Molecular Systematics

SYNOPSIS. Among diverse marine invertebrate taxa, the evolution of a non-planktotrophic larva is often associated with increased rates of cladogenesis, compared to related taxa that retain the ancestral planktotrophic larval form. Molecular phylogenetic analyses of non-planktotrophic (and, presumably species-rich) clades of marine invertebrates are rare. Here we analyze 1542 base pairs of mitochondrial DNA sequence comprising two gene regions, the cytochrome oxidase I gene and the putative control region and flanking sequences, for 23 molecular lineages in the obligately brood-protecting asteroid genus Leptasterias. Using maximum likelihood, minimum evolution, and maximum parsimony methods, five major clades were identified that corresponded to five taxa (species or species complexes) in the subgenus Hexasterias, section camtschatica (following the taxonomy of Walter K. Fisher). Two clades (L. aequalis complex and L. aleutica/L. camtschatica complex) were composed of numerous molecular lineages (7-8 lineages/clade), and several clades had multiple shallow nodes, suggestive of recent radiations. Two of the clades (L. aleutica/L. camtschatica complex and L. hexactis complex), with geographic ranges restricted to latitudes higher than 48؇N, were lacking deep phylogenetic nodes. This pattern is consistent with the hypothesis that high-latitude taxa have high rates of extinction due to repeated climatic crises. A log-likelihood ratio test performed on the camtschatica section, including a member (Leptasterias polaris) of the polaris section and using a representative (L. mü lleri) of Leptasterias subgenus Leptasterias as an outgroup, demonstrated that the camtschatica section is monophyletic.

Four protein-encoding mitochondrial genes (cytochrome b, NADH-dehydrogenase subunits 1, 2 and 4) and one nuclear (c-mos) gene were sequenced to infer phylogenetic relationships among Old and New World representatives of racers and whipsnakes, Coluber (sensu lato). New World Coluber (Coluber sensu stricto, including Masticophis) and Salvadora proved to have affinities with the Old World non-racer colubrine genus Ptyas (and possibly Elaphe s.l. and Coronella), whereas Old World 'Coluber' form several basally related clades; these are (1) Hemorrhois-(Spalerosophis-Platyceps); (2) Hierophis, with Eirenis nested within this paraphyletic genus and (3) 'Coluber' dorri as the sister taxon to Macroprotodon cucullatus. The position of 'Coluber' zebrinus along with Hemerophis socotrae located at the base of the Old World racer radiation forming the possible sister group to all remaining Palearctic racers and whipsnakes remains less well supported. Nevertheless, inter-and subgeneric relationships among many of the Old World racer groups have been resolved.

Species delineation remains one of the most challenging tasks in the study of biodiversity, mostly owing to the application of different species concepts, which results in contrasting taxonomic arrangements. This has important practical consequences, since species are basic units in fields like ecology and conservation biology. We here review molecular genetic evidence relevant to the systematics of toads in the Bufo bufo species group (Anura, Bufonidae). Two studies recently published in this journal (Recuero et al., MPE 62: 71-86 and Garci´a-Porta et al., MPE 63: 113-130) addressed this issue but reached opposing conclusions on the taxonomy of the group (four versus two species). In particular, allozyme data in the latter paper were interpreted as evidence for hybridization across species (between B. bufo-B. spinosus and B. bufo-B. verrucosissimus). We tested claims for hybridization through re-analysis of allozyme data for individuals instead of populations, to be able to distinguish between sympatry with and without admixture, and found no evidence of hybridization across taxa. We propose alternative explanations for the observed patterns that Garci´a-Porta et al. (2012) failed to consider. In the absence of unequivocal evidence for hybridization and introgression, we reject the proposal to downgrade Bufo spinosus and Bufo verrucosissimus to the subspecies level.

Nuclear ribosomal DNA sequences encoding the 5.8S RNA and the Xanking internal transcribed spacers (ITS1 and ITS2) were used to test the phylogenetic relationships within 12 Italian Quercus taxa (Fagaceae). Hypotheses of sequence orthology are tested by detailed inspection of some basic features of oak ITS sequences (i.e., general patterns of conserved domains, thermodynamic stability and predicted conformation of the secondary structure of transcripts) that also allowed more accurate sequence alignment. Analysis of ITS variation supported three monophyletic groups, corresponding to subg. Cerris, Schlerophyllodrys (D Ilex group sensu Nixon) and Quercus, as proposed by Schwarz [Feddes Rep., Sonderbeih. D, 1-200]. A derivation of the "Cerris group" from the "Ilex group" is suggested, with Q. cerris sister to the rest of the "Cerris group." Quercus pubescens was found to be sister to the rest of the "Quercus group." The status of hybrispecies of Q. crenata (Q. cerris £ Q. suber) and Q. morisii (Q. ilex £ Q. suber) was evaluated and discussed. Finally, the phylogenetic position of the Italian species in a broader context of the genus is presented. The utility of the ITS marker to assess the molecular systematics of oaks is therefore conWrmed. The importance of Italy as a region with a high degree of diversity at the population and genetic level is discussed.

Jacquemontia reclinata House (Convolvulaceae) is a federally listed endangered species endemic to coastal strand habitat of south-eastern Florida. In order to identify the closest relatives of J. reclinata, a phylogenetic reconstruction was performed based on nucleotide sequence data from the internal transcribed spacer region of nuclear ribosomal DNA and from the trnH-psbA intergenic spacer of chloroplast DNA. The three putative relatives of J. reclinata and the majority of Jacquemontia Choicy species known to occur in the Caribbean Islands were included. The strict consensus tree concurs with previous morphological studies, indicating that J. reclinata is closely related to the Caribbean species J. cayensis Britton, J. curtisii Hallier f., and J. havanensis (Jacq.) Urb. These three species and J. reclinata form an unresolved clade. Nucleotide divergence within this clade is low, suggesting that the group is recent, perhaps diversifying after the latest glacial period. These taxa need to be studied further using population-level DNA markers. Most species endemic to the Caribbean Basin form a strongly supported clade. Our phylogeny supports Convolvulus nodiflorus Desr. as part of Jacquemontia. In addition, J. ovalifolia (West) Hallier f. ssp. sandwicensis (A. Gray) K.R. Robertson is sister to the Antillean endemic J. solanifolia (L.) Hallier f. © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society, 2007, 154, 443–454.

