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

The first known riodinid ‘cuckoo’ butterfly reveals deep-time convergence and parallelism in ant social parasites

Mutualistic interactions between butterflies and ants can evolve into complex social parasitism. ‘Cuckoo’ caterpillars, known only in the Lycaenidae, use multimodal mimetic traits to achieve social integration into ant societies. Here, we present the first known ‘cuckoo’ butterfly in the family Riodinidae. Aricoris arenarum remained in taxonomic limbo for > 80 years, relegated to nomen dubium and misidentified as Aricoris gauchoana. We located lost type material, designated lectotypes and documented the morphology and natural history of the immature stages. The multifaceted life cycle of A. arenarum can be summarized in three phases: (1) females lay eggs close to honeydew-producing hemipterans tended by specific Camponotus ants; (2) free-living caterpillars feed on liquids (honeydew and ant regurgitations); and (3) from the third instar onward, the caterpillars are fed and tended by ants as ‘cuckoos’ inside the ant nest. This life cycle is remarkably similar to that of the Asian lycaenid Niphanda fusca, despite divergence 90 Mya. Comparable eco-evolutionary pathways resulted in a suite of ecomorphological homoplasies through the ontogeny. This study shows that convergent interactions can be more important than phylogenetic proximity in shaping functional traits of social parasites.

