Characterization of the complete mitochondrial genome of flower-breeding <Emphasis Type="Italic">Drosophila incompta</Emphasis> (Diptera,Drosophilidae)

Drosophila incompta belongs to the flavopilosa group of Drosophila, and has a restricted ecology, being adapted to flowers of Cestrum as feeding and oviposition sites. We sequenced, assembled, and characterized the complete mitochondrial genome (mtDNA) of D. incompta. In addition, we performed phylogenomic and polymorphism analyses to assess evolutionary diversification of this species. Our results suggest that this genome is syntenic with the other published mtDNA of Drosophila. This molecule contains 15,641 bp and encompasses two rRNA, 22 tRNA and 13 protein-coding genes. Regarding nucleotide composition, we found a high A?T bias (76.6 %). The recovered phylogenies indicate D. incompta in the virilis–repleta radiation, as sister to the virilis or repleta groups. The most interesting result is the high degree of polymorphism found throughout the D. incompta mitogenome, revealing pronounced intrapopulational variation. Furthermore, intraspecific nucleotide diversity levels varied between different regions of the genome, thus allowing the use of different mitochondrial molecular markers for analysis of population structure of this species.     

Radiation of the Drosophila nannoptera species group in Mexico

The Drosophila nannoptera species group, a taxon of Mexican cactophilic flies, is an excellent model system to study the influence of abiotic and biotic factors on speciation, the genetic causes of ecological specialization and the evolution of unusual reproductive characters. However, the phylogenetic relationships in the nannoptera species group and its position within the virilis‐repleta phylogeny have not been thoroughly investigated. Using a multilocus data set of gene coding regions of eight nuclear and three mitochondrial genes, we found that the four described nannoptera group species diverged rapidly, with very short internodes between divergence events. Phylogenetic analysis of repleta group lineages revealed that D. inca and D. canalinea are sister to all other repleta group species, whereas the annulimana species D. aracataca and D. pseudotalamancana are sister to the nannoptera and bromeliae species groups. Our divergence time estimates suggest that the nannoptera species group radiated following important geological events in Central America. Our results indicate that a single evolutionary transition to asymmetric genitalia and to unusual sperm storage may have occurred during evolution of the nannoptera group.     

Evolutionary history of alpine and subalpine Daphnia in western North America

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Phylogenetic and diversity patterns of Blanus worm lizards (Squamata: Amphisbaenia): insights from mitochondrial and nuclear gene genealogies and species tree

Phylogenetic and phylogeographic patterns of amphisbaenians are poorly known. Molecular data from mitochondrial and nuclear loci are particularly needed for amphisbaenian phylogeny and taxonomy because their specializations to subterranean habits make morphology poorly informative and the occurrence of cryptic species probable. The Mediterranean genus Blanus includes five species – three of them have been recently studied mainly at the mitochondrial level. In this study, we collected mitochondrial (16S and nd4) and nuclear (mc1r and pomc) sequences from 49 specimens, including multiple individuals for each of the five species. We used multilocus coalescent‐based species‐tree inference and single‐gene analyses to estimate phylogenetic relationships among Blanus and to assess patterns of intraspecific differentiation within all the five species. Species‐tree and single‐gene phylogenies provided strong support for the Anatolian worm lizard B. strauchi lying outside a clade comprising all other congeners, with a sister relationship between the Iberian clade (B. cinereus and B. mariae) and the North African clade (B. tingitanus and B. mettetali). Mitochondrial and nuclear data supported the genetic distinctiveness of the recently described B. mariae and also indicated that the distribution of this species is wider than previously known and overlaps with B. cinereus in central Portugal. Blanus tingitanus showed two phylogeographic groups, from the northern and the southern portion of the range, respectively, having high mitochondrial and nuclear divergence and a possible contact zone in northwestern Morrocco. Finally, high genetic variation was found within B. mettetali and B. strauchi, suggesting in the latter case, the occurrence of cryptic taxa to be tested by further research.     

