Rates of nuclear DNA evolution in pheasant-like birds: evidence from restriction maps

Novel polymorphisms and genetic studies of the shadow of prion protein gene (SPRN) in pheasants

Background

Prion diseases in mammals are caused by the structural conversion of the natural prion protein (PrPC) to a pathogenic isoform, the "scrapie form of prion protein (PrPSc)." Several studies reported that the shadow of prion protein (Sho), encoded by the shadow of prion protein gene (SPRN), is involved in prion disease development by accelerating the conformational conversion of PrPC to PrPSc. Until now, genetic polymorphisms of the SPRN gene and the protein structure of Sho related to fragility to prion disease have not been investigated in pheasants, which are a species of poultry.

Methods

Here, we identified the SPRN gene sequence by polymerase chain reaction (PCR) and compared the SPRN gene and Sho protein sequences among various prion disease-susceptible and -resistant species to identify the distinctive genetic features of pheasant Sho using Clustal Omega. In addition, we investigated genetic polymorphisms of the SPRN gene in pheasants and analyzed genotype, allele, and haplotype frequencies, as well as linkage disequilibrium among the genetic polymorphisms. Furthermore, we used in silico programs, namely Mutpred2, MUpro and AMYCO, to investigate the effect of non-synonymous single nucleotide polymorphisms (SNPs). Finally, the predicted secondary and tertiary structures of Sho proteins from various species were analyzed by Alphafold2.

Results

In the present study, we reported pheasant SPRN gene sequences for the first time and identified a total of 14 novel SNPs, including 7 non-synonymous and 4 synonymous SNPs. In addition, the pheasant Sho protein sequence showed 100% identity with the chicken Sho protein sequence. Furthermore, amino acid substitutions were predicted to affect the hydrogen bond distribution in the 3D structure of the pheasant Sho protein.

Conclusion

To the best of our knowledge, this is the first report of the genetic and structural features of the pheasant SPRN gene.

Analysis of the source of aggressiveness in gamecocks

Although the fighting behaviour in gamecocks has evolved because of artificial selection, it is unknown whether the selection for aggressiveness affects neurotransmitter levels in the avian central nervous system. We sought to identify the source and origin of this trait. We collected the brain samples from 6 female Shamo gamecocks and 5 Shaver Brown chickens (control; bred for egg production). The midbrain levels of norepinephrine (NE) were significantly higher in Shamo gamecocks (P = 0.0087) than in the controls. Moreover, alleles encoding adrenergic receptors differed between the breeds in terms of response to NE. Gene mutations specific to Shamo and potentially associated with fighting behaviour were in sites T440N of ADRα1D; V296I of ADRα2A; and T44I, Q232R, and T277M of ADRβ2. The evolutionary analysis indicated that the ADRβ2 (T44I and Q232R) mutations were heritable in all Galliformes, whereas the T440N mutation of ADRα1D and V296I mutations of ADRα2A were unique to Shamo and originated by artificial selection. A high NE level may confer a selective advantage by enabling gamecocks to be aggressive and pain tolerant. Therefore, the strong fighting behaviour of Shamo has resulted from a combination of naturally inherited and mutant genes derived by artificial selection.

Complete mitochondrial genome of Sri Lankan Junglefowl (Gallus lafayetti) and phylogenetic study

The complete mitochondrial genomes of two Sri Lankan junglefowl (Gallus lafayetti: CJF) individuals were sequenced by using next-generation sequencing technique. Samples were collected from Rathnapura and Pelmadulla areas in Sri Lanka. The complete mitochondrial DNA is 16,839 bp in length, with a typical mitogenome structure composed of a non-coding control region, 22 tRNA, two rRNA, and 13 protein-coding genes. Overall base composition is 30% A, 23.9% T, 32.3% C, and 13.6% G indicating high content of 54.0% A + T for both individuals. Phylogenetic analysis reveals that CJF samples cluster with the clade of the green junglefowl (Gallus varius) and red junglefowl (Gallus gallus) than to grey junglefowl (Gallus sonerattii: GyJF). This result can be subsequently used to provide essential information for junglefowl evolution.

Major Histocompatibility Complex Allele Persistence in Eurasia and America in the Genus Carduelis (Spinus) During Million Years

Introduction:

GenusCarduelis(Fringillidaefamily) includes goldfinches, siskins, redpolls, greenfinches and crossbills. Many of the species classified within this genus and other related genera have been grouped by using molecular systematics and the mitochondrial cytochrome b (mt cyt b) gene. According to this, the Eurasian siskin (C. spinus)is the only one extant direct ancestor of several North American finches; North American / South American radiations may have been originated by Eurasian siskin (or extinct relative). In the present work, we aim to perform a study of transpecies and transcontinental analyses of MHC (Major Histocompatibility Complex) Class I alleles in several genusCarduelis/Spinusspecies in order to draw evolutionary conclusions in several wild bird species belonging to the genusCarduelis / Spinus.

Materials and Methods:

Blood was taken from worldwide wild bird species. Passerine phylogeny was done after analysing mtDNA with Maximun Likelihood and Bayesian dendrograms. Major histocompatibility complex alleles were obtained by standard DNA cloning and sequencing.

Results:

We found two matches between MHC-I DNA alleles from different South American siskins at DNA level. Also, it was observed that the Eurasian siskin shares a protein with pine siskin and another with three South American siskins. Eight South American siskins species also share the same MHC protein. In addition, studied songbirds MHC class I intron 2 is longer than that ofGallus gallus.

Conclusion:

We have drawn the following conclusions: 1) We present the first direct evidence that “Minimal Essential MHC” does not exist for birds; one of its main definition characters,i.e.: small intron size does not hold for songbirds. 2) We also report that MHC genes transpecies evolution exist in birds by showing also for the first time that worldwide bird species keep the same MHC protein and DNA alleles. 3) New evidences on MHC alleles conservation from EurasianCarduelis spinus(most ancient) to South American siskins (most recent) during million years support that Eurasian siskin is the parental species for American GenusCarduelis (Spinus)species. It is uncertain whether Eurasian siskin (or extant relative) had initially an Holoartic distribution, including America.

