Time to update the sectional classification of Ilex (Aquifoliaceae): New insights from Ilex phylogeny,morphology, and distribution

Resolving the infrageneric classification of species-rich genera has been challenging in plant taxonomy. Ilex L. is a subcosmopolitan genus with over 600 species of dioecious trees and shrubs. Many classification systems based on morphological data have been proposed during the past 250 years. However, these systems (such as Loesener's and Galle's systems) may not truly reflect Ilex's evolutionary trajectories because most of those system's infrageneric hierarchies are not monophyletic. In this study, we reconstructed a phylogeny of Ilex L. comprising 15 moderately to highly supported clades using rigorously identified samples (202 species) and closely authenticated gene sequences of three nuclear genes [internal transcribed spacer (ITS), external transcribed spacer (ETS), and nepGS]. The newly generated phylogenetic tree resembles essentially that of the nuclear tree of Manen et al., but shows conspicuous topological differences with the phylogeny of Yao et al. Closely scrutinizing morphological variation and distributional patterns of 202 species, this study found that most lineages of Ilex identified herein are well defined by a particular trait or a combination of morphological and distributional traits, displaying phylogeny–morphology–distribution conformity that has seldom been uncovered in previous studies. Given the general phylogeny–morphology–distribution conformity revealed in this genus, we put forward an updated sectional classification system for Ilex that temporarily contains 14 sections. The new classification will provide a robust framework for studying the evolution and diversification of this ecologically and economically important genus.     

Host range and community structure of avian nest parasites in the genus Philornis (Diptera: Muscidae) on the island of Trinidad

Parasite host range can be influenced by physiological, behavioral, and ecological factors. Combining data sets on host–parasite associations with phylogenetic information of the hosts and the parasites involved can generate evolutionary hypotheses about the selective forces shaping host range. Here, we analyzed associations between the nest‐parasitic flies in the genus Philornis and their host birds on Trinidad. Four of ten Philornis species were only reared from one species of bird. Of the parasite species with more than one host bird species, P. falsificus was the least specific and P. deceptivus the most specific attacking only Passeriformes. Philornis flies in Trinidad thus include both specialists and generalists, with varying degrees of specificity within the generalists. We used three quantities to more formally compare the host range of Philornis flies: the number of bird species attacked by each species of Philornis, a phylogenetically informed host specificity index (Poulin and Mouillot's S_TD), and a branch length‐based S_TD. We then assessed the phylogenetic signal of these measures of host range for 29 bird species. None of these measures showed significant phylogenetic signal, suggesting that clades of Philornis did not differ significantly in their ability to exploit hosts. We also calculated two quantities of parasite species load for the birds – the parasite species richness, and a variant of the S_TD index based on nodes rather than on taxonomic levels – and assessed the signal of these measures on the bird phylogeny. We did not find significant phylogenetic signal for the parasite species load or the node‐based S_TD index. Finally, we calculated the parasite associations for all bird pairs using the Jaccard index and regressed these similarity values against the number of nodes in the phylogeny separating bird pairs. This analysis showed that Philornis on Trinidad tend to feed on closely related bird species more often than expected by chance.     

Molecular phylogenetics of the hummingbird genus Coeligena

Advances in the understanding of biological radiations along tropical mountains depend on the knowledge of phylogenetic relationships among species. Here we present a species-level molecular phylogeny based on a multilocus dataset for the Andean hummingbird genus Coeligena. We compare this phylogeny to previous hypotheses of evolutionary relationships and use it as a framework to understand patterns in the evolution of sexual dichromatism and in the biogeography of speciation within the Andes. Previous phylogenetic hypotheses based mostly on similarities in coloration conflicted with our molecular phylogeny, emphasizing the unreliability of color characters for phylogenetic inference. Two major clades, one monochromatic and the other dichromatic, were found in Coeligena. Closely related species were either allopatric or parapatric on opposite mountain slopes. No sister lineages replaced each other along an elevational gradient. Our results indicate the importance of geographic isolation for speciation in this group and the potential interaction between isolation and sexual selection to promote diversification.     