This study focuses on the phylogenetic relationships within the Polyopisthocotylea and Monopisthocotylea, two groups that are often grouped within the monogeneans, a group of disputed paraphyly. Phylogenetic analyses were conducted with multiple outgroups chosen according to two hypotheses, a paraphyletic Monogenea or a monophyletic Monogenea, and with three methods, namely maximum parsimony, neighbour joining and maximum likelihood. Sequences used were from the partial domain C1, full domain D1, and partial domain C2 (550 nucleotides, 209 unambiguously aligned sites) from the 28S ribosomal RNA gene for 16 species of monopisthocotyleans, 26 polyopisthocotyleans including six polystomatids, and other Platyhelminthes (61 species in total, 27 new sequences). Results were similar with outgroups corresponding to the two hypotheses. Within the Monopisthocotylea, relationships were: {[(Udonella, capsalids), monocotylids], (diplectanids, ancyrocephalids)}; each of these families was found to be monophyletic and their monophyly was supported by high bootstrap values in neighbour joining and maximum parsimony. Within the Polyopisthocotylea, the polystomatids were the sister-group of all others. Among the latter, Hexabothrium, parasite of chondrichthyans, was the most basal, and the mazocraeids, mainly parasites of clupeomorph teleosts, were the sister-groups of all other studied polyopisthocotyleans, these, mainly parasites of euteleosts, being polytomous.

The Resedaceae, containing 6 genera and ca. 85 species, are widely distributed in the Old World, with a major center of species diversity in the Mediterranean basin. Phylogenetic analyses of ITS and plastid trnL-trnF sequences of 66 species from all genera of the Resedaceae reveal (1) monophyly of the family, in congruence with preliminary phylogenetic studies; (2) molecular support for the traditional morphological subdivision of the Resedaceae into three tribes according to ovary and placentation types, and carpel number; (3) two monophyletic genera (Caylusea, Sesamoides), and one natural group (core Reseda), which includes the remaining four genera of the family (Ochradenus, Oligomeris, Randonia, Reseda); (4) a monophyletic origin for four of the six taxonomic sections recognized within Reseda (Leucoreseda, Luteola, Glaucoreseda, Phyteuma). Our results lead us to interpret an increment of the basic chromosome number in the family from x D 5 to x D 6 in at least two independent in...

Because the genus Colletotrichum is among the most important groups of plant pathogenic fungi worldwide, the ability to accurately diagnose species is vital for the implementation of effective disease control and quarantine measures. Although the long-standing, unresolved taxonomic issues in the genus have recently begun to be addressed through multi-locus phylogenetic research, the tools most commonly used for Colletotrichum species identification are either insufficiently variable (e.g. morphology) or homoplasic (e.g. morphology and host range criteria). In this study, using the systematically well-defined falcate-spored, grass-associated group (FG) of Colletotrichum as a model, we test the utility of ITS sequence data to diagnose species affiliations through similarity-based searches of the NCBI GenBank database or by means of gene trees constructed using phylogenetic methods. 43% of all Colletotrichum sequences accessioned by GenBank are from the ITS region, making it the single most common sequence curated by the community; however, 34% of the ITS accessions existed only as sequence data in the database, with no associated publication. Using Colletotrichum ITS sequence data from 53 FG defined isolates and 16 falcate-spored, non-graminicolous isolates to perform GenBank BLAST searches, we found that erroneous identifications were possible for 86% of the 14 species tested. In contrast, the phylogenetic tree generated by the ITS sequence data, although poorly supported by bootstrap values, correctly grouped most of the species, but 10% of the individual isolates were incorrectly placed. From this study, we conclude that the currently available infrastructure of Colletotrichum ITS sequence data may yield unreliable species diagnoses, particularly when sequence similarity alone is the only criterion applied.

A phylogenetic analysis of a combined data set for 560 angiosperms and seven outgroups based on three genes, 18s rDNA (1855 bp), rbcl. (1428 bp), and atpB (1450 bp) representing a total of 4733 bp is presented. Parsimony analysis was expedited by use of a new computer program, the RATCHET. Parsimony jackknifing was performed to assess the support of clades. The combination of three data sets for numerous species has resulted in the most highly resolved and strongly supported topology yet obtained for angiosperms. In contrast to previous analyses based on single genes, much of the spine of the tree and most of the larger clades receive jackknife support 250%. Some of the noneudicots form a grade followed by a strongly supported eudicot clade. The early-branching angiosperms are Amborellaceae, Nymphaeaceae, and a clade of Austrobaileyaceae, Illiciaceae, and Schisandraceae. The remaining noneudicots, except Ceratophyllaceae, form a weakly supported core eumagnoliid clade comprising six well-supported subclades: Chloranthaceae, monocots, WinteraceaeICanellaceae, Piperales, Laurales, and Magnoliales. Ceratophyllaceae are sister to the eudicots. Within the well-supported eudicot clade, the early-diverging eudicots (e.g. Proteales, Ranunculales, Trochodendraceae, Sabiaceae) form a grade, followed by the core eudicots, the monophyly of which is also strongly supported. The core eudicots comprise * Correspondence to 0. E. Soltis.

