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PubMed1991

Nucleotide sequence and evolution of coding and noncoding regions of a quail mitochondrial genome.

Segments of the Japanese quail mitochondrial genome encompassing many tRNA and protein genes, the small and part of the large rRNA genes, and the control region have been cloned and sequenced. Analysis of the relative position of these genes confirmed that the tRNA(Glu) and ND6 genes in galliform mitochondrial DNA are located immediately adjacent to the control region of the molecule instead of between the cytochrome b and ND5 genes as in other vertebrates. Japanese quail and chicken display another distinctive characteristic, that is, they both lack an equivalent to the light-strand replication origin found between the tRNA(Cys) and tRNA(Asn) genes in all vertebrate mitochondrial genomes sequenced thus far. Comparison of the protein-encoding genes revealed that a great proportion of the substitutions are silent and involve mainly transitions. This bias toward transitions also occurs in the tRNA and rRNA genes but is not observed in the control region where transversions account for many of the substitutions. Sequence alignment indicated that the two avian control regions evolve mainly through base substitutions but are also characterized by the occurrence of a 57-bp deletion/addition event at their 5' end. The overall sequence divergence between the two gallinaceous birds suggests that avian mitochondrial genomes evolve at a similar rate to other vertebrate mitochondrial DNAs.

Amino Acid Sequence↗
PubMed1999

Male-driven evolution among Eoaves? A test of the replicative division hypothesis in a heterogametic female (ZW) system.

Because avian females are heterogametic, the reverse of mammals, avian sex chromosomes undergo significantly different patterns and numbers of DNA replications than do those in mammals. This makes the W (female-specific) and the Z chromosomes an excellent model system for the study of the replicative division hypothesis, which purports that DNA substitution rate is determined by the number of germline replications. The sex-specific chromosome in birds (the W) is predicted to change at the slowest rate of all avian chromosomes because it undergoes the fewest rounds of replication per unit of evolutionary time. Using published data on gametogenesis from a variety of sources, we estimated the ratio of male-to-female germline replications (c) in galliforms and anseriforms to be approximately 4.4. The value of c should predict the value of the ratio of male-to-female mutation rates (alpha(m)) if the replicative division hypothesis is true. Homologous DNA sequences including an intron and parts of two exons of the CHD gene were obtained from the W and the Z chromosomes in ostrich, sage grouse, canvasback duck, tundra swan, and snow goose. The exons show significantly different nucleotide composition from the introns, and the W-linked exons show evidence of relaxed constraint. The Z-linked intron is diverging approximately 3.1 times faster than the W-linked intron. From this, alpha(m) was calculated to be approximately 4.1, with a confidence interval of 3.1 to 5.1. The data support the idea that the number of replicative divisions is a major determinant of substitution rate in the Eoavian genome.

Animals↗
PubMed1998

Phylogeny and rapid northern and southern hemisphere speciation of goldfinches during the Miocene and Pliocene epochs.

Mitochondrial cytochrome b (cyt b) from 25 out of 31 extant goldfinches, siskins, greenfinches and redpolls (genus Carduelis) has been sequenced from living samples taken around the world, specimens have also been photographed. Phylogenetic analysis consistently gave the same groups of birds, and this grouping was generally related to geographical proximity. It has been supposed that Pleistocene glaciations played a crucial role in the origin of extant diversity and distribution of Northern Hemisphere vertebrates. Molecular comparison of most extant songbird species belonging to the genus Carduelis does not support this assertion. The fossil record of chicken and pheasant divergence time has been used to calibrate the molecular clock; cyt b DNA dendrograms suggest that speciation in Carduelinae birds occurred during the Miocene and Pliocene Epochs (9-2 million years ago) in both the Northern and Southern Hemispheres. Only about 4% average amount of nucleotide substitution per lineage is found between the most distant Carduelis species; this suggests a remarkably rapid radiation when compared with the radiation of other passerine songbird genera. In addition, a continuum of small songbird speciation may be found during the Miocene Epoch in parallel with speciation of other orders (i.e. Galliformes, chicken/pheasant). Pleistocene glaciations may have been important in subspeciation (i.e. Eastern European grey-headed goldfinches/Western European black-headed goldfinches) and also in ice-induced vicariance (isolation) (i.e. siskin in Western Europe vs. siskin in Far East Asia) around the world. European isolated Serinus citrinella (citril finch) is not a canary, but a true goldfinch. South American siskins have quickly radiated in the last 4 million years coinciding with the emergence of the Isthmus of Panama; probably, a North American siskin related to C. notata invaded a suitable and varied biotope (the South American island) for Carduelis birds. North American goldfinches may be renamed as siskins, because they have a distant genetic relationship with European goldfinches. Genus Acanthis could be dropped, and thus redpolls should be separated from twite and linnet, the latter (Europeans) probably being related to American goldfinches. Also, reproductive barriers are observed between closely related species and not between other more distant ones. Finally, a tentative classification for genus Carduelis species is suggested.

