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Sequencing and comparative analyses of genomes from multiple vertebrates are providing insights about the genetic basis for biological diversity. To date, these efforts largely have focused on eutherian mammals, chicken, and fish. In this article, we describe the generation and study of genomic sequences from noneutherian mammals, a group of species occupying unusual phylogenetic positions. A large sequence data set (totaling > 5 Mb) was generated for the same orthologous region in three marsupial (North American opossum, South American opossum, and Australian tammar wallaby) and one monotreme (platypus) genomes. These ancient mammalian genomes are characterized by unusual architectural features with respect to G + C and repeat content, as well as compression relative to human. Approximately 14% and 34% of the human sequence forms alignments with the orthologous sequence from platypus and the marsupials, respectively; these numbers are distinctly lower than that observed with nonprimate eutherian mammals (45-70%). The alignable sequences between human and each marsupial species are not completely overlapping (only 80% common to all three species) nor are the platypus-alignable sequences completely contained within the marsupial-alignable sequences. Phylogenetic analysis of synonymous coding positions reveals that platypus has a notably long branch length, with the human-platypus substitution rate being on average 55% greater than that seen with human-marsupial pairs. Finally, analyses of the major mammalian lineages reveal distinct patterns with respect to the common presence of evolutionarily conserved vertebrate sequences. Our results confirm that genomic sequence from noneutherian mammals can contribute uniquely to unraveling the functional and evolutionary histories of the mammalian genome. comparative genomics | genome sequencing | genome analysis | phylogenetics | mammalian evolution

Research has been conducted on the sexually selected traits in birds. The relationship between birds' songs and plumage elaboration in finches has been investigated and the results indicate that for the condition-dependent traits birds trade-off trait expression in response to changes in the information content of these traits.

Research has been conducted on the reproduction timing. The effect of this timing on the second brood incidence and parent survival in European coots has been investigated and the results indicate that adult survival does not depend on the season.

Mitochondrial sequence analysis in species of endemic Malagasy and other songbird species reveals that nine of the thirteen Malagasy birds form a clade. Data indicate that this endemic clade is followed by a group of Old World warblers and the clade rivals other island species in its ecological diversity.

Plumage evolution has been studied in orioles (Icterus) with repeated convergence and reversal in patterns found. It appears that sexually selected characters may evolve rapidly and show high levels of convergence and other types of homoplasy. Plumage characters were mapped onto a molecular phylogeny based on two mitochondrial genes. Overall convergence seen in the study is an interesting phenomenon of evolution. However, heavy reliance on plumage characters for constructing phylogenies should be avoided, based on findings of this research.

Little evidence was found for sympatric speciation in island birds based on a search for endemic congeneric species on isolated ocean islands. Of 46 islands and small archipelagos where at least one species of endemic land bird was found, seven paris of endemic congeners, excluding flightless rails, were found. Four pairs of the seven are potentially sister species. Three of the four have always been thought to come from double invasion from a mainland source. The remaining pair may have speciated allopatrically on a small archipelago.

Research suggests that two newly discovered exon 3 insertions in the nuclear proto-oncogene c-myc may be responsible for shared common ancestry between the New World oscines Cardinalinae, Emberizinae, Icteridae, Parulidae and Thraupinae. These groups possess three amino acids inserted at the 991 position within the chicken sequence.

Research concerning the retention of anti-parasitism host defences through evolution from a common ancestor is presented. The Yellow-billed Magpie, although not parasitized, ejects all foreign eggs, a trait shared by its' nearest relative, the Black-billed Magpie, which is parasitized.