Biogeography and evolution of flower color in Veratrum (Melanthiaceae) through inference of a phylogeny based on multiple DNA markers

Veratrum (Melanthiaceae) comprises ca. 27 species with highly variable morphology. This study aims to construct the molecular phylogeny of this genus to infer its floral evolution and historical biogeography, which have not been examined in detail before. Maximum parsimony, maximum likelihood, and Bayesian analyses were performed on the separate and combined ITS, trnL-F, and atpB-rbcL sequences to reconstruct the phylogenetic tree of the genus. All Veratrum taxa formed a monophyletic group, within which two distinct clades were distinguished: species with white-to-green perianth formed one highly supported clade, and the species with black-purple perianth constituted another highly supported clade. Phylogenetic inference on flower color evolution suggested that white-to-green perianth was a plesiomorphic state and black-purple perianth was apomorphic for Veratrum. When species distribution areas were traced as a multi-state character, parsimonious optimization inferred that Veratrum possibly originated in East Asia. Our study confirmed previous phylogenetic and taxonomic suggestions on this genus and provided a typical example of plant radiation across the Northern Hemisphere.     

Molecular phylogeny reveals the repeated evolution of complex male genital traits in the New Zealand moth genus Izatha (Lepidoptera: Xyloryctidae)

Male genitalia are among the most rapidly evolving and divergent morphological structures and sexual selection is known to drive this phenomenon in many taxa. Because of their diversity, even within a single genus, genital characters are frequently used to infer relationships among closely‐related species. Moths within the genus Izatha (Xyloryctidae) are ideal candidates for investigating the phylogenetic patterns of genital evolution as they display great variation in male genital structure and complexity. We determined the evolutionary relationships among 31 species of Izatha by constructing a molecular phylogeny of the genus based on the mitochondrial cytochrome oxidase subunit I gene and the isocitrate dehydrogenase and carbamoylphosphate synthase domain protein nuclear genes. This allowed estimations of ancestral male genital character states and patterns of male genital diversification using maximum‐likelihood models. The genus is divided into two well‐supported clades and two poorly supported clades at the root of the phylogeny with incomplete phylogenetic resolution within two species groups, likely due to rapid speciation. Izatha display a number of apomorphic phallic traits including cornuti (sclerotized spines) which are either discharged into the female during copulation (deciduous cornuti) or fixed to the male phallus (compound and fish‐hook cornuti). Within the genus, there is a reduction of secondary genital characters – the uncus and gnathos – but an elaboration of another grasping structure, the juxta; the potential origin and functionality of these male genital traits are discussed. Overall, some male genital characters provided a good indication of species relationships; however, several parts of the complex male genitalia of Izatha show evidence of homoplasy and convergence highlighting the problems of using these traits in determining species relationships. Additionally, this convergence has highlighted that complex genital structures may evolve repeatedly and independently within a lineage.     

You stay,but I Hop: Host shifting near and far co‐dominated the evolution of Enchenopa treehoppers

The importance and prevalence of phylogenetic tracking between hosts and dependent organisms caused by co‐evolution and shifting between closely related host species have been debated for decades. Most studies of phylogenetic tracking among phytophagous insects and their host plants have been limited to insects feeding on a narrow range of host species. However, narrow host ranges can confound phylogenetic tracking (phylogenetic tracking hypothesis) with host shifting between hosts of intermediate relationship (intermediate hypothesis). Here, we investigated the evolutionary history of the Enchenopa binotata complex of treehoppers. Each species in this complex has high host fidelity, but the entire complex uses hosts across eight plant orders. The phylogenies of E. binotata were reconstructed to evaluate whether (1) tracking host phylogeny; or (2) shifting between intermediately related host plants better explains the evolutionary history of E. binotata. Our results suggest that E. binotata primarily shifted between both distant and intermediate host plants regardless of host phylogeny and less frequently tracked the phylogeny of their hosts. These findings indicate that phytophagous insects with high host fidelity, such as E. binotata, are capable of adaptation not only to closely related host plants but also to novel hosts, likely with diverse phenology and defense mechanisms.     

