Geometric morphometrics and ecological niche modelling for delimitation of Triatoma pallidipennis (Hemiptera: Reduviidae: Triatominae) haplogroups

A recent phylogenetic analysis of Triatoma pallidipennis, an important Chagas disease vector in Mexico, based on molecular markers, revealed five monophyletic haplogroups with validity as cryptic species. Here, we compare T. pallidipennis haplogroups using head and pronotum features, environmental characteristics of their habitats, and ecological niche modeling. To analyze variation in shape, images of the head and pronotum of the specimens were obtained and analyzed using methods based on landmarks and semi-landmarks. Ecological niche models were obtained from occurrence data, as well as a set of bioclimatic variables that characterized the environmental niche of each analyzed haplogroup. Deformation grids for head showed a slight displacement towards posterior region of pre-ocular landmarks. Greatest change in head shape was observed with strong displacement towards anterior region of antenniferous tubercle. Procrustes ANOVA and pairwise comparisons showed differences in mean head shape in almost all haplogroups. However, pairwise comparisons of mean pronotum shape only showed differences among three haplogroups. Correct classification of all haplogroups was not possible using discriminant analysis. Important differences were found among the environmental niches of the analyzed haplogroups. Ecological niche models of each haplogroup did not predict the climatic suitability areas of the other haplogroups, revealing differences in environmental conditions. Significant differences were found between at least two haplogroups, demonstrating distinct environmental preferences among them. Our results show how the analysis of morphometric variation and the characterization of the environmental conditions that define the climatic niche can be used to improve the delimitation of T. pallidipennis haplogroups that constitute cryptic species.

What is adaptive radiation? Many manifestations of the phenomenon in an iconic lineage of Hawaiian spiders

Adaptive radiation provides the ideal context for identifying and testing the processes that drive evolutionary diversification. However, different adaptive radiations show a variety of different patterns, making it difficult to come up with universal rules that characterize all such systems. Diversification may occur via several mechanisms including non-adaptive divergence, adaptation to novel environments, or character displacement driven by competition. Here, we characterize the ways these different drivers contribute to present-day diversity patterns, using the exemplary adaptive radiation of Hawaiian long-jawed orbweaver (Tetragnatha) spiders. We present the most taxonomically comprehensive phylogenetic hypothesis to date for this group, using 10 molecular markers and representatives from every known species across the archipelago. Among the lineages that make up this remarkable radiation, we find evidence for multiple diversification modalities. Several clades appear to have diversified in allopatry under a narrow range of ecological conditions, highlighting the role of niche conservatism in speciation. Others have shifted into new environments and evolved traits that appear to be adaptive in those environments. Still others show evidence for character displacement by close relatives, often resulting in convergent evolution of stereotyped ecomorphs. All of the above mechanisms seem to have played a role in giving rise to the exceptional diversity of morphological, ecological and behavioral traits represented among the many species of Hawaiian Tetragnatha. Taking all these processes into account, and testing how they operate in different systems, may allow us to identify universal principles underlying adaptive radiation.

Environmental filtering is the main assembly rule of ground beetles in the forest and its edge but not in the adjacent grassland

In a fragmented landscape, transitional zones between neighboring habitats are common, and our understanding of community organizational forces across such habitats is important. Edge studies are numerous, but the majority of them utilize information on species richness and abundance. Abundance and taxonomic diversity, however, provide little information on the functioning and phylogeny of the co-existing species. Combining the evaluation of their functional and phylogenetic relationships, we aimed to assess whether ground beetle assemblages are deterministically or stochastically structured along grassland-forest gradients. Our results showed different community assembly rules on opposite sides of the forest edge. In the grassland, co-occurring species were functionally and phylogenetically not different from the random null model, indicating a random assembly process. Contrary to this, at the forest edge and the interior, co-occurring species showed functional and phylogenetic clustering, thus environmental filtering was the likely process structuring carabid assemblages. Community assembly in the grassland was considerably affected by asymmetrical species flows (spillover) across the forest edge: more forest species penetrated into the grassland than open-habitat and generalist species entered into the forest. This asymmetrical species flow underlines the importance of the filter function of forest edges. As unfavorable, human-induced changes to the structure, composition and characteristics of forest edges may alter their filter function, edges have to be specifically considered during conservation management.

Conversion from environmental filtering to randomness as assembly rule of ground beetle assemblages along an urbanization gradient

Urbanization fragments, isolates or eliminates natural habitats, and changes the structure and composition of assemblages living in the remaining natural fragments. Knowing assembly rules is necessary to support and/or maintain biodiversity in urban habitats. We hypothesized that forest communities in rural sites are organized by environmental filtering, but this may be changed by urbanization, and in the suburban and urban forest fragments replaced by randomly organized assemblages, influenced by the colonization of species from the surrounding matrix. Evaluating simultaneously the functional and phylogenetic relationships of co-existing species, we showed that at the rural sites, co-existing ground beetle species were functionally and phylogenetically more similar than expected by chance, indicating that environmental filtering was the likely process structuring these communities. Contrary to this, in urban and suburban sites, the co-occurring species were functionally and phylogenetically not different from the null model, indicating randomly structured assemblages. According to our findings, changes in environmental and habitat characteristics accompanied by urbanization lead to assemblages of randomly colonized species from the surrounding matrix, threatening proper ecosystem functioning. To reassemble stochastically assembled species of urban and suburban fragments to structured, properly functioning communities, appropriate management strategies are needed which simultaneously consider recreational, economic and conservation criteria.

