Molecular phylogenetics of slit‐faced bats (Chiroptera: Nycteridae) reveal deeply divergent African lineages

The bat family Nycteridae contains only the genus Nycteris, which comprises 13 currently recognized species from Africa and the Arabian Peninsula, one species from Madagascar, and two species restricted to Malaysia and Indonesia in South‐East Asia. We investigated genetic variation, clade membership, and phylogenetic relationships in Nycteridae with broad sampling across Africa for most clades. We sequenced mitochondrial cytochrome b (cytb) and four independent nuclear introns (2,166 bp) from 253 individuals. Although our samples did not include all recognized species, we recovered at least 16 deeply divergent monophyletic lineages using independent mitochondrial and multilocus nuclear datasets in both gene tree and species tree analyses. Mean pairwise uncorrected genetic distances among species‐ranked Nycteris clades (17% for cytb and 4% for concatenated introns) suggest high levels of phylogenetic diversity in Nycteridae. We found a large number of designated clades whose members are distributed wholly or partly in East Africa (10 of 16 clades), indicating that Nycteris diversity has been historically underestimated and raising the possibility that additional unsampled and/or undescribed Nycteris species occur in more poorly sampled Central and West Africa. Well‐resolved mitochondrial, concatenated nuclear, and species trees strongly supported African ancestry for SE Asian species. Species tree analyses strongly support two deeply diverged subclades that have not previously been recognized, and these clades may warrant recognition as subgenera. Our analyses also strongly support four traditionally recognized species groups of Nycteris. Mitonuclear discordance regarding geographic population structure in Nycteris thebaica appears to result from male‐biased dispersal in this species. Our analyses, almost wholly based on museum voucher specimens, serve to identify species‐rank clades that can be tested with independent datasets, such as morphology, vocalizations, distributions, and ectoparasites. Our analyses highlight the need for a comprehensive revision of Nycteridae.     

Phylogenetic relationships and evolution of Crassulaceae inferred from matK sequence data

Chloroplast gene matK sequence data were used to estimate the phylogeny of 112 species of Crassulaceae sampled from 33 genera and all six recognized subfamilies. Our analyses suggest that five of six subfamilies recognized in the most recent comprehensive classification of the family are not monophyletic. Instead, we recovered a basal split in Crassulaceae between the southern African CRASSULA: clade (Crassuloideae) and the rest of the family (Sedoideae). These results are compatible with recent studies of cpDNA restriction site analyses. Within Sedoideae, four subclades were also recovered: KALANCHOE:, Leucosedum, Acre, and AEONIUM:; evidence also exists for a TELEPHIUM: clade and SEMPERVIVUM: clade. The genus SEDUM: is highly polyphyletic with representatives spread throughout the large Sedoideae clade. Sympetaly and polymerous flowers have arisen multiple times in Crassulaceae and thus are not appropriate characters upon which to base subfamilial limits, as has been done in the past. One floral character, haplostemy, appears to be confined to the well-supported CRASSULA: clade. Our analyses suggest a southern African origin of the family, with subsequent dispersal northward into the Mediterranean region. From there, the family spread to Asia/eastern Europe and northern Europe; two separate lineages of European Crassulaceae subsequently dispersed to North America and underwent substantial diversification. Our analyses also suggest that the original base chromosome number in Crassulaceae is x = 8 and that polyploidy has played an important role in seven clades. Three of these clades are exclusively polyploid (SEMPERVIVUM: clade and two subclades within the KALANCHOE: and AEONIUM: clades), whereas four (Crassula, Telephium, Leucosedum, and ACRE: clades) comprise both diploid and polyploid taxa. Polyploidy is particularly rampant and cytological evolution especially complex in the ACRE: clade.     

