Kinship,inbreeding and fine‐scale spatial structure influence gut microbiota in a hindgut‐fermenting tortoise

Herbivorous vertebrates rely on complex communities of mutualistic gut bacteria to facilitate the digestion of celluloses and hemicelluloses. Gut microbes are often convergent based on diet and gut morphology across a phylogenetically diverse group of mammals. However, little is known about microbial communities of herbivorous hindgut‐fermenting reptiles. Here, we investigate how factors at the individual level might constrain the composition of gut microbes in an obligate herbivorous reptile. Using multiplexed 16S rRNA gene sequencing, we characterized the faecal microbial community of a population of gopher tortoises (Gopherus polyphemus) and examined how age, genetic diversity, spatial structure and kinship influence differences among individuals. We recovered phylotypes associated with known cellulolytic function, including candidate phylum Termite Group 3, suggesting their importance for gopher tortoise digestion. Although host genetic structure did not explain variation in microbial composition and community structure, we found that fine‐scale spatial structure, inbreeding, degree of relatedness and possibly ontogeny shaped patterns of diversity in faecal microbiomes of gopher tortoises. Our findings corroborate widespread convergence of faecal‐associated microbes based on gut morphology and diet and demonstrate the role of spatial and demographic structure in driving differentiation of gut microbiota in natural populations.     

Re‐mating across years and intralineage polygyny are associated with greater than expected levels of inbreeding in wild red deer

The interaction between philopatry and nonrandom mating has important consequences for the genetic structure of populations, influencing co‐ancestry within social groups but also inbreeding. Here, using genetic paternity data, we describe mating patterns in a wild population of red deer (Cervus elaphus) which are associated with marked consequences for co‐ancestry and inbreeding in the population. Around a fifth of females mate with a male with whom they have mated previously, and further, females frequently mate with a male with whom a female relative has also mated (intralineage polygyny). Both of these phenomena occur more than expected under random mating. Using simulations, we demonstrate that temporal and spatial factors, as well as skew in male breeding success, are important in promoting both re‐mating behaviours and intralineage polygyny. However, the information modelled was not sufficient to explain the extent to which these behaviours occurred. We show that re‐mating and intralineage polygyny are associated with increased pairwise relatedness in the population and a rise in average inbreeding coefficients. In particular, the latter resulted from a correlation between male relatedness and rutting location, with related males being more likely to rut in proximity to one another. These patterns, alongside their consequences for the genetic structure of the population, have rarely been documented in wild polygynous mammals, yet they have important implications for our understanding of genetic structure, inbreeding avoidance and dispersal in such systems.     

Adaptation to monogamy influences parental care but not mating behavior in the burying beetle,Nicrophorus vespilloides

The mating system is expected to have an important influence on the evolution of mating and parenting behaviors. Although many studies have used experimental evolution to examine how mating behaviors evolve under different mating systems, this approach has seldom been used to study the evolution of parental care. We used experimental evolution to test whether adaptation to different mating systems involves changes in mating and parenting behaviors in populations of the burying beetle, Nicrophorus vespilloides. We maintained populations under monogamy or promiscuity for six generations. This manipulation had an immediate impact on reproductive performance and adult survival. Compared to monogamy, promiscuity reduced brood size and adult (particularly male) survival during breeding. After six generations of experimental evolution, there was no divergence between monogamous and promiscuous populations in mating behaviors. Parents from the promiscuous populations (especially males) displayed less care than parents from the monogamous populations. Our results are consistent with the hypothesis that male care will increase with the certainty of paternity. However, it appears that this change is not associated with a concurrent change in mating behaviors.     

