High-quality haploid genomes corroborate 29 chromosomes and highly conserved synteny of genes in Hyles hawkmoths (Lepidoptera: Sphingidae)

BACKGROUND

Morphological and traditional genetic studies of the young Pliocene genus Hyles have led to the understanding that despite its importance for taxonomy, phenotypic similarity of wing patterns does not correlate with phylogenetic relationship. To gain insights into various aspects of speciation in the Spurge Hawkmoth (Hyles euphorbiae), we assembled a chromosome-level genome and investigated some of its characteristics.

RESULTS

The genome of a male H. euphorbiae was sequenced using PacBio and Hi-C data, yielding a 504 Mb assembly (scaffold N50 of 18.2 Mb) with 99.9% of data represented by the 29 largest scaffolds forming the haploid chromosome set. Consistent with this, FISH analysis of the karyotype revealed n = 29 chromosomes and a WZ/ZZ (female/male) sex chromosome system. Estimates of chromosome length based on the karyotype image provided an additional quality metric of assembled chromosome size. Rescaffolding the published male H. vespertilio genome resulted in a high-quality assembly (651 Mb, scaffold N50 of 22 Mb) with 98% of sequence data in the 29 chromosomes. The larger genome size of H. vespertilio (average 1C DNA value of 562 Mb) was accompanied by a proportional increase in repeats from 45% in H. euphorbiae (measured as 472 Mb) to almost 55% in H. vespertilio. Several wing pattern genes were found on the same chromosomes in the two species, with varying amounts and positions of repetitive elements and inversions possibly corrupting their function.

CONCLUSIONS

Our two-fold comparative genomics approach revealed high gene synteny of the Hyles genomes to other Sphingidae and high correspondence to intact Merian elements, the ancestral linkage groups of Lepidoptera, with the exception of three simple fusion events. We propose a standardized approach for genome taxonomy using nucleotide homology via scaffold chaining as the primary tool combined with Oxford plots based on Merian elements to infer and visualize directionality of chromosomal rearrangements. The identification of wing pattern genes promises future understanding of the evolution of forewing patterns in the genus Hyles, although further sequencing data from more individuals are needed. The genomic data obtained provide additional reliable references for further comparative studies in hawkmoths (Sphingidae).

Cryptic diversity in a vagile Hawaiian moth group suggests complex factors drive diversification

Allopatric speciation should be the dominant model of diversification across archipelagos because islands naturally promote isolation. It also follows that ecologically similar, vagile species should be more resistant to this kind of isolation due to dispersal and unifying selection. In a closely-related group of endemic Hawaiian hawkmoths, we found confounding patterns of inter-island connectivity and speciation that did not correlate with vagility, ecological specialization, or island age. Speciation occurred both in allopatric and sympatric taxa, with only the oldest and youngest islands fostering single-island endemic species. The intermediately-sized, central islands supported a combination of endemic and more widely-occurring lineages, suggesting no clear pattern leading to the current diversity in Hawaii. While some species are relatively common, others are apparently extinct or very rare, even on the same island. Further research into the specific mechanisms for these patterns in Hyles may prove broadly informative for understanding both cladogenesis and improving conservation planning. Our study identifies one new species endemic to Kauai and unique mitochondrial lineages in H. perkinsi, which may prove to be new species.

Ancient incomplete lineage sorting of Hyles and Rhodafra (Lepidoptera: Sphingidae)

The hawkmoth genus Rhodafra comprises two African species with unclear relationships, as their wing patterns are markedly different, with one species closely resembling species of a related genus, Hyles. The present paper aims to investigate the monophyly and phylogenetic position of Rhodafra in relation to Hyles and other genera of the subtribe Choerocampina (Sphingidae: Macroglossinae: Macroglossini) using mitochondrial and nuclear sequence data from more species and individuals than have hitherto been studied. As no fresh tissue of Rhodafra was available, ancient-DNA methodology was applied. All data corroborate the genus as monophyletic and that a similar wing pattern is not a good indicator of close phylogenetic relationship in this group of moths. Phylogenetic trees based on mitochondrial data agree in placing Rhodafra within Hyles. In contrast, analysis of nuclear EF1alpha sequences produces a topology in which Rhodafra is placed as the sister clade to Hyles. Although multispecies coalescent analyses suggest a polytomy between Rhodafra, Hyles lineata and the remaining Hyles, total evidence analyses corroborate Rhodafra as sister to Hyles. This relationship is interpreted as the favoured topology. For a more robust result, the question should be re-examined using genomic approaches.

