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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]

Gene trees and species trees: Molecular systematics as one-character taxonomy. Comprehensive taxon sampling, congruent data, gene trees, incomplete lineage sorting, plant molecular systematics, plant taxonomy, species trees, phylogenomic analysis Keywords: comprehensive taxon sampling; congruent data; gene trees; incomplete lineage sorting; phylogenomic analysis; plant molecular systematics; plant taxonomy; species trees EN comprehensive taxon sampling congruent data gene trees incomplete lineage sorting phylogenomic analysis plant molecular systematics plant taxonomy species trees 1 4 4 08/31/23 20230801 NES 230801 In the process of compiling a flora for Montana (Lesica, [21], [21]), we came to realize that many published nomenclatural changes are only weakly supported by the data presented which has often been based on recent findings in the field of molecular evolution. Taxonomists and non-taxonomic botanists should also realize that another source of discordance between gene trees and species trees is transfer of mitochondria or chloroplasts across species boundaries. [Extracted from the article]

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]

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]

Dietary shifts can alter the relative availability of different nutrients and are therefore associated with metabolic adaptation in animals. The Coccinellidae (ladybirds) exhibits three major types of feeding habits and provides a useful model to study the effects of dietary changes on the evolution of mitogenomes, which encode proteins directly involved in energy metabolism. Here, mitogenomes of three coccinellid species were newly sequenced. These data were combined with other ten previously sequenced coccinellid mitogenomes to explore the relationship between mitogenome evolution and diets. Our results indicate that mitogenomic data can be effectively used to resolve phylogenetic relationships of Coccinellidae. Strong codon usage bias in coccinellid mitogenomes was predominantly determined by nucleotide composition. The 13 mitochondrial protein‐coding genes (PCGs) globally evolved under negative constraints, with some PCGs showing a stronger purifying selection. Six PCGs (nad3, nad4L, and nad5 from Complex I; cox1 and cox3 from Complex IV; and atp6 from Complex V) displayed signs of positive selection. Of these, adaptive changes in cox3 were potentially associated with metabolic differences resulting from dietary shifts in Coccinellidae. Our results provide insights into the adaptive evolution of coccinellid mitogenomes in response to both dietary shifts and other life history traits. [ABSTRACT FROM AUTHOR]

Staphylinidae, or rove beetles, are a megadiverse family known for their typically very short elytra exposing most of the abdomen, but the putatively early‐derived subfamily Omaliinae and its relatives have been known to include multiple taxa with unusually long elytra. The ancestral elytral length of the family and of this subfamily have long been debated. We present a phylogenetic analysis of Omaliinae based on partial mitochondrial COI (1488 bp), COII (366 bp), 12S rDNA (353 bp), nuclear 18S rDNA (1814 bp), 28S rDNA (876 bp) and CAD (869 bp) data. In all, 51 species in 31 genera and four outgroup species were included. The concatenated sequences were analysed by both parsimony‐ and model‐based (Bayesian and maximum likelihood) methods. The subfamily Omaliinae was not supported as a monophyletic group. The model‐based analyses (Bayesian and maximum likelihood trees) showed Empelinae nested within Omaliinae (excluding Corneolabiini), whereas parsimony analysis found all three putative ingroup subfamilies, Empelinae, Glypholomatinae and Microsilphinae, grouped within Omaliinae. Within the Omaliinae, the tribes Coryphiini and Eusphalerini were each supported as monophyletic, whereas Anthophagini and Omaliini were each nonmonophyletic. We hypothesize that there have been at least four independent origins of long elytra from short elytra in the omaliine lineage. [ABSTRACT FROM AUTHOR]

Phylogenetic hypotheses of the relationships of Diptera: Anthomyzidae (61 taxa) are discussed with special reference to the genera Fungomyza Roháček, 1999, Anthomyza Fallén, 1810, Epischnomyia Roháček, 2006 and Arganthomyza Roháček, 2009 based on the analysis of 7 combined mitochondrial + nuclear gene markers in comparison with results of the most recent cladistic analysis of morphological characters. The majority of revealed inter‐ and intrageneric relationships of these genera in both analyses were largely congruent except for the topology of Fungomyza and Arganthomyza being equivocal because of different topologies in phylograms generated by alternative molecular methods and Epischnomyia forming a branch within Anthomyza in the molecular data hypothesis. The formerly unsettled Anthomyza drachma proved to be the sister species of the A. umbrosa group while the affinity of A. flavosterna to the A. bellatrix group has not been confirmed. The first phylogenetic hypothesis of Anthomyzinae to include timing of the nodes of divergence is presented. The origin of the subfamily is dated into the Eocene, ca 37.5 (30.6–45.3) MYA, and agrees with the age of the oldest known fossils from Baltic amber. The analysed members of the Anthomyza group of genera were found to have already evolved in the upper Oligocene. The divergences of the Palaearctic and Nearctic sister species in Arganthomyza and Anthomyza were found to occur at several different times during the Neogene (upper Miocene) to lower Quaternary (Pleistocene), from about 7 to 0.7 MYA. These were likely the result of fragmentation of widespread (Holarctic or Sino‐Japanese–Nearctic) ranges of ancestral taxa by vicariance events that were, in turn, caused by multiple interruptions of Beringia Land Bridges or cooling of climate and seem to be consistent with the times of multiple disjunctions of the flora. [ABSTRACT FROM AUTHOR]

Panorpidae is the most species‐rich family in Mecoptera with ca. 470 species in the Northern Hemisphere. However, the intergeneric phylogenetic relationships of Panorpidae remain unsatisfactorily resolved to date. Here, we used molecular and cytogenetic approaches to determine the phylogenetic relationships of Panorpidae in the evolutionary scenario of chromosomes, and estimated their divergence times using fossil‐calibrated Bayesian analysis. In total, 89 species representing all seven genera of Panorpidae were used to reconstruct the phylogenetic trees using maximum parsimony, maximum likelihood and Bayesian inference based on the nuclear 28S rRNA and mitochondrial cox1 and cox2 genes. The results reveal that Panorpidae is a well‐supported monophyletic group that can be categorized into two major clades. Major Clade I comprises Neopanorpa and Leptopanorpa, and Major Clade II consists of all the other genera (Cerapanorpa, Dicerapanorpa, Furcatopanorpa, Panorpa and Sinopanorpa). Neopanorpa and Cerapanorpa are regarded as paraphyletic groups for the first time. BEAST analysis indicates that Panorpidae originated in the Lower Cretaceous approximately 122.5 Ma (96.8–149.3 Ma), and that most diversification occurred from the Selandian (59.8 Ma) to the Middle Pleistocene (0.6 Ma) in the Cenozoic. Cytogenetic data plotted on the cladogram show that the lineage differentiation of Panorpidae is closely related to the chromosomal evolution, especially the reduction of chromosome number. Our study suggests that a taxonomic revision of Panorpidae is urgently needed at the generic level. [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: Interest in methods that estimate speciation and extinction rates from molecular phylogenies has increased over the last decade. The application of such methods requires reliable estimates of tree topology and node ages, which are frequently obtained using standard phylogenetic inference combining concatenated loci and molecular dating. However, this practice disregards population‐level processes that generate gene tree/species tree discordance. We evaluated the impact of employing concatenation and coalescent‐based phylogeny inference in recovering the correct macroevolutionary regime using simulated data based on the well‐established diversification rate shift of delphinids in Cetacea. We found that under scenarios of strong incomplete lineage sorting, macroevolutionary analysis of phylogenies inferred by concatenating loci failed to recover the delphinid diversification shift, while the coalescent‐based tree consistently retrieved the correct rate regime. We suggest that ignoring microevolutionary processes reduces the power of methods that estimate macroevolutionary regimes from molecular data. [ABSTRACT FROM AUTHOR]

