Interspecific gene flow obscures phylogenetic relationships in an important insect pest species complex

As genomic data proliferates, the prevalence of post-speciation gene flow is making species boundaries and relationships increasingly ambiguous. Although current approaches inferring fully bifurcating phylogenies based on concatenated datasets provide simple and robust answers to many species relationships, they may be inaccurate because the models ignore inter-specific gene flow and incomplete lineage sorting. To examine the potential error resulting from ignoring gene flow, we generated both a RAD-seq and a 500 protein-coding loci highly multiplexed amplicon (HiMAP) dataset for a monophyletic group of 12 species defined as the Bactrocera dorsalis sensu lato clade. With some of the world's worst agricultural pests, the taxonomy of the B. dorsalis s.l. clade is important for trade and quarantines. However, taxonomic confusion confounds resolution due to intra- and interspecific phenotypic variation and convergence, mitochondrial introgression across half of the species, and viable hybrids. We compared the topological convergence of our datasets using concatenated phylogenetic and various multispecies coalescent approaches, some of which account for gene flow. All analyses agreed on species delimitation, but there was incongruence between species relationships. Under concatenation, both datasets suggest identical species relationships with mostly high statistical support. However, multispecies coalescent and multispecies network approaches suggest markedly different hypotheses and detected significant gene flow. We suggest that the network approaches are likely more accurate because gene flow violates the assumptions of the concatenated phylogenetic analyses, but the data-reductive requirements of network approaches resulted in reduced statistical support and could not unambiguously resolve gene flow directions. Our study highlights the importance of testing for gene flow, particularly with phylogenomic datasets, even when concatenated approaches receive high statistical support.

Genomics reveals widespread hybridization across insects with ramifications for species boundaries and invasive species

As the amount of genomic data for non-model taxa grows, it is increasingly clear that gene flow across species barriers in insects is much more common than previously thought. In recent years, the decreased cost and increased accuracy of long-read sequencing has enabled the assembly of high-quality, reference genomes and chromosome maps for non-model insects. With this long-read data we can now not only compare variation across the genome among homologous genes between species, which has been the basis of phylogenetics for more than thirty years, but also tease apart evidence of ancient and recent hybridization and gene flow. The implications of hybridization for species adaptation may be more positive than previously considered, explaining its prevalence across many groups of insects. Unfortunately, due to anthropogenic actions, some pest species appear to be benefitting from hybridization and gene flow, facilitating future invasions.

Multi-gene phylogeny of North American clear-winged moths (Lepidoptera: Sesiidae): a foundation for future evolutionary study of a speciose mimicry complex

Sesiids are a diverse group of predominantly diurnal moths, many of which are Batesian mimics of Hymenoptera. However, their diversity and relationships are poorly understood. A multi-gene phylogenetic analysis of 48 North American sesiid species confirmed the traditional taxonomic tribal ranks, demonstrated the paraphyly of Carmenta and Synanthedon with respect to several other genera and ultimately provided minimal phylogenetic resolution within and between North American and European groups. Character support from each gene suggested inconsistency between the phylogenetic signal of the CAD gene and that of the other four genes. However, removal of CAD from subsequent phylogenetic analyses did not substantially change the initial phylogenetic results or return Carmenta and Synanthedon as reciprocally monophyletic, suggesting that it was not impacting the overall phylogenetic signal. The lack of resolution using genes that are typically informative at the species level for other lepidopterans suggests a surprisingly rapid radiation of species in Carmenta/Synanthedon. This group also exhibits a wide range of mimicry strategies and hostplant usage, which could be fertile ground for future study.

Interactions between breeding system and ploidy affect niche breadth in Solanum

Understanding the factors driving ecological and evolutionary interactions of economically important plant species is important for agricultural sustainability. The geography of crop wild relatives, including wild potatoes (Solanum section Petota), have received attention; however, such information has not been analysed in combination with phylogenetic histories, genomic composition and reproductive systems to identify potential species for use in breeding for abiotic stress tolerance. We used a combination of ordinary least-squares (OLS) and phylogenetic generalized least-squares (PGLM) analyses to identify the discrete climate classes that make up the climate niche that wild potato species inhabit in the context of breeding system and ploidy. Self-incompatible diploid or self-compatible polyploid species significantly increase the number of discrete climate classes within a climate niche inhabited. This result was sustained when correcting for phylogenetic non-independence in the linear model. Our results support the idea that specific breeding system and ploidy combinations increase niche breadth through the decoupling of geographical range and niche diversity, and therefore, these species may be of particular interest for crop adaptation to a changing climate.

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.

The Dacini fruit fly fauna of Sulawesi fits Lydekker's line but also supports Wallacea as a biogeographic region (Diptera, Tephritidae)

Although there is scientific consensus on most of the major biogeographic regions in the world, the demarcation of the area connecting Southeast Asia with Australia and Oceania remains debated. Two candidate boundaries potentially explain faunistic diversity patterns in the regions: Lydekker's and Wallace's lines. The islands in between both 'lines' are jointly termed Wallacea, with Sulawesi as the largest landmass. We surveyed Dacini fruit flies (Tephritidae: Dacinae) in Sulawesi between 2016 and 2019 using traps baited with male lures, resulting in 4,517 collected flies. We identified all specimens to species level, which adds 15 new species records to the island, bringing the total number of Dacini species in Sulawesi to 83. The biogeographic affinity of species in the updated checklist reveals a strong connection with former 'Sunda' (41% of species); validating Lydekker's line, but also a high level of endemism (47% of species), confirming the uniqueness of Wallacea as a biogeographic region. We further describe a new species, Bactrocera (Bactrocera) niogreta Doorenweerd, sp. nov. and discuss the taxonomy of several interesting species.

