Showing papers by "Niklas Wahlberg published in 2018"

An updated checklist of the European Butterflies (Lepidoptera, Papilionoidea).

Abstract: This paper presents an updated checklist of the butterflies of Europe, together with their original name combinations, and their occurrence status in each European country. According to this checklist, 496 species of the superfamily Papilionoidea occur in Europe. Changes in comparison with the last version (2.6.2) of Fauna Europaea are discussed. Compared to that version, 16 species are new additions, either due to cryptic species most of which have been discovered by molecular methods (13 cases) or due to discoveries of Asian species on the eastern border of the European territory in the Ural mountains (three cases). On the other hand, nine species had to be removed from the list, because they either do not occur in Europe or lost their species status due to new evidence. In addition, three species names had to be changed and 30 species changed their combination due to new evidence on phylogenetic relationships. Furthermore, minor corrections were applied to some authors' names and years of publication. Finally, the name Polyommatusottomanus Lefebvre, 1831, which is threatened by its senior synonym Lycaenalegeri Freyer, 1830, is declared a nomen protectum, thereby conserving its name in the current combination Lycaenaottomana.

Information Dropout Patterns in Restriction Site Associated DNA Phylogenomics and a Comparison with Multilocus Sanger Data in a Species-Rich Moth Genus

Abstract: 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.

Molecular phylogeny and higher systematics of the metalmark butterflies (Lepidoptera: Riodinidae)

Abstract: Riodinidae is a highly diverse buttery family with the majority of its genera restricted to the Neotropics and, despite previous efforts, its higher systematics remains unresolved. Here, we propose a novel phylogenetic hypothesis, based on a comprehensive sample of riodinids, primarily from the Neotropics, covering 67% of all genera and all of the major lineages. We sequenced nine molecular markers and estimated resulting phylogenies with maximum likelihood and Bayesian approaches, using both timed trees and time-independent trees. We based calibration on three fossil Riodinidae, and reassessed the position of the oldest fossil. We also incorporated 52 samples from a previous study providing a comprehensive maximum likelihood tree for 304 species comprising 80% of all genera. We propose a new higher classication of the Riodinidae with two subfamilies: the Nemeobiinae, including the Old World riodinids and their Neotropical sister Euselasia Hubner; and the Riodininae, comprising all remaining genera. We divided Riodininae into nine tribes (including four new tribes: Calydnini Seraphim, Freitas & Kaminski trib.n.; Sertaniini Seraphim, Freitas & Kaminskitrib.n.; Dianesiini Seraphim, Freitas & Kaminski trib.n.; and Emesidini Seraphim, Freitas & Kaminski trib.n.), with Mesosemiini and Nymphidiini further subdivided into two and seven subtribes (including three new subtribes for Nymphidiini: Zabuellina Seraphim, Freitas & Kaminski subtrib.n.; Pachythonina Seraphim, Freitas & Kaminskisubtrib.n.; and Pandemina Seraphim, Freitas & Kaminski subtrib.n.). Although our phylogenetic hypotheses are generally congruent with the analyses by Espeland et al. (2015), the comprehensive taxon sampling employed here constitutes a large step towards a stable tribal-level classication. All taxonomic changes are summarized in a checklist. Despite most genera being restricted to tropical South and Central America, the oldest known fossil of Riodininae belongs to the Green River formation (42.6–50.2 Ma) in North America. Accordingly, we reassess the family’s crown age at 56 Ma (52.4–60.7 Ma), which is at variance with previous dating using secondary calibrations and a different subset of genes. Nonmonophyletic riodinid genera are ubiquitous, and several groups need further revision, including groups revised recently. Our results point to the need for integrative taxonomy, as adult morphology seems to be have been exhausted as a single data source in this family. This published work has been registered on Zoobank, http://zoobank.org/urn:lsid:zoobank.org:pub:BCA2DDC5-753B-4178-8E7B-B7ED1E995CE8. (Less)

The firefly genus Pteroptyx Olivier revisited (Coleoptera Lampyridae: Luciolinae)

