Harvest and decimation affect genetic drift and the effective population size in wild reindeer

Harvesting and culling are methods used to monitor and manage wildlife diseases. An important consequence of these practices is a change in the genetic dynamics of affected populations that may threaten their long-term viability. The effective population size (N e) is a fundamental parameter for describing such changes as it determines the amount of genetic drift in a population. Here, we estimate N e of a harvested wild reindeer population in Norway. Then we use simulations to investigate the genetic consequences of management efforts for handling a recent spread of chronic wasting disease, including increased adult male harvest and population decimation. The N e/N ratio in this population was found to be 0.124 at the end of the study period, compared to 0.239 in the preceding 14 years period. The difference was caused by increased harvest rates with a high proportion of adult males (older than 2.5 years) being shot (15.2% in 2005-2018 and 44.8% in 2021). Increased harvest rates decreased N e in the simulations, but less sex biased harvest strategies had a lower negative impact. For harvest strategies that yield stable population dynamics, shifting the harvest from calves to adult males and females increased N e. Population decimation always resulted in decreased genetic variation in the population, with higher loss of heterozygosity and rare alleles with more severe decimation or longer periods of low population size. A very high proportion of males in the harvest had the most severe consequences for the loss of genetic variation. This study clearly shows how the effects of harvest strategies and changes in population size interact to determine the genetic drift of a managed population. The long-term genetic viability of wildlife populations subject to a disease will also depend on population impacts of the disease and how these interact with management actions.

Spatial variation in the evolutionary potential and constraints of basal metabolic rate and body mass in a wild bird

An organism's energy budget is strongly related to resource consumption, performance, and fitness. Hence, understanding the evolution of key energetic traits, such as basal metabolic rate (BMR), in natural populations is central for understanding life-history evolution and ecological processes. Here we used quantitative genetic analyses to study evolutionary potential of BMR in two insular populations of the house sparrow (Passer domesticus). We obtained measurements of BMR and body mass (M_b ) from 911 house sparrows on the islands of Leka and Vega along the coast of Norway. These two populations were the source populations for translocations to create an additional third, admixed 'common garden' population in 2012. With the use of a novel genetic group animal model concomitant with a genetically determined pedigree, we differentiate genetic and environmental sources of variation, thereby providing insight into the effects of spatial population structure on evolutionary potential. We found that the evolutionary potential of BMR was similar in the two source populations, whereas the Vega population had a somewhat higher evolutionary potential of M_b than the Leka population. BMR was genetically correlated with M_b in both populations, and the conditional evolutionary potential of BMR (independent of body mass) was 41% (Leka) and 53% (Vega) lower than unconditional estimates. Overall, our results show that there is potential for BMR to evolve independently of M_b , but that selection on BMR and/or M_b may have different evolutionary consequences in different populations of the same species.

Genetic architecture and heritability of early-life telomere length in a wild passerine

Early-life telomere length (TL) is associated with fitness in a range of organisms. Little is known about the genetic basis of variation in TL in wild animal populations, but to understand the evolutionary and ecological significance of TL it is important to quantify the relative importance of genetic and environmental variation in TL. In this study, we measured TL in 2746 house sparrow nestlings sampled across 20 years and used an animal model to show that there is a small heritable component of early-life TL (h²  = 0.04). Variation in TL among individuals was mainly driven by environmental (annual) variance, but also brood and parental effects. Parent-offspring regressions showed a large maternal inheritance component in TL ( h maternal 2  = 0.44), but no paternal inheritance. We did not find evidence for a negative genetic correlation underlying the observed negative phenotypic correlation between TL and structural body size. Thus, TL may evolve independently of body size and the negative phenotypic correlation is likely to be caused by nongenetic environmental effects. We further used genome-wide association analysis to identify genomic regions associated with TL variation. We identified several putative genes underlying TL variation; these have been inferred to be involved in oxidative stress, cellular growth, skeletal development, cell differentiation and tumorigenesis in other species. Together, our results show that TL has a low heritability and is a polygenic trait strongly affected by environmental conditions in a free-living bird.

Artificial size selection experiment reveals telomere length dynamics and fitness consequences in a wild passerine

Telomere dynamics could underlie life-history trade-offs among growth, size and longevity, but our ability to quantify such processes in natural, unmanipulated populations is limited. We investigated how 4 years of artificial selection for either larger or smaller tarsus length, a proxy for body size, affected early-life telomere length (TL) and several components of fitness in two insular populations of wild house sparrows over a study period of 11 years. The artificial selection was expected to shift the populations away from their optimal body size and increase the phenotypic variance in body size. Artificial selection for larger individuals caused TL to decrease, but there was little evidence that TL increased when selecting for smaller individuals. There was a negative correlation between nestling TL and tarsus length under both selection regimes. Males had longer telomeres than females and there was a negative effect of harsh weather on TL. We then investigated whether changes in TL might underpin fitness effects due to the deviation from the optimal body size. Mortality analyses indicated disruptive selection on TL because both short and long early-life telomeres tended to be associated with the lowest mortality rates. In addition, there was a tendency for a negative association between TL and annual reproductive success, but only in the population where body size was increased experimentally. Our results suggest that natural selection for optimal body size in the wild may be associated with changes in TL during growth, which is known to be linked to longevity in some bird species.