Interspecific hybrids of dwarf hamsters and Phasianidae birds as animal models for studying the genetic and developmental basis of hybrid incompatibility

Hybrid incompatibility is important in speciation as it prevents gene flow between closely related populations. Reduced fitness from hybrid incompatibility may also reinforce prezygotic reproductive isolation between sympatric populations. However, the genetic and developmental basis of hybrid incompatibility in higher vertebrates remains poorly understood. Mammals and birds, both amniotes, have similar developmental processes, but marked differences in development such as the XY/ZW sex determination systems and the presence or absence of genomic imprinting. Here, we review the sterile phenotype of hybrids between the Phodopus dwarf hamsters P. campbelli and P. sungorus, and the inviable phenotype of hybrids between two birds of the family Phasianidae, chicken (Gallus gallus domesticus) and Japanese quail (Coturnix japonica). We propose hypotheses for developmental defects that are associated with these hybrid incompatibilities. In addition, we discuss the genetic and developmental basis for these defects in conjunction with recent findings from mouse and avian models of genetics, reproductive biology and genomics. We suggest that these hybrids are ideal animal models for studying the genetic and developmental basis of hybrid incompatibility in amniotes.

A new look at the LTR retrotransposon content of the chicken genome

Background

LTR retrotransposons contribute approximately 10 % of the mammalian genome, but it has been previously reported that there is a deficit of these elements in the chicken relative to both mammals and other birds. A novel LTR retrotransposon classification pipeline, LocaTR, was developed and subsequently utilised to re-examine the chicken LTR retrotransposon annotation, and determine if the proposed chicken deficit is biologically accurate or simply a technical artefact.

Results

Using LocaTR 3.01 % of the chicken galGal4 genome assembly was annotated as LTR retrotransposon-derived elements (nearly double the previous annotation), including 1,073 that were structurally intact. Element distribution is significantly correlated with chromosome size and is non-random within each chromosome. Elements are significantly depleted within coding regions and enriched in gene sparse areas of the genome. Over 40 % of intact elements are found in clusters, unrelated by age or genera, generally in poorly recombining regions. The transcription of most LTR retrotransposons were suppressed or incomplete, but individual domain and full length retroviral transcripts were produced in some cases, although mostly with regularly interspersed stop codons in all reading frames. Furthermore, RNAseq data from 23 diverse tissues enabled greater characterisation of the co-opted endogenous retrovirus Ovex1. This gene was shown to be expressed ubiquitously but at variable levels across different tissues. LTR retrotransposon content was found to be very variable across the avian lineage and did not correlate with either genome size or phylogenetic position. However, the extent of previous, species-specific LTR retrotransposon annotation appears to be a confounding factor.

Conclusions

Use of the novel LocaTR pipeline has nearly doubled the annotated LTR retrotransposon content of the chicken genome compared to previous estimates. Further analysis has described element distribution, clustering patterns and degree of expression in a variety of adult tissues, as well as in three embryonic stages. This study also enabled better characterisation of the co-opted gamma retroviral envelope gene Ovex1. Additionally, this work suggests that there is no deficit of LTR retrotransposons within the Galliformes relative to other birds, or to mammalian genomes when scaled for the three-fold difference in genome size.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3043-1) contains supplementary material, which is available to authorized users.

Assessing phylogenetic relationships among galliformes: a multigene phylogeny with expanded taxon sampling in Phasianidae

Galliform birds (relatives of the chicken and turkey) have attracted substantial attention due to their importance to society and value as model systems. This makes understanding the evolutionary history of Galliformes, especially the species-rich family Phasianidae, particularly interesting and important for comparative studies in this group. Previous studies have differed in their conclusions regarding galliform phylogeny. Some of these studies have suggested that specific clades within this order underwent rapid radiations, potentially leading to the observed difficulty in resolving their phylogenetic relationships. Here we presented analyses of six nuclear intron sequences and two mitochondrial regions, an amount of sequence data larger than many previous studies, and expanded taxon sampling by collecting data from 88 galliform species and four anseriform outgroups. Our results corroborated recent studies describing relationships among the major families, and provided further evidence that the traditional division of the largest family, the Phasianidae into two major groups ("pheasants" and "partridges") is not valid. Within the Phasianidae, relationships among many genera have varied among studies and there has been little consensus for the placement of many taxa. Using this large dataset, with substantial sampling within the Phasianidae, we obtained strong bootstrap support to confirm some previously hypothesized relationships and we were able to exclude others. In addition, we added the first nuclear sequence data for the partridge and quail genera Ammoperdix, Caloperdix, Excalfactoria, and Margaroperdix, placing these taxa in the galliform tree of life with confidence. Despite the novel insights obtained by combining increased sampling of taxa and loci, our results suggest that additional data collection will be necessary to solve the remaining uncertainties.

Evolutionary history of black grouse major histocompatibility complex class IIB genes revealed through single locus sequence-based genotyping

Background

Gene duplications are frequently observed in the Major Histocompatibility Complex (MHC) of many species, and as a consequence loci belonging to the same MHC class are often too similar to tell apart. In birds, single locus genotyping of MHC genes has proven difficult due to concerted evolution homogenizing sequences at different loci. But studies on evolutionary history, mode of selection and heterozygosity correlations on the MHC cannot be performed before it is possible to analyse duplicated genes separately. In this study we investigate the architecture and evolution of the MHC class IIB genes in black grouse. We developed a sequence-based genotyping method for separate amplification of the two black grouse MHC class IIB genes BLB1 and BLB2. Based on this approach we are able to study differences in structure and selection between the two genes in black grouse and relate these results to the chicken MHC structure and organization.

Results

Sequences were obtained from 12 individuals and separated into alleles using the software PHASE. We compared nucleotide diversity measures and employed selection tests for BLB1 and BLB2 to explore their modes of selection. Both BLB1 and BLB2 are transcribed and display classic characteristics of balancing selection as predicted for expressed MHC class IIB genes. We found evidence for both intra- and interlocus recombination or gene conversion, as well as indication for positive but differential selection at both loci. Moreover, the two loci appear to be linked. Phylogenetic analyses revealed orthology of the black grouse MHC class IIB genes to the respective BLB loci in chicken.

