Jon H. Wetton

An Association between Fertility and Cuckoldry in the House Sparrow, Passer domesticus

DNA fingerprinting of 183 broods of house sparrows and their attendant adults revealed that 13.6% of nestlings were unrelated to the attendant male. The occurrence of cuckoldry was unaffected by male age and experience, pair bond duration or time within a breeding season. However, cuckoldry was significantly more frequent in broods that included some infertile eggs. This study suggests that sperm competition can be strongly influenced by the fertility of the cuckolded male, and that females may benefit from extra-pair copulation as an insurance against their mate’s infertility.

Single-locus DNA fingerprinting reveals that male reproductive success increases with age through extra-pair paternity in the house sparrow (Passer domesticus)

Single-locus profiles produced with four cloned minisatellites were used to investigate the paternity of 44 house sparrow nestlings sired through extra-pair copulations. Comparison of the paternal alleles with a profile database of 144 candidate males resulted in 33 paternity assignments to 13 males. Both age and proximity were related to success in cuckoldry. Males achieving extra-pair paternity were usually breeding near to the cuckolded pair. Those at least two years old sired significantly more young through extra-pair matings, resulting in an average reproductive output 36% higher than that of yearlings. Whereas older males gained extra-pair fertilizations during their own breeding attempts, yearlings only achieved extra-pair success outside their own breeding cycle and did not significantly increase their own reproductive success. In contrast to other species in which extra-pair males are apparently chosen for their high quality, male sparrows siring extra-pair young were cuckolded at the same rate as other males.

The Y-Chromosome Tree Bursts into Leaf: 13,000 High-Confidence SNPs Covering the Majority of Known Clades

Many studies of human populations have used the male-specific region of the Y chromosome (MSY) as a marker, but MSY sequence variants have traditionally been subject to ascertainment bias. Also, dating of haplogroups has relied on Y-specific short tandem repeats (STRs), involving problems of mutation rate choice, and possible long-term mutation saturation. Next-generation sequencing can ascertain single nucleotide polymorphisms (SNPs) in an unbiased way, leading to phylogenies in which branch-lengths are proportional to time, and allowing the times-to-most-recent-common-ancestor (TMRCAs) of nodes to be estimated directly. Here we describe the sequencing of 3.7 Mb of MSY in each of 448 human males at a mean coverage of 51×, yielding 13,261 high-confidence SNPs, 65.9% of which are previously unreported. The resulting phylogeny covers the majority of the known clades, provides date estimates of nodes, and constitutes a robust evolutionary framework for analyzing the history of other classes of mutation. Different clades within the tree show subtle but significant differences in branch lengths to the root. We also apply a set of 23 Y-STRs to the same samples, allowing SNP- and STR-based diversity and TMRCA estimates to be systematically compared. Ongoing purifying selection is suggested by our analysis of the phylogenetic distribution of nonsynonymous variants in 15 MSY single-copy genes.

Within-clutch patterns of egg viability and paternity in the House Sparrow

One of the potential benefits of extra-pair copulation is an enhanced likelihood of successful fertilization if the pair male is unable to produce sufficient viable sperm to ensure the fertility of an entire clutch. Low male fertility can be a transient phenomenon associated with higher rates of sperm usage than production, leading to a progressive depletion of sperm reserves. Evidence of a correlation between hatching success and the occurrence of extra-pair fertilizations has been reported in House Sparrows. In this study we have used single-locus minisatellite and microsatellite profiling to investigate the distribution of extra-pair fertilizations within House Sparrow broods to determine whether there are changes in the level of hatching failure or extra-pair paternity during the course of producing a clutch. Embryonic material was collected at mid-incubation to minimize loss of data through pre-sampling mortality and to ensure that laying order was known. A significant clustering of both infertile eggs and extra-pair young was noted in the earliest eggs in a clutch. Possible causes of this phenomenon are discussed.

No evidence for extrapair fertilizations in the merlin revealed by DNA fingerprinting

Broods of young merlins were compared with the adults in attendance at their nest by DNA fingerprinting. No offspring were found that mismatched genetically suggesting that intraspecific brood parasitism and extrapair fertilization are very rare in this population. The results are discussed in the light of the Paternity Assurance Hypothesis.

