Phylogenetic analysis of nuclear and mitochondrial genes reveals evolutionary relationships and mitochondrial introgression in the sertifer species group of the genus Neodiprion (Hymenoptera: Diprionidae)

Whole Genomes Reveal Evolutionary Relationships and Mechanisms Underlying Gene-Tree Discordance in Neodiprion Sawflies

Rapidly evolving taxa are excellent models for understanding the mechanisms that give rise to biodiversity. However, developing an accurate historical framework for comparative analysis of such lineages remains a challenge due to ubiquitous incomplete lineage sorting (ILS) and introgression. Here, we use a whole-genome alignment, multiple locus-sampling strategies, and summary-tree and single nucleotide polymorphism-based species-tree methods to infer a species tree for eastern North American Neodiprion species, a clade of pine-feeding sawflies (Order: Hymenopteran; Family: Diprionidae). We recovered a well-supported species tree that-except for three uncertain relationships-was robust to different strategies for analyzing whole-genome data. Nevertheless, underlying gene-tree discordance was high. To understand this genealogical variation, we used multiple linear regression to model site concordance factors estimated in 50-kb windows as a function of several genomic predictor variables. We found that site concordance factors tended to be higher in regions of the genome with more parsimony-informative sites, fewer singletons, less missing data, lower GC content, more genes, lower recombination rates, and lower D-statistics (less introgression). Together, these results suggest that ILS, introgression, and genotyping error all shape the genomic landscape of gene-tree discordance in Neodiprion. More generally, our findings demonstrate how combining phylogenomic analysis with knowledge of local genomic features can reveal mechanisms that produce topological heterogeneity across genomes.

Recurrent selection shapes the genomic landscape of differentiation between a pair of host-specialized haplodiploids that diverged with gene flow

Understanding the genetics of adaptation and speciation is critical for a complete picture of how biodiversity is generated and maintained. Heterogeneous genomic differentiation between diverging taxa is commonly documented, with genomic regions of high differentiation interpreted as resulting from differential gene flow, linked selection and reduced recombination rates. Disentangling the roles of each of these non-exclusive processes in shaping genome-wide patterns of divergence is challenging but will enhance our knowledge of the repeatability of genomic landscapes across taxa. Here, we combine whole-genome resequencing and genome feature data to investigate the processes shaping the genomic landscape of differentiation for a sister-species pair of haplodiploid pine sawflies, Neodiprion lecontei and Neodiprion pinetum. We find genome-wide correlations between genome features and summary statistics are consistent with pervasive linked selection, with patterns of diversity and divergence more consistently predicted by exon density and recombination rate than the neutral mutation rate (approximated by dS). We also find that both global and local patterns of FST, dXY and π provide strong support for recurrent selection as the primary selective process shaping variation across pine sawfly genomes, with some contribution from balancing selection and lineage-specific linked selection. Because inheritance patterns for haplodiploid genomes are analogous to those of sex chromosomes, we hypothesize that haplodiploids may be especially prone to recurrent selection, even if gene flow occurred throughout divergence. Overall, our study helps fill an important taxonomic gap in the genomic landscape literature and contributes to our understanding of the processes that shape genome-wide patterns of genetic variation.

Evaluating species boundaries using coalescent delimitation in pine-killing Monochamus (Coleoptera: Cerambycidae) sawyer beetles

Plant-feeding beetle species are diverse and often individually highly variable. Accurate classifications can be difficult to establish yet are essential for study of evolutionary patterns and processes. Molecular data are key to further characterizing morphologically difficult groups and defining genus and species boundaries. Monochamus Dejean species are ecologically and economically significant, and in coniferous forests they vector the nematode that causes Pine Wilt Disease. This study uses nuclear and mitochondrial genes to test the monophyly and relationships of Monochamus and applies coalescent methods to further delimit the conifer-feeding species. Monochamus has also included approximately 120 Old World species associated with diverse angiosperm tree species. We sample from these additional morphologically diverse species to determine their placement in the Lamiini. Through supermatrix and coalescent methods, the higher-level relationships of Monochamus show that conifer-feeders are a monophyletic group that includes the type species and has split into Nearctic and Palearctic clades. Molecular dating indicates a single dispersal of conifer-feeders to North America over the second Bering Land Bridge circa 5.3 Ma. All other Monochamus sampled fall in different parts of the Lamiini tree. Small-bodied angiosperm-feeding Monochamus group with the monotypic genus Microgoes Casey. The African Monochamus subgenera sampled are distantly related to the conifer-feeding clade. The multispecies coalescent delimitation methods BPP and STACEY delimit 17 conifer-feeding Monochamus species for a total of 18 species, and supports the retention of all current species. An interrogation with nuclear gene allele phasing reveals that unphased data can be unreliable for accurate delimitations and divergence times. The delimited species are discussed with integrative evidence, highlighting real-world challenges in recognizing the completion of speciation trajectories.