Causes and consequences of variation in early-life telomere length in a bird metapopulation

Environmental conditions during early-life development can have lasting effects shaping individual heterogeneity in fitness and fitness-related traits. The length of telomeres, the DNA sequences protecting chromosome ends, may be affected by early-life conditions, and telomere length (TL) has been associated with individual performance within some wild animal populations. Thus, knowledge of the mechanisms that generate variation in TL, and the relationship between TL and fitness, is important in understanding the role of telomeres in ecology and life-history evolution. Here, we investigate how environmental conditions and morphological traits are associated with early-life blood TL and if TL predicts natal dispersal probability or components of fitness in 2746 wild house sparrow (Passer domesticus) nestlings from two populations sampled across 20 years (1994-2013). We retrieved weather data and we monitored population fluctuations, individual survival, and reproductive output using field observations and genetic pedigrees. We found a negative effect of population density on TL, but only in one of the populations. There was a curvilinear association between TL and the maximum daily North Atlantic Oscillation index during incubation, suggesting that there are optimal weather conditions that result in the longest TL. Dispersers tended to have shorter telomeres than non-dispersers. TL did not predict survival, but we found a tendency for individuals with short telomeres to have higher annual reproductive success. Our study showed how early-life TL is shaped by effects of growth, weather conditions, and population density, supporting that environmental stressors negatively affect TL in wild populations. In addition, shorter telomeres may be associated with a faster pace-of-life, as individuals with higher dispersal rates and annual reproduction tended to have shorter early-life TL.

Density-dependent selection and the maintenance of colour polymorphism in barn owls

The capacity of natural selection to generate adaptive changes is (according to the fundamental theorem of natural selection) proportional to the additive genetic variance in fitness. In spite of its importance for development of new adaptations to a changing environment, processes affecting the magnitude of the genetic variance in fitness-related traits are poorly understood. Here, we show that the red-white colour polymorphism in female barn owls is subject to density-dependent selection at the phenotypic and genotypic level. The diallelic melanocortin-1 receptor gene explained a large amount of the phenotypic variance in reddish coloration in the females ([Formula: see text]). Red individuals (RR genotype) were selected for at low densities, while white individuals (WW genotype) were favoured at high densities and were less sensitive to changes in density. We show that this density-dependent selection favours white individuals and predicts fixation of the white allele in this population at longer time scales without immigration or other selective forces. Still, fluctuating population density will cause selection to fluctuate and periodically favour red individuals. These results suggest how balancing selection caused by fluctuations in population density can be a general mechanism affecting the level of additive genetic variance in natural populations.

Fur colour in the Arctic fox: genetic architecture and consequences for fitness

Genome-wide association studies provide good opportunities for studying the genetic basis of adaptive traits in wild populations. Yet, previous studies often failed to identify major effect genes. In this study, we used high-density single nucleotide polymorphism and individual fitness data from a wild non-model species. Using a whole-genome approach, we identified the MC1R gene as the sole causal gene underlying Arctic fox Vulpes lagopus fur colour. Further, we showed the adaptive importance of fur colour genotypes through measures of fitness that link ecological and evolutionary processes. We found a tendency for blue foxes that are heterozygous at the fur colour locus to have higher fitness than homozygous white foxes. The effect of genotype on fitness was independent of winter duration but varied with prey availability, with the strongest effect in years of increasing rodent populations. MC1R is located in a genomic region with high gene density, and we discuss the potential for indirect selection through linkage and pleiotropy. Our study shows that whole-genome analyses can be successfully applied to wild species and identify major effect genes underlying adaptive traits. Furthermore, we show how this approach can be used to identify knowledge gaps in our understanding of interactions between ecology and evolution.

Variation in generation time reveals density regulation as an important driver of pace of life in a bird metapopulation

Generation time determines the pace of key demographic and evolutionary processes. Quantified as the weighted mean age at reproduction, it can be studied as a life-history trait that varies within and among populations and may evolve in response to ecological conditions. We combined quantitative genetic analyses with age- and density-dependent models to study generation time variation in a bird metapopulation. Generation time was heritable, and males had longer generation times than females. Individuals with longer generation times had greater lifetime reproductive success but not a higher expected population growth rate. Density regulation acted on recruit production, suggesting that longer generation times should be favoured when populations are closer to carrying capacity. Furthermore, generation times were shorter when populations were growing and longer when populations were closer to equilibrium or declining. These results support classic theory predicting that density regulation is an important driver of the pace of life-history strategies.

