Estimating demographic contributions to effective population size in an age-structured wild population experiencing environmental and demographic stochasticity

Effective population size in a partially clonal plant is not predicted by the number of genetic individuals

Estimating effective population size (N _e) is important for theoretical and practical applications in evolutionary biology and conservation. Nevertheless, estimates of N _e in organisms with complex life-history traits remain scarce because of the challenges associated with estimation methods. Partially clonal plants capable of both vegetative (clonal) growth and sexual reproduction are a common group of organisms for which the discrepancy between the apparent number of individuals (ramets) and the number of genetic individuals (genets) can be striking, and it is unclear how this discrepancy relates to N _e. In this study, we analysed two populations of the orchid Cypripedium calceolus to understand how the rate of clonal versus sexual reproduction affected N _e. We genotyped >1000 ramets at microsatellite and SNP loci, and estimated contemporary N _e with the linkage disequilibrium method, starting from the theoretical expectation that variance in reproductive success among individuals caused by clonal reproduction and by constraints on sexual reproduction would lower N _e. We considered factors potentially affecting our estimates, including different marker types and sampling strategies, and the influence of pseudoreplication in genomic data sets on N _e confidence intervals. The magnitude of N _e/N _ramets and N _e/N _genets ratios we provide may be used as reference points for other species with similar life-history traits. Our findings demonstrate that N _e in partially clonal plants cannot be predicted based on the number of genets generated by sexual reproduction, because demographic changes over time can strongly influence N _e. This is especially relevant in species of conservation concern in which population declines may not be detected by only ascertaining the number of genets.

Female reproductive skew exacerbates the extinction risk from poaching in the eastern black rhino

Variation in individual demographic rates can have large consequences for populations. Female reproductive skew is an example of structured demographic heterogeneity where females have intrinsic qualities that make them more or less likely to breed. The consequences of reproductive skew for population dynamics are poorly understood in non-cooperatively breeding mammals, especially when coupled with other drivers such as poaching. We address this knowledge gap with population viability analyses using an age-specific, female-only, individual-based, stochastic population model built with long-term data for three Kenyan populations of the Critically Endangered eastern black rhino (Diceros bicornis michaeli). There was substantial reproductive skew, with a high proportion of females not breeding or doing so at very low rates. This had a large impact on the projected population growth rate for the smaller population on Ol Jogi. Moreover, including female reproductive skew exacerbates the effects of poaching, increasing the probability of extinction by approximately 70% under a simulated poaching pressure of 5% offtake per year. Tackling the effects of reproductive skew depends on whether it is mediated by habitat or social factors, with potential strategies including habitat and biological management respectively. Investigating and tackling reproductive skew in other species requires long-term, individual-level data collection.

Integrating advances in population and evolutionary ecology with conservation strategy through long-term studies of red-billed choughs

Conceptual and methodological advances in population and evolutionary ecology are often pursued with the ambition that they will help identify demographic, ecological and genetic constraints on population growth rate (λ), and ultimately facilitate evidence-based conservation. However, such advances are often decoupled from conservation practice, impeding translation of scientific understanding into effective conservation and of conservation-motivated research into wider conceptual understanding. We summarise key outcomes from long-term studies of a red-billed chough Pyrrhocorax pyrrhocorax population of conservation concern, where we proactively aimed to achieve the dual and interacting objectives of advancing population and evolutionary ecology and advancing effective conservation. Estimation of means, variances and covariances in key vital rates from individual-based demographic data identified temporal and spatial variation in subadult survival as key constraints on λ, and simultaneously provided new insights into how vital rates can vary as functions of demographic structure, natal conditions and parental life history. Targeted analyses showed that first-year survival increased with prey abundance, implying that food limitation may constrain λ. First-year survival then decreased dramatically, threatening population viability and prompting emergency supplementary feeding interventions. Detailed evaluations suggested that the interventions successfully increased first-year survival in some years and additionally increased adult survival and successful reproduction, thereby feeding back to inform intervention refinements and understanding of complex ecological constraints on λ. Genetic analyses revealed novel evidence of expression of a lethal recessive allele, and demonstrated how critically small effective population size can arise, thereby increasing inbreeding and loss of genetic variation. Population viability analyses parameterised with all available demographic and genetic data showed how ecological and genetic constraints can interact to limit population viability, and identified ecological management as of primacy over genetic management to ensure short-term persistence of the focal population. This case study demonstrates a full iteration through the sequence of primary science, evidence-based intervention, quantitative evaluation and feedback that is advocated in conservation science but still infrequently achieved. It thereby illustrates how pure science advances informed conservation actions to ensure the (short-term) stability of the target population, and how conservation-motivated analyses fed back to advance fundamental understanding of population processes.

