Phylogenomics of Tetraopes longhorn beetles unravels their evolutionary history and biogeographic origins.

Tetraopes longhorn beetles are known for their resistance to milkweed plant toxins and their coevolutionary dynamics with milkweed plants (Asclepias). This association is considered a textbook example of coevolution, in which each species of Tetraopes is specialized to feed on one or a few species of Asclepias. A major challenge to investigating coevolutionary hypotheses and conducting molecular ecology studies lies in the limited understanding of the evolutionary history and biogeographical patterns of Tetraopes. By integrating genomic, morphological, paleontological, and geographical data, we present a robust phylogeny of Tetraopes and their relatives, using three inference methods with varying subsets of data, encompassing 2-12 thousand UCE loci. We elucidate the diversification patterns of Tetraopes species across major biogeographical regions and their colonization of the American continent. Our findings suggest that the genus originated in Central America approximately 21 million years ago during the Miocene and diversified from the Mid-Miocene to the Pleistocene. These events coincided with intense geological activity in Central America. Additionally, independent colonization events in North America occurred from the Late Miocene to the early Pleistocene, potentially contributing to the early diversification of the group. Our data suggest that a common ancestor of Tetraopini migrated into North America, likely facilitated by North Atlantic land bridges, while closely related tribes diverged in Asia and Europe during the Paleocene. Establishing a robust and densely sampled phylogeny of Tetraopes beetles provides a foundation for investigating micro- and macroevolutionary phenomena, including clinal variation, coevolution, and detoxification mechanisms in this ecologically important group.

Once upon a fly: The biogeographical odyssey of Labrundinia (Chironomidae, Tanypodinae), an aquatic non-biting midge towards diversification.

Labrundinia is a highly recognizable lineage in the Pentaneurini tribe (Diptera, Chironomidae). The distinct predatory free-swimming larvae of this genus are typically present in unpolluted aquatic environments, such as small streams, ponds, lakes, and bays. They can be found on the bottom mud, clinging to rocks and wood, and dwelling among aquatic vegetation. Labrundinia has been extensively studied in ecological research and comprises 39 species, all but one of which has been described from regions outside the Palearctic. Earlier phylogenetic studies have suggested that the initial diversification of the genus likely occurred in the Neotropical Region, with its current presence in the Nearctic Region and southern South America being the result of subsequent dispersal events. Through the integration of molecular and morphological data in a calibrated phylogeny, we reveal a complex and nuanced evolutionary history for Labrundinia, providing insights into its biogeographical and diversification patterns. In this comprehensive study, we analyze a dataset containing 46 Labrundinia species, totaling 10,662 characters, consisting of 10,616 nucleotide sites and 46 morphological characters. The molecular data was generated mainly by anchored enrichment hybrid methods. Using this comprehensive dataset, we inferred the phylogeny of the group based on a total evidence matrix. Subsequently, we employed the generated tree for time calibration and further analysis of biogeography and diversification patterns. Our findings reveal multiple dispersal events out of the Neotropics, where the group originated in the late Cretaceous approximately 72 million years ago (69-78 Ma). We further reveal that the genus experienced an early burst of diversification rates during the Paleocene, which gradually decelerated towards the present-day. We also find that the Neotropics have played a pivotal role in the evolution of Labrundinia by serving as both a cradle and a museum. By "cradle," we mean that the region has been a hotspot for the origin and diversification of new Labrundinia lineages, while "museum" refers to the region's ability to preserve ancestral lineages over extended periods. In summary, our findings indicate that the Neotropics have been a key source of genetic diversity for Labrundinia, resulting in the development of distinctive adaptations and characteristics within the genus. This evidence highlights the crucial role that these regions have played in shaping the evolutionary trajectory of Labrundinia.

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.

First phylogenetic analysis of Dryophthorinae (Coleoptera, Curculionidae) based on structural alignment of ribosomal DNA reveals Cenozoic diversification.