Dispersal in a house sparrow metapopulation: An integrative case study of genetic assignment calibrated with ecological data and pedigree information

Dispersal has a crucial role determining ecoevolutionary dynamics through both gene flow and population size regulation. However, to study dispersal and its consequences, one must distinguish immigrants from residents. Dispersers can be identified using telemetry, capture-mark-recapture (CMR) methods, or genetic assignment methods. All of these methods have disadvantages, such as high costs and substantial field efforts needed for telemetry and CMR surveys, and adequate genetic distance required in genetic assignment. In this study, we used genome-wide 200K Single Nucleotide Polymorphism data and two different genetic assignment approaches (GSI_SIM, Bayesian framework; BONE, network-based estimation) to identify the dispersers in a house sparrow (Passer domesticus) metapopulation sampled over 16 years. Our results showed higher assignment accuracy with BONE. Hence, we proceeded to diagnose potential sources of errors in the assignment results from the BONE method due to variation in levels of interpopulation genetic differentiation, intrapopulation genetic variation and sample size. We show that assignment accuracy is high even at low levels of genetic differentiation and that it increases with the proportion of a population that has been sampled. Finally, we highlight that dispersal studies integrating both ecological and genetic data provide robust assessments of the dispersal patterns in natural populations.

Fluctuating optimum and temporally variable selection on breeding date in birds and mammals

Temporal variation in natural selection is predicted to strongly impact the evolution and demography of natural populations, with consequences for the rate of adaptation, evolution of plasticity, and extinction risk. Most of the theory underlying these predictions assumes a moving optimum phenotype, with predictions expressed in terms of the temporal variance and autocorrelation of this optimum. However, empirical studies seldom estimate patterns of fluctuations of an optimum phenotype, precluding further progress in connecting theory with observations. To bridge this gap, we assess the evidence for temporal variation in selection on breeding date by modeling a fitness function with a fluctuating optimum, across 39 populations of 21 wild animals, one of the largest compilations of long-term datasets with individual measurements of trait and fitness components. We find compelling evidence for fluctuations in the fitness function, causing temporal variation in the magnitude, but not the direction of selection. However, fluctuations of the optimum phenotype need not directly translate into variation in selection gradients, because their impact can be buffered by partial tracking of the optimum by the mean phenotype. Analyzing individuals that reproduce in consecutive years, we find that plastic changes track movements of the optimum phenotype across years, especially in bird species, reducing temporal variation in directional selection. This suggests that phenological plasticity has evolved to cope with fluctuations in the optimum, despite their currently modest contribution to variation in selection.

Stabilizing selection and adaptive evolution in a combination of two traits in an arctic ungulate

Stabilizing selection is thought to be common in wild populations and act as one of the main evolutionary mechanisms, which constrain phenotypic variation. When multiple traits interact to create a combined phenotype, correlational selection may be an important process driving adaptive evolution. Here, we report on phenotypic selection and evolutionary changes in two natal traits in a semidomestic population of reindeer (Rangifer tarandus) in northern Finland. The population has been closely monitored since 1969, and detailed data have been collected on individuals since they were born. Over the length of the study period (1969-2015), we found directional and stabilizing selection toward a combination of earlier birth date and heavier birth mass with an intermediate optimum along the major axis of the selection surface. In addition, we demonstrate significant changes in mean traits toward earlier birth date and heavier birth mass, with corresponding genetic changes in breeding values during the study period. Our results demonstrate evolutionary changes in a combination of two traits, which agree closely with estimated patterns of phenotypic selection. Knowledge of the selective surface for combinations of genetically correlated traits are vital to predict how population mean phenotypes and fitness are affected when environments change.

Insights into the genetic architecture of morphological traits in two passerine bird species

Knowledge about the underlying genetic architecture of phenotypic traits is needed to understand and predict evolutionary dynamics. The number of causal loci, magnitude of the effects and location in the genome are, however, still largely unknown. Here, we use genome-wide single-nucleotide polymorphism (SNP) data from two large-scale data sets on house sparrows and collared flycatchers to examine the genetic architecture of different morphological traits (tarsus length, wing length, body mass, bill depth, bill length, total and visible badge size and white wing patches). Genomic heritabilities were estimated using relatedness calculated from SNPs. The proportion of variance captured by the SNPs (SNP-based heritability) was lower in house sparrows compared with collared flycatchers, as expected given marker density (6348 SNPs in house sparrows versus 38 689 SNPs in collared flycatchers). Indeed, after downsampling to similar SNP density and sample size, this estimate was no longer markedly different between species. Chromosome-partitioning analyses demonstrated that the proportion of variance explained by each chromosome was significantly positively related to the chromosome size for some traits and, generally, that larger chromosomes tended to explain proportionally more variation than smaller chromosomes. Finally, we found two genome-wide significant associations with very small-effect sizes. One SNP on chromosome 20 was associated with bill length in house sparrows and explained 1.2% of phenotypic variation (V_P), and one SNP on chromosome 4 was associated with tarsus length in collared flycatchers (3% of V_P). Although we cannot exclude the possibility of undetected large-effect loci, our results indicate a polygenic basis for morphological traits.

