Distinguishing the effects of selection from demographic history in the genetic variation of two sister passerines based on mitochondrial-nuclear comparison.

Determining the mechanisms responsible for the distribution of genetic diversity in natural populations has occupied a central role in molecular evolution. Our study was motivated by the unprecedented observation that a widespread Eurasian flycatcher, Ficedula albicilla, exhibited no variation at the mitochondrial DNA (mtDNA) ND2 gene in 75 individuals sampled over a 5000-km distance. In contrast, its sister species, F. parva, had low but considerably higher levels of mtDNA variation. We assessed whether natural selection or demographic factors could explain the absence of mtDNA variation in F. albicilla. Eighteen nuclear genes were sequenced to estimate the two species' phylogeographic histories, and for comparison to the mtDNA data. Multilocus coalescence analyses suggested that F. albicilla experienced a population expansion perhaps following a population bottleneck. Simulations based on this demographic history, however, did not replicate the extremely low level of mtDNA variation. Historical range changes based on ecological niche models also failed to explain the observed mtDNA patterns. Neutrality tests (DHEW and ML-HKA) suggested a non-neutral pattern in the mtDNA of F. albicilla. We found a transmembrane-skewed distribution of nonsynonymous substitutions between the two species, three of which caused functional change; the results implied that positive selection could have targeted mtDNA. Several lines of evidence support selection rather than demographic history as the main force influencing the patterns of mtDNA variation. Despite the influence of natural selection, many of the phylogeographic inferences derived from mtDNA were robust, including species limits and a high level of gene flow among populations within species.

mtDNA haplotypes differ in their probability of being eliminated by a mass die-off in an abundant seabird.

In this study, we take advantage of a natural experiment--a 2004 mass die-off of the Common Murre in Alaska to determine whether closely related mtDNA haplotypes differ in their probability of being eliminated during such a short term but a marked event removing hundreds of thousands of individuals. We sequenced complete mtDNA ND2 gene (1041 bp) for 168 Common Murres sampled from seven breeding colonies across Alaska before the 2004 die-off and 127 dead murres washed ashore during the die-off. We found little mtDNA variation and lack of geographical structuring among the seven Common Murre breeding colonies in Alaska. A comparison of the single-dominant mtDNA haplotype's frequency between live murres sampled on breeding colonies before the die-off (73.2%; 95% confidence interval 66.3-79.9%) and dead murres sampled during the die-off (59.1%; 95% confidence interval 50.4-67.4%; Fisher's exact P=0.01) showed that carriers of the dominant haplotype were significantly less likely to die than carriers of other haplotypes. At the same time, the ratio of non-synonymous to synonymous substitutions did not differ between live (10:35) and dead birds (18:34; Fisher's exact P=0.26), indicating that non-synonymous substitutions were as likely to be eliminated as synonymous substitutions. These results are consistent with the possibility of positive selection on the dominant mtDNA haplotype during the die-off.

The shifting roles of dispersal and vicariance in biogeography.

Dispersal and vicariance are often contrasted as competing processes primarily responsible for spatial and temporal patterns of biotic diversity. Recent methods of biogeographical reconstruction recognize the potential of both processes, and the emerging question is about discovering their relative frequencies. Relatively few empirical studies, especially those employing molecular phylogenies that allow a temporal perspective, have attempted to estimate the relative roles of dispersal and vicariance. In this study, the frequencies of vicariance and dispersal were estimated in six lineages of birds that occur mostly in the aridlands of North America. Phylogenetic trees derived from mitochondrial DNA sequence data were compared for towhees (genus Pipilo), gnatcatchers (genus Polioptila), quail (genus Callipepla), warblers (genus Vermivora) and two groups of thrashers (genus Toxostoma). Different area cladograms were obtained depending on how widespread and missing taxa were coded. Nonetheless, no cladogram was obtained for which all lineages were congruent. Although vicariance was the dominant mode of evolution in these birds, approximately 25% of speciation events could have been derived from dispersal across a preexisting barrier. An expanded database is now needed to estimate the relative roles of each process. Applying a molecular clock calibration, nearly all speciation events are of the order of a million or more years old, much older than typically presumed.