We examined patterns of variation in skeletal morphometrics (29 characters), allozymes (34 loci), mitochondrial DNA (mtDNA) restriction sites (n = 74) and fragments (n = 395), and mtDNA sequences (1,739 bp from cytochrome b, ND2, ND6, and the control region) among all species of Toxostoma. The phenetic pattern of variation in skeletal morphometrics generally matched traditional taxonomic groupings (based on plumage patterns) with the exceptions of T. redivivum, which because of its large size clusters outside of its proper evolutionary group (lecontei), and T. occelatum, which did not cluster with T. curvirostre. Skull characters contributed highly to species discrimination, suggesting that unique feeding adaptations arose in different species groups. Although genetic variation was detected at isozyme loci (average heterozygosity = 3.6%), these data yielded little phylogenetic resolution. Similarly, mtDNA restriction sites were relatively uninformative; hence, phylogenetic conclusions were based on sequence data. Phylogenetic analyses confirmed the monophyly of these traditionally recognized assemblages: rufum group (T. rufum, T. longirostre, and T. guttatum ), lecontei group (T. lecontei, T. crissale, and T. redivivum ), and cinereum group (T. bendirei and T. cinereum). The cinereum and lecontei groups appear to be sister lineages. Monophyly of the curvirostre group (which also includes T. occelatum) was not confirmed. Sequence data suggest that T. occelatum and T. curvirostre, which differ by 7.7% sequence divergence, are probably most closely related to the rufum group. Toxostoma rufum and T. longirostre have similar external appearances and differ by 5.0%. Toxostoma guttatum is restricted to Cozumel Island and often is considered a subspecies of T. tongirostre; it differs by more than 5% from the other two members of the rufum group and is a distinct species constituting the basal member of this group. The phenotypically distinctive T. bendirei and T. cinereum differ in sequence divergence by only 1.6%. Overall, mtDNA distances computed from coding genes (mean 8.5%) exceeded distances computed from the control region (mean 7.6%), contrary to expectation. Because neither allozymes nor mtDNA could unambiguously resolve the placement of T. occelatum and T. curvirostre, a scenario involving contemporaneous speciation is suggested. Application of a molecular clock suggested that most speciation occurred in the late Pliocene or early Pleistocene.

A new species of Confuciusornis, the oldest beaked bird, has been identified as a result of the discovery of an extremely well preserved skeleton within the Yixian Formation in Liaoning, China. This skeleton has feathers and provides the first direct evidence in the Mesozoic record of the shape of a horny beak. The skull shows some critical features of Confuciusornis, while the humerus is typical of Confuciusornis in having a very clear proximal end with an oval depression. The foot has extremely recurved claws and a reversed hallux.

Persistent contradictions in well supported empirical findings usually point to important scientific problems and may even lead to exciting new insights. One of the most enduring problems in evolutionary biology is the apparent conflict between paleontological and embryological evidence regarding the homology of the digits in the avian hand (1, 2). We propose that this problem highlights an important feature of morphological change: namely, the possible dissociation between the developmental origin of a particular repeated element and its subsequent individualization into a fully functional character. We argue that, although comparative embryological evidence correctly identifies the homology of the primordial condensations in avians as CII, CIII, and CIV, subsequent anatomical differentiation reflects a frame shift in the developmental identities of the avian digit anlagen in later ontogeny such that CII becomes DI, CIII becomes DII, and CIV becomes DIII.

We estimated genetic differentiation between morphologically distinct tidal marsh populations of Swamp Sparrows (Melospiza georgiana nigrescens) and the more widespread inland populations (M. g. georgiana and M. g. ericrypta). The tidal marsh populations are consistently grayer with more extensive black markings (particularly in the crown), and their bills are larger These differences are variously shared with other species of salt marsh birds and small mammals. We analyzed mitochondrial DNA sequences (5[prime] end of control region, COII/ t-lys/ATPase8, and ND2) of Swamp Sparrows and found low levels of genetic variation and no evidence of geographic structure. These results suggest a rapid and recent geographic expansion of Swamp Sparrows from restricted Pleistocene populations. Morphological differentiation has occurred without long-term genetic isolation, suggesting that selection on the divergent traits is intense. The grayer and more melanistic plumage is probably cryptic coloration for foraging on tidal mud, which tends to be grayish as a result of the formation of iron sulfides, rather than iron oxides, under anaerobic conditions.