Addressing the "hardest puzzle in American pomology:" Phylogeny of Prunus sect. Prunocerasus (Rosaceae) based on seven noncoding chloroplast DNA regions

Prunus subg. Prunus sect. Prunocerasus (Rosaceae) is a North American taxon with 17 commonly recognized taxa. To test the hypothesis of monophyly for the section we sequenced the trnG and rpL16 introns and the trnH-psbA and trnS-trnG intergenic spacers for at least two representatives of each of the five subgenera in Prunus. Additionally we sampled heavily among Prunus subg. Prunus sections Prunus and Armeniaca and Prunus subg. Amygdalus because these groups are putatively most closely related to Prunocerasus. Once monophyly of sect. Prunocerasus was shown we added the sequences of trnL and rpS16 introns and the trnL-trnF spacer in an attempt to increase resolution within the section. The species of sect. Prunocerasus showed an initial split with P. subcordata, the only species from western North America, sister to the rest of the group. The remaining species fell into three primary clades. Within each of the three primary clades there was little phylogenetic resolution. Lastly, we present evidence that P. texana, previously classified in subg. Amygdalus, may be a plum or at least contain a Prunocerasus chloroplast. This is the first phylogenetic hypothesis presented for sect. Prunocerasus, and the clades recovered contrast sharply with previously defined groups based on morphological characters.     

Molecular phylogeny, character evolution, and biogeography of the grammitid fern genus Lellingeria (Polypodiaceae)

? Premise of the study: The recognition of monophyletic genera for groups that have high levels of homoplastic morphological characters and/or conflicting results obtained by different studies can be difficult. Such is the case in the grammitid ferns, a clade within the Polypodiaceae. In this study, we aim to resolve relationships among four clades of grammitid ferns, which have been previously recovered either as a polytomy or with conflicting topologies, with the goal of circumscribing monophyletic genera. ? Methods: The sampling included 89 specimens representing 61 species, and sequences were obtained for two genes (atpB and rbcL) and four intergenic spacers (atpB-rbcL, rps4-trnS, trnG-trnR, and trnL-trnF), resulting in a matrix of 5091 characters. The combined data set was analyzed using parsimony, likelihood, and Bayesian methods. Ninety-six morphological characters were optimized onto the generated trees, using the parsimony method. ? Key results: Lellingeria is composed of two main clades, the L. myosuroides and the Lellingeria s.s. clades, which together are sister to Melpomene. Sister to all three of these is a clade with two species of the polyphyletic genus Terpsichore. In the L. myosuroides clade, several dispersal events occurred between the neotropics, Africa, and the Pacific Islands, whereas Lellingeria s.s. is restricted to the neotropics, with about 60% of its diversity in the Andes. ? Conclusions: Overall, our results suggest that Lellingeria is monophyletic, with two clades that are easily characterized morphologically and biogeographically. Morphological characters describing the indument are the most important to define the clades within the ingroup. A small clade, previously considered in Terpsichore, should be recognized as a new genus.     

Molecular evolution of southern North American Cyprinidae (Actinopterygii), with the description of the new genus Tampichthys from central Mexico

Most of the recognized species of the genus Dionda inhabit drainages of the Gulf of Mexico from central Mexico to central Texas, USA, and have been considered a monophyletic group based on morphological, osteological, and allozyme investigations. Phylogenetic relationships of 15 species of Dionda and 34 species from closely related genera were inferred from one mitochondrial (cytb) and three nuclear gene sequences (S7, Rhodopsin, Rag1) totaling 4487 nucleotides. Separate analyses of all four genes yield congruent phylogenies; however the 15 putative species of Dionda evaluated were never recovered as a monophyletic group when species from nine related genera were included in the analyses. Among the ingroup taxa, one well-supported and highly divergent clade is consistently recognized and consists of six recognized and three undescribed northern species currently recognized in the genus Dionda. These nine species inhabit present or past tributaries of the Rio Grande basin of northern Mexico and southern USA, and were recovered as a basal clade in all analyses. Another large, also strongly supported clade, consisting of seven genera, include five southern recognized species currently in the genus Dionda, forming the sister group to the Codoma clade. These five species comprise the "Southern Dionda clade" and inhabit headwaters of the Pánuco-Tamesí drainage and some adjacent coastal rivers in the Tampico Embayment. The consistent and repeated identification of eight different clades recovered in most of the separate gene analyses strongly supports a division of the non-natural genus Dionda. A new genus, Tampichthys, is proposed for the clade of species endemic to east-central Mexico and formerly in Dionda. Tampichthys and the putative monotypic genus Codoma are more related to Mexican species of the genera Cyprinella and Notropis than to other species referred to Dionda sensu stricto.     