Aim We sought to illuminate the history of the arachnid orders Schizomida and Uropygi, neither of which have previously been subjected to global molecular phylogenetic and biogeographical analyses. Location Specimens used in this study were collected in all major tropical and subtropical areas where they are presently found, including the Americas, Africa, Australia and the Indo-Pacific region. Methods From field-collected specimens, we sequenced two nuclear and two mitochondrial markers, combined these with publicly available data, and conducted multi-gene phylogenetic analyses on 240 Schizomida, 24 Uropygi and 12 other arachnid outgroups. Schizomid specimens included one specimen from the small family Protoschizomidae; other schizomid specimens were in Hubbardiidae, subfamily Hubbardiinae, which holds 289 of the order's 305 named species. We inferred ancestral areas using the Dispersal-Extinction-Cladogenesis model of range evolution, and we used fossil calibrations to estimate divergence times. Results We recovered monophyletic Schizomida and Uropygi as each other's sister group, forming the clade Thelyphonida, and terminals from the New World were usually positioned as the earliest diverging lineages. The ancestral area for schizomids reconstructed unambiguously to the region comprised of Mexico, Southern California and Florida (the xeric New World subtropics). Optimal trees suggested a single colonization of the Indo-Pacific in both orders, although this did not receive bootstrap support. Molecular dating gave an Upper Carboniferous origin for each order, and a mid-Cretaceous expansion of Schizomida, including the origin and initial diversification of those in the Indo-Pacific. Main conclusions Ancestral area reconstructions, molecular dating and fossil evidence all support an Upper Carboniferous, tropical Pangean origin for Thelyphonida, Schizomida and perhaps Uropygi. Much of this region became unsuitable habitat for these arachnids during the breakup of Pangea, but they persisted in the area that is now Meso- and South America. From there they then expanded to the Indo-Pacific, where schizomids today display an idiosyncratic combination of microendemism and long-range dispersal. [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]

Sticky trap predation, the use of adhesive substances to trap and capture prey, is an intriguing yet poorly studied predatory strategy. Unique among known sticky trap predators, assassin bugs (Reduviidae) have evolved both exogenous and endogenous sticky trap predatory mechanisms: some trap their prey with sticky plant resins, some scavenge insects entrapped by sticky plant trichomes and others self-produce sticky secretions. The evolution of these different strategies in assassin bugs is poorly understood due to the lack of comprehensive phylogenies. We reconstruct a phylogeny of Reduviidae (141 taxa; > 5000 bp) focusing on the Harpactorinae and Bactrodinae that engage in sticky trap predation. Ancestral state reconstruction, and temporal and geographical divergence analyses show that sticky trap predation techniques in assassin bugs evolved at least seven times independently since the late Cretaceous: use of sticky plant trichomes evolved as many as four times, resin-use twice independently and once as a transition from trichome use, and 'self-stickiness' once. Exogenous and endogenous sticky traps first appeared in the Neotropics, with the two exogenous mechanisms (resin and trichome use) subsequently evolving independently in the Old World. This study illustrates, for the first time, the complex evolutionary pattern of sticky trap predation within assassin bugs. [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]

The commercial deep-sea penaeid shrimp genus Parapenaeus contains 15 species, three subspecies and two forms in the Indo-West Pacific and the Atlantic. Novel nucleotide sequence data from five different genes ( COI, 16S, 12S, NaK and PEPCK) were collected to estimate phylogenetic relationships and taxonomic status amongst all but one subspecies in this genus. The phylogenetic results only support two of the four species groups previously proposed for this genus and indicate an evolution direction of the genital organs from simple to complex. The present results suggest that Parapenaeus originated in the shallow waters of the West Pacific with subsequent migration to the deep sea and the Atlantic. The molecular data reveal that there was probably misidentification of females between Parapenaeus australiensis and Parapenaeus ruberoculatus, with females previously assigned as P. australiensis likely being the females of P. ruberoculatus, while material identified as P. australiensis forma nodosa being the true P. australiensis females. On the other hand, Parapenaeus longipes forma denticulata truly represents a variation of the same species, while the subspecies Parapenaeus fissuroides indicus warrants a specific rank. [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]

Aim Lineages in many parts of the world have distributions that have been shaped by range contraction in the face of deteriorating climatic conditions through the Neogene. When such lineages now consist of widely spaced vicariant populations (vicars) they provide opportunities (1) to compare and contrast the timing and pattern of diversification within and between major geographical regions, and (2) to examine how differential interactions with geography, climate and localized adaptation may have shaped idiosyncratic patterns of genetic diversification. Location Australian Arid Zone ( AAZ) and Australian Monsoonal Tropics ( AMT). Methods We compiled and analysed mitochondrial DNA, nuclear DNA and allozyme datasets to determine the evolutionary history and genetic diversity of isolated populations of a gecko lineage (the Oedura marmorata complex and related taxa) distributed across the Australian monsoonal and arid biomes. Results Three widely allopatric lineages in the AAZ diverged during the late Miocene and Plio-Pleistocene. Populations in the AMT display much greater genetic turnover than those in the AAZ over equivalent geographical distances, and also include several lineages that are of equal or greater age than all diversity in the AAZ. Saxicoline lineages tend to show higher genetic diversity and/or have more restricted ranges than arboreal relatives in both biomes. Main conclusions Lineages of Oedura show contrasting patterns of diversification in the two major biomes they inhabit. Diversity in the arid biome is younger and restricted to widely separated refugia, reflecting the younger age and pervasive harshness of this environment. Higher diversity in the AMT is also indicative of persistence, but at much finer geographical scales and broadly over a longer period of time, perhaps reflecting the more continuous spatial and temporal distribution of equitable habitats within this region. Finally, the wider distribution of arboreal lineages in both biomes suggests that ecological flexibility has also shaped the contrasting patterns of distribution in related lineages, and supports the contention that an association with rocks has shaped high lineage diversity in many taxa from the Australian Monsoonal Tropics. [ABSTRACT FROM AUTHOR]

