Phylogenetic analysis of trophic associations

Ecologists frequently collect data on the patterns of association between adjacent trophic levels in the form of binary or quantitative food webs. Here, we develop statistical methods to estimate the roles of consumer and resource phylogenies in explaining patterns of consumer-resource association. We use these methods to ask whether closely related consumer species are more likely to attack the same resource species and whether closely related resource species are more likely to be attacked by the same consumer species. We then show how to use estimates of phylogenetic signals to predict novel consumer-resource associations solely from the phylogenetic position of species for which no other (or only partial) data are available. Finally, we show how to combine phylogenetic information with information about species' ecological characteristics and life-history traits to estimate the effects of species traits on consumer-resource associations while accounting for phylogenies. We illustrate these techniques using a food web comprising species of parasitoids, leaf-mining moths, and their host plants.     

Determinants of parasitoid communities of willow‐galling sawflies: habitat overrides physiology,host plant and space

Studies on the determinants of plant–herbivore and herbivore–parasitoid associations provide important insights into the origin and maintenance of global and local species richness. If parasitoids are specialists on herbivore niches rather than on herbivore taxa, then alternating escape of herbivores into novel niches and delayed resource tracking by parasitoids could fuel diversification at both trophic levels. We used DNA barcoding to identify parasitoids that attack larvae of seven Pontania sawfly species that induce leaf galls on eight willow species growing in subarctic and arctic–alpine habitats in three geographic locations in northern Fennoscandia, and then applied distance‐ and model‐based multivariate analyses and phylogenetic regression methods to evaluate the hierarchical importance of location, phylogeny and different galler niche dimensions on parasitoid host use. We found statistically significant variation in parasitoid communities across geographic locations and willow host species, but the differences were mainly quantitative due to extensive sharing of enemies among gallers within habitat types. By contrast, the divide between habitats defined two qualitatively different network compartments, because many common parasitoids exhibited strong habitat preference. Galler and parasitoid phylogenies did not explain associations, because distantly related arctic–alpine gallers were attacked by a species‐poor enemy community dominated by two parasitoid species that most likely have independently tracked the gallers’ evolutionary shifts into the novel habitat. Our results indicate that barcode‐ and phylogeny‐based analyses of food webs that span forested vs. tundra or grassland environments could improve our understanding of vertical diversification effects in complex plant–herbivore–parasitoid networks.     

Histories of host shifts and cospeciation among free‐living parasitoids of Rhagoletis flies

Host shifts by specialist insects can lead to reproductive isolation between insect populations that use different hosts, promoting diversification. When both a phytophagous insect and its ancestrally associated parasitoid shift to the same novel host plant, they may cospeciate. However, because adult parasitoids are free living, they can also colonize novel host insects and diversify independent of their ancestral host insect. Although shifts of parasitoids to new insect hosts have been documented in ecological time, the long‐term importance of such shifts to parasitoid diversity has not been evaluated. We used a genus of flies with a history of speciation via host shifting (Rhagoletis [Diptera: Tephritidae]) and three associated hymenopteran parasitoid genera (Diachasma, Coptera and Utetes) to examine cophylogenetic relationships between parasitoids and their host insects. We inferred phylogenies of Rhagoletis, Diachasma, Coptera and Utetes and used distance‐based cophylogenetic methods (ParaFit and PACo) to assess congruence between fly and parasitoid trees. We used an event‐based method with a free‐living parasitoid cost model to reconstruct cophylogenetic histories of each parasitoid genus and Rhagoletis. We found that the current species diversity and host–parasitoid associations between the Rhagoletis flies and parasitoids are the primary result of ancient cospeciation events. Parasitoid shifts to ancestrally unrelated hosts primarily occur near the branch tips, suggesting that host shifts contribute to recent parasitoid species diversity but that these lineages may not persist over longer time periods. Our analyses also stress the importance of biologically informed cost models when investigating the coevolutionary histories of hosts and free‐living parasitoids.     