Two therapods bearing feathers and dating from the Upper Jurassic/Lower Cretaceous have been found in the Chaomidianzi Formation of Liaoning province, China. These therapods, designated Protarchaeopteryx and Caudipteryx, have relatively long legs. In both cases, the hallux is positioned high and orientated anteromedially. This indicates that these therapods were ground-dwelling runners, in spite of having downy and plumulaceous feathers covering their bodies. Both lie outside Avialae and are non-avian coelurosaurs.

Farmers in Liaoning, China, discovered two almost complete skeletons of Sinosauropteryx, a dinosaur species closely linked with Compsognathus. The skeletons are from the basal part of the Yixian Formation, which has four fossil-bearing sedimentary intercalations. The skeletons are particularly interesting for their integumentary structures, which are extremely well preserved. There are no structures showing the basic morphological features of modern bird feathers, but they could be protofeathers which have not previously been identified.

Heritability of body size in two experimentally created environments, representing good and poor feeding conditions, respectively, was estimated utilizing cross-fostered collared flycatcher Ficedula albicolis nestlings. Young raised under poor feeding conditions attained smaller body size than their full-sibs raised under good feeding conditions. Parent-offspring regressions indicated lower heritability of body size under poor than under good feeding conditions.

Trilled vocalizations from 34 species of songbirds Passeriformes: Emberizidae were studied. Two acoustic variables, trill rate and frequency bandwidth, were measured for different trill types. Findings indicated that performance constraints have restricted the evolutionary diversification of trills. Specifically, the role of constraints linked with vocal tract modulations during song production and evolution was examined.

The belief that birds originated from the Archaeopteryx was shattered by the discoveries of the fossilized Gansus and Confuciusornis by Chinese scientist Hou Lianhai. The fossils have added another 75 million years to the history of birds. Curator of the China Geological Museum Ji Qiang also discovered another fossil which he named Sinosauropteryx. Dinosaur expert Dong Zhiming thinks that the findings reveal that birds originated from dinosaurs. Both Hou and Ji stressed on the importance of protecting the rich beds of fossils that will yield further clues about the origin of birds.

Recent research has revealed that birds may have descended from dinosaurs which sported short tails and were feathered. The Mesozoic era saw these reptilian creatures acquire new characteristics as they both specialized and diversified and adopted new lifestyles. This time period constituted the first 85 years of avian evolution. Despite the new evidence, there is still much that needs to be discovered to firmly establish interrelationships and cause-and-effect findings.

We amplified and sequenced a 711 base-pair (bp) fragment of mtDNA at the cytochrome-b locus to reexamine relationships within and among species of Sphyrapicus and representatives of two other woodpecker genera (Melanerpes, Colaptes). Sequences were obtained from 10 individuals of 5 taxa: Red-breasted Sapsucker (S. ruber daggetti), n = 2; Red-naped Sapsucker (S. nuchalis), n = 2; hybrid of S. ruber daggetti x S. nuchalis, n = 1; Yellow-bellied Sapsucker (S. varius varius), n = 2; Williamson's Sapsucker (S. thyroideus thyroideus), n = 2; and Red-bellied Woodpecker (M. carolinus), n = 1. The Melanerpes sequence and a comparable published sequence of Andean Flicker (C. rupicola) were used as outgroups. Levels of mtDNA sequence divergence ranged from 0.0 to 0.6% within species and 0.1 to 10.2% among species of Sphyrapicus, and from 12.5 to 14.5% between members of Sphyrapicus and the two outgroup species. One region of sequence (78 bp) was identified as being especially conserved. Branching topologies based on this study corroborated results from a previous analysis of relationships in Sphyrapicus using allozymes: the phenotypically dissimilar species ruber and nuchalis are most closely related; varius, which is very similar in appearance to nuchalis, branches off next; and thyroideus, the most divergent member of the quartet from the standpoint of plumage pattern and degree of sexual dimorphism, is strongly differentiated genetically. Pairwise mtDNA distances within Sphyrapicus showed a strong curvilinear relationship with allozyme distances (r = 0.996). The monophyly of Sphyrapicus is reaffirmed, with S. thyroideus closer to the ancestral species. Members of Sphyrapicus are more similar to Melanerpes than to Colaptes based on their mtDNA. Prior hypotheses regarding the evolutionary history of sapsuckers in North America are discussed. Despite the near genetic identity of ruber and nuchalis based on both allozymes and mtDNA sequences, and their tendency for limited hybridization in sympatry, an earlier study of mating preference supports the biologic-species status of these taxa.

