Improving production efficiency and minimizing the environmental impact of dairy farming are 2 important goals of the dairy industry. Achieving these objectives requires improving the feed-to-milk conversion efficiency. One way to achieve this goal is through genetic selection. However, measuring feed efficiency in commercial herds is currently not feasible. As such, we conducted a study to evaluate the genetic accuracy of various selection indices derived from Fourier transform mid-infrared (FTIR)-spectra or milk composition. We use 7,793 weekly records on 537 genotyped cows (78,964 SNPs), with information on residual feed intake (RFI), and FTIR-spectra. We fitted various types of selection indexes using the complete FTIR-spectra of milk samples. The estimated heritability of RFI was 0.12 ± 0.02. The accuracy of indirect selection using the FTIR-spectra was maximized using a principal components selection index (0.16 ± 0.07), followed by a Lasso-type penalized selection index (0.14 ± 0.06). We determined that an index based on milk spectral data recorded on ~25 daughters produced a progeny average with an accuracy comparable to direct phenotypic selection for RFI. We conclude that indirect selection for RFI using FTIR-spectra data can be effective for sires with progeny; however, future studies with a larger sample size are needed to validate these results.

The evolution of suppressed recombination between sex chromosomes is widely hypothesized to be driven by sexually antagonistic selection (SA), where tighter linkage between the sex-determining gene(s) and nearby SA loci is favored when it couples male-beneficial alleles to the proto-Y chromosome, and female-beneficial alleles to the proto-X. Although difficult to test empirically, the SA selection hypothesis overshadows several alternatives, including an incomplete but often-repeated \"sheltering\" hypothesis which suggests that expansion of the sex-linked region (SLR) reduces the homozygous expression of deleterious mutations at selected loci. Here, we use population genetic models to evaluate the consequences of partially recessive deleterious mutational variation for the evolution of otherwise neutral chromosomal inversions expanding the SLR on proto-Y chromosomes. Both autosomal and SLR-expanding inversions face a race against time: lightly-loaded inversions are initially beneficial, but eventually become deleterious as they accumulate new mutations, after which their chances of fixing become negligible. In contrast, initially unloaded inversions eventually become neutral as their deleterious load reaches the same equilibrium as non-inverted haplotypes. Despite the differences in inheritance and indirect selection, SLR-expanding inversions exhibit similar evolutionary dynamics to autosomal inversions over many biologically plausible parameter conditions. Differences emerge when the population average mutation load is quite high; in this case large autosomal inversions that are lucky enough to be mutation-free can rise to intermediate to high frequencies where selection in homozygotes becomes important (Y-linked inversions never appear as homozygous karyotypes); conditions requiring either high mutation rates, highly recessive deleterious mutations, weak selection, or a combination thereof.

Genetic changes that enabled the evolution of eusociality have long captivated biologists. More recently, attention has focussed on the consequences of eusociality on genome evolution. Studies have reported higher molecular evolutionary rates in eusocial hymenopteran insects compared with their solitary relatives. To investigate the genomic consequences of eusociality in termites, we analysed nine genomes, including newly sequenced genomes from three non-eusocial cockroaches. Using a phylogenomic approach, we found that termite genomes have experienced lower rates of synonymous substitutions than those of cockroaches, possibly as a result of longer generation times. We identified higher rates of non-synonymous substitutions in termite genomes than in cockroach genomes, and identified pervasive relaxed selection in the former (24-31% of the genes analysed) compared with the latter (2-4%). We infer that this is due to reductions in effective population size, rather than gene-specific effects (e.g. indirect selection of caste-biased genes). We found no obvious signature of increased genetic load in termites, and postulate efficient purging of deleterious alleles at the colony level. Additionally, we identified genomic adaptations that may underpin caste differentiation, such as genes involved in post-translational modifications. Our results provide insights into the evolution of termites and the genomic consequences of eusociality more broadly.