Phylogeography and DNA-based species delimitation provide insight into the taxonomy of the polymorphic rose chafer Protaetia (Potosia) cuprea species complex (Coleoptera: Scarabaeidae: Cetoniinae) in the Western Palearctic

The development of modern methods of species delimitation, unified under the "integrated taxonomy" approach, allows a critical examination and re-evaluation of complex taxonomic groups. The rose chafer Protaetia (Potosia) cuprea is a highly polymorphic species group with a large distribution range. Despite its overall commonness, its taxonomy is unclear and subject to conflicting hypotheses, most of which largely fail to account for its evolutionary history. Based on the sequences of two mitochondrial markers from 65 individuals collected across the species range, and a detailed analysis of morphological characters including a geometric morphometry approach, we infer the evolutionary history and phylogeography of the P. cuprea species complex. Our results demonstrate the existence of three separate lineages in the Western Palearctic region, presumably with a species status. However, these lineages are in conflict with current taxonomic concepts. None of the 29 analyzed morphological characters commonly used in the taxonomy of this group proved to be unambiguously species- or subspecies- specific. The geometric morphometry analysis reveals a large overlap in the shape of the analyzed structures (pronotum, meso-metaventral projection, elytra and aedeagus), failing to identify either the genetically detected clades or the classical species entities. Our results question the monophyly of P. cuprea in regard to P. cuprina, as well as the species status of P. metallica. On the other hand, we found support for the species status of the Sicilian P. hypocrita. Collectively, our findings provide a new and original insight into the taxonomy and phylogeny of the P. cuprea species complex. At the same time, the results represent the first attempt to elucidate the phylogeography of these polymorphic beetles.

Geographic patterns of phenotypic diversity in incipient species of North American blister beetles (Coleoptera: Meloidae) are not determined by species niches, but driven by demography along the speciation process

The Epicauta stigmata complex is a group of blister beetles composed of three parapatric or sympatric species that occur in central Mexico to southern USA: E. stigmata, E. uniforma and E. melanochroa. These species are morphologically very similar, and are mainly distinguished by body colour differences. Here we assessed whether phenotypic divergence in coloration patterns define evolutionary units within the complex. We studied the phylogenetic relationships, demographic history and concordances between morphological and ecological traits in the group. The complex apparently had a demographic history of recent population expansion during the last glaciation period 75000 to 9500 years ago. The three species show no reciprocal monophyly, and thus their allospecificity was not confirmed. The current distribution of haplotypes and the genetic divergences in these taxa can be explained by either recent mitochondrial introgression events caused by hybridisation or by incomplete lineage sorting. Colour pattern differences in the complex are not likely a product of local selection acting over a common genetic background. We suggest that phenotypic divergence in colour patterns during an incipient speciation process might be seen as an enhancing factor of cohesion within each of the three evolutionary units.

Estimating and mitigating amplification bias in qualitative and quantitative arthropod metabarcoding

Amplicon based metabarcoding promises rapid and cost-efficient analyses of species composition. However, it is disputed whether abundance estimates can be derived from metabarcoding due to taxon specific PCR amplification biases. PCR-free approaches have been suggested to mitigate this problem, but come with considerable increases in workload and cost. Here, we analyze multilocus datasets of diverse arthropod communities, to evaluate whether amplification bias can be countered by (1) targeting loci with highly degenerate primers or conserved priming sites, (2) increasing PCR template concentration, (3) reducing PCR cycle number or (4) avoiding locus specific amplification by directly sequencing genomic DNA. Amplification bias is reduced considerably by degenerate primers or targeting amplicons with conserved priming sites. Surprisingly, a reduction of PCR cycles did not have a strong effect on amplification bias. The association of taxon abundance and read count was actually less predictable with fewer cycles. Even a complete exclusion of locus specific amplification did not exclude bias. Copy number variation of the target loci may be another explanation for read abundance differences between taxa, which would affect amplicon based and PCR free methods alike. As read abundance biases are taxon specific and predictable, the application of correction factors allows abundance estimates.