Evolution,biogeography and systematics of the western Palaearctic Zamenis ratsnakes

The phylogenetic relationships between western Palaearctic Zamenis and Rhinechis ratsnakes have been troubled, with recent estimates based on the supermatrix approach questioning their monophyly and providing contradictory results. In this study, we generated a comprehensive molecular data set for Zamenis and closely related ratsnakes to assess their phylogenetic and systematic relationships and infer their spatial and temporal modes of diversification. We obtained a fully resolved and well‐supported phylogeny, which is consistent across markers, taxon‐sets and phylogenetic methods. The close phylogenetic relationship between Rhinechis and Zamenis is well‐established. However, the early branching pattern within this clade, and the position of R. scalaris and Z. hohenackeri, remains poorly supported. The Persian ratsnake Z. persicus is sister to the Mediterranean species Z. situla, Z. longissimus and Z. lineatus, of which Z. situla is sister to a clade containing the latter two species. These results are consistent with a recent phylogenomic study on ratsnakes based on hundreds of loci. Whereas, topological tests based on our data and evidence from such phylogenomic study strongly rejected previous phylogenetic estimates based on the supermatrix approach and demonstrate that these “mega‐phylogenies”, with hundreds of taxa and high levels of missing data, have recovered inconsistent relationships with spurious nodal support. Biogeographical and molecular dating analyses suggest an origin of the ancestor of Rhinechis and Zamenis in the Aegean region with early cladogenesis during the Late Miocene associated with the Aegean arch formation and support a scenario of east‐to‐west diversification. Finally, while we have little morphological and phylogenetic evidence for the distinctiveness between Rhinechis and Zamenis, a classification of them in a single genus, and the designation of Zamenis scalaris (Schinz, 1822), reflects better their evolutionary relationships.     

Phylogeny and species delineation in the marine diatom Pseudo‐nitzschia (Bacillariophyta) using cox1, LSU,and ITS2 rRNA genes: A perspective in character evolution

Analyses of the mitochondrial cox1, the nuclear‐encoded large subunit (LSU), and the internal transcribed spacer 2 (ITS2) RNA coding region of Pseudo‐nitzschia revealed that the P. pseudodelicatissima complex can be phylogenetically grouped into three distinct clades (Groups I–III), while the P. delicatissima complex forms another distinct clade (Group IV) in both the LSU and ITS2 phylogenetic trees. It was elucidated that comprehensive taxon sampling (sampling of sequences), selection of appropriate target genes and outgroup, and alignment strategies influenced the phylogenetic accuracy. Based on the genetic divergence, ITS2 resulted in the most resolved trees, followed by cox1 and LSU. The morphological characters available for Pseudo‐nitzschia, although limited in number, were overall in agreement with the phylogenies when mapped onto the ITS2 tree. Information on the presence/absence of a central nodule, number of rows of poroids in each stria, and of sectors dividing the poroids mapped onto the ITS2 tree revealed the evolution of the recently diverged species. The morphologically based species complexes showed evolutionary relevance in agreement with molecular phylogeny inferred from ITS2 sequence–structure data. The data set of the hypervariable region of ITS2 improved the phylogenetic inference compared to the cox1 and LSU data sets. The taxonomic status of P. cuspidata and P. pseudodelicatissima requires further elucidation.     

Molecular phylogeny,biogeography and chromosome evolution of Malagasy dwarf geckos of the genus Lygodactylus (Squamata,Gekkonidae)