Conclusions

The results indicate that the duplication of the BLB gene occurred before the species divergence into black grouse, chicken and pheasant. Further, we conclude that BLB1 and BLB2 in black grouse are subjected to homogenizing concerted evolution due to interlocus genetic exchange after species divergence. The loci are in linkage disequilibrium, which is in line with the theory of tightly coevolving genes within the MHC under the minimal essential MHC hypothesis. Our results support the conclusion that MHC form and function in birds derived from studies on the domesticated chicken are not artefacts of the domestication process.

Spectrum of MHC class II variability in Darwin's finches and their close relatives

The study describes >400 major histocompatibility complex (MHC) class II B exon 2 and 114 intron 2 sequences of 36 passerine bird species, 13 of which belong to the group of Darwin's finches (DFs) and the remaining 23 to close or more distant relatives of DFs in Central and South America. The data set is analyzed by a combination of judiciously selected statistical methods. The analysis reveals that reliable information concerning MHC organization, including the assignment of sequences to loci, and evolution, as well as the process of species divergence, can be obtained in the absence of genomic sequence data, if the analysis is taken several steps beyond the standard phylogenetic tree construction approach. The main findings of the present study are these: The MHC class II B region of the passerine birds is as elaborate in its organization, divergence, and genetic diversity as the MHC of the eutherian mammals, specifically the primates. Hence, the reported simplicity of the fowl MHC is an oddity. With the help of appropriate markers, the divergence of the MHC genes can be traced deep in the phylogeny of the bird taxa. Transspecies polymorphism is rampant at many of the bird MHC loci. In this respect, the DFs behave as if they were a single, genetically undifferentiated population. There is thus far no indication of alleles that could be considered species, genus, or even DF group specific. The implication of these findings is that DFs are in the midst of adaptive radiations, in which morphological differentiation into species is running ahead of genetic differentiation in genetic systems such as the MHC or the mitochondrial DNA. The radiations are so young that there has not been enough time to sort out polymorphisms at most of the loci among the morphologically differentiating species. These findings parallel those on Lake Victoria haplochromine fishes. Several of the DF MHC allelic lineages can be traced back to the MHC genes of the species Tiaris obscura, which we identified previously as the closest extant relative of DFs in continental America.

Phylogeographic population structure of Red-winged Blackbirds assessed by mitochondrial DNA

A continent-wide survey of restriction-site variation in mitochondrial DNA (mtDNA) of the Red-winged Blackbird (Agelaius phoeniceus) was conducted to assess the magnitude of phylogeographic population structure in an avian species. A total of 34 mtDNA genotypes was observed among the 127 specimens assayed by 18 restriction endonucleases. Nonetheless, population differentiation was minor, as indicated by (i) small genetic distances in terms of base substitutions per nucleotide site between mtDNA genotypes (maximum P approximately 0.008) and by (ii) the widespread geographic distributions of particular mtDNA clones and phylogenetic arrays of clones. Extensive morphological differentiation among redwing populations apparently has occurred in the context of relatively little phylogenetic separation. A comparison between mtDNA data sets for Red-winged Blackbirds and deermice (Peromyscus maniculatus) also sampled from across North America shows that intraspecific population structures of these two species differ dramatically. The lower phylogeographic differentiation in redwings is probably due to historically higher levels of gene flow.

The origin and genetic variation of domestic chickens with special reference to junglefowls Gallus g. gallus and G. varius

It is postulated that chickens (Gallus gallus domesticus) became domesticated from wild junglefowls in Southeast Asia nearly 10,000 years ago. Based on 19 individual samples covering various chicken breeds, red junglefowl (G. g. gallus), and green junglefowl (G. varius), we address the origin of domestic chickens, the relative roles of ancestral polymorphisms and introgression, and the effects of artificial selection on the domestic chicken genome. DNA sequences from 30 introns at 25 nuclear loci are determined for both diploid chromosomes from a majority of samples. The phylogenetic analysis shows that the DNA sequences of chickens, red and green junglefowls formed reciprocally monophyletic clusters. The Markov chain Monte Carlo simulation further reveals that domestic chickens diverged from red junglefowl 58,000+/-16,000 years ago, well before the archeological dating of domestication, and that their common ancestor in turn diverged from green junglefowl 3.6 million years ago. Several shared haplotypes nonetheless found between green junglefowl and chickens are attributed to recent unidirectional introgression of chickens into green junglefowl. Shared haplotypes are more frequently found between red junglefowl and chickens, which are attributed to both introgression and ancestral polymorphisms. Within each chicken breed, there is an excess of homozygosity, but there is no significant reduction in the nucleotide diversity. Phenotypic modifications of chicken breeds as a result of artificial selection appear to stem from ancestral polymorphisms at a limited number of genetic loci.

The mitochondrial genome sequence and molecular phylogeny of the turkey, Meleagris gallopavo

The mitochondrial genome (mtGenome) has been little studied in the turkey (Meleagris gallopavo), a species for which there is no publicly available mtGenome sequence. Here, we used PCR-based methods with 19 pairs of primers designed from the chicken and other species to develop a complete turkey mtGenome sequence. The entire sequence (16,717 bp) of the turkey mtGenome was obtained, and it exhibited 85% similarity to the chicken mtGenome sequence. Thirteen genes and 24 RNAs (22 tRNAs and 2 rRNAs) were annotated. An mtGenome-based phylogenetic analysis indicated that the turkey is most closely related to the chicken, Gallus gallus, and quail, Corturnix japonica. Given the importance of the mtGenome, the present work adds to the growing genomic resources needed to define the genetic mechanisms that underlie some economically significant traits in the turkey.