The paradoxical rarity of a fruit fly fungus attacking a broad range of hosts

Understanding the factors that determine the realized and potential distribution of a species requires knowledge of abiotic, physiological, limitations as well as ecological interactions. Fungi of the order Laboulbeniales specialize on arthropods and are typically thought to be highly specialized on a single species or closely related group of species. Because infections are almost exclusively transmitted through direct contact between the hosts, the host ecology, to a large extent, determines the distribution and occurrence of the fungus. We examined ~20,000 fruit flies (Diptera: Dacinae) collected in Malaysia, Sulawesi, Australia, and the Solomon Islands between 2017 and 2019 for fungal infections and found 197 infected flies across eight different Bactrocera species. Morphology and 1,363 bps of small subunit (18S) DNA sequences both support that the infections are from a single polyphagous fungal species Stigmatomyces dacinus-a known ectoparasite of these fruit flies. This leads to the question: why is S. dacinus rare, when its hosts are widespread and abundant? In addition, the hosts are all Bactrocera, a genus with ~480 species, but 37 Bactrocera species found sympatric with the hosts were never infected. Host-selection does not appear to be phylogenetically correlated. These results suggest a hidden complexity in how different, but closely related, host species vary in their susceptibility, which somehow limits the abundance and dispersal capability of the fungus.

Comparing Adaptive Radiations Across Space, Time, and Taxa

Adaptive radiation plays a fundamental role in our understanding of the evolutionary process. However, the concept has provoked strong and differing opinions concerning its definition and nature among researchers studying a wide diversity of systems. Here, we take a broad view of what constitutes an adaptive radiation, and seek to find commonalities among disparate examples, ranging from plants to invertebrate and vertebrate animals, and remote islands to lakes and continents, to better understand processes shared across adaptive radiations. We surveyed many groups to evaluate factors considered important in a large variety of species radiations. In each of these studies, ecological opportunity of some form is identified as a prerequisite for adaptive radiation. However, evolvability, which can be enhanced by hybridization between distantly related species, may play a role in seeding entire radiations. Within radiations, the processes that lead to speciation depend largely on (1) whether the primary drivers of ecological shifts are (a) external to the membership of the radiation itself (mostly divergent or disruptive ecological selection) or (b) due to competition within the radiation membership (interactions among members) subsequent to reproductive isolation in similar environments, and (2) the extent and timing of admixture. These differences translate into different patterns of species accumulation and subsequent patterns of diversity across an adaptive radiation. Adaptive radiations occur in an extraordinary diversity of different ways, and continue to provide rich data for a better understanding of the diversification of life.

Six years of fruit fly surveys in Bangladesh: a new species, 33 new country records and discovery of the highly invasive Bactrocera carambolae (Diptera, Tephritidae)

We engaged in six years of snap-shot surveys for fruit flies in rural environments and ten protected forest areas of Bangladesh, using traps baited with male lures (cue-lure, methyl eugenol, zingerone). Our work has increased the recorded number of species of Tephritidae in the country from seven to 37. We summarize these surveys and report eight new country occurrence records, and a new species (Zeugodacusmadhupuri Leblanc & Doorenweerd, sp. nov.) is described. The highlight among the new records is the discovery, and significant westward range extension, of Bactroceracarambolae Drew & Hancock, a major fruit pest detected in the Chattogram and Sylhet Divisions. We rectify the previously published erroneous record of Bactrocerabogorensis (Hardy), which was based on a misidentification of Zeugodacusdiaphorus (Hendel). We also report the occurrence in Bangladesh of nine other Tephritidae, the rearing of three primary fruit fly parasitoids from Zeugodacus, and records of non-target attraction to fruit fly lures.

Two new day-flying species of Agrotis Ochsenheimer (Lepidoptera: Noctuidae) from the alpine summit of the Maunakea Volcano

Two new endemic Hawaiian species of Agrotis Ochsenheimer (Noctuidae) are described: A. helela and A. kuamauna. Both species are day-flying and occur at high-elevations. Observations of adult and larval morphology and biology are included, as well as illustrations of adult moths and genitalia for both sexes.

Tracking the Origins of Fly Invasions; Using Mitochondrial Haplotype Diversity to Identify Potential Source Populations in Two Genetically Intertwined Fruit Fly Species (Bactrocera carambolae and Bactrocera dorsalis [Diptera: Tephritidae])

Bactrocera carambolae Drew and Hancock and Bactrocera dorsalis (Hendel) (Diptera: Tephritidae) are important pests of many fruits. These flies have been spread across the world through global travel and trade, and new areas are at risk of invasion. Whenever new invasive populations are discovered, quick and accurate identification is needed to mitigate the damage they can cause. Determining invasive pathways can prevent further spread of pests as well as subsequent reinvasions through the same pathway. Molecular markers can be used for both species identification and pathway analysis. We analyzed 1,601 individuals from 19 populations using 765 base pairs of the mitochondrial cytochrome oxidase I (COI) gene to infer the haplotype diversity and population structure within these flies from across their native and invasive ranges. We analyzed these samples by either grouping by species or geographic populations due to the genetic similarity in the mitochondrial genome. We found no genetic structure between B. dorsalis and B. carambolae and our findings suggest recent and most likely ongoing, genetic exchange between these two species in the wild. Hyper-diverse mitochondrial genetic diversity in the native range suggests large population sizes and relatively high mutation rates. Only 52% of the haplotypes found in the trap captures from California are shared with haplotypes from flies found in our global survey, indicating significant genetic diversity in the native range that is missing from our samples. However, these results provide a foundation for the accurate determination of the provenance of invasive populations around the world.