We performed a phylogenetic analysis using nuclear (RAG‐1, RAG‐2) and mitochondrial (16S) markers, a statistical Bayesian reconstruction of ancestral distribution areas and a karyological analysis on most Malagasy species of the gekkonid genus Lygodactylus. The phylogenetic analysis largely confirms major basal branching pattern of previous molecular studies, but highlights significant differences concerning both the relationships between different species groups as well as those within groups. The biogeographic analysis supports a Malagasy origin of Lygodactylus, an oversea dispersal to continental Africa and a return to Madagascar. The L. madagascariensis group (also including a new candidate species identified herein) is the most basal clade in Lygodactylus, and the sister group of a clade with all the remaining species. The second most basal clade is the L. verticillatus group, placed as the sister group of a clade comprising African and Malagasy species. The sister lineage of the L. verticillatus group originated the African radiation through an oversea dispersal out of Madagascar. Eventually, the sister lineage of the L. capensis group originated secondary dispersals from Africa to Madagascar. In Madagascar, lineage diversification in different species groups mainly occurred from southern to northern and eastern regions. Dispersal, vicariance and paleoclimatic refugia probably played a relevant role in the evolutionary history of closely related taxa and in speciation mechanisms. The cytogenetic analysis evidenced a high karyotypic variability in Lygodactylus (from 2n = 34 to 2n = 40), which is at least partly consistent with the phylogenetic relationships and the composition of the various species group. Chromosome evolution occurred independently in different lineages, mainly through a reduction in the chromosome number and starting from a putative primitive karyotype of 2n = 40 with all telocentric elements.     

New data on the phylogeny of Ariantinae (Pulmonata,Helicidae) and the systematic position of Cylindrus obtusus based on nuclear and mitochondrial DNA marker sequences

The phylogenetic relationships among genera of the subfamily Ariantinae (Pulmonata, Helicidae), especially the sister‐group relationship of Cylindrus obtusus, were investigated with three mitochondrial (12S rRNA, 16S rRNA, Cytochrome c oxidase subunit I) and two nuclear marker genes (Histone H4 and H3). Within Ariantinae, C. obtusus stands out because of its aberrant cylindrical shell shape. Here, we present phylogenetic trees based on these five marker sequences and discuss the position of C. obtusus and phylogeographical scenarios in comparison with previously published results. Our results provide strong support for the sister‐group relationship between Cylindrus and Arianta confirming previous studies and imply that the split between the two genera is quite old. The tree reveals a phylogeographical pattern of Ariantinae with a well‐supported clade comprising the Balkan taxa which is the sister group to a clade with individuals from Alpine localities. Additional lineages representing samples from southern Alpine localities as well as from Slovakia split from more basal nodes, but their relationships are not clearly resolved. To achieve more definitive conclusions concerning the geographical origin of Ariantinae, still more sequence data are needed to obtain a tree with better resolution of basal nodes. The genetic data also provided new insights concerning the genus Cepaea, which was used as one of the outgroup taxa. Cepaea vindobonensis is only distantly related to Cepaea nemoralis and Cepaea hortensis, the latter two being more closely related to Eobania vermiculata. Thus, in our tree, the genus Cepaea is paraphyletic.     

Phylogenetic relationships,song and distribution of the endangered Rufous‐headed Robin Larvivora ruficeps

The Rufous‐headed Robin Larvivora ruficeps is one of the world's rarest and least known birds. We summarize the known records since it was first described in 1905 from Shaanxi Province, central China. All subsequent Chinese records are from seven adjacent localities in nearby Sichuan Province. We studied its phylogenetic position for the first time using mitochondrial and nuclear markers for all species of Larvivora and a broad selection of other species in the family Muscicapidae. Our results confirmed that L. ruficeps is appropriately placed in the genus Larvivora, and suggested that it is sister to the Rufous‐tailed Robin Larvivora sibilans, with these two forming a sister clade to a clade comprising both the Japanese Robin Larvivora akahige and Ryukyu Robin Larvivora komadori. Siberian Blue Robin Larvivora cyane and Indian Blue Robin Larvivora brunnea form the sister clade to the other Larvivora species. In contrast, song analyses indicated that the song of L. ruficeps is most similar to that of L. komadori, whereas the song of L. sibilans is relatively more similar to that of L. akahige, and songs of L. cyane and L. brunnea closely resemble each other. We used ecological niche modelling to estimate the suitable habitats of L. ruficeps based on the records from breeding grounds, suggesting that north and central Sichuan, south Gansu, south Shaanxi and south‐east Tibet are likely to contain the most suitable habitats for this species.     