Cross-contamination and strong mitonuclear discordance in Empria sawflies (Hymenoptera, Tenthredinidae) in the light of phylogenomic data

In several sawfly taxa strong mitonuclear discordance has been observed, with nuclear genes supporting species assignments based on morphology, whereas the barcode region of the mitochondrial COI gene suggests different relationships. As previous studies were based on only a few nuclear genes, the causes and the degree of mitonuclear discordance remain ambiguous. Here, we obtained genomic-scale ddRAD data together with Sanger sequences of mitochondrial COI and two to three nuclear protein coding genes to investigate species limits and mitonuclear discordance in two closely related species groups of the sawfly genus Empria. As found previously based on nuclear ITS and mitochondrial COI sequences, species are in most cases supported as monophyletic based on new nuclear data reported here, but not based on mitochondrial COI. This mitonuclear discordance can be explained by occasional mitochondrial introgression with little or no nuclear gene flow, a pattern that might be common in haplodiploid taxa with slowly evolving mitochondrial genomes. Some species in the E. immersa group are not recovered as monophyletic according to either mitochondrial or nuclear data, but this could partly be because of unresolved taxonomy. Preliminary analyses of ddRAD data did not recover monophyly of E. japonica within the E. longicornis group (three Sanger sequenced nuclear genes strongly supported monophyly), but closer examination of the data and additional Sanger sequencing suggested that both specimens were substantially (possibly 10-20% of recovered loci) cross-contaminated. A reason could be specimen identification tag jumps during sequencing library preparation that in previous studies have been shown to affect up to 2.5% of the sequenced reads. We provide an R script to examine patterns of identical loci among the specimens and estimate that the cross-contamination rate is not unusually high for our ddRAD dataset as a whole (based on counting of identical sequences in the immersa and longicornis groups, which are well separated from each other and probably do not hybridise). The high rate of cross-contamination for both E. japonica specimens might be explained by the small number of recovered loci (~1000) compared to most other specimens (>10 000 in some cases) because of poor sequencing results. We caution against drawing unexpected biological conclusions when closely related specimens are pooled before sequencing and tagged only at one end of the molecule or at both ends using a unique combination of limited number of tags (less than the number of specimens).

Climate change and forest plagues: assessing current and future impacts of diprionid sawflies on the pine forests of north-western Mexico

The imminent threat of climate change lies in its potential to disrupt the balance of ecosystems, particularly vulnerable areas such as mountain-top remnant forests. An example of such a fragile ecosystem is the Sierra San Pedro Mártir (SSPM) National Park of Mexico's Baja California state, where high levels of endemism can be found, and which is home to one of the country's few populations of the emblematic Jeffrey pine (Pinus jeffreyi). Recent outbreaks of pine-feeding sawfly larvae in SSPM increase the vulnerability of this forest ecosystem, calling for immediate assessments of the severity of this threat. Here, we present a thorough study of the sawfly's biology and distribution, carrying out molecular and morphology-based identification of the species and creating model-based predictions of the species distribution in the area. The sawfly was found to belong to an undescribed species of the genus Zadiprion (family Diprionidae) with a one-year life-cycle. The distribution of this species appears to be restricted to the SSPM national park and it will probably persist for at least another 50 years, even considering the effects of climate change.

