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Previous phylogenetic analyses indicated that Polygonoideae, the largest subfamily in the Polygonaceae, is monophyletic. Phylogenetic relationships within the Polygonoideae have been substantially controversial. We collected 160 samples representing all currently recognized tribes for a more comprehensive phylogenetic analysis of the subfamily. Here, we reconstructed phylogenetic relationships of the Polygonoideae, inferred ancestral character states, and estimated the divergence time with a dense taxon sampling. This study corroborated and expanded previous results regarding the phylogenetic relationships of the Polygonoideae clade, and resolved the phylogenetic status of some controversial taxa by integrating molecular and morphological evidence. Phylogenetic analyses based on the complete plastomes suggested strong support for six primary clades that correspond to the most recent circumscription of tribes: Polygoneae, Rumiceae, Calligoneae, Pteroxygoneae, Fagopyreae, and Persicarieae. In addition, we provided further morphological data and assessed characters that supported different clades. The 3‐colpate pollen, 5‐parted perianth, and 3 styles were inferred to be the ancestral states of Polygonoideae. Divergence time estimation revealed that Polygonoideae originated around the late Cretaceous, and diversification was concentrated in the Eocene and Miocene. Time estimation indicated that the rapid uplift of the Tibetan Plateau and the intensification of the Asian monsoons might be potential driving forces for the diversification of Polygonoideae. Overall, this study advances our understanding of the phylogeny and diversification of the Polygonoideae and highlights the adaptive evolution of the taxa. [ABSTRACT FROM AUTHOR]

The extant marine mussels which belong to the Mytiloidea are widespread species inhabiting mostly coastal waters, with some distributed in the deep sea. To clarify the classification systems and phylogenetic relationships range from genus to family level within Mytiloidea, new sequence was used in a phylogenetic analysis including all the available Mytiloidea mitochondrial genomes. In this study, the complete mitochondrial genome of Vignadula atrata is 15,624 bp in length and contains 12 protein-coding genes (PCGs, atp8 is absent), two ribosomal RNA genes, and 22 transfer RNA genes. Phylogenetic analysis based on 12 PCGs showed that it has a close relationship to Bathymodiolus. The analysis of gene rearrangements in the Pteriomorphia showed that the arrangements are highly variable across species, novel gene rearrangements were found within Mytiloidea. The V. atrata mitogenome was provided in detail, with notes on the sequence and a key to the species of Vignadula. This study provides a perspective on the taxonomic histories of the marine mussels and refines the unclear relationship between the origin and evolution of species in Mytiloidea within Bivalvia. [ABSTRACT FROM AUTHOR]

The mitochondrial (mt) genome is an important tool when studying the evolution of metazoan animals. The oyster family Gryphaeidae, together with Ostreidae, is one of the two extant taxa of superfamily Ostreoidea. Up until now, the available mitochondrial genomes of oysters were all limited to family Ostreidae. In the present study, the first complete mtDNA of family Gryphaeidae represented by Hyotissa hyotis was sequenced and compared with other available ostreoid mtDNA. The mtDNA of H. hyotis is 22,185 bp in length, encoding 13 protein-coding-genes (PCGs), two ribosomal RNA (rRNA) and 23 transfer RNA (tRNA) genes. Within all the intergenic regions that range from 2 to 1528 bp, two large non-coding regions were identified. The first large non-coding region, located between Cox1 and trnA, contains 1528 nucleotides, while the second one is 1191 bp in length and positioned between Cytb and Nad2. The nucleotide composition of the whole mtDNA is A + T biased, accounting for 59.2%, with a negative AT skew value of −0.20 and a positive GC skew value of 0.33. In contrast to the mtDNA of Ostreidae, neither the split of rrnL nor rrnS was detected in that of H. hyotis. The duplication of trnW of H. hyotis was also discovered for the first time within Ostreoidea. The gene order of H. hyotis is quite different from those of ostreids, indicating extensive rearrangements within superfamily Ostreoidea. The reconstructed phylogeny supported H. hyotis as sister to Ostreidae, with the latter clade formed by Ostrea + (Saccostrea + Crassostrea). This study could provide important information for further understanding the mitochondrial evolution of oysters. [ABSTRACT FROM AUTHOR]

Situated at the junction of three continents, Europe, Asia and Africa, the Eastern Mediterranean is an ideal region to study the effects of palaeogeography, ecology and long human presence on animal evolution. Laudakia stellio (Squamata: Agamidae) is found across this region and offers an excellent opportunity for such studies. The high morphological variation across their range suggests that these lizards might represent a species complex. This is the first study exploring their evolutionary history, using molecular markers and individuals from all described subspecies. We employed the latest phylogenetic and species-delimitation methods to identify all distinct evolutionary lineages, their genetic variation and divergence times. The phenotypical diversity of L. stellio matches its genetic differentiation: almost all subspecies correspond to well-supported retrieved subclades and additional distinct lineages representing intermediate morphs have been retrieved. ' Laudakia stellio ' represents three distinct evolutionary entities that diverged during the Plio-Pleistocene transition, which we propose as distinct species. One includes Greek and Turkish populations, as well as cryptic Anatolian lineages. The second comprises all other Near East populations and the third is endemic to Cyprus. Our results indicate a role of humans in shaping present distribution patterns, and highlight the importance of the Aegean, Anatolia and the Levant as glacial refugia and diversity hotspots. [ABSTRACT FROM AUTHOR]

The distinction of the annual Sagina apetala and S. micropetala (= S. apetala subsp. erecta, S. filicaulis) is based mainly on the position of sepals in fruit and shape and colour of the sepals, but identification of the two species is difficult. A molecular phylogeny of material identified as S. apetala and S. micropetala as well as other species of the genus using two nuclear and two plastid markers showed that there exist two lineages that are sister to each other and can be unambiguously distinguished molecularly. Although many of the morphological characters used in the literature proved useful in distinguishing these two lineages, sepal indumentum is the most reliable character to discriminate between them in Germany. Whereas S. micropetala usually has glabrous sepals, the sepals of S. apetala usually are glandular-pubescent. The chromosome number of 2n = 12 for S. micropetala, here determined for the first time, is identical to that of S. apetala, supporting the close relationship between the two species. Sagina apetala and S. micropetala are sister to S. maritima, an annual species from European coasts, which may imply a coastal origin of the two species. A brief review of the possible origin of other European ruderals from coastal relatives is provided. [ABSTRACT FROM AUTHOR]

Thismia is a genus of > 80 mycoheterotrophic species characterized by a peculiar appearance and complex floral morphology. A significant proportion of the species and morphological diversity of Thismia has only been uncovered in the past two decades, and new discoveries continue to be made. Given that many new data have recently become available, and the most comprehensive taxonomic revision of the genus from 1938 addresses less than half of the currently known species, previous hypotheses for species relationships and infrageneric taxonomic classification in Thismia was in need of review. Extensive molecular phylogenetic studies of Thismia at the genus level have never been presented. We investigate the phylogenetic relationships of 41 species (and one variety) of Thismia from the Old World. Our study comprises 68 specimens (for 28 of which the data were newly generated), including outgroup taxa broadly representing Thismiaceae (= Burmanniaceae p.p. sensu APG IV, 2016), and is based on two nuclear and one mitochondrial marker. We use maximum likelihood and Bayesian inference to infer relationships among the taxa. We also constructed a morphological dataset of 12 mostly floral characters, comparing these characters to hypotheses based on molecular evidence to identify putative synapomorphies for major clades and to discuss hypotheses regarding the evolution of structural traits in the genus. Our analyses indicate that the majority of currently accepted infrageneric taxa of Thismia are polyphyletic. We find support for the monophyly of the Old World group, in which we recognize five well-supported lineages (clades); the only New World species studied appears to be related to the Neotropical genus Tiputinia. Ancestral state reconstructions demonstrate that the evolution of most morphological characters was homoplastic, but we identify characters that provide each of the five clades of Old World Thismia with a unique morphological description. The geographical distribution of the species under study is also shown to be consistent with the major clades. Our investigation provides a phylogenetic basis for the development of a novel sectional classification of Thismia reflecting morphological and geographical traits. [ABSTRACT FROM AUTHOR]

