A New Miocene-Divergent Lineage of Old World Racer Snake from India

A distinctive early Miocene-divergent lineage of Old world racer snakes is described as a new genus and species based on three specimens collected from the western Indian state of Gujarat. Wallaceophis gen. et. gujaratenesis sp. nov. is a members of a clade of old world racers. The monotypic genus represents a distinct lineage among old world racers is recovered as a sister taxa to Lytorhynchus based on ~3047bp of combined nuclear (cmos) and mitochondrial molecular data (cytb, ND4, 12s, 16s). The snake is distinct morphologically in having a unique dorsal scale reduction formula not reported from any known colubrid snake genus. Uncorrected pairwise sequence divergence for nuclear gene cmos between Wallaceophis gen. et. gujaratenesis sp. nov. other members of the clade containing old world racers and whip snake is 21–36%.     

Phylogenetic relationships of North American Antirrhinum (Veronicaceae)

Species of the genus Antirrhinum (Veronicaceae) provide excellent opportunities for research on plant evolution given their extensive morphological and ecological diversity. These opportunities are enhanced by genetic and developmental data from the model organism Antirrhinum majus. The genus Antirrhinum includes 15 New World species in section Saerorhinum and 21 Old World species in sections Antirrhinum and Orontium. Phylogenetic analyses of sequences of the internal transcribed spacer region (ITS) of nuclear ribosomal DNA were conducted for 19 Antirrhinum species, including all species from the New World, and 13 related genera in the tribe Antirrhineae. These analyses confirm the monophyly of Antirrhinum given the inclusion of the small genus Mohavea and exclusion of A. cyathiferum. The New World species, all of which are tetraploid, form a clade that is weakly supported as sister to the Old World sect. Orontium. The Old World species in sect. Antirrhinum form a well-supported clade that is sister to the remainder of the genus. In addition, both molecular and morphological data are used in the most comprehensive effort to date focused on recovering the phylogenetic relationships among the extremely diverse species in section Saerorhinum.     

Genetic divergence and evolutionary relationships of the old and new world emberizidae

Genetic differentiation and evolutionary relationships were surveyed on 12 species of the Old and seven species of the New World Emberizidae by allozyme electrophoresis of 20 loci. Genetic variability of the Emberizidae is similar to those of the other Passeriformes. The degree of genetic differentiation in the family were large among species of the genus Emberiza of the Old World, and also among genera of the New World Emberizidae. Evolutionary relationships of the Emberizidae based on these genetic distances differed considerably from those of previous publications on some points: (1) Emberiza tristrami, E. elegans, E. bruniceps and E. schoeniclus were genetically much diverged from the other Emberiza as a species of the same genus. (2) Some genetic distances between Emberiza were larger than distances between subfamilies of the New World Emberizidae. (3) Species of the Cardinarinae examined genetically, belonged to the Emberizinae of the New World. Genetic data did not support the current classification that the Old World buntings arose from the New World forms by recent colonization. Discussion was made on the evolution of the Old and New World Emberizidae from the genetic view point.     

Molecular phylogenetics of the giant genus Croton and tribe Crotoneae (Euphorbiaceae sensu stricto) using ITS and TRNL-TRNF DNA sequence data

Parsimony, likelihood, and Bayesian analyses of nuclear ITS and plastid trnL-F DNA sequence data are presented for the giant genus Croton (Euphorbiaceae s.s.) and related taxa. Sampling comprises 88 taxa, including 78 of the estimated 1223 species and 29 of the 40 sections previously recognized of Croton. It also includes the satellite genus Moacroton and genera formerly placed in tribe Crotoneae. Croton and all sampled segregate genera form a monophyletic group sister to Brasiliocroton, with the exception of Croton sect. Astraea, which is reinstated to the genus Astraea. A small clade including Moacroton, Croton alabamensis, and C. olivaceus is sister to all other Croton species sampled. The remaining Croton species fall into three major clades. One of these is entirely New World, corresponding to sections Cyclostigma, Cascarilla, and Velamea sensu Webster. The second is entirely Old World and is sister to a third, also entirely New World clade, which is composed of at least 13 of Webster's sections of Croton. This study establishes a phylogenetic framework for future studies in the hyper-diverse genus Croton, indicates a New World origin for the genus, and will soon be used to evaluate wood anatomical, cytological, and morphological data in the Crotoneae tribe.     