Dryophthorinae is an economically important, ecologically distinct, and ubiquitous monophyletic group of pantropical weevils with more than 1,200 species in 153 genera. This study provides the first comprehensive phylogeny of the group with the aim to provide insights into the process and timing of diversification of phytophagous insects, inform classification and facilitate predictions. The taxon sampling is the most extensive to date and includes representatives of all five dryophthorine tribes and all but one subtribe. The phylogeny is based on secondary structural alignment of 18S and 28S rRNA totaling 3,764 nucleotides analyzed under Bayesian and maximum likelihood inference. We used a fossil-calibrated relaxed clock model with two approaches, node-dating and fossilized birth-death models, to estimate divergence times for the subfamily. All tribes except the species-rich Rhynchophorini were found to be monophyletic, but higher support is required to ascertain the paraphyly of Rhynchophorini with more confidence. Nephius is closely related to Dryophthorini and Stromboscerini, and there is strong evidence for paraphyly of Sphenophorina. We find a large gap between the divergence of Dryophthorinae from their sister group Platypodinae in the Jurassic-Cretaceous boundary and the diversification of extant species in the Cenozoic, highlighting the role of coevolution with angiosperms in this group.

Evaluating insect-host interactions as a driver of species divergence in palm flower weevils.

Plants and their specialized flower visitors provide valuable insights into the evolutionary consequences of species interactions. In particular, antagonistic interactions between insects and plants have often been invoked as a major driver of diversification. Here we use a tropical community of palms and their specialized insect flower visitors to test whether antagonisms lead to higher population divergence. Interactions between palms and the insects visiting their flowers range from brood pollination to florivory and commensalism, with the latter being species that feed on decaying-and presumably undefended-plant tissues. We test the role of insect-host interactions in the early stages of diversification of nine species of beetles sharing host plants and geographical ranges by first delimiting cryptic species and then using models of genetic isolation by environment. The degree to which insect populations are structured by the genetic divergence of plant populations varies. A hierarchical model reveals that this variation is largely uncorrelated with the kind of interaction, showing that antagonistic interactions are not associated with higher genetic differentiation. Other aspects of host use that affect plant-associated insects regardless of the outcomes of their interactions, such as sensory biases, are likely more general drivers of insect population divergence.

Whole-genome amplification in double-digest RADseq results in adequate libraries but fewer sequenced loci.

Whole-genome amplification by multiple displacement amplification (MDA) is a promising technique to enable the use of samples with only limited amount of DNA for the construction of RAD-seq libraries. Previous work has shown that, when the amount of DNA used in the MDA reaction is large, double-digest RAD-seq (ddRAD) libraries prepared with amplified genomic DNA result in data that are indistinguishable from libraries prepared directly from genomic DNA. Based on this observation, here we evaluate the quality of ddRAD libraries prepared from MDA-amplified genomic DNA when the amount of input genomic DNA and the coverage obtained for samples is variable. By simultaneously preparing libraries for five species of weevils (Coleoptera, Curculionidae), we also evaluate the likelihood that potential contaminants will be encountered in the assembled dataset. Overall, our results indicate that MDA may not be able to rescue all samples with small amounts of DNA, but it does produce ddRAD libraries adequate for studies of phylogeography and population genetics even when conditions are not optimal. We find that MDA makes it harder to predict the number of loci that will be obtained for a given sequencing effort, with some samples behaving like traditional libraries and others yielding fewer loci than expected. This seems to be caused both by stochastic and deterministic effects during amplification. Further, the reduction in loci is stronger in libraries with lower amounts of template DNA for the MDA reaction. Even though a few samples exhibit substantial levels of contamination in raw reads, the effect is very small in the final dataset, suggesting that filters imposed during dataset assembly are important in removing contamination. Importantly, samples with strong signs of contamination and biases in heterozygosity were also those with fewer loci shared in the final dataset, suggesting that stringent filtering of samples with significant amounts of missing data is important when assembling data derived from MDA-amplified genomic DNA. Overall, we find that the combination of MDA and ddRAD results in high-quality datasets for population genetics as long as the sequence data is properly filtered during assembly.

West meets East: How do rainforest beetles become circum-Pacific? Evolutionary origin of Callipogon relictus and allied species (Cerambycidae: Prioninae) in the New and Old Worlds.