Genetic data from 28 STR loci for forensic individual identification and parentage analyses in 6 bird of prey species

Twenty-eight STR loci were screened in wild populations of six bird of prey species providing allele frequencies and population genetic parameters necessary for the application of STRs in wildlife forensic genetic casework. Individual STR loci were validated according to forensic recommendations in specimens of golden eagle (Aquila chrysaetos), goshawk (Accipiter gentilis), merlin (Falco columbarius), peregrine falcon (Falco peregrinus), gyr falcon (Falco rusticolus) and saker falcon (Falco cherrug). Deviations from Hardy-Weinberg expectations and linkage disequilibrium between locus pairs were examined. The average probability of identity (PI(ave)) and power of exclusion (PE) suggest the profiling systems of golden eagle, goshawk, merlin and peregrine falcons are capable of providing robust and highly discriminatory forensic evidence for legal proceedings. Due to low sample numbers the allele frequency data for gyr and saker falcons is not currently capable of providing an effective probability of identity. Further work should focus on increasing the size of these data sets.

A suite of falcon single‐locus minisatellite probes: a powerful alternative to DNA fingerprinting

Nine falcon single‐locus minisatellite probes have been cloned, characterized and shown to provide a powerful alternative to multilocus DNA fingerprinting for determining the parentage of broods of young. Eight clones derived from size‐selected peregrine Falco peregrinus and merlin F. columbarius charomid libraries were found to detect single minisatellite loci in all tested members of the genus Falco. A further clone (cFti1) randomly selected from a kestrel F. tinnunculus library identified a single locus in other members of the genus and certain species of the Accipitridae. The nine loci display a mean heterozygosity of 88% and considerable allelic diversity in the peregrine and merlin. Pedigree analysis provides evidence consistent with the clustering of minisatellites in linkage groups that are conserved between species. Mutations were observed at five loci among families of peregrines and kestrels. Composite profiles produced with this suite of probes provide an excellent means of confirming identity and parentage. The use of profiling for investigating familial relationships, population dynamics and combating the illegal trade in wild falcons is discussed.

Polymorphic Sex-Specific Sequences in Birds of Prey

A red kite (Milvus milvus) clone, which cross-hybridizes to a human minisatellite, reveals complex polymorphic patterns in members of the Accipitridae, a family of 217 species of birds of prey, which includes the kites, hawks and eagles. The total absence of hybridization to males implies that the sequence is located on the W chromosome, and stable inheritance from mother to daughter suggests that the patterns evolve as haploid matrilines. This has allowed not only the development of a simple and rapid sexing technique but may also provide a means of monitoring matriarchal success and dispersion. As an example, a survey of 36 continental European red kite nests revealed 24 different haplotypes, whereas only 2 were found among 53 Welsh nests. The results show the effect of a dramatic bottleneck in Wales and may provide evidence of recent introgression from the continent.

Single-locus profiling reveals loss of variation in inbred populations of the red kite (Milvus milvus)

The genetic analysis of inbred populations has been facilitated by the development of Variable Number Tandem Repeat (VNTR) probes. We describe here the first use of a synthetic, concatenated simple sequence probe to detect a single VNTR locus and its use in differentiating populations of the red kite, one of Europe’s most threatened birds of prey. Numbering 11000-13000 pairs, this species is patchily distributed, comprising several populations, some of which have recently suffered major bottlenecks. By using the (CCAT)n probe we have examined variation within and among four of these. The levels of heterozygosity and allelic diversity reflect each population’s history but also reveal substructuring within the indigenous British population in Wales. Here a group of peripheral territories, which are amongst the most successful in the population, exhibit significantly lower heterozygosity than the main population, and appear to receive little genetic input from it.

In the blood: the myth and reality of genetic markers of identity

ABSTRACT The differences between copies of the human genome are very small, but tend to cluster in different populations. So, despite the fact that low inter-population differentiation does not support a biological definition of races statistical methods are nonetheless claimed to be able to predict successfully the population of origin of a DNA sample. Such methods are employed in commercial genetic ancestry tests, and particular genetic signatures, often in the male-specific Y-chromosome or maternally-inherited mitochondrial DNA, have become widely identified with particular ancestral or existing groups, such as Vikings, Jews, or Zulus. Here, we provide a primer on genetics, and describe how genetic markers have become associated with particular groups. We describe the conflict between population genetics and individual-based genetics and the pitfalls of over-simplistic genetic interpretations, arguing that although the tests themselves are reliable, the interpretations are unreliable and strongly influenced by cultural and other social forces.