Behavior and temperature modulate a thermoregulation–predation risk trade‐off in juvenile gopher tortoises

Ectotherms frequently thermoregulate behaviorally to improve physiological processes such as digestion and growth, but basking and other thermoregulatory activities can also increase predation risk. Organismal and environmental characteristics can, in some species, influence predation risk associated with thermoregulation and thereby relax or tighten constraints on thermoregulatory behavior, physiological performance, and, ultimately, life history traits. Providing one of the first such investigations in turtles, we examine whether behavior and thermal environment modulate a thermoregulation–predation risk trade‐off in juvenile gopher tortoises (Gopherus polyphemus). Young gopher tortoises experience very high predation pressure, and their declining species faces many challenges, including human‐induced increased shading of its environment. We hypothesized that in response to simulated predator approach, basking hatchling and juvenile tortoises would: (i) hide inside burrows; (ii) hide for shorter durations in cooler burrows presumably due to greater constraints on physiological performance; and (iii) spend greater time at the surface following disturbance in cool environments because individuals would need to bask more to maintain preferred body temperatures. Basking tortoises always hid inside burrows when approached and exhibited very long flight initiation distances ( = 45 m) that increased with age/size. Individuals fled into burrows even when it was not possible for them to see the approaching researcher, suggesting the use of vibrations (aerial/ground) to detect potential predators and a possible antipredator function for exceptionally large otoliths characteristic of the species. Tortoises hid for short durations ( = 18.3 min), especially in cool burrows, suggesting that they optimize hiding responses to balance physiological costs and antipredator benefits. Additionally, surface activity following disturbance consisted primarily of basking and correlated negatively with burrow temperature. These findings suggest that thermal environment influences predation risk in ectotherms whose surface activity is driven primarily by thermoregulatory requirements and highlight potential benefits of warm, well‐insolated habitats, such as endangered longleaf pine (Pinus palustris) ecosystems, for juvenile gopher tortoises.     

Estimating the inbreeding level and genetic relatedness in an isolated population of critically endangered Sichuan taimen (Hucho Bleekeri) using genome‐wide SNP markers

Sichuan taimen (Hucho bleekeri) is critically endangered fish listed in The Red List of Threatened Species compiled by the International Union for Conservation of Nature (IUCN). Specific locus amplified fragment sequencing (SLAF‐seq)‐based genotyping was performed for Sichuan taimen with 43 yearling individuals from three locations in Taibai River (a tributary of Yangtze River) that has been sequestered from its access to the ocean for more than 30 years since late 1980s. Applying the inbreeding level and genetic relatedness estimation using 15,396 genome‐wide SNP markers, we found that the inbreeding level of this whole isolated population was at a low level (2.6 × 10^?3 ± 0.079), and the means of coancestry coefficients within and between the three sampling locations were all very low (close to 0), too. Genomic differentiation was negatively correlated with the geographical distances between the sampling locations (p < .001), and the 43 individuals could be considered as genetically independent two groups. The low levels of genomic inbreeding and relatedness indicated a relatively large number of sexually mature individuals were involved in reproduction in Taibai River. This study suggested a genomic‐relatedness‐guided breeding and conservation strategy for wild fish species without pedigree information records.     

The combined effects of pre‐ and post‐copulatory processes are masking sexual conflict over mating rate in Gerris buenoi

In polygynandrous animals, post‐copulatory processes likely interfere with precopulatory sexual selection. In water striders, sexual conflict over mating rate and post‐copulatory processes are well documented, but their combined effect on reproductive success has seldom been investigated. We combine genetic parentage analyses and behavioural observations conducted in a competitive reproductive environment to investigate how pre‐ and post‐copulatory processes influence reproductive success in Gerris buenoi Kirkaldy. Precopulatory struggles had antagonistic effects on male and female reproductive success: efficiently gaining copulations was beneficial for males, whereas efficiently avoiding copulations was profitable for females. Also, high mating rates and an intermediate optimal resistance level of females supported the hypothesis of convenience polyandry. Contrary to formal predictions, high mating rates (i.e. the number of copulations) did not increase reproductive success in males or decrease reproductive success in females. Instead, the reproductive success of both sexes was higher when offspring were produced with several partners and when there were few unnecessary matings. Thus, male and female G. buenoi displayed different interests in reproduction, but post‐copulatory processes were masking the effects of copulatory mating success on reproductive success. Given the high mating rates observed, sperm competition could easily counter the effect of mating rates, perhaps in interaction with cryptic female choice and/or fecundity selection. Our study presents a complex but realistic overview of sexual selection forces at work in a model organism for the study of sexual conflict, confirming that insights are gained from investigating all episodes in the reproduction cycle of polygynandrous animals.     