Ecological interaction networks, such as those describing the mutualistic interactions between plants and their pollinators or between plants and their frugivores, exhibit non-random structural properties that cannot be explained by simple models of network formation. One factor affecting the formation and eventual structure of such a network is its evolutionary history. We argue that this, in many cases, is closely linked to the evolutionary histories of the species involved in the interactions. Indeed, empirical studies of interaction networks along with the phylogenies of the interacting species have demonstrated significant associations between phylogeny and network structure. To date, however, no generative model explaining the way in which the evolution of individual species affects the evolution of interaction networks has been proposed. We present a model describing the evolution of pairwise interactions as a branching Markov process, drawing on phylogenetic models of molecular evolution. Using knowledge of the phylogenies of the interacting species, our model yielded a significantly better fit to 21% of a set of plant-pollinator and plant-frugivore mutualistic networks. This highlights the importance, in a substantial minority of cases, of inheritance of interaction patterns without excluding the potential role of ecological novelties in forming the current network architecture. We suggest that our model can be used as a null model for controlling evolutionary signals when evaluating the role of other factors in shaping the emergence of ecological networks. [ABSTRACT FROM AUTHOR]

ABSTRACT Petalomonads are particularly important for understanding the early evolution of euglenids, but are arguably the least studied major group within this taxon. We have established a culture of the biflagellate petalomonad Notosolenus urceolatus, and conducted electron microscopy observations and molecular phylogenetic analysis. Notosolenus urceolatus has eight pellicular strips bordered by grooves and underlain by close-set microtubules. There are ventral and dorsal Golgi bodies. Mitochondria apparently contain fibrous inclusions, as in Petalomonas cantuscygni. A previously undocumented type of large, globular extrusome is present instead of the tubular extrusomes characteristic of Euglenozoa. The feeding apparatus lacks rods and vanes, and is partly supported by an 'MTR'. The flagella have complex transition zones that are extremely elongated but unswollen. Only the emergent portion of the anterior flagellum has an organised paraxonemal rod, and also has very fine mastigonemes. The basal bodies are offset and lack connecting fibres. 18S rRNA gene phylogenies show that N. urceolatus is closely related to Petalomonas sphagnophila and P. cantuscygni, not Notosolenus ostium, confirming that current generic assignments based on the number of emergent flagella are phylogenetically unreliable, and making it difficult to infer whether features shared by N. urceolatus and P. cantuscygni (for example) are general for petalomonads. [ABSTRACT FROM AUTHOR]

Despite likely being the most diverse group within the Tricladida, the systematics of land planarians ( Geoplanidae) has received minor attention. The most species-rich ingroup, the subfamily Geoplaninae, is restricted to the Neotropics. The systematics of Geoplaninae remains uncertain. Unique features supporting the genera are scanty; moreover, parts of the known species have been poorly described, making comparative studies difficult. Likewise the evolutionary relationships among land planarians remain insufficiently understood. In the present study, a phylogenetic hypothesis for selected taxa of Geoplaninae based on the molecular data is presented and discussed in the light of morphological features. Our phylogenetic inference is based on the fragments of three nuclear regions (18 S, 28 S rDNA and EF-1α) and a mitochondrial marker (cytochrome oxidase I) for which we considered three optimality criteria (parsimony, maximum likelihood and Bayesian inference). Although our data provide little support for most basal nodes, our phylogenetic trees show a number of well-supported clades, unveiling morphologically homogeneous groups. According to these results, we propose to separate Geoplana into Barreirana (formerly considered a subgenus), Cratera gen. n., Imbira gen. n., Matuxia gen. n., Obama gen. n. and Paraba gen. n., emend the diagnoses of Barreirana, Geoplana, Notogynaphallia, Pasipha and Xerapoa and review the classification of the species within these genera. For Geoplana goetschi sensu Marcus, (1951), a new name is proposed. [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 brown algal genus Padina (Dictyotales, Phaeophyceae) is distributed worldwide in tropical and temperate seas. Global species diversity and distribution ranges, however, remain largely unknown. Species-level diversity was reassessed using DNA-based, algorithmic species delineation techniques based on cox3 and rbcL sequence data from 221 specimens collected worldwide. This resulted in estimates ranging from 39 to 61 putative species ( ESUs), depending on the technique as well as the locus. We discuss the merits, potential pitfalls, and evolutionary and biogeographic significance of algorithmic species delineation. We unveil patterns whereby ESUs are in all but one case restricted to either the Atlantic or Indo- Pacific Ocean. Within ocean basins we find evidence for the vast majority of ESUs to be confined to a single marine realm. Exceptions, whereby ESUs span up to three realms, are located in the Indo- Pacific Ocean. Patterns of range-restricted species likely arise by repeated founder events and subsequent peripatric speciation, hypothesized to dominate speciation mechanisms for coastal marine organisms in the Indo- Pacific. Using a three-gene ( cox3, psaA and rbcL), relaxed molecular clock phylogenetic analysis we estimated divergence times, providing a historical framework to interpret biogeographic patterns. [ABSTRACT FROM AUTHOR]

Vallo, P., Benda, P., Červený, J. & Koubek, P. (2012). Conflicting mitochondrial and nuclear paraphyly in small-sized West African house bats (Vespertilionidae). - Zoologica Scripta, 42, 1-12. Hybridization between species may result in introgression of mitochondrial DNA from one species to another. Phylogenetic inference, therefore, may not recover true evolutionary relationships. In bats, there are only a few reported cases of introgressive hybridization. House bats are a genus with obscure phylogeny and taxonomy, caused mainly by morphological similarity. We undertook a detailed analysis of small-sized West African house bats ( Scotophilus), tentatively identified as S. nigritellus, to clarify relationships between two sympatric colour forms. These forms were recovered in paraphyletic position to each other in both mitochondrial and nuclear phylogenies, signifying that they are two distinct species. While the yellow-bellied form could be assigned beyond doubt to S. nigritellus s. str., the white-bellied form may be an as yet undescribed species. Moreover, the white-bellied form clustered as a sister mitochondrial lineage to another species, Scotophilus leucogaster. These sister lineages differed by only 2.6-2.8% sequence divergence, which lies within the intraspecific range for this genus. Two nuclear markers, however, contradicted the sister relationship, showing them instead to be distantly related. The apparent conflict between the mitochondrial and nuclear signals suggests that past hybridization may have occurred between these morphologically distinct species. [ABSTRACT FROM AUTHOR]

Jadin, R.C., Townsend, J.H., Castoe, T.A. & Campbell, J.A. (2012). Cryptic diversity in disjunct populations of Middle American Montane Pitvipers: a systematic reassessment of Cerrophidion godmani. -Zoologica Scripta, 41, 455-470. The discovery and taxonomic recognition of cryptic species has become increasingly frequent with the application of molecular phylogenetic analyses, particularly for species with broad geographic distributions. In this study we focus on the venomous pitviper species Cerrophidion godmani that is widely distributed throughout the highlands of Central America. We provide evidence based on both molecular phylogenetic analyses and morphological data that C. godmani represents three deeply divergent lineages and is possibly non-monophyletic. These three lineages are relatively conserved in their morphology and tend to be highly variable among individuals, but we do find sufficient morphological characters to diagnose them as evolutionarily distinct. We apply these data, together with known geographic distributions of populations, to infer boundaries of these three divergent evolutionary lineages. Based on the body of evidence, we formally name and describe two new species of Cerrophidion and redescribe C. godmani sensu stricto. [ABSTRACT FROM AUTHOR]

