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

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.

https://pure.rug.nl/ws/files/6668976/2002AnimBehavDingemanse.pdf

Repeatability and heritability of exploratory behaviour in great tits from the wild

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

Robert J. G. Dawson

Papers

A DNA test to sex most birds

A DNA test to sex most birds.