Toward a resolution of a taxonomic enigma: first genetic analyses of Paradoxornis webbianus and Paradoxornis alphonsianus (Aves: Paradoxornithidae) from China and Italy

Paradoxornis webbianus and Paradoxornis alphonsianus naturally occur in South-East Asia. Due to a recent introduction, a mixed population currently occurs in northern Italy. A preliminary phylogeographic analysis using samples from Italy and China found little genetic differentiation between the two taxa and revealed the existence of two molecular lineages, sympatric in some part of China, that do not correspond to the morphological classification. Possible taxonomic changes and preliminary inferences on the relationships between Chinese and the Italian populations and on the likely provenance of the founders introduced in Italy are also discussed.     

上海崇明东滩震旦鸦雀冬季种群栖息地的生境选择

2008年11月-2009年3月,在崇明东滩对震旦鸦雀(Paradoxornis heudei)种群生态进行调查研究,并对震旦鸦雀种群和生境因子的相关性进行分析。运用单因素方差对互花米草(Spartina alterniflora)入侵和芦苇(Phragmites australis)收割造成的芦苇滩涂变化进行分析,并运用多元回归的方法对震旦鸦雀种群的密度和分布以及相关环境因子进行生境选择分析。结果表明,崇明东滩震旦鸦雀种群的密度为(5.08±3.11)只/hm2;震旦鸦雀种群的密度和芦苇直径呈极显著正相关,震旦鸦雀种群的分布和芦苇的高度、密度呈极显著正相关,和食物资源量呈显著正相关;互花米草和震旦鸦雀种群的密度和分布呈显著负相关;互花米草入侵和芦苇收割降低了震旦鸦雀越冬期的栖息地质量,保留一部分生长质量较好的芦苇可以缓解震旦鸦雀冬季种群的生存压力。     

Beyond a morphological paradox: complicated phylogenetic relationships of the parrotbills (Paradoxornithidae, Aves)

The parrotbills (Paradoxornithidae, meaning "birds of paradox," Aves) are a group of Old World passerines with perplexing taxonomic histories due to substantial morphological and ecological variation at various levels. In this study, phylogenetic relationships of the parrotbills were reconstructed based on sequences of two mitochondrial segments and three nuclear coding regions. Three major clades with characteristic body size and plumage coloration were found in both mtDNA and nuclear gene trees. However, mtDNA phylogeny suggested that the Paradoxornithidae is paraphyletic and relationships among three major parrotbill clades were poorly resolved. On the contrary, apparent and well-supported monophyletic relationships among the three major clades of Paradoxornithidae were revealed by concatenated nuclear dataset. Since paraphyly based on mtDNA data has commonly been found within avian taxa, the conflicting phylogenetic signal between mtDNA and nuclear loci revealed in this study indicates that results obtained from mtDNA dataset alone need to be evaluated with caution. Taxonomic implications of our phylogenetic findings are discussed. These phylogenies also point out areas for future investigation regarding the rapid diversification, morphological evolution and environmental adaptation of various parrotbill species or species complexes.     

灰冠鸦雀巢及巢址生境的首次报道

灰冠鸦雀(Paradoxornis przewalskii)是狭域分布的中国特有鸟种,分布区仅局限于岷山北部。近年来关于该种的新发现为我们提供了其栖息地和现有分布范围的宝贵信息,但该种的繁殖情况还从未有观察与报道。2013年6月10日,我们在四川省唐家河国家级自然保护区内发现1对正在育雏的灰冠鸦雀及其3只新生雏鸟,对其巢址生境和巢的结构进行了详细记录。灰冠鸦雀筑巢于稀疏的岷江冷杉(Abies faxoniana)和红桦(Betula albo-sinensis)混交林下的浓密缺苞箭竹(Fargesia denudata)丛中,巢址海拔2700 m,位于陡峭阳坡接近林线处。巢为结构精细的杯状巢,高约6.6 cm,深约5.0 cm,巢口内径4.8 cm,外径7.0 cm。巢由干草叶与竹叶编织而成,巢壁外侧装饰有大量绿色苔藓。本报道为灰冠鸦雀野外繁殖的首次记录,为今后深入开展该珍稀鸟种的繁殖生态和栖息地选择研究提供了基本信息。     

Isolation and characterization of microsatellite markers from reed parrotbill, Paradoxornis heudei (Aves: Timaliidae)

Eleven microsatellite markers were obtained from reed parrotbill, Paradoxornis heudei, using the fast isolation by AFLP of sequences containing repeats (FIASCO) method as part of an effort to compare levels of genetic diversity in different populations of China. Polymorphism levels ranged form 5 to 11 alleles (mean = 9.27) using 32 reed parrotbills, with the observed heterozygosity ranging from 0.037 to 0.80. Six loci were significant deviated from HWE and nine loci showed linkage equilibrium. The utility of these loci on two other Passeriformes species, vinous-throated parrotbill (P. webbianus) and oriental great reed warbler (Acrocephalus orientalis), were also tested.     