Debevec, AH., Cardinal, S & Danforth, BN. Identifying the sister group to the bees: a molecular phylogeny of Aculeata with an emphasis on the superfamily Apoidea. - Zoologica Scripta, 41, 527-535. The hymenopteran superfamily Apoidea includes the bees (Anthophila) as well as four predatory wasp families (Heterogynaidae, Ampulicidae, Sphecidae and Crabronidae) collectively referred to as the 'sphecoid' or 'apoid' wasps. The most widely cited studies suggest that bees are sister to the wasp family Crabronidae, but alternative hypotheses have been proposed based on both morphological and molecular data. We combined DNA sequence data from previously published studies and newly generated data for four nuclear genes (28S, long-wavelength rhodopsin, elongation factor-1α and wingless) to identify the likely sister group to the bees. Analysis of our four-gene data set by maximum likelihood and Bayesian methods indicates that bees most likely arise from within a paraphyletic Crabronidae. Possible sister groups to the bees include Philanthinae, Pemphredoninae or Philanthinae + Pemphredoninae. We used Bayesian methods to explore the robustness of our results. Bayes Factor tests strongly rejected the hypotheses of crabronid monophyly as well as placement of Heterogynaidae within Crabronidae. Our results were also stable to alternative rootings of the bees. These findings provide additional support for the hypothesis that bees arise from within Crabronidae, rather than being sister to Crabronidae, thus altering our understanding of bee ancestry and evolutionary history. [ABSTRACT FROM AUTHOR]

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]

Persistent difficulties in resolving clear lineages in diverging populations of prokaryotes or unicellular eukaryotes (protistan polyphyletic groups) are challenging the classical species concept. Although multiple integrated approaches would render holistic taxonomies, most phylogenetic studies are still based on single-gene or morphological traits. Such methodologies conceal natural lineages, which are considered 'cryptic.' The concept of species is considered artificial and inadequate to define natural populations. Social organisms display differential behaviors toward kin than to nonrelated individuals. In 'social' microbes, kin discrimination has been used to help resolve crypticity. Aggregative behavior could be explored in a nonsocial protist to define phylogenetic varieties that are considered 'cryptic.' Two Entamoeba invadens strains, IP-1 and VK-1:NS are considered close populations of the same 'species.' This study demonstrates that IP-1 and VK-1:NS trophozoites aggregate only with alike members and discriminate members of different strains based on behavioral and chemical signals. Combined morphological, behavioral/chemical, and ecological studies could improve Archamoebae phylogenies and define cryptic varieties. Evolutionary processes in which selection acted continuously and cumulatively on ancestors of Entamoeba populations gave rise to chemical and behavioral signals that allowed individuals to discriminate nonpopulation members and, gradually, to the emergence of new lineages; alternative views that claim a 'Designer' or 'Creator' as responsible for protistan diversity are unfounded. [ABSTRACT FROM AUTHOR]

The phylogeny of morphologically simple algae is problematic due to insufficient morphological characters to aid in distinguishing species and relationships. The problem is further compounded because multiple evolutionary lineages of morphologically similar species occur in most well-sampled biogeographic locations; therefore, location cannot be used as a proxy for species. The phylogeny of the upright members of the Erythropeltidales is partially clarified by combining molecular data, unialgal culture observations, and worldwide sampling. Our results show that there are several well-supported lineages within the Erythropeltidales with only two morphologically recognizable taxa at present. The first is the genus Porphyrostromium, with a well-developed basal crust, which includes two Erythrotrichia species ( Porphyrostromium ligulatum comb. nov. and Porphyrostromium pulvinatum comb. nov.). The second is the branched species Erythrotrichia welwitschii (Rupr.) Batters. There are also six strongly supported Erythrotrichia carnea-like lineages. While not completely satisfactory, we propose that one lineage (lineage 2) with samples close to the type locality be designated as E. carnea with a specific isolate as an epitype. The lack of morphology to differentiate the other lineages leads to a taxonomy based solely on gene sequencing and molecular phylogeny, with rbcL sequences differentiating the lineages proposed. We hold off on proposing more species and genera until more data and samples can be gathered. [ABSTRACT FROM AUTHOR]

Elephant-shrews or sengis (Macroscelidea, Afrotheria) are grouped into two subfamilies, Rhynchocyoninae with a single genus and four species, and Macroscelidinae represented by three genera and 13 species. Our current understanding of the evolutionary relationships within this group is largely based on a molecular phylogeny that suffers from incomplete species representation. We present the first complete phylogeny (with the exception of the recently described East African Rhynchocyon udzungwensis) for Macroscelidea based on mitochondrial and nuclear markers. Novel cytogenetic characters as well as previously described allozyme variation and various morphological features are evaluated and mapped to the molecular topology. Our analyses indicate that Elephantulus is paraphyletic, and that Petrodromus and Macroscelides should be subsumed in Elephantulus. A relaxed Bayesian dating approach supports the hypothesis that an arid-adapted Macroscelidinae lineage dispersed from east Africa at ∼11.5 MYA via an African arid corridor to south-western Africa. The timing of speciation within the east African Rhynchocyoninae (8-10 MYA) is coincidental with the diversification of some other forest specialists. In turn, divergence within the Macroscelidinae coincides with major aridification events across Africa. [ABSTRACT FROM AUTHOR]

Aktipis, S. W., Boehm, E. & Giribet, G. (2010). Another step towards understanding the slit-limpets (Fissurellidae, Fissurelloidea, Vetigastropoda, Gastropoda): a combined five-gene molecular phylogeny. - Zoologica Scripta, 40, 238-259. Fissurellids, commonly known as slit or keyhole limpets, are limpet-shaped gastropods that typically possess a hole, slit or notch in their bilaterally symmetrical shells and usually occur on rocky marine substrates. Competing classifications for Fissurellidae have been circumscribed using various morphological characters such as radular, shell and mantle features; two to five different subfamilies have been recognized. Although fissurellid species are frequently included in larger vetigastropod phylogenies, relatively few phylogenetic studies of the group have been performed. This study presents a phylogenetic investigation of the relationships amongst slit-limpets in the vetigastropod superfamily Fissurelloidea, representing the first molecular phylogeny of this clade. In this study, the monophyly of Fissurelloidea and Fissurellidae varied depending on the analytical method used, but clades compatible with the subfamilies Diodorinae and Fissurellinae were recovered with high bootstrap support in all analyses. Species traditionally classified in Emarginulinae formed two groups identified in this study as Hemitominae ( Puncturella, Cranopsis and Hemitoma) and Emarginulinae sensu stricto ( Emarginula, Montfortula, Tugali, Scutus and Nannoscutum), but Hemitominae was only monophyletic in the maximum likelihood analysis. The results of this study contradict traditional fissurellid classifications as well as theories about the evolution of key fissurellid shell characters. The placement of Puncturella, Cranopsis and Hemitoma sister to all remaining fissurellids suggests that the presence of an anteriorly placed foramen or notch is plesiomorphic, and that an anterior notch or slit evolved multiple times in Fissurellidae. [ABSTRACT FROM AUTHOR]