Molecular techniques are currently the leading tools for reconstructing phylogenetic relationships, but our understanding of ancestral, plesiomorphic and apomorphic characters requires the study of the morphology of extant forms for testing these phylogenies and for reconstructing character evolution. This review highlights the potential of soft body morphology for inferring the evolution and phylogeny of the lophotrochozoan phylum Bryozoa. This colonial taxon comprises aquatic coelomate filter‐feeders that dominate many benthic communities, both marine and freshwater. Despite having a similar bauplan, bryozoans are morphologically highly diverse and are represented by three major taxa: Phylactolaemata, Stenolaemata and Gymnolaemata. Recent molecular studies resulted in a comprehensive phylogenetic tree with the Phylactolaemata sister to the remaining two taxa, and Stenolaemata (Cyclostomata) sister to Gymnolaemata. We plotted data of soft tissue morphology onto this phylogeny in order to gain further insights into the origin of morphological novelties and character evolution in the phylum. All three larger clades have morphological apomorphies assignable to the latest molecular phylogeny. Stenolaemata (Cyclostomata) and Gymnolaemata were united as monophyletic Myolaemata because of the apomorphic myoepithelial and triradiate pharynx. One of the main evolutionary changes in bryozoans is a change from a body wall with two well‐developed muscular layers and numerous retractor muscles in Phylactolaemata to a body wall with few specialized muscles and few retractors in the remaining bryozoans. Such a shift probably pre‐dated a body wall calcification that evolved independently at least twice in Bryozoa and resulted in the evolution of various hydrostatic mechanisms for polypide protrusion. In Cyclostomata, body wall calcification was accompanied by a unique detachment of the peritoneum from the epidermis to form the hydrostatic membraneous sac. The digestive tract of the Myolaemata differs from the phylactolaemate condition by a distinct ciliated pylorus not present in phylactolaemates. All bryozoans have a mesodermal funiculus, which is duplicated in Gymnolaemata. A colonial system of integration (CSI) of additional, sometimes branching, funicular cords connecting neighbouring zooids via pores with pore‐cell complexes evolved at least twice in Gymnolaemata. The nervous system in all bryozoans is subepithelial and concentrated at the lophophoral base and the tentacles. Tentacular nerves emerge intertentacularly in Phylactolaemata whereas they partially emanate directly from the cerebral ganglion or the circum‐oral nerve ring in myolaemates. Overall, morphological evidence shows that ancestral forms were small, colonial coelomates with a muscular body wall and a U‐shaped gut with ciliary tentacle crown, and were capable of asexual budding. Coloniality resulted in many novelties including the origin of zooidal polymorphism, an apomorphic landmark trait of the Myolaemata. [ABSTRACT FROM AUTHOR]

Riethia Kieffer, a genus of the non-biting midge subfamily Chironominae (Diptera: Chironomidae) is distributed in Australia, New Zealand, New Caledonia and South America. This austral distribution could be due to earth history (vicariance) or from Southern Hemisphere dispersal(s). We obtained samples from each area, most intensively from throughout Australia. We included putative sister genus Pseudochironomus Malloch, many genera from tribe Tanytarsini, enigmatic taxa in Chironomini and conventional outgroups from other subfamilies. We assembled a multilocus molecular dataset for four genetic regions from 107 individuals to reconstruct the first dated molecular phylogeny for the group. Four terminal clusters corresponded to unreared (thus unassociated) larvae. Monophyly was supported for 'core' Riethia , Pseudochironomus , putative tribe Pseudochironomini, tribe Tanytarsini (including enigmatic Nandeva Wiedenbrug, Reiss & Fittkau) and subfamily Chironominae. All species are monophyletic except for R. cinctipes Freeman, which includes R. neocaledonica Cranston. Riethia zeylandica Freeman, previously thought to be widespread in eastern Australia, now is a New Zealand endemic with Australian specimens allocated now to several regionally restricted species. The origin of Riethia was at 60.6 Ma ('core') or 52.1 Ma depending on the relationship of two South American species. Both dates are before the break-up of South America and Australia. Diversification within crown group Riethia started before the Cretaceous–Paleogene boundary, with subsequent separation at 52 Ma of an Australian 'clade I' from its sister 'clade II', which comprises Australian, New Zealand and New Caledonian species. Inferred dates for species origins of New Caledonia and New Zealand taxa imply transoceanic dispersals from eastern Australia. Western Australian species diverged during the mid to late Miocene from their eastern Australian sister taxa. This correlates with the onset of drying of Australia and the separation of mesic east from west by the formation of an arid proto-Nullarbor. Taken together, the inferred tempo of diversification in the group included both older ages reflecting earth history, yet with suggested recent intra-Pacific separations due to transoceanic dispersals. Several non-biting midges have exclusively austral (Southern Hemisphere) distributions, suggesting that their distribution and diversification was due to Mesozoic breakup of the megacontinent Gondwana. We estimated a dated phylogeny for Riethia (Kieffer) (Chironomidae), supporting an underlying earth history explanation for its austral distribution. However, dates involving New Zealand, New Caledonia and South America are too young and more likely arise from transoceanic dispersal. Miocene onset of aridification likely influenced two east–west disjunctions in Australia. Diversification in this clade evidently is more complex and nuanced than naively 'Gondwanan'. [ABSTRACT FROM AUTHOR]

Premise: Despite intensive research, the pathways and driving forces behind the evolution of derived woodiness on oceanic islands remain obscure. The genus Daucus comprises mostly herbs (therophytes, hemicryptophytes) with few rosette treelets (chamaephytes) endemic to various Macaronesian archipelagos, suggesting their independent evolution. To elucidate the evolutionary pathways to derived woodiness, we examined phylogenetic relationships and the habit and secondary xylem evolution in Daucus and related taxa. Methods: Sixty taxa were surveyed for molecular markers, life history, and habit traits. Twenty‐one species were considered for wood anatomical characters. A dated phylogeny was estimated using Bayesian methods. The evolution of selected traits was reconstructed using parsimony and maximum likelihood. Results: Daucus dispersed independently to the Canary Islands (and subsequently to Madeira), Cape Verde, and the Azores in the late Miocene and Pleistocene. Life span, reproductive strategy, and life form were highly homoplastic; the ancestor of Daucus was probably a monocarpic, biennial hemicryptophyte. Rosette treelets evolved independently in the Canarian‐Madeiran lineage and in Cape Verde, the latter within the last 0.13 Myr. Treelets and hemicryptophytes did not differ in wood anatomy. Pervasive axial parenchyma in wood occurred more often in polycarpic rather than monocarpic species. Conclusions: Life span and life form in Daucus are evolutionarily labile and may change independently of wood anatomy, which is related to plant reproductive strategy rather than to life form. Insular woodiness may evolve rapidly (as demonstrated in D. bischoffii), and in Daucus, it does not seem to be an adaptation to lower the risk of xylem embolism. [ABSTRACT FROM AUTHOR]

