Phylogeny

2012
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.

2012_talavera_et_al_polyommatus.pdf
2011
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.

ugelvig_lv_et_al._2011_glaucopsyche_mpe.pdf
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
2010
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.

vila_et_al._2010_dot_distrib.pdf
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_stingless.pdf
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.

ramirez_et_al._euglossini_2010.pdf
2009
Russell JA, Moreau CS, Goldman-Huertas B, Fujiwara M, Lohman DJ, Pierce NE. Bacterial gut symbionts are tightly linked with the evolution of herbivory in ants. Proceedings of the National Academy of Sciences of the United States of America. 2009;106 :21236-21241.Abstract

Ants are a dominant feature of terrestrial ecosystems, yet we know little about the forces that drive their evolution. Recent findings illustrate that their diets range from herbivorous to predaceous, with "herbivores'' feeding primarily on exudates from plants and sap-feeding insects. Persistence on these nitrogen-poor food sources raises the question of how ants obtain sufficient nutrition. To investigate the potential role of symbiotic microbes, we have surveyed 283 species from 18 of the 21 ant subfamilies using molecular techniques. Our findings uncovered a wealth of bacteria from across the ants. Notable among the surveyed hosts were herbivorous "turtle ants'' from the related genera Cephalotes and Procryptocerus (tribe Cephalotini). These commonly harbored bacteria from ant-specific clades within the Burkholderiales, Pseudomonadales, Rhizobiales, Verrucomicrobiales, and Xanthomonadales, and studies of lab-reared Cephalotes varians characterized these microbes as symbiotic residents of ant guts. Although most of these symbionts were confined to turtle ants, bacteria from an ant-specific clade of Rhizobiales were more broadly distributed. Statistical analyses revealed a strong relationship between herbivory and the prevalence of Rhizobiales gut symbionts within ant genera. Furthermore, a consideration of the ant phylogeny identified at least five independent origins of symbioses between herbivorous ants and related Rhizobiales. Combined with previous findings and the potential for symbiotic nitrogen fixation, our results strongly support the hypothesis that bacteria have facilitated convergent evolution of herbivory across the ants, further implicating symbiosis as a major force in ant evolution.

2009_russell_et_al.pdf
2008
Canfield MR, Greene E, Moreau CS, Chen N, Pierce NE. Exploring phenotypic plasticity and biogeography in emerald moths: A phylogeny of the genus Nemoria (Lepidoptera: Geometridae). Molecular Phylogenetics and Evolution. 2008;49 :477-487.Abstract

The moth genus Nemoria (Lepidoptera: Geometridae) includes 134 described species whose larvae and adults display a considerable range of phenotypic plasticity in coloration and morphology. We reconstructed the phylogeny of 54 species of Nemoria and seven outgroups using characters from the mitochondrial genes, Cytochrome Oxidase I and II (COI and COII), and the nuclear gene, Elongation Factor-a (EF-1a). Maximum parsimony, maximum likelihood and Bayesian inference were used to infer the phylogeny. The 54 ingroup species represented 13 of the 15 recognized species groups of Nemoria [Ferguson, D.C., 1985. Fasc. 18.1, Geometroidea: Geometridae (in part). In: Dominick, R.B. (Ed.), The Moths of America North of Mexico, Fasc. 18.1. Wedge Entomological Research Foundation, Washington; Pitkin, L.M., 1993. Neotropical emerald moths of the genera Nemoria, Lissochlora and Chavarriella, with particular reference to the species of Costa Rica (Lepidoptera: Geometridae, Geometrinae). Bull. Br. Mus. Nat. Hist. 62, 39–159], and the seven outgroups came from four tribes of Geometrinae. These data support Nemoria as a monophyletic group and largely recover the species groupings proposed in previous taxonomic analyses using morphological characters. Phenotypic plasticity of larvae is not correlated with plasticity of adults among those species of Nemoria where life histories are known, and appears to be evolutionarily labile for both life history stages: Species exhibiting larval phenotypic plasticity, such as N. arizonaria and N. outina, are placed in several distinct clades, suggesting that this trait has evolved multiple times, and species displaying adult phenotypic plasticity are likewise distributed throughout the phylogeny. A comparative analysis of the biogeographic history of Nemoria supports a South American origin for the genus with multiple introductions into North America, and an application of published substitution rates to the phylogram provides an age estimate of 7.5 million years.