The Zygomycota is an ecologically heterogenous assemblage of nonzoosporic fungi comprising two classes, Zygomycetes and Trichomycetes. Phylogenetic analyses have suggested that the phylum is polyphyletic; two of four orders of Trichomycetes are related to the Mesomycetozoa (protists) that diverged near the fungal/animal split. Current circumscription of the Zygomycota includes only orders with representatives that produce zygospores. We present a molecular-based phylogeny including recognized representatives of the Zygomycetes and Trichomycetes with a combined dataset for nuclear rRNA 18S (SSU), 5.8S and 28S (LSU) genes. Tree reconstruction by Bayesian analyses suggests the Zygomycota is paraphyletic. Although 12 clades were identified only some of these correspond to the nine orders of Zygomycota currently recognized. A large superordinal clade, comprising the Dimargaritales, Harpellales, Kickxellales and Zoopagales, grouping together many symbiotic fungi, also is identified in part by a unique septal structure. Although Harpellales and Kickxellales are not monophyletic, these lineages are distinct from the Mucorales, Endogonales and Mortierellales, which appear more closely related to the Ascomycota + Basidiomycota + Glomeromycota. The final major group, the insectassociated Entomophthorales, appears to be polyphyletic. In the present analyses Basidiobolus and Neozygites group within Zygomycota but not with the Entomophthorales. Clades are discussed with special reference to traditional classifications, mapping morphological characters and ecology, where possible, as a snapshot of our current phylogenetic perspective of the Zygomycota.

Recent molecular systematic investigations suggested that Ferula, an umbellifer genus of about 170 species, is polyphyletic, with its members placed in the apioid superclade and within tribe Scandiceae. We analyzed ITS sequence variation from 134 accessions of Apiaceae, including 83 accessions (74 species) of Ferula to ascertain the phylogenetic position of the genus within the family. Phylogenetic analyses of these data using maximum parsimony, Bayesian, and neighbor-joining methods support the monophyly of Ferula upon the addition of Dorema and Leutea (as Ferula sensu lato) and its placement in tribe Scandiceae. Ferula sensu is closely allied with other major lineages of Scandiceae, corresponding to subtribes Scandicinae, Daucinae, and Torilidinae. Therefore, we recognize the Ferula clade as subtribe Ferulinae. Another addition to tribe Scandiceae is a clade composed of genera Glaucosciadium and Mozaffariania. The three accessions of Ferula misplaced in the apioid superclade represent a species of Silaum.

In the most comprehensive study to date we explored the phylogeny and evolution of the genus Asparagus, with emphasis on the southern African species. We included 211 accessions, representing 77 (92%) of the southern African, 6 (17%) of the tropical African, 10 (56%) of the strictly European and 6 (9%) of the Eurasian species. We analysed DNA sequences from three plastid regions (trnH-psbA, trnD-T, ndhF) and from the nuclear region phytochrome C (PHYC) with parsimony and maximum likelihood methods, and recovered a monophyletic Asparagus. The phylogeny conflicts with all previous infra-generic classifications. It has many strongly supported clades, corroborated by morphological characters, which may provide a basis for a revised taxonomy. Additionally, the phylogeny indicates that many of the current species delimitations are problematic. Using biogeographic analyses that account for phylogenetic uncertainty (S-DIVA) and take into account relative branch lengths (Lagrange) we confirm...

Monophyly of Arthropoda is emphatically supported from both morphological and molecular perspectives. Recent work finds Onychophora rather than Tardigrada to be the closest relatives of arthropods. The status of tardigrades as panarthropods (rather than cycloneuralians) is contentious from the perspective of phylogenomic data. A grade of Cambrian taxa in the arthropod stem group includes gilled lobopodians, dinocaridids (e.g., anomalocaridids), fuxianhuiids and canadaspidids that inform on character acquisition between Onychophora and the arthropod crown group. A sister group relationship between Crustacea (itself likely paraphyletic) and Hexapoda is retrieved by diverse kinds of molecular data and is well supported by neuroanatomy. This clade, Tetraconata, can be dated to the early Cambrian by crown group-type mandibles. The rival Atelocerata hypothesis (Myriapoda þ Hexapoda) has no molecular support. The basal node in the arthropod crown group is embroiled in a controversy over whether myriapods unite with chelicerates (Paradoxopoda or Myriochelata) or with crustaceans and hexapods (Mandibulata). Both groups find some molecular and morphological support, though Mandibulata is presently the stronger morphological hypothesis. Either hypothesis forces an unsampled ghost lineage for Myriapoda from the Cambrian to the mid Silurian.

The Indian species Portulaca suffruticosa has been confused with other taxa by many previous authors, due to lack of field collections and a paucity of specimens in Indian herbaria. Following a morphological taxonomic study supported by new field collections, P. suffruticosa is confirmed as an accepted species endemic to southern India and Sri Lanka, and as distinct from P. pilosa and P. tuberosa. The more recently described species P. lakshminarasimhaniana and P. laljii are considered to be conspecific with P. suffruticosa, and P. badamica conspecific with P. tuberosa; their names are accordingly synonymised. Lectotypifications of the names P. suffruticosa Wight, P. tuberosa Roxb. and P. wightiana Wall. ex Wight & Arn. were found to be necessary to avoid future misapplication of names and full descriptions of these three species are provided. A key to all Indian species of Portulaca is provided.

The internal classification of the cosmopolitan and medically important genus Culex is thoroughly reviewed and updated to reflect the multitude of taxonomic changes and concepts which have been published since the classification was last compiled by Edwards in 1932. Both formal and informal taxa are included. The classification is intended to aid researchers and students who are interested in analyzing species relationships, making group comparisons and testing phylogenetic hypotheses. The genus includes 768 formally recognized species divided among 26 subgenera. Many of the subgenera are subdivided hierarchically into nested informal groups of morphologically similar species that are believed to represent monophyletic lineages based on morphological similarity. The informal groupings proposed by researchers include Sections, Series, Groups, Lines, Subgroups and Complexes, which are unlikely to be phylogenetically equivalent categories among the various subgenera.

