A DNA test to sex most birds.

Molecular sexing is an attractive means to determine the sex of sexually monomorphic birds, e.g. chicks of most species. A universal approach for molecular sexing of birds would require that a conserved W chromosome-linked sequence could be analysed, but no single gene has previously been known from any avian W chromosome. The recent discovery of the CHD1W gene, apparently W-linked in all non-ratite birds, has opened new possibilities in this direction, although there is a problem in that the gene also exists in a very similar copy on the Z chromosome (CHD1Z). Here we describe a universal method for molecular sexing of non-ratite birds which is based on the detection of a constant size difference between CHD1W and CHD1Z introns. Using highly conserved primers flanking the intron, PCR amplification and agarose electrophoresis, females are characterised by displaying one (CHD1W) or two fragments (CHD1W and CHD1Z), while males only show one fragment (CHD1Z) clearly different in size from the female-specific CHD1W fragment. With one particular pair of primers (2550F and 2718R) we applied this test to 50 bird species from 11 orders throughout the avian phylogeny, successfully sexing 47 of the species. Using an alternative pair of primers, the three failing species could be reliably sexed. This means that a simple, rapid and cheap universal system for molecular sexing of non-ratite birds is now available.

A simple and universal method for molecular sexing of non-ratite birds

The application of molecular genetic techniques has revolutionized our view of avian mating systems. Contrary to prior expectations, birds are only very rarely sexually monogamous, with ‘extra-pair offspring’ found in approximately 90% of species. Even among socially monogamous species, over 11% of offspring are, on average, the result of extra-pair paternity (EPP). Based on over 150 molecular genetic studies of EPP in birds, we review two topical areas: (i) ecological explanations for interspecific variation in the rate of EPP; and (ii) evidence bearing on the adaptive function of EPP. We highlight the remaining challenges of understanding the relative roles of genes and ecology in determining variation between taxa in the rate of extra paternity, and testing for differences between extra-pair offspring and those sired within-pair.

https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1365-294X.2002.01613.x

Extra pair paternity in birds: a review of interspecific variation and adaptive function.

Many previous estimates of the mutation rate in humans have relied on screens of visible mutants. We investigated the rate and pattern of mutations at the nucleotide level by comparing pseudogenes in humans and chimpanzees to (i) provide an estimate of the average mutation rate per nucleotide, (ii) assess heterogeneity of mutation rate at different sites and for different types of mutations, (iii) test the hypothesis that the X chromosome has a lower mutation rate than autosomes, and (iv) estimate the deleterious mutation rate. Eighteen processed pseudogenes were sequenced, including 12 on autosomes and 6 on the X chromosome. The average mutation rate was estimated to be approximately 2.5 x 10(-8) mutations per nucleotide site or 175 mutations per diploid genome per generation. Rates of mutation for both transitions and transversions at CpG dinucleotides are one order of magnitude higher than mutation rates at other sites. Single nucleotide substitutions are 10 times more frequent than length mutations. Comparison of rates of evolution for X-linked and autosomal pseudogenes suggests that the male mutation rate is 4 times the female mutation rate, but provides no evidence for a reduction in mutation rate that is specific to the X chromosome. Using conservative calculations of the proportion of the genome subject to purifying selection, we estimate that the genomic deleterious mutation rate (U) is at least 3. This high rate is difficult to reconcile with multiplicative fitness effects of individual mutations and suggests that synergistic epistasis among harmful mutations may be common.

http://bioinformatics.bc.edu/~marth/BI820/files/Nachman-MutationRate-G-2000.pdf

Estimate of the Mutation Rate per Nucleotide in Humans

Estimation of avian nest survival has traditionally involved simple measures of apparent nest survival or Mayfield constant-nest-survival models. However, these methods do not allow researchers to build models that rigorously assess the importance of a wide range of biological factors that affect nest survival. Models that incorporate greater detail, such as temporal variation in nest survival and covariates representative of individual nests represent a substantial improvement over traditional estimation methods. In an attempt to improve nest survival estimation procedures, we introduce the nest survival model now available in the program MARK and demonstrate its use on a nesting study of Mountain Plovers (Charadrius montanus Townsend) in Montana, USA. We modeled the daily survival of Mountain Plover nests as a function of the sex of the incubating adult, nest age, year, linear and quadratic time trends, and two weather covariates (maximum daily temperature and daily precipitation) during a six-year stud...

