Information dropout patterns in restriction site associated DNA phylogenomics and a comparison with multilocus Sanger data in a species-rich moth genus

A rapid shift from traditional Sanger sequencing-based molecular methods to the phylogenomic approach with large numbers of loci is underway. Among phylogenomic methods, restriction site associated DNA (RAD) sequencing approaches have gained much attention as they enable rapid generation of up to thousands of loci randomly scattered across the genome and are suitable for nonmodel species. RAD data sets however suffer from large amounts of missing data and rapid locus dropout along with decreasing relatedness among taxa. The relationship between locus dropout and the amount of phylogenetic information retained in the data has remained largely uninvestigated. Similarly, phylogenetic hypotheses based on RAD have rarely been compared with phylogenetic hypotheses based on multilocus Sanger sequencing, even less so using exactly the same species and specimens. We compared the Sanger-based phylogenetic hypothesis (8 loci; 6172 bp) of 32 species of the diverse moth genus Eupithecia (Lepidoptera, Geometridae) to that based on double-digest RAD sequencing (3256 loci; 726,658 bp). We observed that topologies were largely congruent, with some notable exceptions that we discuss. The locus dropout effect was strong. We demonstrate that number of loci is not a precise measure of phylogenetic information since the number of single-nucleotide polymorphisms (SNPs) may remain low at very shallow phylogenetic levels despite large numbers of loci. As we hypothesize, the number of SNPs and parsimony informative SNPs (PIS) is low at shallow phylogenetic levels, peaks at intermediate levels and, thereafter, declines again at the deepest levels as a result of decay of available loci. Similarly, we demonstrate with empirical data that the locus dropout affects the type of loci retained, the loci found in many species tending to show lower interspecific distances than those shared among fewer species. We also examine the effects of the numbers of loci, SNPs, and PIS on nodal bootstrap support, but could not demonstrate with our data our expectation of a positive correlation between them. We conclude that RAD methods provide a powerful tool for phylogenomics at an intermediate phylogenetic level as indicated by its broad congruence with an eight-gene Sanger data set in a genus of moths. When assessing the quality of the data for phylogenetic inference, the focus should be on the distribution and number of SNPs and PIS rather than on loci.Peer reviewe

Taxonomy and nomenclature of some Fennoscandian Sawflies, with descriptions of two new species (Hymenoptera, Symphyta)

While working on an identification guide to the sawflies of Fennoscandia, we encountered numerous taxonomic problems, for some of which we present solutions. Dicrostema Benson, 1952 is a new synonym of Phymatoceropsis Rohwer, 1916, and not congeneric with Paracharactus MacGillivray, 1908. Two species occurring in Europe are transferred to Phymatoceropsis. Dolerus aericepsellus Heidemaa and Mutanen sp. nov. and Heptamelus viitasaarii Liston, Mutanen and Prous sp. nov. are described from Finland. Abia brevicornis Leach, 1817 nom. rev. is the valid name of Abia nitens auct. nec Linnaeus, and Abia nitens (Linnaeus, 1758) is the valid name for what has recently been called Abia sericea (Linnaeus, 1767). Tenthredo haemorrhoidalis Fabricius, 1781 is treated as an unplaced species of Hymenoptera, possibly Ichneumonoidea. Calameuta variabilis (Mocsáry, 1886) is the valid name of the species recently generally called C. haemorrhoidalis. Claremontia confusa (Konow, 1886) sp. rev. and Claremontia brevicornis (Brischke, 1883) are distinct species. Dolerus coracinus (Klug, 1818) is the valid name for D. anthracinus auct. Dolerus anthracinus (Klug, 1818) is a valid species similar to D. nitens Zaddach, 1859. Dolerus coruscans Konow, 1890 sp. rev. is a valid species. Dolerus junci (Stephens, 1835) is the valid name for Dolerus cothurnatus auct. Dolerus timidus (Klug, 1818) sp. rev. is distinguished from the similar D. pratensis (Linnaeus, 1758). A neotype is designated for Astatus punctatus Klug, 1803. Lectotypes are designated for 39 nominal species. 29 species group names are new junior synonyms. We present data on some species recently collected for the first time in Finland, including first records for the Palaearctic and West Palaearctic

Climate shapes the spatiotemporal variation in color morph diversity and composition across the distribution range of Chrysomela lapponica leaf beetle