Molecular phylogeny of the Drosophila virilis section (Diptera: Drosophilidae) based on mitochondrial and nuclear sequences

Regardless of the well-documented virilis species group, most groups of the Drosophila virilis section have not been completely studied at molecular level since it was suggested. Therefore, phylogenetic relationships among and within species groups of the virilis section are generally unknown. In present paper, the complete mitochondrial ND2 gene and fragment of COI gene in combination with a nuclear gene, Adh coding region, were used to derive the most extensive molecular phylogeny to date for the Drosophila virilis section. A total of 111 individuals covering 61 species were sampled in this study. Novel phylogenetic findings included (1) support for the paraphyly of the melanica and robusta species group and at least two subgroups of the robusta species group, the lacertosa and okadai subgroups, were distinguished as paraphyletic taxa. In addition, (2) present results revealed the sister relationship between D. moriwakii and the robusta subgroup, conflicting with current taxonomy regarding D. moriwakii, which was shifted from the robusta species group to the melanica group. (3) In contrast to the robusta and melanica species groups, monophyly of the polychaeta species group, the angor group and the virilis group was confirmed, respectively. However, the monophyletic quadrisetata species group was resolved with uncertainty. (4) Our analyses of combined data set suggested close relationship between the quadrisetata species group and the unpublished clefta group, and the okadai subgroup is sister to the clade comprising of the quadrisetata and clefta species groups. Within the virilis section, D. fluvialis and three tropical species groups, the polychaeta group, the angor group and the repleta group, are found to branch off earlier than other ingroup taxa. This suggests that the virilis section might have originated in the Old World tropics. Besides, the derived status of the close affinities of the quadrisetata group, the clefta group, and the melanica and robusta groups is probably the result of their adaptation to forests between subtropical and cool-temperate climate. Based on the consideration of the phylogenetic placement of the species of the virilis section, we suggest that at least five independent migrations occurred from the Old World to the New World.     

The phylogeny of Dendropsophini (Anura: Hylidae: Hylinae)

The relationships of the hyline tribe Dendropsophini remain poorly studied, with most published analyses dealing with few of the species groups of Dendropsophus. In order to test the monophyly of Dendropsophini, its genera, and the species groups currently recognized in Dendropsophus, we performed a total evidence phylogenetic analysis. The molecular dataset included sequences of three mitochondrial and five nuclear genes from 210 terminals, including 12 outgroup species, the two species of Xenohyla, and 93 of the 108 recognized species of Dendropsophus. The phenomic dataset includes 46 terminals, one per species (34 Dendropsophus, one Xenohyla, and 11 outgroup species). Our results corroborate the monophyly of Dendropsophini and the reciprocal monophyly of Dendropsophus and Xenohyla. Some species groups of Dendropsophus are paraphyletic (the D. microcephalus, D. minimus, and D. parviceps groups, and the D. rubicundulus clade). On the basis of our results, we recognize nine species groups; for three of them (D. leucophyllatus, D. microcephalus, and D. parviceps groups) we recognize some nominal clades to highlight specific morphology or relationships and facilitate species taxonomy. We further discuss the evolution of oviposition site selection, where our results show multiple instances of independent evolution of terrestrial egg clutches during the evolutionary history of Dendropsophus.     

Macroevolutionary persistence of heritable endosymbionts: acquisition,retention and expression of adaptive phenotypes in Spiroplasma

The phylogenetic incongruence between insects and their facultative maternally transmitted endosymbionts indicates that these infections are generally short‐lived evolutionarily. Therefore, long‐term persistence of many endosymbionts must depend on their ability to colonize and spread within new host species. At least 17 species of Drosophila are infected with endosymbiotic Spiroplasma that have various phenotypic effects. We transinfected five strains of Spiroplasma from three divergent clades into Drosophila neotestacea to test their capacity to spread in a novel host. A strain that causes male killing in Drosophila melanogaster (its native host) also does so in D. neotestacea, even though these host species diverged 40–60 mya. A strain native to D. neotestacea (designated sNeo) and the two other strains of the poulsonii clade of Spiroplasma confer resistance to wasp parasitism, suggesting that this trait may be ancestral within this clade of Spiroplasma. Conversely, no strain other than sNeo conferred resistance to the sterilizing effects of nematode parasitism, suggesting that nematode resistance is a recently derived condition. The apparent addition of nematode resistance to a Spiroplasma lineage that already confers resistance to wasp parasitism suggests endosymbionts can increase the repertoire of traits conducive to their spread. The capacity of an endosymbiont to undergo maternal transmission and express adaptive phenotypes in novel hosts, without requiring a period of host–symbiont co‐evolution, enables the spread of such symbionts immediately after the colonization of a new host. This could be critical for the macroevolutionary persistence of facultative endosymbionts whose sojourn times within individual host species are relatively brief.     