Salvia (Lamiaceae) is not monophyletic: implications for the systematics, radiation, and ecological specializations of Salvia and tribe Mentheae

Salvia, with over 900 species from both the Old and New World, is the largest genus in the Lamiaceae. Unlike most members of the subfamily Nepetoideae to which it belongs, only two stamens are expressed in Salvia. Although the structure of these stamens is remarkably variable across the genus, generally each stamen has an elongate connective and divergent anther thecae, which form a lever mechanism important in pollination. In a preliminary investigation of infrageneric relationships within Salvia, the monophyly of the genus and its relationship to other members of the tribe Mentheae were investigated using the chloroplast DNA regions rbcL and trnL-F. Significant conclusions drawn from the data include: Salvia is not monophyletic, Rosmarinus and Perovskia together are sister to an Old World clade of Salvia, the section Audibertia is sister to subgenus Calosphace or the monotypic Asian genus Dorystaechas, and the New World members of section Heterosphace are sister to section Salviastrum. Owing to the non-monophyly of Salvia, relationships at the next clearly monophyletic level, tribe Mentheae, were investigated.     

A molecular phylogeny of the Old World stingless bees (Hymenoptera: Apidae: Meliponini) and the non-monophyly of the large genus Trigona

Abstract.  We examined the inter- and infrageneric relationships of Old World Meliponini with a near-complete sampling of supra-specific taxa. DNA sequences for the taxa were collected from four genes (mitochondrial 16S rRNA, nuclear long-wavelength rhodopsin copy 1 (opsin), elongation factor-1α copy F2 and arginine kinase). Additional sampling of New World taxa indicated that Trigona sensu lato is not monophyletic: Trigona from the Indo-Malayan/Australasian Regions forms a large clade distantly related to the Neotropical Trigona . A separate clade comprises the Afrotropical meliponines, and includes the 'minute' species found in the Afrotropical, Indo-Malayan and Australasian Regions. The Neotropical genus Melipona , by contrast with previous investigations, is not the sister lineage to the remaining stingless bees, but falls within the strongly supported Neotropical clade. These results constitute the framework for a revised classification and ongoing biological investigations of Meliponini. A single taxonomic change, Heterotrigona bakeri stat.n. , is proposed on the basis of sequence divergence.     

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

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

Piecing together the "new" Plantaginaceae

Scrophulariaceae is one of the families that has been divided extensively due to the results of DNA sequence studies. One of its segregates is a vastly enlarged Plantaginaceae. In a phylogenetic study of 47 members of Plantaginaceae and seven outgroups based on 3561 aligned characters from four DNA regions (the nuclear ribosomal ITS region and the plastid trnL-F, rps16 intron, and matK-trnK intron regions), the relationships within this clade were analyzed. The results from parsimony and Bayesian analyses support the removal of the Lindernieae from Gratioleae to a position outside Plantaginaceae. A group of mainly New World genera is paraphyletic with respect to a clade of Old World genera. Among the New World taxa, those offering oil as a pollinator reward cluster together. Ourisia is sister to this clade. Gratioleae consist of Gratiola, Otacanthus, Bacopa, Stemodia, Scoparia, and Mecardonia. Cheloneae plus Russelia and Tetranema together constitute the sister group to a clade predominantly composed of Old World taxa. Among the Old World clade, Ellisiophyllum and Lafuentea have been analyzed for the first time in a molecular phylogenetic analysis. The former genus is sister to Sibthorpia and the latter is surprisingly the sister to Antirrhineae.     