For a better understanding of the complex coevolutionary processes between hosts and parasites, accurate identification of the actors involved in the interaction is of fundamental importance. Blood parasites of the Order Haemosporidia, responsible for malaria, have become the focus of a broad range of studies in evolutionary biology. Interestingly, molecular-based studies on avian malaria have revealed much higher species diversity than previously inferred with morphology. Meanwhile, studies on bat haemosporidian have been largely neglected. In Europe, only one genus ( Polychromophilus) and two species have been morphologically described. To evaluate the presence of potential cryptic species and parasite prevalence, we undertook a molecular characterization of Polychromophilus in temperate zone bats. We used a nested-PCR approach on the cytochrome b mitochondrial gene to detect the presence of parasites in 237 bats belonging to four different species and in the dipteran bat fly Nycteribia kolenatii, previously described as being the vector of Polychromophilus. Polychromophilus murinus was found in the four bat species and in the insect vector with prevalence ranging from 4% for Myotis myotis to 51% for M. daubentoni. By sequencing 682 bp, we then investigated the phylogenetic relationships of Polychromophilus to other published malarial lineages. Seven haplotypes were found, all very closely related, suggesting the presence of a single species in our samples. These haplotypes formed a well-defined clade together with Haemosporidia of tropical bats, revealing a worldwide distribution of this parasite mostly neglected by malarial studies since the 1980s. [ABSTRACT FROM AUTHOR]

To reconstruct the phylogeographic history of the Holarctic carnivorous genus Leptodora (Crustacea: Cladocera: Haplopoda). We studied the DNA of between one and five specimens each from 28 populations distributed across the Holarctic, but with emphasis on Eurasia. We sequenced a mitochondrial (cytochrome c oxidase subunit I) and a nuclear (elongation factor-1α) gene, and combined this molecular information with geological and palaeoclimatological data. Haplotype networks and phylogenetic trees were constructed using a Bayesian and maximum likelihood approach. A molecular clock was applied. Leptodora consists of three clades ( Leptodora kindtii in Europe, Leptodora richardi in China and Japan, and Leptodora sp. in North America), with insular subclades in Japan and in the eastern Mediterranean. The North American clade was not studied in detail. Leptodora richardi is the more thermophilic of the three. It extends from the Tropic of Cancer in the south to the Heilong Basin in the north. The western European L. kindtii is more cold-water adapted than the eastern Mediterranean subclade. 'West European' and 'Chinese' clades are broadly separated by a hybrid zone in Siberia and European Russia as far west as the Volga. These hybrids have the mitochondrial DNA of L. kindtii, the nuclear DNA of L. richardi and the low-temperature preference of L. kindtii, and may have formed as recently as the Holocene hypsithermal. A pure L. kindtii population in the Upper Irtysh catchment, east of the Dzungarian Gates, has been sequestered in endorheic Lake Wulungu, Xinjiang, since the mid-Pleistocene. Application of a molecular clock places the most recent common ancestor of the North American, East Asian and European populations in the mid-Miocene. The North American taxon is still living in isolation, while the Eurasian taxa, separated by the Alpine folding, made contact again in the Pleistocene, when the cold-stenothermic L. kindtii repeatedly moved eastwards across Siberia and back. The population in Xinjiang is a relict of an early wave coming from western Europe: it crossed the Dzungarian Gates during a humid mid-Pleistocene event, probably corresponding to the Apsheron transgression in the Caspian Basin. Later aridity isolated it there, and it started accumulating private haplotypes. The Holocene Euro-Siberian hybrid zone may eventually engulf all European populations. [ABSTRACT FROM AUTHOR]

A molecular phylogenetic study of red algal parasites commonly found in the Northwestern Pacific and the Hawaiian Islands was undertaken. Four species, Benzaitenia yenoshimensis Yendo, Janczewskia hawaiiana Apt, J. morimotoi Tokida, and Ululania stellata Apt et Schlech (Ceramiales), are parasitic on rhodomelacean species belonging to the tribes Chondrieae and Laurencieae. Although Janczewskia and Ululania are classified in the same tribes as their host species, the taxonomic placement of Benzaitenia has been controversial. To infer the phylogenetic positions of these parasites and to clarify the relationships between the parasites and their hosts, phylogenetic analyses of partial nuclear SSU and LSU rRNA genes and the cox1 gene were performed. The SSU rRNA gene analyses clearly show that both Janczewskia species are positioned within the Laurencia s. str. clade with their host species, while Benzaitenia and Ululania are placed in the Chondrieae clade. According to these analyses, J. hawaiiana and U. stellata are not sister to their current hosts; in contrast, B. yenoshimensis and J. morimotoi are closely related to their current hosts. These data suggest that J. hawaiiana and U. stellata have likely evolved from species other than their current hosts and have switched hosts at some point in their evolutionary history. Likelihood ratio tests do not support the monophyly of J. hawaiiana and J. morimotoi, suggesting multiple origins of parasitism within Laurencia s. str. [ABSTRACT FROM AUTHOR]

The cicada genus Psithyristria Stål (Hemiptera: Cicadidae), endemic to Luzon, the Philippines, is reviewed, and its higher taxonomic affiliations are determined using morphology and molecular phylogenetics. Seven new Psithyristria species, P. grandis, sp.n., P. albiterminalis, sp.n., P. incredibilis, sp.n., P. paraspecularis, sp.n., P. peculiaris, sp.n., P. moderabilis, sp.n. and P. genesis, sp.n., are described. A key to the 12 known species is provided. The molecular phylogenetic analyses of Psithyristria and putatively related taxa showed some unexpected generic relationships, leading to changes in higher taxonomic placement for a number of Asian cicada genera. Psithyristria falls within the tribe Cicadini Latreille, 1802, and the tribe Psithyristriini Distant, 1905 syn.n. is therefore synonymized with Cicadini. The subtribe Psithyristriina Distant, 1905 stat.n. is recognized within Cicadini and defined for the genera Psithyristria, transferred from Psithyristriini, and Basa Distant, Pomponia Stål and Semia Matsumura, transferred from Cicadina, synonymizing Pomponiina Kato, 1932 syn.n. with Psithyristriina. The Cicadini subtribe Leptopsaltriina Moulton, 1923 is redefined to include the genera Terpnosia Distant, Euterpnosia Matsumura, Leptosemia Matsumura, Neocicada Kato, Puranoides Moulton, Leptopsaltria Stål, Tanna Distant, Purana Distant, Formosemia Matsumura, Maua Distant, Nabalua Moulton, Taiwanosemia Matsumura, Gudaba Distant and Calcagninus Distant, synonymizing Terpnosiina Kato, 1932 syn.n. The tribe Cicadatrini Distant, 1905 is recognized and redefined to include the genera Cicadatra Kolenati, Psalmocharias Kirkaldy, Mogannia Amyot & Audinet-Serville, Nipponosemia Kato and Emathia Stål, synonymizing Moganniini Distant, 1905 syn.n. The nine Psithyristria species included in the molecular analyses have an uncorrected mitochondrial genetic distance of 2–9%, and most species appear to be related through a single radiation event that occurred approximately 5–10 Ma. No phylogenetic structure was found in two unusually divergent characters, the forewing venation and the shape of the uncal lobes. Psithyristria is found in the northern Luzon mountains and is closely related to Semia of Taiwan and eastern China, Pomponia of east Asia and the Indonesian/Malaysian islands, and probably most closely to Basa of India. Psithyristria may be a cicadid example of a small number of Philippine organisms that trace their ancestry directly back to the temperate Asian mainland, rather than through the island chains to the south of the country. [ABSTRACT FROM AUTHOR]