Descriptions of four new species of Bactrocera and new country records highlight the high biodiversity of fruit flies in Vietnam (Diptera, Tephritidae, Dacinae)

Recent snap-shot surveys for fruit flies in Vietnam in 2015 and 2017 using traps baited with the male Dacinae fruit fly lures methyl eugenol, cue-lure and zingerone, collected 56 species, including 11 new country records and another 11 undescribed species, four of which are described in this paper. This increases the number of described species known to occur in Vietnam from 78 to 93. Species accumulation curves, based on the Chao 2 mean estimate, suggest that we collected 60-85 % of the local fauna at the sites sampled, and that species diversity decreases with increasing latitude. The four new species are named: Bactrocera (Tetradacus) ernesti Leblanc & Doorenweerd sp. n., B. (Asiadacus) connecta Leblanc & Doorenweerd sp. n., B. (Parazeugodacus) clarifemur Leblanc & Doorenweerd sp. n., and B. (Bactrocera) adamantea Leblanc & Doorenweerd sp. n. In addition to morphological data COI DNA sequence data of both the COI-5P and COI-3P mitochondrial DNA gene regions is provided. Three of the four newly described species are morphologically and genetically easily distinguished from all other members of Dacini. Bactroceraclarifemur sp. n. is superficially similar to B.pendleburyi (Perkins) based on morphology, but there are several apomorphic characters to distinguish the two. Both COI and a segment of the nuclear gene Elongation Factor 1 alpha separate the two species as well.

Description of a new species of Dacus from Sri Lanka, and new country distribution records (Diptera, Tephritidae, Dacinae)

A fruit fly survey in the Sinharaja and Knuckles National Parks in Sri Lanka (2016), using traps baited with the male lures methyl eugenol, cue-lure, and zingerone, yielded 21 species of Dacini fruit flies. Of these, three species, viz. Bactroceraamarambalensis Drew, B.dongnaiae Drew & Romig, and B.rubigina (Wang & Zhao), are new country occurrence records, and Dacus (Mellesis) ancoralis Leblanc & Doorenweerd, sp. n. is described as a new species. The Sri Lankan Dacini fruit fly fauna is now comprised of 39 species.

HiMAP: Robust phylogenomics from highly multiplexed amplicon sequencing

High-throughput sequencing has fundamentally changed how molecular phylogenetic data sets are assembled, and phylogenomic data sets commonly contain 50- to 100-fold more loci than those generated using traditional Sanger sequencing-based approaches. Here, we demonstrate a new approach for building phylogenomic data sets using single-tube, highly multiplexed amplicon sequencing, which we name HiMAP (highly multiplexed amplicon-based phylogenomics) and present bioinformatic pipelines for locus selection based on genomic and transcriptomic data resources and postsequencing consensus calling and alignment. This method is inexpensive and amenable to sequencing a large number (hundreds) of taxa simultaneously and requires minimal hands-on time at the bench (<1/2 day), and data analysis can be accomplished without the need for read mapping or assembly. We demonstrate this approach by sequencing 878 amplicons in single reactions for 82 species of tephritid fruit flies across seven genera (384 individuals), including some of the most economically important agricultural insect pests. The resulting filtered data set (>150,000-bp concatenated alignment, ~20% missing character sites across all individuals and amplicons) contained >40,000 phylogenetically informative characters, and although some discordance was observed between analyses, it provided unparalleled resolution of many phylogenetic relationships in this group. Most notably, we found high support for the generic status of Zeugodacus and the sister relationship between Dacus and Zeugodacus. We discuss HiMAP, with regard to its molecular and bioinformatic strengths, and the insight the resulting data set provides into relationships of this diverse insect group.

HiMAP: Robust phylogenomics from highly multiplexed amplicon sequencing

High-throughput sequencing has fundamentally changed how molecular phylogenetic data sets are assembled, and phylogenomic data sets commonly contain 50- to 100-fold more loci than those generated using traditional Sanger sequencing-based approaches. Here, we demonstrate a new approach for building phylogenomic data sets using single-tube, highly multiplexed amplicon sequencing, which we name HiMAP (highly multiplexed amplicon-based phylogenomics) and present bioinformatic pipelines for locus selection based on genomic and transcriptomic data resources and postsequencing consensus calling and alignment. This method is inexpensive and amenable to sequencing a large number (hundreds) of taxa simultaneously and requires minimal hands-on time at the bench (<1/2 day), and data analysis can be accomplished without the need for read mapping or assembly. We demonstrate this approach by sequencing 878 amplicons in single reactions for 82 species of tephritid fruit flies across seven genera (384 individuals), including some of the most economically important agricultural insect pests. The resulting filtered data set (>150,000-bp concatenated alignment, ~20% missing character sites across all individuals and amplicons) contained >40,000 phylogenetically informative characters, and although some discordance was observed between analyses, it provided unparalleled resolution of many phylogenetic relationships in this group. Most notably, we found high support for the generic status of Zeugodacus and the sister relationship between Dacus and Zeugodacus. We discuss HiMAP, with regard to its molecular and bioinformatic strengths, and the insight the resulting data set provides into relationships of this diverse insect group.