Advanced techniques for modeling avian nest survival

Assuming that new mutations arise mainly during DNA replication, sequence evolution in mammals has been seen as 'male driven' (ref. 1) because of the many more cell divisions in spermatogenesis than in oogenesis. Molecular support for this idea has been obtained from the observation of higher substitution rates in genes on the Y than on the X chromosome of primates and rodents, which are species with male heterogamety, but has not been confirmed by the reciprocal analysis of organisms with female heterogamety. The recent suggestion that an intrinsic reduction in the X-chromosome mutation rate may be confounded with male effects in previous comparisons, and the paradoxical finding of low levels of polymorphism on the primate Y chromosome indicate that the idea of male-biased mutation rate needs to be re-examined. We have analysed the molecular evolution of the gene CHD, which is present on the Z and W sex chromosomes of birds. The substitution rate at synonymous positions, as well as in intron DNA, was considerably higher on the Z chromosome than on the female-specific W chromosome, with an estimated male-to-female bias in mutation rate (alpha m) of 3.9-6.5. Thus, evolution appears to be male driven in birds--a situation that supports a neutral model of molecular evolution.

Male-driven evolution of DNA sequences in birds.

The avian egg as a test system for endocrine disrupters: effects of diethylstilbestrol and ethynylestradiol on sex organ develo

Elevated blood plasma cholesterol (hypercholesterolemia) is a major risk factor for coronary artery disease (CAD) in humans. Genetic dissection of polygenic lipid and lipoprotein disorders in swine, a key animal model for the study of familial hypercholesterolemia (FH) and CAD, led to the isolation of a monogenic subphenotype (FH-r), that is inherited in the recessive (r) manner. A genome scan mapped the FH-r locus close to the centromere of chromosome 2. Comparative mapping showed that this region shares homology with a part of human chromosome 19 that harbors the low density lipoprotein receptor (LDLR) locus, and therefore suggested LDLR as the prime candidate gene for FH-r. Cloning and sequencing of hepatic LDLR cDNA from two FH-r/r and one normal (N/N) animals disclosed a single missense mutation (R84C) in a region that corresponds to human exon 4. The C84 mutation cosegregates invariantly with hypercholesterolemia, which strongly suggests that this mutation is responsible for the observed hyperlipidemia.

Identification of a mutation in the low density lipoprotein receptor gene associated with recessive familial hypercholesterolemia in swine

Four microsatellite markers from the willow warbler Phylloscopus trochilus: were isolated and characterised. The combined exclusion probability of the three most polymorphic markers (Phtr1, Phtr2 and Phtr3) was 0.96. These markers were used to test for the occurrence of extra-pair young (EPY) in twelve willow warbler families sampled from the island of Gotland in 1992 and 1993. The mean frequency of extra-pair young was found to be 28% and the mean frequency of families with extra-pair young 58%. These results contrast with an earlier study in a mainland Swedish population, where no EPY were found. The island population in this study has a higher breeding density than the mainland population, rendering support for density dependent factors affecting the frequency of EPY. A cross-species study showed that the willow warbler microsatellite markers can also be used in other European passerines as well as distantly related species, such as the Australian magpie Gymnorhina tibicen.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1601-5223.1997.00127.x

Anna-Karin Fridolfsson

Papers

A simple and universal method for molecular sexing of non-ratite birds

Male-driven evolution of DNA sequences in birds.

The avian egg as a test system for endocrine disrupters: effects of diethylstilbestrol and ethynylestradiol on sex organ develo

Identification of a mutation in the low density lipoprotein receptor gene associated with recessive familial hypercholesterolemia in swine

Microsatellite Markers for Paternity Testing in the Willow Warbler Phylloscopus Trochilus: High Frequency of Extra‐Pair Young in an Island Population