The longhorn beetle genus Callipogon Audinet-Serville represents a small group of large wood-boring beetles whose distribution pattern exhibits a unique trans-Pacific disjunction between the East Asian temperate rainforest and the tropical rainforest of the Neotropics. To understand the biogeographic history underlying this circum-Pacific disjunct distribution, we reconstructed a molecular phylogeny of the subfamily Prioninae with extensive sampling of Callipogon using multilocus sequence data of 99 prionine and four parandrine samples (ingroups), together with two distant outgroup species. Our sampling of Callipogon includes 18 of the 24 currently accepted species, with complete representation of all species in our focal subgenera. Our phylogenetic analyses confirmed the purported affinity between the Palearctic Callipogon relictus and its Neotropical congeners. Furthermore, based on molecular dating under the fossilized birth-death (FBD) model with comprehensive fossil records and probabilistic ancestral range reconstructions, we estimated the crown group Callipogon to have originated in the Paleocene circa 60 million years ago (Ma) across the Neotropics and Eastern Palearctics. The divergence between the Palearctic C. relictus and its Neotropical congeners is explained as the result of a vicariance event following the demise of boreotropical forest across Beringia at the Eocene-Oligocene boundary. As C. relictus represents the unique relictual species that evidentiates the lineage's expansive ancient distribution, we evaluated its conservation importance through species distribution modelling. Though we estimated a range expansion for C. relictus by 2050, we emphasize a careful implementation of conservation programs towards the protection of primary forest across its current habitats, as the species remains highly vulnerable to habitat disturbance.

Phylogenomic Data Yield New and Robust Insights into the Phylogeny and Evolution of Weevils.

The phylogeny and evolution of weevils (the beetle superfamily Curculionoidea) has been extensively studied, but many relationships, especially in the large family Curculionidae (true weevils; > 50,000 species), remain uncertain. We used phylogenomic methods to obtain DNA sequences from 522 protein-coding genes for representatives of all families of weevils and all subfamilies of Curculionidae. Most of our phylogenomic results had strong statistical support, and the inferred relationships were generally congruent with those reported in previous studies, but with some interesting exceptions. Notably, the backbone relationships of the weevil phylogeny were consistently strongly supported, and the former Nemonychidae (pine flower snout beetles) were polyphyletic, with the subfamily Cimberidinae (here elevated to Cimberididae) placed as sister group of all other weevils. The clade comprising the sister families Brentidae (straight-snouted weevils) and Curculionidae was maximally supported and the composition of both families was firmly established. The contributions of substitution modeling, codon usage and/or mutational bias to differences between trees reconstructed from amino acid and nucleotide sequences were explored. A reconstructed timetree for weevils is consistent with a Mesozoic radiation of gymnosperm-associated taxa to form most extant families and diversification of Curculionidae alongside flowering plants-first monocots, then other groups-beginning in the Cretaceous.

Phylogeny of world stag beetles (Coleoptera: Lucanidae) reveals a Gondwanan origin of Darwin's stag beetle.

Stag beetles (family Lucanidae Latreille, 1804) are one of the earliest branching lineages of scarab beetles that are characterized by the striking development of the male mandibles. Despite stag beetles' popularity among traditional taxonomists and amateur collectors, there has been almost no study of lucanid relationships and evolution. Entomologists, including Jeannel (1942), have long recognized resemblance between the austral stag beetles of the tribes Chiasognathini, Colophonini, Lamprimini, Pholidotini, Rhyssonotini, and Streptocerini, but this hypothesis of their close relationship across the continents has never been tested. To gain further insight into lucanid phylogeny and biogeography, we reconstructed the first molecular phylogeny of world stag beetles using DNA sequences from mitochondrial 16S rDNA, nuclear 18S and 28S rDNA, and the nuclear protein-coding (NPC) gene wingless for 93 lucanid species representing all extant subfamilies and 24 out of the 27 tribes, together with 14 representative samples of other early branching scarabaeoid families and two staphyliniform beetle families as outgroups. Both Bayesian inference (BI) and maximum likelihood inference (MLI) strongly supported the monophyly of Lucanidae sensu lato that includes Diphyllostomatidae. Within Lucanidae sensu stricto, the subfamilies Lucaninae and Lampriminae appeared monophyletic under both methods of phylogenetic inferences; however, Aesalinae and Syndesinae were found to be polyphyletic. A time-calibrated phylogeny based on five fossil data estimated the origin of crown group Lucanidae as circa 160 million years ago (MYA). Divergence between the Neotropical and Australasian groups of the Chiasognathini was estimated to be circa 47MYA, with the South African Colophonini branching off from the ancient Chiasognathini lineage around 87MYA. Another Gondwanan relationship was recovered between the Australasian Eucarteria and the Neotropical Casignetus, which diverged circa 58MYA. Lastly, as Jeannel's hypothesis predicted, divergence within Lampriminae between the Australasian Lamprima and the Neotropical Streptocerus was estimated to be circa 37MYA. The split of these lineages were generally concordant with the pattern of continental break-up of the super-continent Gondwana, and our biogeographic reconstructions based on the dispersal-extinction-cladogenesis model (DEC) corroborate our view that the divergences in these austral lineages were caused by vicariance events following the Gondwanan break-up. In addition, the phylogenetic position and geographic origin of the Hawaiian genus Apterocyclus was revealed for the first time. Overall, our results provide the framework toward studying lucanid relationships and divergence time estimates, which allowed for more accurate biogeographic explanations and discussions on ancestral lucanids and the evolutionary origin of the enlarged male mandibles.