A global checklist of the 932 fruit fly species in the tribe Dacini (Diptera, Tephritidae)

The correct application of the scientific names of species is neither easy nor trivial. Mistakes can lead to the wrong interpretation of research results or, when pest species are involved, inappropriate regulations and limits on trade, and possibly quarantine failures that permit the invasion of new pest species. Names are particularly challenging to manage when groups of organisms encompass a large number of species, when different workers employ different philosophical views, or when species are in a state of taxonomic flux. The fruit fly tribe Dacini is a species-rich taxon within Tephritidae and contains around a fifth of all known species in the family. About 10% of the 932 currently recognized species are pests of commercial fruits and vegetables, precipitating quarantines and trade embargos. Authoritative species lists consist largely of scattered regional treatments and outdated online resources. The checklist presented here is the first global overview of valid species names for the Dacini in almost two decades, and includes new lure records. By publishing this list both in paper and digitally, we aim to provide a resource for those studying fruit flies as well as researchers studying components of their impact on agriculture. The list is largely a consolidation of previous works, but following the results from recent phylogenetic work, we transfer one subgenus and eight species to different genera: members of the Bactrocera subgenus Javadacus Hardy, considered to belong to the Zeugodacus group of subgenera, are transferred to genus Zeugodacus; Bactrocera pseudocucurbitae White, 1999, stat. rev., is transferred back to Bactrocera from Zeugodacus; Zeugodacus arisanicus Shiraki, 1933, stat. rev., is transferred back to Zeugodacus from Bactrocera; and Z. brevipunctatus (David & Hancock, 2017), comb. n.; Z. javanensis (Perkins, 1938), comb. n.; Z. montanus (Hardy, 1983), comb. n.; Z. papuaensis (Malloch, 1939), comb. n.; Z. scutellarius (Bezzi, 1916), comb. n.; Z. semisurstyli (Drew & Romig, 2013), comb. n.; and Z. trilineatus (Hardy, 1955), comb. n. are transferred from Bactrocera to Zeugodacus.

A phylogenetic assessment of the polyphyletic nature and intraspecific color polymorphism in the Bactrocera dorsalis complex (Diptera, Tephritidae)

The Bactroceradorsalis complex (Tephritidae) comprises 85 species of fruit flies, including five highly destructive polyphagous fruit pests. Despite significant work on a few key pest species within the complex, little has been published on the majority of non-economic species in the complex, other than basic descriptions and illustrations of single specimens regarded as typical representatives. To elucidate the species relationships within the Bactroceradorsalis complex, we used 159 sequences from one mitochondrial (COI) and two nuclear (elongation factor-1α and period) genes to construct a phylogeny containing 20 described species from within the complex, four additional species that may be new to science, and 26 other species from Bactrocera and its sister genus Dacus. The resulting concatenated phylogeny revealed that most of the species placed in the complex appear to be unrelated, emerging across numerous clades. This suggests that they were placed in the Bactroceradorsalis complex based on the similarity of convergent characters, which does not appear to be diagnostic. Variations in scutum and abdomen color patterns within each of the non-economic species are presented and demonstrate that distantly-related, cryptic species overlap greatly in traditional morphological color patterns used to separate them in keys. Some of these species may not be distinguishable with confidence by means other than DNA data.

Description of a new species and new country distribution records of Bactrocera (Diptera: Tephritidae: Dacinae) from Cambodia

Bactrocera (Bactrocera) kohkongiae Leblanc (Diptera: Tephritidae: Dacinae), from the Koh Kong Province of Cambodia, is described as new. This species belongs to the Oriental fruit fly (B. dorsalis) complex. Genetic sequences (mitochondrial COI and nuclear EF1α and Period) are deposited in GenBank. A haplotype network, based on the COI sequences for 21 specimens, shows high genetic diversity. New country records from Cambodia are included for 22 species.

Genetic Diversity of Bactrocera dorsalis (Diptera: Tephritidae) on the Hawaiian Islands: Implications for an Introduction Pathway Into California

Population genetic diversity of the oriental fruit fly, Bactrocera dorsalis (Hendel), on the Hawaiian islands of Oahu, Maui, Kauai, and Hawaii (the Big Island) was estimated using DNA sequences of the mitochondrial cytochrome c oxidase subunit I gene. In total, 932 flies representing 36 sampled sites across the four islands were sequenced for a 1,500-bp fragment of the gene named the C1500 marker. Genetic variation was low on the Hawaiian Islands with >96% of flies having just two haplotypes: C1500-Haplotype 1 (63.2%) or C1500-Haplotype 2 (33.3%). The other 33 flies (3.5%) had haplotypes similar to the two dominant haplotypes. No population structure was detected among the islands or within islands. The two haplotypes were present at similar frequencies at each sample site, suggesting that flies on the various islands can be considered one population. Comparison of the Hawaiian data set to DNA sequences of 165 flies from outbreaks in California between 2006 and 2012 indicates that a single-source introduction pathway of Hawaiian origin cannot explain many of the flies in California. Hawaii, however, could not be excluded as a maternal source for 69 flies. There was no clear geographic association for Hawaiian or non-Hawaiian haplotypes in the Bay Area or Los Angeles Basin over time. This suggests that California experienced multiple, independent introductions from different sources.

