Phylogeography,population genetics and conservation of the European red deer Cervus elaphus

• 1 During the Last Glacial Maximum, European red deer Cervus elaphus occurred in refugia in Iberia/southern France, Italy, the Balkans and the Carpathians. Most of Europe, including large parts of the east and north‐east, is now inhabited by red deer from the western lineage. The eastern lineage is largely confined to south‐eastern Europe; a third lineage comprises Sardo‐Corsican and Barbary red deer.
• 2 Sardo‐Corsican, Barbary and Mesola red deer are genetically unique units. They exhibit low levels of genetic diversity and deserve particular protection, since conservation strategies should target genetic information.
• 3 Hybridization between sika Cervus nippon and red deer occurs rarely, but may lead to extensive introgression, particularly in parts of the British Isles. Further expansion of both species may lead to increased hybridization in continental Europe.
• 4 Although hunting has an impact on red deer gene pools, the main threat today is habitat fragmentation in human‐dominated landscapes. The resulting increase in genetic drift and inbreeding reduces variability in isolated populations and may lead to inbreeding depression. To support vital meta‐populations, migration corridors should be established.

     

Indirect genetic effects and the genetic bases of social dominance: evidence from cattle

Genetic studies of social behaviour have currently received new impetus from models including indirect genetic effects (IGEs) of social partners. This study aimed at investigating the contribution of conspecifics in social dominance, considered as response of dyadic interaction that is, winning (dominant individual) or losing (subordinate). A genetic correlation of −1 is expected between the attitude to win and the attitude to loose, and because a population always accounts for half winners and half losers, the heritability of the dominant status should be close to zero. Specifically, social dominance was studied in Aosta Chestnut and Aosta Black Pied (Bos taurus) breeds, alpine rustic cattle famous for traditional tournaments where pairs of cows assess dominant status in bloodless fights. The outcomes of 25 590 dyadic interactions performed by 8159 individuals in 11 years were analysed by applying a classical quantitative model and models including indirect effects. Data were analysed via Bayesian approach on a threshold trait. The assessment of variances revealed a genetic correlation of −0.976 between direct and indirect genetic components. The heritability measured on a liability scale was 0.122 for direct phenotype, but decreased to 0.014 when the total heritable variance (TBV) was considered. The trend of estimated breeding values showed that the total TBV was constant over the years, even though its direct component increased and the indirect part decreased. This result confirms the relevance of IGEs on social behaviour and the assumption that the mean individual social dominance cannot evolve within a population, due to the evolutionary constraints imposed by the ‘social environment''.     

Book review of evolutionary genetics: Concepts,analysis, and practice

Recent technological advances have expanded and increased the resolution of studies in evolutionary biology, creating a need for a modern textbook that highlights the latest developments in the field. Evolutionary Genetics: Concepts, Analysis, and Practice, by Glenn‐Peter Sætre and Mark Ravinet (2019), as well as the book's accompanying online tutorials, provide a clear, up‐to‐date, and enjoyable introduction to evolutionary biology and genetics that explains fundamental evolutionary concepts, illustrates recent exciting findings, and offers hands‐on experience in analysing and interpreting genomic data. The book's accessible nature and emphasis on developing practical skills make it a valuable resource for undergraduate courses on evolutionary biology.     

Genetic diversity, gene flow and drift in Bavarian red deer populations (Cervus elaphus)

The red deer (Cervus elaphus) populationof Bavaria in Southern Germany was severelyreduced during the 19th century due toover-hunting. The species has since recoveredwithin designated areas. Subsequent habitatfragmentation presumably has changed thegenetic structure of Bavarian red deer.In order to assess the genetic diversity, weanalysed samples obtained from nine differentBavarian and two adjacent (Thueringen andCzech-Republic) red deer populations,genotyping 19 microsatellite loci. Our analysesrevealed moderate and significant differencesin diversity. Referring to assignment tests,the genetic differentiation of Bavarian reddeer was sufficient to assign an individual'sorigin to the correct population at an averageof 91.6%. The correlation of genetic andgeographic distance matrices revealed noevidence for isolation by distance. Thecoalescent model analysis suggests that thegenetic structure used to be characterized by adrift–gene flow equilibrium and is nowinfluenced by drift and disruption of the geneflow. Only three of the examined populationsshowed a probability of less than 10% that twogenes within these populations share a commonancestor (F _IS-value). Twopopulations had high F _IS values,indicating the influence of drift.Additionally, the intrapopulation indicesrevealed a low variability in thesepopulations. The estimated effective populationsizes (N _e) were generally in thesame range as the actual population sizes. Theinbreeding rates, based on the estimated N _e, and the inbreeding coefficientssuggested that the Bavarian red deerpopulations are in a stable state.     