Animals↗
PubMed2006

Substitution rate heterogeneity and the male mutation bias.

Germline mutation rates have been found to be higher in males than in females in many organisms, a likely consequence of cell division being more frequent in spermatogenesis than in oogenesis. If the majority of mutations are due to DNA replication error, the male-to-female mutation rate ratio (alpha(m)) is expected to be similar to the ratio of the number of germ line cell divisions in males and females (c), an assumption that can be tested with proper estimates of alpha(m) and c. Alpha(m) is usually estimated by comparing substitution rates in putatively neutral sequences on the sex chromosomes. However, substantial regional variation in substitution rates across chromosomes may bias estimates of alpha(m) based on the substitution rates of short sequences. To investigate regional substitution rate variation, we estimated sequence divergence in 16 gametologous introns located on the Z and W chromosomes of five bird species of the order Galliformes. Intron ends and potentially conserved blocks were excluded to reduce the effect of using sequences subject to negative selection. We found significant substitution rate variation within Z chromosome (G15 = 37.6, p = 0.0010) as well as within W chromosome introns (G15 = 44.0, p = 0.0001). This heterogeneity also affected the estimates of alpha(m), which varied significantly, from 1.53 to 3.51, among the introns (ANOVA: F(13,14) = 2.68, p = 0.04). Our results suggest the importance of using extensive data sets from several genomic regions to avoid the effects of regional mutation rate variation and to ensure accurate estimates of alpha(m).

Animals↗
PubMed2000

Male-biased mutation rates revealed from Z and W chromosome-linked ATP synthase alpha-subunit (ATP5A1) sequences in birds.

Whether the mutation rate differs between sexes has been a matter of discussion for years. Molecular analyses of mammals have indicated that males mutate more often than females, as manifested by the faster rate of neutral sequence evolution on the Y chromosome than on the X chromosome. However, these observations can as well be interpreted as specific reduction of the X chromosome mutation rate, which would be adaptive because of reducing the number of slightly deleterious recessive mutations exposed in hemizygote males. Recently, data from birds have suggested that vertebrate mutation rates may indeed be male-biased. In birds, females are the heterogametic sex (ZW), and analyses of the Z-linked CHD1Z gene have shown that it evolves faster than its W-linked and thus female-specific homologue, CHD1W. We have now studied the second avian gene known to exist in a copy on the nonrecombining regions of both the Z and the W chromosome, viz., the ATP synthase alpha-subunit (ATP5A1). In independent comparisons of three pairs of bird species from divergent lineages, intron sequences of the Z-linked copy (ATP5A1Z) were consistently found to evolve faster than the W-linked copy (ATP5A1W). From these data we calculated male-to-female mutation rate ratios (alpha) of 1.8, 2.3, and 5.0 in Galliform, Anseriform, and Ciconiiform lineages, respectively. Therefore, this study provides independent support for a male-biased mutation rate in birds.

Animals↗
PubMed2001

Evolution of a metal-binding cluster in the NH(2)-terminal variable region of avian fast skeletal muscle troponin T: functional divergence on the basis of tolerance to structural drifting.

This study investigated the evolution of a transition metal ion-binding cluster ([H--X--X--X--H](n); Tx) in the alternatively spliced NH(2)-terminal variable region of avian pectoral muscle troponin T (TnT). Encoded by avian fast skeletal muscle TnT-specific P exons, Tx-like structures were expressed in the breast muscle TnT's of almost all birds examined. Their presence results in the developmentally up-regulated high molecular weight pectoral muscle TnT. Sequence analysis and metal affinity chromatography revealed that in Galliformes and Craciformes, the Tx structure evolved into multiple H--X--X--X--H pairs with a high-affinity metal-binding capacity. Turkey, chicken, quail, and curassow breast muscle TnT's contain nine, seven, four, and three consecutive or closely located metal-binding sites, respectively, in the NH(2)-terminal region. The metal-binding affinity of the Tx element increased as the number of His pairs increased due to the duplication of P exons and the conversion of other exon sequences. The data show two related components of avian pectoral muscle TnT evolution: a larger, more acidic NH(2)-terminal segment and a cluster of transition metal-binding sites, both of which may have functional significance for their selection value. The evolution of the Tx segment in the NH(2)-terminal variable region of avian pectoral muscle TnT demonstrates a functional divergence on the basis of tolerance to structural drifting.