The genus Hyperamoeba Alexeieff, 1923 was established to accommodate an aerobic amoeba exhibiting three life stages—amoeba, flagellate, and cyst. As more species/strains were isolated, it became increasingly evident from small subunit (SSU) gene phylogenies and ultrastructure that Hyperamoeba is polyphyletic and its species occupy different positions within the class Myxogastria. To pinpoint Hyperamoeba strains within other myxogastrid genera we aligned numerous myxogastrid sequences: whole small subunit ribosomal (SSU or 18S rRNA) gene for 50 dark-spored (i.e. Stemonitida and Physarida) Myxogastria (including a new “ Hyperamoeba” /Didymium sequence) and a ∼400-bp SSU fragment for 147 isolates assigned to 10 genera of the order Physarida. Phylogenetic analyses show unambiguously that the type species Hyperamoeba flagellata is a Physarum ( Physarum flagellatum comb. nov.) as it nests among other Physarum species as robust sister to Physarum didermoides. Our trees also allow the following allocations: five Hyperamoeba strains to the genus Stemonitis; Hyperamoeba dachnaya, Pseudodidymium cryptomastigophorum, and three other Hyperamoeba strains to the genus Didymium; and two further Hyperamoeba strains to the family Physaridae. We therefore abandon the polyphyletic and redundant genus Hyperamoeba. We discuss the implications for the ecology and evolution of Myxogastria, whose amoeboflagellates are more widespread than previous inventories supposed, being now found in freshwater and even marine environments. [ABSTRACT FROM AUTHOR]

The paradox of a host specificity of the human faecal microbiota otherwise acknowledged as characterized by global functionalities conserved between humans led us to explore the existence of a phylogenetic core. We investigated the presence of a set of bacterial molecular species that would be altogether dominant and prevalent within the faecal microbiota of healthy humans. A total of 10 456 non-chimeric bacterial 16S rRNA sequences were obtained after cloning of PCR-amplified rDNA from 17 human faecal DNA samples. Using alignment or tetranucleotide frequency-based methods, 3180 operational taxonomic units (OTUs) were detected. The 16S rRNA sequences mainly belonged to the phyla Firmicutes (79.4%), Bacteroidetes (16.9%), Actinobacteria (2.5%), Proteobacteria (1%) and Verrumicrobia (0.1%). Interestingly, while most of OTUs appeared individual-specific, 2.1% were present in more than 50% of the samples and accounted for 35.8% of the total sequences. These 66 dominant and prevalent OTUs included members of the genera Faecalibacterium, Ruminococcus, Eubacterium, Dorea, Bacteroides, Alistipes and Bifidobacterium. Furthermore, 24 OTUs had cultured type strains representatives which should be subjected to genome sequence with a high degree of priority. Strikingly, 52 of these 66 OTUs were detected in at least three out of four recently published human faecal microbiota data sets, obtained with very different experimental procedures. A statistical model confirmed these OTUs prevalence. Despite the species richness and a high individual specificity, a limited number of OTUs is shared among individuals and might represent the phylogenetic core of the human intestinal microbiota. Its role in human health deserves further study. [ABSTRACT FROM AUTHOR]

Almost 80 years ago, a radiation scheme based on structural resemblance was first outlined for the marine order Dinophysiales. This hypothetical radiation illustrated the relationship between the dinophysioid genera and included several independent, extant lineages. Subsequent studies have supplied additional information on morphology and ecology to these evolutionary lineages. We have for the first time combined morphological information with molecular phylogenies to test the dinophysioid radiation hypothesis in a modern context. Nuclear-encoded LSU rDNA sequences including domains D1-D6 from 27 species belonging to Dinophysis Ehrenb. , Ornithocercus F. Stein , Phalacroma F. Stein , Amphisolenia F. Stein , Citharistes F. Stein, and Histioneis F. Stein were obtained from the Indian Ocean. Previously, LSU rDNA has only been determined from one of these. In Bayesian analyses, Amphisolenia formed a long basal clade to the other dinophysioids. These diverged into two separate lineages, the first comprised species with a classical Phalacroma outline, also including the type species P. porodictyum F. Stein. Thus, we propose to reinstate the genus Phalacroma. The relationship between the genera in the second lineage was not well resolved. However, the molecular phylogeny supported monophyly of Histioneis and Citharistes and showed the genus Dinophysis to be polyphyletic and in need of a taxonomic revision. Species of Ornithocercus grouped with Citharistes, but this relationship remained unresolved. The phylogenetic trees furthermore revealed convergent evolution of several morphological characters in the dinophysioids. According to the molecular data, the dinophysioids appeared to have evolved quite differently from the radiation schemes previously hypothesized. Four dinophysioid species had identical LSU rDNA sequences to other well-established species. [ABSTRACT FROM AUTHOR]

