A multilocus population genetic survey of the greater sage-grouse across their range.

The distribution and abundance of the greater sage-grouse (Centrocercus urophasianus) have declined dramatically, and as a result the species has become the focus of conservation efforts. We conducted a range-wide genetic survey of the species which included 46 populations and over 1000 individuals using both mitochondrial sequence data and data from seven nuclear microsatellites. Nested clade and structure analyses revealed that, in general, the greater sage-grouse populations follow an isolation-by-distance model of restricted gene flow. This suggests that movements of the greater sage-grouse are typically among neighbouring populations and not across the species, range. This may have important implications if management is considering translocations as they should involve neighbouring rather than distant populations to preserve any effects of local adaptation. We identified two populations in Washington with low levels of genetic variation that reflect severe habitat loss and dramatic population decline. Managers of these populations may consider augmentation from geographically close populations. One population (Lyon/Mono) on the southwestern edge of the species' range appears to have been isolated from all other greater sage-grouse populations. This population is sufficiently genetically distinct that it warrants protection and management as a separate unit. The genetic data presented here, in conjunction with large-scale demographic and habitat data, will provide an integrated approach to conservation efforts for the greater sage-grouse.

A population genetic comparison of argali sheep (Ovis ammon) in Mongolia using the ND5 gene of mitochondrial DNA; implications for conservation.

We sequenced 556 bp of the mitochondrial ND5 gene to infer aspects of population structure and to test subspecific designations of argali sheep (Ovis ammon) in Mongolia. Analysis of molecular variance (AMOVA) revealed greater variation within than among putative subspecies and populations, suggesting high levels female-mediated gene flow. Compared with bighorn sheep (O. canadensis) in North America, substantially less differentiation in mitochondrial DNA was found among argali populations over 1200 km than was found among bighorn populations over 250 km. This result is consistent with differences in argali and bighorn life history traits. Argali run for long distances across open terrain in the presence of a threat rather than running up into steep escape terrain like bighorn sheep do. Our results suggest recognizing only one Evolutionary Significant Unit (subspecies) of argali in Mongolia, but they may support recognizing two Management Units, because two regions do exhibit slightly different haplotype frequencies at the ND5 gene of mtDNA.

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.

Relationships of the extinct moa-nalos, flightless Hawaiian waterfowl, based on ancient DNA.

The extinct moa-nalos were very large, flightless waterfowl from the Hawaiian islands. We extracted, amplified and sequenced mitochondrial DNA from fossil moa-nalo bones to determine their systematic relationships and lend insight into their biogeographical history. The closest living relatives of these massive, goose-like birds are the familiar dabbling ducks (tribe Anatini). Moa-nalos, however, are not closely related to any one extant species, but represent an ancient lineage that colonized the Hawaiian islands and evolved flightlessness long before the emergence of the youngest island, Hawaii, from which they are absent. Ancient DNA yields a novel hypothesis for the relationships of these bizarre birds, whereas the evidence of phylogeny in morphological characters was obscured by the evolutionary transformation of a small, volant duck into a giant, terrestrial herbivore.

Is it possible to construct phylogenetic trees using polypeptide hormone sequences?

Because of the high degree of primary sequence conservation in neuropeptides and low molecular weight polypeptide hormones, these polypeptides are not useful for constructing phylogenetic trees based on maximum parsimony analysis. This review focuses on the organization of neuropeptide and polypeptide hormone precursors and discusses strategies for aligning polypeptide precursors for phylogenetic analysis. Examples are provided to support the hypothesis that some neuropeptide and polypeptide precursors and some high molecular weight polypeptide hormones can be used as data sets for resolving deep divergences among vertebrate taxa.

Mitochondrial gene order adjacent to the control region in crocodile, turtle, and tuatara.