Estimating red deer Cervus elaphus populations: an analysis of variation and cost-effectiveness of counting methods

• 1 Different counting methods are currently used to estimate red deer populations in the open range in Scotland, but there are few data available to compare variation in estimates, or relative cost‐effectiveness.
• 2 While it is impossible to determine the accuracy of counts (as real numbers are unknown), variation within and between different methods can be measured by repeat counts of the same area within as short a period as possible.
• 3 This study aimed to quantify the variation observed from repeat counts using each of four methods (ground, helicopter, infrared helicopter and dung‐counting methods) at one of three study sites in late winters 2003, 2004 and 2005. Additional data from digital camera images of groups from counts in other areas of Scotland were also used to assess the accuracy of visual counts.
• 4 Coefficients of variation (CVs) within any method of between 5% and 16% were recorded, consistent with previous comparisons for red deer open range counts in Scotland. CVs were lowest for ground and helicopter counts. The infrequency of optimal conditions was likely to limit the applicability of infrared counts in Scotland.
• 5 In terms of cost‐effectiveness, helicopter counting was the least labour‐intensive, with costs of other techniques depending on the availability of existing manpower as an overhead cost.
• 6 It is concluded that helicopter counts are most likely to minimize errors while maximizing cost‐efficiency. Accuracy can be improved by the use of digital photography for counting larger deer groups. Estimates are likely to be improved further by increasing the frequency of counts and using the same methods, counters and routes for repeat counts.

     

Repeatability of size and fluctuating asymmetry of antler characteristics in red deer (Cervus elaphus) during ontogeny

Fluctuating asymmetry (FA) has been suggested as a measure of the sensitivity of development to a wide array of genetic and environmental stresses. It has been also suggested that antlers in red deer could be important during social and rutting displays. We used antler measurements of 51 males that were measured over subsequent seasons, from 3–8 years of age, and analysed three antler traits: antler weight, length, and the number of antler tines (antler size). We calculated absolute and relative FA. All three size traits were highly significantly intercorrelated. By contrast to this, the FA of the three traits, did not show such relationships. With increasing age, antler size and FA also increased. When testing the repeatability of FA and antler size, there was a principal difference in the pattern between FA and antler size, with the latter being much more consistent than the former. This suggests that antler size, not FA, may be a good predictor of the bearer's quality in mate selection. This fits well with the good-genes hypothesis that the development of extravagant secondary sexual characters can be an honest advertisement of heritable male quality.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 91 , 215–226.     

Variation of some serum proteins in red deer, Cervus elaphus L

Various electrophoretic techniques, immunoblotting and inhibitions of trypsin and chymotrypsin were used to study the variability of serum proteins in farmed red deer, Cervus elaphus L., of Czechoslovakian origin. Easily interpretable polymorphisms were observed in transferrin (variants A, B1, B2, C) and vitamin D binding protein, GC (variants D, F, I, S). Great variability was observed in the protease inhibitors PI2, PI3, PI4, PI5, and PI8 and in unidentified zones in the vicinity of albumin, but no genetical or physiological interpretation for this variability is yet available. Haemopexin, alpha 1 glycoprotein, protease inhibitors PI1, PI6 and PI7 were monomorphic.     