Incomplete lineage sorting or secondary admixture: disentangling historical divergence from recent gene flow in the Vinous‐throated parrotbill (Paradoxornis webbianus)

Although Pleistocene glaciations had a major impact on the population genetic patterns of many species in North America and Europe, it remains unclear how these climatic fluctuations contributed to species diversification in East Asia. One reason for this is the difficulty of distinguishing genetic admixture following secondary contact from incomplete lineage sorting, both of which can generate similar patterns of genetic variation. Using a combination of multilocus analyses and coalescent simulation, we explore how these two processes occurred in the Pleistocene evolutionary history of a widespread East Asian bird, the Vinous‐throated parrotbill, Paradoxornis webbianus. Maximum likelihood (ML) tree identified two major mitochondrial lineages, which are geographically separated in most parts of its range, but are sympatric at a few sampling sites. NJ tree and Structure analysis of microsatellite data set revealed an extensive level of admixture and little population structure, suggesting recent admixture between two formerly separated groups. Networks from nuclear DNA data sets, however, did not indicate any geographically isolated groups but rather a panmictic population, thus support incomplete lineage sorting. By using coalescent simulation approaches, we show that both processes did occur, although at different temporal scales. During the Pleistocene glaciations, probably around 0.1–0.5 Ma (the Marine Isotope Stage 6, MIS6), P. webbianus contracted into two separate refugia, and subsequently accumulated genetic divergence. During the interglacial MIS5, the species expanded into previously glaciated areas allowing the once separated groups to come into contact and become admixed. Taken together, our results indicate the current genetic variation within P. webbianus is a combination pattern of widespread distribution in pre‐Pleistocene, then contraction and fragmentation into separated refugia during glacial advance, followed by recently postglacial expansion and admixture.     

Speciation in an avian complex endemic to the mountains of Middle America (Ergaticus, Aves: Parulidae)

The implementation of the phylogeographic approach for the study of biodiversity is critical in poorly sampled regions like the montane systems of Middle America, as complex evolutionary histories often result in the presence of independent lineages not properly considered by traditional taxonomy. Herein we sequenced 2370 bp of mtDNA (ND2, cyt b and ATPase) from 81 individuals of Ergaticus, a complex of birds endemic to the montane forests of Middle America. Although current taxonomy recognizes two species, the results reveal considerable genetic structure with the presence of four mtDNA lineages. Two of these lineages within Ergaticus ruber evidence the need of a revaluation of the species limits for this taxon. The general phylogeographic pattern can be explained as a consequence of relative isolation of the populations in different mountain ranges separated by low elevation barriers. Most population groups did not show signals of demographic expansion with the exception of the one corresponding to clade 1. The divergence time estimates point to the Pleistocene as an important time period for the diversification of this complex.     

The digital tendon locking mechanism of the avian foot (Aves)

Summary Representatives of all avian orders were studied in order to establish that the tendon-locking mechanism (TLM), consisting of local specialization of the flexor tendons and the adjacent portion of the flexor tendon sheath, is by no means rare, but rather, constitutes the prevalent condition in a large majority of the avian species sampled. The areas of tubercles on the tendons and the adjacent sheath plications intermesh with one another thereby forming a true tendon-locking mechanism that maintains the distal and other interphalangeal joints of the digits in the flexed position. The TLM seems to function not only in perching, but in a wide variety of other activities of the avian foot including swimming, wading, prey-grasping, clinging, hanging, and tree climbing. The basic structural components of the mechanism are remarkably similar in the divergent avian groups adapted for these activities. Ultrastructural detail of the TLM was studied by means of scanning and transmission electron microscopy. Interdigital variation in distribution of the TLM in all of the digits of individuals were made as were comparisons of the interspecific distribution of the TLM. An analysis of the biomechanics involved in engaging the elements of the TLM and how they produce locking of the flexed joints of the digits includes a consideration of the roles of the podothecal pads, ungual flexor processes, and the elastic flexor and extensor ligaments of the toes. The components of the TLM are differentiated in early fetal development establishing that the TLM components are not acquired adventitiously in response to such factors as posthatching mechanical stresses.     

Construction of the avian skull,as demonstrated by direct magnifying microfocal radiography (Aves)

Summary The new microfocus X-ray technique works with X-ray sources smaller than 10 m in diameter. Thus, in contrast to conventional X-ray systems, it is possible to obtain direct magnifications with high spatial resolution, i.e., well-focused radiographs with better contrast and depth of focus. In this connection, specific construction principles of the avian skull are elucidated, comparing several bird groups. The typical pneumatization effects are demonstrated, as are other biologically important anatomical features, in particular those of the bills/beaks as related to mechanical demands.     