Genomic evidence suggests further changes of butterfly names

Further genomic sequencing of butterflies by our research group expanding the coverage of species and specimens from different localities, coupled with genome-scale phylogenetic analysis and complemented by phenotypic considerations, suggests a number of changes to the names of butterflies, mostly those recorded from the United States and Canada. Here, we present evidence to support these changes. The changes are intended to make butterfly classification more internally consistent at the genus, subgenus and species levels. I.e., considering all available evidence, we attempt to assign similar taxonomic ranks to the clades of comparable genetic differentiation, which on average is correlated with the age of phylogenetic groups estimated from trees. For species, we use criteria devised by genomic analysis of the genetic differentiation across suture zones and comparison of sympatric populations of closely related species. As a result, we resurrect 4 genera and 1 subgenus from subgeneric status or synonymy, change the rank of 8 currently used genera to subgenus, synonymize 7 genus-group names, summarize evidence to support 19 taxa as species instead of subspecies and 1 taxon as subspecies instead of species, along with a number of additional changes. One new genus and one new subspecies are described. Namely, the following taxa are treated as genera Tharsalea Scudder, 1876, Helleia Verity, 1943, Apangea Zhdanko, 1995, and Boldenaria Zhdanko, 1995. Tetracharis Grote, 1898 is a valid subgenus (not a synonym of Anthocharis Boisduval, Rambur, [Duménil] & Graslin, [1833]) that consists of Anthocharis cethura C. Felder & R. Felder, 1865 (Müller, 1764), Anthocharis midea (Hübner, [1809]), and Anthocharis limonea (A. Butler, 1871). The following are subgenera: Speyeria Scudder, 1872 of Argynnis Fabricius, 1807; Aglais Dalman, 1816 and Polygonia Hübner, [1819] of Nymphalis Kluk, 1780; Palaeonympha Butler, 1871 of Megisto Hübner, [1819]; Hyponephele Muschamp, 1915 of Cercyonis Scudder, 1875; Pyronia Hübner, [1819] and Aphantopus Wallengren, 1853 of Maniola Schrank, 1801 and Pseudonymphidia Callaghan, 1985 of Pachythone. Lafron Grishin, gen. n. (type species Papilio orus Stoll, [1780], parent subfamily Lycaeninae [Leach], [1815]) is described. Dipsas japonica Murray, 1875 is fixed as the type species of Neozephyrus Sibatani & Ito, 1942. The following taxa are junior subjective synonyms: Falcapica Klots, 1930 of Tetracharis Grote, 1898; Habrodais Scudder, 1876, Favonius Sibatani & Ito, 1942, Neozephyrus Sibatani & Ito, 1942, Quercusia Verity, 1943, Chrysozephyrus Shirôzu & Yamamoto, 1956, and Sibataniozephyrus Inomata, 1986 of Hypaurotis Scudder, 1876; Plesioarida Trujano & García, 2018 of Roeberella Strand, 1932; Papilio temenes Godart, 1819 (lectotype designated herein) of Heraclides aristodemus (Esper, 1794), Speyeria hydaspe conquista dos Passos & Grey, 1945 of Argynnis hesperis tetonia (dos Passos & Grey, 1945), and Erycides imbreus Plötz, 1879 of Phocides polybius polybius (Fabricius, 1793). The following are revised genus-species combinations: Pachythone lencates (Hewitson, 1875) Pachythone flocculus (Brévignon & Gallard, 1993), Pachythone floccus (Brévignon, 2013), Pachythone heberti (P. Jauffret & J. Jauffret, 2007), Pachythone marajoara (P. Jauffret & J. Jauffret, 2007) and Cissia cleophes (Godman & Salvin, 1889). The following species are transferred between subgenera: Anthocharis lanceolata Lucas, 1852 belongs to Anthocharis Boisduval, Rambur, [Duménil] & Graslin, [1833] instead of Paramidea Kuznetsov, 1929 and Danaus eresimus (Cramer, 1777) belongs to Danaus Kluk, 1780, and not to Anosia Hübner, 1816. The following taxa are distinct species rather than subspecies (of species shown in parenthesis): Heraclides ponceana (Schaus, 1911) (not Heraclides aristodemus (Esper, 1794)), Colias elis Strecker, 1885 (not Colias meadii W. H. Edwards, 1871), Argynnis irene Boisduval, 1869 and Argynnis nausicaa W. H. Edwards, 1874 (not Argynnis hesperis W. H. Edwards, 1864), Coenonympha california Westwood, [1851] (not Coenonympha tullia (Müller, 1764)), Dione incarnata N. Riley, 1926 (not Dione vanillae (Linnaeus, 1758)), Chlosyne coronado (M. Smith & Brock, 1988) (not Chlosyne fulvia (W. H. Edwards, 1879)), Chlosyne chinatiensis (Tinkham, 1944) (not Chlosyne theona (Ménétriés, 1855)), Phocides lilea (Reakirt, [1867]) (not Phocides polybius (Fabricius, 1793)), Cecropterus nevada (Scudder, 1872) and Cecropterus dobra (Evans, 1952) (not Cecropterus mexicana (Herrich-Schäffer, 1869)), Telegonus anausis Godman & Salvin, 1896, (not Telegonus anaphus (Cramer, 1777)), Epargyreus huachuca Dixon, 1955 (not Epargyreus clarus (Cramer, 1775)), Nisoniades bromias (Godman & Salvin, 1894) (not Nisoniades rubescens (Möschler, 1877)), Pholisora crestar J. Scott & Davenport, 2017 (not Pholisora catullus (Fabricius, 1793)), Carterocephalus mandan (W. H. Edwards, 1863) and Carterocephalus skada (W. H. Edwards, 1870) (not Carterocephalus palaemon (Pallas, 1771)), Amblyscirtes arizonae H. Freeman, 1993 (not Amblyscirtes elissa Godman, 1900), and Megathymus violae D. Stallings & Turner, 1956 (not Megathymus ursus Poling, 1902). Resulting from these changes, the following are revised species-subspecies combinations: Heraclides ponceana bjorndalae (Clench, 1979), Heraclides ponceana majasi L. Miller, 1987, Argynnis irene dodgei Gunder, 1931, Argynnis irene cottlei J. A. Comstock, 1925, Argynnis irene hanseni (J. Emmel, T. Emmel & Mattoon, 1998), Argynnis nausicaa elko (Austin, 1984), Argynnis nausicaa greyi (Moeck, 1950), Argynnis nausicaa viola (dos Passos & Grey, 1945), Argynnis nausicaa tetonia (dos Passos & Grey, 1945), Argynnis nausicaa chitone W. H. Edwards, 1879, Argynnis nausicaa schellbachi (Garth, 1949), Argynnis nausicaa electa W. H. Edwards, 1878, Argynnis nausicaa dorothea (Moeck, 1947), and Argynnis nausicaa capitanensis (R. Holland, 1988), Argynnis zerene atossa W. H. Edwards, 1890, Dione incarnata nigrior (Michener, 1942), Chlosyne coronado pariaensis (M. Smith & Brock, 1988), Cecropterus nevada aemilea (Skinner, 1893), Cecropterus nevada blanca (J. Scott, 1981), Telegonus anausis annetta (Evans, 1952), Telegonus anausis anoma (Evans, 1952), Telegonus anausis aniza (Evans, 1952), Epargyreus huachuca profugus Austin, 1998, Carterocephalus mandan mesapano (Scudder, 1868) and Carterocephalus skada magnus Mattoon & Tilden, 1998. American Coenonympha subspecies placed under C. tullia other than Coenonympha tullia kodiak W. H. Edwards, 1869, Coenonympha tullia mixturata Alpheraky, 1897 and Coenonympha tullia yukonensis W. Holland, 1900 belong to C. california. Heraclides ponceana latefasciatus Grishin, ssp. n. is described from Cuba. Argynnis coronis carolae dos Passos & Grey, 1942 is considered a subspecies-level taxon. Unless stated otherwise, all subgenera, species, subspecies and synonyms of mentioned genera and species are transferred together with their parent taxa, and others remain as previously classified.

