Thomas W. Quinn

Chromosome-Specific Intron Size Differences in the Avian CHD Gene Provide an Efficient Method for Sex Identification in Birds

to this problem for some species (e.g. Griffiths and Holland 1990, Quinn et al. 1990, Rabenold et al. 1991, Dvorak et al. 1992, Longmire et al. 1993, Ogawa et al. 1997), but their use requires considerable xpertise, and often their taxonomic range is limited. More recently, PCR-based approaches that are technically simpler and that have broad taxonomic utility have been developed (Ogawa et al. 1997). The discovery of a highly conserved gene (CHD) that is linked to the W and a non-W chromosome in

CHAPTER 1 – Molecular Evolution of the Mitochondrial Genome

The chapter provides an overview of the evolution of the avian mitochondrial genome from a broad perspective, mainly at a level of organization above the primary sequence level. It illustrates similarities and differences among the mitochondrial genomes of Aves and other vertebrate classes, and focuses on how some of these differences have provided unique opportunities to probe deep phylogenetic questions. Studies of systematic relationships frequently make use of direct comparison of DNA sequence information, from which estimates of branching order can be made, using an assortment of methods that include parsimony, maximum likelihood, and distance. Such approaches have provided a wealth of new information, and with the concurrent refinement of statistical or “quasistatistical” methods, allow the relative robustness of conflicting phylogenetic hypotheses to be evaluated. The use of major genomic rearrangements or other such “genomic landmarks” as characters for phylogenetic analysis provides a complementary approach to direct sequence comparison that may be unaffected by the problems of alignment or sequence saturation. Such approaches make the seemingly reasonable but unproven assumption that major rearrangements are unlikely to occur in the same manner more than once in the time period under consideration.

A NEW SPECIES OF SAGE-GROUSE (PHASIANIDAE: CENTROCERCUS) FROM SOUTHWESTERN COLORADO

Abstract The Gunnison Sage-Grouse (Centrocercus minimus) is described as a new species from southwestern Colorado and contrasted with the Sage-Grouse (Centrocercus urophasianus) from northern Colorado and western North America. Gunnison Sage-Grouse differ from all other described sage-grouse (C. u. urophasianus, C. u. phaios) in morphological measurements, plumage, courtship display, and genetics. The species currently is limited to 8 isolated populations in southwestern Colorado and adjacent San Juan County, Utah. Total estimated spring breeding population is fewer than 5000 individuals with the largest population (<3000) in the Gunnison Basin (Gunnison and Saguache counties), Colorado.

A population genetic comparison of large- and small-bodied sage grouse in Colorado using microsatellite and mitochondrial DNA markers

Sage grouse (Centrocercus urophasianus) from southwestern Colorado and southeastern Utah (United States) are 33% smaller than all other sage grouse and have obvious plumage and behavioural differences. Because of these differences, they have been tentatively recog—nized as a separate ‘small‐bodied’ species. We collected genetic evidence to further test this proposal, using mitochondrial sequence data and microsatellite markers to determine whether there was gene flow between the two proposed species. Significant differences in the distribution of alleles between the large‐ and small‐bodied birds were found in both data sets. Analysis of molecular variance (amova) revealed that 65% of the variation in mitochondrial DNA (mtDNA) haplotypes could be explained by the large‐ vs. small‐bodied distinction. Genetic distances and neighbour‐joining trees based on allelic frequency data showed a distinct separation between the proposed species, although cladistic analysis of the phylogenetic history of the mitochondrial sequence haplotypes has shown a lack of reciprocal monophyly. These results further support the recognition of the small‐bodied sage grouse as a distinct species based on the biological species concept, providing additional genetic evidence to augment the morphological and behavioural data. Furthermore, small‐bodied sage grouse had much less genetic variation than large‐bodied sage grouse, which may have implications for conservation issues.

Male-Driven Evolution Among Eoaves? A Test of the Replicative Division Hypothesis in a Heterogametic Female (ZW) System

Abstract. 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 (αm) 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 ≈ 3.1 times faster than the W-linked intron. From this, αm 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.

POPULATION GENETICS OF GUNNISON SAGE-GROUSE: IMPLICATIONS FOR MANAGEMENT

Abstract The newly described Gunnison sage-grouse (Centrocercus minimus) is a species of concern for management because of marked declines in distribution and abundance due to the loss and fragmentation of sagebrush habitat. This has caused remaining populations to be unusually small and isolated. We utilized mitochondrial DNA sequence data and data from 8 nuclear microsatellites to assess the extent of population subdivision among Gunnison sage-grouse populations in southwestern Colorado and southeastern Utah, USA. We found a high degree of population structure and low amounts of gene flow among all pairs of populations except the geographically adjacent Gunnison and Curecanti populations. Population structure for Gunnison sage-grouse was significantly higher than has been reported for greater sage-grouse (C. urophasianus). Further, we documented low levels of genetic diversity in some populations (particularly Dove Creek/Monticello and Piñon Mesa with an average of only 3.00 and 2.13 alleles per locus respectively) indicating that translocations from larger, more genetically diverse populations may be warranted. Bayesian analysis identified 3 potential migrants (involving San Miguel, Dove Creek/Monticello, Crawford, and Curecanti). Further, this analysis showed that 4 individuals from Cerro/Cimarron were more closely related to birds from San Miguel than to its geographically closer neighbors Gunnison and Curecanti. This suggests the Cerro/Cimarron area may act as a stepping stone for gene flow between San Miguel and Gunnison and that habitat restoration and protection in areas between these 2 basins should be a priority in an attempt to facilitate natural movement among these populations. Conservation plans should include monitoring and maintaining genetic diversity, preventing future habitat loss and fragmentation, enhancing existing habitat, and restoring converted sagebrush communities.