The effects of biogeography on ant diversity and activity on the Boston Harbor Islands, Massachusetts, U.S.A.

Many studies have examined how island biogeography affects diversity on the scale of island systems. In this study, we address how diversity varies over very short periods of time on individual islands. To do this, we compile an inventory of the ants living in the Boston Harbor Islands National Recreation Area, Boston, Massachusetts, USA using data from a five-year All Taxa Biodiversity Inventory of the region's arthropods. Consistent with the classical theory of island biogeography, species richness increased with island size, decreased with island isolation, and remained relatively constant over time. Additionally, our inventory finds that almost half of the known Massachusetts ant fauna can be collected in the BHI, and identifies four new species records for Massachusetts, including one new to the United States, Myrmica scabrinodis. We find that the number of species actually active on islands depended greatly on the timescale under consideration. The species that could be detected during any given week of sampling could by no means account for total island species richness, even when correcting for sampling effort. Though we consistently collected the same number of species over any given week of sampling, the identities of those species varied greatly between weeks. This variation does not result from local immigration and extinction of species, nor from seasonally-driven changes in the abundance of individual species, but rather from weekly changes in the distribution and activity of foraging ants. This variation can be upwards of 50% of ant species per week. This suggests that numerous ant species on the BHI share the same physical space at different times. This temporal partitioning could well explain such unexpectedly high ant diversity in an isolated, urban site.

9-genes reinforce the phylogeny of holometabola and yield alternate views on the phylogenetic placement of Strepsiptera.

BACKGROUND: The extraordinary morphology, reproductive and developmental biology, and behavioral ecology of twisted wing parasites (order Strepsiptera) have puzzled biologists for centuries. Even today, the phylogenetic position of these enigmatic "insects from outer space" [1] remains uncertain and contentious. Recent authors have argued for the placement of Strepsiptera within or as a close relative of beetles (order Coleoptera), as sister group of flies (order Diptera), or even outside of Holometabola. METHODOLOGY/PRINCIPAL FINDINGS: Here, we combine data from several recent studies with new data (for a total of 9 nuclear genes and approximately 13 kb of aligned data for 34 taxa), to help clarify the phylogenetic placement of Strepsiptera. Our results unequivocally support the monophyly of Neuropteroidea (=Neuropterida+Coleoptera)+Strepsiptera, but recover Strepsiptera either derived from within polyphagan beetles (order Coleoptera), or in a position sister to Neuropterida. All other supra-ordinal- and ordinal-level relationships recovered with strong nodal support were consistent with most other recent studies. CONCLUSIONS/SIGNIFICANCE: These results, coupled with the recent proposed placement of Strepsiptera sister to Coleoptera, suggest that while the phylogenetic neighborhood of Strepsiptera has been identified, unequivocal placement to a specific branch within Neuropteroidea will require additional study.

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.

Temporal lags and overlap in the diversification of weevils and flowering plants.