Phylogeny of Impatiens (Balsaminaceae): integrating molecular and morphological evidence into a new classification

Impatiens L. is one of the largest angiosperm genera, containing over 1000 species, and is notorious for its taxonomic difficulty. Here, we present, to our knowledge, the most comprehensive phylogenetic analysis of the genus to date based on a total evidence approach. Forty‐six morphological characters, mainly obtained from our own investigations, are combined with sequence data from three genetic regions, including nuclear ribosomal ITS and plastid atpB‐rbcL and trnL‐F. We include 150 Impatiens species representing all clades recovered by previous phylogenetic analyses as well as three outgroups. Maximum‐parsimony and Bayesian inference methods were used to infer phylogenetic relationships. Our analyses concur with previous studies, but in most cases provide stronger support. Impatiens splits into two major clades. For the first time, we report that species with three‐colpate pollen and four carpels form a monophyletic group (clade I). Within clade II, seven well‐supported subclades are recognized. Within this phylogenetic framework, character evolution is reconstructed, and diagnostic morphological characters for different clades and subclades are identified and discussed. Based on both morphological and molecular evidence, a new classification outline is presented, in which Impatiens is divided into two subgenera, subgen. Clavicarpa and subgen. Impatiens; the latter is further subdivided into seven sections.     

Phylogeny of Malpighiaceae: evidence from chloroplast ndhF and trnl-F nucleotide sequences

The Malpighiaceae are a family of ～1250 species of predominantly New World tropical flowering plants. Infrafamilial classification has long been based on fruit characters. Phylogenetic analyses of chloroplast DNA nucleotide sequences were analyzed to help resolve the phylogeny of Malpighiaceae. A total of 79 species, representing 58 of the 65 currently recognized genera, were studied. The 3' region of the gene ndhF was sequenced for 77 species and the noncoding intergenic spacer region trnL-F was sequenced for 65 species; both sequences were obtained for the outgroup, Humiria (Humiriaceae). Phylogenetic relationships inferred from these data sets are largely congruent with one another and with results from combined analyses. The family is divided into two major clades, recognized here as the subfamilies Byrsonimoideae (New World only) and Malpighioideae (New World and Old World). Niedenzu's tribes are all polyphyletic, suggesting extensive convergence on similar fruit types; only de Jussieu's tribe Gaudichaudieae and Anderson's tribes Acmanthereae and Galphimieae are monophyletic. Fleshy fruits evolved three times in the family and bristly fruits at least three times. Among the wing-fruited vines, which constitute more than half the diversity in the family, genera with dorsal-winged samaras are fairly well resolved, while the resolution of taxa with lateral-winged samaras is poor. The trees suggest a shift from radially symmetrical pollen arrangement to globally symmetrical pollen at the base of one of the clades within the Malpighioideae. The Old World taxa fall into at least six and as many as nine clades.     

Plastomic data shed new light on the phylogeny,biogeography, and character evolution of the family Crassulaceae