Phylogenetic test of speciation by host shift in leaf cone moths (Caloptilia) feeding on maples (Acer)

The traditional explanation for the exceptional diversity of herbivorous insects emphasizes host shift as the major driver of speciation. However, phylogenetic studies have often demonstrated widespread host plant conservatism by insect herbivores, calling into question the prevalence of speciation by host shift to distantly related plants. A limitation of previous phylogenetic studies is that host plants were defined at the family or genus level; thus, it was unclear whether host shifts predominate at a finer taxonomic scale. The lack of a statistical approach to test the hypothesis of host-shift-driven speciation also hindered studies at the species level. Here, we analyze the radiation of leaf cone moths (Caloptilia) associated with maples (Acer) using a newly developed, phylogeny-based method that tests the role of host shift in speciation. This method has the advantage of not requiring complete taxon sampling from an entire radiation. Based on 254 host plant records for 14 Caloptilia species collected at 73 sites in Japan, we show that major dietary changes are more concentrated toward the root of the phylogeny, with host shift playing a minor role in recent speciation. We suggest that there may be other roles for host shift in promoting herbivorous insect diversification rather than facilitating speciation per se.

Ecological niche and geographic distribution of the Chagas disease vector, Triatoma dimidiata (Reduviidae: Triatominae): Evidence for niche differentiation among cryptic species

The principal vector of Chagas disease in Central America, Triatoma dimidiata, shows considerable diversity of habitat, phenotype, and genotype across its geographic range (central Mexico to southern Ecuador), suggesting that it constitutes a complex of cryptic species. However, no consistent picture of the magnitude of ecological differentiation among populations of this complex has yet been developed. To assess ecological variation across the complex, we broadened the geographic coverage of phylogeographic data and analyses for the complex into Colombia and Mexico, with additional nuclear (ITS-2) and mitochondrial (ND4) DNA sequences. This information allowed us to describe distributions of previously documented clades in greater detail: Group I, from central Guatemala south to Ecuador; Group II, across Mexico south through the Yucatán Peninsula to Belize and northern Guatemala; and Group III, in northern Guatemala, Belize, and the Yucatán Peninsula. Using ecological niche modeling, we assessed ecological niche differentiation among the groups using four hypotheses of accessible areas (M) across the distribution of the complex. Results indicated clear niche divergence of Group I from Group II: the speciation process thus appears to have involved genetic and ecological changes, suggesting divergence in populations in response to environmental conditions.

What defines an adaptive radiation? Macroevolutionary diversification dynamics of an exceptionally species-rich continental lizard radiation

BACKGROUND

Adaptive radiation theory posits that ecological opportunity promotes rapid proliferation of phylogenetic and ecological diversity. Given that adaptive radiation proceeds via occupation of available niche space in newly accessed ecological zones, theory predicts that: (i) evolutionary diversification follows an 'early-burst' process, i.e., it accelerates early in the history of a clade (when available niche space facilitates speciation), and subsequently slows down as niche space becomes saturated by new species; and (ii) phylogenetic branching is accompanied by diversification of ecologically relevant phenotypic traits among newly evolving species. Here, we employ macroevolutionary phylogenetic model-selection analyses to address these two predictions about evolutionary diversification using one of the most exceptionally species-rich and ecologically diverse lineages of living vertebrates, the South American lizard genus Liolaemus.

RESULTS

Our phylogenetic analyses lend support to a density-dependent lineage diversification model. However, the lineage through-time diversification curve does not provide strong support for an early burst. In contrast, the evolution of phenotypic (body size) relative disparity is high, significantly different from a Brownian model during approximately the last 5 million years of Liolaemus evolution. Model-fitting analyses also reject the 'early-burst' model of phenotypic evolution, and instead favour stabilizing selection (Ornstein-Uhlenbeck, with three peaks identified) as the best model for body size diversification. Finally, diversification rates tend to increase with smaller body size.

CONCLUSIONS

Liolaemus have diversified under a density-dependent process with slightly pronounced apparent episodic pulses of lineage accumulation, which are compatible with the expected episodic ecological opportunity created by gradual uplifts of the Andes over the last ~25My. We argue that ecological opportunity can be strong and a crucial driver of adaptive radiations in continents, but may emerge less frequently (compared to islands) when major events (e.g., climatic, geographic) significantly modify environments. In contrast, body size diversification conforms to an Ornstein-Uhlenbeck model with multiple trait optima. Despite this asymmetric diversification between both lineages and phenotype, links are expected to exist between the two processes, as shown by our trait-dependent analyses of diversification. We finally suggest that the definition of adaptive radiation should not be conditioned by the existence of early-bursts of diversification, and should instead be generalized to lineages in which species and ecological diversity have evolved from a single ancestor.

Anisomeriini diving beetles-an Atlantic-Pacific Island disjunction on Tristan da Cunha and Robinson Crusoe Island, Juan Fernández?