We review recent developments in the debate over species concepts, exploring differences between the biological species concept (BSC) and the phylogenetic species concept (PSC). Three principal flaws in the BSC are reviewed: (1) the occurrence of paraphyletic or nonhistorical groups; (2) the misrepresention of the significance of hybridization among differentiated taxa; and (3) the logical difficulty in handling allopatric populations. Simple cline theory shows that likely times to fusion for hybridizing taxa exceed the average duration of most species in the fossil record. We address criticisms of PSCs (of which there are several), including the application of phylogenetic methods to populations, and whether species can be monophyletic. We suggest that the evolutionary species concept and the PSC might be more similar than generally appreciated. Empirical studies of variation in the Brown Towhee (Pipilo fuscus) complex and Fox Sparrow (Passerella iliaca) reveal that the BSC and PSC can lead to different species limits. Reasons are given for why the PSC is the preferred concept for comparative biology, phylogenetic inference, historical biogeography, estimation of bio-diversity, hybrid-zone analysis, conservation biology, and speciation analysis. Despite problems associated with all species concepts, we think that a concept consistent with the PSC should replace 'biological' species concepts.

Recently, we acquired DNA of two rare species of heron, the Neotropical Zigzag Heron (Zebrilus undulatus) and the African White-crested Bittern (Tigriornis leucolophus). To estimate their phylogenetic relationships to other herons, we compared these species with representatives of the major heron clades using DNA-DNA hybridization. Even though the Zigzag Heron resembles a tiger-heron in its barred plumage and forest habitat, it is most closely related to bitterns. The White-crested Bittern is monophyletic with the New World tiger-herons (Tigrisoma) and, thus, is better termed the White-crested Tiger-Heron. These findings accord well with phylogenetic analyses based on osteology. The remaining uncertainties in higher-level heron phylogeny are principally: (1) the position and composition of some enigmatic genera (e.g. Gorsachius, Agamia, Pilherodius, and Ardeola); and (2) the identification of the basal heron lineage, which appears to be either tiger-herons or the Boat-billed Heron (Cochlearius).

Molecular studies show that most avian species evolved in the Pleistocene Epoch and species' durations decreased through Pleistocene due to heightened speciation rates. A study of the cumulative distribution of reconstructed speciation events in mtDNA phylogenies of 11 avian genera show a decline in net diversification rate throughout the Pleistocene Epoch. It is unclear whether speciation rates decreased or extinction rates increased.

A study has been conducted to examine the phylogenetic relationships among populations of the yellow warbler, Dendroica petechia, from North, Central and South America and the West Indies using DNA restriction mapping. Results revealed 37 haplotypes, with the mtDNAs from North America distinct from those of the other populations, and a sequence divergence ranging from 0.14% to 3.17%. These suggest that multiple colonization may have taken place in faunal groups from the West Indies and the Caribbean Islands.

Data from the phylogenetic analysis of genus Vireo using cytochrome b sequences neither agrees with nor opposes monophyletic nature of the genus Vireo. Two significant clades found in the genus Vireo are eye-lined clade and eye-ringed clade. Among the two confamilial species, Cyclarhis gujanensis had a closer relationship with Vireo than Vireolanius leucotis.

The Humboldt, Magellanic, Jackass and Galapagos Penguins belong to the species Spheniscus. An allozyme phylogeny study was conducted to determine the phylogenetic relations between these penguins. The resulting phenetic and cladistic trees consistently showed the closest relationship between the Jackass and the Magellanic penguins. Two major clades were revealed, and molecular clock calibration suggests that they diverged about 500,000 mya in the mid-Pleistocene. The Jackass and the Magellanic penguins appeared in the late Pleistocene.

