A DNA test to sex most birds.

To achieve a coherent evolutionary theory, it is necessary to account for the effects of the environment on the process of development. Phenotypic plasticity is the change in the expressed phenotype of a genotype as a function of the environment. Various measures of plasticity exist, many of which can be united within the framework of a polynomial function. This function is the norm of reaction. For the special case of a linear reaction norm, genetic variation can be partitioned into portions that are independent and dependent on the environment. From this partition two heritability measures are derived which can be used, alternatively, to compare populations or make predictions about the response to selection. Genetically, plasticity is likely due both to differences in allelic expression across environments and to changes in interactions among loci; plasticity is not a function of heterozygosity. Plasticity responds to both artificial and natural selection. The evolution of plasticity is modeled in thre...

Genetics and Evolution of Phenotypic Plasticity

I Honeybees of the World.- 1 The Genus Apis.- 2 Stingless Bees (Meliponinae).- 3 Evolution.- 4 Geographic Variability.- 5 Methods of Honeybee Taxonomy: Past and Present.- 6 Morphometric Analysis and Classification.- 7 Apis florea Fabricius 1787: 305.- 8 Apis dorsata Fabricius 1793: 328.- 9 Apis cerana Fabricius 1793: 327.- II The Western Honeybee Apis mellifera L. Classification and Natural History.- 10 Apis mellifera Linnaeus 1758: 576 General Introduction to a Polymorphic Species with an Unusual Range of Adaptation.- 11 The Races of the Near East (Irano-Ponto-Mediterranean Area).- 12 Honeybees of Tropical Africa.- 13 Honeybees of the Western Mediterranean.- 14 Honeybees of the Central Mediterranean and Southeastern Europe.- References.

Biogeography and Taxonomy of Honeybees

Population genetics has come of age. Three important components have come together: efficient techniques to examine informative segments of DNA, statistics to analyse DNA data and the availability of easy-to-use computer packages. Single-locus genetic markers and those that produce gene genealogies yield information that is truly comparable among studies. These markers answer biological questions most efficiently and also contribute to much broader investigations of evolutionary, population and conservation biology. For these reasons, single-locus and genealogical markers should be the focus of the intensive genetic data collection that has begun owing to the power of genetics in population biology.

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Efficient genetic markers for population biology.

Amplified fragment length polymorphisms (AFLPs) are polymerase chain reaction (PCR)-based markers for the rapid screening of genetic diversity. AFLP methods rapidly generate hundreds of highly replicable markers from DNA of any organism; thus, they allow high-resolution genotyping of fingerprinting quality. The time and cost efficiency, replicability and resolution of AFLPs are superior or equal to those of other markers [allozymes, random amplified polymorphic DNA (RAPD), restriction fragment length polymorphism (RFLP), microsatellites], except that AFLP methods primarily generate dominant rather than co-dominant markers. Because of their high replicability and ease of use, AFLP markers have emerged as a major new type of genetic marker with broad application in systematics, pathotyping, population genetics, DNA fingerprinting and quantitative trait loci (QTL) mapping.

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AFLP genotyping and fingerprinting

Random amplified polymorphic DNA (RAPD) fragment reproducibility was assayed in three animal species: red deer (Cervus elaphus), wild boar (Sus scrofa) and fruit fly (Drosophila melanogaster). Ten 10-mer primers (Operon) were tested in two replicate reactions per individual under different stringency conditions (annealing temperatures of 35 degrees C or 45 degrees C). Two estimates were generated from the data: autosimilarity, which tests the reproducibility of overall banding patterns, and band repeatability, which tests the reproducibility of specific bands. Autosimilarity (the similarity of individuals with themselves) was lower than 1 for all three species ranging between values of 0.66 for Drosophila at 45 degrees C and 0.88 for wild boar at 35 degrees C. Band repeatability was estimated as the proportion of individuals showing homologous bands in both replicates. The fraction of repeatable bands was 23% for deer, 36% for boar and 26% for fruit fly, all at an annealing temperature of 35 degrees C. Raising the annealing temperature did not improve repeatability. Phage lambda DNA was subjected to amplification and the pattern of bands compared with theoretical expectations based on nucleotide sequence. Observed fragments could not be related to expected ones, even if a 2 bp mismatch is allowed. Therefore, the nature of genetic variation uncovered by the RAPD method is unclear. These data demonstrate that prudence should guide inferences about population structure and nucleotide divergence based on RAPD markers.