Anisomeriini diving beetles contain only two enigmatic species, representing a remarkable disjunction between the Pacific Juan Fernández Islands (Anisomeria bistriata) and the South Atlantic Tristan da Cunha Archipelago (Senilites tristanicola). They belong to the Colymbetinae, which contain 140 species worldwide. Here we aim to reconstruct the evolutionary history of the Anisomerinii and use > 9000 bp DNA sequence data from 13 fragments of 12 loci for a comprehensive sampling of Colymbetinae species. Analyses under different optimization criteria converge on very similar topologies, and show unambiguously that Anisomeria bistriata and Senilites tristanicola belong to the Neotropical Rhantus signatus species group, a comparatively recent clade within Colymbetinae. Anisomeriini therefore are synonomized with Colymbetini and both species are transferred to Rhantus accordingly, resulting in secondary homonymy of Rhantus bistriatus (Brullé, 1835) with Rhantus bistriatus (Bergsträsser, 1778). We propose the replacement name Rhantus selkirki Jäch, Balke & Michat nom. nov. for the Juan Fernández species. Presence of these species on remote islands is therefore not relictary, but the result of more recent range expansions out of mainland South America. Finally, we suggest that Carabdytini should be synonymized with Colymbetini. Our study underpins the Hennigian principle that a natural classification can be derived only from the search for shared apomorphies between species, not from differences.

The evolutionary genetics of highly divergent alleles of the mimicry locus in Papilio dardanus

BACKGROUND

The phylogenetic history of genes underlying phenotypic diversity can offer insight into the evolutionary origin of adaptive traits. This is especially true where single genes have large phenotypic effects, for example in determining polymorphic mimicry in butterflies. Here, we characterise the evolutionary history of two candidate genes for the mimicry switch in the polymorphic Batesian mimic Papilio dardanus coding for the transcription factors engrailed and invected.

RESULTS

We show that phased haplotypes associated with the dominant morphs f. poultoni and f. planemoides are phylogenetically highly divergent, in particular at non-synonymous sites. Some non-synonymous changes are shared between the divergent alleles suggesting either convergence or a shared ancestry. Gene trees for invected do not show this pattern. Despite their great divergence, all engrailed alleles of P. dardanus were monophyletic with respect to alleles of closely related species. Phylogenetic analyses therefore reveal no evidence for introgression from other species. A McDonald-Kreitman test conducted on a population sample from South Africa confirms a significant excess of intraspecific non-synonymous diversity in P. dardanus engrailed, suggesting long-term balanced polymorphism at this locus.

CONCLUSIONS

The divergence between engrailed haplotypes suggests an evolutionary history distorted by selection with multiple changes reflecting recurrent selective sweeps. The high level of intraspecific polymorphism observed is characteristic of balancing selection on this locus, as expected if the gene engrailed is under phenotypic selection for the maintenance of multiple mimetic morphs. Non-synonymous changes in key functional portions of a major transcription factor are likely to be deleterious but if maintained in a dominant allele at low frequency, heterozygosity would reduce the associated genetic load.

Ancyronyx Erichson, 1847 (Coleoptera, Elmidae) from Mindoro, Philippines, with description of the larvae and two new species using DNA sequences for the assignment of the developmental stages

Ancyronyx buhidsp. n. and Ancyronyx tamarawsp. n. are described based on adults and larvae, matched using their cox1 or cob DNA sequence data. Additional records of Ancyronyx schillhammeri Jäch, 1994 and Ancyronyx minerva Freitag & Jäch, 2007 from Mindoro are listed. The previously unknown larva of Ancyronyx schillhammeri is also described here, aided by cox1 data. The new species and larval stages are described in detail and illustrated by SEM and stacked microscopic images. Keys to the adult and larval Ancyronyx species of Mindoro and an updated checklist of Philippine Ancyronyx species are provided. The usefulness as bioindicators, the phylogenetic relationships and biogeographic aspects affecting the distribution patterns are briefly discussed.

Australasian sky islands act as a diversity pump facilitating peripheral speciation and complex reversal from narrow endemic to widespread ecological supertramp

The Australasian archipelago is biologically extremely diverse as a result of a highly puzzling geological and biological evolution. Unveiling the underlying mechanisms has never been more attainable as molecular phylogenetic and geological methods improve, and has become a research priority considering increasing human-mediated loss of biodiversity. However, studies of finer scaled evolutionary patterns remain rare particularly for megadiverse Melanesian biota. While oceanic islands have received some attention in the region, likewise insular mountain blocks that serve as species pumps remain understudied, even though Australasia, for example, features some of the most spectacular tropical alpine habitats in the World. Here, we sequenced almost 2 kb of mitochondrial DNA from the widespread diving beetle Rhantus suturalis from across Australasia and the Indomalayan Archipelago, including remote New Guinean highlands. Based on expert taxonomy with a multigene phylogenetic backbone study, and combining molecular phylogenetics, phylogeography, divergence time estimation, and historical demography, we recover comparably low geographic signal, but complex phylogenetic relationships and population structure within R. suturalis. Four narrowly endemic New Guinea highland species are subordinated and two populations (New Guinea, New Zealand) seem to constitute cases of ongoing speciation. We reveal repeated colonization of remote mountain chains where haplotypes out of a core clade of very widespread haplotypes syntopically might occur with well-isolated ones. These results are corroborated by a Pleistocene origin approximately 2.4 Ma ago, followed by a sudden demographic expansion 600,000 years ago that may have been initiated through climatic adaptations. This study is a snapshot of the early stages of lineage diversification by peripatric speciation in Australasia, and supports New Guinea sky islands as cradles of evolution, in line with geological evidence suggesting very recent origin of high altitudes in the region.