Advantages of an easy-to-use DNA extraction method for minimal-destructive analysis of collection specimens

Here we present and justify an approach for minimal-destructive DNA extraction from historic insect specimens for next generation sequencing applications. An increasing number of studies use insects from museum collections for biodiversity research. However, the availability of specimens for molecular analyses has been limited by the degraded nature of the DNA gained from century-old museum material and the consumptive nature of most DNA extraction procedures. The method described in this manuscript enabled us to successfully extract DNA from specimens as old as 241 years using a minimal-destructive approach. The direct comparison of the DNeasy extraction Kit and the Monarch® PCR & DNA Clean-up Kit showed a significant increase of 17.3-fold higher DNA yield extracted with the Monarch Oligo protocol on average. By using an extraction protocol originally designed for oligonucleotide clean-up, we were able to combine overcoming the restrictions by target fragment size and strand state, with minimising time consumption and labour-intensity. The type specimens used for the minimal-destructive DNA extraction exhibited no significant external change or post-extraction damage, while sufficient DNA was retrieved for analyses.

Genome-wide SNP Data Reveal an Overestimation of Species Diversity in a Group of Hawkmoths

The interface between populations and evolving young species continues to generate much contemporary debate in systematics depending on the species concept(s) applied but which ultimately reduces to the fundamental question of “when do nondiscrete entities become distinct, mutually exclusive evolutionary units”? Species are perceived as critical biological entities, and the discovery and naming of new species is perceived by many authors as a major research aim for assessing current biodiversity before much of it becomes extinct. However, less attention is given to determining whether these names represent valid biological entities because this is perceived as both a laborious chore and an undesirable research outcome. The charismatic spurge hawkmoths (Hyles euphorbiae complex, HEC) offer an opportunity to study this less fashionable aspect of systematics. To elucidate this intriguing systematic challenge, we analyzed over 10,000 ddRAD single nucleotide polymorphisms from 62 individuals using coalescent-based and population genomic methodology. These genome-wide data reveal a clear overestimation of (sub)species-level diversity and demonstrate that the HEC taxonomy has been seriously oversplit. We conclude that only one valid species name should be retained for the entire HEC, namely Hyles euphorbiae, and we do not recognize any formal subspecies or other taxonomic subdivisions within it. Although the adoption of genetic tools has frequently revealed morphologically cryptic diversity, the converse, taxonomic oversplitting of species, is generally (and wrongly in our opinion) accepted as rare. Furthermore, taxonomic oversplitting is most likely to have taken place in intensively studied popular and charismatic organisms such as the HEC.

A highly contiguous genome assembly of the bat hawkmoth Hyles vespertilio (Lepidoptera: Sphingidae)

BACKGROUND

Adapted to different ecological niches, moth species belonging to the Hyles genus exhibit a spectacular diversity of larval color patterns. These species diverged ∼7.5 million years ago, making this rather young genus an interesting system to study a wide range of questions including the process of speciation, ecological adaptation, and adaptive radiation.

RESULTS

Here we present a high-quality genome assembly of the bat hawkmoth Hyles vespertilio, the first reference genome of a member of the Hyles genus. We generated 51× Pacific Biosciences long reads with an average read length of 8.9 kb. Pacific Biosciences reads longer than 4 kb were assembled into contigs, resulting in a 651.4-Mb assembly consisting of 530 contigs with an N50 value of 7.5 Mb. The circular mitochondrial contig has a length of 15,303 bp. The H. vespertilio genome is very repeat-rich and exhibits a higher repeat content (50.3%) than other Bombycoidea species such as Bombyx mori (45.7%) and Manduca sexta (27.5%). We developed a comprehensive gene annotation workflow to obtain consensus gene models from different evidence including gene projections, protein homology, transcriptome data, and ab initio predictions. The resulting gene annotation is highly complete with 94.5% of BUSCO genes being completely present, which is higher than the BUSCO completeness of the B. mori (92.2%) and M. sexta (90%) annotations.

CONCLUSIONS

Our gene annotation strategy has general applicability to other genomes, and the H. vespertilio genome provides a valuable molecular resource to study a range of questions in this genus, including phylogeny, incomplete lineage sorting, speciation, and hybridization. A genome browser displaying the genome, alignments, and annotations is available at https://genome-public.pks.mpg.de/cgi-bin/hgTracks?db=HLhylVes1.

Functional characterization of the Hyles euphorbiae hawkmoth transcriptome reveals strong expression of phorbol ester detoxification and seasonal cold hardiness genes

Background

The European spurge hawkmoth, Hyles euphorbiae (Lepidoptera, Sphingidae), has been intensively studied as a model organism for insect chemical ecology, cold hardiness and evolution of species delineation. To understand species isolation mechanisms at a molecular level, this study aims at determining genetic factors underlying two adaptive ecological trait candidates, phorbol ester (TPA) detoxification and seasonal cold acclimation.