Can sexual selection drive female life histories? A comparative study on Galliform birds

Sexual selection has been identified as a major evolutionary force shaping male life history traits but its impact on female life history evolution is less clear. Here we examine the impact of sexual selection on three key female traits (body size, egg size and clutch size) in Galliform birds. Using comparative independent contrast analyses and directional discrete analyses, based on published data and a new genera-level supertree phylogeny of Galliform birds, we investigated how sexual selection [quantified as sexual size dimorphism (SSD) and social mating system (MS)] affects these three important female traits. We found that female body mass was strongly and positively correlated with egg size but not with clutch size, and that clutch size decreased as egg size increased. We established that SSD was related to MS, and then used SSD as a proxy of the strength of sexual selection. We found both a positive relationship between SSD and female body mass and egg size and that increases in female body mass and egg size tend to occur following increases in SSD in this bird order. This pattern of female body mass increases lagging behind changes in SSD, established using our directional discrete analysis, suggests that female body mass increases as a response to increases in the level of sexual selection and not simply through a strong genetic relationship with male body mass. This suggests that sexual selection is linked to changes in female life history traits in Galliformes and we discuss how this link may shape patterns of life history variation among species.

Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. II. Analysis and discussion

In recent years, avian systematics has been characterized by a diminished reliance on morphological cladistics of modern taxa, intensive palaeornithogical research stimulated by new discoveries and an inundation by analyses based on DNA sequences. Unfortunately, in contrast to significant insights into basal origins, the broad picture of neornithine phylogeny remains largely unresolved. Morphological studies have emphasized characters of use in palaeontological contexts. Molecular studies, following disillusionment with the pioneering, but non-cladistic, work of Sibley and Ahlquist, have differed markedly from each other and from morphological works in both methods and findings. Consequently, at the turn of the millennium, points of robust agreement among schools concerning higher-order neornithine phylogeny have been limited to the two basalmost and several mid-level, primary groups. This paper describes a phylogenetic (cladistic) analysis of 150 taxa of Neornithes, including exemplars from all non-passeriform families, and subordinal representatives of Passeriformes. Thirty-five outgroup taxa encompassing Crocodylia, predominately theropod Dinosauria, and selected Mesozoic birds were used to root the trees. Based on study of specimens and the literature, 2954 morphological characters were defined; these characters have been described in a companion work, approximately one-third of which were multistate (i.e. comprised at least three states), and states within more than one-half of these multistate characters were ordered for analysis. Complete heuristic searches using 10 000 random-addition replicates recovered a total solution set of 97 well-resolved, most-parsimonious trees (MPTs). The set of MPTs was confirmed by an expanded heuristic search based on 10 000 random-addition replicates and a full ratchet-augmented exploration to ascertain global optima. A strict consensus tree of MPTs included only six trichotomies, i.e. nodes differing topologically among MPTs. Bootstrapping (based on 10 000 replicates) percentages and ratchet-minimized support (Bremer) indices indicated most nodes to be robust. Several fossil Neornithes (e.g. Dinornithiformes, Aepyornithiformes) were placed within the ingroup a posteriori either through unconstrained, heursitic searches based on the complete matrix augmented by these taxa separately or using backbone-constraints. Analysis confirmed the topology among outgroup Theropoda and achieved robust resolution at virtually all levels of the Neornithes. Findings included monophyly of the palaeognathous birds, comprising the sister taxa Tinamiformes and ratites, respectively, and the Anseriformes and Galliformes as monophyletic sister-groups, together forming the sister-group to other Neornithes exclusive of the Palaeognathae (Neoaves). Noteworthy inferences include: (i) the sister-group to remaining Neoaves comprises a diversity of marine and wading birds; (ii) Podicipedidae are the sister-group of Gaviidae, and not closely related to the Phoenicopteridae, as recently suggested; (iii) the traditional Pelecaniformes, including the shoebill (Balaeniceps rex) as sister-taxon to other members, are monophyletic; (iv) traditional Ciconiiformes are monophyletic; (v) Strigiformes and Falconiformes are sister-groups; (vi) Cathartidae is the sister-group of the remaining Falconiformes; (vii) Ralliformes (Rallidae and Heliornithidae) are the sister-group to the monophyletic Charadriiformes, with the traditionally composed Gruiformes and Turniciformes (Turnicidae and Mesitornithidae) sequentially paraphyletic to the entire foregoing clade; (viii) Opisthocomus hoazin is the sister-taxon to the Cuculiformes (including the Musophagidae); (ix) traditional Caprimulgiformes are monophyletic and the sister-group of the Apodiformes; (x) Trogoniformes are the sister-group of Coliiformes; (xi) Coraciiformes, Piciformes and Passeriformes are mutually monophyletic and closely related; and (xii) the Galbulae are retained within the Piciformes. Unresolved portions of the Neornithes (nodes having more than one most-parsimonious solution) comprised three parts of the tree: (a) several interfamilial nodes within the Charadriiformes; (b) a trichotomy comprising the (i) Psittaciformes, (ii) Columbiformes and (iii) Trogonomorphae (Trogoniformes, Coliiformes) + Passerimorphae (Coraciiformes, Piciformes, Passeriformes); and (c) a trichotomy comprising the Coraciiformes, Piciformes and Passeriformes. The remaining polytomies were among outgroups, although several of the highest-order nodes were only marginally supported; however, the majority of nodes were resolved and met or surpassed conventional standards of support. Quantitative comparisons with alternative hypotheses, examination of highly supportive and diagnostic characters for higher taxa, correspondences with prior studies, complementarity and philosophical differences with palaeontological phylogenetics, promises and challenges of palaeogeography and calibration of evolutionary rates of birds, and classes of promising evidence and future directions of study are reviewed. Homology, as applied to avian examples of apparent homologues, is considered in terms of recent theory, and a revised annotated classification of higher-order taxa of Neornithes and other closely related Theropoda is proposed. (c) 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1-95.

RATES OF EVOLUTION OF HYBRID INVIABILITY IN BIRDS AND MAMMALS

Almost 30 years ago, A. C. Wilson and colleagues presented results indicating that hybrid inviability between species evolves 10 times faster in mammals than in birds and frogs. Here I revisit this question for birds and mammals using modern molecular data (mitochondrial cytochrome b DNA) and a more phylogenetically appropriate statistical approach. My analyses confirm that diverging mammals lose the ability to form viable hybrids faster than birds. To explain the difference in rates of evolutionary loss of hybridization potential, Wilson and coworkers proposed that mammals have higher rates of regulatory evolution, causing higher probabilities of developmental incompatibilities between mammal species. I briefly discuss this and other potential explanations.