Our ability to correctly reconstruct a phylogenetic tree is strongly affected by both systematic errors and the amount of phylogenetic signal in the data. Current approaches to tackle tree reconstruction artifacts, such as the use of parameter-rich models, do not translate readily to single-gene alignments. This, coupled with the limited amount of phylogenetic information contained in single-gene alignments, makes gene trees particularly difficult to reconstruct. Opsin phylogeny illustrates this problem clearly. Opsins are G-protein coupled receptors utilized in photoreceptive processes across Metazoa and their protein sequences are roughly 300 amino acids long. A number of incongruent opsin phylogenies have been published and opsin evolution remains poorly understood. Here, we present a novel approach, the canary sequence approach, to investigate and potentially circumvent errors in single-gene phylogenies. First, we demonstrate our approach using two well-understood cases of long-branch attraction in single-gene data sets, and simulations. After that, we apply our approach to a large collection of well-characterized opsins to clarify the relationships of the three main opsin subfamilies. [ABSTRACT FROM AUTHOR]

The eight‐eyed haplogyne spider family Plectreuridae Simon, 1893 is one of the oldest of spider families, currently comprising two genera (Kibramoa and Plectreurys), 30 extant species and one subspecies. Plectreuridae have not been rigorously examined since 1958, with only three new species added to Plectreurys. This study revisited a subset of taxa from the genus Kibramoa using a combined morphological and multilocus phylogenetic analysis. Species distribution modeling (SDM) was used to investigate the current and paleo distributional patterns of the genus Kibramoa throughout the biodiverse region of the California Floristic Province (CFP). A reexamination of genitalic morphology reflected cryptic species, yet multilocus Bayesian and maximum likelihood analyses of mitochondrial (COI, 16S) and nuclear (ITS1, 28S) markers consistently suggested several divergent lineages. A time‐calibrated phylogeny indicated that the most recent common ancestor of Kibramoa appeared in the Mid‐Miocene and continued to diversify throughout the Plio‐Pleistocene. Xerophilic Kibramoa, as inferred by SDM, had a much wider distribution during the Mid‐Holocene, when climate was at its warmest. This body of work uncovered novel findings regarding the evolution of plectreurids, provided the first phylogeny of the family, and demonstrated similar biogeographic patterns displayed in other CFP taxa. [ABSTRACT FROM AUTHOR]

Mitochondrial genes are placed on one molecule, which implies that they should carry consistent phylogenetic information. Following this advantage, we present a well-supported phylogeny based on mitochondrial genomes from almost 300 representatives of Passeriformes, the most numerous and differentiated Aves order. The analyses resolved the phylogenetic position of paraphyletic Basal and Transitional Oscines. Passerida occurred divided into two groups, one containing Paroidea and Sylvioidea, whereas the other, Passeroidea and Muscicapoidea. Analyses of mitogenomes showed four types of rearrangements including a duplicated control region (CR) with adjacent genes. Mapping the presence and absence of duplications onto the phylogenetic tree revealed that the duplication was the ancestral state for passerines and was maintained in early diverged lineages. Next, the duplication could be lost and occurred independently at least four times according to the most parsimonious scenario. In some lineages, two CR copies have been inherited from an ancient duplication and highly diverged, whereas in others, the second copy became similar to the first one due to concerted evolution. The second CR copies accumulated over twice as many substitutions as the first ones. However, the second CRs were not completely eliminated and were retained for a long time, which suggests that both regions can fulfill an important role in mitogenomes. Phylogenetic analyses based on CR sequences subjected to the complex evolution can produce tree topologies inconsistent with real evolutionary relationships between species. Passerines with two CRs showed a higher metabolic rate in relation to their body mass. [ABSTRACT FROM AUTHOR]

The subfamily Saprininae is a group of moderately large histerid beetles that exhibits remarkable morphological and biological diversity. Although all species are predaceous, feeding on larvae of flies and other arthropods, numerous ecologically diverse lineages appeared during the evolution of the group, including taxa adapted for life in sand. These psammophiles conquered the Earth's arid and sandy desert regions. They are endowed with profound morphological adaptations, and the beginning of their radiation largely coincides with the Palaeocene–Eocene Thermal Maximum, which constituted the peak of the long-term early Cenozoic global warming. Earth's temperature during that time was believed to be globally ~8 °C warmer than it is today, and the aridification played an important role in the desertification of the planet. Here, we present the first comprehensive phylogenetic analysis of Saprininae to date, based on 115 taxa of 37 (sub)genera, which represent all major Saprininae genera. Our analyses resulted in a well-resolved phylogeny of the group, partly congruent with earlier phylogenetic hypotheses. We find support for the monophyly of the Saprininae and four major clades within it. Ultra-psammophily has evolved at least three times independently, with convergent morphological features arising in different desert regions, as a response to similar selective pressures. [ABSTRACT FROM AUTHOR]

Graphical abstract Highlights • Triturus newts show a correlation between body build and aquatic lifestyle. • The phylogeny of this adaptive radiation is currently unresolved. • We obtain c. 6000 markers with target enrichment by sequence capture. • Distinct phylogenetic methods all support a single topology. • The species tree supports gradual evolution of more elongated and aquatic newts. Abstract Newts of the genus Triturus (marbled and crested newts) exhibit substantial variation in the number of trunk vertebrae (NTV) and a higher NTV corresponds to a longer annual aquatic period. Because the Triturus phylogeny has thwarted resolution to date, the evolutionary history of NTV, annual aquatic period, and their potential coevolution has remained unclear. To resolve the phylogeny of Triturus , we generated a c. 6000 transcriptome-derived marker data set using a custom target enrichment probe set, and conducted phylogenetic analyses using: (1) data concatenation with RAxML, (2) gene-tree summary with ASTRAL, and (3) species-tree estimation with SNAPP. All analyses produce the same, highly supported topology, despite cladogenesis having occurred over a short timeframe, resulting in short internal branch lengths. Our new phylogenetic hypothesis is consistent with the minimal number of inferred changes in NTV count necessary to explain the diversity in NTV observed today. Although a causal relationship between NTV, body form, and aquatic ecology has yet to be experimentally established, our phylogeny indicates that these features have evolved together, and suggest that they may underlie the adaptive radiation that characterizes Triturus. [ABSTRACT FROM AUTHOR]

The taxonomic history of the diatom genus Amphora is one of a broad early morphological concept resulting in the inclusion of a diversity of taxa, followed by an extended period of revision and refinement. The introduction of molecular systematics has increased the pace of revision and has largely resolved the relationships between the major lineages, indicating homoplasy in the evolution of amphoroid symmetry. Within the two largest monophyletic lineages, the genus Halamphora and the now taxonomically refined genus Amphora, the intrageneric morphological and ecological relationships have yet to be explored within a phylogenetic framework. Critical among this is whether the range of morphological features exhibited within these diverse genera are reflective of evolutionary groupings or, as with many previously studied amphoroid features, are nonhomologous when examined phylogenetically. Presented here is a four‐marker molecular phylogeny that includes 31 taxa from the genus Amphora and 77 taxa from the genus Halamphora collected from fresh, brackish, and salt waters from coastal and inland habitats of the United States and Japan. These phylogenies illustrate complex patterns in the evolution of frustule morphology and ecology within the genera and the implications of this on the taxonomy, classification, and organization of the genera are discussed. [ABSTRACT FROM AUTHOR]

Abstract: Here, we evaluate the so‐called Thorson's rule, which posits that direct‐development and larger eggs are favored toward the poles in marine organisms and whose validity been the subject of considerable debate in the literature, combining an expanded phenotypic dataset encompassing 60 species of benthic octopuses with a new molecular phylogeny. Phylogenetic reconstruction shows two clades: clade 1 including species of the families Eledonidae, Megaleledonidae, Bathypolypodidae, and Enteroctopodidae, and clade 2 including species of Octopodidae. Egg size, development mode, and all environmental variables exhibited phylogenetic signal, partly due to differences between the two clades: whereas most species in clade 1 inhabit cold and deep waters, exhibit large eggs and hatchling with holobenthic development, species from clade 2 inhabit tropical‐temperate and shallow waters, evolved small eggs, and generally exhibit merobenthic development. Phylogenetic regressions show that egg size exhibits a conspicuous latitudinal cline, and that both egg size and development mode vary with water temperature. Additionally, analyses suggest that egg size is constrained by body size in lineages with holobenthic development. Taken together, results suggest that the variation in egg size and development mode across benthic octopuses is adaptive and associated with water temperature, supporting Thorson's rule in these organisms. [ABSTRACT FROM AUTHOR]