Lack of demonstratable effects of pollutants on cyt b sequences in wood ducks from a contaminated nuclear reactor cooling pond.

The effects of low levels of radiation on DNA mutation rates are largely unknown for free-living vertebrates. In this study we investigated the effects of contamination from cooling ponds at a nuclear production facility in South Carolina on the mutation rates in mitochondrial DNA in wood ducks (Aix sponsa). Specifically, we sequenced a 433-bp portion of the cytochrome b gene from 18 female-offspring pairs of wood ducks from contaminated ponds and 2 female-offspring pairs from control ponds. Very low haplotype diversity was observed overall, and no case of mutation between female and offspring could be satisfactorily documented. This suggests that the levels of radioactive contamination in these cooling ponds have little effect on the mutation rate of mitochondrial DNA in these waterfowl and that mitochondrial DNA may not be as sensitive an indicator as previously anticipated.

The comparative amino acid sequences, substrate specificities and gene or cDNA nucleotide sequences of some prokaryote and eukaryote amidinotransferases: implications for evolution.

The amino acid sequences of the amidinotransferases and the nucleotide sequences of their genes or cDNA from four Streptomyces species (seven genes) and from the kidneys of rat, pig, human and human pancreas were compared. The overall amino acid and nucleotide sequences of the prokaryotes and eukaryotes were very similar and further, three regions were identified that were highly identical. Evidence is presented that there is virtually zero chance that the overall and high identity regions of the amino acid sequence similarities and the overall nucleotide sequence similarities between Streptomyces and mammals represent random match. Both rat and lamprey amidinotransferases were able to use inosamine phosphate, the amidine group acceptor of Streptomyces. We have concluded that the structure and function of the amidinotransferases and their genes has been highly conserved through evolution from prokaryotes to eukaryotes. The evolution has occurred with: (1) a high degree of retention of nucleotide and amino acid sequences; (2) a high degree of retention of the primitive Streptomyces guanine + cytosine (G + C) third codon position composition in certain high identity regions of the eukaryote cDNA; (3) a decrease in the specificities for the amidine group acceptors; and (4) most of the mutations silent in the regions suggested to code for active sites in the enzymes.

Geographic analysis of nucleotide diversity and song sparrow (Aves: Emberizidae) population history.

Mitochondrial DNA (mtDNA) control-region (CR) sequences were analysed to address three questions regarding the evolution of geographical variation in song sparrows. (i) Are mtDNA sequences more informative about phylogenetic relationships and population history than previously published restriction fragment (RFLP) data? (ii) Are song sparrow CR sequences evolving in a selectively neutral manner? (iii) What do the haplotype cladogram and geographical pattern of nucleotide diversity (pi) suggest about the recent evolutionary history of song sparrow populations? Results from phylogenetic analyses of CR sequences corroborate RFLP results and reveal instances in which haplotypes do not group by locality. Neutrality tests (Tajima 1989a) suggest that song sparrow mtDNA is evolving in a selectively neutral manner, although exceptions are noted. A novel geographical pattern of pi suggests a model of song sparrow population history involving multiple Pleistocene refugia and colonization of some formerly glaciated regions from multiple sources. Moreover, application of coalescence theory to the haplotype cladogram suggests that two different haplotypes (48NF and 151HA) may have predominated in different parts of the song sparrow's range. This model provides insight into the current distribution of song sparrow mtDNA haplotypes and may explain the discordance between evolutionary history inferred from mtDNA and morphology in this species.

Patterns of mtDNA variation in Hawaiian freshwater fishes: the phylogeographic consequences of amphidromy.

