Male-biased mutation rates and the overestimation of extrapair paternity: problem, solution, and illustration using thick-billed murres (Uria lomvia, Alcidae).

The widespread utility of hypervariable loci in genetic studies derives from the high mutation rate, and thus the high polymorphism, of these loci. Recent evidence suggests that mutation rates can be extremely high and may be male biased (occurring in the male germ-line). These two factors combined may result in erroneous overestimates of extrapair paternity, since legitimate offspring with novel alleles will have more mismatches with respect to the biological father than the biological mother. As mutations are male driven, increasing the number of hypervariable loci screened may simply increase the number of mismatches between fathers and their legitimate offspring. Here we describe a simple statistic, the probability of resemblance (PR), to distinguish between mismatches due to parental misassignment versus mutation in either sex or null alleles. We apply this method to parentage data on thick-billed murres (Uria lomvia), and demonstrate that, without considering either mutations or male-biased mutation rates, cases of extrapair paternity (7% in this study) would be grossly overestimated (14.5%-22%). The probability of resemblance can be utilized in parentage studies of any sexually reproducing species when allele or haplotype frequency data are available for putative parents and offspring. We suggest calculating this probability to correctly categorize legitimate offspring when mutations and null alleles may cause mismatches.

High levels of extra-pair paternity in an isolated, low-density, island population of tree swallows (Tachycineta bicolor).

Molecular genetic studies have suggested that apparently nonbreeding males ('floaters') may account for a significant proportion of extra-pair paternity (EPP) in avian populations. Attempts to determine the influence of breeding density on EPP are therefore confounded by the presence of a subpopulation of floaters whose numbers are difficult to estimate. To study EPP in a tree swallow (Tachycineta bicolor) population with few floaters, we chose a nestbox grid on an island with an excess of available breeding sites and very few floaters. We obtained DNA samples from 13 complete families and performed DNA profiling on them using four microsatellite loci. For comparison, we also obtained a sample of 58 extra-pair young (EPY) from a mainland population typed at five microsatellite loci. Paternity assignments among resident males in both populations were made using the microsatellite profiles and a likelihood-based statistical method. Of the 67 island nestlings typed, we found 37 (55%) nestlings from 11 (85%) different nests that were EPY. The proportion of nestlings that were EPY and the proportion of broods containing EPY did not differ significantly between island and mainland populations studied previously. There was no significant difference between island and mainland populations in the proportion of extra-pair paternities assigned among neighbouring resident males. Male breeding density does not appear to affect the ability of female tree swallows to obtain extra-pair fertilizations, at least over the range of densities studied so far. The rate of EPP has remained remarkably consistent over many years, studies and populations implying an important role of active female choice in determining EPP.

Perception and history: molecular phylogeny of a diverse group of neotropical frogs, the 30-chromosome hyla (anura: hylidae).

We used 16S rRNA, 12S rRNA, and cytochrome-b sequence to investigate the history of the "30-chromosome" Hyla, a diverse assemblage of neotropical treefrogs. Three aspects of these frogs were examined: (1) phylogenetic relationships among constituent species groups, among the species of one of these groups (Hyla leucophyllata group), and among populations of Hyla leucophyllata; (2) the apparent age of cladogenetic events; and (3) the phylogeography of H. leucophyllata. Mixed success in resolving the phylogeny is not because of a lack of character variation; levels of genetic divergence are high and suggest pre-Pleistocene diversification, even among populations. Close temporal proximity of ancient cladogenetic events might make resolution of the topology difficult using any character set. At the population level, current geographic proximity is a poor predictor of phylogenetic affinity. A long history of dispersal and colonization may complicate, or even preclude, the accurate recovery of the history of this species in the Amazon Basin. It remains to be seen whether the patterns found here will prove common among neotropical frogs.

Disruptive sexual selection for plumage coloration in a passerine bird.