Abstract: The synchronous firefly genus Pteroptyx Olivier is reassessed from morphological, molecular, and habitat perspectives in Malaysia, and includes some reliably associated females described from morphological features and internal female reproductive anatomy. Phylogenetic analyses using combined morphological and molecular data (where available) for 158 taxa supported all the major features of the existing taxonomic categories within the Indopacific Luciolinae. They revealed a distinct Pteroptyx clade as a morphologically variable genus with Poluninius selangoriensis Ballantyne being newly synonymised with Luciola testacea Motschulsky, the type species, which is redescribed from the type series. Pteroptyx gelasina Ballantyne was shown to be distinct and three of the four morphological subdivisions within Pteroptyx malaccae (Gorham) considered useful. A new species Pt. balingiana Jusoh sp. nov. is described from Sarawak. A second specimen of Pt. gombakia Ballantyne is described and figured. Some females were reliably associated with identified males by molecular data, but investigation of their morphology showed consistent features that were for the most part not useful for species delineation, which still relies on association with the males and colour patterns. All females investigated had bursa plates.Habitat details for most Pteroptyx revealed an association with a riparian environment likely to support mangroves but not necessarily an obligatory association with mangroves or any particular species. Pteroptyx galbina Jusoh was found up to 30 km from the sea, and Pt. bearni Olivier displays in a variety of flowering plants alongside rivers, including mangroves.Keys to species and diagnoses of all species with coloured plates are given.

A simple method for data partitioning based on relative evolutionary rates.

Abstract: Background. Multiple studies have demonstrated that partitioning of molecular datasets is important in model-based phylogenetic analyses. Commonly, partitioning is done a priori based on some known properties of sequence evolution, e.g. differences in rate of evolution among codon positions of a protein-coding gene. Here we propose a new method for data partitioning based on relative evolutionary rates of the sites in the alignment of the dataset being analysed. The rates are inferred using the previously published Tree Independent Generation of Evolutionary Rates (TIGER), and the partitioning is conducted using our novel python script RatePartitions. We conducted simulations to assess the performance of our new method, and we applied it to eight published multi-locus phylogenetic datasets, representing different taxonomic ranks within the insect order Lepidoptera (butterflies and moths) and one phylogenomic dataset, which included ultra-conserved elements as well as introns. Methods. We used TIGER-rates to generate relative evolutionary rates for all sites in the alignments. Then, using RatePartitions, we partitioned the data into partitions based on their relative evolutionary rate. RatePartitions applies a simple formula that ensures a distribution of sites into partitions following the distribution of rates of the characters from the full dataset. This ensures that the invariable sites are placed in a partition with slowly evolving sites, avoiding the pitfalls of previously used methods, such as k- means. Different partitioning strategies were evaluated using BIC scores as calculated by PartitionFinder. Results. Simulations did not highlight any misbehaviour of our partitioning approach, even under difficult parameter conditions or missing data. In all eight phylogenetic datasets, partitioning using TIGER-rates and RatePartitions was significantly better as measured by the BIC scores than other partitioning strategies, such as the commonly used partitioning by gene and codon position. We compared the resulting topologies and node support for these eight datasets as well as for the phylogenomic dataset. Discussion. We developed a new method of partitioning phylogenetic datasets without using any prior knowledge (e.g. DNAsequence evolution). This method is entirely based on the properties of the data being analysed and can be applied to DNA sequences (protein-coding, introns, ultra-conserved elements), protein sequences, as well as morphological characters. A likely explanation for why our method performs better than other tested partitioning strategies is that it accounts for the heterogeneity in the data to a much greater extent than when data are simply subdivided based on prior knowledge. (Less)

Evolution within a language: environmental differences contribute to divergence of dialect groups.