MtDNA sequencing was used to assess the phylogeographic structure of four species of Hawaiian freshwater fishes: Lentipes concolor, Stenogobius hawaiiensis, Sicyopterus stimpsoni, and Awaous guamensis. Samples of each species were collected from streams on the northeast side of Kauai, Maui, Molokai, Oahu, and Hawaii. We sequenced segments from both coding and noncoding regions (638-1391 bp) in each species. Sequence analysis uncovered genetic variability in these fishes but no evidence of strong geographic structure among island populations. This result is most readily explained by the fishes' larval marine life stage (amphidromy), which likely facilitates gene flow among island populations. By constraining genetic differentiation among populations, amphidromy may impede speciation in these fishes, possibly explaining why the Hawaiian freshwater fish fauna is depauperate compared to other species-rich Hawaiian faunas. It may also provide them with a kind of evolutionary flexibility atypical of other, more isolated island faunas and allow natural restocking to occur in streams that have been restored to suitable conditions. Comparisons of restriction site and sequence data suggested similar population genetic conclusions for all species except S. stimpsoni, for which the restriction site data is questioned.

Molecular systematics and biogeography of aridland gnatcatchers (genus Polioptila) and evidence supporting species status of the California gnatcatcher (Polioptila california).

Over 2000 basepairs of mitochondrial DNA (mtDNA) sequences were compared to (1) examine evolution in protein coding versus noncoding [control region (CR)] segments, and (2) test the species-level distinctiveness of the California gnatcatcher (Polioptila californica) and clarify its phylogenetic and biogeographic relationships to other arid-adapted gnatcatchers. Unlike some studies, CR region I (left domain) was not as variable as coding genes. As expected, the central domain of the CR varied little, whereas CR II (right domain) showed high levels of variation. CR sequences tended to be "phylogenetically noisy" as evidenced by lower rescaled consistency indices, relative to those for coding genes. The California gnatcatcher differs from its sister-species, the black-tailed gnatcatcher (P. melanura), by approximately 4.0%, which supports species-level recognition. Two other aridland gnatcatchers, the black-capped gnatcatcher. (P. nigriceps) and white-lored gnatcatcher (P. albiloris), are closely related to the previous two species, also at a level of about 4 to 4.5% sequence divergence. These species evolved over a relatively short time, but prior to the most recent Pleistocene glaciations.

Molecular phylogenetics of the avian genus Pipilo and a biogeographic argument for taxonomic uncertainty.

We sequenced 1709 base pairs (bp) of mitochondrial DNA including parts of cytochrome b, ND 2, and the control region (CR I, II) for seven members of the avian genus Pipilo (towhees), Melozone kieneri (rusty-crowned ground-sparrow), and Arremonops rufivirgatus (olive sparrow). A total of 457 bp was variable and 257 bp were potentially phylogenetically informative. All gene regions were similarly variable (20.2 to 28.4%) except for CR II (38.4%); third position transitions were as common as substitutions in the CR. Tree topology was sensitive to choice of outgroup(s) and individual sequences used as exemplars. Six trees were considered viable phylogenetic hypotheses based on maximum parsimony and maximum likelihood analyses. These trees generally supported two groups of towhees (rufous-sided group, brown towhee group), a sister taxon relationship for P. aberti and P. crissalis, and a sister taxon relationship for P. ocai and P. maculatus. The occurrence of M. kiernei within Pipilo in three trees challenges the monophyly of the latter; the other species of Melozone and other outgroups require study to resolve Pipilo monophyly. The relationships of P. albicollis and P. fuscus were ambiguous, as they were with previous data sets (allozymes, mtDNA restriction sites); they could be sister species or either one could be the basal species in the brown towhee group. We suggest that this taxonomic uncertainty obtains from the contemporaneous origin of P. fuscus, P. albicollis, and the ancestor of P. aberti/P. crissalis. We favor a "star" phylogeny because species in unrelated lineages found in the same region as P. albicollis are similarly difficult to resolve phylogenetically. Synapomorphies from coding genes and the CR did not preferentially support basal and terminal nodes, and hence did not provide different windows of taxonomic resolution, which might be expected from the apparent rapid rate of CR evolution. Phylogenetic trees inferred from allozymes, restriction sites, and mtDNA sequences were congruent, suggesting that each is a useful source of phylogenetic information.