Phylogenetic relationships among nine Turkish Orchis species were inferred from variation in the internal transcribed spacer and maturase Kinase regions. Foreign sequences were also retrieved from NCBI to increase interspecific sampling. The topology of ITS tree was broadly congruent to that of matK tree. The trees showed two major clades; the first one included species from Orchis and Neotinea subgenera and the second included species of Anacamptis subgenus. Phylogenetic separation of some species found in Neotinea and Anacamptis subgenera were previously reported, and the current study also indicated that moving these species into Neotinea and Anacamptis genera could be reasonable. [ABSTRACT FROM AUTHOR]

Aim To unravel the origins and to infer the processes of diversification in the low-vagility nemesiid trap-door spiders of the Balearic Islands. The specific goals were: (1) to determine whether nemesiid spiders colonized the islands by oversea dispersal, or whether they are the result of the fragmentation of a once continuous distribution by continental drift, and (2) to test whether the Balearic lineages have undergone local diversification processes. Locations Balearic Islands, Iberian Peninsula, Western Mediterranean. Methods Multilocus molecular phylogenetic inference using parsimony and model-based methods, and divergence time estimation with relaxed clocks and informed substitution rate priors, and biogeographical ancestral reconstruction inferred in a Bayesian framework. Results Phylogenetic analyses revealed the monophyly of the genera Iberesia and Nemesia. Four independent clades were recovered for the Balearic fauna. One of the clades included a formerly unknown species from Minorca. The Balearic clades split from their continental relatives in the early Tortonian, except for Iberesia brauni, which dates to the Messinian-Zanclean. The biogeographical reconstruction indicated that the Balearic fauna probably originated in the Betic region of the Iberian Peninsula. Main conclusions The presence of Nemesia on the Balearic Islands was explained by fragmentation of an ancestral distribution range that included the Betic region and the islands in the Early Tortonian. The arrival of Iberesia to the islands, however, was the result of a secondary range expansion that was facilitated by the emergence of land bridges with the continent during the Messinian salinity crisis (MSC). Similarly, the drops in the sea level that occurred during the MSC and subsequently in the Quaternary glacial cycles established land passages between Majorca and Minorca. [ABSTRACT FROM AUTHOR]

Prey spectrum and feeding process of the mixotrophic thecate dinoflagellate Fragilidium mexicanum strain Fm-LOHABE01 were examined using a culture isolated from Masan Bay, Korea in 2011 during a summer bloom of the toxic dinoflagellate Alexandrium pacificum . The novel 18S and 28S rDNA sequences for F . mexicanum were also used to explore inter-species relationships within the genus Fragilidium . The F. mexicanum fed on species belonging to four dinoflagellate genera (i.e., Alexandrium , Ceratium , Heterocapsa , and Scrippsiella ) when separately offered a variety of prey, including dinoflagellates, raphidophytes, cryptophytes, and a ciliate. In addition, F . mexicanum displayed different levels of feeding frequency for prey species of Alexandrium . While F . mexicanum consistently fed on A . catenella and A . pacificum , feeding on A . affine was rarely observed. The F . mexicanum ingested prey by direct engulfment through the sulcus, after capturing the prey by a tow filament. Phylogenetic analyses of 18S and 28S rDNA datasets demonstrated that Fragilidium sequences formed a monophyletic group with high statistical supports and diverged into four distinct clades. The F. mexicanum formed a separate clade with Fragilidium sp. EUSK D from Angola and Korean isolate of F. fissile with very strong supports. [ABSTRACT FROM AUTHOR]

We investigated the evolution of the male genitalia of species of Limnebius (Coleoptera, Hydraenidae). This genus is very homogeneous externally but characterized by highly diverse male genitalia, which are in some cases extraordinarily complex. We reconstructed a molecular phylogeny for 70 of the c. 150 known species of the genus with six fragments of mitochondrial and nuclear genes. We found two main lineages of Miocene origin, largely corresponding to the synonymized subgenera Bilimneus and Limnebius, which are here re-erected. Within the Holarctic Limnebius s.s. we found four well-supported lineages, although with poorly supported relationships between them: the L. piceus, L. gracilipes, L. parvulus and L. nitidus species groups. We describe the aedeagus and its different appendages in detail based on the study of 116 species, including serial histological sections to reconstruct the internal structure of seven of them. Using Bayesian methods we reconstructed the ancestral Limnebius as having small males ( c. 1.2 ± 0.5 mm), with a small aedeagus ( c. 0.4 ± 0.3 mm) with a free left paramere, probably an externally fused right paramere, and a possible additional appendage. The species of Bilimneus experienced a reduction in size and a simplification of their genitalia, without free parameres and with a very simple, homogenous structure. Within Limnebius s.s. several independent increases in male body and genital size took place, with a strong correlation as measured with independent contrasts. There was, however, no overall correlation between genital size and number of appendages, even though smaller genitalia tend to be less complex. [ABSTRACT FROM AUTHOR]

The Calopiidae Ponder, 1999 (Caenogastropoda: Truncatelloidea) are a family of aquatic microgastropods endemic to Australia. Of its four known species, three--Calopia minutissima, C. laseroni and C. imitata (all Ponder, 1999)--are broadly distributed, whereas C. burni Ponder, 1999 is restricted to southeastern Victoria. We used a concatenated dataset (1,261 positions), containing fragments of the mitochondrial genes COI and 16S, to generate the first molecular phylogeny of the family. Bayesian inference and maximum likelihood analyses of the combined dataset elucidate evolutionary relationships within the Calopiidae. Furthermore, C. imitata and C. burni were recovered as a strongly supported clade of negligible sequence divergence, so we view these two taxa as conspecific. Consequently, C. burni is synonymized herein with C. imitata, and a taxonomic reassessment of C. imitata is provided. A discriminant function analysis of shell dimensions suggests some morphological differences between populations of C. imitata, possibly expressing ecophenotypic variability. [ABSTRACT FROM AUTHOR]

Within the insect order Lepidoptera (moths and butterflies), the so-called nonditrysian superfamilies are mostly species-poor but highly divergent, offering numerous synapomorphies and strong morphological evidence for deep divergences. Uncertainties remain, however, and tests of the widely accepted morphological framework using other evidence are desirable. The goal of this paper is to test previous hypotheses of nonditrysian phylogeny against a data set consisting of 61 nonditrysian species plus 20 representative Ditrysia and eight outgroups ( Trichoptera), nearly all sequenced for 19 nuclear genes (up to 14 700 bp total). We compare our results in detail with those from previous studies of nonditrysians, and review the morphological evidence for and against each grouping The major conclusions are as follows. (i) There is very strong support for Lepidoptera minus Micropterigidae and Agathiphagidae, here termed Angiospermivora, but no definitive resolution of the position of Agathiphagidae, although support is strongest for alliance with Micropterigidae, consistent with another recent molecular study. (ii) There is very strong support for Glossata, which excludes Heterobathmiidae, but weak support for relationships among major homoneurous clades. Eriocraniidae diverge first, corroborating the morphological clade Coelolepida, but the morphological clades Myoglossata and Neolepidoptera are never monophyletic in the molecular trees; both are contradicted by strong support for Lophocoronoidea + Hepialoidea, the latter here including Mnesarchaeoidea syn.n. (iii) The surprising grouping of Acanthopteroctetidae + Neopseustidae, although weakly supported here, is consistent with another recent molecular study. (iv) Heteroneura is very strongly supported, as is a basal split of this clade into Nepticuloidea + Eulepidoptera. Relationships within Nepticuloidea accord closely with recent studies based on fewer genes but many more taxa. (v) Eulepidoptera are split into a very strongly supported clade consisting of Tischeriidae + Palaephatidae + Ditrysia, here termed Euheteroneura, and a moderately supported clade uniting Andesianidae with Adeloidea. (vi) Relationships within Adeloidea are strongly resolved and Tridentaformidae fam.n. is described for the heretofore problematic genus Tridentaforma Davis, which is strongly supported in an isolated position within the clade. (vii) Within Euheteroneura, the molecular evidence is conflicting with respect to the sister group to Ditrysia, but strongly supports paraphyly of Palaephatidae. We decline to change the classification, however, because of strong morphological evidence supporting palaephatid monophyly. (viii) We review the life histories and larval feeding habits of all nonditrysian families and assess the implications of our results for hypotheses about early lepidopteran phytophagy. The first host record for Neopseustidae, which needs confirmation, suggests that larvae of this family may be parasitoids. This published work has been registered in ZooBank: . [ABSTRACT FROM AUTHOR]

