Toussaint EFA, Breinholt JW, Earl C, Warren AD, Brower JVZ, Yago M, Dexter KM, Espeland M, Pierce NE, Lohman DJ, et al. Anchored phylogenomics illuminates the skipper butterfly tree of life. BMC Evolutionary Biology. 2018. touissant_et_al_2018_s12862-018-1216-z-2.pdf
Kawahara AY, Breinholt JW, Espeland M, Storer C, Plotkin D, Dexter KM, Toussaint EFA, St Laurent RA, Brehm G, Vargas S, et al. Phylogenetics of moth-like butterflies (Papilionoidea: Hedylidae) based on a new 13-locus target capture probe set. Molecular Phylogenetics and Evolution. 2018. kawahara_moth.pdf
Espeland M, Breinholt J, Willmott KR, Warren AD, Vila R, Toussaint EFA, Maunsell SC, Kwaku AP, Talavera G, Eastwood R, et al. Comprehensive higher-level phylogeny of butterflies (Papilionoidea) inferred from genomic data. Current Biology. 2018;28 :770-778. Publisher's Version espeland_et_al_2018_-s2.0-s0960982218300940-main.pdf
Janda MF, Matos-Maravi P, Borovanska M, Zima Jr J, Youngerman E, Pierce NE. Phylogeny and population genetic structure of the ant genus Acropyga (Hymenoptera : Formicidae) in Papua New Guinea. Invertebrate Systematics. 2016;30 :28-40. 2016_Janda_et_al.pdf
Espeland M, Hall JPW, DeVries PJ, Lees DC, Cornwall M, Hsu YF, Wu LW, Campbell DL, Talavera G, Vila R, et al. Ancient Neotropical origin and recent recolonisation: Phylogeny, biogeography and diversification of the Riodinidae (Lepidoptera: Papilionoidea). Molecular Phylogenetics and Evolution. 2015;93 :296-306.Abstract

We present the first dated higher-level phylogenetic and biogeographic analysis of the butterfly family Riodinidae. This family is distributed worldwide, but more than 90% of the c. 1500 species are found in the Neotropics, while the c. 120 Old World species are concentrated in the Southeast Asian tropics, with minor Afrotropical and Australasian tropical radiations, and few temperate species. Morphologically based higher classification is partly unresolved, with genera incompletely assigned to tribes. Using 3666 bp from one mitochondrial and four nuclear markers for each of 23 outgroups and 178 riodinid taxa representing all subfamilies, tribes and subtribes, and 98 out of 145 described genera of riodinids, we estimate that Riodinidae split from Lycaenidae about 96 Mya in the mid-Cretaceous and started to diversify about 81 Mya. The Riodinidae are monophyletic and originated in the Neotropics, most likely in lowland proto-Amazonia. Neither the subfamily Euselasiinae nor the Nemeobiinae are monophyletic as currently constituted. The enigmatic, monotypic Neotropical genera Styx and Corrachia (most recently treated in Euselasiinae: Corrachiini) are highly supported as derived taxa in the Old World Nemeobiinae, with dispersal most likely occurring across the Beringia land bridge during the Oligocene. Styx and Corrachia, together with all other nemeobiines, are the only exclusively Primulaceae-feeding riodinids. The steadily increasing proliferation of the Neotropical Riodininae subfamily contrasts with the decrease in diversification in the Old World, and may provide insights into factors influencing the diversification rate of this relatively ancient clade of Neotropical insects. (C) 2015 Elsevier Inc. All rights reserved.