Aim To reconstruct the temporal, geographical and eco-climatological differentiation of the genus Anthemis (Compositae, Anthemideae) in the circum-Mediterranean region, in order to evaluate the relative importance of geographical vs. climatological differentiation processes in influencing the actual distribution patterns in this plant group. Location The circum-Mediterranean region, including the Iberian Peninsula, northern Africa, the Italian and Balkan peninsulas, the Aegean region and Anatolia, the Caucasus, the Arabian Peninsula and western Asia. Methods The phylogeny of the genus Anthemis was obtained from a maximum likelihood analysis based on nuclear ribosomal DNA (nrDNA) internal transcribed spacer (ITS) sequence data, and the chronology of diversification was derived using a penalized likelihood approach. The reconstruction of the spatial diversification of the genus was based on a dispersal/vicariance (DIVA) analysis. Eco-climatological niche differentiation was inferred by optimizing 19 bioclimatic variables onto the phylogeny. A multi-dimensional hypervolume, proposed as a representation of the eco-climatological niche and defined by the combination of ranges for all bioclimatic variables, was calculated for each taxon and each internal node. To identify ‘eco-climatological vicariance’ events in the phylogeny, the pairwise overlap among hypervolumes of sister groups was calculated. Finally, the temporal and clade-wise relative importance of geographical vs. eco-climatological vicariance events was estimated. Results The temporal reconstruction shows a constant increase of lineages through the last 12 Myr. The geographical reconstruction suggests that Anthemis diverged from the rest of the Compositae–Anthemideae in the eastern Mediterranean region, and from there radiated into the whole circum-Mediterranean region through successive dispersal and vicariance events. The reconstruction of the eco-climatological niches suggests a progressive adaptation from a montane-humid climate towards arid environments and the typical mediterranean climate. Main conclusions The results presented here involved phylogenetic, geographical and eco-climatological reconstructions; joint analyses of all of these aspects have assessed the relative importance of geological vs. climatic forces that have affected the distributional history of the genus Anthemis. Large-scale differentiation patterns triggered by geological forces appear to have influenced the evolutionary history of the genus in a rather constant manner over the last 12 Myr, whereas climatic forces seem to have played an important role in two phases of the radiation process: at around 9 Ma, when the area experienced the onset of a trend towards aridification, and during the last 3.5 Myr, with the establishment of the typical mediterranean climate and the influence of Pleistocene climate oscillations. [ABSTRACT FROM AUTHOR]

Aim The clade Campanulaceae in the Cretan area is rich in endemics, with c. 50% of its species having restricted distributions. These species are analysed in the context of a larger phylogeny of the Campanulaceae. Divergence times are calculated and hypotheses of vicariance and dispersal are tested with the aim of understanding whether Cretan lineages represent remnants of an older continental flora. Location The Cretan area: Crete and the Karpathos Islands (Greece). Methods We obtained chloroplast DNA sequence data from rbcL, atpB and matK genes for 102 ingroup taxa, of which 18 are from the Cretan area, 11 are endemics, and two have disjunct, bi-regional distributions. We analysed the data usingbeast, a Bayesian approach that simultaneously infers the phylogeny and divergence times. We calibrated the tree by placing a seed fossil in the phylogeny, and used published age estimates as a prior for the root. Results The phylogenetic reconstruction shows that all Campanula species fall within a well-supported campanuloid clade; however, Campanula is highly polyphyletic. The Cretan endemics do not form a monophyletic group, and species are scattered throughout the campanuloid clade. Therefore, the Cretan taxa did not evolve following a single vicariance or dispersal event. Most Cretan lineages represent remnants of an older continental flora, with the exception of one clade that radiated in situ after island isolation, and one lineage that appears to have arrived by dispersal. Main conclusions Most Cretan species were present in the islands at the time of their isolation, and very little long-distance dispersal to Crete and diversification within Crete has occurred since then. Endemism is probably driven by loss of species on the mainland after island isolation. Species on the islands may have been more widespread in the past, but they are now restricted to often inaccessible areas, probably as a result of human pressure. [ABSTRACT FROM AUTHOR]

Lampreys (Agnatha) and lungfish (Dipnoi) are representatives of the earliest and the intermediate stages in vertebrate evolution, respectively, and survived in the Cambrian (approximately 540 mA, lampreys) and Devonian (approximately 400 mA, lungfishes) Periods. The unique phylogenetic position of these two groups presents us with an exciting opportunity to understand life in ancient times and to begin to trace the evolution of vision and photoreception in vertebrates. Using a multidisciplinary approach employing anatomical and molecular techniques, the evolution of photoreception is explored in these extant, living fossils to predict the environmental lighting conditions to which our vertebrate ancestors were exposed. Contrary to expectations, the retinae of the southern hemisphere lamprey ( Geotria australis Gray, 1851) and the Australian lungfish ( Neoceratodus forsteri Krefft, 1870) are far from “primitive,” each possessing five types of photoreceptors, many with spectral filters for tuning the light. Detailed ultrastructural analysis reveals that all five receptor types in G. australis are cone-like, whereas N. forsteri possesses four cone types and a single type of rod. Each receptor type also contains a different visual pigment (opsin gene); that is, LWS, SWS1, SWS2, RhA and RhB in G. australis and LWS, SWS1, SWS2, Rh1 and Rh2 in N. forsteri, all of which are expressed within the retina and are sensitive to different parts of the electromagnetic spectrum, providing the potential for pentachromatic and tetrachromatic color vision, respectively. [ABSTRACT FROM AUTHOR]

• LHY/CCA1 genes play a key role in the plant circadian clock system and are highly conserved among plant species. However, the evolutionary process of the LHY/ CCA1 gene family remains unclear in angiosperms. To obtain details of the phylogeny of these genes, this study characterized LHY/CCA1 genes in a model woody plant, Populus tree. • The evolutionary process of angiosperm LHY/CCA1 genes was elucidated using three approaches: comparison of exon–intron structures, reconstruction of phylogenetic trees and examination of syntenic relationships. In addition, the molecular evolutionary rates and the expression patterns of Populus LHYs were analyzed. • Gene duplication events of Populus LHYs and Arabidopsis LHY/CCA1 had occurred independently by different chromosomal duplication events arising in each evolutionary lineage. Populus LHYs were under purifying selection by estimating substitution rates of these genes. Further, Populus LHYs conserved diurnal expressions in leaves and stems but the transcripts of LHY2 were more abundant than those of LHY1 in Populus plants. • This study uncovered phylogenetic relationships of the LHY/ CCA1 gene family in angiosperms. In addition, the transcript abundance and the evolutionary differences between Populus LHY1 and LHY2 imply that Populus LHY2, rather than LHY1, may have a major role in the Populus clock system. [ABSTRACT FROM AUTHOR]

This study presents extensive molecular phylogenetic and morphometric data for Anoplocephaloides dentata (Galli-Valerio, 1905)-like cestodes (Anoplocephalidae) and related species parasitizing arvicoline rodents (voles and lemmings) in the Holarctic region. The molecular phylogeny is based on nucleotide sequences of cytochrome oxidase I (mtDNA) and 28S ribosomal RNA. Anoplocephaloides dentata-like cestodes included three main clades, two in western Eurasia and one in the Holarctic region (excluding western Eurasia). Three well-supported sublineages were included in the southern European clade, one of which represents the true A. dentata from Chionomys nivalis and sympatric Microtus arvalis and Dinaromys bogdanovi. These clades generally had non-overlapping distributions and showed a preference for certain host species. Multivariate analysis of morphometric data failed to discriminate unambiguously the various A. dentata-like lineages recovered in the molecular phylogeny, although two to three of the (sub)lineages were morphologically divergent. The overall evidence suggests, however, that instead of a single host-generalist species there are at least five more or less host-specific species of A. dentata-like cestodes. Colonization of new host lineages seems to have been the predominant mode of diversification, suggested by the considerable incongruence between host and parasite phylogenies at multiple taxonomic levels. Based on the results of the molecular survey, a redescription and neotype designation are provided for A. dentata. [ABSTRACT FROM AUTHOR]