The theory of sexual selection was developed to explain the evolution of highly exaggerated sexual ornaments. Now supported by vast empirical evidence, sexual selection is generally considered to favour individuals with the most extreme trait expression. Here we describe disruptive selection on a sexual ornament, plumage coloration, in yearling male lazuli buntings (Passerina amoena). In habitats with limited good-quality nesting cover, the dullest and the brightest yearlings were more successful in obtaining high-quality territories, pairing with females and siring offspring, than yearlings with intermediate plumage. This pattern reflects the way that territorial adult males vary levels of aggression to influence the structure of their social neighbourhood. Adult males showed less aggression towards dull yearlings than intermediate and bright ones, permitting the dull yearlings to settle on good territories nearby. Fitness comparisons based on paternity analyses showed that both the adults and dull yearlings benefited genetically from this arrangement, revealing a rare example of sexually selected male-male cooperation.

Riverine barriers and the geographic distribution of Amazonian species.

Rivers have been suggested to have played an important role in shaping present-day patterns of ecological and genetic variation among Amazonian species and communities. Recent molecular studies have provided mixed support for the hypothesis that large lowland Amazonian rivers have functioned as significant impediments to gene flow among populations of neotropical species. To date, no study has systematically evaluated the impact that riverine barriers might have on structuring whole Amazonian communities. Our analyses of the phylogeography of frogs and small mammals indicate that a putative riverine barrier (the Juruá River) does not relate to present-day patterns of community similarity and species richness. Rather, our results imply a significant impact of the Andean orogenic axis and associated thrust-and-fold lowland dynamics in shaping patterns of biotic diversity along the Juruá. Combined results of this and other studies significantly weaken the postulated role of rivers as major drivers of Amazonian diversification.

A molecular phylogeny of warbling-finches (Poospiza): paraphyly in a neotropical Emberizid genus.

We investigated the phylogenetic relationships of 12 species within a single genus of neotropical passerine (Poospiza) using 849 bp (283 codons) of the cytochrome b mitochondrial gene. We further explored evolutionary affinities of these taxa using sequence from an additional 47 thraupine (tanagers) and 7 emberizine (sparrows and buntings) genera, members of the predominantly New World family Emberizidae. Poospiza have traditionally been considered part of the emberizine radiation. However, our analyses suggest that members of this genus are more closely related to some thraupine lineages than they are to the other neotropical emberizine genera included in our study (Atlapetes, Embernagra, Melopyrrha, Phrygilus, Saltatricula, Tiaris). Although member taxa are closely related, the genus Poospiza appears to be paraphyletic with representatives of 6 thraupine genera (Cnemoscopus, Cypsnagra, Hemispingus, Nephelornis, Pyrrhocoma, Thylpopsis) interspersed among four well-supported Poospiza clades. The majority of species within this Poospiza-thraupine clade have geographic ranges that are exclusive to, or partially overlap with, the Andes Mountains. It is probable that these mountains have played an important role in driving cladogenesis within this group. Sequence divergence (transversions only; mean 4.7+/-1.3%) within the clade suggests that much of this diversification occurred within the late Miocene and Pliocene, a period coincident with major orogenic activity in central-western South America.

Ridges and rivers: a test of competing hypotheses of Amazonian diversification using a dart-poison frog (Epipedobates femoralis).

Mitochondrial DNA cytochrome b sequence data from a dart-poison frog, Epipedobates femoralis, were used to test two hypotheses of Amazonian diversification: the riverine barrier and the ridge hypotheses. Samples were derived from sites located on both banks of the Rio Juruá and on both sides of the Iquitos Arch in western Amazonia. The phylogeographic structure was inconsistent with predictions of the riverine barrier hypothesis. Haplotypes from opposite river banks did not form monophyletic clades in any of our phylogenetic analyses, nor was the topology within major clades consistent with the riverine hypothesis. Further, the greatest differentiation between paired sites on opposite banks was not at the river mouth where the strongest barrier to gene flow was predicted to occur. The results instead were consistent with the hypothesis that ancient ridges (arches), no longer evident on the landscape, have shaped the phylogeographic relationships of Amazonian taxa. Two robustly supported clades map onto opposite sides of the Iquitos Arch. The mean haplotypic divergence between the two clades, in excess of 12%, suggests that this cladogenic event dates to between five and 15 million years ago. These estimates span a period of major orogenesis in western South America and presumably the formation of these ancient ridges.