Boyle JH, Kaliszewska ZA, Espeland M, Suderman TR, Fleming J, Heath A, Pierce NE. Phylogeny of the Aphnaeinae: myrmecophilous African butterflies with carnivorous and herbivorous life histories. Systematic Entomology. 2015;40 :169-182.Abstract

The Aphnaeinae (Lepidoptera: Lycaenidae) are a largely African subfamily of 278 described species that exhibit extraordinary life-history variation. The larvae of these butterflies typically form mutualistic associations with ants, and feed on a wide variety of plants, including 23 families in 19 orders. However, at least one species in each of 9 of the 17 genera is aphytophagous, parasitically feeding on the eggs, brood or regurgitations of ants. This diversity in diet and type of symbiotic association makes the phylogenetic relations of the Aphnaeinae of particular interest. A phylogenetic hypothesis for the Aphnaeinae was inferred from 4.4kb covering the mitochondrial marker COI and five nuclear markers (wg, H3, CAD, GAPDH and EF1) for each of 79 ingroup taxa representing 15 of the 17 currently recognized genera, as well as three outgroup taxa. Maximum Parsimony, Maximum Likelihood and Bayesian Inference analyses all support Heath's systematic revision of the clade based on morphological characters. Ancestral range inference suggests an African origin for the subfamily with a single dispersal into Asia. The common ancestor of the aphnaeines likely associated with myrmicine ants in the genus Crematogaster and plants of the order Fabales.

Kaliszewska ZA, Lohman DJ, Sommer K, Adelson G, Rand DB, Mathew J, Talavera G, Pierce NE. When caterpillars attack: Biogeography and life history evolution of the Miletinae (Lepidoptera: Lycaenidae). Evolution. 2015;69 :571-588.Abstract

Of the four most diverse insect orders, Lepidoptera contains remarkably few predatory and parasitic species. Although species with these habits have evolved multiple times in moths and butterflies, they have rarely been associated with diversification. The wholly aphytophagous subfamily Miletinae (Lycaenidae) is an exception, consisting of nearly 190 species distributed primarily throughout the Old World tropics and subtropics. Most miletines eat Hemiptera, although some consume ant brood or are fed by ant trophallaxis. A well-resolved phylogeny inferred using 4915 bp from seven markers sampled from representatives of all genera and nearly one-third the described species was used to examine the biogeography and evolution of biotic associations in this group. Biogeographic analyses indicate that Miletinae likely diverged from an African ancestor near the start of the Eocene, and four lineages dispersed between Africa and Asia. Phylogenetic constraint in prey selection is apparent at two levels: related miletine species are more likely to feed on related Hemiptera, and related miletines are more likely to associate with related ants, either directly by eating the ants, or indirectly by eating hemipteran prey that are attended by those ants. These results suggest that adaptations for host ant location by ovipositing female miletines may have been retained from phytophagous ancestors that associated with ants mutualistically.

Price SL, Powell S, Kronauer DJC, Tran LAP, Pierce NE, Wayne RK. Renewed diversification is associated with new ecological opportunity in the Neotropical turtle ants. Journal of Evolutionary Biology. 2014;27 :242-258.Abstract

Ecological opportunity, defined as access to new resources free from competitors, is thought to be a catalyst for the process of adaptive radiation. Much of what we know about ecological opportunity, and the larger process of adaptive radiation, is derived from vertebrate diversification on islands. Here, we examine lineage diversification in the turtle ants (Cephalotes), a species-rich group of ants that has diversified throughout the Neotropics. We show that crown group turtle ants originated during the Eocene (around 46 mya), coincident with global warming and the origin of many other clades. We also show a marked lineage-wide slowdown in diversification rates in the Miocene. Contrasting this overall pattern, a species group associated with the young and seasonally harsh Chacoan biogeographic region underwent a recent burst of diversification. Subsequent analyses also indicated that there is significant phylogenetic clustering within the Chacoan region and that speciation rates are highest there. Together, these findings suggest that recent ecological opportunity, from successful colonization of novel habitat, may have facilitated renewed turtle ant diversification. Our findings highlight a central role of ecological opportunity within a successful continental radiation.