Application of agriculture-developed demographic analysis for the conservation of the Hawaiian alpine wekiu bug

Insects that should be considered for conservation attention are often overlooked because of a lack of data. The detailed information necessary to assess population growth, decline, and maximum range is particularly difficult to acquire for rare and cryptic species. Many of these difficulties can be overcome with the use of life table analyses and heat energy accumulation models common in agriculture. The wekiu bug (Nysius wekiuicola), endemic to the summit of one volcanic mountain in Hawaii, is a rare insect living in an environmentally sensitive alpine stone desert, where field-based population assessments would be inefficient or potentially detrimental to natural and cultural resources. We conducted laboratory experiments with the insects by manipulating rearing temperatures of laboratory colonies and made detailed observations of habitat conditions to develop life tables representing population growth parameters and environmental models for wekiu bug phenology and demographic change. Wekiu bugs developed at temperatures only found in its environment on sunny days and required the thermal buffer found on cinder cones for growth and population increase. Wekiu bugs required approximately 3.5 months to complete one generation. The bug developed optimally from 26 to 30 °C, temperatures that are much higher than the air temperature attains in its elevational range. The developmental temperature range of the species confirmed a physiological reason why the wekiu bug is only found on cinder cones. This physiology information can help guide population monitoring and inform habitat restoration and conservation. The wekiu bug was a candidate for listing under the U.S. Endangered Species Act, and the developmental parameters we quantified were used to determine the species would not be listed as endangered or threatened. The use of developmental threshold experiments, life table analyses, and degree day modeling can directly inform otherwise unobservable habitat needs and demographic characteristics of extremely rare insects.

Convergent evolution of morphology and habitat use in the explosive Hawaiian fancy case caterpillar radiation

Species occurring in unconnected, but similar habitats and under similar selection pressures often display strikingly comparable morphology, behaviour and life history. On island archipelagos where colonizations and extinctions are common, it is often difficult to separate whether similar traits are a result of in situ diversification or independent colonization without a phylogeny. Here, we use one of Hawaii's most ecologically diverse and explosive endemic species radiations, the Hawaiian fancy case caterpillar genus Hyposmocoma, to test whether in situ diversification resulted in convergence. Specifically, we examine whether similar species utilizing similar microhabitats independently developed largely congruent larval case phenotypes in lineages that are in comparable, but isolated environments. Larvae of these moths are found on all Hawaiian Islands and are characterized by an extraordinary array of ecomorphs and larval case morphology. We focus on the 'purse cases', a group that is largely specialized for living within rotting wood. Purse cases were considered a monophyletic group, because morphological, behavioural and ecological traits appeared to be shared among all members. We constructed a phylogeny based on nuclear and mitochondrial DNA sequences from 38 Hyposmocoma species, including all 14 purse case species and 24 of non-purse case congeners. Divergence time estimation suggests that purse case lineages evolved independently within dead wood and developed nearly identical case morphology twice: once on the distant Northwest Hawaiian Islands between 15.5 and 9 Ma and once on the younger main Hawaiian Islands around 3.0 Ma. Multiple ecomorphs are usually found on each island, and the ancestral ecomorph of Hyposmocoma appears to have lived on tree bark. Unlike most endemic Hawaiian radiations that follow a clear stepwise progression of colonization, purse case Hyposmocoma do not follow a pattern of colonization from older to younger island. We postulate that the diversity of microhabitats and selection from parasitism/predation from endemic predators may have shaped case architecture in this extraordinary endemic radiation of Hawaiian insects.

Conservation implications of changes in endemic Hawaiian Drosophilidae diversity across land use gradients

Endemic Hawaiian Drosophilidae, a radiation of nearly 1000 species including 13 federally listed as endangered, occur mostly in intact native forest, 500–1500 m above sea level. But their persistence in disturbed forest and agricultural areas has not been documented. Thus, control efforts for agricultural pests may impact endemic species if previously undocumented refugia in agricultural areas may play a role in their conservation. To quantify whether invasive plants and agriculture habitats may harbor endemic Drosophilidae, we established standardized trapping arrays, with traps typically designed to control invasive fruit flies (Tephritidae), with 81 sites across native, disturbed and agricultural land use gradients on the islands of Hawai’i and Maui. We collected and identified, to species level, over 22,000 specimens. We found 121 of the possible 292 species expected to occur in the sampled areas, and the majority (91%) of the captured specimens belonged to 24 common species. Species diversity and numbers were greatest in the native forest, but 55% of the species occurred in the invasive strawberry guava belt and plantation forest, adjacent to and almost 500 m from native forest, and 22 species were collected in orchards and nonnative forest as far as 10 km from native habitats. Their persistence outside of native forest suggests that more careful management of disturbed forest and a reassessment of its conservation value are in order. Conservation efforts and assessments of native forest integrity should include the subset of species restricted to intact native forest, since these species are highly localized and particularly sensitive. Additionally, future efforts to control invasive pest fruit flies should consider the nontarget impacts of maintaining traps in and near native forest. This survey project demonstrates the utility of thorough biotic surveys and taxonomic expertise in developing both sensitive species lists and baseline diversity indices for future conservation and monitoring efforts.