Abstract: The processes leading to the diversity of over 7000 present-day languages have been the subject of scholarly interest for centuries Several factors have been suggested to contribute to the spatial segregation of speaker populations and the subsequent linguistic divergence However, their formal testing and the quantification of their relative roles is still missing We focussed here on the early stages of the linguistic divergence process, that is, the divergence of dialects, with a special focus on the ecological settings of the speaker populations We adopted conceptual and statistical approaches from biological microevolution and parallelled intra-lingual variation with genetic variation within a species We modelled the roles of geographical distance, differences in environmental and cultural conditions and in administrative history on linguistic divergence at two different levels: between municipal dialects (cf in biology, between individuals) and between dialect groups (cf in biology, between populations) We found that geographical distance and administrative history were important in separating municipal dialects However, environmental and cultural differences contributed markedly to the divergence of dialect groups In biology, increase in genetic differences between populations together with environmental differences may suggest genetic differentiation of populations through adaptation to the local environment However, our interpretation of this result is not that language itself adapts to the environment Instead, it is based on Homo sapiens being affected by its environment, and its capability to adapt culturally to various environmental conditions The differences in cultural adaptations arising from environmental heterogeneity could have acted as nonphysical barriers and limited the contacts and communication between groups As a result, linguistic differentiation may emerge over time in those speaker populations which are, at least partially, separated Given that the dialects of isolated speaker populations may eventually evolve into different languages, our result suggests that cultural adaptation to local environment and the associated isolation of speaker populations have contributed to the emergence of the global patterns of linguistic diversity

Phylogenetic relationships, biogeography and diversification of Coenonymphina butterflies (Nymphalidae: Satyrinae) : intercontinental dispersal of a southern Gondwanan group?

Abstract: The origins, evolutionary history and diversification of the Australian butterfly fauna are poorly known and uncertain. Two competing hypotheses have been proposed to explain the occurrence of butterflies on this isolated continental landmass. The common view is that all Australian butterflies entered the continent relatively recently from the northern hemisphere via Southeast Asia and/or mainland New Guinea (i.e. northern dispersal origin hypothesis). The alternative view is that part or all of the Australian butterfly fauna ultimately evolved in remnant or Southern Gondwana when Australia was connected to South America through Antarctica (i.e. Southern Gondwanan origin hypothesis). However, robust phylogenies with strong support for monophyly are lacking for the majority of Australian endemic butterfly lineages, thereby precluding determination of their systematic relationships and hence their geographic origins. Here, we use molecular data to reconstruct phylogenetic relationships of the globally distributed butterfly subtribe Coenonymphina (Satyrinae: Satyrini). This group represents a major component of the butterfly fauna of the wider Australasian region, with 19 genera and 71 species endemic to the region. Dating estimates extrapolated from secondary calibration sources indicate that the subtribe arose c. 48 Ma (95% credibility interval, 52–42 Ma), and the crown group first diverged in the Eocene (c. 44 Ma, 95% credibility interval 51–37 Ma). Rapid speciation events subsequently followed around the Eocence–Oligocene boundary, resulting in a near-hard polytomy comprising short basal branches with nodes that are difficult to resolve. Based on strongly supported phylogenetic relationships and estimates of divergence times, we conclude that the group probably had its origin in the fragment of Southern Gondwana consisting of Australia, Antarctica and South America. However, we are unable to rule out the northern dispersal scenario, particularly as Coenonymphina are closely related to a set of predominantly Asian lineages. Dispersal and extinction events following the final break-up of Gondwana have played a pivotal role in shaping the extant distributions of the group. (Less)

Molecular systematics of the subfamily Limenitidinae (Lepidoptera: Nymphalidae)

Abstract: We studied the systematics of the subfamily Limenitidinae (Lepidoptera: Nymphalidae) using molecular methods to reconstruct a robust phylogenetic hypothesis. The molecular data matrix comprised 205 Limenitidinae species, four outgroups, and 11,327 aligned nucleotide sites using up to 18 genes per species of which seven genes (CycY, Exp1, Nex9, PolII, ProSup, PSb and UDPG6DH) have not previously been used in phylogenetic studies. We recovered the monophyly of the subfamily Limenitidinae and seven higher clades corresponding to four traditional tribes Parthenini, Adoliadini, Neptini, Limenitidini as well as three additional independent lineages. One contains the genera Harma + Cymothoe and likely a third, Bhagadatta, and the other two independent lineages lead to Pseudoneptis and to Pseudacraea. These independent lineages are circumscribed as new tribes. Parthenini was recovered as sister to rest of Limenitidinae, but the relationships of the remaining six lineages were ambiguous. A number of genera were found to be non-monophyletic, with Pantoporia, Euthalia, Athyma, and Parasarpa being polyphyletic, whereas Limenitis, Neptis, Bebearia, Euryphura, and Adelpha were paraphyletic.