Phylogenetic relationships in Rosaceae inferred from chloroplast matK and trnL-trnF nucleotide sequence data

 Phylogenetic relationships in Rosaceae were studied using parsimony analysis of nucleotide sequence data from two regions of the chloroplast genome, the matK gene and the trnL-trnF region. As in a previously published phylogeny of Rosaceae based upon rbcL sequences, monophyletic groups were resolved that correspond, with some modifications, to subfamilies Maloideae and Rosoideae, but Spiraeoideae were polyphyletic. Three main lineages appear to have diverged early in the evolution of the family: 1) Rosoideae sensu stricto, including taxa with a base chromosome number of 7 (occasionally 8); 2) actinorhizal Rosaceae, a group of taxa that engage in symbiotic nitrogen fixation; and 3) the rest of the family. The spiraeoid genus Gillenia, not included in the rbcL study, was strongly supported as the sister taxon to Maloideae sensu lato. A New World origin of Maloideae is suggested. The position of the economically important genus Prunus and the status of subfamily Amygdaloideae remain unresolved. Received February 27, 2001 Accepted October 11, 2001     

Phylogenetic Framework for Trema (Celtidaceae)

We used ITS and trnL sequence data, analyzed separately and combined by MP, to explore species relationships and concepts in Trema (Celtidaceae), a pantropical genus of pioneer trees. Whether Trema is monophyletic or includes Parasponia is still unresolved. Three clades within Trema received moderate to high support, one from the New World and two from the Old World, but their relationships were not resolved. In the New World, specimens of T. micrantha formed two groups consistent with endocarp morphology. Group I, with smaller brown endocarps, is a highly supported clade sister to T. lamarckiana. Group II, with larger black endocarps, is poorly resolved with several subclades, including the highly supported T. integerrima clade. Both Old World clades contain Asian and African species, with three or more species in each region. Trema orientalis is not monophyletic: specimens from Africa formed a highly supported clade sister to T. africana, while those from Asia were sister to T. aspera from Australia.     

A multi-gene phylogeny of aquiline eagles (Aves: Accipitriformes) reveals extensive paraphyly at the genus level

The phylogeny of the tribe Aquilini (eagles with fully feathered tarsi) was investigated using 4.2 kb of DNA sequence of one mitochondrial (cyt b) and three nuclear loci (RAG-1 coding region, LDH intron 3, and adenylate-kinase intron 5). Phylogenetic signal was highly congruent and complementary between mtDNA and nuclear genes. In addition to single-nucleotide variation, shared deletions in nuclear introns supported one basal and two peripheral clades within the Aquilini. Monophyly of the Aquilini relative to other birds of prey was confirmed. However, all polytypic genera within the tribe, Spizaetus, Aquila, Hieraaetus, turned out to be non-monophyletic. Old World Spizaetus and Stephanoaetus together appear to be the sister group of the rest of the Aquilini. Spizastur melanoleucus and Oroaetus isidori are nested among the New World Spizaetus species and should be merged with that genus. The Old World 'Spizaetus' species should be assigned to the genus Nisaetus (Hodgson, 1836). The sister species of the two spotted eagles (Aquila clanga and Aquila pomarina) is the African Long-crested Eagle (Lophaetus occipitalis). Hieraaetus fasciatus/spilogaster are closest to Aquila verreauxii and should be merged with that genus. Wahlberg's Eagle H. wahlbergi, formerly placed in Aquila, is part of a clade including three small Hieraaetus species (pennatus, ayresii, and morphnoides). The Martial Eagle (Polemaetus bellicosus) is the sister species of the Aquila/Hieraaetus/Lophaetus clade. Basal relationships within this clade remained unresolved. Parsimony reconstruction of the evolution of plumage pattern within Aquilini suggests that: (1) transverse barring of parts of the body plumage was lost in the Palearctic Aquila-Hieraaetus clade, (2) pale underparts in adult plumage evolved three times independently, and (3) dimorphic adult plumage is a derived character of the small-bodied Hieraaetus clade.     