Color polymorphism offers rich opportunities for studying the eco-evolutionary mechanisms that drive the adaptations of local populations to heterogeneous and changing environments. We explored the color morph diversity and composition in a Chrysomela lapponica leaf beetle across its entire distribution range to test the hypothesis that environmental and climatic variables shape spatiotemporal variation in the phenotypic structure of a polymorphic species. We obtained information on 13 617 specimens of this beetle from museums, private collections, and websites. These specimens (collected from 1830-2020) originated from 959 localities spanning 33 degrees latitude, 178 degrees longitude, and 4200 m altitude. We classified the beetles into five color morphs and searched for environmental factors that could explain the variation in the level of polymorphism (quantified by the Shannon diversity index) and in the relative frequencies of individual color morphs. The highest level of polymorphism was found at high latitudes and altitudes. The color morphs differed in their climatic requirements; composition of colour morphs was independent of the geographic distance that separated populations but changed with collection year, longitude, mean July temperature and between-year temperature fluctuations. The proportion of melanic beetles, in line with the thermal melanism hypothesis, increased with increasing latitude and altitude and decreased with increasing climate seasonality. Melanic morph frequencies also declined during the past century, but only at high latitudes and altitudes where recent climate warming was especially strong. The observed patterns suggest that color polymorphism is especially advantageous for populations inhabiting unpredictable environments, presumably due to the different climatic requirements of coexisting color morphs

Climate shapes the spatiotemporal variation in color morph diversity and composition across the distribution range of Chrysomela lapponica leaf beetle

Color polymorphism offers rich opportunities for studying the eco-evolutionary mechanisms that drive the adaptations of local populations to heterogeneous and changing environments. We explored the color morph diversity and composition in a Chrysomela lapponica leaf beetle across its entire distribution range to test the hypothesis that environmental and climatic variables shape spatiotemporal variation in the phenotypic structure of a polymorphic species. We obtained information on 13 617 specimens of this beetle from museums, private collections, and websites. These specimens (collected from 1830-2020) originated from 959 localities spanning 33 degrees latitude, 178 degrees longitude, and 4200 m altitude. We classified the beetles into five color morphs and searched for environmental factors that could explain the variation in the level of polymorphism (quantified by the Shannon diversity index) and in the relative frequencies of individual color morphs. The highest level of polymorphism was found at high latitudes and altitudes. The color morphs differed in their climatic requirements; composition of colour morphs was independent of the geographic distance that separated populations but changed with collection year, longitude, mean July temperature and between-year temperature fluctuations. The proportion of melanic beetles, in line with the thermal melanism hypothesis, increased with increasing latitude and altitude and decreased with increasing climate seasonality. Melanic morph frequencies also declined during the past century, but only at high latitudes and altitudes where recent climate warming was especially strong. The observed patterns suggest that color polymorphism is especially advantageous for populations inhabiting unpredictable environments, presumably due to the different climatic requirements of coexisting color morphs

A molecular-based identification resource for the arthropods of Finland

Publisher Copyright: © 2021 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.To associate specimens identified by molecular characters to other biological knowledge, we need reference sequences annotated by Linnaean taxonomy. In this study, we (1) report the creation of a comprehensive reference library of DNA barcodes for the arthropods of an entire country (Finland), (2) publish this library, and (3) deliver a new identification tool for insects and spiders, as based on this resource. The reference library contains mtDNA COI barcodes for 11,275 (43%) of 26,437 arthropod species known from Finland, including 10,811 (45%) of 23,956 insect species. To quantify the improvement in identification accuracy enabled by the current reference library, we ran 1000 Finnish insect and spider species through the Barcode of Life Data system (BOLD) identification engine. Of these, 91% were correctly assigned to a unique species when compared to the new reference library alone, 85% were correctly identified when compared to BOLD with the new material included, and 75% with the new material excluded. To capitalize on this resource, we used the new reference material to train a probabilistic taxonomic assignment tool, FinPROTAX, scoring high success. For the full-length barcode region, the accuracy of taxonomic assignments at the level of classes, orders, families, subfamilies, tribes, genera, and species reached 99.9%, 99.9%, 99.8%, 99.7%, 99.4%, 96.8%, and 88.5%, respectively. The FinBOL arthropod reference library and FinPROTAX are available through the Finnish Biodiversity Information Facility (www.laji.fi) at https://laji.fi/en/theme/protax. Overall, the FinBOL investment represents a massive capacity-transfer from the taxonomic community of Finland to all sectors of society.Peer reviewe