ECOLOGICAL VERSUS PHYLOGENETIC DETERMINANTS OF TROPHIC ASSOCIATIONS IN A PLANT–LEAFMINER–PARASITOID FOOD WEB

Specialized trophic interactions in plant–herbivore–parasitoid food webs can spur “bottom–up” diversification if speciation in plants leads to host‐shift driven divergence in insect herbivores, and if the effect then cascades up to the third trophic level. Conversely, parasitoids that search for victims on certain plant taxa may trigger “top–down” diversification by pushing herbivores into “enemy‐free space” on novel hosts. We used phylogenetic regression methods to compare the relative importance of ecology versus phylogeny on associations between Heterarthrinae leafmining sawflies and their parasitoids. We found that: (1) the origin of leafmining led to escape from most parasitoids attacking external‐feeding sawflies; (2) the current enemies mainly consist of generalists that are shared with other leafmining taxa, and of more specialized lineages that may have diversified by shifting among heterarthrines; and (3) parasitoid–leafminer associations are influenced more by the phylogeny of the miners’ host plants than by relationships among miner species. Our results suggest that vertical diversifying forces have a significant—but not ubiquitous—role in speciation: many of the parasitoids have remained polyphagous despite niche diversification in the miners, and heterarthrine host shifts also seem to be strongly affected by host availability.     

COSPECIATION ANALYSIS OF AN OBLIGATE POLLINATION MUTUALISM: HAVEGLOCHIDION TREES (EUPHORBIACEAE) AND POLLINATING EPICEPHALA MOTHS(GRACILLARIIDAE) DIVERSIFIED IN PARALLEL?

Species-specific obligate pollination mutualism between Glochidion trees (Euphorbiaceae) and Epicephala moths (Gracillariidae) involves a large number of interacting species and resembles the classically known fig-fig wasp and yucca-yucca moth associations. To assess the extent of parallel cladogenesis in Glochidion-Epicephala association, we reconstruct phylogenetic relationships of 18 species of Glochidion using nuclear ribosomal DNA sequences (internal and external transcribed spacers) and those of the corresponding 18 Epicephala species using mitochondrial (the cytochrome oxidase subunit I gene) and nuclear DNA sequences (the arginine kinase and elongation factor-1alpha genes). Based on the obtained phylogenies, we determine whether Glochidion and Epicephala have undergone parallel diversification using several different methods for investigating the level of cospeciation between phylogenies. These tests indicate that there is generally a greater degree of correlation between Glochidion and Epicephala phylogenies than expected in a random association, but the results are sensitive to selection of different phylogenetic hypotheses and analytical methods for evaluating cospeciation. Perfect congruence between phylogenies is not found in this association, which likely resulted from host shift by the moths. The observed significant discrepancy between Glochidion and Epicephala phylogenies implies that the one-to-one specificity between the plants and moths has been maintained through a complex speciation process or that there is an underestimated diversity of association between Glochidion trees and Epicephala moths.     

Host conservatism,geography, and elevation in the evolution of a Neotropical moth radiation

The origins of evolutionary radiations are often traced to the colonization of novel adaptive zones, including unoccupied habitats or unutilized resources. For herbivorous insects, the predominant mechanism of diversification is typically assumed to be a shift onto a novel lineage of host plants. However, other drivers of diversification are important in shaping evolutionary history, especially for groups residing in regions with complex geological histories. We evaluated the contributions of shifts in host plant clade, bioregion, and elevation to diversification in Eois (Lepidoptera: Geometridae), a hyper‐diverse genus of moths found throughout the Neotropics. Relationships among 107 taxa were reconstructed using one mitochondrial and two nuclear genes. In addition, we used a genotyping‐by‐sequencing approach to generate 4641 SNPs for 137 taxa. Both datasets yielded similar phylogenetic histories, with relationships structured by host plant clade, bioregion, and elevation. While diversification of basal lineages often coincided with host clade shifts, more recent speciation events were more typically associated with shifts across bioregions or elevational gradients. Overall, patterns of diversification in Eois are consistent with the perspective that shifts across multiple adaptive zones synergistically drive diversification in hyper‐diverse lineages.     