Multiple colonization of Madagascar and Socotra by colubrid snakes: evidence from nuclear and mitochondrial gene phylogenies

Colubrid snakes form a speciose group of unclarified phylogeny. Their almost cosmopolitan distribution could be interpreted as a product of plate-tectonic vicariance. We used sequences of the nuclear c-mos, the mitochondrial cytochrome b and the 16S rRNA genes in 41 taxa to elucidate the relationships between the endemic colubrid genera found in Madagascar and in the Socotra archipelago. The well-resolved trees indicate multiple origins of both the Malagasy and the Socotran taxa. The Malagasy genus Mimophis was nested within the Psammophiinae, and the Socotran Hemerophis was closely related to Old World representatives of the former genus Coluber. The remaining 14 genera of Malagasy colubrids formed a monophyletic sister group of the Socotran Ditypophis (together forming the Pseudoxyrhophiinae). Molecular-clock estimates place the divergence of Malagasy and Socotran colubrids from their non-insular sister groups into a time-frame between the Eocene and Miocene. Over-seas rafting is the most likely hypothesis for the origin of at least the Malagasy taxa. The discovery of a large monophyletic clade of colubrids endemic to Madagascar indicates a need for taxonomic changes. The relationship of this radiation to the Socotran Ditypophis highlights the potential of the Indian Ocean islands to act as an evolutionary reservoir for lineages that have become extinct in Africa and Asia.     

The RAG-1 exon in the avian order Caprimulgiformes: phylogeny, heterozygosity, and base composition

We sequenced 2.8 kb of the RAG-1 exon for most of the extant genera in the avian order Caprimulgiformes to investigate monophyly of the order and phylogeny within the traditional families. The order is not monophyletic: the Aegothelidae (owlet-nightjars) were the sister group of the Apodiformes (swifts and hummingbirds). There was no support for the monophyly of a clade containing the remaining families of Caprimulgiformes. However, the RAG-1 data strongly supported a relationship between the Podargidae (frogmouths) and Caprimulgidae (nightjars). Within the Caprimulgidae, the Australasian genus Eurostopodus was sister to the rest of the family, which in turn was composed of four major clades, three of which were restricted to the New World and primarily to the Neotropics. The Old World caprimulgids form a monophyletic clade embedded within the New World taxa; consequently, most Old World nightjars are probably the result of a single expansion out of the Neotropics. The genus Caprimulgus was not found to be monophyletic. Several species in the Caprimulgidae have both elevated heterozygosity and high GC3 content; it is likely that these are causally related.     

A complete generic phylogeny of Malpighiaceae inferred from nucleotide sequence data and morphology

? Premise of the study: The Malpighiaceae include ～1300 tropical flowering plant species in which generic definitions and intergeneric relationships have long been problematic. The goals of our study were to resolve relationships among the 11 generic segregates from the New World genus Mascagnia, test the monophyly of the largest remaining Malpighiaceae genera, and clarify the placement of Old World Malpighiaceae. ? Methods: We combined DNA sequence data for four genes (plastid ndhF, matK, and rbcL and nuclear PHYC) from 338 ingroup accessions that represented all 77 currently recognized genera with morphological data from 144 ingroup species to produce a complete generic phylogeny of the family. ? Key results and conclusions: The genera are distributed among 14 mostly well-supported clades. The interrelationships of these major subclades have strong support, except for the clade comprising the wing-fruited genera (i.e., the malpighioid+Amorimia, Ectopopterys, hiraeoid, stigmaphylloid, and tetrapteroid clades). These results resolve numerous systematic problems, while others have emerged and constitute opportunities for future study. Malpighiaceae migrated from the New to Old World nine times, with two of those migrants being very recent arrivals from the New World. The seven other Old World clades dispersed much earlier, likely during the Tertiary. Comparison of floral morphology in Old World Malpighiaceae with their closest New World relatives suggests that morphological stasis in the New World likely results from selection by neotropical oil-bee pollinators and that the morphological diversity found in Old World flowers has evolved following their release from selection by those bees.     