Evolutionary history of Gymnocarpos (Caryophyllaceae) in the arid regions from North Africa to Central Asia

Gymnocarpos has only about ten species distributed in the arid regions of Asia and Africa, but it exhibits a geographical disjunction between eastern Central Asia and western North Africa and Minor Asia. We sampled eight species of the genus and sequenced two chloroplast regions (rps16 and psbB–psbH), and the nuclear rDNA (ITS) to study the phylogeny and biogeography. The results of the phylogenetic analyses corroborated that Gymnocarpos is monophyletic, in the phylogenetic tree two well supported clades are recognized: clade 1 includes Gymnocarpos sclerocephalus and G. decandrus, mainly the North African group, whereas clade 2 comprises the remaining species, mainly in the Southern Arabian Peninsula. Molecular dating analysis revealed that the divergence age of Gymnocarpos was c. 31.33 Mya near the Eocene and Oligocene transition boundary, the initial diversification within Gymnocarpos dated to c. 6.69 Mya in the late Miocene, and the intraspecific diversification mostly occurred during the Quaternary climate oscillations. Ancestral area reconstruction suggested that the Southern Arabian Peninsula was the ancestral area for Gymnocarpos. Our conclusions revealed that the aridification since mid‐late Miocene significantly affected the diversification of the genus in these areas.     

MOLECULAR PHYLOGENY OF THE GREEN ALGAL ORDER PRASIOLALES (TREBOUXIOPHYCEAE,CHLOROPHYTA)1

The systematics of the Prasiolales was investigated by phylogenetic inference based on analyses of the rbcL and 18S rRNA genes for representatives of all four genera currently attributed to this order (Prasiococcus, Prasiola, Prasiolopsis, Rosenvingiella), including all type species. The rbcL gene had higher sequence divergence than the 18S rRNA gene and was more useful for phylogenetic inference at the ranks of genus and species. In the rbcL gene phylogeny, three main clades were observed, corresponding to Prasiola, Prasiolopsis, and Rosenvingiella. Prasiococcus was nested among species of Prasiola occurring in subaerial and supralittoral habitats. Trichophilus welckeri Weber Bosse, a subaerial alga occurring in the fur of sloths in Amazonia, was closely related to Prasiolopsis ramosa Vischer. The species of Prasiola were grouped into three well‐supported clades comprising (i) marine species, (ii) freshwater and terrestrial species with linear blades, and (iii) terrestrial species with rounded or fan‐shaped blades. Sequence divergence was unexpectedly low in the marine group, which included species with different morphologies. For the 18S rRNA gene, the phylogenetic analyses produced several clades observed for the rbcL gene sequence analysis, but, due to very little sequence variation, it showed considerably lower resolution for inference at the species and genus levels. Due to the low support of some internal branches, the results of the analyses did not allow an unambiguous clarification of the origin and the early evolution of the Prasiolales.     

A complex biogeographic history of diversification in Neotropical lancehead pitvipers (Serpentes,Viperidae)

Based on the literature, we had predicted that the diversification within the Neotropical snake genus Bothrops occurred along a latitudinal gradient from north to south, with diversification into unoccupied niches through ecological opportunity, not correlated with geoclimatic events. Using a dated phylogeny and estimating likelihoods of ancestral states at cladogenesis events, we reconstructed ancestral areas and assessed major events of the diversification of Bothrops clades, and we also discuss systematic implications for this group. Based on the phylogeny we produced, B. lojanus was not considered as part of the genus Bothrops since the results recovered this species nested within the Bothrocophias clade. We infer that the diversification of the Miocene Bothrops pictus and Bothrops alternatus clades may be related to the uplift of the western slopes of the Andes and the Argentinian Patagonian Andes, respectively. The Pliocene Bothrops taeniatus and Bothrops osbornei clades may be related to the uplift of the eastern and northern Andes, respectively. The Plio-Pleistocene Bothrops neuwiedi clade may be related to the habitat transitions from a warmer and forested environment to a cooler and open landscape; the Bothrops jararaca (i.e. island endemic species) and Bothrops lanceolatus clades to over-water dispersal with island speciation; and Bothrops atrox clade to the appearance of the Panamanian land bridge. We found that a multitemporal and multidirectional history of diversification may be correlated with geoclimatic and dispersalist events. We argue that the vacant niche hypothesis by itself does not explain Bothrops diversification.     