Genital variation in moths—evolutionary and systematic perspectives

Abstract genital characteristics have peculiar morphological patterns. They show great divergence between species. At the same time, they are assumed to vary little within species by taxonomists who frequently use genital features to delimit species. I studied moth (Lepidoptera) genital size and shape variation within and between species. I also tested hypotheses proposed to explain rapid genital diversification among species. Studies were carried out using traditional distance measurement morphometrics and modern geometric morphometrics. Several moth species were analyzed. d that genital structures show variation that in closely related species may show structural overlap. More surprisingly, the amount of variation in internal genitalia was equal to non-genital traits. These and some other findings are against the predictions of the lock-and-key hypothesis, which suggests that genital differences form a mechanical isolation system between species. Meanwhile, the findings are in good accordance with the various mechanisms of the sexual selection hypothesis. I found that external genital traits express varying amounts of variability. However, both external and internal genitalia consistently show small variation in size so that large individuals have disproportionately small genitalia and vice versa. This finding is consistent with the lock-and-key theory, but also with the cryptic female choice hypothesis. In conclusion, the results suggest that sexual selection plays a major role in genital diversification, but the exact mechanism remained unclear in this study. Some structures in moth genitalia strongly suggest that sexual conflict is present as well. It is possible that several mechanisms of sexual selection are in action simultaneously. dings have implications to insect taxonomy. Genital characters, although often useful, should not be considered superior to other characters because they may vary considerably within species. I have shown that subjective visual evaluation of genital characteristics and a priori assumption of their low variability may easily lead to unsound taxonomic conclusions. Sophisticated morphometric tools are very useful and objective in delimiting sibling species. Geometric morphometrics is particularly useful since it helps to evaluate limits of variation. There are, however, no theoretical grounds to assume that genitalia are not subject to intraspecific geographic variation. Such variation was detected in this study as well. Geographic relationships should therefore be taken into consideration more frequently when delimiting populations into different species

Revision of the West Palaearctic Euura bergmanni and oligospila groups (Hymenoptera, Tenthredinidae)

Abstract Eight Western Palaearctic Euura species are here assigned to the bergmanni group (bergmanni, brevivalvis, dispar, glutinosae, leptocephalus, respondens, sylvestris, and viridis) and two species to the oligospila group (frenalis and oligospila). Euura pallens (Konow, 1903) (bergmanni group) is removed from the list of West Palaearctic taxa. Euura pyramidalis (Hellén, 1948) is treated as incertae sedis within the bergmanni group. Definitions of the bergmanni and oligospila groups are primarily based on genetic sequence data (mitochondrial COI and nuclear NaK and POL2). We report likely occurrence of heteroplasmy and amplification of NUMTs among some of the treated species, complicating the use of DNA barcoding in species discrimination. Based on morphological and genetic evidence, we establish that the correct name for the invasive willow sawfly in the southern hemisphere (South America, southern Africa, Australia, New Zealand), known there only in the female sex, is Euura respondens (Förster, 1854). The species is probably native to the Palaearctic (or even Holarctic) where males are common: possibly as common as females (examined from Europe and Central Asia). The name Euura oligospila (Förster, 1854) has been incorrectly used for the species in the southern hemisphere. The examination of type material and reliable association of males and females based on genetics revealed that females of E. oligospila are morphologically extremely similar to E. respondens (and to some other E. bergmanni group species), but male penis valves and genetics enable reliable separation of these species. Morphological separation of females of E. oligospila and E. respondens is possible, but challenging. Identification keys for males and females of the bergmanni and oligospila groups are provided. The following 15 new synonymies are proposed: Nematus validicornis Förster, 1854, syn. nov. with Euura bergmanni (Dahlbom, 1835); Pteronidea woollatti Lindqvist, 1971, syn. nov. and Nematus turgaiensis Safjanov, 1977, syn. nov. with Euura brevivalvis (Thomson, 1871); Pteronidea pseudodispar Lindqvist, 1969, syn. nov. with Euura dispar (Zaddach, 1876); Nematus (Pteronidea) fastosus var. ponojense Hellén, 1948, syn. nov. and N. (P.) fastosus var. punctiscuta Hellén, 1948, syn. nov. with Euura frenalis (Thomson, 1888); Nematus declaratus Muche, 1974, syn. nov. and N. desantisi D.R. Smith, 1983, syn. nov. with Euura respondens (Förster, 1854); Pteronidea straminea Lindqvist, 1958, syn. nov., P. angustiserra Lindqvist, 1969, syn. nov., and P. disparoides Lindqvist, 1969, syn. nov. with Euura sylvestris (Cameron, 1884); Pteronidea breviseta Lindqvist, 1946, syn. nov., P. breviseta Lindqvist, 1949, syn. nov., P. abscondita Lindqvist, 1949, syn. nov., and P. lauroi Lindqvist, 1960, syn. nov. with Euura viridis (Stephens, 1835). Lectotypes are designated for 18 nominal taxa: Amauronematus longicornis Konow, 1897; A. spurcus Konow, 1904; Nematus bergmanni Dahlbom, 1835; N. brevivalvis Thomson, 1871; N. curtispina Thomson, 1871; N. (Pteronidea) fastosus var. ponojense Hellén, 1948; N. (P.) fastosus var. punctiscuta Hellén, 1948; N. glutinosae Cameron, 1882; N. microcercus Thomson, 1871; N. polyspilus Förster, 1854; N. prasinus Hartig, 1837; N. respondens Förster, 1854; N. salicivorus Cameron, 1882; N. validicornis Förster, 1854; N. virescens Hartig, 1837; Pteronidea curtispina var. luctuosa Enslin, 1916; Pteronus fastosus Konow, 1904; and P. pallens Konow, 1903