Genetic Basis of Body Color and Spotting Pattern in Redheaded Pine Sawfly Larvae (Neodiprion lecontei)

Pigmentation has emerged as a premier model for understanding the genetic basis of phenotypic evolution, and a growing catalog of color loci is starting to reveal biases in the mutations, genes, and genetic architectures underlying color variation in the wild. However, existing studies have sampled a limited subset of taxa, color traits, and developmental stages. To expand the existing sample of color loci, we performed QTL mapping analyses on two types of larval pigmentation traits that vary among populations of the redheaded pine sawfly (Neodiprion lecontei): carotenoid-based yellow body color and melanin-based spotting pattern. For both traits, our QTL models explained a substantial proportion of phenotypic variation and suggested a genetic architecture that is neither monogenic nor highly polygenic. Additionally, we used our linkage map to anchor the current N. lecontei genome assembly. With these data, we identified promising candidate genes underlying (1) a loss of yellow pigmentation in populations in the mid-Atlantic/northeastern United States [C locus-associated membrane protein homologous to a mammalian HDL receptor-2 gene (Cameo2) and lipid transfer particle apolipoproteins II and I gene (apoLTP-II/I)], and (2) a pronounced reduction in black spotting in Great Lakes populations [members of the yellow gene family, tyrosine hydroxylase gene (pale), and dopamine N-acetyltransferase gene (Dat)]. Several of these genes also contribute to color variation in other wild and domesticated taxa. Overall, our findings are consistent with the hypothesis that predictable genes of large effect contribute to color evolution in nature.

Gregariousness does not vary with geography, developmental stage, or group relatedness in feeding redheaded pine sawfly larvae

Aggregations are widespread across the animal kingdom, yet the underlying proximate and ultimate causes are still largely unknown. An ideal system to investigate this simple, social behavior is the pine sawfly genus Neodiprion, which is experimentally tractable and exhibits interspecific variation in larval gregariousness. To assess intraspecific variation in this trait, we characterized aggregative tendency within a single widespread species, the redheaded pine sawfly (N. lecontei). To do so, we developed a quantitative assay in which we measured interindividual distances over a 90‐min video. This assay revealed minimal behavioral differences: (1) between early‐feeding and late‐feeding larval instars, (2) among larvae derived from different latitudes, and (3) between groups composed of kin and those composed of nonkin. Together, these results suggest that, during the larval feeding period, the benefits individuals derive from aggregating outweigh the costs and that this cost‐to‐benefit ratio does not vary dramatically across space (geography) or ontogeny (developmental stage). In contrast to the feeding larvae, our assay revealed a striking reduction in gregariousness following the final larval molt in N. lecontei. We also found some intriguing interspecific variation: While N. lecontei and N. maurus feeding larvae exhibit significant aggregative tendencies, feeding N. compar larvae do not aggregate at all. These results set the stage for future work investigating the proximate and ultimate mechanisms underlying developmental and interspecific variation in larval gregariousness across Neodiprion.

Ancient and modern genome shuffling: Reticulate mito-nuclear phylogeny of four related allopatric species of Gyrodactylus von Nordmann, 1832 (Monogenea: Gyrodactylidae), ectoparasites on the Eurasian minnow Phoxinus phoxinus (L.) (Cyprinidae)

Phylogenetic analyses including four allopatric species of Gyrodactylus von Nordmann, 1832 on the Eurasian minnow Phoxinus phoxinus (L.) (Cyprinidae) revealed incongruence between the nuclear ITS1-5.8S-ITS2 and mitochondrial cox1 phylogenies due to ancient hybridisation. Gyrodactylus pannonicus Molnár, 1968 was sampled close to its type-locality, the upper reaches of River Tisza, tributary of Danube in the Black Sea Basin. Faunistic search detected three new related species with maximum composite likelihood distances in cox1 between 16.8-23.2% (tentatively 1.3 to 1.8 My of divergence). Gyrodactylus albolacustris n. sp. recorded in the White Sea Basin, eastern Baltic Basin and Mongolia was close to G. pannonicus in the nuclear ITS (divergence of 0.9%), but diverged in cox1 by 19.8%. The Mongolian isolate of G. albolacustris n. sp. diverged from the European isolates in cox1 by 8.9%, suggesting 0.7 My of isolation. The two other new species differed from G. pannonicus by >4% in ITS and some large indels in ITS1, and by >20% in cox1. Gyrodactylus danastriae n. sp. was found in River Strwiąż, a tributary of the River Dniester (Black Sea Basin) and was characterised by smaller size of anchors and by 29-41 bp dimorphic insertion in ITS1. Gyrodactylus botnicus n. sp. is considered endemic in the Baltic Basin, but was also found in the White Sea Basin as a postglacial immigrant, where it had hybridised with G. albolacustris n. sp. in spite of the high divergence in ITS (3.9%) and cox1 (22%). The discordant nuclear and mitochondrial phylogenies revealed an ancient mitochondrial introgression: G. albolacustris n. sp. was derived from a hybridisation combining proto-pannonicus ITS with proto-danastriae mitochondria, perhaps 1.3 My ago. The postglacial hybridisation of G. albolacustris n. sp. (as the donor of mtDNA^alb and ITS^alb) and G. botnicus n. sp. (donor of the ITS^bot) offered a model of shuffling of the genomic components: the process of the homogenisation and stabilisation of nuclear ITS (concerted evolution) and the lineage sorting has hardly begun.