The extraordinary diversity of herbivorous beetles is usually attributed to coevolution with angiosperms. However, the degree and nature of contemporaneity in beetle and angiosperm diversification remain unclear. Here we present a large-scale molecular phylogeny for weevils (herbivorous beetles in the superfamily Curculionoidea), one of the most diverse lineages of insects, based on approximately 8 kilobases of DNA sequence data from a worldwide sample including all families and subfamilies. Estimated divergence times derived from the combined molecular and fossil data indicate diversification into most families occurred on gymnosperms in the Jurassic, beginning approximately 166 Ma. Subsequent colonization of early crown-group angiosperms occurred during the Early Cretaceous, but this alone evidently did not lead to an immediate and major diversification event in weevils. Comparative trends in weevil diversification and angiosperm dominance reveal that massive diversification began in the mid-Cretaceous (ca. 112.0 to 93.5 Ma), when angiosperms first rose to widespread floristic dominance. These and other evidence suggest a deep and complex history of coevolution between weevils and angiosperms, including codiversification, resource tracking, and sequential evolution.

The thoracic morphology of Archostemata and the relationships of the extant suborders of Coleoptera (Hexapoda).

Thoracic structures of Tetraphalerus bruchi are described in detail. The results were compared with features found in other representatives of Archostemata and other coleopteran suborders. Differences between thoracic structures of Tetraphalerus and members of other archostematan subgroups are discussed. External and internal characters of larval and adult representatives of 37 genera of the coleopteran suborders are outlined, coded and analysed cladistically, with four groups of Neuropterida as outgroup taxa. The results strongly suggest the branching pattern Archostemata + [Adephaga + (Myxophaga + Polyphaga)]. Coleoptera excluding Archostemata are supported with a high Bremer support. Important evolutionary changes linked with this branching event are simplifications of the thoracic skeleton resulting in reduced degrees of freedom (i.e. a restricted movability, especially at the leg bases), and a distinct simplification of the muscle system. This development culminates in Polyphaga, which are also strongly supported as a clade. Internalization of the partly reduced propleura, further muscle losses, and the fusion of the mesoventrites and metaventrites-with reversal in Scirtoidea and Derodontidae-are autapomorphies of Polyphaga. Archostemata is a small relict group in contrast to highly successful xylobiontic groups of Polyphaga. The less efficient thoracic locomotor apparatus, the lack of cryptonephric Malpighian tubules, and the rise of angiosperms with beetle groups primarily adjusted to them may have contributed to the decline of Archostemata. © The Willi Hennig Society 2008.

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.

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

Neodiprion Rohwer (Hymenoptera: Diprionidae) is a Holarctic genus of conifer-feeding sawflies with a remarkable amount of inter- and intraspecific diversity in host use, behavior, and development. This variation is thought to play a central role in Neodiprion diversification, but speciation hypotheses remain untested due to a lack of a robust phylogenetic estimate. Here, we utilize sequence data from three nuclear genes (CAD, ANL43, EF1alpha) to obtain a phylogenetic estimate for the genus. These analyses suggest that: (1) North American and Eurasian Neodiprion are monophyletic sister clades, (2) the sertifer group is paraphyletic with respect to the monophyletic lecontei group, and (3) on at least two occasions, dispersal from eastern to western North America proceeded via southern host bridges. Based on these results and host biogeography, we revise a previous scenario for the evolution of Neodiprion and suggest maximum ages for the genus and for the lecontei group (25 My and 14 My, respectively). In addition, because a previous study reported rampant mitochondrial introgression in the lecontei group, we assess its prevalence in the sertifer group. Analysis of three mitochondrial genes (COI, tRNA-leucine, and COII) reveals that mito-nuclear discordance is prevalent in the sertifer group, and patterns of species monophyly are consistent with those expected under frequent mitochondrial introgression. As was the case for lecontei group species, we find that introgression appears to be most pronounced between species that occasionally share hosts, suggesting that divergent host use is an important barrier to gene flow in Neodiprion. Finally, we suggest that the lack of phylogenetic resolution and prevalence of species non-monophyly in the non-Pinus feeding Neodiprion may result from the rapid divergence (possibly with gene flow) of these species following their entry into a novel adaptive zone.

Mitonuclear discordance is caused by rampant mitochondrial introgression in Neodiprion (Hymenoptera: Diprionidae) sawflies.