Alternative Splicing↗
PubMed2000

Mhc diversity in two passerine birds: no evidence for a minimal essential Mhc.

Humans express an array of Mhc genes, while the chicken has an Mhc that is relatively small and compact with fewer expressed genes. Here we ask whether the "minimal essential Mhc" of the chicken is representative for birds. We investigated the RFLP genotypes in 55 great reed warblers Acrocephalus arundinaceus and 10 willow warblers Phylloscopus trochilus to obtain an overview of the number of class II B genes. There were 13-17 bands per individual in the great reed warblers and 25-30 in the willow warblers, and every individual had a unique RFLP genotype. The high number of RFLP bands indicates that both species have a large number of class II B genes although some may be pseudogenes. Seven different class II B sequences were detected in a great reed warbler cDNA library. There was considerable sequence divergence between the cDNA sequences in exon 2 (peptide-binding region, PBR), whereas they were very similar in exon 3. The cDNA sequences were easily alignable to a classical chicken class II B sequence, and balancing selection was acting in the PBR. One of the cDNA sequences had two deletions and is likely nonfunctional. Finally, the polymorphic class I and class II B RFLP fragments seemed to be linked in the five studied great reed warbler families. These and previous results suggest that birds of the order Passeriformes in general have more Mhc class I and II B genes than birds of the order Galliformes. This difference could be caused by their phylogenetic past, and/or by variance in the selection pressure for maintaining a high number of Mhc genes.

Amino Acid Sequence↗
PubMed2005

New host and locality records for the Ixodes auritulus (Acari: Ixodidae) species group, with a review of host relationships and distribution in the Neotropical Zoogeographic Region.

New Neotropical records are presented for ticks belonging to the Ixodes auritulus Neumann, 1904, species group, together with a review of hosts and localities from which members of this complex have previously been collected. The range of the I. auritulus species group is now understood to include Colombia, and 15 bird species are listed as new hosts. From Guatemala to southern Argentina and Chile, specimens of the I. auritulus group have been found on birds belonging to the orders Ciconiiformes, Columbiformes, Falconiformes, Galliformes, Passeriformes, Piciformes, Procellariiformes and Tinamiformes. Passeriform birds are probably the principal hosts, sustaining tick populations throughout the Neotropics. Collection data have yielded four areas--southern South America (from 56 degrees S to 51 degrees S), southern Brazil (25 degrees S-22 degrees S), south-central Peru (14 degrees S-10 degrees S) and Central America (10 degrees N-15 degrees N)--where the I. auritulus group appears to commonly parasitize birds, but additional collections may show that the range of this complex is less discontinuous than currently perceived. Several morphological differences are described for ticks within and among these areas, but it is still unclear whether the I. auritulus group comprises more than one species.

Animals↗
PubMed2005

Molecular and cytogenetic characterization of site-specific repetitive DNA sequences in the Chinese soft-shelled turtle (Pelodiscus sinensis, Trionychidae).

A novel family of repetitive DNA sequences that are components of constitutive heterochromatin were cloned from BglI-digested genomic DNA of the Chinese soft-shelled turtle (Pelodiscus sinensis, Trionychidae), and characterized by filter hybridization and chromosome in-situ hybridization. The BglI-family of repetitive sequences were classified into four types by their genome organization and chromosomal distribution as follows: the repeated sequences located on (1) two pairs of microchromosomes, (2) four pairs of microchromosomes,(3) about half the number of microchromosomes and (4) the interstitial region of the short arm of chromosome 2. The presence of microchromosome-specific repetitive sequences has also been reported in the Struthioniformes and Galliformes, suggesting that turtle chromosomes retain some similarity to the chromosome structure as well as the karyotypes of avian species.

Animals↗
PubMed2007

Comparison of the chicken and zebra finch Z chromosomes shows evolutionary rearrangements.

Using fluorescent in-situ hybridization (FISH) of zebra finch (Taeniopygia guttata) bacterial artificial chromosome (BAC) clones, we determined the chromosomal localizations of 14 zebra finch genes that are Z-linked in chickens: ATP5A1, CHD1, NR2F1, DMRT1, PAM, GHR, HSD17B4, NIPBL, ACO1, HINT1, SMAD2, SPIN, NTRK2 and UBE2R2. All 14 genes also map to the zebra finch Z chromosome, indicating substantial conservation of gene content on the Z chromosome in the two avian lineages. However, the physical order of these genes on the zebra finch Z chromosome differed from that of the chicken, in a pattern that would have required several inversions since the two lineages diverged. Eight of 14 zebra finch BAC DNA showed cross-hybridization to the W chromosome, usually to the entire W chromosome, suggesting that repetitive sequences are shared by the W and Z chromosomes. These repetitive sequences likely evolved in the finch lineage after it diverged from the Galliform lineage.