Oviposition traits generate extrinsic postzygotic isolation between two pine sawfly species

BACKGROUND

Although empirical data indicate that ecological speciation is prevalent in nature, the relative importance of different forms of reproductive isolation and the traits generating reproductive isolation remain unclear. To address these questions, we examined a pair of ecologically divergent pine-sawfly species: while Neodiprion pinetum specializes on a thin-needled pine (Pinus strobus), N. lecontei utilizes thicker-needled pines. We hypothesized that extrinsic postzygotic isolation is generated by oviposition traits. To test this hypothesis, we assayed ovipositor morphology, oviposition behavior, and host-dependent oviposition success in both species and in F1 and backcross females.

RESULTS

Compared to N. lecontei, N. pinetum females preferred P. strobus more strongly, had smaller ovipositors, and laid fewer eggs per needle. Additionally, we observed host- and trait-dependent reductions in oviposition success in F1 and backcross females. Hybrid females that had pinetum-like host preference (P. strobus) and lecontei-like oviposition traits (morphology and egg pattern) fared especially poorly.

CONCLUSIONS

Together, these data indicate that maladaptive combinations of oviposition traits in hybrids contribute to extrinsic postzygotic isolation between N. lecontei and N. pinetum, suggesting that oviposition traits may be an important driver of divergence in phytophagous insects.

Timeframes of speciation, reticulation, and hybridization in the bulldog bat explained through phylogenetic analyses of all genetic transmission elements

Phylogenetic comparisons of the different mammalian genetic transmission elements (mtDNA, X-, Y-, and autosomal DNA) is a powerful approach for understanding the process of speciation in nature. Through such comparisons the unique inheritance pathways of each genetic element and gender-biased processes can link genomic structure to the evolutionary process, especially among lineages which have recently diversified, in which genetic isolation may be incomplete. Bulldog bats of the genus Noctilio are an exemplar lineage, being a young clade, widely distributed, and exhibiting unique feeding ecologies. In addition, currently recognized species are paraphyletic with respect to the mtDNA gene tree and contain morphologically identifiable clades that exhibit mtDNA divergences as great as among many species. To test taxonomic hypotheses and understand the contribution of hybridization to the extant distribution of genetic diversity in Noctilio, we used phylogenetic, coalescent stochastic modeling, and divergence time estimates using sequence data from cytochrome-b, cytochrome c oxidase-I, zinc finger Y, and zinc finger X, as well as evolutionary reconstructions based on amplified fragment length polymorphisms (AFLPs) data. No evidence of ongoing hybridization between the two currently recognized species was identified. However, signatures of an ancient mtDNA capture were recovered in which an mtDNA lineage of one species was captured early in the noctilionid radiation. Among subspecific mtDNA clades, which were generally coincident with morphology and statistically definable as species, signatures of ongoing hybridization were observed in sex chromosome sequences and AFLP. Divergence dating of genetic elements corroborates the diversification of extant Noctilio beginning about 3 Ma, with ongoing hybridization between mitochondrial lineages separated by 2.5 myr. The timeframe of species' divergence within Noctilio supports the hypothesis that shifts in the dietary strategies of gleaning insects (N. albiventris) or fish (N. leporinus) are among the most rapid instances of dietary evolution observed in mammals. This study illustrates the complex evolutionary dynamics shaping gene pools in nature, how comparisons of genetic elements can serve for understanding species boundaries, and the complex considerations for accurate taxonomic assignment.

