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.

Whiteman NK, Gloss AD, Sackton TB, Groen SC, Humphrey PT, Lapoint RT, Sonderby IE, Halkier BA, Kocks C, Ausubel FM, et al. Genes Involved in the Evolution of Herbivory by a Leaf-Mining, Drosophilid Fly. Genome Biology and Evolution. 2012;4 :900-916.Abstract

Herbivorous insects are among the most successful radiations of life. However, we know little about the processes underpinning the evolution of herbivory. We examined the evolution of herbivory in the fly, Scaptomyza flava, whose larvae are leaf miners on species of Brassicaceae, including the widely studied reference plant, Arabidopsis thaliana (Arabidopsis). Scaptomyza flava is phylogenetically nested within the paraphyletic genus Drosophila, and the whole genome sequences available for 12 species of Drosophila facilitated phylogenetic analysis and assembly of a transcriptome for S. flava. A time-calibrated phylogeny indicated that leaf mining in Scaptomyza evolved between 6 and 16 million years ago. Feeding assays showed that biosynthesis of glucosinolates, the major class of antiherbivore chemical defense compounds in mustard leaves, was upregulated by S. flava larval feeding. The presence of glucosinolates in wild-type (WT) Arabidopsis plants reduced S. flava larval weight gain and increased egg-adult development time relative to flies reared in glucosinolate knockout (GKO) plants. An analysis of gene expression differences in 5-day-old larvae reared on WT versus GKO plants showed a total of 341 transcripts that were differentially regulated by glucosinolate uptake in larval S. flava. Of these, approximately a third corresponded to homologs of Drosophila melanogaster genes associated with starvation, dietary toxin-, heat-, oxidation-, and aging-related stress. The upregulated transcripts exhibited elevated rates of protein evolution compared with unregulated transcripts. The remaining differentially regulated transcripts also contained a higher proportion of novel genes than the unregulated transcripts. Thus, the transition to herbivory in Scaptomyza appears to be coupled with the evolution of novel genes and the co-option of conserved stress-related genes.

2012_whiteman_et_al_gbe.pdf faculty_1000_recommendation_clark.jpg
Russell JA, Funaro CF, Giraldo YM, Goldman-Huertas B, Suh D, Kronauer DJC, Moreau CS, Pierce NE. A Veritable Menagerie of Heritable Bacteria from Ants, Butterflies, and Beyond: Broad Molecular Surveys and a Systematic Review. Plos One. 2012;7.Abstract

Maternally transmitted bacteria have been important players in the evolution of insects and other arthropods, affecting their nutrition, defense, development, and reproduction. Wolbachia are the best studied among these and typically the most prevalent. While several other bacteria have independently evolved a heritable lifestyle, less is known about their host ranges. Moreover, most groups of insects have not had their heritable microflora systematically surveyed across a broad range of their taxonomic diversity. To help remedy these shortcomings we used diagnostic PCR to screen for five groups of heritable symbionts-Arsenophonus spp., Cardinium hertigii, Hamiltonella defensa, Spiroplasma spp., and Wolbachia spp.-across the ants and lepidopterans (focusing, in the latter case, on two butterfly families-the Lycaenidae and Nymphalidae). We did not detect Cardinium or Hamiltonella in any host. Wolbachia were the most widespread, while Spiroplasma (ants and lepidopterans) and Arsenophonus (ants only) were present at low levels. Co-infections with different Wolbachia strains appeared especially common in ants and less so in lepidopterans. While no additional facultative heritable symbionts were found among ants using universal bacterial primers, microbes related to heritable enteric bacteria were detected in several hosts. In summary, our findings show that Wolbachia are the dominant heritable symbionts of ants and at least some lepidopterans. However, a systematic review of symbiont frequencies across host taxa revealed that this is not always the case across other arthropods. Furthermore, comparisons of symbiont frequencies revealed that the prevalence of Wolbachia and other heritable symbionts varies substantially across lower-level arthropod taxa. We discuss the correlates, potential causes, and implications of these patterns, providing hypotheses on host attributes that may shape the distributions of these influential bacteria.

Funaro CF, Kronauer DJC, Moreau CS, Goldman-Huertas B, Pierce NE, Russell JA. Army Ants Harbor a Host-Specific Clade of Entomoplasmatales Bacteria. Applied and Environmental Microbiology. 2011;77 :346-350.Abstract

In this article, we describe the distributions of Entomoplasmatales bacteria across the ants, identifying a novel lineage of gut bacteria that is unique to the army ants. While our findings indicate that the Entomoplasmatales are not essential for growth or development, molecular analyses suggest that this relationship is host specific and potentially ancient. The documented trends add to a growing body of literature that hints at a diversity of undiscovered associations between ants and bacterial symbionts.