Ancient host shifts followed by host conservatism in a group of ant parasitoids

While ant colonies serve as host to a diverse array of myrmecophiles, few parasitoids are able to exploit this vast resource. A notable exception is the wasp family Eucharitidae, which is the only family of insects known to exclusively parasitize ants. Worldwide, approximately 700 Eucharitidae species attack five subfamilies across the ant phylogeny. Our goal is to uncover the pattern of eucharitid diversification, including timing of key evolutionary events, biogeographic patterns and potential cophylogeny with ant hosts. We present the most comprehensive molecular phylogeny of Eucharitidae to date, including 44 of the 53 genera and fossil-calibrated estimates of divergence dates. Eucharitidae arose approximately 50 Ma after their hosts, during the time when the major ant lineages were already established and diversifying. We incorporate host association data to test for congruence between eucharitid and ant phylogenies and find that their evolutionary histories are more similar than expected at random. After a series of initial host shifts, clades within Eucharitidae maintained their host affinity. Even after multiple dispersal events to the New World and extensive speciation within biogeographic regions, eucharitids remain parasitic on the same ant subfamilies as their Old World relatives, suggesting host conservatism despite access to a diverse novel ant fauna.     

Lithinine moths on ferns: a phylogenetic study of insect-plant interactions

We examine host association patterns in pteridophagous moths of the tribe Lithinini (Lepidoptera: Geometridae). This represents the first study where the host associations of oligophagous, pteridophagous Lepidoptera are analysed in a phylogenetic context. We compare the observed phylogenetic patterns of lithinine moths and their hosts with the contrasting coevolutionary scenarios proposed by Mitter et ai , and discuss the support for various hypotheses relative to Thompson's concept of coevolution as 'escape with radiation', and the chemical facilitation model of Jermy. The patterns observed support a scenario where host shifting subsequent to a single colonization event has resulted in lack of strict concordance (i.e. parallel cladogenesis) between moth and fern phylogenies.     

Phylogenetics and evolution of host-plant use in leaf-mining sawflies (Hymenoptera: Tenthredinidae: Heterarthrinae)

The habit of mining within leaves has evolved convergently in numerous plant-feeding insect taxa. Many leaf-mining groups contain a large number of species with distinct feeding preferences, which makes them highly suitable for studies on the evolutionary history of host-plant use and on the role of niche shifts in speciation. We aimed to clarify the origin, classification, and ecological evolution of the tenthredinid sawfly subfamily Heterarthrinae, which contains c. 150 leaf-mining species that collectively feed on over 20 plant genera around the world. For this, we reconstructed the phylogeny of representative heterarthrine species and diverse outgroups from the superfamily Tenthredinoidea on the basis of DNA sequence data collected from two mitochondrial (CoI and Cytb) and two nuclear (EF-1α and NaK) genes. Thereafter, we inferred the history of niche diversification within Heterarthrinae by plotting larval host-plant associations on the trees, and by contrasting a time-calibrated leaf-miner phylogeny with the phylogeny of their host plants. The results show that: (1) heterarthrine leaf-miners constitute a monophyletic group that arose from external-feeding blennocampine lineages within the Tenthredinidae c. 110-80 million years ago; (2) heterarthrines generally radiated well after their host taxa, and extant host-plant associations therefore result from a combination of host conservatism and occasional shifts among available plant taxa; and (3) diversification in Heterarthrinae apparently occurs by multiple mechanisms, including sympatric or allopatric ecological speciation, non-ecological allopatric speciation, and possibly allochronic speciation. Overall, both present and historical host-use patterns within the Heterarthrinae exhibit striking similarities to patterns found in co-occurring herbivore taxa.     

Are most species small? Not within species-level phylogenies.

The robust macro-ecological observation that there are more small-bodied species implies that small-bodied organisms have experienced elevated net rates of diversification. We investigate the role of body size in creating non-random differences in rates of cladogenesis using a set of 38 species-level phylogenies drawn from a range of animal groups. We use independent contrasts to explore the relationship between body size and species richness within individual phylogenies and across related sets of phylogenies. We also carry out a meta-analysis looking for associations between body size and species richness across the taxa. We find little evidence for increased cladogenesis among small-bodied organisms within taxa, and no evidence for any consistent differences between taxa. We explore possible explanations for the inconsistency of our findings with macro-ecological patterns.     