A high‐quality pedigree and genetic markers both reveal inbreeding depression for quality but not survival in a cooperative mammal

Inbreeding depression, the reduced fitness of offspring of closely related parents, is commonplace in both captive and wild populations and has important consequences for conservation and mating system evolution. However, because of the difficulty of collecting pedigree and life‐history data from wild populations, relatively few studies have been able to compare inbreeding depression for traits at different points in the life cycle. Moreover, pedigrees give the expected proportion of the genome that is identical by descent (IBD_g) whereas in theory with enough molecular markers realized IBD_g can be quantified directly. We therefore investigated inbreeding depression for multiple life‐history traits in a wild population of banded mongooses using pedigree‐based inbreeding coefficients (f_ped) and standardized multilocus heterozygosity (sMLH) measured at 35–43 microsatellites. Within an information theoretic framework, we evaluated support for either f_ped or sMLH as inbreeding terms and used sequential regression to determine whether the residuals of sMLH on f_ped explain fitness variation above and beyond f_ped. We found no evidence of inbreeding depression for survival, either before or after nutritional independence. By contrast, inbreeding was negatively associated with two quality‐related traits, yearling body mass and annual male reproductive success. Yearling body mass was associated with f_ped but not sMLH, while male annual reproductive success was best explained by both f_ped and residual sMLH. Thus, our study not only uncovers variation in the extent to which different traits show inbreeding depression, but also reveals trait‐specific differences in the ability of pedigrees and molecular markers to explain fitness variation and suggests that for certain traits, genetic markers may capture variation in realized IBD_g above and beyond the pedigree expectation.     

Interplay between age‐based competitive asymmetries within the brood and direct competition between inbred and outbred offspring in a burying beetle

Theory suggests that intraspecific competition associated with direct competition between inbred and outbred individuals should be an important determinant of the severity of inbreeding depression. The reason is that, if outbred individuals are stronger competitors than inbred ones, direct competition should have a disproportionate effect on the fitness of inbred individuals. However, an individual's competitive ability is not only determined by its inbreeding status but also by competitive asymmetries that are independent of an individual's inbreeding status. When this is the case, such competitive asymmetries may shape the outcome of direct competition between inbred and outbred individuals. Here, we investigate the interface between age‐based competitive asymmetries within broods and direct competition between inbred and outbred offspring in the burying beetle Nicrophorus vespilloides. We found that inbred offspring had lower survival than outbred ones confirming that there was inbreeding depression. Furthermore, seniors (older larvae) grew to a larger size and had higher survival than juniors (younger larvae), confirming that there were age‐based competitive asymmetries. Nevertheless, there was no evidence that direct competition between inbred and outbred larvae exacerbated inbreeding depression, no evidence that inbreeding depression was more severe in juniors and no evidence that inbred juniors suffered disproportionately due to competition from outbred seniors. Our results suggest that direct competition between inbred and outbred individuals does not necessarily exacerbate inbreeding depression and that inbred individuals are not always more sensitive to poor and stressful conditions than outbred ones.     

Genetic isolation among mountains but not between stream types in a tropical high‐altitude mayfly

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Maternal predator‐exposure affects offspring size at birth but not telomere length in a live‐bearing fish

The perception of predation risk could affect prey phenotype both within and between generations (via parental effects). The response to predation risk could involve modifications in physiology, morphology, and behavior and can ultimately affect long‐term fitness. Among the possible modifications mediated by the exposure to predation risk, telomere length could be a proxy for investigating the response to predation risk both within and between generations, as telomeres can be significantly affected by environmental stress. Maternal exposure to the perception of predation risk can affect a variety of offspring traits but the effect on offspring telomere length has never been experimentally tested. Using a live‐bearing fish, the guppy (Poecilia reticulata), we tested if the perceived risk of predation could affect the telomere length of adult females directly and that of their offspring with a balanced experimental setup that allowed us to control for both maternal and paternal contribution. We exposed female guppies to the perception of predation risk during gestation using a combination of both visual and chemical cues and we then measured female telomere length after the exposure period. Maternal effects mediated by the exposure to predation risk were measured on offspring telomere length and body size at birth. Contrary to our predictions, we did not find a significant effect of predation‐exposure neither on female nor on offspring telomere length, but females exposed to predation risk produced smaller offspring at birth. We discuss the possible explanations for our findings and advocate for further research on telomere dynamics in ectotherms.     