Spread of a Gammabaculovirus within Larval Populations of Its Natural Balsam Fir Sawfly (Neodiprion abietis) Host Following Its Aerial Application

Field trials and assessments of the balsam fir sawfly (Neodiprion abietis) nucleopolyhedrovirus (NeabNPV: Baculoviridae, Gammabaculovirus) against its natural host were conducted in July and August 2002 near Corner Brook, Newfoundland and Labrador, Canada, in naturally regenerated, precommercially thinned stands dominated by balsam fir (Abies balsamea). Two experimental blocks, each with its own untreated control, were established. The purpose of the Island Pond block was to examine the spread of NeabNPV from a 313-ha aerial treatment block out into adjacent populations of balsam fir sawflies. The purpose of the Old Man's Pond block (2,093 ha) was to determine whether NeabNPV could disperse into populations of balsam fir sawflies within a 200-m zone between spray swaths. NeabNPV was applied to treatment blocks by a Cessna 188B AgTruck aircraft equipped with MicronAir AU4000 rotary atomizers at an application rate equivalent to 1 × 10⁸ NeabNPV occlusion bodies/ha in 2.5 L of 20% aqueous molasses. At Island Pond, NeabNPV infection increased with time following the spray, especially for individuals close to the treatment block, and infection rate decreased to a measured distance of 400 m from the treatment block. At Old Man's Pond, NeabNPV infection rose higher (80% vs. 15%) and sawfly densities declined more (84% vs. 60%) in the area between spray swaths than in the control block.

Recent speciation in three closely related sympatric specialists: inferences using multi-locus sequence, post-mating isolation and endosymbiont data

Shifting between unrelated host plants is relatively rare for phytophagous insects, and distinct host specificity may play crucial roles in reproductive isolation. However, the isolation status and the relationship between parental divergence and post-mating isolation among closely related sympatric specialists are still poorly understood. Here, multi-locus sequence were used to estimate the relationship among three host plant–specific closely related flea beetles, Altica cirsicola, A. fragariae and A. viridicyanea (abbreviated as AC, AF and AV respectively). The tree topologies were inconsistent using different gene or different combinations of gene fragments. The relationship of AF+(AC+AV) was supported, however, by both gene tree and species tree based on concatenated data. Post-mating reproductive data on the results of crossing these three species are best interpreted in the light of a well established phylogeny. Nuclear-induced but not Wolbachia-induced unidirectional cytoplasmic incompatibility, which was detected in AC-AF and AF-AV but not in AC-AV, may also suggest more close genetic affinity between AC and AV. Prevalence of Wolbachia in these three beetles, and the endosymbiont in most individuals of AV and AC sharing a same wsp haplotype may give another evidence of AF+(AC+AV). Our study also suggested that these three flea beetles diverged in a relative short time (0.94 My), which may be the result of shifting between unrelated host plants and distinct host specificity. Incomplete post-mating isolation while almost complete lineage sorting indicated that effective pre-mating isolation among these three species should have evolved.

Identification of molecular markers for DNA barcoding in the Aphidiinae (Hym. Braconidae)

Reliable identification of Aphidiinae species (Braconidae) is a prerequisite for conducting studies on aphid-parasitoid interactions at the community level. However, morphological identification of Aphidiinae species remains problematic even for specialists and is almost impossible with larval stages. Here, we compared the efficiency of two molecular markers [mitochondrial cytochrome c oxydase I (COI) and nuclear long wavelength rhodopsin (LWRh)] that could be used to accurately identify about 50 species of Aphidiinae that commonly occur in aphid-parasitoid networks in northwestern Europe. We first identified species on a morphological basis and then assessed the consistency of genetic and morphological data. Probably because of mitochondrial introgression, Aphidius ervi and A. microlophii were indistinguishable on the basis of their COI sequences, whereas LWRh sequences discriminated these species. Conversely, because of its lower variability, LWRh failed to discriminate two pairs of species (Aphidius aquilus, Aphidius salicis, Lysiphlebus confusus and Lysiphlebus fabarum). Our study showed that no unique locus but a combination of two genes should be used to accurately identify members of Aphidiinae.