Male-biased mutation rate and divergence in autosomal, z-linked and w-linked introns of chicken and Turkey

To investigate mutation-rate variation between autosomes and sex chromosomes in the avian genome, we have analyzed divergence between chicken (Gallus gallus) and turkey (Meleagris galopavo) sequences from 33 autosomal, 28 Z-linked, and 14 W-linked introns with a total ungapped alignment length of approximately 43,000 bp. There are pronounced differences in the mean divergence among autosomes and sex chromosomes (autosomes [A] = 10.08%, Z chromosome = 10.99%, and W chromosome = 5.74%), and we use these data to estimate the male-to-female mutation-rate ratio (alpha(m)) from Z/A, Z/W, and A/W comparisons at 1.71, 2.37, and 2.52, respectively. Because the alpha(m) estimates of the three comparisons do not differ significantly, we find no statistical support for a specific reduction in the Z chromosome mutation rate (Z reduction estimated at 4.89%, P = 0.286). The idea of mutation-rate reduction in the sex chromosome hemizygous in one sex (i.e., X in mammals, Z in birds) has been suggested on the basis of theory on adaptive mutation-rate evolution. If it exists in birds, the effect would, thus, seem to be weak; a preliminary power analysis suggests that it is significantly less than 18%. Because divergence may vary within chromosomal classes as a result of variation in mutation and/or selection, we developed a novel double-bootstrapping method, bootstrapping both by introns and sites from concatenated alignments, to estimate confidence intervals for chromosomal class rates and for alpha(m). The narrowest interval for the alpha(m) estimate is 1.88 to 2.97 from the Z/W comparison. We also estimated alpha(m) using maximum likelihood on data from all three chromosome classes; this method yielded alpha(m) = 2.47 and approximate 95% confidence intervals of 2.27 to 2.68. Our data are broadly consistent with the idea that mutation-rate differences between chromosomal classes can be explained by the male mutation bias alone.

Calibration of galliform molecular clocks using multiple fossils and genetic partitions

For more than a century, members of the traditional avian order Galliformes (i.e., pheasants, partridges, junglefowl, and relatives) have been among the most intensively studied birds, but still a comprehensive timeframe for their evolutionary history is lacking. Thanks to a number of recent cladistic interpretations for several galliform fossils, candidates now exist that can potentially be used as accurate internal calibrations for molecular clocks. Here, we describe a molecular timescale for Galliformes based on cytochrome b and ND2 using nine mostly internal fossil-based anchorpoints. Beyond application of calibrations spanning the entire evolutionary history of Galliformes, care was taken to investigate the effects of calibration choice, substitution saturation, and rate heterogeneity among lineages on divergence time estimation. Results show broad consistency in time estimation with five out of the nine total calibrations. Our divergence time estimates, based on these anchorpoints, indicate that the early history of Galliformes took place in the Cretaceous, including the origin of the basal-most megapode and perhaps cracid lineages, but that the remaining morphological diversification likely started in the earliest Tertiary. The multi-calibration/multi-genetic partition approach used here highlights the importance of understanding the genetic saturation, variation, and rate constancy spectra for the accurate calculation of divergence times by use of molecular clocks.

Phylogeny of Tetraoninae and other galliform birds using mitochondrial 12S and ND2 genes

The avian subfamily Tetraoninae (grouse and ptarmigan) is a Holarctic group in the order Galliformes distinguished by morphological adaptations to cold environments and behavioral traits associated with elaborate courtship. Here we investigate the relationships of 17 tetraonines and 12 other galliform species using mitochondrial 12S and ND2 sequence data. We found support for the recent phylogenetic classification that separates the genus Dendragapus into two genera, Falcipennis and Dendragapus. In addition, we found support for a tetraonine clade in which the first divergence is between Bonasa umbellus and all others, followed by divergence between a Bonasa bonasia/Bonasa sewerzowi clade and the remaining tetraonines. Falcipennis canadensis is sister to a clade with four Tetrao species, and the genus Centrocercus is sister to a Dendragapus obscurus/Tympanuchus clade. Our data indicate a basal position for Cracidae and Megapodiidae among the five recognized galliform families. We also found strong support for the monophyly of Phasianidae, although the relative positions of Numididae and Odontiphoridae remains unresolved. We use a maximum likelihood approach to infer ages of 37mya for divergence of Numididae and Phasianidae and 28mya for the divergence of Tetraoninae and Meleagris gallopavo. These estimates must be viewed as tentative as they depend on tests of rates of molecular evolution and accurate fossil dates.

Effects of body size on take-off flight performance in the Phasianidae (Aves)

To evaluate the mechanisms responsible for relationships between body mass and maximum take-off performance in birds, we studied four species in the Phasianidae: northern bobwhite (Colinus virginianus), chukar (Alectoris chukar), ring-necked pheasant (Phasianus colchicus) and wild turkey (Meleagris gallopavo). These species vary in body mass from 0.2 to 5.3 kg, and they use flight almost solely to escape predators. During take-off, all the species used a similar wingbeat style that appeared to be a vortex-ring gait with a tip reversal during the upstroke. The tip reversal is unusual for birds with rounded wings; it may offer an aerodynamic advantage during rapid acceleration. Flight anatomy generally scaled geometrically, except for average wing chord and wing area, which increased more than expected as body mass (m) increased. Pectoralis strain varied from 19.1 to 35.2 % and scaled in proportion to m(0.23). This positive scaling is not consistent with the widely held assumption that muscle strain is independent of body mass among geometrically similar species. The anatomy of the species precluded measurements of in vivo pectoralis force using the strain-gauge technique that has been employed successfully in other bird species, so we could not directly test in vivo pectoralis force-velocity relationships. However, whole-body kinematics revealed that take-off power (P(ta)), the excess power available for climbing and accelerating in flight, scaled in proportion to m(0.75) and that pectoralis mass-specific P(ta) decreased in proportion to m(−)(0.26) and was directly proportional to wingbeat frequency. These trends suggest that mass-specific pectoralis work did not vary with body mass and that pectoralis stress and strain were inversely proportional, as expected from classical force-velocity models for skeletal muscle. Our observations of P(ta) were consistent with evidence from other species engaged in escape flight and, therefore, appear to contradict evidence from studies of take-off or hovering with an added payload.