Crassulaceae is a mid-sized family of angiosperms, most species of which are herbaceous succulents, usually with 5-merous flowers and one or two whorls of stamens. Although previous phylogenetic studies revealed seven major “clades” in Crassulaceae and greatly improved our understanding of the evolutionary history of the family, relationships among major clades are still contentious. In addition, the biogeographic origin and evolution of important morphological characters delimiting infrafamilial taxa have not been subject to formal biogeographic and character evolution analyses based on a well-supported phylogeny backbone. In this study, we used plastomic data of 52 species, representing all major clades revealed in previous studies to reconstruct a robust phylogeny of Crassulaceae, based on which we unraveled the spatiotemporal framework of diversification of the family. We found that the family may originate in southern Africa and then dispersed to the Mediterranean, from there to eastern Asia, Macaronesia, and North America. The crown age of Crassulaceae was dated at ca. 63.93 million years ago, shortly after the Cretaceous–Paleogene (K-Pg) boundary. We also traced the evolution of six important morphological characters previously used to delimit infrafamilial taxa and demonstrated widespread parallel and convergent evolution of both vegetative (life form and phyllotaxis) and floral characters (number of stamen whorls, petals free or fused, and flower merism). Our results provide a robust backbone phylogeny as a foundation for further investigations, and also some important new insights into biogeography and evolution of the family Crassulaceae.     

Bat Systematics in the Light of Unconstrained Analyses of a Comprehensive Molecular Supermatrix

Bats (Chiroptera) represent the largest diversification of extant mammals after rodents. Here we report the results of a large-scale phylogeny of bats based on unconstrained searches for a data matrix of 804 non-chimeric, taxonomically updated bat terminals (796 species represented by a single terminal plus three species represented by ≥2 genetically distinct subspecies), able to preliminary test the systematics of most groups simultaneously. We used nine nuclear and mitochondrial DNA sequence markers fragmentary represented for ingroups (c. 90% and 64% of extant diversity at genus and species level, respectively) and 20 diverse placental outgroups. Maximum Likelihood and Parsimony analyses applied to the concatenated dataset yielded a highly resolved, variously supported phylogeny that recovered the majority of currently recognized clades at all levels of the chiropteran tree. Calibration points based on 44 key fossils allowed the Bayesian dating of bat origins at c. 4 my after the K-Pg boundary, and the determination of stem and crown ages of intraordinal clades. As expected, bats appeared nested in Laurasiatheria and split into Yinpterochiroptera and Yangochiroptera. More remarkable, all polytypic, currently recognized families were monophyletic, including Miniopteridae, Cistugidae, and Rhinonycteridae, as well as most polytypic genera with few expected exceptions (e.g., Hipposideros). The controversial Myzopodidae appeared in a novel position as sister of Emballonuroidea―a result with interesting biogeographic implications. Most recently recognized subfamilies, genera, and species groups were supported or only minor adjustments to the current taxonomy would be required, except Molossidae, which should be revised thoroughly. In light of our analysis, current bat systematics is strongly supported at all levels; the emergent perception of a strong biogeographic imprint on many recovered bat clades is emphasized.     

From a comb to a tree: phylogenetic relationships of the comb-footed spiders (Araneae, Theridiidae) inferred from nuclear and mitochondrial genes

The family Theridiidae is one of the most diverse assemblages of spiders, from both a morphological and ecological point of view. The family includes some of the very few cases of sociality reported in spiders, in addition to bizarre foraging behaviors such as kleptoparasitism and araneophagy, and highly diverse web architecture. Theridiids are one of the seven largest families in the Araneae, with about 2200 species described. However, this species diversity is currently grouped in half the number of genera described for other spider families of similar species richness. Recent cladistic analyses of morphological data have provided an undeniable advance in identifying the closest relatives of the theridiids as well as establishing the family's monophyly. Nevertheless, the comb-footed spiders remain an assemblage of poorly defined genera, among which hypothesized relationships have yet to be examined thoroughly. Providing a robust cladistic structure for the Theridiidae is an essential step towards the clarification of the taxonomy of the group and the interpretation of the evolution of the diverse traits found in the family. Here we present results of a molecular phylogenetic analysis of a broad taxonomic sample of the family (40 taxa in 33 of the 79 currently recognized genera) and representatives of nine additional araneoid families, using approximately 2.5kb corresponding to fragments of three nuclear genes (Histone 3, 18SrDNA, and 28SrDNA) and two mitochondrial genes (16SrDNA and CoI). Several methods for incorporating indel information into the phylogenetic analysis are explored, and partition support for the different clades and sensitivity of the results to different assumptions of the analysis are examined as well. Our results marginally support theridiid monophyly, although the phylogenetic structure of the outgroup is unstable and largely contradicts current phylogenetic hypotheses based on morphological data. Several groups of theridiids receive strong support in most of the analyses: latrodectines, argyrodines, hadrotarsines, a revised version of spintharines and two clades including all theridiids without trace of a colulus and those without colular setae. However, the interrelationships of these clades are sensitive to data perturbations and changes in the analysis assumptions.     