Understanding the influence of social interactions on individual fitness is key to improving our predictions of phenotypic evolution. However, we often overlook the different components of selection regimes arising from interactions among organisms, including social, correlational, and indirect selection. This is due to the challenging sampling efforts required in natural populations to measure phenotypes expressed during interactions and individual fitness. Furthermore, behaviours are crucial in mediating social interactions, yet few studies have explicitly quantified these selection components on behavioural traits. In this study, we capitalize on an online multiplayer video game as a source of extensive data recording direct social interactions among prey, where prey collaborate to escape a predator in realistic ecological settings. We estimate natural and social selection and their contribution to total selection on behavioural traits mediating competition, cooperation, and predator-prey interactions. Behaviours of other prey in a group impact an individual\'s survival, and thus are under social selection. Depending on whether selection pressures on behaviours are synergistic or conflicting, social interactions enhance or mitigate the strength of natural selection, although natural selection remains the main driving force. Indirect selection through correlations among traits also contributed to the total selection. Thus, failing to account for the effects of social interactions and indirect selection would lead to a misestimation of the total selection acting on traits. Dissecting the contribution of each component to the total selection differential allowed us to investigate the causal mechanisms relating behaviour to fitness and quantify the importance of the behaviours of conspecifics as agents of selection. Our study emphasizes that social interactions generate complex selective regimes even in a relatively simple ecological environment.

The growth of Nelore cattle was analysed considering the following performance parameters; the effect of the calving order of cows on the phenotypic expression of birth weight (BW), average daily gain from birth to weaning (BWG), and weaning weight (WW), the estimated genetic parameters for the traits, including the covariance components between direct and maternal genetic effects. Genetic trends and correlated responses were also obtained for the studied traits. The calving order of cows, as well as other fixed effects used to obtain the adjusted phenotypic means, were statistically significant (p < 0.001) for studied traits. Direct heritability was estimated at 0.24 ± 0.01 (BW), 0.15 ± 0.01 (BWG), and 0.18 ± 0.01 (WW), while maternal heritability was 0.06 ± 0.01 (BW), 0.12 ± 0.01 (BWG), and 0.11 ± 0.01 (WW). The correlations between direct and maternal effects within the same trait were negligible. Moderate to higher direct genetic correlations (ranging from 0.54 ± 0.04 to 0.98 ± 0.01) and maternal genetic correlations (ranging from 0.34 ± 0.09 to 0.99 ± 0.002) were estimated between the studied traits. Unlike direct genetic effects, there was no significant change in maternal genetic effects over time (p > 0.05). These results indicated the need for revising selection indexes for enhancing maternal ability. Correlated responses were generally lower compared to direct responses, except for BWG. The selection for BWG, considering the maternal genetic effect, would be more efficient to improve maternal ability of the cows for pre-weaning growth in relation to selection for WW. Our results found that direct genetic merit improves pre-weaning weight and this trait can be incorporated into the breeding goal as reflected in the WW.

Fisher proposed that female preference for mates with extreme traits could evolve as an essentially arbitrary outcome of a self-reinforcing process. Although Fisher\'s runaway has been shown to be a theoretical possibility, it is not clear whether it occurs in real populations, in part because existing models express the necessary conditions in terms of parameters that would be nearly impossible to estimate in the wild. Here, I reformulate models of the runaway in terms of two estimable parameters, the heritability and phenotypic variance of realized mate choices. Higher values of both quantities make the runaway more likely. In the most realistic model considered, in which mate choices are based on a mixture of absolute and relative criteria, a runaway cannot occur unless mate choice increases the variance of the male trait, which seems incompatible with the strong directional mating preferences typically observed in polygynous species. Even in the most favourable case for the runaway, purely relative preference without direct selection on preference, a substantial heritability of realized mate choices would be required if there is moderately strong stabilizing selection on the male trait. These results cast some doubt on whether the runaway is a plausible outcome in natural populations.

As selection acts on multivariate phenotypes, the evolution of traits within populations not only depends on the genetic basis of each trait, but also on the genetic relationships among traits. As metabolic rate is often related to vital traits such as growth, physiology and behaviour, its variation and evolution is expected to have important repercussions on individual fitness. However, the majority of the correlations between metabolic rate and other traits has been based on phenotypic correlations, while genetic correlations, basis for indirect selection and evolution, have been overlooked. Using a case study, we explore the importance of properly estimating genetic correlations to understand and predict evolution of multivariate phenotypes. We show that selection on metabolic traits could result in indirect selection mainly on growth-related traits, owing to strong genetic correlations, but not on swimming or risk-taking and sociability behaviour even if they covary phenotypically. While phenotypic correlation can inform about genetic correlation direction, caution is needed in predicting the magnitude of genetic correlation. Therefore, even though phenotypic correlations among physiological and behavioural traits could be useful, deriving evolutionary conclusions based purely on them is not robust. In short, proper estimation of genetic correlations is needed when predicting evolutionary consequences. This article is part of the theme issue \'The evolutionary significance of variation in metabolic rates\'.