Miocene Diversification and High-Altitude Adaptation of Parnassius Butterflies (Lepidoptera: Papilionidae) in Qinghai-Tibet Plateau Revealed by Large-Scale Transcriptomic Data

Simple Summary

Parnassius butterflies have contributed to fundamental studies in biogeography, insect–plant interactions, and other fields of conservation biology and ecology. However, the early evolutionary pattern and molecular adaptation mechanism of this alpine butterfly group to high altitudes in Qinghai–Tibet Plateau are poorly understood up to now. In this study, we report for the first time, a relatively large-scale transcriptomic dataset of eight Parnassius species and their two closely related papilionid species, a dated phylogeny based on hundreds of gene sequences, and potential genetic mechanisms underlying the high-altitude adaptation by investigating changes in evolutionary rates and positively selected genes. Overall, our findings indicate that the transcriptome data sets reported here can provide some new insights into the spatiotemporally evolutionary pattern and high altitude adaptation of Parnassius butterflies from the extrinsic and intrinsic view, and will support further expressional and functional studies that will help interested researchers to address evolution, biodiversity and conservation questions concerning Parnassius and other butterfly species.

Abstract

The early evolutionary pattern and molecular adaptation mechanism of alpine Parnassius butterflies to high altitudes in Qinghai–Tibet Plateau are poorly understood up to now, due to difficulties in sampling, limited sequence data, and time calibration issues. Here, we present large-scale transcriptomic datasets of eight representative Parnassius species to reveal the phylogenetic timescale and potential genetic basis for high-altitude adaptation with multiple analytic strategies using 476 orthologous genes. Our phylogenetic results strongly supported that the subgenus Parnassius formed a well-resolved basal clade, and the subgenera Tadumia and Kailasius were closely related in the phylogenetic trees. In addition, molecular dating analyses showed that the Parnassius began to diverge at about 13.0 to 14.3 million years ago (middle Miocene), correlated with their hostplant’s spatiotemporal distributions, as well as geological and palaeoenvironmental changes of the Qinghai–Tibet Plateau. Moreover, the accelerated evolutionary rate, candidate positively selected genes and their potentially functional changes were detected, probably contributed to the high-altitude adaptation of Parnassius species. Overall, our study provided some new insights into the spatiotemporally evolutionary pattern and high altitude adaptation of Parnassius butterflies from the extrinsic and intrinsic view, which will help to address evolution, biodiversity, and conservation questions concerning Parnassius and other butterfly species.

Butterfly dichromatism primarily evolved via Darwin's, not Wallace's, model

Sexual dimorphism is typically thought to result from sexual selection for elaborated male traits, as proposed by Darwin. However, natural selection could reduce expression of elaborated traits in females, as proposed by Wallace. Darwin and Wallace debated the origins of dichromatism in birds and butterflies, and although evidence in birds is roughly equal, if not in favor of Wallace's model, butterflies lack a similar scale of study. Here, we present a large‐scale comparative phylogenetic analysis of the evolution of butterfly coloration, using all European non‐hesperiid butterfly species (n = 369). We modeled evolutionary changes in coloration for each species and sex along their phylogeny, thereby estimating the rate and direction of evolution in three‐dimensional color space using a novel implementation of phylogenetic ridge regression. We show that male coloration evolved faster than female coloration, especially in strongly dichromatic clades, with male contribution to changes in dichromatism roughly twice that of females. These patterns are consistent with a classic Darwinian model of dichromatism via sexual selection on male coloration, suggesting this model was the dominant driver of dichromatism in European butterflies.