Contrasting Phylogenetic and Diversity Patterns in Octodontoid Rodents and a New Definition of the Family Abrocomidae

Octodontoidea is the most species-rich clade among hystricomorph rodents. Based on a combined parsimony analysis of morphological and molecular data of extinct and extant species, we analyze the history of South American octodontoids and propose ages of divergence older than interpreted so far. Early Abrocomidae are recognized for the first time, and a new definition of the family is provided. Traditionally accepted fossil-based times of origin for the southern clades are reinterpreted as later stages of differentiation markedly uncoupled from the origin, differentiation implying specializations for open environments as shown in a morphospace of skull variation. Origin of crown groups is also strongly uncoupled from origin of clades as a consequence of extinction of deep lineages. In the resulting diversity pattern of modern southern clades of octodontoids, the combination of greater disparity, less content of evolutionary history, and lower taxonomic diversity, compared to their northern counterparts, appears at first counterintuitive. We propose that primary components of diversity derived from evolutionary transformation or anagenesis, on the one hand, and from cladogenesis and extinction, on the other, should not be considered associated, or at least not necessarily. Certain patterns of relationships between these distinct components could be driven by environmental dynamics. Like environments, octodontoid diversity would have been more stable in northern South America, whereas in the south, both strong adaptive change and extinction would have been triggered by emerging derived environments.     

Phylogeny of the Gadidae (sensu Svetovidov, 1948) based on their morphology and two mitochondrial genes

Although Codfishes are probably one of the most studied groups of all teleost fishes worldwide owing to their great importance to fisheries, their phylogeny and classification are still far from being firmly established. In this study, we present phylogenetic relationships of 19 out of 22 genera traditionally included in the Gadidae based on the analysis of entire cytochrome b and partial cytochrome oxidase I genes (1530 bp). Maximum Parsimony, Maximum Likelihood, and Bayesian analyses all recovered five main clades that correspond to traditionally recognized groupings within Gadoids. The same clades were recovered with MP analysis based on 30 morphological characters (collected from the literature). Given these findings, we propose a revised provisional classification of Gadoids: one suborder Gadoidei containing two families, the Merlucciidae (1 genus) and the Gadidae (21 genera) distributed into four subfamilies: the Gadinae (12 genera), the Lotinae (3 genera), the Gaidropsarinae (3 genera), and the Phycinae (3 genera). Lastly, nuclear inserts of mitochondrial DNA (Numts) were identified in two species, i.e., Gadiculus argenteus and Melanogrammus aeglefinus.     

Traditional taxonomic groupings mask evolutionary history: a molecular phylogeny and new classification of the chromodorid nudibranchs

Chromodorid nudibranchs (16 genera, 300+ species) are beautiful, brightly colored sea slugs found primarily in tropical coral reef habitats and subtropical coastal waters. The chromodorids are the most speciose family of opisthobranchs and one of the most diverse heterobranch clades. Chromodorids have the potential to be a model group with which to study diversification, color pattern evolution, are important source organisms in natural products chemistry and represent a stunning and widely compelling example of marine biodiversity. Here, we present the most complete molecular phylogeny of the chromodorid nudibranchs to date, with a broad sample of 244 specimens (142 new), representing 157 (106 new) chromodorid species, four actinocylcid species and four additional dorid species utilizing two mitochondrial markers (16s and COI). We confirmed the monophyly of the Chromodorididae and its sister group relationship with the Actinocyclidae. We were also able to, for the first time, test generic monophyly by including more than one member of all 14 of the non-monotypic chromodorid genera. Every one of these 14 traditional chromodorid genera are either non-monophyletic, or render another genus paraphyletic. Additionally, both the monotypic genera Verconia and Diversidoris are nested within clades. Based on data shown here, there are three individual species and five clades limited to the eastern Pacific and Atlantic Oceans (or just one of these ocean regions), while the majority of chromodorid clades and species are strictly Indo-Pacific in distribution. We present a new classification of the chromodorid nudibranchs. We use molecular data to untangle evolutionary relationships and retain a historical connection to traditional systematics by using generic names attached to type species as clade names.     