Evolution of Manduca sexta hornworms and relatives: biogeographical analysis reveals an ancestral diversification in Central America

The hawkmoth genus Manduca is a diverse group of very large, conspicuous moths that has served as an important model across many biological disciplines. Two species in particular, the tobacco hornworm (Manduca sexta) and the tomato hornworm (Manduca quinquemaculatus) have been researched extensively. Studies across biological fields have referred to these two species as being closely related or even sister species, but the extent to which these two model organisms are related remains largely unknown. We conducted a comprehensive multi-gene phylogenetic analysis of Manduca, based on both an ML and Bayesian framework, which resulted in a monophyletic Manduca but only when two other genera, Dolba and Euryglottis are included. We tentatively conclude that the sister group to Manduca sexta comprises the Caribbean M. afflicta and M. johanni, and the sister lineage to this clade includes M. quinquemaculatus and the Hawaiian M. blackburni. Thus, M. sexta and M. quinquemaculatus are closely related, but are not sister species. Biogeographical analyses reveal an ancestral center of diversification in Central America, and Manduca appears to have subsequently colonized North and South America. Our phylogeny provides an important foundation for comparative studies of two model organisms and their relatives.

Three new species of Fancy Case caterpillars from threatened forests of Hawaii (Lepidoptera, Cosmopterigidae, Hyposmocoma)

The endemic Hawaiian moth genus Hyposmocoma includes 348 described species and perhaps twice as many that remain undescribed. The genus is unusual within Lepidoptera in that its larvae create distinctive silk cases in which they perambulate while protected and camouflaged. An extraordinary diversity of case types exists, and to date more than ten different types have been identified, each corresponding roughly to a separate evolutionary lineage. In this study, we describe three new species of Hyposmocoma: Hyposmocoma ipohapuusp. n. from Big Island, Hyposmocoma makawaosp. n. from Makawao Forest Reserve in Mauiand Hyposmocoma tantalasp. n. from Mt. Tantalus, Oahu, all of which produce tubular purse cases during their larval stage. We also describe the female of Hyposmocoma inversella Walsingham, which was previously undescribed, and re-describe two closely related species, Hyposmocoma auropurpurea Walsingham and Hyposmocoma nebulifera Walsingham, neither which have been formally described in recent years. We present for the first time, primer sequences for a 705 bp fragment of CAD, designed for Hyposmocoma and relatives. The molecular phylogeny based on mitochondrial and nuclear loci demonstrates that all are distinct species. The discovery of a new, endemic species from Mt. Tantalus, an area with many invasive species, suggests that even relatively degraded areas in Hawaii would be worthy of active conservation efforts.

Geographic proximity not a prerequisite for invasion: Hawaii not the source of California invasion by light brown apple moth (Epiphyas postvittana)

BACKGROUND

The light brown apple moth (LBAM), Epiphyas postvittana (Walker), is native to Australia but invaded England, New Zealand, and Hawaii more than 100 years ago. In temperate climates, LBAM can be a major agricultural pest. In 2006 LBAM was discovered in California, instigating eradication efforts and quarantine against Hawaiian agriculture, the assumption being that Hawaii was the source of the California infestation. Genetic relationships among populations in Hawaii, California, and New Zealand are crucial to understanding LBAM invasion dynamics across the Pacific.

METHODOLOGY/PRINCIPAL FINDINGS

We sequenced mitochondrial DNA (mtDNA) from 1293 LBAM individuals from California (695), Hawaii (448), New Zealand (147), and Australia (3) to examine haplotype diversity and structure among introduced populations, and evaluate the null hypothesis that invasive populations are from a single panmictic source. However, invasive populations in California and New Zealand harbor deep genetic diversity, whereas Hawaii shows low level, shallow diversity.

CONCLUSIONS/SIGNIFICANCE

LBAM recently has established itself in California, but was in Hawaii and New Zealand for hundreds of generations, yet California and New Zealand show similar levels of genetic diversity relative to Hawaii. Thus, there is no clear relationship between duration of invasion and genetic structure. Demographic statistics suggest rapid expansion occurring in California and past expansions in New Zealand; multiple introductions of diverse, genetically fragmented lineages could contribute to these patterns. Hawaii and California share no haplotypes, therefore, Hawaii is not the source of the California introduction. Paradoxically, Hawaii and California share multiple haplotypes with New Zealand. New Zealand may be the source for the California and Hawaii infestations, but the introductions were independent, and Hawaii was invaded only once. This has significant implications for quarantine, and suggests that probability of invasion is not directly related to geographic distance. Surprisingly, Hawaiian LBAM populations have much lower genetic diversity than California, despite being older.

Captures of pest fruit flies (Diptera: Tephritidae) and nontarget insects in BioLure and torula yeast traps in Hawaii

MultiLure traps were deployed in a Hawaiian orchard to compare the attraction of economically important fruit flies and nontarget insects to the three-component BioLure and torula yeast food lures. Either water or a 20% propylene glycol solution was used to dissolve the torula yeast or as capture fluid in BioLure traps. Torula yeast in water was more attractive than BioLure for male and female Bactrocera cucurbitae (Coquillett) and Bactrocera dorsalis (Hendel) and as attractive for Ceratitis capitata (Wiedemann), and the addition of propylene glycol significantly inhibited the attractiveness of torula yeast. The known synergistic effect of propylene glycol with BioLure, resulting in increased captures of Anastrepha flies, was not observed with Bactrocera. Nontarget Drosophilidae, Neriidae, Phoridae, Calliphoridae, Sarcophagidae, and Muscidae were more strongly attracted to BioLure, and both lures collected Chloropidae equally. As with fruit flies, propylene glycol in torula yeast significantly decreased nontarget captures. The results therefore suggest that torula yeast in water is a more effective attractant than BioLure for pest Bactrocera while minimizing nontarget captures.