2008_canfield_et_al.pdf
Lohman DJ, Peggie D, Pierce NE, Meier R. Phylogeography and genetic diversity of a widespread Old World butterfly, Lampides boeticus (Lepidoptera: Lycaenidae). Bmc Evolutionary Biology. 2008;8.Abstract

Background: Evolutionary genetics provides a rich theoretical framework for empirical studies of phylogeography. Investigations of intraspecific genetic variation can uncover new putative species while allowing inference into the evolutionary origin and history of extant populations. With a distribution on four continents ranging throughout most of the Old World, Lampides boeticus ( Lepidoptera: Lycaenidae) is one of the most widely distributed species of butterfly. It is placed in a monotypic genus with no commonly accepted subspecies. Here, we investigate the demographic history and taxonomic status of this widespread species, and screen for the presence or absence of the bacterial endosymbiont Wolbachia.Results: We performed phylogenetic, population genetic, and phylogeographic analyses using 1799 bp of mitochondrial sequence data from 57 specimens collected throughout the species' range. Most of the samples(> 90%) were nearly genetically identical, with uncorrected pairwise sequence differences of 0 0.5% across geographic distances > 9,000 km. However, five samples from central Thailand, Madagascar, northern Australia and the Moluccas formed two divergent clades differing from the majority of samples by uncorrected pairwise distances ranging from 1.79-2.21%. Phylogenetic analyses suggest that L. boeticus is almost certainly monophyletic, with all sampled genes coalescing well after the divergence from three closely related taxa included for outgroup comparisons. Analyses of molecular diversity indicate that most L. boeticus individuals in extant populations are descended from one or two relatively recent population bottlenecks.Conclusion: The combined analyses suggest a scenario in which the most recent common ancestor of L. boeticus and its sister taxon lived in the African region approximately 7 Mya; extant lineages of L. boeticus began spreading throughout the Old World at least 1.5 Mya. More recently, expansion after population bottlenecks approximately 1.4 Mya seem to have displaced most of the ancestral polymorphism throughout its range, though at least two early-branching lineages still persist. One of these lineages, in northern Australia and the Moluccas, may have experienced accelerated differentiation due to infection with the bacterial endosymbiont Wolbachia, which affects reproduction. Examination of a haplotype network suggests that Australia has been colonized by the species several times. While there is little evidence for the existence of morphologically cryptic species, these results suggest a complex history affected by repeated dispersal events.

lohman_bmc.pdf
2007
Ramirez SR, Gravendeel B, Singer RB, Marshall CR, Pierce NE. Dating the origin of the Orchidaceae from a fossil orchid with its pollinator. Nature. 2007;448 :1042-1045.Abstract

Since the time of Darwin(1), evolutionary biologists have been fascinated by the spectacular adaptations to insect pollination exhibited by orchids. However, despite being the most diverse plant family on Earth(2), the Orchidaceae lack a definitive fossil record and thus many aspects of their evolutionary history remain obscure. Here we report an exquisitely preserved orchid pollinarium (of Meliorchis caribea gen. et sp. nov.) attached to the mesoscutellum of an extinct stingless bee, Proplebeia dominicana, recovered from Miocene amber in the Dominican Republic, that is 15-20 million years (Myr) old(3). This discovery constitutes both the first unambiguous fossil of Orchidaceae(4) and an unprecedented direct fossil observation of a plant-pollinator interaction(5,6). By applying cladistic methods to a morphological character matrix, we resolve the phylogenetic position of M. caribea within the extant subtribe Goodyerinae (subfamily Orchidoideae). We use the ages of other fossil monocots and M. caribea to calibrate a molecular phylogenetic tree of the Orchidaceae. Our results indicate that the most recent common ancestor of extant orchids lived in the Late Cretaceous (76-84 Myr ago), and also suggest that the dramatic radiation of orchids began shortly after the mass extinctions at the K/T boundary. These results further support the hypothesis of an ancient origin for Orchidaceae.