Phylum Tardigrada consists of ∼1000 tiny, hardy metazoan species distributed throughout terrestrial, limno-terrestrial and oceanic habitats. Their phylogenetic status has been debated, with current evidence placing them in the Ecdysozoa. Although there have been efforts to explore tardigrade phylogeny using both morphological and molecular data, limitations such as their few morphological characters and low genomic DNA concentrations have resulted in restricted taxonomic coverage. Using a protocol that allows us to identify and extract DNA from individuals, we have sequenced 18S rDNA from 343 tardigrades from across the globe. Using maximum parsimony and Bayesian analyses we have found support for dividing Order Parachela into three super-families and further evidence that indicates the traditional taxonomic perspective of families in the class Eutardigrada are nonmonophyletic and require re-working. It appears that conserved morphology within Tardigrada has resulted in conservative taxonomy as we have found cases of several discrete lineages grouped into single genera. Although this work substantially adds to the understanding of the evolution and taxonomy of the phylum, we highlight that inferences gained from this work are likely to be refined with the inclusion of further taxa—specifically representatives of the nine families yet to be sampled. © The Willi Hennig Society 2008. [ABSTRACT FROM AUTHOR]

Molecular phylogenetic studies of the extant Pantherinae have resulted in a variety of different hypotheses of relationships. This study presents the results of a cladistic study encompassing 45 osteological and dental characters in the skull and mandible, as well as 13 soft-tissue and behavioural characters. Analyzing extant pantherines with osteological data only resulted in two equally parsimonious trees, which differed only with respects to the jaguar, a taxon which shows morphological affinity to the tiger as well as the lion + leopard. Addition of soft-tissue characters resolved this ambiguity, and led to markedly improved bootstrap values. The inclusion of fossil taxa did not have an impact on topology, but was important for a correct understanding of character evolution, due to the fossils having a combination of characters unlike those of any extant taxon. The clouded leopard is the most basal pantherine, followed by the snow leopard. The large pantherines are a well supported group, to which the snow leopard does not belong, contrary to some molecular studies. Panthera palaeosinensis is no tiger, but may be close to the stem group from which the tiger evolved. P. atrox and P. spelaea are not on the lion lineage, as traditionally assumed, but are successive outgroups to the lion + leopard, although the position of P. spelaea is tentative, but is supported by other lines of evidence such as brain anatomy. © The Willi Hennig Society 2008. [ABSTRACT FROM AUTHOR]

We present a molecular phylogeny of 26 out of the 28 currently accepted genera in the subfamily Chrysophylloideae (Sapotaceae) using parsimony, parsimony jackknifing, and Bayesian inference. A data matrix of 8984 characters was obtained from DNA sequences of seven chloroplast loci, two nuclear loci, indels coded as binary characters, and morphology. Our phylogenetic reconstruction suggests that Chrysophyllum, Pouteria, and Pradosia, as well as some sections within Chrysophyllum and Pouteria, are all polyphyletic. These taxa were previously described largely on the basis of unique combinations of states for a set of morphological characters. Mapping some of these characters onto one of the most parsimonious trees indicates that the symplesiomorphic flower in the subfamily was probably 5-merous, had stamens inserted in the tube orifice, staminodes, seeds with foliaceous cotyledons, exserted radicle, and endosperm. These characters have subsequently been lost multiple times and cannot be used as synapomorphies to support broad generic concepts. Despite the high degree of homoplasy some well-defined clades can be described on the basis of alternative character state combinations. Also, many of these well-supported clades appear to be restricted to particular geographical areas (e.g. all taxa in Australasia form a monophyletic group). Hence, we suggest that the segregate genera Aningeria, Malacantha, and Martiusella may ultimately be resurrected, and probably also Donella and Gambeya, but their circumscriptions are still unclear. One species, Chrysophyllum cuneifolium, may have originated from a hybridization event between continents where the maternal genome (cpDNA) comes from South America and the nuclear genome comes from Africa. © The Willi Hennig Society 2008. [ABSTRACT FROM AUTHOR]

Phylogenetic relationships of 25 genera of Holarctic Teleiodini (Gelechiidae) are postulated based on morphology and molecular characters, including CO-I, CO-II, and 28S genes. The phylogenetic analysis of the morphology matrix yielded four equal most-parsimonious trees (length 330 steps, CI = 0.36, RI = 0.55) and a strict consensus tree (length 335 steps, CI = 0.36, RI = 0.54) with one polytomy and one trichotomy. The phylogenetic analysis of the combined morphology and CO-I + CO-II + 28S matrices yielded two equally most-parsimonious trees (length 1184 steps, CI = 0.50, RI = 0.42) and a strict consensus tree (length 1187 steps, CI = 0.50, RI = 0.42) that reinforced results from the morphological analysis and resolved the one polytomy present in the morphology consensus tree. Teleiodini are defined as a monophyletic clade with a Bremer support value greater than 5 in the consensus tree based on morphological and molecular data. Twenty-three clades of genera are defined with Bremer support values provided. An analysis of larval host-plant preferences based on the consensus tree for combined data indicates derivation of feeding on woody hosts from genera feeding on herbaceous hosts and a single origin of feeding on coniferous hosts. An area cladogram indicates five independent origins of Nearctic genera from Holarctic ancestors and one origin from a Palearctic genus. [ABSTRACT FROM AUTHOR]

A phylogeny of the tribe Aphidini (Hemiptera: Aphididae) was reconstructed from three gene fragments: two mitochondrial regions, partial tRNA-leucine + cytochrome oxidase II (tRNA/COII), partial 12S rRNA + tRNA-valine + 16S rRNA (12S/16S) and one nuclear gene, the elongation factor-1 alpha (EF1α). Bayesian phylogenetic (BP) analyses were performed on each individual dataset of tRNA/COII, 12S/16S and EF1α, and maximum parsimony (MP), Bremer support test, maximum likelihood (ML) and BP analysis were performed on the combined dataset. After comparing our molecular phylogenetic results with the classic classification based on morphological and ecological data, we analysed three main issues: the monophyletic relationships among tribes and subtribes, the validities of the latest taxonomic positions of genera and species and the status of certain Aphis species groups. Our results indicate that 36 of the species analysed, with the exception of Cryptosiphum artemisiae, are clustered within the clade of Aphidini. Also, the 28 species representative of the subtribe Aphidina were separated from the eight species representative of Rhopalosiphina; each monophyletic subtribe was supported by significant P-values in the combined analysis. According to our results, Cryptosiphum should be moved to Macrosiphini because it is more closely related to the genera Lipaphis and Brevicoryne. The genus Toxoptera was recovered as non-monophyletic. In Rhopalosiphina, three genera, Hyalopterus, Rhopalosiphum and Schizaphis, were relatively closer to each other than to the genus Melanaphis. In the relationships between species-groups among Aphis, most species were separated into two main lineages; the fabae group seemed to be more closely related to the spiraecola and craccivora group rather than to the gossypii group. [ABSTRACT FROM AUTHOR]