▪ Abstract A moment estimator of θ, the coancestry coefficient for alleles within a population, was described by Weir & Cockerham in 1984 (100) and is still widely cited. The estimate is used by population geneticists to characterize population structure, by ecologists to estimate migration rates, by animal breeders to describe genetic variation, and by forensic scientists to quantify the strength of matching DNA profiles. This review extends the work of Weir & Cockerham by allowing different levels of coancestry for different populations, and by allowing non-zero coancestries between pairs of populations. All estimates are relative to the average value of θ between pairs of populations. Moment estimates for within- and between-population θ values are likely to have large sampling variances, although these may be reduced by combining information over loci. Variances also decrease with the numbers of alleles at a locus, and with the numbers of populations sampled. This review also extends the work of Weir ...

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Estimating F-statistics.

In vertebrates, melanin-based coloration is often associated with variation in physiological and behavioural traits. We propose that this association stems from pleiotropic effects of the genes regulating the synthesis of brown to black eumelanin. The most important regulators are the melanocortin 1 receptor and its ligands, the melanocortin agonists and the agouti-signalling protein antagonist. On the basis of the physiological and behavioural functions of the melanocortins, we predict five categories of traits correlated with melanin-based coloration. A review of the literature indeed reveals that, as predicted, darker wild vertebrates are more aggressive, sexually active and resistant to stress than lighter individuals. Pleiotropic effects of the melanocortins might thus account for the widespread covariance between melanin-based coloration and other phenotypic traits in vertebrates.

https://serval.unil.ch/resource/serval:BIB_2EC1D375BAD5.P001/REF.pdf

Pleiotropy in the melanocortin system, coloration and behavioural syndromes.

Genetic stochasticity due to small population size contributes to population extinction, especially when population fragmentation disrupts gene flow. Estimates of effective population size (Ne) can therefore be informative about population persistence, but there is a need for an assessment of their consistency and informative relevance. Here we review the body of empirical estimates of Ne for wild populations obtained with the temporal genetic method and published since Frankham's (1995) review. Theoretical considerations have identified important sources of bias for this analytical approach, and we use empirical data to investigate the extent of these biases. We find that particularly model selection and sampling require more attention in future studies.

We report a median unbiased Ne estimate of 260 (among 83 studies) and find that this median estimate tends to be smaller for populations of conservation concern, which may therefore be more sensitive to genetic stochasticity. Furthermore, we report a median Ne/N ratio of 0.14, and find that this ratio may actually be higher for small populations, suggesting changes in biological interactions at low population abundances. We confirm the role of gene flow in countering genetic stochasticity by finding that Ne correlates strongest with neutral genetic metrics when populations can be considered isolated. This underlines the importance of gene flow for the estimation of Ne, and of population connectivity for conservation in general. Reductions in contemporary gene flow due to ongoing habitat fragmentation will likely increase the prevalence of genetic stochasticity, which should therefore remain a focal point in the conservation of biodiversity.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-294X.2008.03842.x

Genetic estimates of contemporary effective population size: what can they tell us about the importance of genetic stochasticity for wild population persistence?

The study of pigmentation has played an important role in the intersection of evolution, genetics, and developmental biology. Pigmentation's utility as a visible phenotypic marker has resulted in over 100 years of intense study of coat color mutations in laboratory mice, thereby creating an impressive list of candidate genes and an understanding of the developmental mechanisms responsible for the phenotypic effects. Variation in color and pigment patterning has also served as the focus of many classic studies of naturally occurring phenotypic variation in a wide variety of vertebrates, providing some of the most compelling cases for parallel and convergent evolution. Thus, the pigmentation model system holds much promise for understanding the nature of adaptation by linking genetic changes to variation in fitness-related traits. Here, I first discuss the historical role of pigmentation in genetics, development and evolutionary biology. I then discuss recent empirically based studies in vertebrates, which rely on these historical foundations to make connections between genotype and phenotype for ecologically important pigmentation traits. These studies provide insight into the evolutionary process by uncovering the genetic basis of adaptive traits and addressing such long-standing questions in evolutionary biology as (1) are adaptive changes predominantly caused by mutations in regulatory regions or coding regions? (2) is adaptation driven by the fixation of dominant mutations? and (3) to what extent are parallel phenotypic changes caused by similar genetic changes? It is clear that coloration has much to teach us about the molecular basis of organismal diversity, adaptation and the evolutionary process.

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Genetics, development and evolution of adaptive pigmentation in vertebrates.

Museums and other natural history collections (NHC) worldwide house millions of specimens. With the advent of molecular genetic approaches these collections have become the source of many fascinating population studies in conservation genetics that contrast historical with present-day genetic diversity. Recent developments in molecular genetics and genomics and the associated statistical tools have opened up the further possibility of studying evolutionary change directly. As we discuss here, we believe that NHC specimens provide a largely underutilized resource for such investigations. However, because DNA extracted from NHC samples is degraded, analyses of such samples are technically demanding and many potential pitfalls exist. Thus, we propose a set of guidelines that outline the steps necessary to begin genetic investigations using specimens from NHC.

/pdf/back-to-the-future-museum-specimens-in-population-genetics-ifzt2u4g9s.pdf

Back to the future: museum specimens in population genetics.

