the caddisfly species Sericostoma personatum and Thremma gallicum were sequenced on a 454 FLX and Illumina MiSeq platform, respectively. Reads were assembled de novo and remaining gaps in the S. personatum mitogenome closed by Sanger sequencing. The lengths of the assembled mitogenomes were 15,260 bp and 15,343 bp for S. personatum and T. gallicum, respectively. Both mitogenomes contained all 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and the control region. The mitochondrial gene order of both caddisflies is identical with the typical insect gene order. These are the third and fourth published mitogenomes of the order Trichoptera of two formerly unexplored families and thus will be useful in future phylogenetic analysis.

Regional differentiation and extensive hybridization between mitochondrial clades of the Southern Ocean giant sea spider Colossendeis megalonyx.

Assessing the enormous diversity of Southern Ocean benthic species and their evolutionary histories is a central task in the era of global climate change. Based on mitochondrial markers, it was recently suggested that the circumpolar giant sea spider Colossendeis megalonyx comprises a complex of at least six cryptic species with mostly small and non-overlapping distribution ranges. Here, we expand the sampling to include over 500 mitochondrial COI sequences of specimens from around the Antarctic. Using multiple species delimitation approaches, the number of distinct mitochondrial OTUs increased from six to 15-20 with our larger dataset. In contrast to earlier studies, many of these clades show almost circumpolar distributions. Additionally, analysis of the nuclear internal transcribed spacer region for a subset of these specimens showed incongruence between nuclear and mitochondrial results. These mito-nuclear discordances suggest that several of the divergent mitochondrial lineages can hybridize and should not be interpreted as cryptic species. Our results suggest survival of C. megalonyx during Pleistocene glaciations in multiple refugia, some of them probably located on the Antarctic shelf, and emphasize the importance of multi-gene datasets to detect the presence of cryptic species, rather than their inference based on mitochondrial data alone.

Exploring Pandora's box: potential and pitfalls of low coverage genome surveys for evolutionary biology.

High throughput sequencing technologies are revolutionizing genetic research. With this "rise of the machines", genomic sequences can be obtained even for unknown genomes within a short time and for reasonable costs. This has enabled evolutionary biologists studying genetically unexplored species to identify molecular markers or genomic regions of interest (e.g. micro- and minisatellites, mitochondrial and nuclear genes) by sequencing only a fraction of the genome. However, when using such datasets from non-model species, it is possible that DNA from non-target contaminant species such as bacteria, viruses, fungi, or other eukaryotic organisms may complicate the interpretation of the results. In this study we analysed 14 genomic pyrosequencing libraries of aquatic non-model taxa from four major evolutionary lineages. We quantified the amount of suitable micro- and minisatellites, mitochondrial genomes, known nuclear genes and transposable elements and searched for contamination from various sources using bioinformatic approaches. Our results show that in all sequence libraries with estimated coverage of about 0.02-25%, many appropriate micro- and minisatellites, mitochondrial gene sequences and nuclear genes from different KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways could be identified and characterized. These can serve as markers for phylogenetic and population genetic analyses. A central finding of our study is that several genomic libraries suffered from different biases owing to non-target DNA or mobile elements. In particular, viruses, bacteria or eukaryote endosymbionts contributed significantly (up to 10%) to some of the libraries analysed. If not identified as such, genetic markers developed from high-throughput sequencing data for non-model organisms may bias evolutionary studies or fail completely in experimental tests. In conclusion, our study demonstrates the enormous potential of low-coverage genome survey sequences and suggests bioinformatic analysis workflows. The results also advise a more sophisticated filtering for problematic sequences and non-target genome sequences prior to developing markers.

The mitochondrial genome of Colossendeis megalonyx supports a basal position of Colossendeidae within the Pycnogonida.

We present the almost complete (16,007 bp) mitochondrial genome of a Colossendeis megalonyx specimen from the Southern Ocean and discuss gene order and tRNA structure in a comparative phylogenetic context. Our data suggest a basal position of the colossendeid lineage corroborating earlier phylogenetic studies but disagreeing with results of a recently published study that supported a highly derived sister-group relationship of Colossendeidae and Nymphonidae. Our results, together with BLAST searches and phylogenetic comparisons, indicate that the specimen presented as Colossendeis sp. in a series of recent studies had been misidentified. It has now been identified as a nymphonid species.