Molecular phylogeny and biogeography of the eastern Tapaculos (Aves: Rhinocryptidae: Scytalopus, Eleoscytalopus): Cryptic diversification in Brazilian Atlantic Forest

Scytalopus and the recently erected Eleoscytalopus are among the Neotropical groups of birds whose taxonomy is most difficult to resolve given their very conservative morphology. We investigated the phylogeny and species limits of Eleoscytalopus and the eastern Scytalopus using two mitochondrial genes and two nuclear introns of multiple individuals from all species of these groups. The eastern Scytalopus are separated in three well defined clades also supported by morphological or vocal characteristics, although the relationships between these clades could not be resolved. We found several allopatric and very divergent lineages in these genera whose characteristics are consistent with species-level divergence, especially in S. speluncae. The great divergence between E. psychopompus and its sister species supports the former as a valid species. Our results corroborate the importance of the Bahia refuge as an avian center of endemism.     

Systematics and biogeography of the Andean genusEriocnemis (Aves: Trochilidae)

Summary With 11 currently recognised species, the genusEriocnemis (Reichenbach, 1849) is one of the most diversified Andean trochilid groups occupying mainly open montane habitats such as the edges of cloud forest or páramos. On the basis of distributional and morphological patterns, this study highlights the geographical variation and biogeography of the taxon. Characteristics common to all these species are the greenish dorsal plumage, the conspicuous and mostly whitish tibial tufts, and a fairly pronounced tail bifurcation. With the help of plumage synapomorphies for a cladistic analysis (PAUP*), several species groups or superspecies can be distinguished: theE. vestitus group (incl.E. vestitus, E. godini, E. nigrivestis), theE. luciani group (incl.E. luciani, E. cupreoventris, E. sapphiropygia), and theE. alinae group (incl.E. alinae, E. mirabilis).E. glaucopoides, E. mosquera, andE. derbyi differ quite widely in morphology and ecological requirements from the other species. Three new subspecies are described,E. vestitus arcosi from southern Ecuador and northern Peru, andE. luciani baptistae from central and southern Ecuador. A previously overlooked specimen ofE. luciani from the Andes of Mérida represents the first species record for Venezuela, about 1100 km northeast of the main population range, and should be recognised taxonomically asE. luciani meridae, subsp. nov., on the basis of its unique plumage morphology and geographical separation. Additionally, the unique type ofE. ventralis (Salvin, 1891) is probably of hybrid origin (E. vestitus × cupreoventris). The genus may have evolved in the northern Andes, subsequently spreading southward and invading the central Andes. Its recent range and phylogenetic patterns indicate vicariance events as the major speciation factor inEriocnemis.In memoriam Dr. Luis F. Baptista (1941–2000)     

Hidden generic diversity in Neotropical birds: molecular and anatomical data support a new genus for the "Scytalopus"indigoticus species-group (Aves: Rhinocryptidae)

The genus Scytalopus is a species-rich and taxonomically complicated component of the Neotropical avian family Rhinocryptidae. Probably because Scytalopus is a superficially uniform assemblage, its monophyly has not been seriously questioned. We investigated phylogenetic relationships of a representative set of species in the genus using nuclear and mitochondrial DNA sequences as well as anatomical data, and provided the first test of its presumed monophyly by including in the analyses its hypothesized closest relatives (the genera Myornis, Eugralla, and Merulaxis) as well as most rhinocryptid genera. We found strong support for the paraphyly of the genus Scytalopus, with the Scytalopus indigoticus species-group forming a clade with Merulaxis. A well-supported clade including the genera Eugralla, Myornis, and the remaining Scytalopus was also recovered. Because these results were recovered independently and with strong support using mitochondrial and nuclear data, and were entirely consistent with anatomical data, we erect a new genus for the S.indigoticus species-group. These findings illustrate the importance of formally testing hypotheses of monophyly even for well-accepted groups of Neotropical birds.     