Non‐concordant phylogeographical patterns of three widely codistributed endemic Western Balkans lacertid lizards (Reptilia,Lacertidae) shaped by specific habitat requirements and different responses to Pleistocene climatic oscillations

The Balkan Peninsula is a hot spot for European herpetofaunal biodiversity and endemism. The rock climbing lizards Dalmatolacerta oxycephala and Dinarolacerta mosorensis and the ground‐dwelling Dalmatian wall lizard Podarcis melisellensis are endemic to the Western Balkans, and their ranges largely overlap. Here, we present a comparative phylogeographical study of these three species in the area of their codistribution in order to determine the level of concordance in their evolutionary patterns. Phylogenetic analyses were performed based on two mitochondrial genes (cytochrome b and 16S rRNA), and a molecular clock approach was used to date the most important events in their evolutionary histories. We also tested for correlations regarding genetic differentiation among populations and their geographical distances. For all three species, a significant correlation between genetic and geographical distances was found. Within D. oxycephala, two deeply separated clades (‘island’ and ‘mainland clade’), with further subdivision of the ‘mainland clade’ into two subclades (‘south‐eastern’ and ‘north‐western’), were found. High sequence divergences were observed between these groups. From our data, the time of separation of the two main clades of D. oxycephala can be estimated at about 5 mya and at about 0.8 mya for the two subclades of the mainland clade. Within D. mosorensis, coalescence time may be dated at about 1 mya, while D. mosorensis and D. montenegrina separated around 5 mya. The results imply the existence of complex palaeo‐biogeographical and geological factors that probably influenced the observed phylogeographical patterns in these lacertid species, and point to the presence of numerous glacial/interglacial refugia. Furthermore, the observed cryptic genetic diversity within the presently monotypic species D. oxycephala prompts for a revision of its taxonomic and conservation status.     

Gene and species trees reveal mitochondrial and nuclear discordance in the Drosophila cardini group (Diptera: Drosophilidae)

Abstract. The Drosophila cardini group includes 15 species, which are subdivided into the D. cardini and D. dunni subgroups. Although many phylogenetic hypotheses have been proposed for this group during the last five decades (based on patterns of reproductive isolation, morphology of male genitalia, chromosomal inversions, isozyme variation, or molecular sequence data), these are mostly discordant with each other. We aimed to clarify some of the evolutionary patterns related to the origin of this incongruence, while also attempting to provide a better-supported phylogenetic hypothesis for the D. cardini subgroup. For this purpose, sequences from three mitochondrial and three nuclear loci were gathered for at least eight species, and both individual gene trees and joint species tree estimates were evaluated. Although there was concordance among gene trees within each of the nuclear and mitochondrial sets, considerable incongruence was revealed in the comparisons between these two data sets. The branching position of D. neocardini was the main source of incongruence, and species trees reconstructed using different approaches with and without this species were particularly incongruent. In addition to providing a better approximation of the evolutionary history of the D. cardini group, this study suggests that incomplete lineage sorting or introgression may be biasing previous species tree estimates. More generally, the results also suggest that the use of supermatrix methods can lead to an overestimation of support for the inferred relationships, and highlight the potential effects of different taxon sampling strategies in phylogenetic reconstruction.     