Development and characterization of expressed sequence tags for the turkey (Meleagris gallopavo) genome and comparative sequence analysis with other birds

Twenty-one randomly selected clones from a turkey (Meleagris gallopavo) pituitary complementary DNA (cDNA) library were sequenced to develop expressed sequence tags (ESTs) for this economically important avian species whose genome is among the least understood. Primers specific for the ESTs were used to produce amplicons from the genomic DNA of turkey, chicken (Gallus gallus), guinea fowl (Numidia meleagris), pigeon (Columba domestica), and quail (Corturnix japonica). The amplicons were sequenced and analyzed for sequence variation within- and similarity among-species and with GenBank database sequences. The proportion of shared bases between the turkey sequence and the consensus sequence from each of the other species ranged from 72% to 93% between turkey and pigeon and quail and between turkey and chicken, respectively. The total number of single nucleotide polymorphisms (SNPs) observed ranged from 3 in quail to 18 in chicken out of 4898 and 5265 bases analyzed, respectively. The most frequent nucleotide variation observed was a C-->T transition. Linkage analysis of one such SNP in the backcross progeny of the East Lansing reference DNA panel, localized TUS0005, the chicken sequence derived from primers specific for turkey TUT2E EST, to chromosome 4. The ESTs reported, as well as the SNPs may provide a useful resource for ongoing efforts to develop high utility genome maps for the turkey and chicken. The primers described can also be used as a tool in future investigations directed at further understanding the biology of the guinea fowl, pigeon and quail and their relatedness to the turkey.

Turkey and chicken interleukin-2 cross-react in in vitro proliferation assays despite limited amino acid sequence identity

We cloned the cDNA of turkey interleukin-2 (IL-2), initially using oligonucleotide primers based on the sequence of the chicken IL-2 gene. Compared with the only other cytokines available for comparison, the interferons (IFN), the coding regions of the turkey and chicken IL-2 genes are much less conserved (86.24% nucleotide identical and 69.93% amino acid identical). The lack of nucleotide conservation was spread across the entire length of the coding region. In comparison, the promoters of the two avian IL-2 genes shared a high degree of identity (95.71% identical over 380 nucleotides). Phylogenetic analysis shows that turkey and chicken IL-2 have diverged to a greater extent than IL-2 from closely related mammalian species. Surprisingly, considering the low level of amino acid identity, including residues known to be important in binding the IL-2 receptor in mammalian species, both turkey and chicken IL-2 cross-react in functional assays.

Resolution of the phylogenetic position of the Congo peafowl, Afropavo congensis: a biogeographic and evolutionary enigma

Afropavo congensis, the Congo peafowl, has long fascinated ornithologists because of its uncertain phylogenetic position and unusual geographic distribution. While some researchers have placed Afropavo as a sister taxon to the true peafowl, Pavo species, others have suggested relationships with the guineafowl or an Old World partridge, Francolinus. These divergent opinions are due, at least in part, to (i) the unique morphological characteristics, lack of elaborate ornamentation, and monogamous mating system in Afropavo which differentiates it from Pavo; and (ii) the restricted distribution of Afropavo in Zaire, which is far removed from the Asian distribution of all other pheasant species. We obtained complete cytochrome b and partial D-loop sequences of Afropavo and compared them to Pavo, guineafowl, Francolinus and other galliform taxa. Our results strongly support a close relationship between Afropavo and Pavo, and we were able to reject alternative phylogenetic hypotheses. Molecular clock estimates of the divergence time place the separation of Afropavo and Pavo in the late Miocene. We also discuss other relatives of Afropavo and Pavo and use this information to propose hypotheses regarding the evolution of ornamentation and sexual dimorphism within this group of pheasants.

How large was the founding population of Darwin's finches?

A key assumption of many allopatric speciation models is that evolution in peripheral or isolated populations is facilitated by drastic reductions in population size. Population bottlenecks are believed to lead to rapid changes in gene frequencies through genetic drift, to facilitate rapid emergence of novel phenotypes, and to enhance reproductive isolation via genetic revolutions. For such effects to occur, founding populations must be very small, and remain small for some time after founding. This assumption has, however, rarely been tested in nature. One approach is to exploit the polymorphism of the major histocompatibility complex (Mhc ) to obtain information about the founding population. Here, we use the Mhc polymorphism to estimate the size of the founding population of Darwin's finches in the Galápagos Archipelago. The results indicate that the population could not have been smaller than 30 individuals.

Characterization of Mhc genes in a multigenerational family of ring-necked pheasants

Little is known about the major histocompatibility (Mhc) genes of birds in different taxonomic groups or about how Mhc genes may be organized in avian species divergent by evolution or habitat. Yet it seems likely that much might be learned from birds about the evolution, organization, and function of this intricate complex of polymorphic genes. In this study a close relative of the chicken, the ring-necked pheasant (Phasianus colchicus), was examined for the presence and organization of Mhc B-G genes. The patterns of restriction fragments revealed by chicken B-G probes in Southern hybridizations and the patterns of pheasant erythrocyte polypeptides revealed in immunoblots by antisera raised against chicken B-G polypeptides provide genetic, molecular, and biochemical data confirming earlier serological evidence for the presence of B-G genes in the pheasant, and hence, the presence of a family of B-G genes in at least a second species of birds. The high polymorphism exhibited by the pheasant B-G gene family allowed genetic differences among individuals within the small experimental population in this study to be detected easily by restriction fragment patterns. Further evidence was found for the organization of the pheasant Mhc class I and class II genes into genetically independent clusters. Whether these gene clusters are fully comparable to the B and Rfp-Y systems in the chicken or whether yet another organization of Mhc genes has been encountered in the pheasant remains to be determined.