A revision of the family Ciconiidae (Aves)

Behavioural and morphological characteristics of all members of the stork family are summarized. References are given to other papers where these subjects are discussed in greater detail for each group of storks. Based on the evidence now available, a revised classification is suggested (Table II) which divides the Ciconiidae into three tribes, six genera, and 17 species. The following genera (of Peters, 1931) are synonymized with other existing genera: Ibis, Sphenorhynchus, Dissoura, Euxenura , and Xenorhynchus. It is further suggested that Scopus should be placed in a suborder of its own and that Balaeniceps be placed in a monotypic family adjacent to the Ciconiidae, pending further study.     

The arachiform vacuolar body: an overlooked shared character in the ascospores of a large monophyletic group within Parmeliaceae (Xanthoparmelia clade, Lecanorales)

Sections of apothecia were used to study the internal morphology of ascospores in the largest monophyletic clade within Parmeliaceae composed of Xanthoparmelia and related genera. The results were compared with fertile representative species of most other parmelioid clades. All the Xanthoparmelia species had spores with a single smooth vacuole, which was peanut-shaped, with different degrees of constriction in the equatorial plane. This differs from the ellipsoid vacuole of other parmelioids. In the Xanthoparmelia clade, sexual reproduction seems much more common than in other parmelioids. Thus, we suggest that the presence of this unique spore morphology might contribute to the evolutionary success of this monophyletic group. Further, the discovery of this useful ascospore character demonstrates that detailed ascospore morphological studies significantly enhance molecular phylogenetic analyses. Ascospore features may be more taxonomically significant in Parmeliaceae than hitherto considered.     

Systematic relationships of the palaeogene family Presbyornithidae (Aves: Anseriformes)

The early Tertiary (Paleocene and Eocene) family Presbyornithidae is one of the most completely known group of fossil birds. Essentially all parts of the skeleton are represented in the fossil record, allowing a thorough analysis of the phylogenetic position of the family. Forty-two families of nonpasserine birds representing the orders Ciconiiformes, Anseriformes, Galliformes, Gruiformes and Charadriiformes, were included in a cladistic analysis of 71 skeletal characters. The previously suggested anseriform affinity of the Presbyornithidae was confirmed. Furthermore, the family proved to be closer to the Anatidae than to the Anhimidae or Anseranatidae. The many postcranial similarities with certain charadriiform birds as the Burhinidae, obviously are plesiomorphies. By this observation, a better undestanding of character evolution in nonpasserine skeletal morphology is gained. The often suggested close relationship of anseriform and galliform birds is not confirmed by osteology. Instead, the Anseriformes and the Phoenicopteridae form a monophyletic clade that is the sister to the remaining ciconiiform birds. This result renders the Ciconiiformes sensu Wetmore (1960) polyphyletic.     

Circumscription of taxa in the chasmophilous Iranian Stachys species (Lamiaceae: sect. Fragilicaulis, subsect. Fragiles) inferred from isoenzyme variation patterns

Fresh leaves of 150 individuals from 15 populations representing five putative species of Stachys sect. Fragilicaulis, subsect. Fragiles distributed in the Zagros mountains in western Iran were analyzed for isoenzyme variation. Four enzyme systems (peroxidase, esterase, superoxide dismutase and ascorbate peroxidase) have been studied and a total of 32 bands representing seven putative loci have been analyzed by UPGMA using the Euclidean distances. UPGMA analysis resulted in the recognition of three distinct clusters among the considered populations. The average value of Shannon diversity index (H′) estimated for each population ranged from 0.05 to 2.17. The mean number of bands per isoenzyme ranges from 1.60 to 2.50. The value of Euclidean distance ranges from 0.85 to 3.79. The analysis of isoenzyme variation patterns suggests recognizing following species in Stachys sect. Fragilicaulis subsect. Fragiles: Stachys benthamiana (including Stachys megalodonta), Stachys kurdica (including Stachys ballotiformis) and Stachys asterocalyx. These data also suggest paying more attention to geographical distribution of taxa in Stachys for their taxonomic delimitation. This study provides another strong support for application of electrophoretic analysis of isoenzymes in taxonomy at species level.     