The evolutionary history of Eryngium (Apiaceae, Saniculoideae): rapid radiations, long distance dispersals, and hybridizations

Eryngium is the largest and arguably the most taxonomically complex genus in the family Apiaceae. Infrageneric relationships within Eryngium were inferred using sequence data from the chloroplast DNA trnQ-trnK 5'-exon and nuclear ribosomal DNA ITS regions to test previous hypotheses of subgeneric relationships, explain distribution patterns, reconstruct ancestral morphological features, and elucidate the evolutionary processes that gave rise to this speciose genus. In total, 157 accessions representing 118 species of Eryngium, 15 species of Sanicula (including the genus Hacquetia that was recently reduced to synonymy) and the monotypic Petagnaea were analyzed using maximum parsimony and Bayesian methods. Both separate and simultaneous analyses of plastid and nuclear data sets were carried out because of the prevalence of polyploids and hybrids within the genus. Eryngium is confirmed as monophyletic and is divided into two redefined subgenera: Eryngium subgenus Eryngium and E. subgenus Monocotyloidea. The first subgenus includes all examined species from the Old World (Africa, Europe, and Asia), except Eryngium tenue, E. viviparum, E. galioides, and E. corniculatum. Eryngium subgenus Monocotyloidea includes all examined species from the New World (North, Central and South America, and Australia; herein called the "New World sensu stricto" clade) plus the aforementioned Old World species that fall at the base of this clade. Most sectional and subgeneric divisions previously erected on the basis of morphology are not monophyletic. Within the "New World sensu stricto" group, six clades are well supported in analyses of plastid and combined plastid and nuclear data sets; the relationships among these clades, however, are unresolved. These clades are designated as "Mexican", "Eastern USA", "South American", "North American monocotyledonous", "South American monocotyledonous", and "Pacific". Members of each clade share similar geographical distributions and/or morphological or ecological traits. Evidence from branch lengths and low sequence divergence estimates suggests a rapid radiation at the base of each of these lineages. Conflict between chloroplast and nuclear data sets is weak, but the disagreements found are suggestive that hybrid speciation in Eryngium might have been a cause, but also a consequence, of the different rapid radiations observed. Dispersal-vicariance analysis indicates that Eryngium and its two subgenera originated from western Mediterranean ancestors and that the present-day distribution of the genus is explained by several dispersal events, including one trans-Atlantic dispersal. In general, these dispersals coincide with the polytomies observed, suggesting that they played key roles in the diversification of the genus. The evolution of Eryngium combines a history of long distance dispersals, rapid radiations, and hybridization, culminating in the taxonomic complexity observed today in the genus.     

Evolution, biogeography, and patterns of diversification in passerine birds

This paper summarizes and discusses the many new insights into passerine evolution gained from an increased general interest in avian evolution among biologists, and particularly from the extensive use of DNA sequence data in phylogenetic reconstruction. The sister group relationship between the New Zealand rifleman and all other passerines, indicates the importance of the former southern supercontinent Gondwana in the earliest evolution of this group. Following the break-up of Gondwana, the ancestors of other major passerine groups became isolated in Australia (oscines), South America (New World suboscines), and possibly, the then connected Kerguelen Plateau/India/Madagascar tectonic plates (Old World suboscines). The oscines underwent a significant radiation in the Australo-Papuan region and only a few oscine lineages have spread further than to the nearby Southeast Asia. A remarkable exception is the ancestor to the vast Passerida radiation, which now comprises 35% of all bird species. This group obviously benefitted greatly from the increased diversity in plant seed size and morphology during the Tertiary. The lyrebirds (and possibly scrub-birds) constitute the sister group to all other oscines, which renders "Corvida" ( sensu Sibley and Ahlquist 1990) paraphyletic. Sequence data suggests that Passerida, the other clade of oscines postulated based on the results of DNA–DNA hybridizations, is monophyletic, and that the rockfowl and rock-jumpers are the most basal members of this clade. The suboscines in the Old World (Eurylamides) and the New World (Tyrannides), respectively, are sister groups. A provisional, working classification of the passerines is presented based on the increased understanding of the major patterns of passerine evolution.     

