Number Of Independent Loci Research Articles

Consequences of Single-Locus and Tightly Linked Genomic Architectures for Evolutionary Responses to Environmental Change.

Genetic and genomic architectures of traits under selection are key factors influencing evolutionary responses. Yet, knowledge of their impacts has been limited by a widespread assumption that most traits are controlled by unlinked polygenic architectures. Recent advances in genome sequencing and eco-evolutionary modeling are unlocking the potential for integrating genomic information into predictions of population responses to environmental change. Using eco-evolutionary simulations, we demonstrate that hypothetical single-locus control of a life history trait produces highly variable and unpredictable harvesting-induced evolution relative to the classically applied multilocus model. Single-locus control of complex traits is thought to be uncommon, yet blocks of linked genes, such as those associated with some types of structural genomic variation, have emerged as taxonomically widespread phenomena. Inheritance of linked architectures resembles that of single loci, thus enabling single-locus-like modeling of polygenic adaptation. Yet, the number of loci, their effect sizes, and the degree of linkage among them all occur along a continuum. We review how linked architectures are often associated, directly or indirectly, with traits expected to be under selection from anthropogenic stressors and are likely to play a large role in adaptation to environmental disturbance. We suggest using single-locus models to explore evolutionary extremes and uncertainties when the trait architecture is unknown, refining parameters as genomic information becomes available, and explicitly incorporating linkage among loci when possible. By overestimating the complexity (e.g., number of independent loci) of the genomic architecture of traits under selection, we risk underestimating the complexity (e.g., nonlinearity) of their evolutionary dynamics.

The evolution of phylogeographic data sets.

Empirical phylogeographic studies have progressively sampled greater numbers of loci over time, in part motivated by theoretical papers showing that estimates of key demographic parameters improve as the number of loci increases. Recently, next-generation sequencing has been applied to questions about organismal history, with the promise of revolutionizing the field. However, no systematic assessment of how phylogeographic data sets have changed over time with respect to overall size and information content has been performed. Here, we quantify the changing nature of these genetic data sets over the past 20 years, focusing on papers published in Molecular Ecology. We found that the number of independent loci, the total number of alleles sampled and the total number of single nucleotide polymorphisms (SNPs) per data set has improved over time, with particularly dramatic increases within the past 5 years. Interestingly, uniparentally inherited organellar markers (e.g. animal mitochondrial and plant chloroplast DNA) continue to represent an important component of phylogeographic data. Single-species studies (cf. comparative studies) that focus on vertebrates (particularly fish and to some extent, birds) represent the gold standard of phylogeographic data collection. Based on the current trajectory seen in our survey data, forecast modelling indicates that the median number of SNPs per data set for studies published by the end of the year 2016 may approach ~20,000. This survey provides baseline information for understanding the evolution of phylogeographic data sets and underscores the fact that development of analytical methods for handling very large genetic data sets will be critical for facilitating growth of the field.

Root peroxidases and Rhizobium, Bradyrhizobium nodulation affinities of Phaseolus vulgaris L. and P. acutifolius A. Gray congruity backcross populations

Four parents [P. acutifolius var.acutifolius (A19), P. a.var. latifolius `Serowi' (A9),P. a. var. latifolius(A10), and P. vulgaris `Red Cloud' kidney (V1)] were used to create six interspecific recurrent and congruity backcross pedigrees (V1 × A9, A9 × V1, V1 × A10, A10 × V1, V1 × A19, A19 × V1) for evaluation of Rhizobium, Bradyrhizobium nodulation affinities and root peroxidase banding patterns. Most primary hybrids nodulated with all Rhizobium, Bradyrhizobium strains, while recurrent generations nodulated with strains of the recurrent parent, suggesting a number of independent loci and random assortment for strain-specific nodulation. A proximity matrix of nodulation phenotypes produced a cluster with V1, two recurrent and two congruity backcross hybrids with V1 as the cytoplasmic parent; a separate cluster with all primary interspecific and balanced, congruity backcross hybrids. A9 and A10were clustered the farthest away from V1. Root peroxidase zymograms of primary hybrids were the summation of the parents and controlled by independent loci. Advanced hybrids exhibited new root peroxidases, matching those found for otherPhaseolus spp., including ancestralP. coccineus. A proximity matrix of root peroxidase phenotypes produced a cluster with only A9 3V1F1, a cluster containing only A19 3V1 F2, and a large cluster with all P. acutifoliusparents and hybrids with P. acutifolius as the cytoplasmic parent in balanced hybrids or the majority parent in unbalanced hybrids. Estimation of genetic distances showed primary, interspecific hybrids to be more closely related with the cytoplasmic parent. Recurrent and congruity backcross generations varied in genetic distances between each respective parent. This is the first report of congruity backcrossing creating hybrids with biochemical traits of nonparental species.