Terrestrialization, miniaturization and rates of diversification in African puddle frogs (Anura: Phrynobatrachidae)

Terrestrialization, the evolution of non-aquatic oviposition, and miniaturization, the evolution of tiny adult body size, are recurring trends in amphibian evolution, but the relationships among the traits that characterize these phenomena are not well understood. Furthermore, these traits have been identified as possible "key innovations" that are predicted to increase rates of speciation in those lineages in which they evolve. We examine terrestrialization and miniaturization in sub-Saharan puddle frogs (Phrynobatrachidae) in a phylogenetic context to investigate the relationship between adaptation and diversification through time. We use relative dating techniques to ascertain if character trait shifts are associated with increased diversification rates, and we evaluate the likelihood that a single temporal event can explain the evolution of those traits. Results indicate alternate reproductive modes evolved independently in Phrynobatrachus at least seven times, including terrestrial deposition of eggs and terrestrial, non-feeding larvae. These shifts towards alternate reproductive modes are not linked to a common temporal event. Contrary to the "key innovations" hypothesis, clades that exhibit alternate reproductive modes have lower diversification rates than those that deposit eggs aquatically. Adult habitat, pedal webbing and body size have no effect on diversification rates. Though these traits putatively identified as key innovations for Phrynobatrachus do not seem to be associated with increased speciation rates, they may still provide opportunities to extend into new niches, thus increasing overall diversity.

Biology, immature and adult morphology, and molecular characterization of a new species of the genus Entedon (Hymenoptera: Eulophidae) associated with the invasive pest Specularius impressithorax (Coleoptera: Chrysomelidae, Bruchinae) on Erythrina plants

Entedon erythrinae sp. n. (Hymenoptera: Eulophidae), a gregarious egg-larval endoparasitoid of the Erythrina bruchine Specularius impressithorax, an invasive pest of the coral tree seeds (Erythrina spp.), is described from the Hawaiian Islands and Africa (South Africa, Tanzania and Mozambique). The biology and morphology of preimaginal stages of this new species are described in details.It is remarkable that the early embryo of the parasitoid represents a mass of undifferentiated cells surrounded by a peculiar membrane formed by the peripheral enlarged polygonal cells. The young larva developing inside this membrane corresponds morphologically to the second instar of congeneric species. Various peculiarities of the parasitoid-host relationships in gregarious and solitary Entedon parasitoids are discussed. The DNA sequences of 28S D2 (nuclear), Cytochrome Oxidase I (COI, mitochondrial) and Cytochrome B (CytB, mitochondrial) genes are provided for this new species and compared with the sequences of some other Afrotropical and Palearctic species of the genus.

Larvae and a new species of Ancyronyx Erichson, 1847 (Insecta, Coleoptera, Elmidae) from Palawan, Philippines, using DNA sequences for the assignment of the developmental stages

Ancyronyx montanussp. n. is described based on adults and larvae, matched using their cox1 DNA sequence data. Larvae of six additional species of Ancyronyx Erichson, 1847 were also described here for the first time, aided by cox1 or cob data: Ancyronyx helgeschneideri Freitag & Jäch, 2007, Ancyronyx minerva Freitag & Jäch, 2007, Ancyronyx patrolus Freitag & Jäch, 2007, Ancyronyx procerus Jäch, 1994, Ancyronyx punkti Freitag & Jäch, 2007, Ancyronyx pseudopatrolus Freitag & Jäch, 2007. Ancyronyx procerus is newly recorded from the Philippines by a larval specimen from Busuanga island. The new species and larval stages are described in detail and illustrated by digital and SEM images. A key to the Ancyronyx larvae of Palawan and an updated checklist of Philippine Ancyronyx is provided.

Islands beneath islands: phylogeography of a groundwater amphipod crustacean in the Balearic archipelago

Background

Metacrangonyctidae (Amphipoda, Crustacea) is an enigmatic continental subterranean water family of marine origin (thalassoid). One of the species in the genus, Metacrangonyx longipes, is endemic to the Balearic islands of Mallorca and Menorca (W Mediterranean). It has been suggested that the origin and distribution of thalassoid crustaceans could be explained by one of two alternative hypotheses: (1) active colonization of inland freshwater aquifers by a marine ancestor, followed by an adaptative shift; or (2) passive colonization by stranding of ancestral marine populations in coastal aquifers during marine regressions. A comparison of phylogenies, phylogeographic patterns and age estimations of clades should discriminate in favour of one of these two proposals.