The automating skeletal and muscular mechanisms of the avian wing (Aves)

The avian wing possesses the ability to synchronize flexion or extension of the elbow and wrist joints automatically. Skeletal and muscular mechanisms are involved in generating this phenomenon. The drawing-parallels action of the radius and ulna coordinates the movements of the forearm with the carpus. Movement of the radius along the length of the forearm isnot dependent on the shape disparity between the dorsal and ventral condyles of the humerus, nor is it generated by the shape of the dorsal condyle itself. Instead, shifting of the radius toward the wrist occurs during humeroulnar flexion when the radius, being pushed by muscles toward the ulna, is deflected off theIncisura radialis toward the wrist. Movement of the radius toward the elbow occurs during the latter stages of humeroulnar extension when, as the dorsal condyle of the humerus and the articular surface of the ulna's dorsal cup roll apart, the radius gets pulled by the humerus and its ligaments away from the wrist. Synchronization of the forearm with the manus is accomplished by twojoint muscles and tendons.M. extensor metacarpi radialis and the propatagial tendons act to extend the manus in unison with the forearm, whileM. extensor metacarpi ulnaris helps these limb segments flex simultaneously.M. flexor carpi ulnaris, in collaboration with the drawing-parallels mechanisms, flexes the carpus automatically when the elbow is flexed, thereby circumducting the manus from the plane of the wing toward the body. In a living bird, these skeletal and muscular coordinating mechanisms may function to automate the internal kinematics of the wing during flapping flight. A mechanized wing may also greatly facilitate the initial flight of fledgling birds. The coordinating mechanisms of the wing can be detected in a bird's osteology, thereby providing researchers with a new avenue by which to gauge the flight capabilities of avian fossil taxa.     

Chromosome studies in four species of Ratitae (Aves)

Chromosomes were studied in female specimens of the ostrich, Struthio camelus L., cassowary, Casuarius casuarius (L.), emu, Dromiceius novaehollandiae (Lath.) and rhea, Rhea americana L. by means of blood and feather pulp culture techniques. Male karyotypes were also studied in the emu and rhea. The diploid chromosome number was most likely 80 in the ostrich and rhea and 82 in the emu, while the exact number could not be determined in the cassowary. Karyotypes of the 4 species were strikingly similar and apparently interchangeable with one another with slight modifications of the centromeric position in one or two pairs of macrochromosomes. No heteromorphic macrochromosomal pair was found either in female specimens or in male ones of the ratite species so far examined, except for a female rhea. This specimen was found to possess an acrocentric chromosome which was evidently a member of nos. 4–6, but considerably smaller than any other chromosome of the group. ³H-thymidine autoradiography provided no more information than the straightforward morphological analysis with regard to the differentiation of the sex-chromosomes.Contributions from the Chromosome Research Unit, Hokkaido University. Dedicated to Emeritus Professor Sajiro Makino on the occasion of his retirement, in honor of his 40 years' service with the University. Supported by a grant from the Scientific Research Fund of the Ministry of Education (No. 584099).     

Characterization of polymorphic microsatellites in the logrunner,Orthonyx temminckii (Aves: Orthonychidae)

We isolated and characterized 10 polymorphic microsatellite loci in the logrunner (Orthonyx temminckii), a rainforest‐dwelling Australian bird. The number of alleles per locus observed within two populations ranged from three to 39, with observed heterozygosities of between 0.12 and 1.00. We demonstrate that these markers are useful for both population‐ and individual‐level analyses.     

Microsatellite loci characterized in three African crane species (Gruidae, Aves)

Forty-three microsatellite loci originally isolated in Grus americana and G. japonensis were tested for polymorphism in the blue crane (G. paradisea). Amplified products were sequenced in the blue crane to aid in the design of blue crane-specific primers. When characterized in 20 unrelated blue crane individuals from South Africa, 14 loci were polymorphic, with each locus displaying between 2 and 7 alleles. Eight polymorphic loci were characterized in the grey-crowned crane (Balearica regulorum) and ten in the wattled crane (G. carunculatus).     