We used the polymerase chain reaction and sequencing of mitochondrial gene junctions adjacent to the 5' end of the control region (light strand orientation) and the 3' end of ND6 to assess whether a representative crocodilian, turtle, or tuatara shares a unique mitochondrial gene order that is found in birds but not in mammals or amphibians. Turtles and crocodiles have the same gene order as mammals, except that crocodile has a tRNAPhe gene inserted between tRNAPro and the 5' end of the control region. Two different arrangements were detected at the 5' end of the control region in the tuatara, one resembling the mammalian (but with tRNAThr absent) and one resembling the avian gene order. Our data are consistent with the hypothesis that some tuatara mtDNAs within a single individual have undergone a deletion that removed the genes coding for cytochrome b and tRNAPro as well as 87 bp of the control region.

Phylogenetic analysis of the Coscoroba coscoroba using mitochondrial srRNA gene sequences.

In order to study the phylogenetic relationships among Coscoroba, goose, and swan lineages, sequences for the complete mitochondrial small ribosomal RNA (srRNA) gene were determined from five waterfowl species. Parsimony and distance analyses support the branching of Coscoroba prior to the divergence of geese and swans, and maximum likelihood analyses give almost equal support to that pattern and to the sister group relationship between Coscoroba and swans. The monophyly of the geese was confirmed at a statistically significant level. In sequence comparisons among waterfowl, transitions increase linearly with transversions, and so we conclude that the lack of complete resolution of Coscoroba's position is not due to sequence saturation alone, but also reflects relatively close branching times.

Sequence evolution in and around the mitochondrial control region in birds.

By cloning and sequencing 3.4 kilobases of snow goose mtDNA we found that the ND5 gene is followed by the genes for cytochrome b, tRNA(Thr), tRNA(Pro), ND6, tRNA(Glu), the control region, tRNA(Phe), and srRNA. This order is identical to that of chicken, quail, and duck mtDNA but differs from that of mammals and a frog (Xenopus). The mean extent of difference due to base substitution between goose and chicken is generally closer to the same comparison between rat and mouse but less than that between human and cow. For one of the nine regions compared (tRNA(Glu)), the bird differences appear to be anomalous, possibly implicating altered functional constraints. Within the control region, several short sequences common to mammals are also conserved in the birds. Comparison of the goose control region with that of quail and chicken suggests that a sequence element with similarity to CSB-1 duplicated once prior to the divergence of goose and chicken and again on the lineage leading to chicken. Between goose (or duck) and chicken there are four times more transversions at the third positions of fourfold-degenerate codons in mitochondrial than in nuclear genes.

The genetic legacy of Mother Goose--phylogeographic patterns of lesser snow goose Chen caerulescens caerulescens maternal lineages.

By using the polymerase chain reaction to amplify and sequence 178 bp of a rapidly evolving region of the mtDNA genome (segment I of the control region) from 81 individuals, approximately 11% of the variation present in the lesser snow goose Chen caerulescens caerulescens L. mitochondrial genome was surveyed. The 26 types of mtDNA detected formed two distinct mitochondrial clades that differ by an average of 6.7% and are distributed across the species range. Restriction analysis of amplified fragments was then used to assign the mtDNA of an additional 29 individuals to either of these clades. Within one major clade, sequence among mtDNAs was concordant with geographic location. Within the other major clade the degree of sequence divergence among haplotypes was lower and no consistent geographic structuring was evident. The two major clades presumably result from vicariant separation of lesser snow geese during the Pleistocene.

Identification of restriction-fragment-length polymorphisms in genomic DNA of the lesser snow goose (Anser caerulescens caerulescens).

A genomic library of partially EcoRI-digested DNA from the lesser snow goose, Anser caerulescens caerulescens, was constructed in the phage vector Charon 4. Phage containing only unique sequences were identified by screening plaques with 32P-labeled genomic DNA. Restriction-fragment-length polymorphisms (RFLPs) were identified by probing DNA from 11-13 male birds from the breeding colony at La Perouse Bay. Of the 17 probes examined, all detected RFLPs with at least one of EcoRi, HindIII, Msp1, and Taq1. Several of them identified highly variable regions with multiple alleles. These RFLPs are valuable DNA markers that can be used for (1) the examination of DNA variation, relatedness, and genetic distance and (2) assessing paternity and maternity. These data suggest that there are higher levels of variation of DNA sequence in birds than had previously been thought to exist.