Wahlberg N, Rota J, Braby MF, Pierce NE, Wheat CW. Revised systematics and higher classification of pierid butterflies (Lepidoptera: Pieridae) based on molecular data. Zoologica Scripta. 2014;43 :641-650.Abstract

The butterfly family Pieridae comprises approximately 1000 described species placed in 85 genera, but the higher classification has not yet been settled. We used molecular data from eight gene regions (one mitochondrial and seven nuclear protein-coding genes) comprising a total of similar to 6700bp from 96 taxa to infer a well-supported phylogenetic hypothesis for the family. Based on this hypothesis, we revise the higher classification for all pierid genera. We resurrect the tribe Teracolini stat. rev. in the subfamily Pierinae to include the genera Teracolus, Pinacopteryx, Gideona, Ixias, Eronia, Colotis and most likely Calopieris. We transfer Hebomoia to the tribe Anthocharidini and assign the previously unplaced genera Belenois and Dixeia to the subtribe Aporiina. Three lineages near the base of Pierinae (Leptosia, Elodina and Nepheronia + Pareronia) remain unplaced. For each of these, we describe and delineate new tribes: Elodinini Braby tribus nova, Leptosiaini Braby tribus nova and Nepheroniini Braby tribus nova. The proposed higher classification is based on well-supported monophyletic groups and is likely to remain stable even with the addition of more data.

Talavera G, Lukhtanov VA, Rieppel L, Pierce NE, Vila R. In the shadow of phylogenetic uncertainty: The recent diversification of Lysandra butterflies through chromosomal change. Molecular Phylogenetics and Evolution. 2013;69 :469-478.Abstract

The phylogeny of the butterfly genus Lysandra (Lycaenidae, Polyommatinae) has been intractable using both molecular and morphological characters, which could be a result of speciation due to karyotype instability. Here we reconstruct the phylogeny of the group using multi-locus coalescent-based methods on seven independent genetic markers. While the genus is ca. 4.9 Mya old, the diversification of the extant lineages was extremely recent (ca. 1.5 Mya) and involved multiple chromosomal rearrangements. We find that relationships are uncertain due to both incomplete lineage sorting and hybridization. Minimizing the impact of reticulation in inferring the species tree by testing for mitochondria] introgression events yields a partially resolved tree with three main supported clades: L. punctifera + L. bellargus, the corydonius taxa, and L coridon + the Iberian taxa, plus three independent lineages without apparently close relatives (L. ossmar, L syriaca and L. dezina). Based on these results and new karyotypic data, we propose a rearrangement recognizing ten species within the genus. Finally, we hypothesize that chromosomal instability may have played a crucial role in the Lysandra recent diversification. New chromosome rearrangements might be fixed in populations after severe bottlenecks, which at the same time might promote rapid sorting of neutral molecular markers. We argue that population bottlenecks might be a prerequisite for chromosomal speciation in this group. (C) 2013 Elsevier Inc. All rights reserved.

2013_talavera_et_al.pdf 2013_talavera_et_al_supplement.pdf
Talavera G, Lukhtanov VA, Pierce NE, Villa R. Establishing criteria for higher-level classification using molecular data: the systematics of Polyommatusblue butterflies (Lepidoptera, Lycaenidae). Cladistics. 2012 :1-27.Abstract

Most taxonomists agree on the need to adapt current classifications to recognize monophyletic units. However, delineations between higher taxonomic units can be based on the relative ages of different lineages and ⁄or the level of morphological differentiation. In this paper, we address these issues in considering the species-rich Polyommatus section, a group of butterflies whose taxonomy has been highly controversial. We propose a taxonomy-friendly, flexible temporal scheme for higher-level classification. Using molecular data from nine markers (6666 bp) for 104 representatives of the Polyommatus section, representing all but two of the 81 described genera ⁄subgenera and five outgroups, we obtained a complete and well resolved phylogeny for this clade. We use this to revise the systematics of the Polyommatus blues, and to define criteria that best accommodate the described genera within a phylogenetic framework. First, we normalize the concept of section (Polyommatus) and propose the use of subtribe (Polyommatina) instead. To preserve taxonomic stability and traditionally recognized taxa, we designate an age interval (4–5 Myr) instead of a fixed minimum age to define genera. The application of these criteria results in the retention of 31 genera of the 81 formally described generic names, and necessitates the description of one new genus (Rueckbeilia gen. nov.). We note that while classifications should be based on phylogenetic data, applying a rigid universal scheme is rarely feasible. Ideally, taxon age limits should be applied according to the particularities and pre-existing taxonomy of each group. We demonstrate that the concept of a morphological gap may be misleading at the genus level and can produce polyphyletic genera, and we propose that recognition of the existence of cryptic genera may be useful in taxonomy.

