The northern spotted owl (Strix occidentalis caurina) is a threatened subspecies and the California spotted owl (Strix occidentalis occidentalis) is a subspecies of special concern in the western United States. Concern for their continued viability has arisen because of habitat loss caused by timber harvesting. The taxonomic status of the northern subspecies has been the subject of continuing controversy. We investigated the phylogeographical and population genetic structure of northern and California spotted owls with special reference to their region of contact. Mitochondrial DNA (mtDNA) control region sequences confirmed the existence of two well-differentiated lineages connected by a narrow hybrid zone in a region of low population density in north central California. Maximum-likelihood estimates indicated bidirectional gene flow between the lineages but limited introgression outside the region of contact. The lengths of both the mtDNA hybrid zone and the reduced density patch were similar and slightly exceeded estimates of natal dispersal distances. This suggests that the two subspecies were in secondary contact in a hybrid zone trapped by a population density trough. Consequently, the zone of interaction is expected to be geographically stable. We discovered a third, rare clade of haplotypes, which we interpreted to be a result of incomplete lineage sorting; those haplotypes result in a paraphyletic northern spotted owl with respect to the California spotted owl. A congeneric species, the barred owl (Strix varia), occasionally hybridizes with spotted owls; our results indicated an upper bound for the frequency of barred owl mtDNA haplotypes in northern spotted owl populations of 3%.

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Mitochondrial DNA control region sequences of spotted owls (Strix occidentalis) allowed us to investigate gene flow, genetic structure, and biogeographic relationships among these forest-dwelling birds of western North America Estimates of gene flow based on genetic partitioning and the phylogeography of haplotypes indicate substantial dispersal within three long-recognized subspecies. However, patterns of individual phyletic relationships indicate a historical absence of gene flow among the subspecies, which are essentially monophyletic. The pattern of haplotype coalescence enabled us to identify the approximate timing and direction of a recent episode of gene flow from the Sierra Nevada to the northern coastal ranges. The three subspecies comprise phylogenetic species, and the northern spotted owl (S. o. caurina) is sister to a clade of California (S. o. occidentalis) plus Mexican spotted owls (S o lucida); this represents a novel biogeographic pattern within birds. The California spotted owl had substantially lower nucleotide diversity than the other two subspecies; this result is inconsistent with present patterns of population density A causal explanation requires postulating a severe bottleneck or a selective sweep, either of which was confined to only one geographic region.

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Mitochondrial DNA control region sequences of spotted owls (Strix occidentalis) allowed us to investigate gene flow, genetic structure, and biogeographic relationships among these forest-dwelling birds of western North America Estimates of gene flow based on genetic partitioning and the phylogeography of haplotypes indicate substantial dispersal within three long-recognized subspecies. However, patterns of individual phyletic relationships indicate a historical absence of gene flow among the subspecies, which are essentially monophyletic. The pattern of haplotype coalescence enabled us to identify the approximate timing and direction of a recent episode of gene flow from the Sierra Nevada to the northern coastal ranges. The three subspecies comprise phylogenetic species, and the northern spotted owl (S. o. caurina) is sister to a clade of California (S. o. occidentalis) plus Mexican spotted owls (S o lucida); this represents a novel biogeographic pattern within birds. The California spotted owl had substantially lower nucleotide diversity than the other two subspecies; this result is inconsistent with present patterns of population density A causal explanation requires postulating a severe bottleneck or a selective sweep, either of which was confined to only one geographic region.

We propose a new classification of the grouse that brings their taxonomy into agreement with our molecular phylogenetic studies. Our analyses provide, for the first time, a robust estimate of the evolutionary history of these birds. These analyses are based on aligned sequences of 3,809 basepairs of five complete mitochondrial genes. Our classification does not require novel genera and gen erally results in the maintenance o f accepted generic names. Only two monotypic genera are required. We recognize the grouse as a subfamily, Tetraoninae, within the family Phasianidae. We recognize three tribes; these include a tribe (Bonasini, a new taxon) for the ruffed grouse Bonasa umbellus, a tribe (Tetrastini, a new rank) for hazel hens in the genus Tetrastes, and a tribe (Tetraonini, a new rank) for all the remaining species. We divide this last, derived tribe into five subtribes that correspond to 1) Falcipennina (a new taxon) for the sharp-winged grouse Falcipennis falcipennis, 2) Canachitina (a new taxon) for the New World spruce grouse in the genus Canachites, 3) Tetraonina (a new rank) for the capercaillies and black grouse in the genera Tetrao and Lyrums, respectively, 4) Centrocercina (a new taxon) for the New World prairie and forest grouse in the genera Tympanuchus, Centrocercus and Dendragapus, and 5) Lagopodina (a new taxon) for the ptarmigans in the genus Lagopus. All the taxa in our classification, at all ranks, are monophyletic with bootstrap support of 95% or more.

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We used mitochondrial and nuclear DNA sequences to examine patterns of differentiation and evolution in the Musophagidae, an avian family endemic to sub-Saharan Africa; attention was focused on the subfamily Musophaginae, the turacos, or louries. Phylogeographic analysis of 410 individual ND2 sequences from throughout the ranges of the currently recognized species revealed multiple instances of unexpectedly large genetic divergences and cryptic taxa. Within both montane and lowland species, including Tauraco hartlaubi and T: schalowi, Menelikornis leucotis, Musophaga macrorhyncha, and Gallirex johnstoni, fixed private haplotypes were found in disjunct portions of the ranges, suggesting negligible recent gene flow and evolutionary independence of populations. Two taxa originally described as subspecies (T: schalowi loitanus and T. s. marungensis), but not recognized for over 50 years, were found to be 100% diagnosable based on the mitochondrial sequences. The data also revealed the existence of two polyphyletic traditional species, Tauraco livingstonii and T. schuettii, as well as the polyphyly or paraphyly of all traditional superspecies complexes involving members of the genus Tauraco. Overall, our analyses of genetic and morphological variation revealed substantial and unexpected geographic diversity within the Musophagidae. We recognize 33 species-level taxa that represent the appropriate units for phylogenetic and biogeographic analyses (phylogenetic species). We used complete mitochondrial ND2 sequences and nuclear DNA sequences of an Aconitase intron and of the RAG-1 exon to infer the phylogenetic relationships among those species. The results include all the phylogenetic species and, for the first time, nuclear data. We present ' Division of Vertebrate Zoology (Ornithology), American Museum of Natural History.