The Trials and Tribulations of Priors and Posteriors in Bayesian Timing of Divergence Analyses: the Age of Butterflies Revisited

Abstract: The need for robust estimates of times of divergence is essential for downstream analyses, yet assessing this robustness is still rare. We generated a time-calibrated genus-level phylogeny of butterflies (Papilionoidea), including 994 taxa, up to 10 gene fragments and an unprecedented set of 12 fossils and 10 host-plant node calibration points. We compared marginal priors and posterior distributions to assess the relative importance of the former on the latter. This approach revealed a strong influence of the set of priors on the root age but for most calibrated nodes posterior distributions shifted from the marginal prior, indicating significant information in the molecular dataset. We also tested the effects of changing assumptions for fossil calibration priors and the tree prior. Using a very conservative approach we estimated an origin of butterflies at 107.6 Ma, approximately equivalent to the Early Cretaceous Late Cretaceous boundary, with a credibility interval ranging from 89.5 Ma (mid Late Cretaceous) to 129.5 Ma (mid Early Cretaceous). This estimate was robust to alternative analyses changing core assumptions. With 994 genera, this tree provides a comprehensive source of secondary calibrations for studies on butterflies.

Species limits in butterflies (Lepidoptera: Nymphalidae): Reconciling classical taxonomy with the multispecies coalescent

Abstract: Species delimitation is at the core of biological sciences. During the last decade, molecular-based approaches have advanced the field by providing additional sources of evidence to classical, morphology-based taxonomy. However, taxonomy has not yet fully embraced molecular species delimitation beyond threshold-based, single-gene approaches, and taxonomic knowledge is not commonly integrated to multi-locus species delimitation models. Here we aim to bridge empirical data (taxonomic and genetic) with the latest coalescent-based species delimitation approaches. We use the multispecies coalescent model as implemented in two recently developed Bayesian methods (DISSECT/STACEY and BP&P) to infer species hypotheses. In both cases, we account for phylogenetic uncertainty (by not using any guide tree) and taxonomic uncertainty (by measuring the impact of using or not a priori taxonomic assignment to specimens). We focus on an entire Neotropical tribe of butterflies, the Haeterini (Nymphalidae: Satyrinae). We contrast divergent taxonomic opinion-splitting, lumping and misclassifying species-in the light of different phenotypic classifications proposed to date. Our results provide a solid background for the recognition of 22 species. The synergistic approach presented here overcomes limitations in both traditional taxonomy (e.g., by recognizing cryptic species) and molecular-based methods (e.g., by recognizing structured populations, and not raise them to species). Our framework provides a step forward towards standardization and increasing reproducibility of species delimitations.

Biodiversity seen through the perspective of insects: 10 simple rules on methodological choices, common challenges, and experimental design for genomic studies

Abstract: The study of biodiversity within the spatiotemporal continuum of evolution, e.g., 30 studying local communities, population dynamics, or phylogenetic diversity, has been important 31 to properly identify and describe the current biodiversity crisis. However, it has become clear 32 that a multi-scale approach – from the leaves of phylogenetic trees to its deepest branches – is 33 necessary to fully comprehend, and predict, biodiversity dynamics. Massive parallel DNA 34 sequencing opens up opportunities for bridging multiple dimensions in biodiversity research, 35 thanks to its efficiency to recover millions of nucleotide polymorphisms, both under neutral or 36 selective pressure. Here we aim to identify the current status, discuss the main challenges, and 37 look into future perspectives on biodiversity genomics research focusing on insects, which 38 arguably constitute the most diverse and ecologically important group of metazoans. We suggest 39 10 simple rules that every biologist could follow to 1) provide a succinct step-by-step guide and 40 best-practices to anyone interested in biodiversity research through insect genomics, 2) review 41 and show relevant literature on biodiversity and evolutionary research in the field of entomology, 42 and 3) make available a perspective on biodiversity studies using insect genomics. Our 43 compilation is targeted at researchers and students who may not yet be specialists in entomology 44 or genomics, but plan to carry out own research in insect genomics. We foresee that the genomic 45 revolution and its application to the study of non-model insect lineages will represent a major 46 leap to our understanding of insect diversity, and by consequence the largest portion of Earth‟s 47 biodiversity, and its evolution in time and space. 48