A phylogenetic overview of the family Pyronemataceae (Ascomycota, Pezizales)

Partial sequences of nuLSU rDNA were obtained to investigate the phylogenetic relationships of Pyronemataceae, the largest and least studied family of Pezizales. The dataset includes sequences for 162 species from 51 genera of Pyronemataceae, and 39 species from an additional 13 families of Pezizales. Parsimony, ML, and Bayesian analyses suggest that Pyronemataceae is not monophyletic as it is currently circumscribed. Ascodesmidaceae is nested within Pyronemataceae, and several pyronemataceous taxa are resolved outside the family. Glaziellaceae forms the sister group to Pyronemataceae in ML analyses, but this relationship, as well as those of Pyronemataceae to the other members of the lineage, are not resolved with support. Fourteen clades of pyronemataceous taxa are well supported and/or present in all recovered trees. Several pyronemataceous genera are suggested to be non-monophyletic, including Anthracobia, Cheilymenia, Geopyxis, Humaria, Lasiobolidium, Neottiella, Octospora, Pulvinula, Stephensia, Tricharina, and Trichophaea. Cleistothecial and truffle or truffle-like ascomata forms appear to have evolved independently multiple times within Pyronemataceae. Results of these analyses do not support previous classifications of Pyronemataceae, and suggest that morphological characters traditionally used to segregate the family into subfamilial groups are not phylogenetically informative above the genus level.     

In search of monophyletic taxa in the family Desmidiaceae (Zygnematophyceae, Viridiplantae): the genus Cosmarium

Nuclear-encoded small subunit (SSU) rDNA, 1506 group I introns, and chloroplast rbcL genes were sequenced from 97 strains representing the largest desmid genus Cosmarium (45 spp.), its putative relatives Actinotaenium (5 spp.), Xanthidium (4 spp.), Euastrum (9 spp.), Staurodesmus (13 spp.), and other Desmidiaceae (Zygnematophyceae, Streptophyta) and used to assess phylogenetic relationships in the family. Analyses of single genes and of a concatenated data set (3260 nt) established 10 well-supported clades in the family with Cosmarium species distributed in six clades and one nonsupported assemblage. Most of the clades contained representatives of at least two genera highlighting the polyphyletic nature of the genera Cosmarium, Euastrum, Staurodesmus, and Actinotaenium. To enhance resolution between clades, we extended the data set by sequencing the slowly evolving chloroplast-encoded large subunit (LSU) rRNA gene from 40 taxa. Phylogenetic analyses of a concatenated data set (5509 nt) suggested a sister relationship between two clades that consisted mainly of Cosmarium species and included C. undulatum, the type species of the genus. We describe molecular signatures in the SSU rRNA for two clades and conclude that more studies involving new isolates, additional molecular markers, and reanalyses of morphological traits are necessary before the taxonomic revision of the genus Cosmarium can be attempted.     

Molecular characterization of the rbcS multi-gene family of Petunia (Mitchell)

Summary The small subunit (RbcS) of ribulose bisphosphate carboxylase (RuBPCase) is encoded by eight genes in Petunia (Mitchell). These genes can be divided into three subfamilies (51, 117 and 71) based upon hybridization to three petunia rbcS cDNA clones. The nucleotide sequence of six of the eight petunia rbcS genes is presented here and the structure of the genes is discussed with respect to their genomic linkage and their expression levels in petunia leaf tissue. The rbcS genes belonging to the same subfamily encode an identical mature RbcS polypeptide, however the different subfamilies encode distinguishable polypeptides. All the genes, except one, contian two introns within the mature subunit coding region; one gene contains one extra intron within the coding region. There are large regions of nucleotide sequence homology within the introns of genes within a subfamily, but significantly less homology between the introns of genes of different subfamilies. A complex pattern of homology within the multiple genes of the 51 subfamily is observed. There are regions within these genes which share high levels of sequence homology; this homology does not extend throughout the whole gene and the regions of homology do not always occur in adjacent genes. Two 3 rbcS gene fragments which we isolated from the petunia genome show high levels of homology to two of the intact rbcS genes.     