Taxonomy and biogeography of Diapensia (Diapensiaceae) based on chloroplast genome data

Diapensia L. is the second largest genus of Diapensiaceae. The taxonomic treatment within Diapensia and relationships within Diapensiaceae have been disputed. Chloroplast genome sequence data have proved to be useful for plant phylogenetic analyses and species delimitation. In this study, we de novo sequenced and assembled 22 chloroplast genomes of 15 species of Diapensiaceae, including all recognized species of Diapensia with multiple samples. A super‐matrix containing a total of 107 genes and 18 taxa was constructed for phylogenetic analyses to resolve phylogenetic relationships among genera of the family and within Diapensia. The resulting phylogenetic tree showed the following strongly supported relationships: (Galax, (Pyxidanthera, (Berneuxia, ((Schizocodon, Diapensia), and Shortia s.s.)))). The dated phylogeny and reconstructed lineage‐through‐time plot for the family indicated rapid diversification in the Neogene and an acceleration of diversification rate after c. 8 Ma. Biogeographic analysis suggested that Diapensia originated in the Northeast Asian mountains approximately 6.06 Ma, followed by northward dispersal to the Arctic and southwestward dispersal to the Himalaya–Hengduan Mountains. Phylogenetic relationships within Diapensia were well resolved. Based on the phylogenetic results, we proposed to reinstate the species status of Diapensia bulleyana Forrest ex Diels, and raised D. purpurea f. albida to the species rank (D. albida [W. E. Evans] J. F. Ye comb. & stat. nov.). The distribution ranges of all species delineated based on the phylogenetic results were revised accordingly based on specimen occurrences. Our study adds new examples for the power of plastid genome data for resolving phylogenetic relationships and clarifying taxonomic disputes among closely related species.     

ECOLOGICAL DIVERSIFICATION AND COMMUNITY STRUCTURE IN THE OLD WORLD LEAF WARBLERS (GENUS PHYLLOSCOPUS): A PHYLOGENETIC PERSPECTIVE

I investigated the historical basis for variation in regional species diversity. I used a molecular phylogenetic analysis within a single genus of birds (the Old World leaf warblers, genus Phylloscopus) in conjunction with ecological studies in Europe, the Himalayas, and Japan to evaluate the importance of historical events in shaping the present constellation of morphology and behavior in the three different regions. The relatively depauperate assemblages have different histories. In Japan, there was invasion of several lineages, which have more closely related species elsewhere in Asia, whereas in Europe there was also limited in situ speciation. Much of the structure of peripheral communities is attributable to invasions from species-rich Asia, with little in situ morphological diversification. Within the Phylloscopus there are several phylogenetic clades with nonoverlapping size distributions. Major ecological and morphological shifts occurred early in the history of diversification within the group, and rarely since.     

Molecular evolution of tephritid fruit flies in the genus Bactrocera based on the cytochrome oxidase I gene

Fruit flies of the genus Bactrocera (Diptera: Tephritidae) are one of the major economically important insects in Asia and Australia. Little attention has been given to analyses of molecular phylogenetic relationships among Bactrocera subgenera. By using mitochondrial cytochrome oxidase I gene (COI) sequences, the phylogenetic relationships among four subgenera, Asiadacus, Bactrocera, Hemigymnodacus, and Zeugodacus, were investigated. Nucleotide diversity within subgenera ranged from 11.7 to 12.4%, and the net divergence among subgenera ranged from 11.2 to 15.7%. Phylogenetic trees calculated from both maximum parsimony and neighbor-joining phylogenetic analysis methods were highly congruent in terms of tree topologies. Phylogenetic analysis of mitochondrial COI sequences suggests that tephritid fruit fly species, which attack cucurbit plants, that is, Asiadacus, Hemigymnodacus and Zeugodacus, were more closely related to each other than to fruit fly species of the subgenus Bactrocera, which attack plants of numerous families. Our data supports previous classification of Bactrocera based on morphological characters. However, the phylogenetic tree showed the polyphyletic of fruit flies in subgenus Zeugodacus. Possible causes of speciation among fruit flies species in this genus were also discussed.     