We investigate the pervasiveness of hybridization and mitochondrial introgression in Neodiprion Rohwer (Hymenoptera; Diprionidae), a Holarctic genus of conifer-feeding sawflies. A phylogenetic analysis of the lecontei species group revealed extensive discordance between a contiguous mitochondrial region spanning three genes (COI, tRNA-leucine, and COII) and three nuclear loci (EF1alpha, CAD, and an anonymous nuclear locus). Bayesian tests of monophyly and Shimodaira-Hasegawa (SH) tests of topological congruence were consistent with mitochondrial introgression; however, these patterns could also be explained by lineage sorting (i.e., deep coalescence). Therefore, to explicitly test the mitochondrial introgression hypothesis, we used a novel application of coalescent-based isolation with migration (IM) models to measure interspecific gene flow at each locus. In support of our hypothesis, mitochondrial gene flow was consistently higher than nuclear gene flow across 120 pairwise species comparisons (P < 1 x 10(-12)). We combine phylogenetic and coalescent evidence to identify likely cases of recent and ancient introgression in Neodiprion, and based on these observations, we hypothesize that shared hosts and/or pheromones facilitate hybridization, whereas disparate abundances between hybridizing species promote mitochondrial introgression. Our results carry implications for phylogenetic analysis, and we advocate the separation of high and low gene flow regions to inform analyses of hybridization and speciational history, respectively.

Larval habits, host-plant associations, and speciation in nematine sawflies (Hymenoptera: Tenthredinidae).

Adaptive radiations consist of two intertwined processes, diversification of species and diversification of their ecological niches, but it is unclear whether there is a causal link between the processes. In phytophagous insects, ecological diversification mainly involves shifts in host-plant associations and in larval feeding habits (internal or external) on different plant parts, and several observations indicate that speciation is facilitated by host shifts. Data on host use in individual species suggest that internal feeders are less likely to colonize new hosts than external-feeding taxa and, consequently, increases in collective host ranges and species numbers should be slowed down in endophagous lineages. We tested these related hypotheses by using phylogenetic information to reconstruct the evolutionary history of larval resource use in the sawfly subfamily Nematinae, a group of 1000 plus species with a broad range of niches: the subfamily's combined host range includes over 20 plant families, and larvae may feed externally on leaves or needles, or internally, for example, in buds, fruits, leaves, or galls. The results show that: (1) Most internally feeding groups have evolved independently from external-feeding ancestors, but several distinct internal habits have appeared convergently multiple times; (2) Shifts among host taxa are clearly more common than changes in larval habits; (3) The majority of host switches have occurred among phylogenetically close plant groups, but many shifts are manifest among distantly related, ecologically proximate hosts; (4) Although external feeding characteristic of the common ancestor of Nematinae is associated with relatively high rates of host-shifting, internal feeders are very conservative in their host use; (5) In contrast, the effect of endophagy on speciation probabilities is more variable: net speciation rates are lowered in most internal-feeding groups, but a striking exception is found in species that induce galls on Salicaceae. The loose connection between collective host ranges and species diversity provides empirical support for theoretical models suggesting that speciation rates are a function of a complex interplay between "intrinsic" niche width and resource heterogeneity.

Tropical forests are both evolutionary cradles and museums of leaf beetle diversity.

The high extant species diversity of tropical lineages of organisms is usually portrayed as a relatively recent and rapid development or as a consequence of the gradual accumulation or preservation of species over time. These explanations have led to alternative views of tropical forests as evolutionary "cradles" or "museums" of diversity, depending on the organisms under study. However, biogeographic and fossil evidence implies that the evolutionary histories of diversification among tropical organisms may be expected to exhibit characteristics of both cradle and museum models. This possibility has not been explored in detail for any group of terrestrial tropical organisms. From an extensively sampled molecular phylogeny of herbivorous Neotropical leaf beetles in the genus Cephaloleia, we present evidence for (i) comparatively ancient Paleocene-Eocene adaptive radiation associated with global warming and Cenozoic maximum global temperatures, (ii) moderately ancient lineage-specific diversification coincident with the Oligocene adaptive radiation of Cephaloleia host plants in the genus Heliconia, and (iii) relatively recent Miocene-Pliocene diversification coincident with the collision of the Panama arc with South America and subsequent bridging of the Isthmus of Panama. These results demonstrate that, for Cephaloleia and perhaps other lineages of organisms, tropical forests are at the same time both evolutionary cradles and museums of diversity.