Results

Phylogenetic relationships within M. longipes based on three mitochondrial DNA (mtDNA) and one nuclear marker revealed five genetically divergent and geographically structured clades. Analyses of cytochrome oxidase subunit 1 (cox1) mtDNA data showed the occurrence of a high geographic population subdivision in both islands, with current gene flow occurring exclusively between sites located in close proximity. Molecular-clock estimations dated the origin of M. longipes previous to about 6 Ma, whereas major cladogenetic events within the species took place between 4.2 and 2.0 Ma.

Conclusions

M. longipes displayed a surprisingly old and highly fragmented population structure, with major episodes of cladogenesis within the species roughly correlating with some of the major marine transgression-regression episodes that affected the region during the last 6 Ma. Eustatic changes (vicariant events) -not active range expansion of marine littoral ancestors colonizing desalinated habitats-explain the phylogeographic pattern observed in M. longipes.

Deep mtDNA subdivision within Linnean species in an endemic radiation of tiger beetles from New Zealand (genus Neocicindela)

The invertebrate fauna of New Zealand is of great interest as a geologically tractable model for the study of species diversification, but direct comparisons with closely related lineages elsewhere are lacking. Integrating population-level analyses with studies of taxonomy and clade diversification, we performed mtDNA analysis on Neocicindela (Cicindelidae, tiger beetles) for a broad sample of populations from 11 of 12 known species and 161 specimens (three loci, 1883 nucleotides), revealing 123 distinct haplotypes. Phylogenetic reconstruction recovered two main lineages, each composed of 5-6 Linnean species whose origin was dated to 6.66 and 7.26 Mya, while the Neocicindela stem group was placed at 10.82 ± 0.48 Mya. Species delimitation implementing a character-based (diagnostic) species concept recognized 19 species-level groups that were in general agreement with Linnean species but split some of these into mostly allopatric subgroups. Tree-based methods of species delimitation using a mixed Yule-coalescence model were inconclusive, and recognized 32-51 entities (including singletons), splitting existing species into up to 8 partially sympatric groups. These findings were different from patterns in the Australian sister genus Rivacindela, where character-based and tree-based methods were previously shown to produce highly congruent groupings. In Neocicindela, the pattern of mtDNA variation was characterized by high intra-population and intra-species haplotype divergence, the coexistence of divergent haplotypes in sympatry, and a poor correlation of genetic and geographic distance. These observations combined suggest a scenario of phylogeographic divergence and secondary contact driven by orogenetic and climatic changes of the Pleistocene/Pliocene. The complex evolutionary history of most species of Neocicindela due to the relative instability of the New Zealand biota resulted in populations of mixed ancestry but not in a general loss of genetic variation.

Sexual selection is involved in speciation in a land snail radiation on crete

We investigated the importance of sexual selection in facilitating speciation in a land snail radiation on Crete. We used differences in the genitalia of the Cretan Xerocrassa species as potential indices of sexual selection. First, we rejected the hypothesis that differences in the genitalia of the Xerocrassa species can be explained by genetic drift using coalescent simulations based on a mitochondrial gene tree. Second, we showed that there is no evidence for the hypothesis that the differences in the genitalia can be explained by natural selection against hybrids under the assumption that this is more likely in geographically overlapping species pairs and clades. Third, we showed that there is a positive scaling between male spermatophore-producing organs and female spermatophore-receiving organs indicating sexual coevolution. The spermatophore enables the sperm to escape from the female gametolytic organ. Thus, the coevolution might be a consequence of sexual conflict or cryptic female choice. Finally, we showed that the evolution of differences in the length of the flagellum that forms the tail of the spermatophore is concentrated toward the tips of the tree indicating that it is involved in speciation. If speciation is facilitated by sexual selection, niches may remain conserved and nonadaptive radiation may result.

Density-dependent diversification in North American wood warblers

Evidence from both molecular phylogenies and the fossil record suggests that rates of species diversification often decline through time during evolutionary radiations. One proposed explanation for this pattern is ecological opportunity, whereby an initial abundance of resources and lack of potential competitors facilitate rapid diversification. This model predicts density-dependent declines in diversification rates, but has not been formally tested in any species-level radiation. Here we develop a new conceptual framework that distinguishes density dependence from alternative processes that also produce temporally declining diversification, and we demonstrate this approach using a new phylogeny of North American Dendroica wood warblers. We show that explosive lineage accumulation early in the history of this avian radiation is best explained by a density-dependent diversification process. Our results suggest that the tempo of wood warbler diversification was mediated by ecological interactions among species and that lineage and ecological diversification in this group are coupled, as predicted under the ecological opportunity model.