Intra‐ and interspecific divergence in the nuclear sequences of the clock gene period in species of the Drosophila buzzatii cluster

We have measured nucleotide variation in the CLOCK/CYCLE heterodimer inhibition domain (CCID) of the clock X‐linked gene period in seven species belonging to the Drosophila buzzatii cluster, namely D. buzzatii, Drosophila koepferae, Drosophila antonietae, Drosophila serido, Drosophila gouveai, Drosophila seriema and Drosophila borborema. We detected that the purifying selection is the main force driving the sequence evolution in period, in agreement with the important role of CCID in clock machinery. Our survey revealed that period provides valuable phylogenetic information that allowed to resolve phylogenetic relationships among D. gouveai, D. borborema and D. seriema, which composed a polytomic clade in preliminary studies. The analysis of patterns of intraspecific variation revealed two different lineages of period in D. koepferae, probably reflecting introgressive hybridization from D. buzzatii, in concordance with previous molecular data.     

The striking polyphyly of Suiriri: Convergent evolution and social mimicry in two cryptic Neotropical birds

Two species of Suiriri (Aves: Tyrannidae) inhabit semi‐open habitats in South America: the polytypic Suiriri Flycatcher (S. suiriri) and the monotypic Chapada Flycatcher (S. affinis). The phylogenetic relationship between these congeneric species has never been investigated in detail. Here we used molecular tools—three nuclear introns and two mitochondrial genes—to investigate the systematic position of the Chapada Flycatcher, comparing the results found with morphological and behavioral data. We found that the polytypic Suiriri Flycatcher to be monophyletic and that it is included in a clade of Elaeniini flycatchers including Phyllomyias, Phaeomyias, and Capsiempis among other genera. The Chapada Flycatcher, on the other hand, is a member of the Fluvicolini, sister to Sublegatus, and should be allocated on its own monospecific genus, which we herein describe. We suggest that social mimicry is responsible for the remarkable convergence in size, shape, plumage coloration, and behavior in the adults of the Suiriri Flycatcher and the Chapada Flycatcher.     

Mitogenomic phylogenetics of Diochus occultus n. sp., a palaeoendemic endogean species within the tribe Diochini (Coleoptera: Staphylinidae: Staphylininae)

The tribe Diochini has a worldwide distribution, with 2 and 74 epigean species within the genera Antarctothius and Diochus, respectively. Recent phylogenetic studies suggest a sister relationship of Diochini and a lineage formed by Xantholinini, Maorothiini, and Othiini, within the subfamily Staphylininae. Here, we describe the first known endogean representative of Diochini, Diochus occultus n. sp., and provide the first two complete mitogenomes for the tribe, corresponding to the two European Diochus species: Diochus occultus n. sp. and Diochus staudingeri. These sequences were combined with 40 additional mitogenomes from representatives within Staphylininae, Paederinae, Silphidae, and Aleocharinae, and COI sequences from 5 additional species of Diochus to conduct a series of mitogenomic phylogenetic and dating analyses. The estimated molecular phylogeny is fully consistent with previous studies based on morphology and molecular data, finding a sister relationship of Diochini with a clade formed by Xantholinini and Othiini (Maorothiini not sampled). Dating analyses inferred an early split of the tribe Diochini at 140–156 Mya. Morphology shows clear differences in the aedeagal and external morphology of D. occultus n. sp. and D. staudingeri, whereas a sister relationship of these taxa is found in the phylogenetic analyses, with the split dated at 48–61 Mya. Although the study of additional Palaearctic Diochus species will be required to conclusively establish that D. occultus n. sp. is a palaeoendemic taxon sister to D. staudingeri, associated with forests of Abies pinsapo in the south of the Iberian Peninsula, this conclusion is consistent with the ancient estimated age of speciation, endogean habitat specificity, low dispersal capacity (flightless species), and microendemicity of D. occultus. This is also consistent with the continued emersion of the Betic sub‐plate along its tectonic evolution. The estimated ages of diversification of the Paederinae‐Staphylininae lineage are also discussed.     