Phylogenetic inference is generally performed on the basis of multiple sequence alignments (MSA). Because errors in an alignment can lead to errors in tree estimation, there is a strong interest in identifying and removing unreliable parts of the alignment. In recent years several automated filtering approaches have been proposed, but despite their popularity, a systematic and comprehensive comparison of different alignment filtering methods on real data has been lacking. Here, we extend and apply recently introduced phylogenetic tests of alignment accuracy on a large number of gene families and contrast the performance of unfiltered versus filtered alignments in the context of single-gene phylogeny reconstruction. Based on multiple genome-wide empirical and simulated data sets, we show that the trees obtained from filtered MSAs are on average worse than those obtained from unfiltered MSAs. Furthermore, alignment filtering often leads to an increase in the proportion of well-supported branches that are actually wrong. We confirm that our findings hold for a wide range of parameters and methods. Although our results suggest that light filtering (up to 20% of alignment positions) has little impact on tree accuracy and may save some computation time, contrary to widespread practice, we do not generally recommend the use of current alignment filteringmethods for phylogenetic inference. By providing away to rigorously and systematically measure the impact of filtering on alignments, the methodology set forth here will guide the development of better filtering algorithms. [ABSTRACT FROM AUTHOR]

Diatoms possess a remarkable life cycle in which cell size decreases slowly during vegetative cell division and then increases rapidly via special expanding cells called ‘auxospores’, which are usually formed as a result of biparental sexual reproduction. However, auxospores are sometimes produced by single unpaired cells, i.e. uniparentally. We examined the nature of uniparental auxosporulation inSellaphoraand used a two-gene dataset to study phylogenetic relationships between uniparental and biparentalSellaphorademes and species; we tested whether uniparental reproduction has evolved once or repeatedly in the genus. In at least two of the uniparental demes auxosporulation occurred through autogamy (i.e. intra-tetrad mating within an undivided cell). Maximum likelihood phylogenies indicated four lineages of uniparentalSellaphoraand significance tests of alternative topologies, in which combinations of uniparentalSellaphorawere constrained to be monophyletic, coupled with likelihood reconstruction of ancestral character states, led to rejection of the hypothesis that uniparental auxosporulation evolved only once in the genus. Uniparentally reproducing lineages appear to arise not infrequently in diatoms but do not persist. Two small extranuclear bodies, apparently containing DNA and lying outside the chloroplast (one close to each pole of the cell), were revealed by DAPI staining. [ABSTRACT FROM PUBLISHER]

The role of natural selection in phenotypic evolution is central to evolutionary biology. Phenotypic evolution is affected by various factors other than adaptation, and recent focus has been placed on the effects of phylogenetic constraints and niche conservatism on phenotypic evolution. Here, we investigate the relationship between the shell morphology and habitat use of bradybaenid land snails of the genus Aegista and clarify the causes of the divergence in shell morphology among phylogenetically related species. The results of ancestral state reconstruction showed that arboreal species have evolved independently from ground-dwelling species at least four times. A significant association was found between shell shape and habitat use, despite the existence of a certain degree of phylogenetic constraint between these traits. A principal component analysis showed that arboreal species tend to have a relatively high-spired shell with a narrow umbilicus. By contrast, ground-dwelling species have a low-spired shell with a wide umbilicus. Although the latitude and elevation of the sampling locations showed no relationship with shell morphology, the geology of the sampling locations affected the shell size of arboreal species. The development of a well-balanced shell shape is one effective method for reducing the cost of locomotion under the force of gravity in each life habitat, resulting in the divergence in shell morphology and the independent evolution of morphologically similar species among different lineages. The present study suggests that ecological divergence is probably the cause of shell morphology divergence in land snails. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 114, 229-241. [ABSTRACT FROM AUTHOR]

Background: Rodents of the genus Mus represent one of the most valuable biological models for biomedical and evolutionary research. Out of the four currently recognized subgenera, Nannomys (African pygmy mice, including the smallest rodents in the world) comprises the only original African lineage. Species of this subgenus became important models for the study of sex determination in mammals and they are also hosts of potentially dangerous pathogens. Nannomys ancestors colonized Africa from Asia at the end of Miocene and Eastern Africa should be considered as the place of their first radiation. In sharp contrast with this fact and despite the biological importance of Nannomys, the specimens from Eastern Africa were obviously under-represented in previous studies and the phylogenetic and distributional patterns were thus incomplete. Results: We performed comprehensive genetic analysis of 657 individuals of Nannomys collected at approximately 300 localities across the whole sub-Saharan Africa. Phylogenetic reconstructions based on mitochondrial (CYTB) and nuclear (IRBP) genes identified five species groups and three monotypic ancestral lineages. We provide evidence for important cryptic diversity and we defined and mapped the distribution of 27 molecular operational taxonomic units (MOTUs) that may correspond to presumable species. Biogeographical reconstructions based on data spanning all of Africa modified the previous evolutionary scenarios. First divergences occurred in Eastern African mountains soon after the colonization of the continent and the remnants of these old divergences still occur there, represented by long basal branches of M. (previously Muriculus) imberbis and two undescribed species from Ethiopia and Malawi. The radiation in drier lowland habitats associated with the decrease of body size is much younger, occurred mainly in a single lineage (called the minutoides group, and especially within the species M. minutoides), and was probably linked to aridification and climatic fluctuations in middle Pliocene/Pleistocene Conclusions: We discovered very high cryptic diversity in African pygmy mice making the genus Mus one of the richest genera of African mammals. Our taxon sampling allowed reliable phylogenetic and biogeographic reconstructions that (together with detailed distributional data of individual MOTUs) provide a solid basis for further evolutionary, ecological and epidemiological studies of this important group of rodents [ABSTRACT FROM AUTHOR]