ramirez2007fossilorchidpollinator.pdf
Quek SP, Davies SJ, Ashton PS, Itino T, Pierce NE. The geography of diversification in mutualistic ants: a gene's-eye view into the Neogene history of Sundaland rain forests. Molecular Ecology. 2007;16 :2045-2062.Abstract

We investigate the geographical and historical context of diversification in a complex of mutualistic Crematogaster ants living in Macaranga trees in the equatorial rain forests of Southeast Asia. Using mitochondrial DNA from 433 ant colonies collected from 32 locations spanning Borneo, Malaya and Sumatra, we infer branching relationships, patterns of genetic diversity and population history. We reconstruct a time frame for the ants' diversification and demographic expansions, and identify areas that might have been refugia or centres of diversification. Seventeen operational lineages are identified, most of which can be distinguished by host preference and geographical range. The ants first diversified 16-20 Ma, not long after the onset of the everwet forests in Sundaland, and achieved most of their taxonomic diversity during the Pliocene. Pleistocene demographic expansions are inferred for several of the younger lineages. Phylogenetic relationships suggest a Bornean cradle and major axis of diversification. Taxonomic diversity tends to be associated with mountain ranges; in Borneo, it is greatest in the Crocker Range of Sabah and concentrated also in other parts of the northern northwest coast. Within-lineage genetic diversity in Malaya and Sumatra tends to also coincide with mountain ranges. A series of disjunct and restricted distributions spanning northern northwest Borneo and the major mountain ranges of Malaya and Sumatra, seen in three pairs of sister lineages, further suggests that these regions were rain-forest refuges during drier climatic phases of the Pleistocene. Results are discussed in the context of the history of Sundaland's rain forests.

quek_et_al_2007._geography_of_diversification.pdf
Kandul NR, Lukhtanov VA, Pierce NE. Karyotypic diversity and speciation in Agrodiaetus butterflies. Evolution. 2007;61 :546-559.Abstract

That chromosomal rearrangements may play an important role in maintaining postzygotic isolation between well-established species is part of the standard theory of speciation. However, little evidence exists on the role of karyotypic change in speciation itself-in the establishment of reproductive barriers between previously interbreeding populations. The large genus' Agrodiaetus (Lepidoptera: Lycaenidae) provides a model system to study this question. Agrodiaetus butterflies exhibit unusual interspecific diversity in chromosome number, from n = 10 to n = 134; in contrast, the majority of lycaenid butterflies have n = 23/24. We analyzed the evolution of karyotypic diversity by mapping chromosome numbers on a thoroughly sampled mitochondrial phylogeny of the genus. Karyotypic differences accumulate gradually between allopatric sister taxa, but more rapidly between sympatric sister taxa. Overall, sympatric sister taxa have a higher average karyotypic diversity than allopatric sister taxa. Differential fusion of diverged populations may account for this pattern because the degree of karyotypic difference acquired between allopatric populations may determine whether they will persist as nascent biological species in secondary sympatry. This study therefore finds evidence of a direct role for chromosomal rearrangements in the final stages of animal speciation. Rapid karyotypic diversification is likely to have contributed to the explosive speciation rate observed in Agrodiaetus, 1.6 species per million years.

kandul_et_al_07.pdf
Braby MF, Pierce NE, Vila R. Phylogeny and historical biogeography of the subtribe Aporiina (Lepidoptera : Pieridae): implications for the origin of Australian butterflies. Biological Journal of the Linnean Society. 2007;90 :413-440.Abstract