Method

A draft transcriptome of H. euphorbiae was generated using Illumina sequencing, providing the first genomic resource for the hawkmoth subfamily Macroglossinae. RNA expression levels in tissues of experimental TPA feeding larvae and cooled pupae was compared to levels in control larvae and pupae using 26 bp RNA sequence tag libraries (DeepSuperSAGE). Differential gene expression was assessed by homology searches of the tags in the transcriptome.

Results

In total, 389 and 605 differentially expressed transcripts for detoxification and cold hardiness, respectively, could be identified and annotated with proteins. The majority (22 of 28) of differentially expressed detox transcripts of the four 'drug metabolism' enzyme groups (cytochrome P450 (CYP), carboxylesterases (CES), glutathione S-transferases (GST) and lipases) are up-regulated. Triacylglycerol lipase was significantly over proportionally annotated among up-regulated detox transcripts. We record several up-regulated lipases, GSTe2, two CESs, CYP9A21, CYP6BD6 and CYP9A17 as candidate genes for further H. euphorbiae TPA detoxification analyses. Differential gene expression of the cold acclimation treatment is marked by metabolic depression with enriched Gene Ontology terms among down-regulated transcripts almost exclusively comprising metabolism, aerobic respiration and dissimilative functions. Down-regulated transcripts include energy expensive respiratory proteins like NADH dehydrogenase, cytochrome oxidase and ATP synthase. Gene expression patterns show shifts in carbohydrate metabolism towards cryoprotectant production. The Glycolysis enzymes, G1Pase, A1e, Gpi and an Akr isoform are up-regulated. Glycerol, an osmolyte which lowers the body liquid supercooling point, appears to be the predominant polyol cryoprotectant in H. euphorbiae diapause pupae. Several protein candidates involved in glucose, glycerol, myo-inositol and potentially sorbitol and trehalose synthesis were identified.

Conclusions

A majority of differently expressed transcripts unique for either detoxification or cold hardiness indicates highly specialized functional adaptation which may have evolved from general cell metabolism and stress response.The transcriptome and extracted candidate biomarkers provide a basis for further gene expression studies of physiological processes and adaptive traits in H. euphorbiae.

Endemics or strangers? The integrative re-appraisal of taxonomy and phylogeny of the Greenland Lymnaeidae (Mollusca: Gastropoda)

The Lymnaeidae constitute a significant part of the freshwater molluscan diversity of Greenland. Since 1842, not less than 10 nominal taxa of the species and variety rank were described to organize the diversity of the Greenland lymnaeid snails. All previous attempts to revise these taxa were systematically based on morphological evidence only. Here, we provide a molecular analysis of the phylogenetic affinity and systematic status of three alleged species of the Greenland Lymnaeidae: Lymnaea vahlii (Møller, 1842), L. holboellii (Møller, 1842), and L. pingelii (Møller, 1842). We examined the newly collected material and inspected the type series of the three species. Our results show a very tight relationship between the Greenland snails and the Nearctic species Ladislavella catascopium (Say, 1817) s. lato. From the genetic point of view, the Greenland populations should be classified within L. catascopium, albeit probably with the merit of a subspecies status. The three nominal species of lymnaeids described by Møller (1842) are apparently synonyms of each other. Our findings assume a rather recent colonization of Greenland by snails arriving from the North American mainland, which is compatible with the so-called "tabula rasa" hypothesis, proposed to explain the currently observed taxonomic diversity of continental animals and plants of the North Atlantic islands. No lymnaeid species endemic to Greenland is thus revealed.

Molecular phylogeny, morphology and taxonomy of Moroccan Triops granarius (Lucas, 1864) (Crustacea: Notostraca), with the description of two new species

We used three molecular markers to investigate populations of Triops granarius from a study area in western Morocco that had a north-south span of approx. 434 km, the most distant populations situated at more than 470 km distance from each other. Previous studies had already investigated two Triops granarius populations from this region and revealed their affiliation to the major phylogenetic lineage that includes Triops cancriformis. By contrast, based on the geographic position of the type locality and the morphology of the type, Triops granarius s.s. likely belongs to a clade that forms the sister group to American and Australian Triops, i.e. including Triops longicaudatus and Triops australiensis. In the present study a second, hitherto unknown phylogenetic lineage was discovered among Moroccan populations of Triops granarius s.l. Our phylogenetic analyses show that both Moroccan lineages of Triops granarius s.l. represent a pair of genetically and morphologically well differentiated sister species that should be separated from Triops granarius. We therefore formally describe them as two new species, Triops maximus sp. nov. and Triops multifidus sp. nov. The early larval stages of both species show a peculiar morphology with 10 to 15 setae on the exopodite of the 2^nd antenna. The number of these setae was generally thought to span five to seven in Notostraca. Despite the fact that the antennal setae form a central part of the main locomotory organ in early instars, we found their number to vary by up to two between body-sides of single individuals.