Individual quality and age but not environmental or social conditions modulate costs of reproduction in a capital breeder

Costs associated with reproduction are widely known to play a role in the evolution of reproductive tactics with consequences to population and eco‐evolutionary dynamics. Evaluating these costs as they pertain to species in the wild remains an important goal of evolutionary ecology. Individual heterogeneity, including differences in individual quality (i.e., among‐individual differences in traits associated with survival and reproduction) or state, and variation in environmental and social conditions can modulate the costs of reproduction; however, few studies have considered effects of these factors simultaneously. Taking advantage of a detailed, long‐term dataset for a population of feral horses (Sable Island, Nova Scotia, Canada), we address the question of how intrinsic (quality, age), environmental (winter severity, location), and social conditions (group size, composition, sex ratio, density) influence the costs of reproduction on subsequent reproduction. Individual quality was measured using a multivariate analysis on a combination of four static and dynamic traits expected to depict heterogeneity in individual performance. Female quality and age interacted with reproductive status of the previous year to determine current reproductive effort, while no effect of social or environmental covariates was found. High‐quality females showed higher probabilities of giving birth and weaning their foal regardless of their reproductive status the previous year, while those of lower quality showed lower probabilities of producing foals in successive years. Middle‐aged (prime) females had the highest probability of giving birth when they had not reproduced the year before, but no such relationship with age was found among females that had reproduced the previous year, indicating that prime‐aged females bear higher costs of reproduction. We show that individual quality and age were key factors modulating the costs of reproduction in a capital breeder but that environmental or social conditions were not, highlighting the importance of considering multiple factors when studying costs of reproduction.     

Reproductive trade‐offs in a long‐lived bird species: condition‐dependent reproductive allocation maintains female survival and offspring quality

Life history theory is an essential framework to understand the evolution of reproductive allocation. It predicts that individuals of long‐lived species favour their own survival over current reproduction, leading individuals to refrain from reproducing under harsh conditions. Here we test this prediction in a long‐lived bird species, the Siberian jay Perisoreus infaustus. Long‐term data revealed that females rarely refrain from breeding, but lay smaller clutches in unfavourable years. Neither offspring body size, female survival nor offspring survival until the next year was influenced by annual condition, habitat quality, clutch size, female age or female phenotype. Given that many nests failed due to nest predation, the variance in the number of fledglings was higher than the variance in the number of eggs and female survival. An experimental challenge with a novel pathogen before egg laying largely replicated these patterns in two consecutive years with contrasting conditions. Challenged females refrained from breeding only in the unfavourable year, but no downstream effects were found in either year. Taken together, these findings demonstrate that condition‐dependent reproductive allocation may serve to maintain female survival and offspring quality, supporting patterns found in long‐lived mammals. We discuss avenues to develop life history theory concerning strategies to offset reproductive costs.     

Morph‐dependent fitness and directional change of morph frequencies over time in a Dutch population of Common buzzards Buteo buteo

How genetic polymorphisms are maintained in a population is a key question in evolutionary ecology. Previous work on a plumage colour polymorphism in the common buzzard Buteo buteo suggested heterozygote advantage as the mechanism maintaining the co‐existence of three morphs (light, intermediate and dark). We took advantage of 20 years of life‐history data collected in a Dutch population to replicate earlier studies on the relationship between colour morph and fitness in this species. We examined differences between morphs in adult apparent survival, breeding success, annual number of fledglings produced and cumulative reproductive success. We found that cumulative reproductive success differed among morphs, with the intermediate morph having highest fitness. We also found assortative mating for colour morph, whereby assortative pairs were more likely to produce offspring and had longer‐lasting pair bonds than disassortative pairs. Over the 20‐year study period, the proportion of individuals with an intermediate morph increased. This apparent evolutionary change did not just arise from selection on individual phenotypes, but also from fitness benefits of assortative mating. The increased frequency of intermediates might also be due to immigration or drift. We hypothesize that genetic variation is maintained through spatial variation in selection pressures. Further studies should investigate morph‐dependent dispersal behaviour and habitat choice.     