Disarticulating and Reassembling Amphipyrinae (Lepidoptera, Noctuoidea, Noctuidae)

Abstract: Just as every home has a junk drawer, most diverse higher taxa have one or more subordinate groups for their putative members that are unassignable to neighboring subordinate groups or are otherwise poorly understood. Amphipyrinae have long been a catchall taxon for Noctuidae, with most members lacking discernible synapomorphies that would allow their assignment to one of the many readily diagnosable noctuid subfamilies. Here we use data from seven gene regions (>5,500 base pairs) for more than 120 noctuid genera to infer a phylogeny for Amphipyrinae and related subfamilies. Sequence data for fifty-seven amphipyrine genera — most represented by the type species of the genus — are examined (most for the first time). We present the first large-scale molecular phylogenetic study of Amphipyrinae sensu lato ; propose several nomenclatural changes for strongly supported results; and identify areas of noctuid phylogeny where greater taxon sampling and/or genomic-scale data are needed. We also discuss morphological (both adult and larval) and life history data for several of the higher taxonomic groupings most relevant to our results. Amphipyrinae are significantly redefined; many former amphipyrines, excluded as a result of our analyses, are reassigned to one of eight other noctuid subfamily-level taxa. For some amphipyrine genera for which phylogenetic placement to subfamily remains uncertain, we assign them to incertae sedis positions in Noctuidae.

Towards Resolving and Redefining Amphipyrinae (Lepidoptera, Noctuoidea, Noctuidae): a Massively Polyphyletic Taxon

Abstract: Amphipyrinae have long been a catchall taxon for Noctuidae, with most members lacking discernible morphological synapomorphies that would allow their assignment to one of the many readily diagnosable noctuid subfamilies. Here data from seven gene regions (>5,500 base pairs) for more than 120 noctuid genera are used to infer a phylogeny for Amphipyrinae and related subfamilies. Sequence data for 57 amphipyrine genera (most represented by the type species of the genus) are examined. Presented here are: the first large-scale molecular phylogenetic study of Amphipyrinae and largest molecular phylogeny of Noctuidae to date; several proposed nomenclatural changes for well supported results; and the identification of areas of noctuid phylogeny where greater taxon sampling and/or genomic-scale data are needed. Adult and larval morphology, along with life history traits, for taxonomic groupings most relevant to the results are discussed. Amphipyrinae are significantly redefined; many former amphipyrines, excluded as a result of these analyses, are reassigned to other noctuid subfamily-level taxa. Four genera, Chamaeclea Grote, Heminocloa Barnes & Benjamin, Hemioslaria Barnes & Benjamin, and Thurberiphaga Dyar are transferred to the tribe Chamaecleini Keegan & Wagner New Tribe in Acontiinae. Stiriina is elevated to Stiriinae Revised Status, Grotellina is elevated to Grotellinae Revised Status, and Annaphilina is elevated to Annaphilini Revised Status. Acopa Harvey is transferred to Bryophilinae, Aleptina Dyar is transferred to Condicinae, Leucocnemis Hampson and Oxycnemis gracillinea (Grote) are transferred to Oncocnemidinae, Nacopa Barnes & Benjamin is transferred to Noctuinae, and Narthecophora Smith is transferred to Stiriinae. Azenia Grote (and its subtribe Azeniina), Cropia Walker, Metaponpneumata Moeschler, Sexserrata Barnes & Benjamin, and Tristyla Smith are transferred to Noctuidae incertae sedis. Hemigrotella Barnes & McDunnough (formerly in subtribe Grotellina) is retained in Amphipyrinae.