Ramirez SR, Eltz T, Fujiwara MK, Gerlach G, Goldman-Huertas B, Tsutsui ND, Pierce NE. Asynchronous Diversification in a Specialized Plant-Pollinator Mutualism. Science. 2011;333 :1742-1746.Abstract

Most flowering plants establish mutualistic associations with insect pollinators to facilitate sexual reproduction. However, the evolutionary processes that gave rise to these associations remain poorly understood. We reconstructed the times of divergence, diversification patterns, and interaction networks of a diverse group of specialized orchids and their bee pollinators. In contrast to a scenario of coevolution by race formation, we show that fragrance-producing orchids originated at least three times independently after their fragrance-collecting bee mutualists. Whereas orchid diversification has apparently tracked the diversification of orchids' bee pollinators, bees appear to have depended on the diverse chemical environment of neotropical forests. We corroborated this apparent asymmetrical dependency by simulating co-extinction cascades in real interaction networks that lacked reciprocal specialization. These results suggest that the diversification of insect-pollinated angiosperms may have been facilitated by the exploitation of preexisting sensory biases of insect pollinators.

Archetti M, Scheuring I, Hoffman M, Frederickson ME, Pierce NE, Yu DW. Economic game theory for mutualism and cooperation. Ecology Letters. 2011;14 :1300-1312.Abstract

We review recent work at the interface of economic game theory and evolutionary biology that provides new insights into the evolution of partner choice, host sanctions, partner fidelity feedback and public goods. (1) The theory of games with asymmetrical information shows that the right incentives allow hosts to screen-out parasites and screen-in mutualists, explaining successful partner choice in the absence of signalling. Applications range from ant-plants to microbiomes. (2) Contract theory distinguishes two longstanding but weakly differentiated explanations of host response to defectors: host sanctions and partner fidelity feedback. Host traits that selectively punish misbehaving symbionts are parsimoniously interpreted as pre-adaptations. Yucca-moth and legume-rhizobia mutualisms are argued to be examples of partner fidelity feedback. (3) The theory of public goods shows that cooperation in multi-player interactions can evolve in the absence of assortment, in one-shot social dilemmas among non-kin. Applications include alarm calls in vertebrates and exoenzymes in microbes.

Pierce NE, Berry AJ. The herbivore's dilemma: Never enough nitrogen. In: Losos J (ed) In the Light of Evolution: Essays From the Laboratory and Field. 1st ed. Roberts & Company ; 2011. pp. 121-134. 2011_pierce_berry_herbivores_dilemma.pdf
Archetti M, Ubeda F, Fudenberg D, Green J, Pierce NE, Yu DW. Let the Right One In: A Microeconomic Approach to Partner Choice in Mutualisms. American Naturalist. 2011;177 :75-85.Abstract

One of the main problems impeding the evolution of cooperation is partner choice. When information is asymmetric (the quality of a potential partner is known only to himself), it may seem that partner choice is not possible without signaling. Many mutualisms, however, exist without signaling, and the mechanisms by which hosts might select the right partners are unclear. Here we propose a general mechanism of partner choice, "screening," that is similar to the economic theory of mechanism design. Imposing the appropriate costs and rewards may induce the informed individuals to screen themselves according to their types and therefore allow a noninformed individual to establish associations with the correct partners in the absence of signaling. Several types of biological symbioses are good candidates for screening, including bobtail squid, ant-plants, gut microbiomes, and many animal and plant species that produce reactive oxygen species. We describe a series of diagnostic tests for screening. Screening games can apply to the cases where by-products, partner fidelity feedback, or host sanctions do not apply, therefore explaining the evolution of mutualism in systems where it is impossible for potential symbionts to signal their cooperativeness beforehand and where the host does not punish symbiont misbehavior.

Whiteman NK, Groen SC, Chevasco D, Bear A, Beckwith N, Gregory TR, Denoux C, Mammarella N, Ausubel FM, Pierce NE. Mining the plant-herbivore interface with a leafmining Drosophila of Arabidopsis. Molecular Ecology. 2011;20 :995-1014.Abstract

Experimental infections of Arabidopsis thaliana (Arabidopsis) with genomically characterized plant pathogens such as Pseudomonas syringae have facilitated the dissection of canonical eukaryotic defence pathways and parasite virulence factors. Plants are also attacked by herbivorous insects, and the development of an ecologically relevant genetic model herbivore that feeds on Arabidopsis will enable the parallel dissection of host defence and reciprocal resistance pathways such as those involved in xenobiotic metabolism. An ideal candidate is Scaptomyza flava, a drosophilid fly whose leafmining larvae are true herbivores that can be found in nature feeding on Arabidopsis and other crucifers. Here, we describe the life cycle of S. flava on Arabidopsis and use multiple approaches to characterize the response of Arabidopsis to S. flava attack. Oviposition choice tests and growth performance assays on different Arabidopsis ecotypes, defence-related mutants, and hormone and chitin-treated plants revealed significant differences in host preference and variation in larval performance across Arabidopsis accessions. The jasmonate and glucosinolate pathways in Arabidopsis are important in mediating quantitative resistance against S. flava, and priming with jasmonate or chitin resulted in increased resistance. Expression of xenobiotic detoxification genes was reduced in S. flava larvae reared on Arabidopsis jasmonate signalling mutants and increased in plants pretreated with chitin. These results and future research directions are discussed in the context of developing a genetic model system to analyse insect-plant interactions.