Occurrence,costs and heritability of delayed selfing in a free‐living flatworm

Evolutionary theory predicts that in the absence of outcrossing opportunities, simultaneously hermaphroditic organisms should eventually switch to self‐fertilization as a form of reproductive assurance. Here, we report the existence of facultative self‐fertilization in the free‐living flatworm Macrostomum hystrix, a species in which outcrossing occurs via hypodermic insemination of sperm into the parenchyma of the mating partner. First, we show that isolated individuals significantly delay the onset of reproduction compared with individuals with outcrossing opportunities (‘delayed selfing’) as predicted by theory. Second, consistent with the idea of M. hystrix being a preferential outcrosser under natural conditions, we report likely costs of selfing manifested via reduced hatchling production and offspring survival. Third, we demonstrate that selfing propensity has a genetic basis in this species, with a heritability estimated at 0.43 ± 0.11. Variation in selfing propensity could arise due to differing costs of inbreeding among families; despite marked inter‐family variation in apparent costs of inbreeding, we found no evidence for such a link. Alternatively, selfing propensity might differ across families because of heritable variation in reproductive traits that determine the likelihood of selfing. We speculate that adaptations to hypodermic insemination under outcrossing, most notably a highly modified copulatory stylet (male copulatory organ) and reduced sperm complexity, could also facilitate facultative selfing in this species.     

High MHC gene copy number maintains diversity despite homozygosity in a Critically Endangered single‐island endemic bird,but no evidence of MHC‐based mate choice

Small population sizes can, over time, put species at risk due to the loss of genetic variation and the deleterious effects of inbreeding. Losing diversity in the major histocompatibility complex (MHC) could be particularly harmful, given its key role in the immune system. Here, we assess MHC class I (MHC‐I) diversity and its effects on mate choice and survival in the Critically Endangered Raso lark Alauda razae, a species restricted to the 7 km² islet of Raso, Cape Verde, since ~1460, whose population size has dropped as low as 20 pairs. Exhaustively genotyping 122 individuals, we find no effect of MHC‐I genotype/diversity on mate choice or survival. However, we demonstrate that MHC‐I diversity has been maintained through extreme bottlenecks by retention of a high number of gene copies (at least 14), aided by cosegregation of multiple haplotypes comprising 2–8 linked MHC‐I loci. Within‐locus homozygosity is high, contributing to low population‐wide diversity. Conversely, each individual had comparably many alleles, 6–16 (average 11), and the large and divergent haplotypes occur at high frequency in the population, resulting in high within‐individual MHC‐I diversity. This functional immune gene diversity will be of critical importance for this highly threatened species’ adaptive potential.     

Heterozygosity correlates with body size,nest site quality and productivity in a colonial waterbird,the whiskered tern (Chlidonias hybrida,Aves: Sternidae)

Positive effects of individual heterozygosity on naturally selected traits have been reported in wild populations of many animal taxa. The aim of this study was to test whether heterozygosity predicts the quality of acquired nest sites and productivity in a colonially breeding waterbird, the whiskered tern (Chlidonias hybrida). For this purpose, 40 adult terns from a small, recently established population in Central Poland were typed at eight microsatellite loci. We demonstrate that individual heterozygosity is positively related to hatching success. We hypothesize that this association could be mediated by direct effects of heterozygosity on the competitive abilities of individuals. We found that more heterozygous terns tended to breed in better protected central parts of the colony, suggesting that they had capabilities of outcompeting less heterozygous individuals and relegating them to the less attractive peripheries of the colony. It was also demonstrated that the link between heterozygosity and individual abilities to acquire more attractive nest site could be mediated by the larger size of heterozygous individuals. Although no correlations between heterozygosity and different components of condition were found, there was a positive association between female heterozygosity and both clutch size and egg size. We suggest that demonstrated heterozygosity‐fitness correlations could be primarily caused by inbreeding depression in the studied whiskered tern population.     