Evolutionary diversification of the gall midge genus Asteromyia (Cecidomyiidae) in a multitrophic ecological context

Gall-forming insects provide ideal systems to analyze the evolution of host–parasite interactions and understand the ecological interactions that contribute to evolutionary diversification. Flies in the family Cecidomyiidae represent the largest radiation of gall-forming insects and are characterized by complex trophic interactions with plants, fungal symbionts, and predators. We analyzed the phylogenetic history and evolutionary associations of the North American cecidomyiid genus Asteromyia, which is engaged in a complex and perhaps co-evolving community of interactions with host-plants, fungi, and parasitoids. Mitochondrial gene trees generally support current classifications, but reveal extensive cryptic diversity within the eight named species. Asteromyia likely radiated after their associated host-plants in the Astereae, but species groups exhibit strong associations with specific lineages of Astereae. Evolutionary associations with fungal mutualists are dynamic, however, and suggest rapid and perhaps coordinated changes across trophic levels.     

Fossil-calibrated molecular phylogenies reveal that leaf-mining moths radiated millions of years after their host plants

Coevolution has been hypothesized as the main driving force for the remarkable diversity of insect-plant associations. Dating of insect and plant phylogenies allows us to test coevolutionary hypotheses and distinguish between the contemporaneous radiation of interacting lineages vs. insect 'host tracking' of previously diversified plants. Here, we used nuclear DNA to reconstruct a molecular phylogeny for 100 species of Phyllonorycter leaf-mining moths and 36 outgroup taxa. Ages for nodes in the moth phylogeny were estimated using a combination of a penalized likelihood method and a Bayesian approach, which takes into account phylogenetic uncertainty. To convert the relative ages of the moths into dates, we used an absolute calibration point from the fossil record. The age estimates of (a selection of) moth clades were then compared with fossil-based age estimates of their host plants. Our results show that the principal radiation of Phyllonorycter leaf-mining moths occurred well after the main radiation of their host plants and may represent the dominant associational mode in the fossil record.     

Rapid diversification associated with ecological specialization in Neotropical Adelpha butterflies

Rapid diversification is often associated with morphological or ecological adaptations that allow organisms to radiate into novel niches. Neotropical Adelpha butterflies, which comprise over 200 species and subspecies, are characterized by extraordinary breadth in host plant use and wing colour patterns compared to their closest relatives. To examine the relationship between phenotypic and species diversification, we reconstructed the phylogenetic history of Adelpha and its temperate sister genus Limenitis using genomewide restriction‐site‐associated DNA (RAD) sequencing. Despite a declining fraction of shared markers with increasing evolutionary distance, the RAD‐Seq data consistently generated well‐supported trees using a variety of phylogenetic methods. These well‐resolved phylogenies allow the identification of an ecologically important relationship with a toxic host plant family, as well as the confirmation of widespread, convergent wing pattern mimicry throughout the genus. Taken together, our results support the hypothesis that evolutionary innovations in both larvae and adults have permitted the colonization of novel host plants and fuelled adaptive diversification within this large butterfly radiation.     