Recent molecular phylogenetic studies on Elymus have added to our understanding of the origination of Elymus species. However, evolutionary dynamics and speciation of most species in Elymus are unclear. Molecular phylogeny has demonstrated that reticulate evolution has occurred extensively in the genus, as an example, the largest subunit of RNA polymerase II ( rpb2) and phosphoenolpyruvate carboxylase ( pepC) data revealed two versions of the St genome, St1 and St2 contributing to speciation of E. caninus. Phylogenetic analyses of E. pendulinus uncovered additional genome-level complexity. Our data indicated that both chloroplast and nuclear gene introgression have occurred in the evolutionary process of E. pendulinus. Non-donor species genomes have been detected in several Elymus species, such as in allohexaploid E. repens ( StStStStHH), a Taeniatherum-like ( Ta genome in Triticeae) GBSSI sequence, Bromus- (Bromeae) and Panicum-like (Paniceae) ITS sequences have been detected. The chloroplast DNA data indicated that Pseudoroegneria is the maternal genome donor to Elymus species, but whether different Elymus species originated from different St donors remains an open question. The origin of the Y genome in Elymus is puzzling. It is clear that the Y genome is distinct from the St genome, but unclear on the relationships of Y to other genomes in Triticeae. Introgressive hybridization may be an important factor complicating the evolutionary history of the species in Elymus. The extent of introgression and its role in creating diversity in Elymus species should be the objective of further investigations. [ABSTRACT FROM AUTHOR]

Highlights: [•] A highly resolved phylogeny of the palm subtribe Ptychospermatinae is presented. [•] The subtribe is supported as a clade, but some genera are clearly not monophyletic. [•] The phylogeny was used to optimize the highly variable character stamen number. [•] No obvious pattern was detected in the evolution of stamen number. [•] Our study raises questions about the adaptive significance of this character in palms. [ABSTRACT FROM AUTHOR]

Highlights: [•] The first study of arctic species of Pedicularis in a molecular phylogenetic context. [•] Arctic Pedicularis evolved 12–14 times independently. [•] Most arctic Pedicularis have high mountain origin. [•] The arctic taxa show considerable niche conservatism with respect to soil moisture. [•] Morphological traits of arctic Pedicularis show a non-uniform pattern of evolution. [ABSTRACT FROM AUTHOR]

We reconstructed the phylogeny of representatives from nine genera and three families of the Cymbellales using two nuclear and three chloroplast genes. After rooting with Anomoeoneis, Placoneis was found as sister to a clade composed of Cymbella, Cymbopleura, Encyonema, Gomphonema, and Gomphoneis. The latter group was divided into lineages with mainly heteropolar and dorsiventral valve symmetry. The data and chloroplast morphology also supported a close relationship between Geissleria decussis and Placoneis. Expectedly, the sequenced genes exhibited substantial across-site rate variation (ASRV) that prompted us to assess the stability of the inferred relationships in the face of different approaches for modelling ASRV. While the overall topology remained stable across analyses, relationships between Cymbella and Cymbopleura and within one clade of Gomphonema varied dependent on the employed model. In some cases a strongly supported relationship in one analysis was not recovered by another that differed solely in how the data were partitioned. These topological fluctuations appeared in areas of the tree with the least balanced taxon sampling, and they altered the outcomes of phylogenetic hypotheses tests of monophyly. Assessing how different models for ASRV affect tree topology and clade support values, therefore, seems important in cases of sparse or unbalanced taxon sampling or when assessing the phylogenetic affinity of previously unsampled taxa when lineage-specific biases in base composition or evolutionary rate are more difficult to detect. [ABSTRACT FROM AUTHOR]

Highlights: [•] First comprehensive molecular phylogeny of Sparassidae and Eusparassus. [•] RTA-clade and Sparassidae were monophyletic, but not so “Laterigradae” and Dionycha. [•] Major Sparassidae subfamilies recovered monophyletic. [•] Eusparassinae were polyphyletic, with Eusparassus out of the “African Clade”. [•] Sparassidae and Eusparassus originated 186 and 70 million years ago respectively. [ABSTRACT FROM AUTHOR]

Highlights: [•] First molecular phylogenetic study of the family Harpagophoridae. [•] Genus Thyropygus was recovered as monophyletic under all analyses. [•] Gonopodal characters are typically suitable for classification of harpagophorids. [•] Harpagophorid millipedes have a high degree of endemicity: limited natural dispersal. [Copyright &y& Elsevier]

Highlights: [•] The first complete species-level phylogeny of Icteridae is presented. [•] Results from mitochondrial and nuclear loci were largely congruent. [•] Relationships among 4 major lineages of blackbirds were resolved robustly. [•] A new monotypic genus, Anumara, is described for the former Curaeus forbesi. [Copyright &y& Elsevier]

Highlights: [•] Our data does not support the monophyly of the family Ctenizidae. [•] The family has an ancient origin and long history in the Mediterranean region. [•] We demonstrate the vicariant origin of the amphiatlantic distribution of Ummidia. [•] The dynamic geology of the Mediterranean drove diversification of local genera. [•] Deep divergences support Cteniza and Cyrtocarenum as independent lineages. [ABSTRACT FROM AUTHOR]

Highlights: [•] We reviewed the molecular approaches used to characterize dermatophyte species. [•] Dermatophytes taxonomy changed based on phylogenetic analyses of the ITS region. [•] Micro-satellite and sequence analyses of the NTS region of rDNA typed dermatophytes. [•] Microsporum and Trichophyton species have a recent radiation. [ABSTRACT FROM AUTHOR]

The taxonomic status of two southern African coastal pipefish species, Syngnathus temminckii and Syngnathus watermeyeri, was investigated using a combination of morphological and genetic data. Morphological data showed that S. temminckii is distinct from the broadly distributed European pipefish Syngnathus acus, and a molecular phylogeny reconstructed using mitochondrial DNA recovered S. temminckii and S. watermeyeri as sister taxa. The southern African species share an evolutionary origin with north-eastern Atlantic Ocean and Mediterranean Sea species, including S. acus. These data support the existence of a distinct southern African clade of Syngnathus pipefishes that has diverged in situ to form the two species present in the region today. [ABSTRACT FROM AUTHOR]

The family Aplodontiidae contains a single, monotypic extant genus, Aplodontia (mountain beaver), which was first described by Rafinesque in 1817. Phylogenetic studies have shown that it is the sister lineage to squirrels. Aplodontia rufa is endemic to the Pacific Northwest and ranges from central California to British Columbia, Canada. Currently, 7 described subspecies are recognized based on morphological taxonomic studies. In this study, mitochondrial and nuclear genes were sequenced to infer molecular phylogenies of A. rufa. One of the goals of this study was to use molecular data to test the current taxonomic hypothesis based on morphology. Another goal was to incorporate geographic information to elucidate distributions of major clades. Our results support the previously held subspecies designations based on morphological taxonomy, with 1 main exception: we determined that within A. rufa, the subspecies A. rufa rainieri and A. rufa rufa north of the Columbia River represent a single lineage and should revert to the name A. rufa olympica. Although we revised geographic boundaries for some groups (A. r. rufa, A. r. olympica, and A. r. pacifica), only the conservation status and management of A. r. olympica (previously 2 subspecies) in Canada may be affected. Our findings support the continued conservation efforts for the isolated and endangered lineages present in coastal California. [ABSTRACT FROM AUTHOR]

Abstract: Barnacles of the superfamily Coronuloidea are obligate epibionts of various marine mammals, marine reptiles and large crustaceans. We used five molecular markers: 12S rDNA, 16S rDNA, 18S rDNA, 28S rDNA and Histone 3 to infer phylogenetic relationships among sixteen coronuloids, representing most of the recent genera of barnacles of this superfamily. Our analyses confirm the monophyly of Coronuloidea and that this superfamily and Tetraclitoidea are sister groups. The six-plated Austrobalanus clusters with these two superfamilies. Based on BEAST and ML trees, Austrobalanus is basal and sister to the Coronuloidea, but the NJ tree places Austrobalanus within the Tetraclitoidae, and in the MP tree it is sister to both Coronuloidea and Tetraclitoidae. Hence the position of Austrobalanus remains unresolved. Within the Coronuloidea we identified four clades. Chelonibia occupies a basal position within the Coronuloidea which is in agreement with previous studies. The grouping of the other clades does not conform to previous studies. Divergence time analyses show that some of the time estimates are congruent with the fossil record while some others are older, suggesting the possibility of gaps in the fossil record. [Copyright &y& Elsevier]