Adult nutrition,but not inbreeding,affects male primary sexual traits in the leaf‐footed cactus bug Narnia femorata (Hemiptera: Coreidae)

Adverse conditions may be the norm rather than the exception in natural populations. Many populations experience poor nutrition on a seasonal basis. Further, brief interludes of inbreeding can be common as population density fluctuates and because of habitat fragmentation. Here, we investigated the effects of poor nutrition and inbreeding on traits that can be very important to reproductive success and fitness in males: testes mass, sperm concentration, and sperm viability. Our study species was Narnia femorata, a species introduced to north‐central Florida in the 1950s. This species encounters regular, seasonal changes in diet that can have profound phenotypic effects on morphology and behavior. We generated inbred and outbred individuals through a single generation of full‐sibling mating or outcrossing, respectively. All juveniles were provided a natural, high‐quality diet of Opuntia humifusa cactus cladode with fruit until they reached adulthood. New adult males were put on a high‐ or low‐quality diet for at least 21 days before measurements were taken. As expected, the low‐quality diet led to significantly decreased testes mass in both inbred and outbred males, although there were surprisingly no detectable effects on sperm traits. We did not find evidence that inbreeding affected testes mass, sperm concentration, and sperm viability. Our results highlight the immediate and overwhelming effects of nutrition on testes mass, while suggesting that a single generation of inbreeding might not be detrimental for primary sexual traits in this particular population.     

Stochastic modelling of shifts in allele frequencies reveals a strongly polygynous mating system in the re‐introduced Asiatic wild ass

Small populations are prone to loss of genetic variation and hence to a reduction in their evolutionary potential. Therefore, studying the mating system of small populations and its potential effects on genetic drift and genetic diversity is of high importance for their viability assessments. The traditional method for studying genetic mating systems is paternity analysis. Yet, as small populations are often rare and elusive, the genetic data required for paternity analysis are frequently unavailable. The endangered Asiatic wild ass (Equus hemionus), like all equids, displays a behaviourally polygynous mating system; however, the level of polygyny has never been measured genetically in wild equids. Combining noninvasive genetic data with stochastic modelling of shifts in allele frequencies, we developed an alternative approach to paternity analysis for studying the genetic mating system of the re‐introduced Asiatic wild ass in the Negev Desert, Israel. We compared the shifts in allele frequencies (as a measure of genetic drift) that have occurred in the wild ass population since re‐introduction onset to simulated scenarios under different proportions of mating males. We revealed a strongly polygynous mating system in which less than 25% of all males participate in the mating process each generation. This strongly polygynous mating system and its potential effect on the re‐introduced population's genetic diversity could have significant consequences for the long‐term persistence of the population in the Negev. The stochastic modelling approach and the use of allele‐frequency shifts can be further applied to systems that are affected by genetic drift and for which genetic data are limited.     

Evolution of life‐history traits and mating strategy in males: a case study on two populations of a Drosophila parasitoid

Abiotic and biotic factors affect life‐history traits and lead populations to exhibit different behavioural strategies. Due to the direct link between their behaviour and fitness, parasitoid females have often been used to test the theories explaining these differences. In male parasitoids, however, such investigations are vastly understudied, although their mating strategy directly determines their fitness. In this study, we compared the pattern of life history traits and the mating strategy of males in two populations of the Drosophila parasitoid Asobara tabida, exposed to different biotic and abiotic conditions, with the major difference being that one of them was recently exposed to strong competition with the dominant competitor Leptopilina boulardi after recent climate change, the other population being settled in a location where L. boulardi has not been recorded. The results showed that individuals of both populations have a different reproductive strategy: in one population, females produced a more female‐biased sex ratio, while males accumulated more lipids during their larval development, invested more energy in reproduction and decreased their locomotor activity, suggesting a higher proportion of matings on their emergence patch, all of these factors being possibly linked to the new competition pressure. In both populations, mating without sperm transfer may persist for several days after males become sperm‐depleted, and may be more frequent than mating with sperm transfer over their whole lifespan. This point is discussed from an evolutionary point of view.