Historical diversification of floodplain forest specialist species in the Amazon: a case study with two species of the avian genus Xiphorhynchus (Aves: Dendrocolaptidae)

Phylogeographical and population genetics methods are used to reconstruct the diversification history of two species of the genus Xiphorhynchus (Aves: Dendrocolaptidae) associated with seasonally flooded forest types in Amazonia. Sequences of the mitochondrial gene cytochrome b were assessed for 21 and 30 individuals, belonging to eight and ten populations, of Xiphorhynchus kienerii and Xiphorhynchus obsoletus , respectively. Uncorrected genetic distances among unique haplotypes recovered ranged only from 0.01% to 0.4% for both species. Over 90% of the genetic variation detected in both species was partitioned within populations, and therefore was not structured geographically. Mismatch distributions and values of Tajima's D -tests indicate that both X. kienerii and X. obsoletus have had small evolutionary effective population sizes, but experienced a recent demographic expansion. These demographic expansions are tentatively dated as occurring over the last 18 000 years BP, a time frame which coincides with the establishment of the early and mid-Holocene age floodplain forest in most of central and eastern Amazonia, following a period of increased river stages throughout the basin. Based on phylogenetic, phylogeographical, and populations genetics data obtained for X. kienerii and X. obsoletus , an evolutionary scenario is proposed to account for the historical diversification of floodplain specialist species in Amazonia.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 89 , 383–395.     

Non-monophyly of the avian genus Seicercus (Aves: Sylviidae) revealed by mitochondrial DNA

The phylogeny of all species and nearly all subspecies of Seicercus and representatives of all subgenera in Phylloscopus was estimated based on two mitochondrial genes. According to the gene tree, and supported by non-molecular data, Seicercus belongs in three separate clades. Two of these include only taxa currently classified as Seicercus , while the third comprises S. xanthoschistos and P. occipitalis . These results suggest that both Seicercus and Phylloscopus are paraphyletic. The gene tree suggests two more cases of non-monophyly: (1) the ' S. burkii complex' is separated into two different clades, one of which also includes S. affinis and S. poliogenys ; (2) two populations of S. affinis intermedius are more closely related to S. affinis ocularis than to a third population of intermedius . A recent proposal to split the ' S. burkii complex' into six species is corroborated, as is the recognition of the taxon cognitus as a colour morph of S. affinis intermedius . Our study also revealed unexpectedly large genetic divergences between three different populations of the monotypic S. poliogenys , indicating the presence of cryptic species. Our results underscore the importance of dense sampling at the specific and infraspecific levels in intrageneric phylogenetic studies.     

Characterization of microsatellite loci In The hihi Notiomystis cincta (Notiomystidae, Aves)

We have characterized 20 polymorphic microsatellite loci in the hihi Notiomystis cincta. Loci were identified by testing loci originally isolated in other avian species and by isolating new microsatellites from a hihi genomic library. These loci were characterized in unrelated hihi from a single population on Tiritiri Matangi Island (n = 98). Each locus displayed between two and 10 alleles, and observed heterozygosities ranged between 0.29 and 0.91. Nineteen of the 20 polymorphic loci could be assigned a chromosome location in the zebra finch, Taeniopygia guttata genome based on sequence homology.     

Characterization of microsatellite loci in the Blue‐and‐gold Macaw,Ara ararauna (Psittaciformes: Aves)

Microsatellite loci were isolated from the Blue‐and‐gold Macaw (Ara ararauna), a Neotropical parrot, from a GT_n and CT_n enriched genomic library. Six loci were characterized varying from one to 11 alleles per locus. Five loci exhibited greater than 50% heterozygosity within the 49 individuals genotyped. Furthermore, the primers also amplified the DNA from two additional genera of Neotropical parrots, indicating the potential utility of these markers for population‐level studies and conservation efforts of Neotropical parrots.     

Pathway position constrains the evolution of an ecologically important pathway in aspens (Populus tremula L.)

Many ecological interactions of aspens and their relatives (Populus spp.) are affected by products of the phenylpropanoid pathway synthesizing condensed tannins (CTs), whose production involves trade‐offs with other ecologically important compounds and with growth. Genes of this pathway are candidates for investigating the role of selection on ecologically important, polygenic traits. We analysed sequences from 25 genes representing 10 steps of the CT synthesis pathway, which produces CTs used in defence and lignins used for growth, in 12 individuals of European aspen (Populus tremula). We compared these to homologs from P. trichocarpa, to a control set of 77 P. tremula genes, to genome‐wide resequencing data and to RNA‐seq expression levels, in order to identify signatures of selection distinct from those of demography. In Populus, pathway position exerts a strong influence on the evolution of these genes. Nonsynonymous diversity, divergence and allele frequency shifts (Tajima's D) were much lower than for synonymous measures. Expression levels were higher, and the direction of selection more negative, for upstream genes than for those downstream. Selective constraints act with increasing intensity on upstream genes, despite the presence of multiple paralogs in most gene families. Pleiotropy, expression level, flux control and codon bias appear to interact in determining levels and patterns of variation in genes of this pathway, whose products mediate a wide array of ecological interactions for this widely distributed species.