The Australian fauna is composed of several major biogeographical elements reflecting different spatial and temporal histories. Two groups of particular interest are the Gondwanan Element, reflecting an ancient origin in Gondwana or southern Gondwana (southern vicariance hypothesis), and the Asian Element, reflecting a more recent origin in Asia, Eurasia or Laurasia (northern dispersal hypothesis). Theories regarding the origin and evolution of butterflies (Hesperioidea, Papilionoidea) in Australia are controversial, with no clear consensus. Here, we investigate the phylogenetic and historical biogeographical relationships of the subtribe Aporiina, a widespread taxon with disjunct distributions in each of the major zoogeographical regions. Attention is paid to origins of the subtribe in the Australian Region for which several conflicting hypotheses have been proposed for the Old World genus Delias Hubner. Our phylogenetic reconstruction was based on analysis of fragments of two nuclear genes (elongation factor-1 alpha, wingless) and one mitochondrial gene (cytochrome oxidase subunit 1) for 30 taxa. Phylogenetic analyses based on maximum parsimony, maximum likelihood and Bayesian inference of the combined data set (2729 bp; 917 parsimony informative characters) recovered six major lineages within the monophyletic Aporiina, with the following topology: (Cepora + Prioneris + (Mylothris + (Aporia + Delias group + Catasticta group))). Given a probable age of origin of the stem-group near the Cretaceous/Tertiary boundary (69-54 Mya), followed by diversification of the crown-group in the early to mid Tertiary (57-45 Mya), we show that an origin of the Aporiina in either southern Gondwana or Laurasia is equally parsimonious, and that dispersal has played a major role in shaping the underlying phylogenetic pattern. We tentatively conclude that an origin in southern Gondwanan is more likely; however, neither hypothesis satisfactorily explains the present-day distribution, and additional lower-level phylogenies are needed to determine the directionality of dispersal events of several taxa and to reject one hypothesis over the other. Dispersal is inferred to have occurred primarily during cooler periods when land bridges or stepping-stones were available between many of the zoogeographical regions. (c) 2007 The Linnean Society of London.

braby_phylo.pdf
Braby MF, Pierce NE. Systematics, biogeography and diversification of the Indo-Australian genus Delias Hubner (Lepidoptera : Pieridae): phylogenetic evidence supports an 'out-of-Australia' origin. Systematic Entomology. 2007;32 :2-25.Abstract

Two alternative hypotheses for the origin of butterflies in the Australian Region, that elements dispersed relatively recently from the Oriental Region into Australia (northern dispersal hypothesis) or descended from ancient stocks in Gondwana (southern vicariance hypothesis), were tested using methods of cladistic vicariance biogeography for the Delias group, a diverse and widespread clade in the Indo-Australian Region. A phylogenetic hypothesis of the twenty-four species-groups recognized currently in Delias and its sister genus Leuciacria is inferred from molecular characters generated from the nuclear gene elongation factor-1 alpha (EF-1 alpha) and the mitochondrial genes cytochrome oxidase subunits I and II (COI/COII) and NADH dehydrogenase 5 (ND5). Phylogenetic analyses based on maximum parsimony, maximum likelihood and Bayesian inference of the combined dataset (3888 bp, 1014 parsimony informative characters) confirmed the monophyly of Delias and recovered eight major lineages within the genus, informally designated the singhapura, belladonna, hyparete, chrysomelaena, eichhorni, cuningputi, belisama and nigrina clades. Species-group relationships within these clades are, in general, concordant with current systematic arrangements based on morphology. The major discrepancies concern the placement of the aganippe, belisama and chrysomelaena groups, as well as several species-groups endemic to mainland New Guinea. Two species (D. harpalyce (Donovan), D. messalina Arora) of uncertain group status are currently misplaced based on strong evidence of paraphyly, and are accordingly transferred to the nigrina and kummeri groups, respectively. Based on this phylogeny, a revised systematic classification is presented at the species-group level. An historical biogeographical analysis of the Delias group revealed that the most parsimonious reconstruction is an origin in the Australian Region, with at least seven dispersal events across Wallacea to the Oriental Region. The eight major clades of Delias appear to have diverged rapidly following complete separation of the Australian plate from Gondwana and its collision with the Asian plate in the late Oligocene. Further diversification and dispersal of Delias in the Miocene-Pliocene are associated with major geological and climatic changes that occurred in Australia-New Guinea during the late Tertiary. The 'out-of-Australia' hypothesis for the Delias group supports an origin of the Aporiina in southern Gondwana (southern vicariance hypothesis), which proposes that the ancestor of Delias + Leuciacria differentiated vicariantly on the Australian plate.