An incomplete European barcode library has a strong impact on the identification success of Lepidoptera from Greece

Abstract Species identification by means of DNA barcodes depends essentially on the scope and quality of a relevant reference library. The first analysis of a large number (about 600 morphospecies) of southern European Lepidoptera (Greece: Peloponnese) shows both the advantages and disadvantages with regard to a reliable identification of Mediterranean species. We determined 946 DNA barcode sequences from 47 families, of which 929 sequences from 46 families were successfully assigned to a Barcode Index Number (BIN) in the global Barcode of Life Data Systems (BOLD) database. A species level identification for 485 BINs representing 477 Linnaean names was successful. These taxa include 34 new records for Greece. However, 128 BINs (c. 20% of the inventory) could not be attached to a Linnaean name from referenced sequences available in BOLD. Of these BINs, 99 are new and hence represent unique records for BOLD. Intra- and inter-BIN divergences are presented and discussed. An initial and preliminary in-depth analysis of randomly selected species indicates an incomplete DNA barcode library in terms of Linnean taxa, in addition to a considerable number of probably undescribed species. It is therefore strongly recommended that the already advanced European barcode library of Lepidoptera should be supplemented with not-yet-sequenced taxa from the Mediterranean

Cross-contamination and strong mitonuclear discordance in Empria sawflies (Hymenoptera, Tenthredinidae) in the light of phylogenomic data

Abstract In several sawfly taxa strong mitonuclear discordance has been observed, with nuclear genes supporting species assignments based on morphology, whereas the barcode region of the mitochondrial COI gene suggests different relationships. As previous studies were based on only a few nuclear genes, the causes and the degree of mitonuclear discordance remain ambiguous. Here, we obtained genomic-scale ddRAD data together with Sanger sequences of mitochondrial COI and two to three nuclear protein coding genes to investigate species limits and mitonuclear discordance in two closely related species groups of the sawfly genus Empria. As found previously based on nuclear ITS and mitochondrial COI sequences, species are in most cases supported as monophyletic based on new nuclear data reported here, but not based on mitochondrial COI. This mitonuclear discordance can be explained by occasional mitochondrial introgression with little or no nuclear gene flow, a pattern that might be common in haplodiploid taxa with slowly evolving mitochondrial genomes. Some species in the E. immersa group are not recovered as monophyletic according to either mitochondrial or nuclear data, but this could partly be because of unresolved taxonomy. Preliminary analyses of ddRAD data did not recover monophyly of E. japonica within the E. longicornis group (three Sanger sequenced nuclear genes strongly supported monophyly), but closer examination of the data and additional Sanger sequencing suggested that both specimens were substantially (possibly 10–20% of recovered loci) cross-contaminated. A reason could be specimen identification tag jumps during sequencing library preparation that in previous studies have been shown to affect up to 2.5% of the sequenced reads. We provide an R script to examine patterns of identical loci among the specimens and estimate that the cross-contamination rate is not unusually high for our ddRAD dataset as a whole (based on counting of identical sequences in the immersa and longicornis groups, which are well separated from each other and probably do not hybridise). The high rate of cross-contamination for both E. japonica specimens might be explained by the small number of recovered loci (~1000) compared to most other specimens (>10 000 in some cases) because of poor sequencing results. We caution against drawing unexpected biological conclusions when closely related specimens are pooled before sequencing and tagged only at one end of the molecule or at both ends using a unique combination of limited number of tags (less than the number of specimens)