Generalized linear mixed models provide a flexible framework for modeling a range of data, although with non-Gaussian response variables the likelihood cannot be obtained in closed form. Markov chain Monte Carlo methods solve this problem by sampling from a series of simpler conditional distributions that can be evaluated. The R package MCMCglmm implements such an algorithm for a range of model fitting problems. More than one response variable can be analyzed simultaneously, and these variables are allowed to follow Gaussian, Poisson, multi(bi)nominal, exponential, zero-inflated and censored distributions. A range of variance structures are permitted for the random effects, including interactions with categorical or continuous variables (i.e., random regression), and more complicated variance structures that arise through shared ancestry, either through a pedigree or through a phylogeny. Missing values are permitted in the response variable(s) and data can be known up to some level of measurement error as in meta-analysis. All simu- lation is done in C/ C++ using the CSparse library for sparse linear systems.

https://cran.r-project.org/web//packages/MCMCglmm/vignettes/Overview.pdf

MCMC Methods for Multi-Response Generalized Linear Mixed Models: The MCMCglmm R Package

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

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

Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.

/pdf/comparative-genomics-reveals-insights-into-avian-genome-3gamkx0zqj.pdf

Comparative genomics reveals insights into avian genome evolution and adaptation.

Birds are difficult to sex. Nestlings rarely show sex-linked morphology and we estimate that adult females appear identical to males in over 50% of the world's bird species. This problem can hinder both evolutionary studies and human-assisted breeding of birds. DNA-based sex identification provides a solution. We describe a test based on two conserved CHD (chromo-helicase-DNA-binding) genes that are located on the avian sex chromosomes of all birds, with the possible exception of the ratites (ostriches, etc.; Struthioniformes). The CHD-W gene is located on the W chromosome; therefore it is unique to females. The other gene, CHD-Z, is found on the Z chromosome and therefore occurs in both sexes (female, ZW; male, ZZ). The test employs PCR with a single set of primers. It amplifies homologous sections of both genes and incorporates introns whose lengths usually differ. When examined on a gel there is a single CHD-Z band in males but females have a second, distinctive CHD-W band.

/pdf/a-dna-test-to-sex-most-birds-4qsdrdaafe.pdf

A DNA test to sex most birds

Sex differences in the foraging behaviour of adults have been observed in a number of sexually size-dimorphic birds, and the usual inference has been that these sex-specific differences are driven primarily by differences in body size. An alternative explanation is that foraging differences result from sex differences unrelated to size, such as sex-specific nutritional requirements. To examine these alternative hypotheses, the foraging behaviour of parents was compared between two sympatric and congeneric species of seabird, the Brown Booby Sula leucogaster , which is highly sexually size-dimorphic (females 38% larger) and the Red-footed Booby S. sula , in which sex differences in body size are less marked (females 15% larger). Using temperature and depth loggers, we found that there were highly significant differences in the foraging trip durations and diving behaviour of male and female Brown Boobies. These sex differences were less marked in Red-footed Boobies. Thus, our interspecies comparison revealed that the magnitude of the difference between the sexes matched the sexual size dimorphism of the species, providing support for the size hypothesis.

Sex-specific foraging behaviour in tropical boobies: does size matter?

Sex identification is a problem in research and conservation. It can often be solved using a DNA test but this is only an option if a sex-specific marker is available. Such markers can be identified using the amplified fragment length polymorphism (AFLP) technique. This is usually a taxonomic method, as it produces a DNA fingerprint of 50-100 PCR bands. However, if male and female AFLP products are compared, sex-specific markers are confined to the heterogametic sex and can rapidly be identified. Once a marker is found, AFLP can be used to sex organisms directly or the marker can be sequenced and a standard PCR test designed.

The use of amplified fragment length polymorphism (AFLP) in the isolation of sex-specific markers.

Sex allocation studies seek to ascertain whether mothers manipulate offspring sex ratio prior to ovulation. To do so, DNA for molecular sexing should be collected as soon after conception as possible, but instead neonates are usually sampled. Here, we aim to identify and quantify some of the problems associated with using molecular techniques to identify the sex of newly laid avian eggs. From both fertilized and unfertilized chicken (Gallus gallus) eggs, we sampled (1) the blastoderm/disc, (2) vitelline membrane and (3) a mixture of (1) and (2). Thus, we replicated scenarios under which contaminated samples are taken and/or unfertilized eggs are not identified as such and are sampled. We found that two commonly used molecular sexing tests, based on the CHD-1 genes, differed in sensitivity, but this did not always predict their ability to sex egg samples. The vitelline membrane was a considerable source of maternal and probably paternal contamination. Fertile eggs were regularly assigned the wrong sex when vitelline membrane contaminated the blastoderm sample. The membrane of unfertilized eggs was always female, i.e. maternal DNA had been amplified. DNA was amplified from 47 to 63% of unfertilized blastodiscs, even though it was highly unlikely that DNA from a single haploid cell could be amplified reliably using these polymerase chain reaction (PCR) techniques. Surprisingly, the blastodiscs were identified as both males and females. We suggest that in these cases only maternal DNA was amplified, and that 'false' males, Z not ZZ, were detected. This was due to the reduced ability of both sets of primers to anneal to the W chromosome compared to the Z chromosome at low DNA concentrations. Overall, our data suggested that estimates of primary sex ratios based on newly laid eggs will be appreciably inaccurate.

/pdf/primary-sex-ratios-in-birds-problems-with-molecular-sex-4j7igye49h.pdf

Kate Orr

Papers

A DNA test to sex most birds

A DNA test to sex most birds.

Sex-specific foraging behaviour in tropical boobies: does size matter?

The use of amplified fragment length polymorphism (AFLP) in the isolation of sex-specific markers.

Primary sex ratios in birds: problems with molecular sex identification of undeveloped eggs