Antler size and fluctuating asymmetry in red deer (Cervus elaphus) stags and probability of becoming a harem holder in rut

Red deer hinds play a significant role in selecting stags for mating. We tested the hypotheses that in red deer ( Cervus elaphus ) the probability of becoming a harem holder (and hence achieving reproductive success) occurs in stags bearing larger, branched antlers and showing low fluctuating asymmetry (FA). Eleven antler characteristics were measured; absolute and relative FA were calculated on 51 cast antler sets from 19 individually recognized stags. Probability of becoming a harem holder (PBHH) was originally analysed separately, i.e. for antler size and FA of each antler characteristic and calculated factors for both antler size and FA. If analysed separately, large antler size and low relative but high absolute FA increased PBHH. When we combined antler size and FA of antler characteristics in one model using antler size and FA factors, however, PBHH and achieving reproductive success were mainly dependent on increasing antler size and enhanced antler branching rather than on FA. We conclude that in contrast to antler size, FA is unlikely to play any significant role in sexual selection as an indicator of individual quality.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 87 , 59–68.     

Genetic polymorphism of erythrocyte diaphorase in red deer, Cervus elaphus L.

NADH diaphorase polymorphism was identified in red deer erythrocyte lysates using starch gel electrophoresis and activity staining. The inheritance of the polymorphism was consistent with predictions of autosomal codominant inheritance of two alleles DIA1F and DIAS. In New Zealand's four main feral red deer populations (n = 188) the DIA1F allele frequency ranged from 0.491 to 0.985. A sample of North American wapiti (n = 42) was monomorphic for the DIA1F allele.     

Social traits,social networks and evolutionary biology

The social environment is both an important agent of selection for most organisms, and an emergent property of their interactions. As an aggregation of interactions among members of a population, the social environment is a product of many sets of relationships and so can be represented as a network or matrix. Social network analysis in animals has focused on why these networks possess the structure they do, and whether individuals’ network traits, representing some aspect of their social phenotype, relate to their fitness. Meanwhile, quantitative geneticists have demonstrated that traits expressed in a social context can depend on the phenotypes and genotypes of interacting partners, leading to influences of the social environment on the traits and fitness of individuals and the evolutionary trajectories of populations. Therefore, both fields are investigating similar topics, yet have arrived at these points relatively independently. We review how these approaches are diverged, and yet how they retain clear parallelism and so strong potential for complementarity. This demonstrates that, despite separate bodies of theory, advances in one might inform the other. Techniques in network analysis for quantifying social phenotypes, and for identifying community structure, should be useful for those studying the relationship between individual behaviour and group‐level phenotypes. Entering social association matrices into quantitative genetic models may also reduce bias in heritability estimates, and allow the estimation of the influence of social connectedness on trait expression. Current methods for measuring natural selection in a social context explicitly account for the fact that a trait is not necessarily the property of a single individual, something the network approaches have not yet considered when relating network metrics to individual fitness. Harnessing evolutionary models that consider traits affected by genes in other individuals (i.e. indirect genetic effects) provides the potential to understand how entire networks of social interactions in populations influence phenotypes and predict how these traits may evolve. By theoretical integration of social network analysis and quantitative genetics, we hope to identify areas of compatibility and incompatibility and to direct research efforts towards the most promising areas. Continuing this synthesis could provide important insights into the evolution of traits expressed in a social context and the evolutionary consequences of complex and nuanced social phenotypes.     

The quantitative genetics of indirect genetic effects: a selective review of modelling issues

Indirect genetic effects (IGE) occur when the genotype of an individual affects the phenotypic trait value of another conspecific individual. IGEs can have profound effects on both the magnitude and the direction of response to selection. Models of inheritance and response to selection in traits subject to IGEs have been developed within two frameworks; a trait-based framework in which IGEs are specified as a direct consequence of individual trait values, and a variance-component framework in which phenotypic variance is decomposed into a direct and an indirect additive genetic component. This work is a selective review of the quantitative genetics of traits affected by IGEs, with a focus on modelling, estimation and interpretation issues. It includes a discussion on variance-component vs trait-based models of IGEs, a review of issues related to the estimation of IGEs from field data, including the estimation of the interaction coefficient Ψ (psi), and a discussion on the relevance of IGEs for response to selection in cases where the strength of interaction varies among pairs of individuals. An investigation of the trait-based model shows that the interaction coefficient Ψ may deviate considerably from the corresponding regression coefficient when feedback occurs. The increasing research effort devoted to IGEs suggests that they are a widespread phenomenon, probably particularly in natural populations and plants. Further work in this field should considerably broaden our understanding of the quantitative genetics of inheritance and response to selection in relation to the social organisation of populations.     