Kronauer DJC, Pierce NE. Myrmecophiles. Current Biology. 2011;21 :R208-R209. 2011_kronauer_and_pierce.pdf
Kronauer DJC, Boomsma JJ, Pierce NE. Nine novel microsatellite markers for the army ant Simopelta pergandei (subfamily Ponerinae). Conservation Genetics Resources. 2011;3 :61-63.Abstract

Simopelta (subfamily Ponerinae) army ants are specialized predators of other ants in New World tropical forests. Although they show a striking convergence in overall life-history with the well known army ants of the subfamilies Aenictinae, Dorylinae, and Ecitoninae, the genus has been little studied. We developed and characterized nine novel microsatellite loci for S. pergandei with 2-8 observed alleles (mean: 5.2) and expected heterozygosities between 0.16 and 0.87 (mean: 0.68). Three of these loci reliably cross-amplified in a second species, S. pentadentata, with 4-8 alleles (mean: 8.0) and expected heterozygosities between 0.32 and 0.85 (mean: 0.65). These genetic markers will be useful in studying the sociobiology and molecular ecology of Simopelta army ants and in elucidating convergent evolutionary trajectories that have culminated in the army ant lifestyle.

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
Weyl EG, Frederickson ME, Yu DW, Pierce NE. Reply to Kiers et al.: Economic and biological clarity in the theory of mutualism. Proceedings of the National Academy of Sciences of the United States of America. 2011;108 :E8-E8. 2011_weyl_et_al_reply.pdf
Kronauer DJC, O'Donnell S, Boomsma JJ, Pierce NE. Strict monandry in the ponerine army ant genus Simopelta suggests that colony size and complexity drive mating system evolution in social insects. Molecular Ecology. 2011;20 :420-428.Abstract

Altruism in social insects has evolved between closely related full-siblings. It is therefore of considerable interest why some groups have secondarily evolved low within-colony relatedness, which in turn affects the relatedness incentives of within-colony cooperation and conflict. The highest queen mating frequencies, and therefore among the lowest degrees of colony relatedness, occur in Apis honeybees and army ants of the subfamilies Aenictinae, Ecitoninae, and Dorylinae, suggesting that common life history features such as reproduction by colony fission and male biased numerical sex-ratios have convergently shaped these mating systems. Here we show that ponerine army ants of the genus Simopelta, which are distantly related but similar in general biology to other army ants, have strictly monandrous queens. Preliminary data suggest that workers reproduce in queenright colonies, which is in sharp contrast to other army ants. We hypothesize that differences in mature colony size and social complexity may explain these striking discrepancies.

Weyl EG, Frederickson ME, Yu DW, Pierce NE. Economic contract theory tests models of mutualism. Proceedings of the National Academy of Sciences. 2010;107 (36) :15712-15716.Abstract

Although mutualisms are common in all ecological communities and have played key roles in the diversification of life, our current understanding of the evolution of cooperation applies mostly to social behavior within a species. A central question is whether mutualisms persist because hosts have evolved costly punishment of cheaters. Here, we use the economic theory of employment contracts to formulate and distinguish between two mechanisms that have been proposed to prevent cheating in host–symbiont mutualisms, partner fidelity feedback (PFF) and host sanctions (HS). Under PFF, positive feedback between host fitness and symbiont fitness is sufficient to prevent cheating; in contrast, HS posits the necessity of costly punishment to maintain mutualism. A coevolutionary model of mutualism finds that HS are unlikely to evolve de novo, and published data on legume–rhizobia and yucca–moth mutualisms are consistent with PFF and not with HS. Thus, in systems considered to be textbook cases of HS, we find poor support for the theory that hosts have evolved to punish cheating symbionts; instead, we show that even horizontally transmitted mutualisms can be stabilized via PFF. PFF theory may place previously underappreciated constraints on the evolution of mutualism and explain why punishment is far from ubiquitous in nature.

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.

Sodhi NS, Lee TM, Sekercioglu CH, Webb EL, Prawiradilaga DM, Lohman DJ, Pierce NE, Diesmos AC, Rao M, Ehrlich PR. Local people value environmental services provided by forested parks. Biodiversity and Conservation. 2010;19 :1175-1188.Abstract

Garnering support from local people is critical for maintaining ecologically viable and functional protected areas. However, empirical data illustrating local people's awareness of the importance of nature's services is limited; hence possibly impeding effective ecosystem (environmental)-services based conservation efforts. Using data from five protected forests in four developing Southeast Asian countries, we provide evidence that local people living near parks value a wide range of environmental services, including cultural, provisioning, and regulating services, provided by the forests. Local people with longer residency valued environmental services more. Educated as well as poor people valued forest ecosystem services more. Conservation education has some influence on people's environmental awareness. For conservation endeavors to be successful, large-scale transmigration programs should be avoided and local people must be provided with alternative sustenance opportunities and basic education in addition to environmental outreach to reduce their reliance on protected forests and to enhance conservation support.

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.