The fragmentary effects of Pleistocene glacial activity have been implicated in speciation among avifauna endemic to the Central Plains of North America. The prairiegrouse complex (genus Tympanuchus), distributed throughout the central United States and Canada, contains three sister taxa believed to have originated from the expansion of late Pleistocene refugial populations. We assayed mitochondrial-DNA (mtDNA) restriction-site and allozyme variation in prairie grouse obtained from localities throughout their current range in North America to examine the nature and timing of events promoting differentiation in Tympanuchus. The genetic data were not consistent with Pleistocene isolation of sufficient duration to allow a taxonomically or geographically structured pattern of genetic variation to emerge. No clear genetic differences among species were observed. Allozymes could not distinguish populations belonging to different species and frequencies were generally similar across taxa. The mtDNA differentiation was characterized by a predominant haplotype shared by all taxa; the remainder (15) were generally infrequent and closely related to the prevalent (and presumably ancestral) haplotype. The presence of unique mtDNA haplotypes within species and absence of certain allozyme alleles from particular taxa implied a degree of isolation and restrictions to gene flow. However, the mtDNA haplotypes did not sort phylogenetically, which suggests recent common ancestry of the lineages and may explain the lack of congruence between genetic variation and species designations. Despite the absence of quantitative genetic differentiation, considerable morphological and behavioral differences are apparent among the putative species. Adult male plumage, vocalization structures, and courtship behaviors form the basis for taxonomic divisions among prairie grouse, but, considering their close association with reproduction, such characters may be subject to sexual selection and may evolve rapidly relative to mtDNA or allozymes. Received 27 January 1993, accepted 19 August 1993.

Mitochondrial-DNA (mtDNA) polymorphisms were studied in the Oilbird (Steatornis caripensis). Twelve closely related (P = 0.06 to 0.35%) mtDNA haplotypes were found in Oilbird colonies studied in northeastern and northwestern Venezuela. Eleven of the mtDNA clones are related to the ancestral one by one or two mutational steps. Female-mediated gene flow is high (Nm > 1) among the colonies studied. As a consequence of the high female-mediated gene flow, no phylogeographic structuring among the mtDNA composite haplotypes was observed. Evidence from mtDNA analysis suggests that Oilbird populations in Venezuela have gone through a bottleneck. Results also seem to indicate that the annual postbreeding migrations of Oilbirds from the Guacharo Cave to the caves in the Mata de Mango area involve mostly the breeding adults, whereas juveniles disperse from the Guacharo Cave to the Mata de Mango cave system for longer periods. Received 3 August 1993, accepted 15 November 1993.

We studied relationships among species of the Neotropical flycatcher genus Leptopogon (Tyrannidae), which have modern-day distributions that include a lowland-tropical-zone member, an upper-tropical-zone member, and two subtropical-zone members. Along the eastern slope of the eastern Andes, species inhabiting the different elevational zones occur parapatrically to one another. Both allozymes and restriction-fragment-length polymorphisms of mitochondrial DNA suggest the same phylogenetic hypothesis: the lowland-tropical-zone species (L. amaurocephalus) is the basal member of the clade, and the upper-tropical-zone species (L. superciliaris) is the sister taxon of the two subtropical-zone species, L. taczanowskii and L. rufipectus. These data are consistent with diversification into successively higher-elevation habitats in the Andes. The biochemical data also suggest that this genus is substantially differentiated from the genera near it in traditional classifications (Mionectes, Phyllomyias, Lophotriccus). Received 6 August 1992, accepted 31 December 1992.

It has been suggested that the distribution of forest and nonforest birds in subtropical South America is the result of forest expansion along the Bermejo and Pilcomayo rivers during the Quaternary. However, this conclusion has a number of flaws, namely, lack of paleoecological support, use of questionable assumptions, problems with habitat classification and the questionable authenticity of a secondary contact zone in the central Chaco.