Ecological controls of mammalian diversification vary with phylogenetic scale

Aim

Diversity dynamics remain controversial. Here, we examine these dynamics, together with the ecological factors governing them, across mammalian clades of different ages and sizes, representing different phylogenetic scales. Specifically, we investigate whether the dynamics are bounded or unbounded, biotically or abiotically regulated, stochastic or ecologically deterministic.

Location

Worldwide.

Time period

150 Myr.

Major taxa studied

Mammals.

Methods

Integrating the newest phylogenetic and distributional data by means of several distinct methods, we study the ecology of mammalian diversification within a predictive framework, inspired by classic theory. Specifically, we evaluate the effects of several classes of factors, including climate, topography, geographical area, rates of climatic‐niche evolution, and regional coexistence between related and unrelated species. Next, we determine whether the relative effects of these factors change systematically across clades representing different phylogenetic scales.

Results

We find that young clades diversify at approximately constant rates, medium‐sized clades show diversification slowdowns, and large clades are mostly saturated, suggesting that diversification dynamics change as clades grow and accumulate species. We further find that diversification slowdowns intensify with the degree of regional coexistence between related species, presumably because increased competition for regional resources suppresses the diversification process. The richness at which clades eventually saturate depends on climate; clades residing in tropical climates saturate at low richness, implying that niches become progressively densely packed towards the tropics.

Main conclusions

The diversification process is influenced by a variety of ecological factors, whose relative effects change across phylogenetic scales, producing scale‐dependent dynamics. Different segments of the same phylogeny might therefore support seemingly conflicting results (bounded or unbounded, biotically or abiotically regulated, stochastic or ecologically deterministic diversification), which might have contributed to several outstanding controversies in the field. These conflicts can be reconciled, however, when accounting for phylogenetic scale, which might, in turn, produce a more integrated understanding of global diversity dynamics.     

Climate,host phylogeny and the connectivity of host communities govern regional parasite assembly

Aim

Identifying barriers that govern parasite community assembly and parasite invasion risk is critical to understand how shifting host ranges impact disease emergence. We studied regional variation in the phylogenetic compositions of bird species and their blood parasites (Plasmodium and Haemoproteus spp.) to identify barriers that shape parasite community assembly.

Location

Australasia and Oceania.

Methods

We used a data set of parasite infections from >10,000 host individuals sampled across 29 bioregions. Hierarchical models and matrix regressions were used to assess the relative influences of interspecies (host community connectivity and local phylogenetic distinctiveness), climate and geographic barriers on parasite local distinctiveness and composition.

Results

Parasites were more locally distinct (co‐occurred with distantly related parasites) when infecting locally distinct hosts, but less distinct (co‐occurred with closely related parasites) in areas with increased host diversity and community connectivity (a proxy for parasite dispersal potential). Turnover and the phylogenetic symmetry of parasite communities were jointly driven by host turnover, climate similarity and geographic distance.

Main conclusions

Interspecies barriers linked to host phylogeny and dispersal shape parasite assembly, perhaps by limiting parasite establishment or local diversification. Infecting hosts that co‐occur with few related species decreases a parasite's likelihood of encountering related competitors, perhaps increasing invasion potential but decreasing diversification opportunity. While climate partially constrains parasite distributions, future host range expansions that spread distinct parasites and diminish barriers to host shifting will likely be key drivers of parasite invasions.     