The human-caused extinction of the Passenger Pigeon (Ectopistes migratorius) is one of the best known and documented of any bird. This event was particularly alarming because the Passenger Pigeon went from being one of the most numerous avian species in the world to extinct in a period of decades, when the last individual died in captivity in a Cincinnati Zoo in 1914. While a great deal of information exists on the likely direct and indirect causes of its demise, as well as information on life-history, the phylogenetic relationships of this species have been subject to considerable speculation. Here we use DNA sequences obtained from museum specimens to resolve the phylogenetic position of this species with respect to other pigeons and doves (Columbiformes). We show that the Passenger Pigeon is not related to the New World mourning doves (Zenaida) as many authors have suggested, but is the sister taxon of all other New World pigeons (Patagioenas). Biogeographic analysis suggests the Passenger Pigeon lineage may have colonized North America from Asia, and subsequently dispersed into South America, leading to a more extensive radiation of New World pigeons.

This paper presents a phylogenetic analysis of Lamiaceae subfam. Lamioideae (including subfamily Pogostemonoideae)
based on sequences of the trnL intron, trnL-trnF intergenic spacer, and rps16 intron of the plastid genome. It is the first
analysis that includes all major lamioid and pogostemonoid genera. Monophyly of Lamioideae s.l. (i.e., including
Pogostemonoideae) is strongly supported, with Cymaria Benth. as its sister group, and Pogostemonoideae, which sometimes
has been recognized as a subfamily, is subsumed in Lamioideae. On the basis of the phylogenetic hypothesis, Lamioideae is
divided into nine tribes. Three new tribes are established: Gomphostemmateae Scheen & Lindqvist, Phlomideae Mathiesen,
and Leucadeae Scheen & Ryding. The other six tribes are: Pogostemoneae Briq., Synandreae Raf., Stachydeae Dumort.,
Leonureae Dumort., Lamieae Coss. & Germ., and Marrubieae Vis. The genus Betonica L. is reestablished. The results also
strongly suggest that the genera Stachys L., Sideritis L., Ballota L., and Leucas R. Br. are polyphyletic or paraphyletic. The
results were used to examine evolution of non-molecular characters.

Phenylhydrazine (PHZ), a potent chemical causes toxicity on various tissues at various levels. Administration of phenylhydrazine mainly causes haematotoxicity which leads to the haemolytic anemia. In mammals PHZ induced anemia increased the iron absorption in spleen, liver and duodenum and finally iron metabolism was altered. Local demand and supply of Fe would increase erythropoeitic activity of the spleen so the size of spleen was increased that create the splenomegaly. PHZ induced anemia activate immune response which triggers phagocytosis in the spleen and liver. Apart from this administration of PHZ interfere the binding of erythropoietin (EPO) with erythropoietin receptors (EPOR) so that JAK-STAT would be affected.PHZ also showed genotoxic effect by creating single strand DNA damage.

Sequence analyses of the plastid genes atpB and rbcL support an expanded order Malvales. Within this alliance, core Malvales are clearly supported and comprise most genera that have previously been included in Sterculiaceae, Tiliaceae, Bombacaceae, and Malvaceae. Additional well supported malvalean alliances include the bixalean clade (Bixaceae, Diego-dendraceae, and Cochlospermaceae), the cistalean clade (Cistaceae, Dipterocarpaceae, and Sarcolaenaceae) and Thymelaeaceae (including Gonystyloideae and Aquilarioideae). Our results indicate sister-group relationships between (1) Neuradaceae and the cistalean clade; (2) Sphaerosepalaceae and Thymelaeaceae; (3) these two clades (1 and 2); and (4) all these and an alliance comprising the bixalean clade and core Malvales, but this pattern is weakly supported by the bootstrap. The affinities of Muntingiaceae and Petenaea are especially ambiguous, although almost certainly they are Malvales s.l. The traditional delimitation of families within core Malvales is untenable. Instead, we propose to merge Sterculiaceae, Tiliaceae and Bombacaceae with Malvaceae and subdivide this enlarged family Malvaceae into nine subfamilies based on molecular, morphological, and biogeographical data: (1) Byttnerioideae, including tribes Byttnerieae, Lasiopetaleae and Theobromeae (all of which have cucullate petals) and Hermannieae; (2) Grewioideae, including most genera of former Tiliaceae; (3) Tilioideae, monogeneric in our analysis; (4) Helicteroideae, comprising most of the taxa previously included in Helictereae, plus Mansonia, Triplochiton (indicating that apocarpy evolved at least twice within Malvaceae) and possibly Durioneae; (5) Sterculioideae, defined by apetalous, apocarpous, usually unisexual flowers with androgynophores; (6) Brownlowioideae, circumscribed as in previous classifications; (7) Dombeyoideae, expanded to include Burretiodendron, Eriolaena, Pterospermum, and Schoutmia; (8) Bombacoideae, corresponding to former Bombacaceae (without Durioneae) but including Fremontodendreae

The highlands of northeastern Honduras remain under-characterized in terms of biological diversity, as exemplified by the regularity of new amphibian and reptile taxa discoveries. Following the recent description of a new species of Nototriton from the Sierra de Agalta in northeastern Honduras, we report the discovery of a second new species of Nototriton from the nearby Parque Nacional Montaña de Botaderos. This new taxon, Nototriton mime sp. nov., is distinguished from other Nototriton by its distinctive pale brown dorsal coloration in adult males, relatively large nares, a relatively broad head, mitochondrial sequence divergence, and phylogenetic relationships, and is geographically isolated from other populations of Nototriton.

The phylogenetic pattern and timing of the radiation of Old World deer was determined based on the complete mitochondrial cytochrome b gene from 33 Cervinae taxa. Using rooted and unrooted phylogenies derived from distinct theoretical approaches, strong support was achieved for monophyly of the Old World deer with muntjacs as sister group as well as for the divergence of at least three distinct genera: Rucervus, Dama, and Cervus. The latter clade comprises what have previously been regarded as the genera or subgenera Panolia, Rusa, Cervus, Sika, and probably Przewalskium. Our data also consistently confirmed paraphyly of nominate C. elaphus and did not support the monophyly of Axis. We used these molecular phylogenies to assess the homoplastic evolution of morphological, geographical, ecological, and selected behavioural character state differences within the Cervinae. Reliable fossil calibrations, large molecular data sets, and improved dating methods are shaping a molecular time scale for the evolutionary radiation of Old World deer that occurred at the Miocene/Pliocene transition and is largely compatible with existing palaeontological evidence. Using node ages estimated from sequence data, we estimated an average per-lineage diversification rate of 0.51 ± 0.1 species per million years (my) over roughly the last 6 mya.