Attraction of Ceratitis capitata (Diptera: Tephritidae) and endemic and introduced nontarget insects to BioLure bait and its individual components in Hawaii

BioLure, a synthetic food attractant for Mediterranean fruit fly [Ceratitis capitata (Wiedemann)], is composed of three chemicals (ammonium acetate, trimethylamine hydrochloride, and putrescine). We deployed these components together and in separate MultiLure traps across predominantly native forests, non-native forests, farmlands, orchards, and residential areas on the islands of Hawaii and Maui, to evaluate attraction of C. capitata and nontarget insects. Large numbers (as many as 186 per trap per day) of mainly saprophagous nontarget flies (primarily Drosophilidae, Chloropidae, Lonchaeidae, Neriidae, Otitidae, and Calliphoridae) were attracted to BioLure. Very few predators, parasitoids, or pollinators were attracted. Native species, predominantly drosophilid and calliphorid flies, were attracted in large numbers in endemic forests, but mostly (at least 88%) introduced species were collected in orchards, backyards, and non-native forest. A comparison of attraction to the three separate components versus combined components in traps revealed that ammonium acetate and, to a lesser extent, putrescine are the key components attractive to nontarget species. Omitting the putrescine ingredient from BioLure did not drastically decrease C. capitata catches but reduced nontarget captures by 20%.

Attraction of nontarget species to fruit fly (Diptera: tephritidae) male lures and decaying fruit flies in traps in hawaii

Synthetic male lures are commonly used to monitor and mass trap pestiferous fruit flies (Diptera: Tephritidae: Dacinae). However, there has been much dispute as to the nontarget impacts of such lures on beneficial and native insects. To evaluate nontarget attraction effects, traps baited with Cue-Lure and methyl eugenol were maintained and emptied weekly in a range of native and non-native forest and commercial orchard and backyard sites on Hawaii and Maui Islands. Lure trap captures were compared against those from unbaited control traps and traps artificially baited with decaying fruit flies to mimic the effect of accumulation of dead trapped target flies in male lure traps. Cue-Lure did not attract nontargets, and methyl eugenol attracted low but significant numbers of five species of flower-associated insects (honey bees, syrphid flies, nitidulid beetles, and endemic crambid moths) and two endemic Hawaiian species of sciarids (Diptera) and mirids (Hemiptera). Saprophagous nontargets, mostly Diptera, were abundant and diverse in traps baited with decaying flies and in male lure traps where accumulation of dead flies occurred but not in male lure traps with few or no fruit fly captures. Most of the previously published records of attraction to methyl eugenol are shown to actually be secondary attraction to decaying fruit flies. Endemic nontargets were collected in native and adjacent forest, but almost exclusively invasive species were attracted to traps placed in non-native habitats. Attraction of flower-associated species may be minimized if methyl eugenol traps are placed in trees after flowering season in orchards.

Evidence of repeated and independent saltational evolution in a peculiar genus of sphinx moths (Proserpinus: Sphingidae)

BACKGROUND

Saltational evolution in which a particular lineage undergoes relatively rapid, significant, and unparalleled change as compared with its closest relatives is rarely invoked as an alternative model to the dominant paradigm of gradualistic evolution. Identifying saltational events is an important first-step in assessing the importance of this discontinuous model in generating evolutionary novelty. We offer evidence for three independent instances of saltational evolution in a charismatic moth genus with only eight species.

METHODOLOGY/PRINCIPAL FINDINGS

Maximum parsimony, maximum likelihood and Bayesian search criteria offered congruent, well supported phylogenies based on 1,965 base pairs of DNA sequence using the mitochondrial gene cytochrome oxidase subunit I, and the nuclear genes elongation factor-1 alpha and wingless. Using a comparative methods approach, we examined three taxa exhibiting novelty in the form of Batesian mimicry, host plant shift, and dramatic physiological differences in light of the phylogenetic data. All three traits appear to have evolved relatively rapidly and independently in three different species of Proserpinus. Each saltational species exhibits a markedly different and discrete example of discontinuous trait evolution while remaining canalized for other typical traits shared by the rest of the genus. All three saltational taxa show insignificantly different levels of overall genetic change as compared with their congeners, implying that their divergence is targeted to particular traits and not genome-wide.

CONCLUSIONS/SIGNIFICANCE

Such rapid evolution of novel traits in individual species suggests that the pace of evolution can be quick, dramatic, and isolated--even on the species level. These results may be applicable to other groups in which specific taxa have generated pronounced evolutionary novelty. Genetic mechanisms and methods for assessing such relatively rapid changes are postulated.

Phylogeography and ecology of an endemic radiation of Hawaiian aquatic case-bearing moths (Hyposmocoma: Cosmopterigidae)

The endemic moth genus Hyposmocoma (Lepidoptera: Cosmopterigidae) may be one of the most speciose and ecologically diverse genera in Hawaii. Among this diversity is the Hyposmocoma saccophora clade with previously unrecorded aquatic larvae. I present a molecular phylogeny based on 773 base pairs (bp) of the mitochondrial gene cytochrome c oxidase subunit I and 762 bp of the nuclear gene elongation factor 1-alpha. Topologies were constructed from data using maximum-parsimony, maximum-likelihood and Bayesian search criteria. Results strongly support the monophyly of the H. saccophora clade and the monophyly of the genus Hyposmocoma. The H. saccophora clade has single-island endemic species on Oahu, Molokai and West Maui. By contrast, there are three species endemic to Kauai, two being sympatric. The H. saccophora clade appears to follow the progression rule, with more basal species on older islands, including the most basal species on 11 Myr-old Necker Island, one of the Northwestern Hawaiian Islands. Aquatic behaviour either evolved recently in the species on the main Hawaiian Islands or was secondarily lost on the arid northwestern Necker Island. The phylogeny suggests that Hyposmocoma is older than any of the current main islands, which may, in part, explain Hyposmocoma's remarkable diversity.