Phylogeny estimation of the radiation of western North American chipmunks (Tamias) in the face of introgression using reproductive protein genes

The causes and consequences of rapid radiations are major unresolved issues in evolutionary biology. This is in part because phylogeny estimation is confounded by processes such as stochastic lineage sorting and hybridization. Because these processes are expected to be heterogeneous across the genome, comparison among marker classes may provide a means of disentangling these elements. Here we use introns from nuclear-encoded reproductive protein genes expected to be resistant to introgression to estimate the phylogeny of the western chipmunks (Tamias: subgenus: Neotamias), a rapid radiation that has experienced introgressive hybridization of mitochondrial DNA (mtDNA). We analyze the nuclear loci using coalescent-based species-tree estimation methods and concatenation to estimate a species tree and we use parametric bootstraps and coalescent simulations to differentiate between phylogenetic error, coalescent stochasticity and introgressive hybridization. Results indicate that the mtDNA gene tree reflects several introgression events that have occurred between taxa of varying levels of divergence and at different time points in the tree. T. panamintinus and T. speciosus appear to be fixed for ancient mitochondrial introgressions from T. minimus. A southern Rocky Mountains clade appears well sorted (i.e., species are largely monophyletic) at multiple nuclear loci, while five of six taxa are nonmonophyletic based on cytochrome b. Our simulations reject phylogenetic error and coalescent stochasticity as causes. The results represent an advance in our understanding of the processes at work during the radiation of Tamias and suggest that sampling reproductive-protein genes may be a viable strategy for phylogeny estimation of rapid radiations in which reproductive isolation is incomplete. However, a genome-scale survey that can statistically compare heterogeneity of genealogical process at many more loci will be necessary to test this conclusion.

Genetic divergence and geographic variation in the deep-water Conus orbignyi complex (Mollusca: Conoidea)

Puillandre, N. et al. (2010) Genetic divergence and geographic variation in a deep-water cone lineage: molecular and morphological analyses of the Conus orbignyi complex (Mollusca: Conoidea).The cone snails (family Conidae) are a hyperdiverse lineage of venomous gastropods. Two standard markers, COI and ITS2, were used to define six genetically-divergent groups within a subclade of Conidae that includes Conus orbignyi; each of these was then evaluated based on their shell morphology. We conclude that three forms, previously regarded as subspecies of Conus orbignyi are distinct species, now recognized as Conus orbignyi, Conus elokismenos and Conus coriolisi. In addition, three additional species (Conus pseudorbignyi, Conus joliveti and Conus comatosa) belong to this clade. Some of the proposed species (e.g., Conus elokismenos) are possibly in turn complexes comprising multiple species. Groups such as Conidae illustrate the challenges generally faced in species delimitation in biodiverse lineages. In the case of the Conus orbignyi complex, not only are there definable, genetically divergent lineages, but also considerable geographic variation within each group. Our study suggests that an intensive analysis of multiple specimens within a single locality helps to minimize the confounding effects of geographic variation and can be a useful starting point for circumscribing different species within such a confusing complex.

The organization of the antennal lobe correlates not only with phylogenetic relationship, but also life history: a Basal hymenopteran as exemplar

The structure of the brain is a consequence of selective pressures and the ancestral brain structures modified by those pressures. The Hymenoptera are one of the most behaviorally complex insect orders, and the olfactory system of honeybees (one of the most derived members) has been extensively studied. To understand the context in which the olfactory system of the Hymenoptera evolved, we performed a variety of immunocytochemical and anatomical labeling techniques on the antennal lobes (ALs) of one of its most primitive members, the sawflies, to provide a comparison between the honeybee and other insect model species. The olfactory receptor neurons project from the antennae to fill the entire glomerular volume but do not form distinct tracts as in the honeybee. Labeling of projection neurons revealed 5 output tracts similar to those in moths and immunolabeling for several transmitters revealed distinct populations of local interneurons and centrifugal neurons that were also similar to moths. There were, however, no histaminergic or dopaminergic AL neurons. The similarities between sawflies and moths suggest that along with the great radiation and increased complexity of behavioral repertoire of the Hymenoptera, there were extensive modifications of AL structure.