Phylogeny and geography predict pathogen community similarity in wild primates and humans

In natural systems, host species are often co-infected by multiple pathogen species, and recent work has suggested that many pathogens can infect a wide range of host species. An important question therefore is what determines the host range of a pathogen and the community of pathogens found within a given host species. Using primates as a model, we show that infectious diseases are more often shared between species that are closely related and inhabit the same geographical region. We find that host relatedness is the best overall predictor of whether two host species share the same pathogens. A higher frequency of pathogen host shifts between close relatives or inheritance of pathogens from a common ancestor may explain this result. For viruses, geographical overlap among neighbouring primate hosts is more important in determining host range. We suggest this is because rapid evolution within viral lineages allows host jumps across larger evolutionary distances. We also show that the phylogenetic pattern of pathogen sharing with humans is the same as that between wild primates. For humans, this means we share a higher proportion of pathogens with the great apes, including chimpanzees and gorillas, because these species are our closest relatives.

Do pollen feeding, pupal-mating and larval gregariousness have a single origin in Heliconius butterflies? Inferences from multilocus DNA sequence data

Phylogenetic information is useful in understanding the evolutionary history of adaptive traits. Here, we present a well-resolved phylogenetic hypothesis for Heliconius butterflies and related genera. We use this tree to investigate the evolution of three traits, pollen feeding, pupal-mating behaviour and larval gregariousness. Phylogenetic relationships among 60 Heliconiina species (86% of the subtribe) were inferred from partial DNA sequences of the mitochondrial genes cytochrome oxidase I, cytochrome oxidase II and 16S rRNA, and fragments of the nuclear genes elongation factor-1α, apterous, decapentaplegic and wingless (3834 bp in total). The results corroborate previous hypotheses based on sequence data in showing that Heliconius is paraphyletic, with Laparus doris and Neruda falling within the genus, demonstrating a single origin for pollen feeding but with a loss of the trait in Neruda. However, different genes are not congruent in their placement of Neruda; therefore, monophyly of the pollen feeding species cannot be ruled out. There is also a highly supported monophyletic ‘pupal-mating clade’ suggesting that pupal mating behaviour evolved only once in the Heliconiina. Additionally, we observed at least three independent origins for larval gregariousness from a solitary ancestor, showing that gregarious larval behaviour arose after warning coloration.

THE GEOGRAPHICAL PATTERN OF SPECIATION AND FLORAL DIVERSIFICATION IN THE NEOTROPICS: THE TRIBE SINNINGIEAE (GESNERIACEAE) AS A CASE STUDY

The geographical pattern of speciation and the relationship between floral variation and species ranges were investigated in the tribe Sinningieae (Gesneriaceae), which is found mainly in the Atlantic forests of Brazil. Geographical distribution data recorded on a grid system of 0.5 x 0.5 degree intervals and a near-complete species-level phylogenetic tree of Sinningieae inferred from a simultaneous analysis of seven DNA regions were used to address the role of geographical isolation in speciation. Geographical range overlaps between sister lineages were measured across all nodes in the phylogenetic tree and analyzed in relation to relative ages estimated from branch lengths. Although there are several cases of species sympatry in Sinningieae, patterns of sympatry between sister taxa support the predominance of allopatric speciation. The pattern of sympatry between sister taxa is consistent with range shifts following allopatric speciation, except in one clade, in which the overlapping distribution of recent sister species indicates speciation within a restricted geographical area and involving changes in pollinators and habitats. The relationship between floral divergence and regional sympatry was also examined by analyzing floral contrasts, phenological overlap, and the degree of sympatry between sister clades. Morphological contrast between flowers is not increased in sympatry and phenological divergence is more apparent between allopatric clades than between sympatric clades. Therefore, our results failed to indicate a tendency for sympatric taxa to minimize morphological and phenological overlap (geographic exclusion and/or character displacement hypotheses). Instead, they point toward adaptation in phenology to local conditions and buildup of sympatries at random with respect to flower morphology. Additional studies at a lower geographical scale are needed to identify truely coexisting species and the components of their reproductive isolation.

Karyotypic diversity and speciation in Agrodiaetus butterflies

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

Species co-existence and character divergence across carnivores

Co-occurring species might be morphologically similar because they are adapted to the same environment, or morphologically dissimilar to minimize competition. We use sister species comparisons to evaluate the relationship between morphological disparity and regional patterns of co-occurrence across carnivores. Up to 63% of the variation in range overlap can be explained by morphological divergence in dentition. Species that differ more in carnassial tooth length overlap more in their geographical range. Carnassials are the primary teeth associated with food processing, and hence difference in carnassial size may be a good indicator of difference in resource use. We suggest this pattern is consistent with competition in sympatry driving ecological character displacement, or competitive exclusion among ecologically similar species. Our study uses newly available data on global distributions, morphology and phylogeny, and is the first to demonstrate a close relationship between morphological disparity and co-occurrence at a regional scale encompassing multiple communities.