There is a wealth of published molecular population genetic studies, however, most do not include historic samples and thus implicitly assume temporal genetic stability. We tested for changes in genetic diversity and structure in three populations of steelhead trout (Oncorhynchus mykiss) from a northern British Columbia watershed using seven microsatellite loci over 40 years. We found little change in genetic diversity (mean allele numbers and observed and expected heterozygosity), despite large variation in the estimated numbers of steelhead returning to the watershed over the same time period. However, the temporal stability in genetic diversity is not reflected in population structure, which appears to be high among populations, yet significantly variable over time. The neighbour-joining tree showed that, overall, two of the populations (Zymoetz and Kispiox) clustered separately from the third (Babine); a finding which was not consistent with their geographical separation. The clustering pattern was also not temporally consistent. We used the temporal method to estimate the effective number of breeders (Nb ) for the three populations; our values (Nb = 17-102) were low for the large and presumed vigorous populations of steelhead trout sampled. The low Nb values were also not consistent with the generally high genetic diversity estimates, suggesting the possibility of intermittent gene flow among the three populations. The use of temporal analyses in population genetic samples should be a priority; first, to verify observed patterns in contemporary data, and second, to build a dataset of temporal analyses to allow generalizations to be made concerning temporal genetic stability and effective population size in natural populations.

Temporal change in genetic structure and effective population size in steelhead trout (Oncorhynchus mykiss).

The melanocortin-1 receptor (MC1R) forms a critical switch in the production of orange/red pheomelanin and black/brown eumelanin pigments during hair development in mammals. The molecular evolution of the melanocortin-1 receptor gene was investigated in a broad range of primate species, including several groups with large differences in distribution of orange/red and black hairs. Primate MC1R has been subject to purifying selection throughout most of its evolution, with small changes in selective constraint being detected early in primate evolution. In contrast to the situation in humans and domestic mammals, many intraspecific and intrageneric differences in primate coat color cannot be attributed to changes in the MC1R coding sequence. Nevertheless, important changes in the biochemical function of MC1R are suggested by mutations in sites of known functional importance, particularly in New World monkeys and lemurs. The evolution of the MC1R in lion tamarins is anomalous, with a combination of a high nonsynonymous to synonymous substitution rate (dN/dS) ratio, deletions, and substitutions. Am J Phys Anthropol 121:000–000, 2003. © 2003 Wiley-Liss, Inc.

Evolution of a pigmentation gene, the melanocortin-1 receptor, in primates.

Correlations of various measures of individual genetic variation with fitness have been reported in a number of taxa; however, the genetic nature of such correlations remains uncertain. To explore ...

Relationships between heterozygosity, allelic distance (d2), and reproductive traits in chinook salmon, Oncorhynchus tshawytscha

We investigated variation in the gene encoding the agouti signaling protein (ASIP) in relation to coat color evolution in primates. We found little evidence that mutations in the coding region of ASIP have been involved in color changes among closely related primate species. Among many closely related species with differing coat color, the coding region of ASIP was identical. In two cases (Sulawesi macaque and black lion tamarin) where species with almost completely black coat color had derived point mutations in exon 4 of the ASIP coding sequence, the same mutations did not alter coloration in other mammals and so probably do not affect ASIP function. Evolutionary reconstructions of two key phenotypes that are typically related to ASIP function—transverse phaeomelanin bands on hairs and pale ventral coloration—showed that these usually evolved concurrently, suggesting that loci acting downstream of ASIP may be involved. Analysis of dN/dS ratios revealed a likely change in functional constraint on ASIP following loss of agouti-banded hairs + pale ventral coloration, particularly in catarrhine primates (humans, apes, and Old World monkeys). Together with previous results on a lack of association of coat color with MC1R variation, these results suggest that other loci probably have an important role in primate coat color evolution.

Investigation of the role of the agouti signaling protein gene (ASIP) in coat color evolution in primates.

We have characterized the biochemical function of the melanocortin 1 receptor (MC1R), a critical regulator of melanin synthesis, from 9 phylogenetically diverse primate species with varying coat colors. There is substantial diversity in melanocyte-stimulating hormone (MSH) binding affinity and basal levels of activity in the cloned MC1Rs. MSH binding was lost independently in lemur and New World monkey lineages, whereas high basal levels of MC1R activity occur in lemurs and some New World monkeys and Old World monkeys. Highest levels of basal activity were found in the MC1R of ruffed lemurs, which have the E94K mutation that leads to constitutive activation in other species. In 3 species (2 lemurs and the howler monkey), we report the novel finding that binding and inhibition of MC1R by agouti signaling protein (ASIP) can occur when MSH binding has been lost, thus enabling continuing regulation of the melanin type via ASIP expression. Together, these findings can explain the previous paradox of a predominantly pheomelanic coat in the red ruffed lemur (Varecia rubra). The presence of a functional, MSH-responsive MC1R in orangutan demonstrates that the mechanism of red hair generation in this ape is different from the prevalent mechanism in European human populations. Overall, we have found unexpected diversity in MC1R function among primates and show that the evolution of the regulatory control of MC1R activity occurs by independent variation of 3 distinct mechanisms: basal MC1R activity, MSH binding and activation, and ASIP binding and inhibition. This diversity of function is broadly associated with primate phylogeny and does not have a simple relation to coat color phenotype within primate clades.

High Diversity in Functional Properties of Melanocortin 1 Receptor (MC1R) in Divergent Primate Species Is More Strongly Associated with Phylogeny than Coat Color

Joanne Kelly

Papers

Temporal change in genetic structure and effective population size in steelhead trout (Oncorhynchus mykiss).

Evolution of a pigmentation gene, the melanocortin-1 receptor, in primates.

Relationships between heterozygosity, allelic distance (d2), and reproductive traits in chinook salmon, Oncorhynchus tshawytscha

Investigation of the role of the agouti signaling protein gene (ASIP) in coat color evolution in primates.

High Diversity in Functional Properties of Melanocortin 1 Receptor (MC1R) in Divergent Primate Species Is More Strongly Associated with Phylogeny than Coat Color