Contrasting histories of avian and mammalian Mhc genes revealed by class II B sequences from songbirds

To explore the evolutionary dynamics of genes in the major histocompatibility complex (Mhc) in nonmammalian vertebrates, we have amplified complete sequences of the polymorphic second (beta1) and third (beta2) exons of class II beta chain genes of songbirds. The pattern of nucleotide substitution in the antigen-binding site of sequences cloned from three behaviorally and phylogenetically divergent songbirds [scrub jays Aphelocoma coerulescens), red-winged blackbirds (Agelaius phoeniceus), and house finches (Carpodacus mexicanus) reveals that class II B genes of songbirds are subject to the same types of diversifying forces as those observed at mammalian class II loci. By contrast, the tree of avian class II B genes reveals that orthologous relationships have not been retained as in placental mammals and that, unlike class II genes in mammals, genes in songbirds and chickens have had very recent common ancestors within their respective groups. Thus, whereas the selective forces diversifying class II B genes of birds are likely similar to those in mammals, their long-term evolutionary dynamics appear to be characterized by much higher rates of concerted evolution.

Genomic organization and evolution of the soybean SB92 satellite sequence

Repetitive DNA sequences comprise a large percentage of plant genomes, and their characterization provides information about both species and genome evolution. We have isolated a recombinant clone containing a highly repeated DNA element (SB92) that is homologous to ca. 0.9% of the soybean genome or about 10(5) copies. This repeated sequence is tandemly arranged and is found in four or five major genomic locations. FISH analysis of metaphase chromosomes suggests that two of these locations are centromeric. We have determined the sequence of two cloned repeats and performed genomic sequencing to obtain a consensus sequence. The consensus repeat size was 92 bp and exhibited an average of 10% nucleotide substitution relative to the two cloned repeats. This high level of sequence diversity suggests an ancient origin but is inconsistent with the limited phylogenetic distribution of SB92, which is found at high copy number only in the annual soybeans. It therefore seems likely that this sequence is undergoing very rapid evolution.

Molecular characterization of three Mhc class II B haplotypes in the ring-necked pheasant

We investigated the class II B genes in a free-ranging population of the ring-necked pheasant Phasianus colchicus by a combination of restriction fragment length polymorphism (RFLP), polymerase chain reaction (PCR), and DNA sequencing. Special attention was paid to the variation in the second exon, which encodes the peptide-binding beta 1-domain. The population was introduced, but it still exhibited major histocompatibility complex polymorphism with at least three segregating class II B haplotypes and consequently six genotypes. We found two class II B genes associated with each haplotype. The class II B genes of birds had until then only been molecularly characterized in the domestic chicken. The pheasant genes were highly variable, although one of the amplified sequences was found in two different haplotypes. Taken together, the most polymorphic positions (residues 37 and 38) were not identical in any of the predicted protein sequences, but all except one of the motifs had already been found in the domestic chicken. Structurally important features in mammalian class II B genes were generally conserved also in the pheasant sequences, but the loss of a potential salt bridge constituent (Arg72) in several sequences may suggest a slightly different structure of the adjacent parts of the peptide-binding groove. The pheasant genes are most closely related to the so called B-LBII family in the chicken, indicating that this represents a major line of development among avian class II B genes.

Pathways of lysozyme evolution inferred from the sequences of cytochrome b in birds

A reliable phylogeny relating the major groups of Galliformes was sought in order to shed light on an unusual case of coupled amino acid replacements in the lysozymes c of these birds. The New World quail and the African guinea fowl share a unique trio of amino acids at three internal positions but have been separated phylogenetically by the majority of trees based on morphological characters. Alternative hypotheses based on molecular data have suggested an arrangement that would be more parsimonious with regard to the lysozyme data. The entire mitochondrial cytochrome b gene (1,143 bp) was amplified via the polymerase chain reaction (PCR) and sequenced for nine galliforms and a representative anseriform to provide DNA sequence data for a phylogenetic reconstruction. The mode and tempo of change in these sequences were analyzed to determine the characters most appropriate for phylogenetic reconstruction. Our results place the New World quail outside all other representative game birds except the cracids. Although in conflict with various morphological analyses, this finding is consistent with the results of DNA-DNA hybridization studies. A model to account for the coupled replacements in the lysozymes is presented. Our results also suggest a rapid but ancient radiation among the Galliformes such that the majority of cytochrome b sequence differences among taxa have accumulated on the terminal branches of the reconstructed phylogenetic trees.

Ancestral lysozymes reconstructed, neutrality tested, and thermostability linked to hydrocarbon packing

The controversy surrounding the idea that neutral mutations dominate protein evolution is attributable in part to the inadequacy of the tools available to evolutionary investigators. With a few exceptions, most investigations into the force driving protein evolution have relied on indirect criteria for distinguishing neutral and non-neutral variants. To investigate a particular pathway of molecular evolution, we have reconstructed by site-directed mutagenesis likely ancestral variants of the lysozymes of modern game birds (order Galliformes), tested their activity and thermostability and determined their three-dimensional structure. We focused on amino acids at three positions that are occupied in all known game birds either by the triplet Thr 40, Ile 55, Ser 91, or by the triplet Ser 40, Val 55, Thr 91. We have synthesized proteins representing intermediates along the possible three-step evolutionary pathways between these triplets. Although all of these are active and stable, none of these intermediates is found in known lysozymes. A comparison of the structures and thermostabilities of the variants reveals a linear correlation between the side-chain volume of the triplet and the thermostability of the protein. Each pathway connecting the two extant triplet sequences includes a variant with a thermostability outside the range of the extant proteins. This observation is consistent with a non-neutral evolutionary pathway. The existence of variants that are more stable than the extant proteins suggests that selection for maximum thermostability may not have been an important factor in the evolution of this enzyme.