Indirect facilitation by a liana might explain the dominance of a small tree in a temperate forest

Aims Lianas are expected to influence composition, structure and functioning of forest systems due to unequal distribution across the potential set of host plants. However, our understanding of mechanisms associated with preferences for specific hosts is still limited, and so is our ability to discern between endogenous and exogenous forces driving forest dynamics in the long run. In this paper, we evaluated whether the dominant liana Hedera helix can indirectly contribute to the eventual dominance of the small multi-stemmed tree Corylus avellana in a remnant temperate forest in central Iberian Peninsula from comparatively reduced liana infestation on C. avellana relative to co-occurring woody species.Methods Through principal component analysis and co-occurrence analysis, we studied the distribution and spatial association between woody species and the liana H. helix. We analyzed the relationship between the number of species in a plot and the number of species infested by the liana to test the hypothesis that H. helix is a generalist liana. Through generalized linear mixed models, we tested the dynamic-multi-stemmed growth form of C. avellana as a plausible life strategy to withstand, in the long run, the liana infestation. In particular, we tested (i) the relationship between stem size and the probability of H. helix infestation including all the tree species within plots and (ii) the relationship between stem size and mortality as evidence of the stem turn over in the tree C. avellana .Important findings Our results indicate that H. helix and C. avellana significantly co-occur in mature stands of this remnant temperate forest where pioneer woody species are absent. Hedera helix severely infests all the woody species whenever stem size exceed ≈25 cm perimeter and there is physical contact at the base of the stem. This implies that all the trees in the community are potential hosts for H. helix. Mixed models indicate that both, infestation by H. helix and stem mortality, are positively related to C. avellana stem perimeter. Reduced long-term infestation of the liana by means of a multi-stemmed growth form with high stem turnover in C. avellana might be an advantage with respect to unipodial tree species. Thus, the liana-tree coexistence pattern may be interpreted as an indirect positive interaction that, contrary to previous findings, results here in species dominance instead of species coexistence.     

Genetic polymorphism of plasminogen and vitamin D binding protein in red deer (Cervus elaphus L.)

Genetic polymorphism was detected in the red deer (Cervus elaphus L.), plasma proteins, plasminogen (PLG) and vitamin D binding protein (GC) using antiserum to human proteins. The affinity of the antisera to deer plasma was less than 10% that of a human standard but they bound specifically to proteins of molecular weight expected for GC and PLG. Three codominant alleles of GC and five of PLG were observed. In a set 124 farmed deer calves and their parents, six calves had genotypes which were not consistent with the expectations of inheritance. Further inconsistencies were found when variation in isocitrate dehydrogenase (IDH) and transferrin (TRF) was examined. Using genetic models which included pedigree error parameters the data were shown to be consistent with genetic inheritance of all loci in a data set containing approximately 4.8% (SE 1.4%) parent-progeny pedigree mismatches. In samples from four deer populations representative of the red deer introduced to New Zealand the GC and PLG polymorphisms provided a probability of paternity exclusion (PE) of between 0.34 and 0.54 and when IDH and TRF were also included the PE was between 0.46 and 0.66. The four populations differed significantly in allele frequency, which supports historical evidence that they originate from separate introductions of small numbers of European red deer.     

Adaptation and the genetics of social behaviour

In recent years much progress has been made towards understanding the selective forces involved in the evolution of social behaviour including conflicts over reproduction among group members. Here, I argue that an important additional step necessary for advancing our understanding of the resolution of potential conflicts within insect societies is to consider the genetics of the behaviours involved. First, I discuss how epigenetic modifications of behaviour may affect conflict resolution within groups. Second, I review known natural polymorphisms of social organization to demonstrate that a lack of consideration of the genetic mechanisms involved may lead to erroneous explanations of the adaptive significance of behaviour. Third, I suggest that, on the basis of recent genetic studies of sexual conflict in Drosophila, it is necessary to reconsider the possibility of within-group manipulation by means of chemical substances (i.e. pheromones). Fourth, I address the issue of direct versus indirect genetic effects, which is of particular importance for the study of behaviour in social groups. Fifth, I discuss the issue of how a genetic influence on dominance hierarchies and reproductive division of labour can have secondary effects, for example in the evolution of promiscuity. Finally, because the same sets of genes (e.g. those implicated in chemical signalling and the responses that are triggered) may be used even in species as divergent as ants, cooperative breeding birds and primates, an integration of genetic mechanisms into the field of social evolution may also provide unifying ideas.     