A comprehensive phylogeography of the Hyles euphorbiae complex (Lepidoptera: Sphingidae) indicates a 'glacial refuge belt'

We test the morphology based hypothesis that the Western Palaearctic spurge hawkmoths represent two species, the Eurasian H. euphorbiae and Afro-Macaronesian H. tithymali. It has been suggested that these species merged into several hybrid swarm populations, although a mitochondrial phylogeography revealed substructure with local differentiation. We analysed a three-gene mt-dataset (889 individuals) and 12 microsatellite loci (892 individuals). Microsatellite analyses revealed an overall weak differentiation and corroborated the superordinate division into two clusters. The data indicate that the populations studied belong to only one species according to the biological species concept, refuting the opening hypothesis. A future taxonomic revision appears necessary to reflect the division into two subgroups. Ancestral mitochondrial polymorphisms are retained in H. euphorbiae, indicating gene flow within a broad 'glacial refuge belt' and ongoing postglacial gene flow. Diverse patterns of extensive mito-nuclear discordance in the Mediterranean and the Middle East presumably evolved by more recent processes. This discordance indicates introgression of H. tithymali-related mitochondrial haplogroups, accompanied (to a lesser degree) by nuclear alleles, into Italian and Aegean H. euphorbiae populations as recently as the late Holocene. The complex mosaic of divergence and reintegration is assumed to have been influenced by locally differing environmental barriers to gene flow.

A MOLECULAR GENETIC EVIDENCE OF THE OCCURRENCE OF THE FRESHWATER SNAIL RADIX LAGOTIS (SCHRANK, 1803) (GASTROPODA: LYMNAEIDAE) IN BULGARIA

Radix lagotis (Schrank, 1803) was found in the Dragoman marshes in Bulgaria. By comparison of the mitochondrial cyt-b sequences (fragment of 329 bp) and sequence data obtained from the nuclear ITS-2 spacer these specimens fell into one cluster with sequences from R. lagotis from Germany, Austria and Czech Republic confirming the morphological determination and the first record of this species for Bulgaria.

Response to cold acclimation in diapause pupae of Hyles euphorbiae (Lepidoptera: Sphingidae): candidate biomarker identification using proteomics

The distribution range of Hyles euphorbiae covers distinct climates across the Palaearctic. Previous investigations showed a correlation between mitochondrial DNA identity of populations and climatic conditions related to winter; however, the lack of biomarkers hampers investigations to test whether geographically distinct populations do show specific molecular responses to low temperatures or whether they possess specific genetic identity at loci functionally related to cold response. The present study was designed to identify candidate protein biomarkers and biological processes that are associated with cold acclimation of overwintering H. euphorbiae diapause pupae. Specimens taken from a single central European population were gradually cooled from 20 °C to -2 °C over 36 days and 12 differentially abundant proteins were identified. In addition, DeepSuperSAGE sequencing technology was applied to study differentially regulated genes. There was incongruence between differentially abundant proteins and differentially expressed genes, but functional characteristics of regulated proteins and analyses of gene ontology term enrichment among differentially regulated genes pointed to activation of the same biological processes, e.g. oxidative stress response. As proteins represent biologically active molecules, candidate biomarkers derived from proteomics are considered well suited to explore intraspecific patterns of local adaptation to different climates.