A genomic perspective on the shortcomings of mitochondrial DNA for "barcoding" identification

Approximately 600-bp sequences of mitochondrial DNA (mtDNA) have been designated as "DNA barcodes" and have become one of the most contentious and animated issues in the application of genetic information to global biodiversity assessment and species identification. Advocates of DNA barcodes have received extensive attention and promotion in many popular and refereed scientific publications. However, we suggest that the utility of barcodes is suspect and vulnerable to technical challenges that are particularly pertinent to mtDNA. We review the natural history of mtDNA and discuss problems for barcoding which are particularly associated with mtDNA and inheritance, including reduced effective population size, maternal inheritance, recombination, inconsistent mutation rate, heteroplasmy, and compounding evolutionary processes. The aforementioned could significantly limit the application and utility of mtDNA barcoding efforts. Furthermore, global use of barcodes will require application and acceptance of a barcode-based species concept that has not been evaluated in the context of the extensive literature concerning species designation. Implementation of mtDNA barcodes in spite of technical and practical shortcomings we discuss may degrade the longstanding synthesis of genetic and organism-based research and will not advance studies ranging from genomic evolution to biodiversity assessment.

Utility of mitochondrial DNA barcodes in species conservation

Molecular tools are a standard part of many conservation studies and can be informative at many different levels of analysis, although there are inherent limitations and strengths of different genes or parts of genes to inform specific questions. Animal DNA barcodes, 600- to 800-base-pair segments of the mitochondrial gene cytochrome oxidase I, have been proposed as a means to quantify global biodiversity. Although mitochondrial (mt) DNA has a long history of use at the species level, recent analyses suggest that the use of a single gene, particularly mitochondrial, is unlikely to yield data that are balanced, universally acceptable, or sufficient in taxonomic scope to recognize many species lineages. Mitochondrial and nuclear genomes have different patterns of evolution and modes of inheritance, which can result in very different assessments of biodiversity. The ramifications of choosing a particular definition of species (species concept) need to be carefully considered because current efforts have designated DNA barcodes as the universal species concept without demonstrating its superiority over preexisting concepts. The results of such a barcoding paradigm may include a failure to recognize significant portions of biodiversity or nuclear/mitochondrial mixed lineages and could spuriously focus conservation resources on populations with relatively minor mtDNA divergence. DNA barcodes are most likely to provide potentially useful information for groups that are already well studied, and such taxa do not constitute the majority of biodiversity or those in most need of research attention. DNA barcode-length sequences are an important source of data but, when used alone or out of context, may offer only a fraction of the information needed to characterize species while taking resources from broader studies that could produce information essential to robust and informed conservation decisions.

Are plant DNA barcodes a search for the Holy Grail?

In a recent study, Kress et al. compared two plant genomes to seek out plant DNA barcodes. Two promising markers balanced the variability that is needed to distinguish species with conserved primer regions that enable universal amplification. Although this study is the most rigorous effort to date, problems from earlier barcoding efforts, such as the use of non-evolutionary species concepts and differential sorting of genes and species, could reemerge. Single-gene barcoding might not be universally effective owing to inherent inaccuracies. Kress et al. suggest the use of multiple genes, reflecting an integrated approach that is likely to be the best answer to identifying species quickly and accurately.

Web-spinning caterpillar stalks snails

Moths and butterflies compose one of the most diverse insect orders, but they are overwhelmingly herbivorous. Less than 0.2% are specialized predators, indicating that lepidopteran feeding habits are highly constrained. We report a Hawaiian caterpillar that specializes on snails, a unique food source requiring an unusual feeding strategy. The caterpillar uses silk to restrain live prey. All caterpillars have silk glands, but none are known to use silk in this spiderlike fashion. Considering the canalization of caterpillar diets, evolution to attack and feed on snails is an anomaly. Hawaii s isolation and consequently disharmonic biota likely promote evolutionary experiments that occur nowhere else.

Evolution of ecological traits and wing morphology in Hemileuca (Saturniidae) based on a two-gene phylogeny

We present a molecular phylogeny for the genus Hemileuca (Saturniidae), based on 624 bp of mitochondrial cytochrome oxidase I (COI) and 932 bp of the nuclear gene elongation factor 1 alpha (EF1alpha). Combined analysis of both gene sequences increased resolution and supported most of the phylogenetic relationships suggested by separate analysis of each gene. However, a maximum parsimony (MP) model for just COI sequence from one sample of most taxa produced a phylogeny incongruent with EF1alpha and combined dataset analyses under either MP or ML models. Time of year and time of day during which adult moths fly corresponded strongly with the phylogeny. Although most Hemileuca are diurnal, ancestral Hemileuca probably were nocturnal, fall-flying insects. The two-gene molecular phylogeny suggests that wing morphology is frequently homoplastic. There was no correlation between the primary larval hostplants and phylogenetic placement of taxa. No phylogenetic pattern of specialization was evident for single hostplant families across the genus. Our results suggest that phenological behavioral characters may be more conserved than the wing morphology characters that are more commonly used to infer phylogenetic relationships in Lepidoptera. Inclusion of a molecular component in the re-evaluation of systematic data is likely to alter prior assumptions of phylogenetic relationships in groups where such potentially homoplastic characters have been used.