The radiation of the Seicercus burkii complex and its congeners (Aves: Sylviidae): molecular genetics and bioacoustics

Cryptic species of passerine birds lack notable morphological differentiation and can best be identified by molecular and bioacoustic markers. Here we investigate seven cryptic species of the golden-spectacled warbler (Seicercus burkii complex) with respect to territorial song and cytochrome-b (cyt-b) sequences. Their phylogenetic relations to other Seicercus species and to members of the genus Phylloscopus are inferred by the same methods. Three separate lineages of Seicercus are nested within different branches of the molecular Phylloscopus tree. The S. burkii complex is a monophyletic unit comprising seven species (S. burkii s. str., S. whistleri, S. valentini, S. soror, S. omeiensis, S. tephrocephalus and S. affinis). S. xanthoschistos turned out to be a close relative of Phylloscopus davisoni within the P. reguloides group. Two isolated sister taxa, S. grammiceps and S. castaniceps, also branch together with the P. reguloides group. Within the S. burkii complex the overall haplotype and nucleotide diversity is highest in taxa from the Chinese middle and upper mountain belt (S. valentini, S. omeiensis and S. soror), indicating at least partially restricted gene flow in these species. This is explained by the fragmentation of high-altitude habitats in China while in the Himalayas the vicariant species S. whistleri inhabits a more continuous mountain belt at the same altitude. For the Chinese species from medium and high altitudes, past range expansion is indicated by significantly negative Tajima Ds. According to pairwise genetic distances, most species of the S. burkii complex have diverged 5 myr ago, the most recent split between S. burkii and S. tephrocephalus is dated 2 myr ago. Coalescence times for haplotype lineages of the different species range from 9 up to 12 myr, and between 5 and 6 myr for S. burkii and S. tephrocephalus.

Within Seicercus divergence of song features such as frequency parameters and syntax structures correlate with genetic distances between taxa. The three cyt-b lineages of Seicercus correspond to different clusters in a discriminant analysis by acoustic parameters. Common syntax structures of territorial song in the Phylloscopus/Seicercus assemblage are: (1) an introductory element derived from specific calls and (2) a syntax of trills and repeated element groups or a combination of both. There are clear indications that these song structures have repeatedly emerged, were lost or were altered in different branches of the phylogenetic tree at different times. Absolute differences between taxa in frequency parameters or in an acoustic divergence index increase significantly with growing genetic distances. However, due to multiple parallel evolution phylogenetic information provided by single acoustic traits decreases with increasing numbers of taxa involved in the investigation.     

A Case of Rapid Diversification in the Neotropics: Phylogenetic Relationships among Cranioleuca Spinetails (Aves, Furnariidae)

Relationships among the 18-19 species of spinetails of the genus Cranioleuca are difficult to establish. Attempts based on traditional taxonomic characters have failed because of a high degree of homoplasy. Most morphological characters vary independently, producing leap-frog patterns of variation along the Eastern Brazilian Andean track, and behavior and vocalizations vary little. We use mtDNA sequence data from the cyt b and ND2 genes in an attempt to clarify relationships within the genus. We show (i) that Cranioleuca represents a recent burst of speciation and (ii) that a set of species thought by Maijer and Fjelds? (1997) to form a natural group is in fact a paraphyletic assemblage which also includes humid forest species with different pigmentations and vocalizations. However, synapomorphic variation in the sequences is not sufficient to unambiguously resolve the relationships within the genus. Several species (C. baroni, C. antisiensis, C. pyrrhophia, C. albiceps) show more than one haplotype, without any obvious correlation between genetic and geographic or morphological variation, and the different species do not always show reciprocal monophyly in haplotype diversity. Nevertheless, low genetic differentiation characterizes not only allopatric taxa but also some forms which are essentially sympatric, supporting species rank for the former. Our data suggest a recent diversification and proliferation possibly linked to Pleistocene climatic variation and its consequent vegetational shifts, at least in the Andean species.     