Parallel diversification of Australian gall-thrips on Acacia

The diversification of gall-inducing Australian Kladothrips (Insecta: Thysanoptera) on Acacia has produced a pair of sister-clades, each of which includes a suite of lineages that utilize virtually the same set of 15 closely related host plant species. This pattern of parallel insect-host plant radiation may be driven by cospeciation, host-shifting to the same set of host plants, or some combination of these processes. We used molecular-phylogenetic data on the two gall-thrips clades to analyze the degree of concordance between their phylogenies, which is indicative of parallel divergence. Analyses of phylogenetic concordance indicate statistically-significant similarity between the two clades. Their topologies also fit with a hypothesis of some degree of host-plant tracking. Based on phylogenetic and taxonomic information regarding the phylogeny of the Acacia host plants in each clade, one or more species has apparently shifted to more-divergent Acacia host-plant species, and in each case these shifts have resulted in notable divergence in aspects of the phenotype including morphology, life history and behaviour. Our analyses indicate that gall-thrips on Australian Acacia have undergone parallel diversification as a result of some combination of cospeciation, highly restricted host-plant shifting, or both processes, but that the evolution of novel phenotypic diversity in this group is a function of relatively few shifts to divergent host plants. This combination of ecologically restricted and divergent radiation may represent a microcosm for the macroevolution of host plant relationships and phenotypic diversity among other phytophagous insects.     

Diversification and coevolution in brood pollination mutualisms: Windows into the role of biotic interactions in generating biological diversity

Brood pollination mutualisms—interactions in which specialized insects are both the pollinators (as adults) and seed predators (as larvae) of their host plants—have been influential study systems for coevolutionary biology. These mutualisms include those between figs and fig wasps, yuccas and yucca moths, leafflowers and leafflower moths, globeflowers and globeflower flies, Silene plants and Hadena and Perizoma moths, saxifrages and Greya moths, and senita cacti and senita moths. The high reciprocal diversity and species‐specificity of some of these mutualisms have been cited as evidence that coevolution between plants and pollinators drives their mutual diversification. However, the mechanisms by which these mutualisms diversify have received less attention. In this paper, we review key hypotheses about how these mutualisms diversify and what role coevolution between plants and pollinators may play in this process. We find that most species‐rich brood pollination mutualisms show significant phylogenetic congruence at high taxonomic scales, but there is limited evidence for the processes of both cospeciation and duplication, and there are no unambiguous examples known of strict‐sense contemporaneous cospeciation. Allopatric speciation appears important across multiple systems, particularly in the insects. Host‐shifts appear to be common, and widespread host‐shifts by pollinators may displace other pollinator lineages. There is relatively little evidence for a “coevolution through cospeciation” model or that coevolution promotes speciation in these systems. Although we have made great progress in understanding the mechanisms by which brood pollination mutualisms diversify, many opportunities remain to use these intriguing symbioses to understand the role of biotic interactions in generating biological diversity.     

A test of host-associated differentiation across the 'parasite continuum' in the tri-trophic interaction among yuccas, bogus yucca moths, and parasitoids

Parasitic taxa span an antagonistic continuum, with some parasites inflicting no fitness costs to some that kill the host after feeding. Host-associated differentiation is postulated as a major process facilitating speciation in many parasitic taxa. Here, I examined the importance of host-associated differentiation in a parasitoid wasp that develops on yucca moths in the genus Prodoxus. Prodoxus are specialists on Yucca , and moth speciation is closely tied to differences in microhabitat use within a plant and among host plant species. Parasitoids in the genus Eusandalum have been reared from Prodoxus species distributed across Yucca . Estimates of host-use patterns obtained through rearings of adult wasps were combined with surveys of mitochondrial DNA cytochrome oxidase I sequence data and amplified fragment length polymorphism markers to determine if populations of Eusandalum were genetically structured based on host use. Eusandalum populations were genetically structured based on geographical distance rather than moth host species, microhabitats within plants, or Yucca species. The results are contrary to the patterns observed in the host genus Prodoxus . Although parasitoids exhibit parasite-like characteristics, these results suggest that Eusandalum may be best viewed as a predator. Female wasps are able to utilize any moth species present at a given locality, and there is little likelihood that host specialization may facilitate population subdivision and speciation.     