An evaluation of RAPD fragment reproducibility and nature

Starting from a completely homozygous population of Drosophila melanogaster, two groups of 100 inbred lines each were established and maintained for 46 generations, by a single brother-sister mating and two double first cousin matings, respectively. Sternopleural bristle number, wing length and wing width were simultaneously scored in all lines every 4-5 generations. The means of four lines in each group departed significantly from the overall mean and, in each case, this was attributed to a single mutation of relatively large effect on at least one trait (0.3-1.4 environmental standard deviations in absolute value). Further analyses revealed widespread pleiotropy, similar gene action of a given mutation for all traits affected, and predominant additive action. No apparent association was found between the magnitudes of mutational effects on the traits and fitness. However, all recessive mutations were deleterious. The distribution of mutant effects was asymmetrical (positive for bristles and negative for wing measurements). Moreover, these distributions had a high variance and may be leptokurtic, due to the presence of major genes. Estimates of the ratio of new mutational variance to environmental variance ranged within (0.7-3.4) x 10(-3), those for wing measurements being generally larger. In agreement with theory, the rate of between-line differentiation was independent of population size.

https://www.genetics.org/content/genetics/132/3/771.full.pdf

The distribution of spontaneous mutations on quantitative traits and fitness in Drosophila melanogaster.

The Cantabrian brown bear Ursus arctos population can be seen as a paradigm in conservation biology due to its endangerment status and genetic uniqueness. Therefore, the need to obtain basic demographic data to inform management actions for conservation is imperative. Despite this, empirical data on the size and trends of the Cantabrian bear population are scarce. Here we present the first estimates of population size (Nc) and effective population size (Ne) of the whole Cantabrian brown bear population. We genotyped 270 non-invasive samples collected during 2006 throughout the entire range of the population and subsequently identified 130 individuals. Different model estimators of Nc based on capture—markrecapture (CMR) procedures were compared. The average for the best three models (Mh Chao, Mh Darroch and CAPWIRE TIRM) yielded a total estimate of Nc = 223 individuals (CI95% = 183–278) and Ne 50 (CI95% = 36–75) providing an Ne / Nc ratio of 0.22. Estimates for the two subpopulations commonly recognized i...

/pdf/estimating-the-population-size-of-the-endangered-cantabrian-5ejhkf29qi.pdf

Estimating the population size of the endangered Cantabrian brown bear through genetic sampling

Phylogeography of chamois (Rupicapra spp.) inferred from microsatellites

The Brown Bear (Ursus arctos) population present in the Cantabrian Mountains has suffered a dramatic decline in recent centuries and is now threatened with extinction. This situation has led to the development and implementation of a species recovery plan. To accomplish this plan, we need to improve our knowledge about the ecology, demography and genetics of this population. This paper presents the genetic analysis of the Cantabrian brown bear population using non-invasive samples (faeces and hairs) collected between 2004 and 2006. It was necessary to optimize a set of 18 microsatellite loci and a sex marker (several new multiplex reactions were developed) to obtain a suitable probability of identity among genotypes to work with this small, deeply structured population. Genotyping of 48 individuals was carried out using a two-step PCR protocol to increase the quality of the multilocus genotypes. Validation of genotypes was performed using a multi-tube approach combined with different software programmes to measure their error rate and reliability. Diversity in the Cantabrian population was low (He = 0.51) and the population was markedly subdivided into two subpopulations (western and eastern) without current gene flow between them. The level of divergence between the two subpopulations (Fst = 0.41) and the extremely low diversity in the eastern group (He = 0.25) indicate that this has had an extremely low effective population size and had been isolated from the main group during the last century. Connectivity between the two subpopulations will be of prime importance for the long-term survival of this species in the Cantabrian Mountains.

Jesús Albornoz

Papers

An evaluation of RAPD fragment reproducibility and nature

The distribution of spontaneous mutations on quantitative traits and fitness in Drosophila melanogaster.

Estimating the population size of the endangered Cantabrian brown bear through genetic sampling

Phylogeography of chamois (Rupicapra spp.) inferred from microsatellites

Non-invasive genetic study of the endangered Cantabrian brown bear (Ursus arctos)