Abstract: Determining whether a conflict between gene trees and species trees represents incomplete lineage sorting (ILS) or hybridization involving native and/or invasive species has implications for reconstructing evolutionary relationships and guiding conservation decisions. Among vertebrates, turtles represent an exceptional case for exploring these issues because of the propensity for even distantly related lineages to hybridize. In this study we investigate a group of freshwater turtles (Trachemys) from a part of its range (the Greater Antilles) where it is purported to have undergone reticulation events from both natural and anthropogenic processes. We sequenced mtDNA for 83 samples, sequenced three nuDNA markers for 45 samples, and cloned 29 polymorphic sequences, to identify species boundaries, hybridization, and intergrade zones for Antillean Trachemys and nearby mainland populations. Initial coalescent analyses of phased nuclear alleles (using *BEAST) recovered a Bayesian species tree that strongly conflicted with the mtDNA phylogeny and traditional taxonomy, and appeared to be confounded by hybridization. Therefore, we undertook exploratory phylogenetic analyses of mismatched alleles from the “coestimated” gene trees (Heled and Drummond, 2010) in order to identify potential hybrid origins. The geography, morphology, and sampling context of most samples with potential introgressed alleles suggest hybridization over ILS. We identify contact zones between different species on Jamaica (T. decussata × T. terrapen), on Hispaniola (T. decorata × T. stejnegeri), and in Central America (T. emolli × T. venusta). We are unable to determine whether the distribution of T. decussata on Jamaica is natural or the result of prehistoric introduction by Native Americans. This uncertainty means that the conservation status of the Jamaican T. decussata populations and contact zone with T. terrapen are unresolved. Human-mediated dispersal events were more conclusively implicated for the prehistoric translocation of T. stejnegeri between Puerto Rico and Hispaniola, as well as the more recent genetic pollution of native species by an invasive pet turtle native to the USA (T. scripta elegans). Finally, we test the impact of introgressed alleles using the multispecies coalescent in a Bayesian framework and show that studies that do not phase heterozygote sequences of hybrid individuals may recover the correct species tree, but overall support for clades that include hybrid individuals may be reduced. [Copyright &y& Elsevier]

Abstract: In addition to the well known “classical” porcine parvovirus (PPV1; responsible for reproductive failure of susceptible sows) several new porcine parvoviruses have been recognized (PPV2, PPV3 and PPV4) in recent years. The genetic variation, characteristics and evolutionary factors shaping these novel PPVs were studied by comparing the complete capsid (cap) genes of PPVs from domestic pigs and wild boars. Using Bayesian coalescent methods we estimated the rate of nucleotide substitution for PPV2, PPV3 and PPV4 to be of the order of 3.86×10−4–8.23×10−4 subs site−1 year−1, similar to those commonly measured for RNA viruses, although this rate in case of PPV2 is probably influenced by frequent recombination events. Given such rapid evolutionary dynamics, it is likely that novel PPVs will continue to improve their capacity to spread among Suidae hosts worldwide. The mean time to the most recent common ancestor for the sampled genetic diversity of the newly discovered porcine parvoviruses was estimated. The results indicated that novel PPVs originated within approximately the last 70years. Incongruent phylogenetic relationships of several strains suggested recombination events supported by several recombination-detecting methods and by split-decomposition phylogenetic networks. Analyses of the selective constraints acting on each codon suggest that some regions of PPV cap genes were under positive selection. This study showed that inter- and intraspecies recombination and diversifying selection pressures are prevalent across the cap genes of novel PPVs, and beside host switching and gene flow are important driving forces of their evolution and may be significant factors in the emergence of new viral variants. [Copyright &y& Elsevier]

Abstract: The pelicans are a charismatic group of large water birds, whose evolutionary relationships have been long debated. Here we use DNA sequence data from both mitochondrial and nuclear genes to derive a robust phylogeny of all the extant species. Our data rejects the widespread notion that pelicans can be divided into white- and brown-plumaged groups. Instead, we find that, in contrast to all previous evolutionary hypotheses, the species fall into three well-supported clades: an Old World clade of the Dalmatian, Spot-billed, Pink-backed and Australian Pelicans, a New World clade of the American White, Brown and Peruvian Pelicans, and monospecific clade consisting solely of the Great White Pelican, weakly grouped with the Old World clade. We discuss possible evolutionary scenarios giving rise to this diversity. [Copyright &y& Elsevier]

Abstract: Phylogenetic hypotheses for the large cosmopolitan genus Hypericum (St. John’s wort) have previously been based on morphology, and molecular studies have thus far included only a few species. In this study, we used 360 sequences of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA (nrDNA) for 206 species representing Hypericum (incl. Triadenum and Thornea) and three other genera of Hypericaceae to generate an explicit phylogenetic hypothesis for the genus using parsimony and model-based methods. The results indicate that the small genus Triadenum is nested in a clade within Hypericum containing most of the New World species. Sister to Hypericum is Thornea from Central America. Within Hypericum, three large clades and two smaller grades were found; these are based on their general morphology, especially characters used previously in taxonomy of the genus. Relative to the most recent classification, around 60% of the sections of Hypericum were monophyletic. We used a Bayesian approach to reconstruct ancestral states of selected morphological characters, which resulted in recognition of characters that support major clades within the genus and a revised interpretation of morphological evolution in Hypericum. The shrubby habit represents the plesiomorphic state from which herbs evolved several times. Arborescent species have radiated convergently in high-elevation habitats in tropical Africa and South America. [Copyright &y& Elsevier]

A fossil pygmy right whale (Cetacea, Mysticeti, Neobalaenidae) with exquisitely preserved baleen is described for the first time in the history of cetacean palaeontology, providing a wealth of information about the evolutionary history and palaeobiogeography of Neobalaenidae. This exquisitely preserved specimen is assigned to a new genus and species, Miocaperea pulchra gen. et sp. nov., and differs from Caperea marginata Gray, 1846, the only living taxon currently assigned to Neobalaenidae, in details of the temporal fossa and basicranium. A thorough comparative analysis of the skeleton of M. pulchra gen. et sp. nov. and C. marginata is also provided, and forms the basis of an extensive osteology-based phylogenetic analysis, confirming the placement of M. pulchra gen. et sp. nov. within Neobalaenidae as well as the monophyly of Neobalaenidae and Balaenidae; the phylogenetic results support the validity of the superfamily Balaenoidea. No relationship with Balaenopteroidea was found by the present study, and thus the balaenopterid-like morphological features observed in C. marginata must have resulted from parallel evolution. The presence of M. pulchra gen. et sp. nov. around 2000 km north from the northernmost sightings of C. marginata suggests that different ecological conditions were able to support pygmy right whale populations in what is now Peru, and that subsequent environmental change caused a southern shift in the distribution of the living neobalaenid whales. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 166, 876-911. [ABSTRACT FROM AUTHOR]

Abstract: In this study, we analyzed the nuclear ITS2 rRNA primary sequence and secondary structure in Veneridae and comparatively with 20 Bivalvia taxa to test the phylogenetic resolution of this marker and its suitability for molecular diagnosis at different taxonomic levels. Maximum likelihood and Bayesian trees based on primary sequences were congruent with (profile-) neighbor-joining trees based on a combined model of sequence-structure evolution. ITS2 showed higher resolution below the subfamily level, providing a phylogenetic signal comparable to (mitochondrial/nuclear) gene fragments 2–5 times longer. Structural elements of the ITS2 folding, such as specific mismatch pairing and compensatory base changes, provided further support for the monophyly of some groups and for their phylogenetic relationships. Veneridae ITS2 folding is structured in six domains (DI–VI) and shows five striking sequence-structure features. Two of them, the Basal and Apical STEMs, are common to Bivalvia, while the presence of both the Branched STEM and the Y/R stretches occurs in five superfamilies of the two Heterodonta orders Myoida and Veneroida, thus questioning their reciprocal monophyly. Our results validated the ITS2 as a suitable marker for venerids phylogenetics and taxonomy, and underlined the significance of including secondary structure information for both applications at several systematic levels within bivalves. [Copyright &y& Elsevier]