Molecular phylogenies of fig pollinating and non-pollinating wasps and the implications for the origin and evolution of the fig-fig wasp mutualism

Abstract. Figs host three ecologically distinct groups of wasps: pollinators, non-pollinators (parasitic wasps) and parasitoids. Both pollinators and non-pollinators complete their life cycles using fig tissue, while parasitoids appear to attack some groups of non-pollinators. We used nucleotide sequence data to address a series of questions concerning genealogical associations, host specificities and degree of strict-sense co-evolution exhibited by members of these groups. We used the relatively conserved 12S rRNA gene of the mitochondria to estimate high level relationships among pollinator, parasitic and parasitoid taxa by sampling species collected from host figs representing five sections (three subgenera) from Asia, Africa, Europe and Central America. We found that all pollinators formed a clear monophyletic group. However, we could not resolve whether or not all of the non-parasitoid wasps associated with figs (Agaonidae, sensu Bouček) formed a single monophyletic group. Further, we used the more variable COII mitochondrial gene to attempt to determine relationships among closely related species of pollinators within two New World genera. Using sequences from the same gene we estimated the phylogenetic relationships among the parasites collected from the same New World host fig species and compared them with those of the pollinators. At fine taxonomic scale, we found that for both pollinator and parasites, species were generally specific to a given fig host. Moreover, the phylogenies of the non-pollinators are largely congruent with those of the pollinators, suggesting the predominance of strict-sense co-evolution on shared host fig species. The implications of these findings and opportunities for future research are discussed.     

HOST PLANT UTILIZATION,HOST RANGE OSCILLATIONS AND DIVERSIFICATION IN NYMPHALID BUTTERFLIES: A PHYLOGENETIC INVESTIGATION

It has been suggested that phenotypic plasticity is a major factor in the diversification of life, and that variation in host range in phytophagous insects is a good model for investigating this claim. We explore the use of angiosperm plants as hosts for nymphalid butterflies, and in particular the evidence for past oscillations in host range and how they are linked to host shifts and to diversification. At the level of orders of plants, a relatively simple pattern of host use and host shifts emerges, despite the 100 million years of history of the family Nymphalidae. We review the evidence that these host shifts and the accompanying diversifications were associated with transient polyphagous stages, as suggested by the “oscillation hypothesis.” In addition, we investigate all currently polyphagous nymphalid species and demonstrate that the state of polyphagy is rare, has a weak phylogenetic signal, and a very apical distribution in the phylogeny; we argue that these are signs of its transient nature. We contrast our results with data from the bark beetles Dendroctonus, in which a more specialized host use is instead the apical state. We conclude that plasticity in host use is likely to have contributed to diversification in nymphalid butterflies.     

Coevolution between Lamellodiscus (Monogenea: Diplectanidae) and Sparidae (Teleostei): the study of a complex host-parasite system

Abstract.— Host-parasite coevolution was studied between Sparidae (Teleostei) fishes and their parasites of the genus Lamellodiscus (Monogenea, Diplectanidae) in the northwestern Mediterranean Sea. Molecular phylogenies were reconstructed for both groups. The phylogenetic tree of the Sparidae was obtained from previously published 16S mitochondrial DNA (mtDNA) sequences associated with new cytochrome-b mtDNA sequences via a "total evidence" procedure. The phylogeny of Lamellodiscus species was reconstructed from 18S rDNA sequences that we obtained. Host-parasite coevolution was studied through different methods: TreeFitter, TreeMap, and a new method, ParaFit. If the cost of a host switch is not assumed to be high for parasites, all methods agree on the absence of widespread cospeciation processes in this host-parasite system. Host-parasite associations were interpreted to be due more to ecological factors than to coevolutionary processes. Host specificity appeared not to be related to host-parasite cospeciation.     

Reciprocal diversification in a complex plant-herbivore-parasitoid food web

Background  

Plants, plant-feeding insects, and insect parasitoids form some of the most complex and species-rich food webs. According to the classic escape-and-radiate (EAR) hypothesis, these hyperdiverse communities result from coevolutionary arms races consisting of successive cycles of enemy escape, radiation, and colonization by new enemy lineages. It has also been suggested that "enemy-free space" provided by novel host plants could promote host shifts by herbivores, and that parasitoids could similarly drive diversification of gall form in insects that induce galls on plants. Because these central coevolutionary hypotheses have never been tested in a phylogenetic framework, we combined phylogenetic information on willow-galling sawflies with data on their host plants, gall types, and enemy communities.