Rapid capture of DNA targets

A rapid capture technique was developed to efficiently isolate specific DNA targets from a variety of genomes. The specificity can be easily adapted to any target for which partial sequence is known, allowing for the isolation of a wide set of target molecules from either characterized or uncharacterized genomes. These targets include but are not limited to transposable elements, microsatellites, repetitive sequences, and possibly unique sequences. Additionally, because the thermodynamics of nucleic acid hybridizations differ from processes such as PCR, a wider variety of targets with a range of mismatches to any customized probe can be isolated. Further this method allows sequences flanking known internal regions to be co-isolated, facilitating the development of flanking primers for downstream applications. Considerable reduction in the frequency of nonspecific binding between key components (background) obviates the need for subsequent screening steps. Rapid capture of DNA targets quickly provides information about target and flanking sequences.

Evaluation of the eastern (Centrocercus urophasianus urophasianus) and western (Centrocercus urophasianus phaios) subspecies of Sage-grouse using mitochondrial control-region sequence data

The status of Sage-grouse (Centrocercusurophasianus) is of increasing concern, aspopulations throughout its range havecontracted as a result of habitat loss anddegradation. Historically, Sage-grouse wereclassified into two subspecies: eastern(C. u. urophasianus) and westernSage-grouse (C. u. phaios) based onslight differences in coloration noted amongeight individuals sampled from Washington,Oregon, and California. We sequenced a rapidlyevolving portion of the mitochondrial controlregion in 332 birds from 16 populations. Although our sampling area covers the proposedboundary between the eastern and westernsubspecies, no genetic evidence to support thedelineation of these subspecies was found. However, a population straddling southwesternNevada and eastern California was found tocontain an unusually high proportion of uniquehaplotypes, consistent with its geneticisolation from other Sage-grouse populations. Of additional interest was the lack ofdiversity in the two populations sampled fromWashington, one of which contained only asingle haplotype. We suggest that multiplelines of evidence are valuable for theformulation of conservation strategies andhence the southwestern Nevada/easternCalifornia population merits furthermorphological, behavioral, and molecular investigation.

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.

POPULATION GENETIC ANALYSIS OF MOUNTAIN PLOVER USING MITOCHONDRIAL DNA SEQUENCE DATA

Abstract Mountain Plover (Charadrius montanus) distribution and abundance have been reduced drastically in the past 30 years and the conversion of shortgrass prairie to agriculture has caused breeding populations to become geographically isolated. This, coupled with the fact that Mountain Plovers are thought to show fidelity to breeding grounds, leads to the prediction that the isolated breeding populations would be genetically distinct. This pattern, if observed, would have important management implications for a species at risk of extinction. Our study examined genetic variation at two mitochondrial regions for 20–30 individuals from each of four breeding sites. We found no evidence of significant population differentiation in the data from the control region or the ATPase 6/8 region. Nested-clade analysis revealed no relationship between haplotype phylogeny, and geography among the 47 control region haplotypes. In the ATPase 6/8 region, however, one of the two clades provided information suggesting that, historically, there has been continuous range expansion. Analysis of mismatch distributions and Tajimas D suggest that the Mountain Plover underwent a population expansion, following the Pleistocene glacial period. To explain the lack of detectable genetic differentiation among populations, despite their geographic isolation and fidelity to breeding locations, we speculate that there is sufficient female-mediated gene flow to homogenize gene pools among populations. Such gene flow might ensue if pair bonds are formed in mixed flocks on wintering grounds rather than on the summer breeding grounds. Análisis Genéticos de Poblaciones de Charadrius montanus Usando Secuencias de ADN Mitocondrial Resumen. La distribución y la abundancia de Charadrius montanus se han reducido drásticamente desde hace 30 años y las poblaciones han quedado más aisladas geográficamente debido a la transformación de las praderas de pastos cortos a tierras agrícolas. Estos cambios, combinados con el hecho de que se cree que C. montanus presenta fidelidad a sus áreas de nidificación, sugieren que las poblaciones reproductivas aisladas podrían ser distintas genéticamente. De observarse este patrón, tendría consecuencias importantes para el manejo de esta especie en peligro de extinción. En nuestro estudio, investigamos el patrón de variación genética en dos regiones mitocondriales en 20–30 individuos de C. montanus provenientes de cuatro sitios de nidificación. No encontramos evidencia de diferencias poblacionales significativas en los datos de la región de control, ni en la región de ATPasa 6/ 8. Un análisis de clados anidados reveló que no hay ninguna relación entre haplotipos filogenia y geografía entre los 47 haplotipos de la región de control. Sin embargo, en la región ATPasa 6/8, uno de los dos clados proveyó información que sugiere que la especie ha aumentado históricamente su rango de distribución. Análisis de distribuciones “mismatch” y de la D de Tajima sugieren que la población se expandió después del período glacial del Pleistoceno. Para explicar la falta de diferenciación genética entre las poblaciones, a pesar de su aislamiento geográfico y de la fidelidad a sus sitios de nidificación, especulamos que el flujo de genes es controlado por las hembras de la población de tal modo que los acervos génicos son bastante homogéneos entre las poblaciones. Dicho flujo de genes podría ocurrir si se formaran las parejas en las bandadas mixtas en el invierno, no en el verano cuando están en sus áreas de nidificación.