Towards unravelling Wolbachia global exchange: a contribution from the Bicyclus and Mylothris butterflies in the Afrotropics

Background

Phylogenetically closely related strains of maternally inherited endosymbiotic bacteria are often found in phylogenetically divergent, and geographically distant insect host species. The interspecies transfer of the symbiont Wolbachia has been thought to have occurred repeatedly, facilitating its observed global pandemic. Few ecological interactions have been proposed as potential routes for the horizontal transfer of Wolbachia within natural insect communities. These routes are however likely to act only at the local scale, but how they may support the global distribution of some Wolbachia strains remains unclear.

Results

Here, we characterize the Wolbachia diversity in butterflies from the tropical forest regions of central Africa to discuss transfer at both local and global scales. We show that numerous species from both the Mylothris (family Pieridae) and Bicyclus (family Nymphalidae) butterfly genera are infected with similar Wolbachia strains, despite only minor interclade contacts across the life cycles of the species within their partially overlapping ecological niches. The phylogenetic distance and differences in resource use between these genera rule out the role of ancestry, hybridization, and shared host-plants in the interspecies transfer of the symbiont. Furthermore, we could not identify any shared ecological factors to explain the presence of the strains in other arthropod species from other habitats, or even ecoregions.

Conclusion

Only the systematic surveys of the Wolbachia strains from entire species communities may offer the material currently lacking for understanding how Wolbachia may transfer between highly different and unrelated hosts, as well as across environmental scales.

Supplementary information

Supplementary information accompanies this paper at 10.1186/s12866-020-02011-2.

Is Sexual Conflict a Driver of Speciation? A Case Study With a Tribe of Brush-footed Butterflies

Understanding the evolutionary mechanisms governing the uneven distribution of species richness across the tree of life is a great challenge in biology. Scientists have long argued that sexual conflict is a key driver of speciation. This hypothesis, however, has been highly debated in light of empirical evidence. Recent advances in the study of macroevolution make it possible to test this hypothesis with more data and increased accuracy. In the present study, we use phylogenomics combined with four different diversification rate analytical approaches to test whether sexual conflict is a driver of speciation in brush-footed butterflies of the tribe Acraeini. The presence of a sphragis, an external mating plug found in most species among Acraeini, was used as a proxy for sexual conflict. Diversification analyses statistically rejected the hypothesis that sexual conflict is associated with shifts in diversification rates in Acraeini. This result contrasts with earlier studies and suggests that the underlying mechanisms driving diversification are more complex than previously considered. In the case of butterflies, natural history traits acting in concert with abiotic factors possibly play a stronger role in triggering speciation than does sexual conflict. [Acraeini butterflies; arms race; exon capture phylogenomics; Lepidoptera macroevolution; sexual selection; sphragis.].

Speciation through chromosomal fusion and fission in Lepidoptera

Changes in chromosome numbers may strongly affect reproductive barriers, because individuals heterozygous for distinct karyotypes are typically expected to be at least partially sterile or to show reduced recombination. Therefore, several classic speciation models are based on chromosomal changes. One import mechanism generating variation in chromosome numbers is fusion and fission of existing chromosomes, which is particularly likely in species with holocentric chromosomes, i.e. chromosomes that lack a single centromere. Holocentric chromosomes evolved repeatedly across the tree of life, including in Lepidoptera. Although changes in chromosome numbers are hypothesized to be an important driver of the spectacular diversification of Lepidoptera, comparative studies across the order are lacking. We performed the first comprehensive literature survey of karyotypes for Lepidoptera species since the 1970s and tested if, and how, chromosomal variation might affect speciation. Even though a meta-analysis of karyological differences between closely related taxa did not reveal an effect on the degree of reproductive isolation, phylogenetic diversification rate analyses across the 16 best-covered genera indicated a strong, positive association of rates of chromosome number evolution and speciation. These findings suggest a macroevolutionary impact of varying chromosome numbers in Lepidoptera and likely apply to other taxonomic groups, especially to those with holocentric chromosomes. This article is part of the theme issue 'Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.