Subspecies and body size allometry affect milk production and composition, and calf growth in red deer: comparison of Cervus elaphus hispanicus and Cervus elaphus scoticus

Studies comparing lactation in wild mammals have shown that maternal weight scales with offspring weight, milk production, or its energy. However, no study appears to have scaled milk composition with maternal or offspring weight. Although diet affects milk composition and production, their effects in biological studies have almost never seemed to be controlled. In this study, we compare two subspecies of red deer, Scottish deer, Cervus elaphus scoticus (10 lactations), and Iberian deer, Cervus elaphus hispanicus (14 lactations), kept under the same diet and housing to assess differences in hind and calf weights and their trends, milk production and composition, and their allometric relationships. Scottish hinds were heavier, and calf weight and gains were greater than Iberian ones, with greater milk production and milk protein content, but they did not differ in fat or lactose content. Calf birth weight, milk production, and protein content showed significant allometric relationships with maternal weight, but no relationship was found for fat, lactose, or any of these variables with calf birth weight. Protein content correlated with calf birth weight, and calf weight trend depended on milk protein production rather than on that of fat or lactose. Protein may be the most important milk component to explain growth and milk composition differences between closely related mammals.     

Phenotypic and genetic integration of personality and growth under competition in the sheepshead swordtail,Xiphophorus birchmanni

Competition for resources including food, physical space, and potential mates is a fundamental ecological process shaping variation in individual phenotype and fitness. The evolution of competitive ability, in particular social dominance, depends on genetic (co)variation among traits causal (e.g., behavior) or consequent (e.g., growth) to competitive outcomes. If dominance is heritable, it will generate both direct and indirect genetic effects (IGE) on resource‐dependent traits. The latter are expected to impose evolutionary constraint because winners necessarily gain resources at the expense of losers. We varied competition in a population of sheepshead swordtails, Xiphophorus birchmanni, to investigate effects on behavior, size, growth, and survival. We then applied quantitative genetic analyses to determine (i) whether competition leads to phenotypic and/or genetic integration of behavior with life history and (ii) the potential for IGE to constrain life history evolution. Size, growth, and survival were reduced at high competition. Male dominance was repeatable and dominant individuals show higher growth and survival. Additive genetic contributions to phenotypic covariance were significant, with the G matrix largely recapitulating phenotypic relationships. Social dominance has a low but significant heritability and is strongly genetically correlated with size and growth. Assuming causal dependence of growth on dominance, hidden IGE will therefore reduce evolutionary potential.     

Genetic structure and assignment tests demonstrate illegal translocation of red deer (Cervus elaphus) into a continuous population

Molecular forensic methods are being increasingly used to help enforce wildlife conservation laws. Using multilocus genotyping, illegal translocation of an animal can be demonstrated by excluding all potential source populations as an individual's population of origin. Here, we illustrate how this approach can be applied to a large continuous population by defining the population genetic structure and excluding suspect animals from each identified cluster. We aimed to test the hypothesis that recreational hunters had illegally introduced a group of red deer into a hunting area in Luxembourg. Reference samples were collected over a large area in order to test the possibility that the suspect individuals might be recent immigrants. Due to isolation-by-distance relationships in the data set, inferring the number of genetic clusters using Bayesian methods was not straightforward. Biologically meaningful clusters were only obtained by simultaneously analysing spatial and genetic information using the program baps 4.1. We inferred the presence of three genetic clusters in the study region. Using partial Mantel tests, we detected barriers to gene flow other than distance, probably created by a combination of urban areas, motorways and a river valley used for viticulture. The four focal animals could be excluded with a high certainty from the three genetic subpopulations and it was therefore likely that they had been released illegally.