The deuterostomes are a monophyletic group of multicellular animals that include the Chordata, a phylum that exhibits a unique body plan within the metazoans. Deuterostomes classically contained three phyla, Echinodermata, Hemichordata, and Chordata. Protochordata describes two invertebrate chordate subphyla, the Tunicata (Urochordata) and the Cephalochordata. Tunicate species are key to understanding chordate origins, as they have tadpole larvae with a chordate body plan. However, molecular phylogenies show only weak support for the Tunicata as the sister-group to the rest of the chordates, suggesting that they are highly divergent from the Cephalochordata and Vertebrata. We believe that members of the Tunicata exhibit a unique adult body plan and should be considered a separate phylum rather than a subphylum of Chordata. The molecular phylogeny of the deuterostomes is reviewed and discussed in the context of likely morphological evolutionary scenarios and the possibility is raised that the ancestor of the Tunicata was colonial. In this scenario, the colonial tadpole larva would more resemble an ancestral chordate than the solitary tadpole larva. In contrast, the true chordates (vertebrates and cephalochordates) would have evolved from filter-feeding benthic worms with cartilaginous gill slits, similar to extant enteropneust hemichordates.

The Eleutherodactylus subgenus Syrrhophus has a complex taxonomic history. For many years the species were classified into series and groups of species based on morphological and allozyme data. However, most of the species have conservative morphology, and their phylogenetic relationships have not been resolved. Furthermore, recent studies employing molecular tools have shown that Syrrhophus diversity is highly underestimated. Here, we present a near-complete phylogenetic hypothesis based on mitochondrial data (16S rRNA, cytochrome c oxidase subunit I, and cytochrome b) and employing maximum likelihood and Bayesian methods. The Bayesian tree has high support values (posterior probabilities ≥0.95) whereas the maximum likelihood hypothesis has generally low values (bootstrap support <70). Both phylogenetic analyses recovered Syrrhophus as monophyletic and composed of four main, allopatric clades (E. symingtoni clade, E. longipes clade, E. modestus clade, and E. nitidus clade) concordant with geography. Based on the molecular and morphological data, we describe a new species from the state of San Luis Potosí, Mexico. The new species is most closely related to E. campi and E. cystignathoides from which it has a genetic distance >7% in 16S rRNA. Finally, based on the phylogenetic results, we resurrect E. rubrimaculatus from synonymy. Our results increase the number of species in the subgenus Syrrhophus to 41. We highlight the importance of efforts to study this important component of Mexican biodiversity.

Kingsnakes of the Lampropeltis getula complex range throughout much of temperate and
subtropical North America. Studies over the last century have used morphology and color pattern to
describe numerous subspecies. More recently, DNA analyses have made invaluable contributions
to our understanding of their evolution and taxonomy. We use genetic and ecological methods
to test previous hypotheses of distinct evolutionary lineages by examining 66 total snakes and
1) analyzing phylogeographic structure using 2 mtDNA loci and 1 nuclear locus, 2) estimating
divergence dates and historical demography among lineages in a Bayesian coalescent framework,
and 3) applying ecological niche modeling (ENM). Our molecular data and ENMs illustrate
that 3 previously recognized subspecies in the eastern United States comprise well-supported
monophyletic lineages that diverged during the Pleistocene. The geographic boundaries of these
3 lineages correspond closely to known biogeographic barriers (Florida peninsula, Appalachian
Mountains, and Apalachicola River) previously identified for other plants and animals, indicating
shared geographic influences on evolutionary history. We conclude that genetic, ecological, and
morphological data support recognition of these 3 lineages as distinct species (Lampropeltis
floridana, Lampropeltis getula, and Lampropeltis meansi).

The Framework for Post-Phylogenetic Systematics reframes biological systematics to reconcile classical and cladistic schools. It combines scientific intuition and statistical inference in a new form of total evidence analysis developing a joint macroevolutionary process-based causal theory. Discrepancies between classical results and morphological and molecular cladograms are explained through heterophyletic inference of deep ancestral taxa, coarse priors leading to Bayesian Solution of total evidence, self-nesting ladders that can reverse branching order, and a superoptimization protocol that aids in distinguishing pseudoextinction from budding evolution. It determines direction of transformative evolution through Dollo evaluation at the taxon level. The genus as a basic, practical unit of evolution is postulated for taxa with dissilient evolution.

Scientific intuition is defended as highly developed heuristics based on physical principles. The geometric mean and Fibonacci series in powers of the golden ratio explain distributions of measurements of the form (a–)b–c(–d) when close to zero. This series is basic both to S. J. Gould’s speciational reformulation of macroevolution and to psychologically salient numbers. The effect of molecular systematics on conservation and bio¬diversity research is shown to be of immediate concern.

The value of cladistic study for serial macroevolutionary reconstruction is reduced to—in morphological studies, evaluation of relatively primitive or advanced taxa, and distinction of taxa by autapomorphies, and—in molecular studies, identification of deep ancestors via heterophyly or unreasonable patristic distance not explainable by extinct or unsampled extended paraphyly. Evolutionary paraphyly is common in cladistics and is to be avoided; phylogenetic paraphyly, however, can be informative.