A test of the sympatric host race formation hypothesis in Neodiprion (Hymenoptera: Diprionidae)

Theory suggests that sympatric speciation is possible; however, its prevalence in nature remains unknown. Because Neodiprion sawflies are host specialists and mate on their hosts, sympatric speciation via host shifts may be common in this genus. Here, we test this hypothesis using near-complete taxonomic sampling of a species group, comprehensive geographical and ecological data, and multiple comparative methods. Host-use data suggest that host shifts contributed to the evolution of reproductive isolation in Neodiprion and previous work has shown that gene flow accompanied divergence. However, geographical data provide surprisingly little support for the hypothesis that host shifts occurred in sympatry. While these data do not rule out sympatric host race formation in Neodiprion, they suggest that this speciation mode is uncommon in the genus and possibly in nature.

To speciate, or not to speciate? Resource heterogeneity, the subjectivity of similarity, and the macroevolutionary consequences of niche-width shifts in plant-feeding insects

Coevolutionary studies on plants and plant-feeding insects have significantly improved our understanding of the role of niche shifts in the generation of new species. Evolving plant lineages essentially constitute moving islands and archipelagoes in resource space, and host shifts by insects are usually preceded by colonizations of novel resources. Critical to hypotheses concerning ecological speciation is what happens immediately before and after colonization attempts: if an available plant is too similar to the current host(s), it simply will be incorporated into the existing diet, but if it is too different, it will not be colonized in the first place. It thus seems that the probability of speciation is maximized when alternative hosts are at an 'intermediate' distance in resource space. In this review, I wish to highlight the possibility that resource similarity and, thus, the definition of 'intermediate', are subjective concepts that depend on the herbivore lineage's tolerance to dietary variation. This subjectivity of similarity means that changes in tolerance can either decrease or increase speciation probabilities depending on the distribution of plants in resource space: insect lineages with narrow tolerances are likely to speciate by 'island-hopping' on young, species-rich plant groups, whereas more generalized lineages could speciate by shifting among resource archipelagoes formed by higher plant taxa. Repeated and convergent origins of traits known to broaden or to restrict host-plant use in multiple different insect groups provide opportunities for studying how tolerance and resource heterogeneity may interact to determine speciation rates.

Comparison of methods for species-tree inference in the sawfly genus Neodiprion (Hymenoptera: Diprionidae)

Conifer-feeding sawflies in the genus Neodiprion provide an excellent opportunity to investigate the origin and maintenance of barriers to reproduction, but obtaining a phylogenetic estimate for comparative studies of Neodiprion speciation has proved difficult. Specifically, nonmonophyly within and discordance between individual gene trees, both of which are common in groups that diverged recently and/or rapidly, make it impossible to infer a species tree using methods that are designed to estimate gene trees. Therefore, in this study, we estimate relationships between members of the lecontei species group using four approaches that are intended to estimate species, not gene, trees: (1) minimize deep coalescences (MDC), (2) shallowest divergences (SD), (3) Bayesian estimation of species trees (BEST), and (4) a novel approach that combines concatenation with monophyly constraints (CMC). Multiple populations are sampled for most species and all four methods incorporate this intraspecific variation into estimates of interspecific relationships. We investigate the sensitivity of each method to taxonomic sampling, and, for the BEST method, we assess the impact of prior choice on species-tree inference. We also compare species-tree estimates to one another and to a morphologically based hypothesis to identify clades that are supported by multiple analyses and lines of evidence. We find that both taxonomic sampling and method choice impact species-tree estimates and that, for these data, the BEST method is strongly influenced by Theta and branch-length priors. We also find that the CMC method is the least sensitive to taxonomic sampling. Finally, although interspecific genetic variation is low due to the recent divergence of the lecontei group, our results to date suggest that incomplete lineage sorting and interspecific gene flow are the main factors complicating species-tree inference in Neodiprion. Based on these analyses, we propose a phylogenetic hypothesis for the lecontei group. Finally, our results suggest that, even for very challenging groups like Neodiprion, an underlying species-tree signal can be extracted from multi-locus data as long as intraspecific variation is adequately sampled and methods that focus on the estimation of species trees are used.