New feather mites of the family Pterolichidae (Acari: Pterolichoidea) from parrots (Aves: Psittaciformes) in Australia

Abstract Seven new feather mite species of the family Pterolichidae are described from various Australian parrots: Apexolichus lathami sp. n. from the swift parrot, Lathamus discolor (Shaw); Titanolichus platycerci sp. n. and Rhytidelasma punctata sp. n. from the pale-headed rosella, Platycercus adscitus (Latham); R. striata sp. n. from the Australian king-parrot, Alisterus scapularis (Lichtenstein); Lorilichus stenolobus sp. n. and Lorilichus curvilobus sp. n. from the rainbow lorikeet, Trichoglossus haematodus (Linnaeus); Psittophagus galahi sp. n. from the galah, Eolophus roseicapillus (Vieillot). We give a brief overview of taxonomic studies of pterolichid mites living on Psittaciformes, and discuss the main diagnostic characters of different generic groups of these mites.     

Wild hybrids of Lesser White-fronted Goose (Anser erythropus)×Greater White-fronted Goose (A. albifrons) (Aves: Anseriformes) from the European migratory flyway

The Lesser White-fronted Goose [Anser erythropus (Linnaeus, 1758)] is one of the most threatened Palearctic goose species, with the Fennoscandinavian subpopulation in particular having seen a drastic decline over the last century. In the 1990s, captive-bred Lesser White-fronted Geese were used successfully for reintroduction and restocking in Sweden and Finland. The discovery of Greater White-fronted Goose [Anser albifrons (Scopoli, 1769)] mtDNA haplotypes in some of these captive-bred birds (Ruokonen et al. 2000) suggested that hybridisation had occurred during captive propagation and led to the discontinuation of the release of captive goslings. Here we report two hybrids of Lesser×Greater White-fronted Geese that were collected on their wintering grounds in England in 1936 and Holland in 1966. Birds from western Russia normally do not migrate south to Western Europe. Hence, these birds most likely originated from the Fennoscandinavian subpopulation and were collected prior to the commencement of the captive-breeding programmes. Both specimens show a heterogeneous set of morphological characters, some of which shared with the putative parent species and others being intermediate between the two White-fronted Goose species. A Canonical Discriminant Function analysis positions both specimens between the two putative parent species, making their hybrid status likely. We show, thus, that hybridisation between Greater and Lesser White-fronted Geese does occur naturally, albeit perhaps infrequently, and argue that the presence of Greater White-fronted Goose mtDNA haplotypes in Lesser White-fronted Goose may be the result of this naturally occurring hybridisation. Our data provide additional information on the debate whether the restocking programmes were halted for the right reasons and whether it is desirable to re-commence with the reintroduction programme.     

A distinctive new subspecies of Scytalopus griseicollis (Aves,Passeriformes, Rhinocryptidae) from the northern Eastern Cordillera of Colombia and Venezuela

We describe a new subspecies of Pale-bellied Tapaculo Scytalopus griseicollis from the northern Eastern Cordillera of Colombia and Venezuela. This form differs diagnosably in plumage from described subspecies Scytalopus griseicollis griseicollis and Scytalopus griseicollis gilesi and from the latter in tail length. It is also differentiated non-diagnosably in voice from both these populations. Ecological niche modelling analysis suggests that the new subspecies is restricted to the Andean montane forest and páramo north of both the arid Chicamocha valley and the Sierra Nevada del Cocuy.     

Tyrant flycatchers coming out in the open: phylogeny and ecological radiation of Tyrannidae (Aves, Passeriformes)