Following a critical review of the species concepts and stressing the need for a single, general classification system to serve both systematists and evolutionary biologists, the author seeks to identify a conceptual framework where matching of taxonomic characters to the biological properties of species is maximized. Sympatric and synchronic populations of amphigonic organisms can almost unequivocally be identified as species when reproductive gaps occur between them. In such situations species are recognized by appropriate descriptors (characters) as genetic units and ecological units. Multivariate statistical methods provide a powerful tool to analyse more complex situations where non-amphigonic organisms and/or allopatric populations are investigated, on condition that appropriate character sets are considered. The increasing availability of molecular data for analysis certainly enhances the recognition of species as genetic unities, whilst much of the ecological role of an organism may be read from a careful choice of morphometric and ethological descriptors. On these premises it is suggested that species can be defined as groups of individuals (populations) which are discretely separated from other such groups in the character space. This definition is phenetical in its form but biological in its meaning since character sifting and weighting are considered essential features at the operational level.

Background: EST sequencing is a versatile approach for rapidly gathering protein coding sequences. They provide direct access to an organism's gene repertoire bypassing the still errorprone procedure of gene prediction from genomic data. Therefore, ESTs are often the only source for biological sequence data from taxa outside mainstream interest. The widespread use of ESTs in evolutionary studies and particularly in molecular systematics studies is still hindered by the lack of efficient and reliable approaches for automated ortholog predictions in ESTs. Existing methods either depend on a known species tree or cannot cope with redundancy in EST data.

Monophyly of Arthropoda is emphatically supported from both morphological and molecular perspectives. Recent work finds Onychophora rather than Tardigrada to be the closest relatives of arthropods. The status of tardigrades as panarthropods (rather than cycloneuralians) is contentious from the perspective of phylogenomic data. A grade of Cambrian taxa in the arthropod stem group includes gilled lobopodians, dinocaridids (e.g., anomalocaridids), fuxianhuiids and canadaspidids that inform on character acquisition between Onychophora and the arthropod crown group. A sister group relationship between Crustacea (itself likely paraphyletic) and Hexapoda is retrieved by diverse kinds of molecular data and is well supported by neuroanatomy. This clade, Tetraconata, can be dated to the early Cambrian by crown group-type mandibles. The rival Atelocerata hypothesis (Myriapoda þ Hexapoda) has no molecular support. The basal node in the arthropod crown group is embroiled in a controversy over whether myriapods unite with chelicerates (Paradoxopoda or Myriochelata) or with crustaceans and hexapods (Mandibulata). Both groups find some molecular and morphological support, though Mandibulata is presently the stronger morphological hypothesis. Either hypothesis forces an unsampled ghost lineage for Myriapoda from the Cambrian to the mid Silurian.

Background: The Philippine archipelago is globally one of the most important model island systems for studying evolutionary processes. However, most plant species on this archipelago have not yet been studied in sufficient detail. The main aim of this study is to unravel the evolutionary history and biogeographic relationships of the Philippine members of the pantropical genus Ixora.
Results: The complex plastid and nuclear divergence patterns in Philippine Ixora, documented using tree and network approaches, reveal a highly dynamic evolution in Ixora, involving several phases of radiation and recolonization. Philippine Ixora comprises at least five lineages, of which one is most closely related to species from Wallacea, and the remaining four to species from Asia.
Conclusions: Our study highlights the importance of Philippine species for understanding phytogeographic patterns in the Indomalayan-Australasian eco-region. The overall genetic differentiation, as well as the incongruence between genealogies based on the biparentally inherited nucleome and the maternally inherited plastome in Ixora, reflect the complex tectonic history of the Philippine archipelago. The Ixora lineage related to Wallacean species supports the delimitation of different ecozones along Huxley’s line, because it is absent from Palawan. The remaining four lineages are all allied with Asian taxa, reflecting several waves of colonization. Close relationships between some widespread Philippine species and locally adapted narrow endemics suggest that the widespread, genetically diverse species act as pools for the formation of new species in a process of ongoing speciation. Our results suggest that the species concepts of some of the more widespread taxa need to be revised.

We investigated genetic divergence and phylogenetic relationships amongst all known species of Palaearctic butterflies of the genus Melanargia using sequence information from three genes [mitochondrial cox1 barcode region (658 bp), ribosomal 16S rRNA (c. 518 bp), and nuclear wg (404 bp)]. Results show a lack of DNA divergence among several poorly characterized taxa, as well as deep divergences within and between others. We corroborated the molecular information with morphological and genitalic characters as well as with geographic data. We revise the taxonomy of Melanargia, and propose a new systematic scheme for the group. We revive some previous synonymies (M. lucasi meadwaldoi stat. rev., M. ines fathme stat. rev., M. ines jahandiezi stat. rev., M. meridionalis tapaishanensis stat. rev.), revise the status of some subspecies into species (M. transcaspica stat. nov., M. lucida stat. nov., M. wiskotti stat. nov.) and of several species into subspecies of other taxa (M. evartianae sadjadii stat. nov., M. larissa hylata stat. nov., M. larissa grumi stat. nov., M. larissa syriaca stat. nov., M. larissa titea stat. nov., M. lugens montana stat. nov., M. epimede ganymedes stat. nov.), revise the status of subspecies and transfer them to other species (M. larissa lorestanensis stat. nov., M. larissa iranica stat. nov., M. larissa karabagi stat. rev., M. larissa kocaki stat. nov., M. transcaspica eberti stat. nov.), and propose new synonymies (M. larissa titea = M. titea standfussi syn. nov. = M. titea titania syn. nov., M. leda leda = M. leda yunnana syn. nov., M. lugens lugens = M. lugens ahyoui syn. nov., M. lugens hengshanensis = M. lugens hoenei syn. nov., M. halimede halimede = M. halimede gratiani syn. nov., M. asiatica asiatica = M. asiatica dejeani syn. nov., = M. asiatica elisa syn. nov., = M. asiatica sigberti syn. nov.). further phylogenetic relationships with other Satyrines remaining unclear. Previous molecular studies have suggested various members of Erebiini, Maniolini or Satyrini (Martin et al., 2000; Yin et al., 2007), or the Asiatic Orsotriaena, Neotropical Cyllopsis or Afrotropical Neocoenyra (Peña et al., 2006) as closest relatives of Melanargiini. Within Melanargia, three subgenera are often recognized: Melanargia (including the taxa M. galathea, M. russiae, M. larissa, M. hylata, M. titea, M. syriaca, etc.); Argeformia (including M. arge, M. ines, M. occitanica and M. pherusa); and Halimede (including eight species confined to eastern Asia) . Disagreement over the status and placement of species within these subgenera (e.g. see Wagener,