Molecular phylogeny of the Notostraca

We used a combined analysis of one nuclear (28S rDNA) and three mitochondrial markers (COI, 12S rDNA, 16S rDNA) to infer the molecular phylogeny of the Notostraca, represented by samples from the six continents that are inhabited by this group of branchiopod crustaceans. Our results confirm the monophyly of both extant notostracan genera Triops and Lepidurus with good support in model based and maximum parsimony analyses. We used branchiopod fossils as a calibration to infer divergence times among notostracan lineages and accounted for rate heterogeneity among lineages by applying relaxed-clock models. Our divergence date estimates indicate an initial diversification into the genera Triops and Lepidurus in the Mesozoic, most likely at a minimum age of 152.3-233.5 Ma, i.e., in the Triassic or Jurassic. Implications for the interpretation of fossils and the evolution of notostracan morphology are discussed. We further use the divergence date estimates to formulate a biogeographic hypothesis that explains distributions of extant lineages predominantly by overland dispersal routes. We identified an additional hitherto unrecognised highly diverged lineage within Lepidurus apus lubbocki and three additional previously unknown major lineages within Triops. Within T. granarius we found deep differentiation, with representatives distributed among three major phylogenetic lineages. One of these major lineages comprises T. cancriformis, the T. mauritanicus species group and two hitherto unrecognised T. granarius lineages. Samples that were morphologically identified as T. granarius diverged from the most basal nodes within this major lineage, and divergence dates suggested an approximate age of 23.7-49.6 Ma for T. cancriformis, indicating the need for a taxonomic revision of Triassic and Permian fossils that are currently attributed to the extant T. cancriformis. We thus elevate T. cancriformis minor to full species status as Triops minorTrusheim, 1938 and include in this species the additional Upper Triassic samples that were attributed to T. cancriformis. We further elevate T. cancriformis permiensis to full species status as Triops permiensisGand et al., 1997.

Intraspecific morphological and genetic variability in the European freshwater snail Radix labiata (Rossmaessler, 1835) (Gastropoda: Basommatophora: Lymnaeidae)

Radix labiata is a widely distributed Palaearctic freshwater snail. This work aims to improve the knowledge of the intraspecific variability in the most important characters used for its determination. To find out which characters are really suitable to distinguish this species from other similar Radix species an integrative approach was applied, involving morphological and molecular data.Molecular sequences of the nuclear spacer fragment ITS-2 and/or the mitochondrial gene fragment cyt-b were obtained from 26 individuals of R. labiata from different regions of Europe, including type localities of Limnaeus pereger labiatus. From the subsample of 24 specimens of which sequences of both gene fragments were available, the variability of several characters that are commonly used for species identification (shell morphology, mantle pigmentation, shape and position of the bursa copulatrix, length and position of the bursa duct, length ratio of praeputium to penial sheath) were measured or documented. Morphological characters distinguishing R. labiata from R. balthica, R. lagotis and the genus Stagnicola are discussed. The best morphological character to differentiate these species is the position of the bursa and the bursa duct. Mantle pigmentation and the ratio of the length of the praeputium to that of the penial sheath are not useful for differentiating R. labiata and R. balthica. Analysis of the network of haplotypes (cyt-b) revealed no correlation between recognisable clusters and geography amongst the studied specimens.

Overlooked cryptic endemism in copepods: systematics and natural history of the calanoid subgenus Occidodiaptomus Borutzky 1991 (Copepoda, Calanoida, Diaptomidae)

Our comprehension of the phylogeny and diversity of most inland-water crustaceans is currently hampered by their pronounced morphological bradytely, which contributed to the affirmation of the "Cosmopolitanism Paradigm" of freshwater taxa. However, growing evidence of the existence of cryptic diversity and molecular regionalism is available for calanoid copepods, thus stressing the need for careful morphological and molecular studies in order to soundly investigate the systematics, diversity and distribution patterns of the group. Diaptomid copepods were here chosen as model taxa, and the morphological and molecular diversity of the species belonging to the west-Mediterranean diaptomid subgenus Occidodiaptomus were investigated with the aim of comparing the patterns of morphological and molecular evolution in freshwater copepods. Three species currently lumped under the binomen Hemidiaptomus (Occidodiaptomus) ingens and two highly divergent clades within H. (O.) roubaui were distinguished, thus showing an apparent discordance between the molecular distances recorded and Occidodiaptomus morphological homogeneity, and highlighting a noteworthy decoupling between the morphological and molecular diversity in the subgenus. Current Occidodiaptomus diversity pattern is ascribed to a combined effect of ancient vicariance and recent dispersal events. It is stressed that the lack of sound calibration points for the molecular clock makes it difficult to soundly temporally frame the diversification events of interest in the taxon studied, and thus to asses the role of morphological bradytely and of accelerated molecular evolutionary rates in shaping the current diversity of the group.

New source of genetic polymorphisms in Lepidoptera?

The variability level of the ISSR (inter-simple sequences repeat) primer (GACA)4 was examined in the three Lepidoptera families Pyralidae, Sphingidae and Pieridae. Our study shows that the tetra-repeat (GACA)n is evidently present in sufficient numbers in these butterflies to provide informative DNA fingerprints. The variability is mostly rather high, but within a comparable range to other ISSR studies. Although less polymorphisms may be encountered in some butterfly families, this study indicates that high variability of this marker may be a common characteristic of Lepidoptera genomes. An appeal for a minimal level of standardization of ISSR-PCR data analysis is formulated to enable an exact comparison between the groups of organisms studied with this fingerprint technique.