A complete time-calibrated multi-gene phylogeny of the European butterflies

With the aim of supporting ecological analyses in butterflies, the third most species-rich superfamily of Lepidoptera, this paper presents the first time-calibrated phylogeny of all 496 extant butterfly species in Europe, including 18 very localised endemics for which no public DNA sequences had been available previously. It is based on a concatenated alignment of the mitochondrial gene COI and up to eleven nuclear gene fragments, using Bayesian inferences of phylogeny. To avoid analytical biases that could result from our region-focussed sampling, our European tree was grafted upon a global genus-level backbone butterfly phylogeny for analyses. In addition to a consensus tree, the posterior distribution of trees and the fully concatenated alignment are provided for future analyses. Altogether a complete phylogenetic framework of European butterflies for use by the ecological and evolutionary communities is presented.

Contrasting genomic and phenotypic outcomes of hybridization between pairs of mimetic butterfly taxa across a suture zone

Hybrid zones, whereby divergent lineages come into contact and eventually hybridize, can provide insights on the mechanisms involved in population differentiation and reproductive isolation, and ultimately speciation. Suture zones offer the opportunity to compare these processes across multiple species. In this paper we use reduced-complexity genomic data to compare the genetic and phenotypic structure and hybridization patterns of two mimetic butterfly species, Ithomia salapia and Oleria onega (Nymphalidae: Ithomiini), each consisting of a pair of lineages differentiated for their wing colour pattern and that come into contact in the Andean foothills of Peru. Despite similarities in their life history, we highlight major differences, both at the genomic and phenotypic level, between the two species. These differences include the presence of hybrids, variations in wing phenotype, and genomic patterns of introgression and differentiation. In I. salapia, the two lineages appear to hybridize only rarely, whereas in O. onega the hybrids are not only more common, but also genetically and phenotypically more variable. We also detected loci statistically associated with wing colour pattern variation, but in both species these loci were not over-represented among the candidate barrier loci, suggesting that traits other than wing colour pattern may be important for reproductive isolation. Our results contrast with the genomic patterns observed between hybridizing lineages in the mimetic Heliconius butterflies, and call for a broader investigation into the genomics of speciation in Ithomiini - the largest radiation of mimetic butterflies.

A glide over the Indo-Australian geological maze: repeated transgressions of Lydekker’s and Wallace’s Lines in archdukes, barons and dukes (Nymphalidae: Limenitidinae: Adoliadini)

Archdukes, barons, counts, dukes and marquises are forest-dwelling butterflies found in mainland Asia and most islands of the Indo-Australian archipelago west of Wallace’s Line, with only a few species occurring as far east as the Bismarck Archipelago. This pattern is unusual among butterfly groups of the region, which often present more widespread geographical ranges bearing little signature of Lydekker’s and Wallace’s Lines. Using a molecular multimarker matrix, we infer the first dated phylogeny for this clade and estimate its biogeographical history. We recover the Oriental genus Euthalia as polyphyletic, although other genera are monophyletic. The clade originated in continental Indomalaya in the late Oligocene ~24 Mya, when the Indo-Australian archipelago was at one of the most dynamic stages of its orogeny. Multiple independent colonization events towards the Lesser Sunda Islands, Moluccas, Australia and New Guinea suggest the relative permeability of Lydekker’s and Wallace’s Lines to these butterflies. Colonization of Melanesia took place twice, probably before the recent formation of Sulawesi. The study of Indo-Australian Adoliadini provides additional evidence that biogeographical barriers long thought to prevent exchange between the Asian and Australian biotas are, in fact, permeable especially to vagile insect lineages in the region.

Phenological shifts alter the seasonal structure of pollinator assemblages in Europe

Pollinators play an important role in terrestrial ecosystems by providing key ecosystem functions and services to wild plants and crops, respectively. The sustainable provision of such ecosystem functions and services requires diverse pollinator communities over the seasons. Despite evidence that climate warming shifts pollinator phenology, a general assessment of these shifts and their consequences on pollinator assemblages is still lacking. By analysing phenological shifts of over 2,000 species, we show that, on average, the mean flight date of European pollinators shifted to be 6 d earlier over the last 60 yr, while their flight period length decreased by 2 d. Our analysis further reveals that these shifts have probably altered the seasonal distribution of pollination function and services by decreasing the overlap among pollinators' phenologies within European assemblages, except in the most northeastern part of Europe. Such changes are expected to decrease the functional redundancy and complementarity of pollinator assemblages and, therefore, might alter the performance of pollination function and services and their robustness to ongoing pollinator extinctions.