Sorting out the Snakebirds: The species status,phylogeny, and biogeography of the Darters (Aves: Anhingidae)

Although the avian family Anhingidae is unequivocally monophyletic, the number and relationships of the component species within the single genus (Anhinga) have long remained unclear. Here, we use extensive mitochondrial and nuclear DNA sequence data (8,878 bp) to show that four species should be recognized. Our fully resolved and well‐supported tree shows that the American Anhinga (Anhinga anhinga) is sister to the three Old World species, with the Oriental (A. melanogaster) and African (A. rufa) Darters sister within the Old World clade, which also includes the Australian Darter (A. novaehollandiae). We estimate that the divergence between the New World and Old World branches occurred 19–22 mya, with the Australian Darter separating from its Old World congeners 14–16 mya and the Oriental and African species splitting ~10 mya. The genus is yet another example of osteological conservatism in the Suliformes, which is comparable to that shown by the cormorants and shags. Nevertheless, the relationships we infer are congruent with recent plumage studies and are biogeographically plausible. We suggest that further investigation of the variation within the African and Australian Darters would be of interest.     

Multiple nuclear genes stabilize the phylogenetic backbone of the genus Quercus

Phylogenetic relationships among 108 oak species (genus Quercus L.) were inferred using DNA sequences of six nuclear genes selected from the existing genomic resources of the genus. Previous phylogenetic reconstructions based on traditional molecular markers are inconclusive at the deeper nodes. Overall, weak phylogenetic signals were obtained for each individual gene analysis, but stronger signals were obtained when gene sequences were concatenated. Our data support the recognition of six major intrageneric groups Cyclobalanopsis, Cerris, Ilex, Quercus, Lobatae and Protobalanus. Our analyses provide resolution at deeper nodes but with moderate support and a more robust infrageneric classification within the two major clades, the ‘Old World Oaks’ (Cyclobalanopsis, Cerris, Ilex) and ‘New World Oaks’ (Quercus, Lobatae, Protobalanus). However, depending on outgroup choice, our analysis yielded two alternative placements of the Cyclobalanopsis clade within the genus Quercus. When Castanea Mill. was chosen as outgroup, our data suggested that the genus Quercus comprised two clades corresponding to two subgenera as traditionally recognized by Camus: subgenus Euquercus Hickel and Camus and subgenus Cyclobalanopsis Øersted (Schneider). However, when Notholithocarpus Manos, Cannon and S. Oh was chosen as an outgroup subgenus Cyclobalanopsis clustered with Cerris and Ilex groups to form the Old World clade. To assess the placement of the root, we complemented our dataset with published data of ITS and CRC sequences. Based on the concatenated eight gene sequences, the most likely root position is at the split between the ‘Old World Oaks’ and the ‘New World Oaks’, which is one of the alternative positions suggested by our six gene analysis. Using a dating approach, we inferred an Eocene age for the primary divergences in Quercus and a root age of about 50–55 Ma, which agrees with palaeobotanical evidence. Finally, irrespective of the outgroup choice, our data boost the topology within the New World clade, where (Protobalanus + Quercus) is a sister clade of Lobatae. Inferred divergence ages within this clade and the Cerris–Ilex clade are generally younger than could be expected from the fossil record, indicating that morphological differentiation pre-dates genetic isolation in this clade.     

Mito‐nuclear discordance with evidence of shared ancestral polymorphism and selection in cactophilic species of Drosophila

The Drosophila serido haplogroup is a monophyletic group composed of the following four cryptic and cactophilic species that are endemic to eastern Brazil: D. borborema, D. gouveai, D. seriema and D. serido. Here, we investigate the mito‐nuclear discordance in these species found among the cytochrome c oxidase subunit I (COI) mitochondrial gene, the autosomal alpha‐Esterase‐5 (α‐Est5) and the X‐linked period gene (per). Our analysis indicates that shared polymorphisms in these three molecular markers may be explained by the maintenance of ancestral polymorphisms rather than introgressive hybridization. The primary structures of COI, per and α‐Est5 genes evolve primarily under purifying selection, but we detected some sites that evolved under positive selection in α‐Est5. Considering the high variability of cacti species in eastern Brazil and the role attributed to Drosophila esterases in digestion metabolism and/or the detoxification of several compounds found in cactus tissues, we conjecture about the role of natural selection triggered by host shifts as an important factor in the intraspecific diversification of the D. serido haplogroup.