Molecular phylogeny of the entomopathogenic fungi of the genus Cordyceps (Ascomycota: Clavicipitaceae) and its evolutionary implications

Abstract Cordyceps is an endoparasite ascomycetous genus containing approximately 450 species with a diversity of insect hosts, traditionally included in the family Clavicipitaceae of Ascomycota. Establishing the relationships among species with a varied range of morphologies and hosts is of importance to our understanding of the phylogeny and co‐evolution of parasites and hosts in entomopathogenic ascomycetes. To this end, we used a combination of molecular index and morphological characters from 40 representative species to carry out comprehensive molecular phylogenetic analyses. Based on the phylogenetic tree, we used the program DISCRETE for inferring the rates of evolution and finding ancestral states of morphological character. The phylogenetic analyses revealed two important points. (i) Types of perithecia attached to stroma reflected an evolutionary trend in Cordyceps. The vertically immersed perithecia form was the ancestral state, superficial and obliquely immersed perithecia were derived characters, obliquely immersed was irreversible. Species with obliquely immersed perithecia were in a closely related group and were the derived group. (ii) A strong correlation between fungal relatedness and the microhabitat supported the hypothesis that the host jumps through commingling in soil microhabitats. Based on the results of these analyses, host switching explains the diversity of entomopathogenic fungi of the genus Cordyceps.     

Independent origins of the feather lice (Insecta: Degeeriella) of raptors

Although diurnal birds of prey have historically been placed in a single order due to a number of morphological characters, recent molecular phylogenies have suggested that this is a case of convergence rather than homology, with hawks (Accipitridae) and falcons (Falconidae) forming two distantly related groups within birds. The feather lice of birds have often been used as a model for comparing host and parasite phylogenies, and in some cases there is significant congruence between the two. Thus, studying the phylogeny of the lice of diurnal raptors may be of particular interest with respect to the independent evolution of hawks vs. falcons. Using one mitochondrial gene and three nuclear genes, we inferred a phylogeny for the feather louse genus Degeeriella (which are all obligate raptor ectoparasites) and related genera. This phylogeny indicated that Degeeriella is polyphyletic, with lice from falcons vs. hawks forming two distinct clades. Falcon lice were sister to lice from African woodpeckers, whereas Capraiella, a genus of lice from rollers lice, was embedded within Degeeriella from hawks. This phylogeny showed significant geographical structure, with host geography playing a larger role than host taxonomy in explaining louse phylogeny, particularly within clades of closely related lice. However, the louse phylogeny does reflect host phylogeny at a broad scale; for example, lice from the hawk genus Accipiter form a distinct clade. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 114 , 837–847.     

Phylogeny and Evolutionary History of the Ground Squirrels (Rodentia: Marmotinae)

Although ground squirrels (Spermophilus) and prairie dogs (Cynomys) are among the most intensively studied groups of mammals with respect to their ecology and behavior, a well-resolved phylogeny has not been available to provide a framework for comparative and historical analyses. We used complete mitochondrial cytochrome b sequences to construct a phylogeny that includes all 43 currently recognized species in the two genera, as well as representatives of two closely related genera (Marmota and Ammospermophilus). In addition, divergence times for ground squirrel lineages were estimated using Bayesian techniques that do not assume a molecular clock. All methods of phylogenetic analysis recovered the same major clades, and showed the genus Spermophilus to be paraphyletic with respect to both Marmota and Cynomys. Not only is the phylogeny at odds with previous hypotheses of ground squirrel relationships, but it suggests that convergence in morphology has been a common theme in ground squirrel evolution. A well-supported basal clade, including Ammospermophilus and two species in the subgenus Otospermophilus, diverged from all other ground squirrels an estimated 17.5 million years ago. Between 10 and 14 million years ago, a relatively rapid diversification gave rise to lineages leading to marmots and to several distinct groups of ground squirrels. The Eurasian ground squirrels diverged from their North American relatives during this period, far earlier than previously hypothesized. This period of diversification corresponded to warming climate and spread of grasslands in western North America and Eurasia. Close geographic proximity of related forms suggests that most species evolved in or near their current ranges.     