39 Phylogeny of aulacoseira (bacillariophyta)

Ochromonas sensu lato is the largest genus in the Chrysophyceae, containing over 100 names. Ochromonas species are biflagellate, naked, plastid-bearing single cells, distinguished from loricate, scaled, colonial and colorless genera. Most, if not all, species of Ochromonas are mixotrophic, i.e., they photosynthesize but they also engulf bacteria and other small prey. Preliminary evidence from SSU rRNA sequences show that Ochromonas is a polyphyletic genus. Ochromonas tuberculata is the most distinct from all other Ochromonas species. The other Ochromonas species (examined thus far) are scattered in three clades. For example, O. danica and O. sphaerocystis are sister to Poterioochromonas stipitata and P. malhamensis . Four additional species (identified by light microscopy as O. elegans Doflein, O. globosa Skuja, O. ovalis Dolfein, O. sociabilis Pringheim ) have SSU rRNA sequences identical to P. malhamensis . Of these, only O. sociabilis has been transferred to Poterioochromonas . Thus, at least some species may be synonymous with others. Two clades of marine species are also known, one containing coastal species and the other containing open ocean species. A number of genera (some also polyphyletic) are interspersed amongst the Ochromonas species (e.g., Chrysolepidomonas, Chrysonephele, Chrysoxys, Cyclonexis, Dinobryon, Epipyxis, Uroglena, Uroglenopsis ). The goal of this research (just beginning) is to establish a monophyletic Ochromonas , probably by assigning some species to other genera (existing or new). One major problem is that the type species, O. triangulata Vysotskii , hasn't been observed in over 100 years, and it is unclear which of several clades of Ochromonas contains the type. Results will be discussed.     

Densely sampled phylogenetic analyses of the Lesser Short-toed Lark (Alaudala rufescens) — Sand Lark (A. raytal) species complex (Aves,Passeriformes) reveal cryptic diversity

The taxonomy of the Lesser/Asian Short-toed Lark Alaudala rufescens–cheleensis complex has been debated for decades, mainly because of minor morphological differentiation among the taxa within the complex, and different interpretations of the geographical pattern of morphological characters among different authors. In addition, there have been few studies based on non-morphological traits. It has recently been suggested based on a molecular study of the lark family Alaudidae that the Sand Lark A. raytal is nested within this complex. We here analysed mitochondrial cytochrome b (cyt b) from 130 individuals across the range of this complex (hereafter called Alaudala rufescens–raytal complex), representing all except two of the 18 currently recognized subspecies. We also analysed 11 nuclear markers from a subsample of these individuals, representing all of the clades found in the cyt b tree. Five primary clades were recovered, which confirmed that A. raytal is nested within this complex. Divergence time estimates among these five clades ranged from 1.76 to 3.16 million years (my; 95% highest posterior density [HPD] 1.0–4.51 my) or 1.99–2.53 my (95% HPD 0.96–4.3 my) in different analyses. Only four of the currently recognized subspecies were recovered as monophyletic in the cyt b tree. Our results call for a taxonomic revision, and we tentatively suggest that at least four species should be recognized, although we stress the need for an approach integrating molecular, morphological and other data that are not yet available.     