Animals↗
PubMed2006

On the positions of centromeres in chicken lampbrush chromosomes.

Using immunostaining with antibodies against cohesin subunits, we show here that cohesin-enriched structures analogous to the so-called centromere protein bodies (PB) are the characteristic of galliform lampbrush chromosomes. Their centromeric location was verified by FISH with certain DNA probes. PB-like structures were used as markers for centromere localization in chicken lampbrush chromosomes. The gap predicted to be centromeric in current chicken chromosome 3 sequence assembly was found to correspond to the non-centromeric cluster of CNM repeat on the q-arm of chromosome 3; the centromere is proposed to be placed at another position. The majority of chicken microchromosomes were found to be acrocentric, in contrast to Japanese quail microchromosomes which are biarmed. Centromere cohesin-enriched structures on chicken and quail lampbrush microchromosomes co-localize with pericentromeric CNM and BglII- repeats respectively. FISH to the nascent transcripts on chicken lampbrush chromosomes revealed numerous non-centromeric CNM clusters in addition to pericentromeric arrays. Complementary CNM transcripts from both C- and G-rich DNA strands were revealed during the lampbrush stage.

Animals↗
PubMed2005

Plasmodium dominicana n. sp. (Plasmodiidae: Haemospororida) from Tertiary Dominican amber.

Plasmodium dominicana n. sp. is described from Tertiary Dominican Republic amber. The description is based on oocysts, sporozoites and possible microgametes and an ookinete in the body-cavity of a female Culex mosquito (Diptera: Culicidae: Culicinae). The large pedunculated oocysts, together with the culicine vector, align the fossil with the extant avain malaria species, P. juxtanucleare Versiani & Gomes, 1941. Based on the host range of P. juxtanucleare, a possible primary host would have been a member of the order Galliformes. This discovery establishes a minimum age for the genus Plasmodium Marchiafava & Celli, 1885 and places avian malaria in the Americas by the mid-Tertiary. It also supports earlier theories that some species of primate malaria could have evolved in the Americas.

Amber↗
PubMed2005

A new species of Pterothominx Freitas, 1959 (Nematoda: Capillariidae) parasitising psittacine birds (Psittaciformes).

A new species, Pterothominx (Pterothominx) moraveci n. sp. (Trichinelloidea: Capillariidae) is described from an Australian parrot, Barnardius zonarius Shaw (Psittacidae: Psittaciformes), imported from Germany and kept in captivity in the Czech Republic. Males of the new taxon differ from all other species of the subgenus Pterothominx Freitas, 1959, which mainly parasitise galliform birds, in having a shorter spicule (0.925-1.338; mean 1.050 mm), a shorter body length and a different form of armed spicular sheath and bursa. Females differ in having the smallest eggs (40-50 x 20-25; mean 48 x 23 microm) and in other morphometrical characters. From the species P. (P.) totani (Linstow, 1875), which parasitises charadriiform birds, the new species differs in its smaller number of stichocytes (females 42-46, mean 44; versus 50-54), different form of the bursa and praebursal alae, and other characters. This is the only species of Pterothominx that parasitises psittacine birds.

Animals↗
PubMed1983

Annual variation in the concentrations of circulating hormones in capercaillie (Tetrao urogallus).

Seasonal variation in the levels of immunoreactive lutropin (LH), follitropin (FSH), prolactin (PRL), corticosterone (B), thyroxine (T4), and triiodothyronine (T3) was measured in the plasma of male and female capercaillies (Tetrao urogallus, Galliformes) in captivity (latitude N 67 degrees). In male capercaillies there was an increase in the concentrations of LH and FSH beginning in March and reaching their maxima in May, which correlated with the nesting period. The concentration of plasma PRL increased from the end of April and reached its highest level simultaneously with the rapid fall of plasma LH and FSH concentrations. It remained elevated until August, Plasma T4 level was depressed after levels of plasma FSH and LH had reached their maxima and was correlated to simultaneous elevation of plasma PRL level. No dramatic seasonal changes in plasma T3 level were noted. In the female capercaillie no marked changes in plasma FSH and LH concentrations were observed. Although four of six females laid eggs only one of them managed to terminate its nesting successfully; five eggs hatched. Changes in prolactin concentration in females parallel those in males. No marked variations were observed in plasma corticosterone concentrations. On the basis of these results it seems probable that captive female capercaillie show depressed gonadotrophin secretion, resulting in unsuccessful nesting. On the other hand it has to be emphasized that gonadotrophin assays may not be sensitive enough, especially in the female, to measure LH and FSH in the volumes of plasma put in the assays.