The evolutionary origin and diversification of the reptilian venom system is described. The resolution of higher-order molecular phylogenetics has clearly established that a venom system is ancestral to snakes. The diversification of the venom system within lizards is discussed, as is the role of venom delivery in the behavioural ecology of these taxa (particularly Varanus komodoensis ). The more extensive diversification of the venom system in snakes is summarised, including its loss in some clades. Finally, we discuss the contentious issue of a definition for “venom”, supporting an evolutionary definition that recognises the homology of both the venom delivery systems and the toxins themselves. [ABSTRACT FROM AUTHOR]

The majority of proteins in eukaryotes are composed of multiple domains, and the number and order of these domains is an important determinant of protein function. Although multidomain proteins with a particular domain architecture were initially considered to have a common evolutionary origin, recent comparative studies of protein families or whole genomes have reported that a minority of multidomain proteins could have appeared multiple times independently. Here, we test this scenario in detail for the signaling molecules netrin and secreted frizzled-related proteins (sFRPs), two groups of netrin domain-containing proteins with essential roles in animal development. Our primary phylogenetic analyses suggest that the particular domain architectures of each of these proteins were present in the eumetazoan ancestor and evolved a second time independently within the metazoan lineage from laminin and frizzled proteins, respectively. Using an array of phylogenetic methods, statistical tests, and character sorting analyses, we show that the polyphyly of netrin and sFRP is well supported and cannot be explained by classical phylogenetic reconstruction artifacts. Despite their independent origins, the two groups of netrins and of sFRPs have the same protein interaction partners (Deleted in Colorectal Cancer/neogenin and Unc5 for netrins and Wnts for sFRPs) and similar developmental functions. Thus, these cases of convergent evolution emphasize the importance of domain architecture for protein function by uncoupling shared domain architecture from shared evolutionary history. Therefore, we propose the terms merology to describe the repeated evolution of proteins with similar domain architecture and discuss the potential of merologous proteins to help understanding protein evolution. [ABSTRACT FROM AUTHOR]

Abstract: Porcine parvovirus (PPV) is widespread among swine and is responsible for reproductive failure of susceptible sows, characterized by embryonic and fetal death. Studies showed that PPV in domestic pig is genetically diverse and some strains differ from the ones used for vaccination. Organ samples from wild boars and domestic pigs were collected in Transylvania (Romania) and tested for the presence of PPV by polymerase chain reaction. Positive samples were grouped and 14 from the wild boar and 1 from the domestic pig PPVs were selected for VP1/VP2 sequence analysis and comparison with available GenBank data. The molecular clock analysis revealed that PPV has a relatively recent evolutionary history, originated approximately 120years ago and the main divergence occurred in the last 20–60years. Phylogenetic and residue substitution analysis showed that the viruses could be divided into 6 distinct clusters and that wild boar PPVs were partially different and independent from domestic pig PPVs. PPVs of wild boars proved to be more diverse than viruses of domestic pigs. The presence of the highly virulent 27a-like PPV strains in wild boars was also detected. [Copyright &y& Elsevier]

Abstract: We review morphological characters considered important for understanding butterfly phylogeny and evolution in the light of recent large-scale molecular phylogenies of the group. A number of the most important morphological works from the past half century are reviewed and morphological character evolution is reassessed based on the most recent phylogenetic results. In particular, higher level butterfly morphology is evaluated based on a very recent study combining an elaborate morphological dataset with a similar molecular one. Special attention is also given to the families Papilionidae, Nymphalidae and Hesperiidae which have all seen morphological and molecular efforts come together in large, combined works in recent years. In all of the examined cases the synergistic effect of combining elaborate morphological datasets with ditto molecular clearly outweigh the merits of either data type analysed on its own (even for ‘genome size’ molecular datasets). It is evident that morphology, far from being obsolete or arcane, still has an immensely important role to play in butterfly (and insect) phylogenetics. Not least because understanding morphology is essential for understanding and evaluating the evolutionary scenarios phylogenetic trees are supposed to illustrate. [Copyright &y& Elsevier]

Although archigregarines are poorly understood intestinal parasites of marine invertebrates, they are critical for understanding the earliest stages in the evolution of the Apicomplexa. Previous studies suggest that archigregarines are a paraphyletic stem group from which other lineages of gregarines, and possibly all other groups of apicomplexans, evolved. However, substantiating this inference is difficult because molecular phylogenetic data from archigregarines, in particular, and other gregarines, in general, are severely limited. In an attempt to help fill gaps in our knowledge of archigregarine diversity and phylogeny, we set out to discover and characterize novel lineages of archigregarines with high-resolution light and scanning electron microscopy and analyses of small subunit ( SSU) rDNA sequences derived from single-cell ( SC) PCR techniques. Here, we describe two novel species of Selenidium, namely Selenidium idanthyrsae n. sp. and S. boccardiellae n. sp., and demonstrate the surface morphology and molecular phylogenetic position of the previously reported species S. cf. mesnili. We also describe a novel genus of archigregarine, Veloxidium leptosynaptae n. gen., n. sp., which branches with an environmental sequence and, together, forms the nearest sister lineage to a diverse clade of marine eugregarines (i.e. lecudinids and urosporids). This molecular phylogenetic result is consistent with the hypothesis that archigregarines are deeply paraphyletic within apicomplexans, and suggests that convergent evolution played an important role in shaping the diversity of eugregarine trophozoites. [ABSTRACT FROM AUTHOR]

Abstract: Phylogenetic relationships in the genus Anthyllis (Leguminosae: Papilionoideae: Loteae) were investigated using data from the nuclear ribosomal internal transcribed spacer regions (ITS) and three plastid regions (psbA–trnH intergenic spacer, petB–petD region and rps16 intron). Bayesian and maximum parsimony (MP) analysis of a concatenated plastid dataset recovered well-resolved trees that are topologically similar, with many clades supported by unique indels. MP and Bayesian analyses of the ITS sequence data recovered trees that have several well-supported topological differences, both among analyses, and to trees inferred from the plastid data. The most substantial of these concerns A. vulneraria and A. lemanniana, whose placement in the parsimony analysis of the ITS data appears to be due to a strong long-branch effect. Analysis of the secondary structure of the ITS1 spacer showed a strong bias towards transitions in A. vulneraria and A. lemanniana, many of which were also characteristic of certain outgroup taxa. This may contribute to the conflicting placement of this clade in the MP tree for the ITS data. Additional conflicts between the plastid and ITS trees were more taxonomically focused. These differences may reflect the occurrence of reticulate evolution between closely related species, including a possible hybrid origin for A. hystrix. The patterns of incongruence between the plastid and the ITS data seem to correlate with taxon ranks. All of our phylogenetic analyses supported the monophyly of Anthyllis (incl. Hymenocarpos). Although they are often taxonomically associated with Anthyllis, the genera Dorycnopsis and Tripodion are shown here to be more closely related to other genera of Loteae. We infer up to six major clades in Anthyllis that are morphologically well-characterized, and which could be recognized as sections. Four of these agree with various morphology-based classifications, while the other two are novel. We reconstruct the evolution of several morphological characteristics found only in Anthyllis or tribe Loteae. Some of these characters support major clades, while others show evidence of homoplasy within Anthyllis. [Copyright &y& Elsevier]