braby_delias.pdf
2006
Eastwood R, Pierce NE, Kitching RL, Hughes JM. Do ants enhance diversification in lycaenid butterflies? Phylogeographic evidence from a model myrmecophile, Jalmenus evagoras. Evolution. 2006;60 :315-327.Abstract

Abstract. The ant-tended Australian butterfly, Jalmenus evagoras, has been a model system for studying the ecology and evolution of mutualism. A phylogeographic analysis of mitochondrial DNA cytochrome oxidase I sequences from 242 butterflies (615 bp) and 66 attendant ants (585 bp) from 22 populations was carried out to explore the relationship between ant association and butterfly population structure. This analysis revealed 12 closely related butterfly haplotypes in three distinct clades roughly corresponding to three allopatric subpopulations of the butterflies. Minimal genetic diversity and widespread haplotypes within biogeographical regions suggest high levels of matrilineal gene flow. Attendant ants are significantly more diverse than was previously thought, with at least seven well-defined clades corresponding to independent morphological determinations, distributed throughout the range of the butterflies. Nested analysis of molecular variance showed that biogeography, host plant, and ant associate all contribute significantly in explaining variation in butterfly genetic diversity, but these variables are not independent of one another. Major influences appear to come from fragmentation due to large-scale biogeographical barriers, and diversification following a shift in habitat preference. A consequence of such a shift could be codiversification of the butterfly with habitatadapted ants, resulting in apparent phylogenetic concordance between butterflies and ants. The implications of these results are discussed in terms of possible effects of ant attendance on the diversification of Lycaenidae as a whole.

2006_eastwood_et_al.pdf
Braby MF, Villa R, Pierce NE. Molecular phylogeny and systematics of the Pieridae (Lepidoptera: Papilionoidea): higher classification and biogeography. Zoological Journal of the Linnaean Society. 2006;147 :239-275.Abstract

The systematic relationships of the butterfly family Pieridae are poorly understood. Much of our current understanding is based primarily on detailed morphological observations made 50–70 years ago. However, the family and its putative four subfamilies and two tribes, have rarely been subjected to rigorous phylogenetic analysis. Here we present results based on an analysis of molecular characters used to reconstruct the phylogeny of the Pieridae in order to infer higher-level classification above the generic level and patterns of historical biogeography. Our sample contained 90 taxa representing 74 genera and six subgenera, or 89% of all genera recognized in the family. Three complementary approaches were employed: (1) a combined analysis of a 30 taxon subset for sequences from four gene regions, including elongation factor-1 alpha (EF-1α), wingless, cytochrome oxidase subunit I (COI), and 28S (3675 bp, 1031 parsimony-informative characters), mainly to establish higher-level relationships, (2) a single-gene analysis of the 90 taxon data set for sequences from EF-1α (1066 bp, 364 parsimony-informative characters), mainly to establish lower-level relationships, and (3) an all available data analysis of the entire data set for sequences from the four genes, to recover both deep and shallow nodes. Analyses using maximum parsimony, maximum likelihood and Bayesian inference provided similar results. All supported monophyly for the four subfamilies but not for the two tribes, with the Anthocharidini polyphyletic and the Pierini paraphyletic. The combined and all available data analyses support the following relationships among the subfamilies: ((Pseudopontiinae + Dismorphiinae) + (Coliadinae + Pierinae)), corroborating Ehrlich’s 1958 phenetic hypothesis. On the basis of these analyses, and additional morphological and life history evidence, we propose a reclassification of the subfamily Pierinae into two tribes (Anthocharidini s.s., Pierini s.s.) and two informal groups (Colotis group, Leptosia), with the tribe Pierini s.s. subdivided into three subtribes (Appiadina, Pierina, Aporiina) and three genera (Elodina, Dixeia, Belenois) of uncertain status (incertae sedis). The combined and all available data analyses support the following relationships among the Pierinae: (Colotis group + Anthocharidini s.s. + Leptosia + (Elodina + ((Dixeia + Belenois) + Appiadina + Pierina + Aporiina))). Application of a molecular clock calibrated using fossil evidence and semiparametric rate smoothing suggests that divergence between the Pierina and Aporiina occurred no later than the Palaeocene (> 60 Myr). The minimum estimate for the age of the crown-group of the Pieridae was 112–82 Myr, with a mean of 95 Myr. A historical biogeographical hypothesis is proposed to explain the present-day distribution of the clade Pseudopontiinae + Dismorphiinae, which argues for an origin of the two subfamilies in western Gondwana (Africa + South America) during the Late Cretaceous.