The Phylogeny and Systematics of Blind Cambrian Ptychoparioid Trilobites

The paraphyletic trilobite suborder Ptychopariina includes a large proportion of Cambrian trilobite diversity and is probably ancestral to most groups of post-Cambrian trilobites. Resolution of the phylogenetic relationships within the group is therefore crucial to a better understanding of the initial radiation of trilobites. The recognition of approaches that can successfully resolve the relationships of ptychoparioid taxa is an important first step towards this aim. Cladistic analysis was used to determine relationships within the Cambrian ptychoparioid trilobite family Conocoryphidae, and to test claims that the family is polyphyletic. Ninety-seven characters were coded for 40 conocoryphid species and nine non-conocoryphids. The results indicate that the family consists of four distantly related clades. Three are recognized here as distinct families, including an extensively revised Conocoryphidae, and the families Holocephalidae and Atopidae. The fourth clade is referred to the subfamily Acontheinae (Corynexochida) as the new Tribe Hartshillini. Analysis of the disparity of these four clades shows that they are significantly less morphologically variable than the original polyphyletic taxon, demonstrating the possible effects of taxonomic error on macroevolutionary studies of morphological disparity.     

Phylogeny of the genus Merluccius based on mitochondrial and nuclear genes

Genus Merluccius is considered one of the most important groups within the Teleostei, and comprises 12 extant species distributed along the coasts of America, Europe and Africa, being its fisheries very important in these continents. Despite their noticeable economical importance for humans, to date the phylogeny of hakes has not been clearly established. In this study we used mitochondrial sequences (the ribosomal genes 12S rDNA and 16S rDNA, the coding gene cytochrome b and the control region) and the nuclear 5S rDNA conserved region in order to determine the phylogenetic and biogeographical relationships within the genus Merluccius. This is the first time that all the species of this genus recognized by the FAO are included in a phylogeny. Maximum Parsimony, Maximum Likelihood and Bayesian analyses of the mitochondrial sequences suggest that the geographical origin of the genus was the North Atlantic Ocean, and indicate that two main clades, early separated in the evolution, exist within the genus: one American (7 species) and one Euro-African (5 species). Among the American species, M. bilinearis seems to be the most ancient one, and the rise of the Panama Isthmus could act as a physical barrier leading to further processes of speciation. Within the Euro-African clade, successive events of geographical differentiation could explain the observed pattern of species distribution. Therefore, we propose both vicariant speciation and geographical dispersion as main mechanisms to explain the evolutionary history of the genus Merluccius.     

Molecular classification and phylogenetic relationships of selected edible Basidiomycetes species

Morphological identification of edible mushrooms can sometimes prove troublesome, because phenotypic variation in fungi can be affected by substrate and environmental factors. One of the most important problems for mushroom breeders is the lack of a systematic consensus tool to distinguish different species, which are sometimes morphologically identical. Basidiomycetes as one of the largest groups of edible mushrooms have become more important in recent times for their medicinal and nutritional properties. Partial rDNA sequences, including the Internal Transcribed Spacer I-5.8SrDNA-Internal Transcribed Spacer II, were used in this study for molecular identification and assessment of phylogenetic relationships between selected edible species of the Basidiomycetes. Phylogenetic trees showed five distinct clades; each clade belonging to a separate family group. The first clade included all the species belonging to the Pleurotaceae (Pleurotus spp.) family; similarly, the second, third, fourth, and fifth clades consist of species from the Agaricaceae (Agaricus sp.), Lyophllaceae (Hypsigygus sp.), Marasmiaceae (Lentinula edodes sp.) and Physalacriaceae (Flammulina velutipes sp.) families, respectively. Moreover, different species of each family were clearly placed in a distinct sub-cluster and a total of 13 species were taken for analysis. Species differentiation was re-confirmed by AMOVA analysis (among the populations: 99.67%; within: 0.33%), nucleotide divergence, haplotyping and P value. Polymorphism occurred throughout the ITS regions due to insertion-deletion and point mutations, and can be clearly differentiated within the families as well as genera. Moreover, this study proves that the sequence of the ITS region is a superior molecular DNA barcode for taxonomic identification of Basidiomycetes.     