Ugelvig LV, Vila R, Pierce NE, Nash DR. A phylogenetic revision of the Glaucopsyche section (Lepidoptera: Lycaenidae), with special focus on the Phengaris-Maculinea clade. Molecular Phylogenetics and Evolution. 2011;61 :237-243.Abstract

Despite much research on the socially parasitic large blue butterflies (genus Maculinea) in the past 40 years, their relationship to their closest relatives, Phengaris, is controversial and the relationships among the remaining genera in the Glaucopsyche section are largely unresolved. The evolutionary history of this butterfly section is particularly important to understand the evolution of life history diversity connected to food-plant and host-ant associations in the larval stage. In the present study, we use a combination of four nuclear and two mitochondrial genes to reconstruct the phylogeny of the Glaucopsyche section, and in particular, to study the relationships among and within the Phengaris-Maculinea species.We find a clear pattern between the clades recovered in the Glaucopsyche section phylogeny and their food-plant associations, with only the Phengaris-Maculinea clade utilising more than one plant family. Maculinea is, for the first time, recovered with strong support as a monophyletic group nested within Phengaris, with the closest relative being the rare genus Caerulea. The genus Glaucopsyche is polyphyletic, including the genera Sinia and lolana. Interestingly, we find evidence for additional potential cryptic species within the highly endangered Maculinea, which has long been suspected from morphological, ecological and molecular studies. (C) 2011 Elsevier Inc. All rights reserved.

Vila R, Bell CD, Macniven R, Goldman-Huertas B, Ree RH, Marshall CR, Balint Z, Johnson K, Benyamini D, Pierce NE. Phylogeny and palaeoecology of Polyommatus blue butterflies show Beringia was a climate-regulated gateway to the New World. Proceedings of the Royal Society B-Biological Sciences. 2011;278 :2737-2744.Abstract

Transcontinental dispersals by organisms usually represent improbable events that constitute a major challenge for biogeographers. By integrating molecular phylogeny, historical biogeography and palaeoecology, we test a bold hypothesis proposed by Vladimir Nabokov regarding the origin of Neotropical Polyommatus blue butterflies, and show that Beringia has served as a biological corridor for the dispersal of these insects from Asia into the New World. We present a novel method to estimate ancestral temperature tolerances using distribution range limits of extant organisms, and find that climatic conditions in Beringia acted as a decisive filter in determining which taxa crossed into the New World during five separate invasions over the past 11 Myr. Our results reveal a marked effect of the Miocene-Pleistocene global cooling, and demonstrate that palaeoclimatic conditions left a strong signal on the ecology of present-day taxa in the New World. The phylogenetic conservatism in thermal tolerances that we have identified may permit the reconstruction of the palaeoecology of ancestral organisms, especially mobile taxa that can easily escape from hostile environments rather than adapt to them.

vila_et_al._2011_evol_of_nabokovs_blues_esm_5.pdf vila_et_al._2011_evol_of_nabokovs_blues_ms.pdf
Vila R, Lukhtanov VA, Talavera G, Gil F, Pierce NE. How common are dot-like distributions? Taxonomical oversplitting in western European Agrodiaetus (Lepidoptera: Lycaenidae) revealed by chromosomal and molecular markers. Biological Journal of the Linnean Society. 2010;101 :130-154.Abstract