2006_braby_et_al.pdf
Moreau CS, Bell CD, Vila R, Archibald SB, Pierce NE. Phylogeny of the ants: Diversification in the age of angiosperms. Science. 2006;312 :101-104.Abstract

We present a large-scale molecular phylogeny of the ants (Hymenoptera: Formicidae), based on 4.5 kilobases of sequence data from six gene regions extracted from 139 of the 288 described extant genera, representing 19 of the 20 subfamilies. All but two subfamilies are recovered as monophyletic. Divergence time estimates calibrated by minimum age constraints from 43 fossils indicate that most of the subfamilies representing extant ants arose much earlier than previously proposed but only began to diversify during the Late Cretaceous to Early Eocene. This period also witnessed the rise of angiosperms and most herbivorous insects.

moreau_phylo.pdf
2005
Lukhtanov VA, Kandul NP, Plotkin JB, Dantchenko AV, Haig D, Pierce NE. Reinforcement of pre-zygotic isolation and karyotype evolution in Agrodiaetus butterflies. Nature. 2005;436 :385-389.Abstract

The reinforcement model of evolution argues that natural selection enhances pre-zygotic isolation between divergent populations or species by selecting against unfit hybrids(1,2) or costly interspecific matings(3). Reinforcement is distinguished from other models that consider the formation of reproductive isolation to be a by-product of divergent evolution(4,5). Although theory has shown that reinforcement is a possible mechanism that can lead to speciation(6-8), empirical evidence has been sufficiently scarce to raise doubts about the importance of reinforcement in nature(6,9,10). Agrodiaetus butterflies ( Lepidoptera: Lycaenidae) exhibit unusual variability in chromosome number. Whereas their genitalia and other morphological characteristics are largely uniform, different species vary considerably in male wing colour, and provide a model system to study the role of reinforcement in speciation. Using comparative phylogenetic methods, we show that the sympatric distribution of 15 relatively young sister taxa of Agrodiaetus strongly correlates with differences in male wing colour, and that this pattern is most likely the result of reinforcement. We find little evidence supporting sympatric speciation: rather, in Agrodiaetus, karyotypic changes accumulate gradually in allopatry, prompting reinforcement when karyotypically divergent races come into contact.

lukhtanovnature03704.pdf
Wahlberg N, Braby MF, Brower AVZ, de Jong R, Lee MM, Nylin S, Pierce NE, Sperling FAH, Vila R, Warren AD, et al. Synergistic effects of combining morphological and molecular data in resolving the phylogeny of butterflies and skippers. Proceedings of the Royal Society B-Biological Sciences. 2005;272 :1577-1586.Abstract