Morphology disentangles the systematics of a ubiquitous but elusive meiofaunal group (Kinorhyncha: Pycnophyidae)

Kinorhyncha is a group of benthic, microscopic animals distributed worldwide in marine sediments. The phylum is divided into two classes, Cyclorhagida and Allomalorhagida, congruent with the two major clades recovered in recent phylogenetic analyses. Allomalorhagida accommodates more than one‐third of the described species, most of them assigned to the family Pycnophyidae. All previous phylogenetic analyses of the phylum recovered the two genera within Pycnophyidae, Pycnophyes and Kinorhynchus, as paraphyletic and polyphyletic. A major problem in these studies was the lack of molecular data of most pycnophyids, due to the limited and highly localized distribution of most species, often in the Arctic and the deep‐sea. We here overcame the problem by adding a morphological partition with data for 79 Pycnophyidae species, 15 of them also represented by molecular data. Model‐based analyses yielded seven clades, which each was supported by several morphological apomorphies. Accordingly, Kinorhynchus is synonymized with Pycnophyes and six new genera are described for the remaining recovered clades: Leiocanthus gen. nov., Cristaphyes gen. nov., Higginsium gen. nov., Krakenella gen. nov., Setaphyes gen. nov. and Fujuriphyes gen. nov.     

The beetle tree of life reveals that Coleoptera survived end‐Permian mass extinction to diversify during the Cretaceous terrestrial revolution

Here we present a phylogeny of beetles (Insecta: Coleoptera) based on DNA sequence data from eight nuclear genes, including six single‐copy nuclear protein‐coding genes, for 367 species representing 172 of 183 extant families. Our results refine existing knowledge of relationships among major groups of beetles. Strepsiptera was confirmed as sister to Coleoptera and each of the suborders of Coleoptera was recovered as monophyletic. Interrelationships among the suborders, namely Polyphaga (Adephaga (Archostemata, Myxophaga)), in our study differ from previous studies. Adephaga comprised two clades corresponding to Hydradephaga and Geadephaga. The series and superfamilies of Polyphaga were mostly monophyletic. The traditional Cucujoidea were recovered in three distantly related clades. Lymexyloidea was recovered within Tenebrionoidea. Several of the series and superfamilies of Polyphaga received moderate to maximal clade support in most analyses, for example Buprestoidea, Chrysomeloidea, Coccinelloidea, Cucujiformia, Curculionoidea, Dascilloidea, Elateroidea, Histeroidea and Hydrophiloidea. However, many of the relationships within Polyphaga lacked compatible resolution under maximum‐likelihood and Bayesian inference, and/or lacked consistently strong nodal support. Overall, we recovered slightly younger estimated divergence times than previous studies for most groups of beetles. The ordinal split between Coleoptera and Strepsiptera was estimated to have occurred in the Early Permian. Crown Coleoptera appeared in the Late Permian, and only one or two lineages survived the end‐Permian mass extinction, with stem group representatives of all four suborders appearing by the end of the Triassic. The basal split in Polyphaga was estimated to have occurred in the Triassic, with the stem groups of most series and superfamilies originating during the Triassic or Jurassic. Most extant families of beetles were estimated to have Cretaceous origins. Overall, Coleoptera experienced an increase in diversification rate compared to the rest of Neuropteroidea. Furthermore, 10 family‐level clades, all in suborder Polyphaga, were identified as having experienced significant increases in diversification rate. These include most beetle species with phytophagous habits, but also several groups not typically or primarily associated with plants. Most of these groups originated in the Cretaceous, which is also when a majority of the most species‐rich beetle families first appeared. An additional 12 clades showed evidence for significant decreases in diversification rate. These clades are species‐poor in the Modern fauna, but collectively exhibit diverse trophic habits. The apparent success of beetles, as measured by species numbers, may result from their associations with widespread and diverse substrates – especially plants, but also including fungi, wood and leaf litter – but what facilitated these associations in the first place or has allowed these associations to flourish likely varies within and between lineages. Our results provide a uniquely well‐resolved temporal and phylogenetic framework for studying patterns of innovation and diversification in Coleoptera, and a foundation for further sampling and resolution of the beetle tree of life.