The fossil record and estimating divergence times between lineages: maximum divergence times and the importance of reliable phylogenies

Bounded estimates on divergence times between lineages are crucial to the calculation of absolute rates of molecular evolution. Upper (minimum) bounds on divergence times are easily estimated based on earliest fossil finds. Lower (maximum) bounds are more difficult to estimate; the age of putative ancestors may be used, though in practice it is virtually impossible to distinguish ancestors from primitive sister groups, which do not, of logical necessity, constitute lower bounds on divergence times. Two relatively new approaches to estimating lower bounds directly assess the incompleteness of the fossil record. The first uses taphonomic control groups to distinguish real absences from nonpreservation, while the second, and probably more powerful, uses the quality of the fossil record to estimate confidence intervals on the bases of stratigraphic ranges. For some groups, especially vertebrates, the inclusion or exclusion of problematic fossils can dramatically affect estimated lower bounds on divergence times, often swamping the uncertainties due to the incompleteness of the fossil record and/or correlation and dating errors. When datable paleogeographic events reflect ancient divisions of faunas, a lower bound on the divergence time of species within a fauna can be established based on the geologic, rather than fossil, record. The fossil records of hominids, eutherian mammals, echinoids, and geese are used as examples.

Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers

With a standard set of primers directed toward conserved regions, we have used the polymerase chain reaction to amplify homologous segments of mtDNA from more than 100 animal species, including mammals, birds, amphibians, fishes, and some invertebrates. Amplification and direct sequencing were possible using unpurified mtDNA from nanogram samples of fresh specimens and microgram amounts of tissues preserved for months in alcohol or decades in the dry state. The bird and fish sequences evolve with the same strong bias toward transitions that holds for mammals. However, because the light strand of birds is deficient in thymine, thymine to cytosine transitions are less common than in other taxa. Amino acid replacement in a segment of the cytochrome b gene is faster in mammals and birds than in fishes and the pattern of replacements fits the structural hypothesis for cytochrome b. The unexpectedly wide taxonomic utility of these primers offers opportunities for phylogenetic and population research.

Rates of molecular evolution and the fraction of nucleotide positions free to vary

Selective constraints on DNA sequence change were incorporated into a model of DNA divergence by restricting substitutions to a subset of nucleotide positions. A simple model showed that both mutation rate and the fraction of nucleotide positions free to vary are strong determinants of DNA divergence over time. When divergence between two species approaches the fraction of positions free to vary, standard methods that correct for multiple mutations yield severe underestimates of the number of substitutions per site. A modified method appropriate for use with DNA sequence, restriction site, or thermal renaturation data is derived taking this fraction into account. The model also showed that the ratio of divergence in two gene classes (e.g., nuclear and mitochondrial) may vary widely over time even if the ratio of mutation rates remains constant. DNA sequence divergence data are used increasingly to detect differences in rates of molecular evolution. Often, variation in divergence rate is assumed to represent variation in mutation rate. The present model suggests that differing divergence rates among comparisons (either among gene classes or taxa) should be interpreted cautiously. Differences in the fraction of nucleotide positions free to vary can serve as an important alternative hypothesis to explain differences in DNA divergence rates.

Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers

With a standard set of primers directed toward conserved regions, we have used the polymerase chain reaction to amplify homologous segments of mtDNA from more than 100 animal species, including mammals, birds, amphibians, fishes, and some invertebrates. Amplification and direct sequencing were possible using unpurified mtDNA from nanogram samples of fresh specimens and microgram amounts of tissues preserved for months in alcohol or decades in the dry state. The bird and fish sequences evolve with the same strong bias toward transitions that holds for mammals. However, because the light strand of birds is deficient in thymine, thymine to cytosine transitions are less common than in other taxa. Amino acid replacement in a segment of the cytochrome b gene is faster in mammals and birds than in fishes and the pattern of replacements fits the structural hypothesis for cytochrome b. The unexpectedly wide taxonomic utility of these primers offers opportunities for phylogenetic and population research.

Primary structure of the hemoglobin alpha-chain of rose-ringed parakeet (Psittacula krameri)

The structure of the hemoglobin alpha-chain of Rose-ringed Parakeet was determined by sequence degradations of the intact subunit, the CNBr fragments, and peptides obtained by digestion with staphylococcal Glu-specific protease and trypsin. Using this analysis, the complete alpha-chain structure of 21 avian species is known, permitting comparisons of the protein structure and of avian relationships. The structure exhibits differences from previously established avian alpha-chains at a total of 61 positions, five of which have residues unique to those of the parakeet (Ser-12, Gly-65, Ser-67, Ala-121, and Leu-134). The analysis defines hemoglobin variation within an additional avian order (Psittaciformes), demonstrates distant patterns for evaluation of relationships within other avian orders, and lends support to taxonomic conclusions from molecular data.

Evolution in bacteria: evidence for a universal substitution rate in cellular genomes

This paper constructs a temporal scale for bacterial evolution by tying ecological events that took place at known times in the geological past to specific branch points in the genealogical tree relating the 16S ribosomal RNAs of eubacteria, mitochondria, and chloroplasts. One thus obtains a relationship between time and bacterial RNA divergence which can be used to estimate times of divergence between other branches in the bacterial tree. According to this approach, Salmonella typhimurium and Escherichia coli diverged between 120 and 160 million years (Myr) ago, a date which fits with evidence that the chief habitats occupied now by these two enteric species became available that long ago. The median extent of divergence between S. typhimurium and E. coli at synonymous sites for 21 kilobases of protein-coding DNA is 100%. This implies a silent substitution rate of 0.7-0.8%/Myr--a rate remarkably similar to that observed in the nuclear genes of mammals, invertebrates, and flowering plants. Similarities in the substitution rates of eucaryotes and procaryotes are not limited to silent substitutions in protein-coding regions. The average substitution rate for 16S rRNA in eubacteria is about 1%/50 Myr, similar to the average rate for 18S rRNA in vertebrates and flowering plants. Likewise, we estimate a mean rate of roughly 1%/25 Myr for 5S rRNA in both eubacteria and eucaryotes. For a few protein-coding genes of these enteric bacteria, the extent of silent substitution since the divergence of S. typhimurium and E. coli is much lower than 100%, owing to extreme bias in the usage of synonymous codons. Furthermore, in these bacteria, rates of amino acid replacement were about 20 times lower, on average, than the silent rate. By contrast, for the mammalian genes studied to date, the average replacement rate is only four to five times lower than the rate of silent substitution.