Animals↗
PubMed1991

Assay validation and characterization of hepatic 5'-deiodinase activity in ring doves using reverse-T3 as substrate.

Adult ring dove hepatic 5'-deiodinase (5'D) activity was studied in vitro using reverse T3 (rT3) as substrate. A previous study of ring dove hepatic deiodinase in our laboratory did not include characterization studies and was unsuccessful in relating the pattern of 5'D development to that of plasma T3. In the present study we established valid assay conditions and characterized the hepatic 5'D in doves to provide a comparison with other avian species and 5'D activity is proportional to enzyme concentration (as postmitochondrial fraction (PMF) protein) over the range measured (0-0.163 mg PMF protein/ml, representing 0-2.19 mg original tissue/ml). Activity was linear with time from 5 to 30 min of incubation at 0.163 mg PMF protein/ml. Our 5'D assays used 20 mM DTT; activity was maximal from 5 to 30 mM DTT. Using the validated conditions the following characteristics were found: the apparent Km was 0.44 microM rT3, Vmax was 255 pM rT3 degraded/min-mg PMF protein, and activity was completely inhibited by 1 mM PTU. Activity was maximal at pH 8.04 and at 37.5 degrees (although this did not differ from activity at 41.5 degrees, the body temperature of doves). In summary, this study demonstrates conditions that measure 5'D at initial velocities in dove liver and demonstrates that the hepatic 5'D enzyme in ring doves is similar to the deiodinase activity in liver of galliform birds and mammals.

Animals↗
PubMed1995

Testosterone-induced changes of call structure, midbrain and syrinx anatomy in partridges.

Testosterone (T) treated Grey partridges (Perdix perdix) of both sexes uttered significantly longer and lower-pitched calls than controls; both these acoustic features play a critical role in mate choice. A morphometrical analysis of the midbrain nucleus intercollicularis showed a cell size increase in T-treated birds regardless of their sex. Histological study of the syrinx did not reveal any sexually dimorphic structure in experimental and control birds; the major T-induced change was a thickening of the external membranes, reported to be the main sound source in Galliforms. In conclusion, T appears able to modify not only some acoustic parameters, but also certain anatomical structures at the peripheral and central levels of the vocal system in a nonoscine species.

Animals↗
PubMed1988

Comparative studies on the structure of biliary immunoglobulins of some avian species. II. Antigenic properties of the biliary immunoglobulins of chicken, turkey, duck and goose.

Studies on the immunological cross-reactivity of the Igs+ from the bile of chicken and turkey (order Galliformes) as well as duck and goose (order Anseriformes) to Igs with antigenic known properties carried out by a series of RIA. Various class-specific anti-Ig sera produced in rabbits, guinea-pigs and mice were used. The following results were obtained: (1) A high extent of antigenic relationship between the chicken and turkey biliary Igs was demonstrated by a radiobinding system consisting of 125I-turkey biliary Ig and class-specific rabbit anti-turkey biliary Ig antibodies. The biliary Igs of duck and goose did not inhibit this antigen binding system. (2) The duck and goose biliary Igs were able to inhibit the binding of 125I-carp IgM to Fc-fragment-specific rabbit anti-carp IgM antibodies and of 125I-human IgM to Fc-fragment-specific guinea-pig anti-human IgM antibodies, respectively. (3) None of the biliary Igs show cross-reactive properties common with human and porcine IgA. That was detected by inhibition of the radio-binding system from 125I-human IgA and alpha chain-specific mouse anti-human IgA antibodies. Therefore, the conclusion was made that in anseriform birds IgM-like Igs are the secretory Igs, while in galiform birds biliary Igs with special antigenic properties occur.

Animals↗
PubMed1986

Multiple molecular forms of soluble esterases in the digestive system of the developing chicken.

Soluble esterases in tissues of endodermic origin and of various developmental ages of Gallus gallus were analysed by polyacrylamide slab gel electrophoresis and characterized as carboxylesterases, acetylesterases and cholinesterases. Esterase bands were observed from day 9 in the liver and from day 6 in stomach, intestine and yolk sac. The electrophoretic profiles became more complex after hatching with concomitant increase in the staining intensity. On isoelectric focusing of liver extracts only a major form with pI 5.4 was observed. An eserine sensitive band designated EL-1 was found to be tissue (liver) and age (upon hatching) specific. EL-1-like isozymes were also observed in other species of the Galliformes order.

Aging↗