Phylogenomics reveals the evolutionary timing and pattern of butterflies and moths

Lepidoptera play key roles in many biological systems. Butterflies are hypothesized to have evolved contemporaneously with flowering plants, and moths are thought to have gained anti-bat defenses in response to echolocating predatory bats, but these hypotheses have largely gone untested. Using a transcriptomic, dated evolutionary tree of Lepidoptera, we demonstrate that the most recent common ancestor of Lepidoptera is considerably older than previously hypothesized. The oldest moths in crown Lepidoptera were present in the Carboniferous, some 300 million years ago, and began to diversify largely in synchrony with angiosperms. We show that multiple lineages of moths independently evolved hearing organs well before the origin of bats, rejecting the hypothesis that lepidopteran hearing organs arose in response to these predators.

Butterflies and moths (Lepidoptera) are one of the major superradiations of insects, comprising nearly 160,000 described extant species. As herbivores, pollinators, and prey, Lepidoptera play a fundamental role in almost every terrestrial ecosystem. Lepidoptera are also indicators of environmental change and serve as models for research on mimicry and genetics. They have been central to the development of coevolutionary hypotheses, such as butterflies with flowering plants and moths’ evolutionary arms race with echolocating bats. However, these hypotheses have not been rigorously tested, because a robust lepidopteran phylogeny and timing of evolutionary novelties are lacking. To address these issues, we inferred a comprehensive phylogeny of Lepidoptera, using the largest dataset assembled for the order (2,098 orthologous protein-coding genes from transcriptomes of 186 species, representing nearly all superfamilies), and dated it with carefully evaluated synapomorphy-based fossils. The oldest members of the Lepidoptera crown group appeared in the Late Carboniferous (∼300 Ma) and fed on nonvascular land plants. Lepidoptera evolved the tube-like proboscis in the Middle Triassic (∼241 Ma), which allowed them to acquire nectar from flowering plants. This morphological innovation, along with other traits, likely promoted the extraordinary diversification of superfamily-level lepidopteran crown groups. The ancestor of butterflies was likely nocturnal, and our results indicate that butterflies became day-flying in the Late Cretaceous (∼98 Ma). Moth hearing organs arose multiple times before the evolutionary arms race between moths and bats, perhaps initially detecting a wide range of sound frequencies before being co-opted to specifically detect bat sonar. Our study provides an essential framework for future comparative studies on butterfly and moth evolution.

Recalibration of the insect evolutionary time scale using Monte San Giorgio fossils suggests survival of key lineages through the End-Permian Extinction

Insects are a highly diverse group of organisms and constitute more than half of all known animal species. They have evolved an extraordinary range of traits, from flight and complete metamorphosis to complex polyphenisms and advanced eusociality. Although the rich insect fossil record has helped to chart the appearance of many phenotypic innovations, data are scarce for a number of key periods. One such period is that following the End-Permian Extinction, recognized as the most catastrophic of all extinction events. We recently discovered several 240-million-year-old insect fossils in the Mount San Giorgio Lagerstätte (Switzerland-Italy) that are remarkable for their state of preservation (including internal organs and soft tissues), and because they extend the records of their respective taxa by up to 200 million years. By using these fossils as calibrations in a phylogenomic dating analysis, we present a revised time scale for insect evolution. Our date estimates for several major lineages, including the hyperdiverse crown groups of Lepidoptera, Hemiptera: Heteroptera and Diptera, are substantially older than their currently accepted post-Permian origins. We found that major evolutionary innovations, including flight and metamorphosis, appeared considerably earlier than previously thought. These results have numerous implications for understanding the evolution of insects and their resilience in the face of extreme events such as the End-Permian Extinction.

Molecular phylogeny and historical biogeography of Parnara butterflies (Lepidoptera: Hesperiidae)