Molecular phylogenetic evidence for the evolution of specialization in anemonefishes.

Anemonefishes (genera: Amphiprion and Premnas; family Pomacentridae) are a group of 28 species of coral reef fishes that are found in obligate symbiosis with large tropical sea anemones. A phylogenetic hypothesis based on morphological analyses of this group suggests that the ancestral anemonefish was a generalist with similar morphology to other pomacentrids, and that it gave rise to other anemonefish species that were more specialized for living with particular species of host anemones. To test this hypothesis we constructed a molecular phylogeny for the anemonefishes by sequencing 1140 base pairs of the cytochrome b gene and 522 base pairs of the 16S rRNA gene for six species of anemonefishes (representatives of all subgenera and species complexes) and two other pomacentrid species. Three methods of phylogenetic analysis all strongly supported the conclusion that anemonefishes are a monophyletic group. The molecular phylogeny differs from the tree based on morphological data in that the two species of specialized anemonefishes (Premnas biaculeatus and Amphiprion ocellaris) were assigned to a basal position within the clade, and the extreme host generalist (Amphiprion clarkii) to a more derived position. Thus, the initial anemonefish ancestors were probably host specialists and subsequent speciation events led to a combination of generalist and specialist groups. Further phylogenetic studies of additional anemonefish species are required to substantiate this hypothesis.

The effects of physostigmine and scopolamine on memory for food caches in the black-capped chickadee.

The possible effects of anticholinesterases on the central nervous system and, in particular, on learning and memory, have generated considerable interest. Food caching in the black-capped chickadee is an excellent natural paradigm of spatial working memory. Its susceptibility to cholinergically active drugs was explored in the present study. Our ultimate objective was to use food caching as a natural paradigm for the study of the consequences in birds of sublethal exposure to anticholinesterase insecticides. Biochemical analyses showed that administration of the anticholinesterase physostigmine (eserine) led to a short-lived effect, with recovery of brain cholinesterase levels already underway 5 min after an intramuscular injection. Birds administered the anticholinergic scopolamine before caching demonstrated significantly impaired recall compared to birds given physostigmine. Birds given saline only had an intermediate performance. Giving the drugs between caching and recovery had no measurable effect. These findings suggest that effects of cholinergic agents on cache recovery in chickadees are comparable to their effects in tests of working memory in mammals.

Characterization and assessment of an avian repetitive DNA sequence as an icterid phylogenetic marker.

The first tandemly repeated sequence examined in a passerine bird, a 431-bp PstI fragment named pMAT1, has been cloned from the genome of the brown-headed cowbird (Molothrus ater). The sequence represents about 5-10% of the genome (about 4 x 10(5) copies) and yields prominent ethidium bromide stained bands when genomic DNA cut with a variety of restriction enzymes is electrophoresed in agarose gels. A particularly striking ladder of fragments is apparent when the DNA is cut with HinfI, indicative of a tandem arrangement of the monomer. The cloned PstI monomer has been sequenced, revealing no internal repeated structure. There are sequences that hybridize with pMAT1 found in related nine-primaried oscines but not in more distantly related oscines, suboscines, or nonpasserine species. Little sequence similarity to tandemly repeated PstI cut sequences from the merlin (Falco columbarius), saurus crane (Grus antigone), or Puerto Rican parrot (Amazona vittata) or to HinfI digested sequence from the Toulouse goose (Anser anser) was detected. The isolated sequence was used as a probe to examine DNA samples of eight members of the tribe Icterini. This examination revealed phylogenetically informative characters. The repeat contains cutting sites from a number of restriction enzymes, which, if sufficiently polymorphic, would provide new phylogenetic characters. Sequences like these, conserved within a species, but variable between closely related species, may be very useful for phylogenetic studies of closely related taxa.