Because the universe of possible DNA sequences is inconceivably vast, organisms have evolved mechanisms for exploring DNA sequence space while substantially reducing the hazard that would otherwise accrue to any process of random, accidental mutation. One such mechanism is meiotic recombination. Although sexual reproduction imposes a seemingly paradoxical 50% cost to fitness, sex evidently prevails because this cost is outweighed by the advantage of equipping offspring with genetic variation to accommodate environmental vicissitudes. The potential adaptive utility of additional mechanisms for producing genetic variation has long been obscured by a presumption that the vast majority of mutations are deleterious. Perhaps surprisingly, the probability for adaptive variation can be increased by several mechanisms that generate mutations abundantly. Such mechanisms, here called \'mutation protocols\', implement implicit \'constraints that deconstrain\'. Like meiotic recombination, they produce genetic variation in forms that minimize potential for harm while providing a reasonably high probability for benefit. One example is replication slippage of simple sequence repeats (SSRs); this process yields abundant, reversible mutations, typically with small quantitative effect on phenotype. This enables SSRs to function as adjustable \'tuning knobs\'. There exists a clear pathway for SSRs to be shaped through indirect selection favouring their implicit tuning-knob protocol. Several other molecular mechanisms comprise probable components of additional mutation protocols. Biologists might plausibly regard such mechanisms of mutation not primarily as sources of deleterious genetic mistakes but also as potentially adaptive processes for \'exploring\' DNA sequence space.

Pyrethroids are primarily used for mosquito control in Korea. However, high frequencies of mutations conferring resistance to not only pyrethroids but also to other insecticides have been found in mosquito populations. This study aimed to examine the hypothesis that insecticides used outside of public health may play a role in selection. Briefly, the resistance mutation frequencies to three insecticide groups (pyrethroids, organophosphates, and cyclodienes) were estimated in two representative groups of mosquito species (Anopheles Hyrcanus Group and Culex pipiens complex). The relationship between these frequencies and the land-use status of the collection sites was investigated through multiple regression analysis. In the Anopheles Hyrcanus Group, the frequencies of both ace1 (organophosphate resistance) and rdl (cyclodiene resistance) mutations were positively correlated with \'proximity to golf course\', possibly be due to the insecticides used for turf maintenance. They also showed positive correlations with field area and rice paddy area, respectively, suggesting the role of agricultural insecticides in the selection of these resistance traits. For the Cx. pipiens complex, the kdr (pyrethroid resistance), ace1, and rdl mutations were positively correlated with the residential area, field, and rice paddy, respectively. Therefore, pyrethroids used for public health could serve as a direct source of resistance selection pressure against kdr, whereas non-public health insecticides may pose primary selection pressure against the ace1 and rdl traits. The current findings suggest that the insecticides used in agriculture and the golf industry play a significant role in mosquito selection, despite variations in the extent of indirect selection pressure according to the mosquito groups and insecticide classes.

Sexual selection has a rich history of mathematical models that consider why preferences favor one trait phenotype over another (for population genetic models) or what specific trait value is preferred (for quantitative genetic models). Less common is exploration of the evolution of choosiness or preference strength: i.e., by how much a trait is preferred. We examine both population and quantitative genetic models of the evolution of preferences, specifically developing \"baseline models\" of the evolution of preference strength during the Fisher process. Using a population genetic approach, we find selection for stronger and stronger preferences when trait variation is maintained by mutation. However, this force is quite weak and likely to be swamped by drift in moderately-sized populations. In a quantitative genetic model, unimodal preferences will generally not evolve to be increasingly strong without bounds when male traits are under stabilizing viability selection, but evolve to extreme values when viability selection is directional. Our results highlight that different shapes of fitness and preference functions lead to qualitatively different trajectories for preference strength evolution ranging from no evolution to extreme evolution of preference strength.