Enigmatic phylogeny of skuas (Aves:Stercorariidae)

Multiple sources of evidence show that the skuas (Aves:Stercorariidae) are a monophyletic group, closely related to gulls (Laridae. On morphological and behavioural evidence the Stercorariidae are divided into two widely divergent genera, Catharacta and Stercorarius, consistent with observed levels of nuclear and mitochondrial gene divergence. Catharacta skuas are large-bodied and with one exception breed in the Southern Hemisphere. Stercorarius skuas otherwise known as jaegers) are smaller bodied and breed exclusively in the Northern Hemisphere. Evidence from both mitochondrial and nuclear genomes and from ectoparasitic lice (Insecta:Phthiraptera) shows that the Pomarine skua, S. pomarinus, which has been recognized as being somewhat intermediate in certain morphological and behavioural characteristics, is much more closely related to species in the genus Catharacta, especially to the Northern Hemisphere-breeding Great skua, C. skua, than it is to the other two Stercorarius skuas, the Arctic skua, S. parasiticus and the Longtailed skua, S. longicaudus. Three possible explanations that might account for this discordant aspect of skua phylogeny are explored. These involve (i) the segregation of ancestral polymorphism, (ii) convergent evolution of morphology and behaviour or (iii) inter-generic hybridization. The available evidence from both nuclear and mitochondrial genomes does not exclude any of these hypotheses. Thus, resolution of this enigma of skua phylogeny awaits further work.

Evidence from molecular systematics for decreased avian diversification in the pleistocene Epoch.

Pleistocene glaciations have been suggested as major events influencing speciation rates in vertebrates. Avian paleontological studies suggest that most extant species evolved in the Pleistocene Epoch and that species' durations decreased through the Pleistocene because of heightened speciation rates. Molecular systematic studies provide another data base for testing these predictions. In particular, rates of diversification can be determined from molecular phylogenetic trees. For example, an increasing rate of speciation (but constant extinction) requires shorter intervals between successive speciation events on a phylogenetic tree. Examination of the cumulative distribution of reconstructed speciation events in mtDNA phylogenies of 11 avian genera, however, reveals longer intervals between successive speciation events as the present time is approached, suggesting a decrease in net diversification rate through the Pleistocene Epoch. Thus, molecular systematic studies do not indicate a pulse of Pleistocene diversification in passerine birds but suggest, instead, that diversification rates were lower in the Pleistocene than for the preceding period. Documented habitat shifts likely led to the decreased rate of diversification, although from molecular evidence we cannot discern whether speciation rates decreased or extinction rates increased.

Associations between heterozygosity and morphological variance.

Recent studies have contrasted the expression of phenotypic traits, such as variance in morphological characters, with levels of genetic variation (heterozygosity) as determined by electrophoretic analysis of protein-coding loci. The theoretical basis for interpreting significant covariation stems in part from Lerner's work on genetic homeostasis, which predicts that within populations increased heterozygosity will produce decreased morphological variance, owing to a buffering effect of heterosis during development. However, the prediction for the relationship between genic heterozygosity and the variance of morphological traits among populations is unclear. To determine if a relationship existed between heterozygosity and morphological variance, we compared estimates of heterozygosity and morphological variance across 15 population samples of the fox sparrow and 17 samples of the pocket gopher. The estimates of morphological variance included coefficients of variation for each character and the variance of individual scores about the population mean in a principal components analysis. Although several recent studies have reported a significant relationship between heterozygosity and morphological variance, we found that the two measures do not covary significantly.