Sizing bands on autoradiograms: a study of precision for scoring DNA fingerprints.

We replicated DNA fingerprints of snapping turtles (Chelydra serpentina) and hypervariable restriction fragments of red-winged blackbirds (Agelaius phoeniceus) to estimate the between-blot and between-lane components of variance in molecular weights of restriction fragments. Molecular weight standards were included in every lane, and bands were sized using a sonic digitizer. In both studies, a strong positive correlation was found between band size and coefficient of variation (CV; mean = 0.7%). In the DNA fingerprint study, 26% of the variance in estimates of band size was due to differences between blots, 10% due to differences between lanes on the same blot, and 64% due to error in the digitizing process. In the restriction fragment length polymorphism (RFLP) study, 16% of the variance was due to difference between lanes, and 84% to digitizing. Statistical models were developed to measure the effect of sizing error on identifying identical fragments in different lanes or on different blots, in categorizing distinct alleles, and in determining the size of bins in operational allele definitions. We suggest that the distance between bands be at least 2.8 standard deviations (SD) before they are declared different at alpha = 0.05, and 3.7 SD for alpha = 0.01. A variation in CVs strongly indicates that empirical relationships between SD and band size must be used to decide if two bands represent the same allele. Alleles must be at least 3.9 SD apart before the chance of assigning new observations in error falls below 0.05. We suggest that a minimum bin width of 16 SD is necessary before the chances of assigning a band to the wrong bin falls below 0.05.

Realized reproductive success of polygynous red-winged blackbirds revealed by DNA markers.

Hypervariable genetic markers, including a novel locus-specific marker detected by a mouse major histocompatibility complex probe, reveal that multiple paternity is common in families of polygynous red-winged blackbirds (Agelaius phoeniceus). Almost half of all nests contained at least one chick resulting from an extra-pair fertilization, usually by a neighboring male. Genetically based measures of reproductive success show that individual males realize more than 20% of their overall success from extra-pair fertilizations, on average, and that this form of mating behavior confounds traditional measures of male success. The importance of alternative reproductive tactics in a polygynous bird is quantified, and the results challenge previous explanations for the evolution of avian polygny.

Effects of the organophosphorus pesticide fenitrothion on behavior and reproduction in zebra finches.

Activity was significantly altered in zebra finch pairs orally dosed with fenitrothion insecticide at rates of 1.04 and 3.80 mg/kg. Both the level and the dirunal pattern of activity were affected. Recovery of normal activity required 1-2 days, depending on the dosage administered. Fenitrothion had only a slight effect on reproduction when parents were dosed at the egg-laying stage of the breeding cycle. The implications of these results for the interpretation of field monitoring studies are discussed.

Recurrent patterns of natural selection in a population of Darwin's finches.

The adaptive significance of morphological traits can be assessed by measuring and identifying the forces of selection acting on them. Boag and Grant documented directional selection in a small population of Darwin's medium ground finches, Geospiza fortis, on I. Daphne Major, Galápagos, in 1977. Large beak and body size were favoured at a time of diminishing food supply and high adult mortality. We show here that in two subsequent periods of moderate to high adult mortality (1980 and 1982), the population was subject to the same selection. We have used a recently developed technique to ascertain the targets of direct selection. Beak depth and body weight were commonly under direct selection to increase but, surprisingly, beak width was directly selected to decrease, over all three periods of mortality. The results have implications for our understanding of evolutionary change in morphological traits of Darwin's finches.

Intense Natural Selection in a Population of Darwin's Finches (Geospizinae) in the Galapagos.

Survival of Darwin's finches through a drought on Daphne Major Island was nonrandom. Large birds, especially males with large beaks, survived best because they were able to crack the large and hard seeds that predominated in the drought. Selection intensities, calculated by O'Donald's method, are the highest yet recorded for a vertebrate population.