Sarcostemma R.Br. (Apocynaceae — Asclepiadoideae) — a controversial generic circumscription reconsidered: Evidence fromtrnL-F spacers

The polyphyly ofSarcostemma sensu latu, suspected on morphological and karyological reasons is confirmed by analysis of thetrnL-F spacer region. With the exception ofCynanchum montevidense (subgen.Mellichampia, Sundell 1981), Old World and New World taxa belong to different clades.Sarcostemma sensu stricto andPlatykeleba show a strong affinity to Old WorldCynanchum; the affinities ofOxystelma cannot be determined at present.Philibertia andBlepharodon are sister groups, both are sister toFunastrum, andPentacyphus is basal to the New World clade.     

啄木鸟科内谱系生物地理学新探

啄木鸟群体共包含254种,但早期对啄木鸟的分类学研究局限于形态学、行为学和鸣唱法等方向,分子研究结果又彼此存在差异,因此啄木鸟分类系统目前还有争议。分子数据的大量累积为啄木鸟系统发育的研究提供了条件。利用从GenBank获取的ND2基因序列,对啄木鸟科179种啄木鸟采用NJ法、MP法以及ML法分别进行了分子进化树构建,同时用NJ法重建了Picumnus属分子进化树。此外又利用cytb基因序列采用NJ法对Dryobates属和Picoides属进行分子进化树重建。我们的结果显示,姬啄木亚科Picumnus属新大陆物种彼此的进化关系仍需进一步研究,而该属唯一一种旧大陆种P.innominatus,种内遗传差异在种间水平依然显著,这说明其种内遗传差异一直被低估了。在啄木鸟亚科内,Hemicircus属和Nesoctites属为姐妹关系,而Geocolaptes olivaceus插入了Campethera属支系中,并非与其构成姐妹群体。此外,一些姐妹群在新旧大陆上的分布,推测这种分布可能与第四纪冰川有关。啄木鸟从旧大陆向新大陆迁移,在第四纪冰川作用下不断发生分布范围的扩张与收缩,最终形成现存的分布格局。     

Biogeography of Old World emballonurine bats (Chiroptera: Emballonuridae) inferred with mitochondrial and nuclear DNA

Extant bats of the genus Emballonura have a trans-Indian Ocean distribution, with two endemic species restricted to Madagascar, and eight species occurring in mainland southeast Asia and islands in the western Pacific Ocean. Ancestral Emballonura may have been more widespread on continental areas, but no fossil identified to this genus is known from the Old World. Emballonura belongs to the subfamily Emballonurinae, which occurs in the New and Old World. Relationships of all Old World genera of this subfamily, including Emballonura and members of the genera Coleura from Africa and western Indian Ocean islands and Mosia nigrescens from the western Pacific region, are previously unresolved. Using 1833 bp of nuclear and mitochondrial genes, we reconstructed the phylogenetic history of Old World emballonurine bats. We estimated that these lineages diverged around 30 million years ago into two monophyletic sister groups, one represented by the two taxa of Malagasy Emballonura, Coleura and possibly Mosia, and the other by a radiation of Indo-Pacific Emballonura, hence, rendering the genus Emballonura paraphyletic. The fossil record combined with these phylogenetic relationships suggest at least one long-distance dispersal event across the Indian Ocean, presumably of African origin, giving rise to all Indo-Pacific Emballonura species (and possibly Mosia). Cladogenesis of the extant Malagasy taxa took place during the Quaternary giving rise to two vicariant species, E. atrata in the humid east and E. tiavato in the dry west.