Phylogenetic relationships among major clades of butterflies and skippers have long been controversial, with no general consensus even today. Such lack of resolution is a substantial impediment to using the otherwise well studied butterflies as a model group in biology. Here we report the results of a combined analysis of DNA sequences from three genes and a morphological data matrix for 57 taxa (3258 characters, 1290 parsimony informative) representing all major lineages from the three putative butterfly super-families (Hedyloidea, Hesperioidea and Papilionoidea), plus out-groups representing other ditrysian Lepidoptera families. Recently, the utility of morphological data as a source of phylogenetic evidence has been debated. We present the first well supported phylogenetic hypothesis for the butterflies and skippers based on a total-evidence analysis of both traditional morphological characters and new molecular characters from three gene regions (GOI, EF-1 alpha and wingless). All four data partitions show substantial hidden support for the deeper nodes, which emerges only in a combined analysis in which the addition of morphological data plays a crucial role. With the exception of Nymphalidae, the traditionally recognized families are found to be strongly supported monophyletic clades with the following relationships: (Hesperiidae+(Papilionidae+(Pieridae+(Nymphalidae+(Lycaenidae+Riodinidae))))). Nymphalidae is recovered as a monophyletic clade but this clade does not have strong support. Lycaenidae and Riodinidae are sister groups with strong support and we suggest that the latter be given family rank. The position of Pieridae as the sister taxon to nymphalids, lycaenids and riodinids is supported by morphology and the EF-1 alpha data but conflicted by the COI and wingless data. Hedylidae are more likely to be related to butterflies and skippers than geometrid moths and appear to be the sister group to Papilionoidea + Hesperioidea.

wahlberg_et_al_2005.pdf
2004
Quek SP, Davies SJ, Itino T, Pierce NE. Codiversification in an ant-plant mutualism: Stem texture and the evolution of host use in Crematogaster (Formicidae : Myrmicinae) inhabitants of Macaranga (Euphorbiaceae). Evolution. 2004;58 :554-570.Abstract

We investigate the evolution of host association in a cryptic complex of mutualistic Crematogaster (Decacrema) ants that inhabits and defends Macaranga trees in Southeast Asia. Previous phylogenetic studies based on limited samplings of Decacrema present conflicting reconstructions of the evolutionary history of the association, inferring both cospeciation and the predominance of host shifts. We use cytochrome oxidase I (COI) to reconstruct phylogenetic relationships in a comprehensive sampling of the Decacrema inhabitants of Macaranga. Using a published Macaranga phylogeny, we test whether the ants and plants have cospeciated. The COI phylogeny reveals 10 well-supported lineages and an absence of cospeciation. Host shifts, however, have been constrained by stem traits that are themselves correlated with Macaranga phylogeny. Earlier lineages of Decacrema exclusively inhabit waxy stems, a basal state in the Pachystemon clade within Macaranga, whereas younger species of Pachystemon, characterized by nonwaxy stems, are inhabited only by younger lineages of Decacrema. Despite the absence of cospeciation, the correlated succession of stem texture in both phylogenies suggests that Decacrema and Pachystemon have diversified in association, or codiversified. Subsequent to the colonization of the Pachystemon clade, Decacrema expanded onto a second clade within Macaranga, inducing the development of myrmecophytism in the Pruinosae group. Confinement to the aseasonal wet climate zone of western Malesia suggests myrmecophytic Macaranga are no older than the wet forest community in Southeast Asia, estimated to be about 20 million years old (early Miocene). Our calculation of COI divergence rates from several published arthropod studies that relied on tenable calibrations indicates a generally conserved rate of approximately 1.5% per million years. Applying this rate to a rate-smoothed Bayesian chronogram of the ants, the Decacrema from Macaranga are inferred to be at least 12 million years old (mid-Miocene). However, using the extremes of rate variation in COI produces an age as recent as 6 million years. Our inferred timeline based on 1.5% per million years concurs with independent biogeographical events in the region reconstructed from palynological data, thus suggesting that the evolutionary histories of Decacrema and their Pachystemon hosts have been contemporaneous since the mid-Miocene. The evolution of myrmecophytism enabled Macaranga to radiate into enemy-free space, while the ants' diversification has been shaped by stem traits, host specialization, and geographic factors. We discuss the possibility that the ancient and exclusive association between Decacrema and Macaranga was facilitated by an impoverished diversity of myrmecophytes and phytoecious (obligately plant inhabiting) ants in the region.

2004_quek_et_al.pdf

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