Infrequent and unidirectional colonization of hyperdiverse Papuadytes diving beetles in New Caledonia and New Guinea

We present a molecular phylogenetic analysis of 2808 aligned bp of rrnL, cox1, cob, H3 and 18S rRNA of all major morphological groups of Papuadytes diving beetles (Coleoptera: Dytiscidae) which are diverse in running water habitats throughout the Australian region. We focus on the origin of the fauna of the megadiverse islands of New Guinea and New Caledonia. Parsimony as well as Bayesian analyses suggest a basal position of Australian species in a paraphyletic series, with more recent nested radiations in New Caledonia and New Guinea. According to molecular clock analyses, both landmasses were colonized during the Miocene, which matches geological data and corroborates similar findings in other taxonomic groups. Our analyses suggest that dispersal played an important role in the formation of these large insular faunas, although successful colonization appears to be a rare event, and, in this case, is unidirectional. Whether or not a lineage is present on an island is due to chance: Papuadytes are absent from Fiji, where related Copelatus have radiated extensively in the same habitats occupied by Papuadytes in New Caledonia and New Guinea, while Copelatus are absent from New Caledonia. Lineages of Papuadytes apparently colonized New Caledonia twice, around 14 and 9 MYA according to the molecular calibration, and both lineages are derived from an Australian ancestor. The older clade is represented only by two apparently relictual mountain species (one morphologically strongly adapted to highly ephemeral habitats), while the younger clade contains at least 18 species exhibiting a great morphological diversity. The 150+ species in New Guinea are monophyletic, apparently derived from an Australian ancestor, and constitute a morphologically rather homogenous group. The tree backbone remains insufficiently supported under parsimony and Bayesian analyses, where shorter branches suggest a rapid sequence of major branching events.

The phylogenetic pattern of speciation and wing pattern change in neotropical Ithomia butterflies (Lepidoptera: nymphalidae)

Species level phylogenetic hypotheses can be used to explore patterns of divergence and speciation. In the tropics, speciation is commonly attributed to either vicariance, perhaps within climate-induced forest refugia, or ecological speciation caused by niche adaptation. Mimetic butterflies have been used to identify forest refugia as well as in studies of ecological speciation, so they are ideal for discriminating between these two models. The genus Ithomia contains 24 species of warningly colored mimetic butterflies found in South and Central America, and here we use a phylogenetic hypothesis based on seven genes for 23 species to investigate speciation in this group. The history of wing color pattern evolution in the genus was reconstructed using both parsimony and likelihood. The ancestral pattern for the group was almost certainly a transparent butterfly, and there is strong evidence for convergent evolution due to mimicry. A punctuationist model of pattern evolution was a significantly better fit to the data than a gradualist model, demonstrating that pattern changes above the species level were associated with cladogenesis and supporting a model of ecological speciation driven by mimicry adaptation. However, there was only one case of sister species unambiguously differing in pattern, suggesting that some recent speciation events have occurred without pattern shifts. The pattern of geographic overlap between clades over time shows that closely related species are mostly sympatric or, in one case, parapatric. This is consistent with modes of speciation with ongoing gene flow, although rapid range changes following allopatric speciation could give a similar pattern. Patterns of lineage accumulation through time differed significantly from that expected at random, and show that most of the extant species were present by the beginning of the Pleistocene at the latest. Hence Pleistocene refugia are unlikely to have played a major role in Ithomia diversification.

DNA taxonomy, phylogeny and Pleistocene diversification of the Cicindela hybrida species group (Coleoptera: Cicindelidae)

Species delimitation is complicated where morphological variation is continuous or poorly subdivided, but for taxonomic convenience it is common practice to separate and name geographical groups to capture this variation. DNA-based approaches may be used to test if these groups in fact represent historically divided, discrete species entities. The Cicindela hybrida complex (Coleoptera: Cicindelidae) is an assemblage of up to seven morphologically recognized species and 15 subspecies with wide distribution in the Palaearctic region. We sequenced a discontinuous segment of 1899 bp of mtDNA including three regions (coxI, rrnL+trnL2+nad1, cob) for a total of 99 specimens from 36 sampling localities across Europe, revealing 48 haplotypes. Four major clades could be identified corresponding to geographical groups from central Iberia, Ukraine, central Europe, and a band from the Atlantic Iberian coast to northern Europe. Taking into account further subdivisions within these clades, four of the six named species included in the analysis were recognizable by applying various procedures for species delimitation. Age estimates from calibrated molecular clocks date the diversification of the hybrida group within the past 2 million years (Myr), and the separation of the northern clade within 0.4 Myr. Nested clade analysis revealed the rapid range expansion of the northern group consistent with postglacial dispersal, but we did not find support for specific source population(s) in the postulated southern refugia. The evolutionary framework based on mtDNA sequences is shown to identify species entities as discrete clusters of closely related sequences and provides an objective system for delineating and recognizing hierarchically structured groups. In the case of the C. hybrida complex, these groups largely coincided with those established from morphology. The study adds further support to the utility of mtDNA-based sequence profiles (the 'DNA taxonomy') as a rapid and objective synthesis of evolutionary diversity and as reference system for communication.