Psathyrella species growing on dung or occasionally on dung in the Nordic countries were studied using morphological characters and nu-rDNA sequence data and type collections were examined when available. Fourteen species capable of growing on dung were identified. Descriptions are given of all dung-inhabiting species and to a lesser extent of the species occasionally growing on dung. Three new species are described: Psathyrella fimiseda, P. merdicola, and P. scatophila. P. stercoraria is described as a new species in order to validate the name. A key to the coprophilous species in Europe including the species described by Peck & Smith from North America is provided. The phylogenetic analyses recovered four major supported clades within Psathyrellaceae corresponding to Parasola, Coprinopsis, Lacrymaria/Spadiceae pro parte, and Psathyrella. The status of Coprinellus was ambiguous. The current morphology-based infrageneric classification of Psathyrella was not supported by the phylogenetic analyses and a coprophilous habit has apparently evolved on multiple occasions. Three new combinations are proposed: Parasola conopilus, Coprinopsis marcescibilis, and Coprinopsis pannucioides.

This study is the most extensive molecular study of the gastropod families Trochidae and Calliostomatidae published to date, in terms of both numbers of taxa and of gene sequences. As a result of Bayesian phylogenetic analyses of molecular sequence data from one nuclear gene and three mitochondrial genes, we propose dramatic changes to Trochidae family systematics, present the first molecular phylogeny for Calliostomatidae and include the first published sequence data for the enigmatic subfamily Thysanodontinae. Our phylogeny demonstrates that within the family Trochidae there is strong support for three subfamilies new to traditional classifications: Alcyninae subfam. nov., Fossarininae and Chrysostomatinae subfam. nov. As proposed, Alcyninae consists only of the nominotypical genus Alcyna, which is sister to all other trochids. The subfamily Fossarininae, as defined here, includes Fossarina, Broderipia, Synaptocochlea and ''Roya" eximia and probably also Clydonochilus and Minopa. The subfamily Chrysostomatinae comprises the genera Chrysostoma and Chlorodiloma. Additional molecular support is also obtained for recently redefined Trochinae, Monodontinae, and Cantharidinae and for the traditionally recognised subfamilies Umboniinae and Stomatellinae. The subfamily Lirulariinae is not supported by the molecular data, but rather is incorporated into Umboniinae. We also demonstrate that the current concept of the subfamily Margaritinae (previously a trochid subfamily, but recently and provisionally assigned to Turbinidae) is not monophyletic. We provide preliminary evidence that whereas Margarella rosea (previously a member of Margaritinae) belongs in the trochid subfamily Cantharidinae, its presumptive congener M. antarctica is not a trochid, but instead clusters with the thysanodontine genus Carinastele. Based on the phylogenetic placement of C. kristelleae, we agree with previous proposals based on morphological data that Thysanodontinae are more closely related to Calliostomatidae than Trochidae. Both Calliostoma and Carinastele are carnivorous and if a sister relationship can be confirmed between Carinastele and Margarella antarctica it might mean that carnivory evolved twice in Trochoidea. The direction of dietary changes was not investigated in this study, but mapping diet onto the phylogeny suggests that true herbivory is predominantly a derived character. The new classification system also means that five trochid subfamilies are predominantly associated with hard substrata, one with soft substrata (Umboniinae) and two with algae and seagrass (Alcyninae and Cantharidinae). There has been a shift back to hard substrata in one umboniine clade. Two of three clades within Calliostomatidae were predominantly associated with hard substrata, but one Japanese clade is associated with sand. The finding of three new, unidentified species from very deep water means that Trochidae, like Calliostomatidae, now includes species found at bathyal depths. More deep-water species may be found as increased sampling leads to the discovery of new species.

The taxonomy of the British elms is notoriously complicated and a satisfactory consensus classification remains elusive. This taxonomic complexity appears to be attributable to the reproductive biology of the species. Ulmus glabra Huds. reproduces sexually and its taxonomic status is widely (albeit not universally) accepted. In contrast, the suckering elms of the U. minor complex (U. minor Mill. emend. Richens sensu latissimo) rarely reproduce by seed in Britain. Instead they perpetuate predominantly by vegetative reproduction; arguments regarding their taxonomy are legion. We have used molecular markers (RAPDs) to investigate the amounts and partitioning of clonal diversity and taxon inter-relationships in the British elms, focusing on a particularly enigmatic suckering elm, U. plotii Druce. Our molecular data suggest that all samples of U. plotii that precisely match the type description are ramets of a single genet, the distribution of which is attributable to human planting. Morphologically similar samples, which have many but not all of the U. plotii diagnostic characters, do not cluster with U. plotii when the RAPD data are analysed using principal coordinates analysis (PCO). Instead, they are scattered on the PCO plots throughout the broader range of variability of the U. minor complex. The implications of these results for the taxonomy of the British elms are discussed, and the need to combine knowledge of population structure with taxonomic pragmatism is emphasized.