MOLECULAR PHYLOGEOGRAPHY, RETICULATION, AND LINEAGE SORTING IN MEDITERRANEAN SENECIO SECT. SENECIO (ASTERACEAE)

Abstract The Mediterranean species complex of Senecio serves to illustrate evolutionary processes that are likely to confound phylogenetic inference, including rapid diversification, gene tree‐species tree discordance, reticulation, interlocus concerted evolution, and lack of complete lineage sorting. Phylogeographic patterns of chloroplast DNA (cpDNA) haplotype variation were studied by sampling 156 populations (502 individuals) across 18 species of the complex, and a species phylogeny was reconstructed based on sequences from the internal transcribed spacer (ITS) regions of nuclear ribosomal DNA. For a subset of species, randomly amplified polymorphic DNAs (RAPDs) provided reference points for comparison with the cpDNA and ITS datasets. Two classes of cpDNA haplotypes were identified, with each predominating in certain parts of the Mediterranean region. However, with the exception of S. gallicus, intraspecific phylogeographic structure is limited, and only a few haplotypes detected were species‐specific. Nuclear sequence divergence is low, and several unresolved phylogenetic groupings are suggestive of near simultaneous diversification. Two well‐supported ITS clades contain the majority of species, amongst which there is a pronounced sharing of cpDNA haplotypes. Our data are not capable of diagnosing the relative impact of reticulation versus insufficient lineage sorting for the entire complex. However, there is firm evidence that S. flavus subsp. breviflorus and S. rupestris have acquired cpDNA haplotypes and ITS sequences from co‐occurring species by reticulation. In contrast, insufficient lineage sorting is a viable hypothesis for cpDNA haplotypes shared between S. gallicus and its close relatives. We estimated the minimum coalescent times for these haplotypes by utilizing the inferred species phylogeny and associated divergence times. Our data suggest that ancestral cpDNA polymorphisms may have survived for ca. 0.4–1.0 million years, depending on molecular clock calibrations.     

Linking patterns and processes of species diversification in the cone flies Strobilomyia (Diptera: Anthomyiidae)

Phytophagous insects provide useful models for the study of ecological speciation. Much attention has been paid to host shifts, whereas situations where closely related lineages of insects use the same plant during different time periods have been relatively neglected in previous studies of insect diversification. Flies of the genus Strobilomyia are major pests of conifers in Eurasia and North America. They are specialized feeders in cones and seeds of Abies (fir), Larix (larch) ,and Picea (spruce). This close association is accompanied by a large number of sympatric Strobilomyia species coexisting within each tree genus. We constructed a molecular phylogeny with a 1320 base-pair fragment of mitochondrial DNA that demonstrated contrasting patterns of speciation in larch cone flies, as opposed to spruce and fir cone flies; this despite their comparable geographic distributions and similar resource quality of the host. Species diversity is the highest on larch, and speciation is primarily driven by within-host phenological shifts, followed by allopatric speciation during geographical expansion. By contrast, fewer species exploit spruce and fir, and within-host phenological shifts did not occur. This study illustrates within-host adaptive radiation through phenological shifts, a neglected mode of sympatric speciation.     

Tracing the radiation of Maniola (Nymphalidae) butterflies: new insights from phylogeography hint at one single incompletely differentiated species complex

The use of DNA sequence data often leads to the recognition of cryptic species within putatively well‐known taxa. The opposite case, detecting less diversity than originally described, has, however, far more rarely been documented. Maniola jurtina, the Meadow Brown butterfly, occurs all over Europe, whereas all other six species in the genus Maniola are restricted to the Mediterranean area. Among them, three are island endemics on Sardinia, Cyprus, and Chios, respectively. Maniola species are almost indistinguishable morphologically, and hybridization seems to occur occasionally. To clarify species boundaries and diversification history of the genus, we reconstructed the phylogeography and phylogeny of all seven species within Maniola analyzing 138 individuals from across its range using mitochondrial and nuclear genetic markers. Examination of variation in mitochondrial and nuclear DNA surprisingly revealed a case of taxonomic “oversplitting”. The topology of the recovered phylogenetic tree is not consistent with accepted taxonomy, but rather reveals haplotype clades that are incongruent with nominal species boundaries: instead of seven species, we recognized only two major, yet incompletely segregated, lineages. Our results are consistent with the hypothesis that Maniola originated in Africa. We suggest that one lineage dispersed over the Strait of Gibraltar and the Iberian Peninsula to the west of Europe, while the other lineage spreads eastward through Asia Minor and over the Bosporus to Eastern Europe.