Tyrant flycatchers constitute a substantial component of the land bird fauna in all South American habitats. Past interpretations of the morphological and ecological evolution in the group have been hampered by the lack of a well‐resolved hypothesis of their phylogenetic interrelationships. Here, we present a well‐resolved phylogeny based on DNA sequences from three nuclear introns for 128 taxa. Our results confirm much of the overall picture of Tyrannidae relationships, and also identify several novel relationships. The genera Onychorhynchus, Myiobius and Terenotriccus are placed outside Tyrannidae and may be more closely related to Tityridae. Tyrannidae consists of two main lineages. An expanded pipromorphine clade includes flatbills, tody‐tyrants and antpipits, and also Phylloscartes and Pogonotriccus. The spadebills, Neopipo and Tachuris are their closest relatives. The remainder of the tyrant flycatchers forms a well‐supported clade, subdivided in two large subclades, which differ consistently in foraging behaviour, the perch‐gleaning elaeniines and the sallying myiarchines, tyrannines and fluvicolines. A third clade is formed by the genera Myiotriccus, Pyrrhomyias, Hirundinea and three species currently placed in Myiophobus. Ancestral habitat reconstruction and divergence date estimation suggest that early divergence events in Tyrannida took place in a humid forest environment during the Oligocene. Large‐scale diversification in open habitats is confined to the clade consisting of the elaeniines, myiarchines, tyrannines and fluvicolines. This radiation correlates in time to the expansion of semi‐open and open habitats from the mid‐Miocene (c. 15 Mya) onwards. The pipromorphine, elaeniine and myiarchine–tyrannine–fluvicoline clades each employ distinct foraging strategies (upward striking, perch‐gleaning and sallying, respectively), but the degree of diversity in morphology and microhabitat exploitation is markedly different between these clades. While the pipromorphines and elaeniines each are remarkably homogenous in morphology and exploit a restricted range of microhabitats, the myiarchine–tyrannine–fluvicoline clade is more diverse in these respects. This greater ecological diversity, especially as manifested in their success in colonizing a wider spectrum of open habitats, appears to be connected to a greater adaptive flexibility of the search‐and‐sally foraging behaviour.     

Predicting the distribution of the crested tinamous, Eudromia spp. (Aves, Tinamiformes)

A bioclimatic analysis of the crested tinamous was conducted to explore climatic factors underpinning the distribution of both Eudromia elegans and E. formosa and to evaluate its potential application in paleontological studies. The study utilized records throughout the entire known range of Eudromia spp. in southern South America. Relationships between 20 environmental parameters and the presence of Eudromia species were established, mapping and characterizing their spatial distribution in a geographic information system using BIOCLIM and MAXENT algorithms. The MAXENT prediction map shows a more homogeneous pattern while BIOCLIM showed a patchier pattern. The models applied here generated maps that adjust to the well-known previous distributions of both species. Nevertheless, for Eudromia elegans, the distribution predicted by MAXENT includes areas where it is actually considered absent, and the BIOCLIM prediction does not include some areas where it is presumed present. Eudromia formosa were found in warmer and wetter sites than E. elegans. Low precipitation areas were identified as suitable for Eudromia elegans. Strong differences between the climatic profiles for both Eudromia spp distributions occurred, with the precipitation the most important influence. E. formosa tolerates the highest maximum temperatures, whereas E. elegans supports the lowest temperatures.     

Evolution of the trnF(GAA) gene in Arabidopsis relatives and the brassicaceae family: monophyletic origin and subsequent diversification of a plastidic pseudogene

Recently, we used the 5'-trnL(UAA)-trnF(GAA) region of the chloroplast DNA for phylogeographic reconstructions and phylogenetic analysis among the genera Arabidopsis, Boechera, Rorippa, Nasturtium, and Cardamine. Despite the fact that extensive gene duplications are rare among the chloroplast genome of higher plants, within these taxa the anticodon domain of the trnF(GAA) gene exhibit extensive gene duplications with one to eight tandemly repeated copies in close 5' proximity of the functional gene. Interestingly, even in Arabidopsis thaliana we found six putative pseudogenic copies of the functional trnF gene within the 5'-intergenic trnL-trnF spacer. A reexamination of trnL(UAA)-trnF(GAA) regions from numerous published phylogenetic studies among halimolobine, cardaminoid, and other cruciferous taxa revealed not only extensive trnF gene duplications but also favor the hypothesis about a single origin of trnF pseudogene formation during evolution of the Brassicaceae family 16-21 MYA. Conserved sequence motifs from this tandemly repeated region are codistributed nonrandomly throughout the plastome, and we found some similarities with a DNA sequence duplication in the rps7 gene and its adjacent spacer. Our results demonstrate the potential evolutionary dynamics of a plastidic region generally regarded as highly conserved and probably cotranscribed and, as shown here for several genera among cruciferous plants, greatly characterized by parallel gains and losses of duplicated trnF copies.