The butterfly genus Parnara (Hesperiinae: Baorini), of which some are major pests of economic crops (e.g., rice, wild rice stems and sugarcane), currently consists of 10 species and several subspecies and has a highly disjunct distribution in Australia, Africa, and Asia. We determined the systematic relationships and biogeographical history of the genus by reconstructing the phylogeny based on eight genes and 101 specimens representing all 10 recognized species. Four species delimitation methods (ABGD, bPTP, GMYC and BPP) were also employed to assess the taxonomic status of each species. Based on these results and analyses, we recognize 11 extant species in the genus. The status of the taxon P. naso poutieri (Boisduval, 1833) from Madagascar is revised as a distinct species, Parnara poutieri (Boisduval, 1833) stat. rev. The subspecies P. guttata mangala (Moore, 1866) syn. nov. is synonymized with P. guttata guttata (Bremer & Grey, 1853), while P. bada (Moore, 1878) is provisionally treated as a complex of two species, namely P. bada and P. apostata (Snellen, 1886). The monophyly of Parnara is strongly supported, with the following relationships: P. amalia + ((P. monasi + (P. poutieri + P. naso)) + ((P. kawazoei + P. bada complex) + (P. ganga + (P. ogasawarensis + (P. guttata + P. batta))))). Divergence time and ancestral range estimates indicate that the common ancestor of Parnara originated in an implausible area of Australia, Africa, and Oriental region in the mid-Oligocene and then differentiated in the late Miocene-late Pliocene. Dispersal and range expansion have played an important role in diversification of the genus in Asia and Afica. Relatively stable geotectonic plates at the time when most extant lineages appeared during the late Miocene-early Pliocene might have been the factor responsible for the relatively constant low dynamic rate of diversification within the group.

Whole Genome Shotgun Phylogenomics Resolves the Pattern and Timing of Swallowtail Butterfly Evolution

Evolutionary relationships have remained unresolved in many well-studied groups, even though advances in next-generation sequencing and analysis, using approaches such as transcriptomics, anchored hybrid enrichment, or ultraconserved elements, have brought systematics to the brink of whole genome phylogenomics. Recently, it has become possible to sequence the entire genomes of numerous nonbiological models in parallel at reasonable cost, particularly with shotgun sequencing. Here, we identify orthologous coding sequences from whole-genome shotgun sequences, which we then use to investigate the relevance and power of phylogenomic relationship inference and time-calibrated tree estimation. We study an iconic group of butterflies—swallowtails of the family Papilionidae—that has remained phylogenetically unresolved, with continued debate about the timing of their diversification. Low-coverage whole genomes were obtained using Illumina shotgun sequencing for all genera. Genome assembly coupled to BLAST-based orthology searches allowed extraction of 6621 orthologous protein-coding genes for 45 Papilionidae species and 16 outgroup species (with 32% missing data after cleaning phases). Supermatrix phylogenomic analyses were performed with both maximum-likelihood (IQ-TREE) and Bayesian mixture models (PhyloBayes) for amino acid sequences, which produced a fully resolved phylogeny providing new insights into controversial relationships. Species tree reconstruction from gene trees was performed with ASTRAL and SuperTriplets and recovered the same phylogeny. We estimated gene site concordant factors to complement traditional node-support measures, which strengthens the robustness of inferred phylogenies. Bayesian estimates of divergence times based on a reduced data set (760 orthologs and 12% missing data) indicate a mid-Cretaceous origin of Papilionoidea around 99.2 Ma (95% credibility interval: 68.6–142.7 Ma) and Papilionidae around 71.4 Ma (49.8–103.6 Ma), with subsequent diversification of modern lineages well after the Cretaceous-Paleogene event. These results show that shotgun sequencing of whole genomes, even when highly fragmented, represents a powerful approach to phylogenomics and molecular dating in a group that has previously been refractory to resolution.

Molecular Phylogeny and Historical Biogeography of the Butterfly Tribe Aeromachini Tutt (Lepidoptera: Hesperiidae) from China

: The butterfly tribe Aeromachini Tutt, 1906 is a large group of skippers. In this study, a total of 10 genera and 45 species of putative members of this tribe, which represent most of the generic diversity and nearly all the species diversity of the group in China, were sequenced for two mitochondrial genes and three nuclear genes (2093 bp). The combined dataset was analyzed with maximum likelihood inference using IQtree. We found strong support for monophyly of Aeromachini from China and support for the most recent accepted species in the tribe. Two paraphyletic genera within Aeromachini are presented and discussed. The divergence time estimates with BEAST and ancestral-area reconstructions with RASP provide a detailed description about the historical biogeography of the Aeromachini from China. The tribe very likely originated from the Hengduan Mountains in the late Ecocene and expanded to the Himalaya Mountains and Central China Regions. A dispersal-vicariance analysis suggests that dispersal events have played essential roles in the distribution of extant species, and geological and climatic changes have been important factors driving current distribution patterns.