DNA sequences obtained from four evolving genes, mitochondrial 12S and 16S rRNA, nuclear alpha-enolase and tRNA(val), reaffirmed the hypothesis regarding the bird-crocodilian relations which suggests that the birds' closest living relatives are the crocodilians. This hypothesis was based on fossil records of amniote vetebrates that existed for a short period during the end of the Paleozoic Era.

The Noronha Vireo (Vireo gracilirostris) is endemic to the small oceanic island of Fernando de Noronha off the easternmost tip of Brazil. Although derived from the Red-eyed Vireo (V. olivaceus) complex, the Noronha Vireo is differentiated strongly in coloration, plumage pattern, and morphology and fully merits recognition as a distinct species. It is a smaller bird with a much more rounded wing, longer, more slender bill and a more elongated tail and tarsus. These appear to be specializations for gleaning small insects from foliage, particularly the undersides of leaves. The birds are abundant where appropriate habitat is maintained. The few available data on reproductive and molt cycles, nesting, and vocalizations in V. gracilirostris are summarized.

Evolutionary relationships among obligate ant-following birds in the genus Gymnopithys were addressed using phenetic and phylogenetic analyses of allozyme characters. Genetic variation at 37 gene loci was analyzed across all four species in the genus and within two species (Bicolored Antbird (G. leucaspis), and White-throated Antbird (G. salvini)). Interspecific genetic distances were high, and comparable to other studies of Neotropical birds, which exceed those in many temperate zone species. Within the genus, Lunulated Antbird (G. lunulata) and G. salvini were sister taxa. There was only weak support for a sister-taxon relationship between G. leucaspis and the Rufous-throated Antbird (G. rufigula). Within G. leucaspis and G. salvini, high F(sub st) indicated substantial genetic subdivision, again comparable to other Neotropical birds and much greater than temperate zone birds. Increased age of population isolation is proposed to account for the high genetic divergence in Neotropical birds.

Scientists are starting to accept the belief that long tails in birds are the result of sexual selection, but this analysis fails to take into account aerodynamics. Certain tail types, such as shallow-forked, long tails, actually improve aerodynamics and therefore may be the result of natural selection rather than sexual selection. However, certain un-aerodynamically beneficial long-tail types such as graduated tails do appear to be the result of sexual selection and are more common in species that do not fly long distances.

The finding that lekking birds were not significantly more sexually size- or plumage-dimorphic than non-lekking birds when phylogenetic history is accounted for was evaluated. Felsenstein's matched pairwise independent comparisons showed that lekking birds were significantly more size-dimorphic than their non-lekking close relatives. This result was obtained because Felsenstein's method can be used with continuous variables, and confounding third variables are eliminated by comparing only close taxonomic groups sharing similar ecologies and selection pressures. Ancestor transitions are calculated from, and therefore dependent on, descendant states.

Multilocus protein electrophoresis of tissue samples from Mediterranean Alectoris revealed their evolutionary development. Calculated genetic distances demonstrated the species diversity among Barbary Partridge (A. barabara) and Chukar (A. chukar) while establishing the consaguinity of Rock Partridge (A. graeca) and Red-legged Partridge (A. rufa). These observations indicate the slow evolution of Alectoris species and their independence from one another.

Allozyme electrophoresis was used in the evaluation of genetic variation among four Mexican populations each of Common Bush-tanagers (Chlorospingus ophthalmicus) and Chestnut-capped Brush-finches (Atlapetes brunneinucha). Within-population genetic variation in Chlorospingus and Atlapetes is typical of bird species diversity, but among-populations of both species are strongly genetically differentiated. Geographic distance among populations is does not affect variation. Both species have sufficient genetic isolation so that most of the populations must differentiate by genetic drift alone.

Parus (P.) bicolor and P. inornatus are more evolutionarily related than P. wollweberi, which diverged earlier in the geologic timescale. The patterns of mitochondrial DNA divergence among the three titmice species provides a critical assessment of genetic divergence in the present taxonomy of titmice. A high mitochondrial DNA divergence existed between two subspecies of P. inornatus in contrast to the low divergence between subspecies of bicolor and wollweberi. Further research may separate the interior and coastal P. inornatus as two distinct species.