Great advances have been made in our understanding of the phylogeny and classification of Aga-vaceae in the last 20 years. In older systems Agavaceae were paraphyletic due to overemphasis of ovary position or habit. Discovery of a unique bimodal karyotype in Agave and Yucca eventually led to a reexamination of concepts and relationships in all the lilioid monocots, which continues to the present day. Developments in cytogenetics, microscopy, phylogenetic systematics, and most recently DNA technology have led to remarkable new insights. Large-scale rbcL sequence studies placed Agavaceae with the core Asparagales and identified closely related taxa. Analysis of cpDNA restriction sites, rbcL, and ITS nrDNA sequences all supported removal of Dracaenaceae, Nolinaceae, and clarified relationships. Agavaceae s.s. presently consists of Agave, Beschorneria, Furcraea, Hesperaloe, Hes-peroyucca, Manfreda, Polianthes, Prochnyanthes, and Yucca. In this paper we analyze recently obtained ndhF sequence data from Agavaceae and Asparagales and discuss the implications for classification. Parsimony analysis of ndhF data alone resolves most genera of Agavaceae and supports the inclusion of Camassia, Chlorogalum, Hesperocallis, and Hosta within Agavaceae s.l. Analysis of combined ndhF and rbcL data sets of selected Asparagales results in better resolution and stronger bootstrap support for many relationships. Combination of all available ndhF, rbcL, and ITS data in a single analysis results in the best resolution currently available for Agavaceae s.l. Implications for classification schemes past and present are discussed.

Although tribe Stachydeae (Lamiaceae) is considered monophyletic, relationships within the tribe are still
poorly understood. The complexity of Stachydeae includes paraphyletic genera, considerable morphological
plasticity, a range of ploidy levels, and presumably frequent natural hybridization. We performed
parsimony and Bayesian phylogenetic analyses of nuclear (ribosomal ITS) and plastid (trnL intron, trnL–
trnF spacer, rps16 intron) DNA sequence data from a taxonomically and geographically broad sampling
of the tribe to identify major evolutionary lineages and to test taxonomic hypotheses within this largest
of all lamioid tribes. We included 143 accessions corresponding to 121 species, representing both Old and
New World species, and all 12 recognized genera of tribe Stachydeae. Both nuclear and plastid data
corroborate monophyly of the tribe, with Melittis as sister to all remaining Stachydeae. For the latter
well-supported clade, we suggest the phylogenetic name Eurystachys. Within Eurystachys, although
monophyly is supported by both nuclear and plastid data for several named and unnamed groups, the
majority of recognized taxa appear to be para- or polyphyletic. The taxon compositions of most subclades
are congruent between the plastid and nuclear tree topologies, whereas their relative phylogenetic
placements are often not. This level of plastid–nuclear incongruence suggests considerable impact of
hybridization in the evolution of Stachydeae.

Phylogenetic analyses of four nuclear genes, namely the large and small subunits of the nuclear ribosomal RNA, transcription elongation factor 1-alpha and the second largest RNA polymerase II subunit, established that the ecological group of marine bitunicate ascomycetes has representatives in the orders Capnodiales, Hysteriales, Jahnulales, Mytilinidiales, Patellariales and Pleosporales. Most of the fungi sequenced were intertidal mangrove taxa and belong to members of 12 families in the Pleosporales: Aigialaceae, Didymellaceae, Leptosphaeriaceae, Lenthitheciaceae, Lophiostomataceae, Massarinaceae, Montagnulaceae, Morosphaeriaceae, Phaeosphaeriaceae, Pleosporaceae, Testudinaceae and Trematosphaeriaceae. Two new families are described: Aigialaceae and Morosphaeriaceae, and three new genera proposed: Halomassarina, Morosphaeria and Rimora. Few marine species are reported from the Dothideomycetidae (e.g. Mycosphaerellaceae, Capnodiales), a group poorly studied at the molecular level. New marine lineages include the Testudinaceae and Manglicola guatemalensis in the Jahnulales. Significantly, most marine Dothideomycetes are intertidal tropical species with only a few from temperate regions on salt marsh plants (Spartina species and Juncus roemerianus), and rarely totally submerged (e.g. Halotthia posidoniae and Pontoporeia biturbinata on the seagrasses Posidonia oceanica and Cymodocea nodosum). Specific attention is given to the adaptation of the Dothideomycetes to the marine milieu, new lineages of marine fungi and their host specificity.

Phylogenetic relationships, limits of species, and genera within Lycoperdaceae, were inferred by use of ITS and LSU nu-rDNA sequence data. Lycoperdaceae was confirmed as monophyletic, and Mycenastrum corium as a sister taxon to the ingroup. Four major clades were identified and received weak to moderate support and correspond with the genera Lycoperdon, Bovista, Calvatia, and Disciseda. The Lycoperdon clade includes species from Lycoperdon, Vascellum, Morganella, Handkea, Bovistella, and Calvatia. The structure within the Lycoperdon clade is unresolved and several clades are more or less unsupported, which suggests treating the supported Lycoperdon clade as the genus Lycoperdon. L. nigrescens and L. caudatum occur on single branches and their phylogenetic positions could not be resolved. The phylogenetic analyses identified 31 species of Lycoperdon, 11 species of Bovista, six species of Calvatia, and two species of Disciseda. In Lycoperdon three new species were recognized. A new species closely related to B. limosa is identified and discussed. A classification of Lycoperdaceae is proposed based on the results of the phylogenetic analyses.

Species of Ulva occur worldwide in all aquatic habitats from freshwater through brackish to fully saline environments. The scarcity of stable morphological characters and the morphological plasticity linked to environmental conditions typical of species referred to this genus make identification and circumscription problematic. In Ireland and Britain the taxonomy of Ulva species has been uncertain, and only three species have been reported: Ulva lactuca, U. rigida and U. olivascens (later reassigned to Umbraulva olivascens). We reassessed the taxonomic status of this genus by combining morphological investigations with analyses of rbcL sequence data for 24 selected specimens from the Irish and southern British shores. This combination of methods allowed the identification of seven lineages, which were considered to represent the following species: Ulva rigida, U. scandinavica, U. lactuca, U. gigantea, U. rotundata, U. californica and Umbraulva olivascens. Of these, U. scandinavica, U. gigantea, U. rotundata and U. californica are newly reported; the distribution of U. olivascens was shown to be much wider than previously thought. The use of morphological features proved to be largely inconclusive and of limited value for circumscription of species. In the rbcL phylogeny, U. olivascens formed a sister clade to all other species. The results support the conspecificity of U. rigida, U. scandinavica and U. armoricana and the conspecificity of U. pseudocurvata and U. compressa already suggested in previous studies.