Harvest-induced phenotypic selection in an island population of moose, Alces alces

Empirical evidence strongly indicates that human exploitation has frequently led to rapid evolutionary changes in wild populations, yet the mechanisms involved are often poorly understood. Here, we applied a recently developed demographic framework for analyzing selection to data from a 20-year study of a wild population of moose, Alces alces. In this population, a genetic pedigree has been established all the way back to founders. We demonstrate harvest-induced directional selection for delayed birth dates in males and reduced body mass as calf in females. During the study period, birth date was delayed by 0.81 days per year for both sexes, whereas no significant changes occurred in calf body mass. Quantitative genetic analyses indicated that both traits harbored significant additive genetic variance. These results show that selective harvesting can induce strong selection that oppose natural selection. This may cause evolution of less favorable phenotypes that become maladaptive once harvesting ceases.

On being the right size: increased body size is associated with reduced telomere length under natural conditions

Evolution of body size is likely to involve trade-offs between body size, growth rate and longevity. Within species, larger body size is associated with faster growth and ageing, and reduced longevity, but the cellular processes driving these relationships are poorly understood. One mechanism that might play a key role in determining optimal body size is the relationship between body size and telomere dynamics. However, we know little about how telomere length is affected when selection for larger size is imposed in natural populations. We report here on the relationship between structural body size and telomere length in wild house sparrows at the beginning and end of a selection regime for larger parent size that was imposed for 4 years in an isolated population of house sparrows. A negative relationship between fledgling size and telomere length was present at the start of the selection; this was extended when fledgling size increased under the selection regime, demonstrating a persistent covariance between structural size and telomere length. Changes in telomere dynamics, either as a correlated trait or a consequence of larger size, could reduce potential longevity and the consequent trade-offs could thereby play an important role in the evolution of optimal body size.

Estimating phenotypic selection in age-structured populations by removing transient fluctuations

An extension of the selection differential in the Robertson-Price equation for the mean phenotype in an age-structured population is provided. Temporal changes in the mean phenotype caused by transient fluctuations in the age-distribution and variation in mean phenotype among age classes, which can mistakenly be interpreted as selection, will disappear if reproductive value weighting is applied. Changes in any weighted mean phenotype in an age-structured population may be decomposed into between- and within-age class components. Using reproductive value weighting the between-age class component becomes pure noise, generated by previous genetic drift or fluctuating selection. This component, which we call transient quasi-selection, can therefore be omitted when estimating age-specific selection on fecundity or viability within age classes. The final response can be computed at the time of selection, but can not be observed until lifetime reproduction is realized unless the heritability is one. The generality of these results is illustrated further by our derivation of the selection differential for the continuous time age-structured model with general age-dependent weights. A simple simulation example as well as estimation of selection components in a house sparrow population illustrates the applicability of the theory to analyze selection on the mean phenotype in fluctuating age-structured populations.

Correlates of egg size variation in a population of house sparrow Passer domesticus

Propagule size represents an important life-history trait under maternal control. Despite a positive relationship between propagule size and components of fitness, propagule size displays tremendous amounts of variation which causes are poorly understood within natural populations. With a study of a house sparrows Passer domesticus, we investigate maternal and environmental correlates of egg size, quantify variation in egg size within and between females and broods, and estimate heritability. Egg size had a curvilinear relationship with clutch size and decreased significantly in subsequent broods within seasons. Furthermore, egg size increased with maternal body mass, was positively affected by spring temperatures and curvilinearly related to temperature during the 2 weeks prior to egg laying. Some 46.4 % of variation in egg size was due to differences between females, and 21.9 % was explained by variation between broods by the same female. The heritability of egg size was low (h (2) = 0.26) compared to estimates from other studies (h (2) > 0.6). The present study challenges the recent idea that egg size is an inflexible maternal characteristic with very high additive genetic variance, and suggests that females are subject to both intrinsic and extrinsic constraints prior to and during egg formation, leading to the observed plasticity in egg size. In a general sense, propagule size could be expected to be both limited by and adaptively adjusted in accordance to prevailing environmental conditions.