Approximately 50 taxa of butterflies in Western Europe have been described as new species or elevated to the level of species during the last 40 years. Many, especially those belonging to the genus Agrodiaetus, have unusually localized, 'dot-like' distributional ranges. In the present study, we use a combination of chromosomal and molecular markers to re-evaluate the species status of Agrodiaetus distributed west of the 17th meridian. The results obtained do not support the current designations of Agrodiaetus galloi, Agrodiaetus exuberans, and Agrodiaetus agenjoi as endemic species with highly restricted distribution ranges, but indicate that these taxa are more likely to be local populations of a widely distributed species, Agrodiaetus ripartii. Agrodiaetus violetae is shown to be a polytypic species consisting of at least two subspecies, including Agrodiaetus violetae subbaeticus comb. nov. and Agrodiaetus violetae violetae. Agrodiaetus violetae is genetically (but not chromosomally) distinct from Agrodiaetus fabressei and has a wider distribution in southern Spain than previously believed. Agrodiaetus humedasae from northern Italy is supported as a highly localized species that is distinct from its nearest relatives. We propose a revision of the species lists for Agrodiaetus taking these new data into account. The results reported in the present study are relevant to animal conservation efforts in Europe because of their implications for IUCN Red List priorities. (C) 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 101, 130-154.

Ramirez SR, Nieh JC, Quental TB, Roubik DW, Imperatriz-Fonseca VL, Pierce NE. A molecular phylogeny of the stingless bee genus Melipona (Hymenoptera: Apidae). Molecular Phylogenetics and Evolution. 2010;56 :519-525.Abstract

Stingless bees (Meliponini) constitute a diverse group of highly eusocial insects that occur throughout tropical regions around the world. The meliponine genus Melipona is restricted to the New World tropics and has over 50 described species. Melipona, like Apis, possesses the remarkable ability to use representational communication to indicate the location of foraging patches. Although Melipona has been the subject of numerous behavioral, ecological, and genetic studies, the evolutionary history of this genus remains largely unexplored. Here, we implement a multigene phylogenetic approach based on nuclear, mitochondrial, and ribosomal loci, coupled with molecular clock methods, to elucidate the phylogenetic relationships and antiquity of subgenera and species of Melipona. Our phylogenetic analysis resolves the relationship among subgenera and tends to agree with morphology-based classification hypotheses. Our molecular clock analysis indicates that the genus Melipona shared a most recent common ancestor at least similar to 14-17 million years (My) ago. These results provide the groundwork for future comparative analyses aimed at understanding the evolution of complex communication mechanisms in eusocial Apidae. (C) 2010 Elsevier Inc. All rights reserved.

Ramirez SR, Roubik DW, Skov C, Pierce NE. Phylogeny, diversification patterns and historical biogeography of euglossine orchid bees (Hymenoptera: Apidae). Biological Journal of the Linnean Society. 2010;100 :552-572.Abstract

The orchid bees constitute a clade of prominent insect pollinators distributed throughout the Neotropical region. Males of all species collect fragrances from natural sources, including flowers, decaying vegetation and fungi, and store them in specialized leg pockets to later expose during courtship display. In addition, orchid bees provide pollination services to a diverse array of Neotropical angiosperms when foraging for food and nesting materials. However, despite their ecological importance, little is known about the evolutionary history of orchid bees. Here, we present a comprehensive molecular phylogenetic analysis based on similar to 4.0 kb of DNA from four loci [cytochrome oxidase (CO1), elongation factor 1-alpha (EF1-alpha), arginine kinase (ArgK) and RNA polymerase II (Pol-II)] across the entire tribe Euglossini, including all five genera, eight subgenera and 126 of the approximately 200 known species. We investigated lineage diversification using fossil-calibrated molecular clocks and the evolution of morphological traits using disparity-through-time plots. In addition, we inferred past biogeographical events by implementing model-based likelihood methods. Our dataset supports a new view on generic relationships and indicates that the cleptoparasitic genus Exaerete is sister to the remaining orchid bee genera. Our divergence time estimates indicate that extant orchid bee lineages shared a most recent common ancestor at 27-42 Mya. In addition, our analysis of morphology shows that tongue length and body size experienced rapid disparity bursts that coincide with the origin of diverse genera (Euglossa and Eufriesea). Finally, our analysis of historical biogeography indicates that early diversification episodes shared a history on both sides of Mesoamerica, where orchid bees dispersed across the Caribbean, and through a Panamanian connection, thus reinforcing the hypothesis that recent geological events (e.g. the formation of the isthmus of Panama) contributed to the diversification of the rich Neotropical biota. (C) 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 100, 552-572.