SNP-based analysis reveals unexpected features of genetic diversity, parental contributions and pollen contamination in a white spruce breeding program

Accurate monitoring of genetic diversity levels of seedlots and mating patterns of parents from seed orchards are crucial to ensure that tree breeding programs are long-lasting and will deliver anticipated genetic gains. We used SNP genotyping to characterize founder trees, five bulk seed orchard seedlots, and trees from progeny trials to assess pollen contamination and the impact of severe roguing on genetic diversity and parental contributions in a first-generation open-pollinated white spruce clonal seed orchard. After severe roguing (eliminating 65% of the seed orchard trees), we found a slight reduction in the Shannon Index and a slightly negative inbreeding coefficient, but a sharp decrease in effective population size (eightfold) concomitant with sharp increase in coancestry (eightfold). Pedigree reconstruction showed unequal parental contributions across years with pollen contamination levels between 12 and 51% (average 27%) among seedlots, and 7-68% (average 30%) among individual genotypes within a seedlot. These contamination levels were not correlated with estimates obtained using pollen flight traps. Levels of pollen contamination also showed a Pearson's correlation of 0.92 with wind direction, likely from a pollen source 1 km away from the orchard under study. The achievement of 5% genetic gain in height at rotation through eliminating two-thirds of the orchard thus generated a loss in genetic diversity as determined by the reduction in effective population size. The use of genomic profiles revealed the considerable impact of roguing on genetic diversity, and pedigree reconstruction of full-sib families showed the unanticipated impact of pollen contamination from a previously unconsidered source.

Phenotypic evolution in stochastic environments: The contribution of frequency- and density-dependent selection

Understanding how environmental variation affects phenotypic evolution requires models based on ecologically realistic assumptions that include variation in population size and specific mechanisms by which environmental fluctuations affect selection. Here we generalize quantitative genetic theory for environmentally induced stochastic selection to include general forms of frequency- and density-dependent selection. We show how the relevant fitness measure under stochastic selection relates to Fisher's fundamental theorem of natural selection, and present a general class of models in which density regulation acts through total use of resources rather than just population size. In this model, there is a constant adaptive topography for expected evolution, and the function maximized in the long run is the expected factor restricting population growth. This allows us to generalize several previous results and to explain why apparently " K -selected" species with slow life histories often have low carrying capacities. Our joint analysis of density- and frequency-dependent selection reveals more clearly the relationship between population dynamics and phenotypic evolution, enabling a broader range of eco-evolutionary analyses of some of the most interesting problems in evolution in the face of environmental variation.

The evolution of polymorphism in the warning coloration of the Amazonian poison frog Adelphobates galactonotus

While intraspecific variation in aposematic signals can be selected for by different predatory responses, their evolution is also contingent on other processes shaping genetic variation. We evaluate the relative contributions of selection, geographic isolation, and random genetic drift to the evolution of aposematic color polymorphism in the poison frog Adelphobates galactonotus, distributed throughout eastern Brazilian Amazonia. Dorsal coloration was measured for 111 individuals and genetic data were obtained from 220 individuals at two mitochondrial genes (mtDNA) and 7963 Single Nucleotide Polymorphisms (SNPs). Four color categories were described (brown, blue, yellow, orange) and our models of frog and bird visual systems indicated that each color was distinguishable for these taxa. Using outlier and correlative analyses we found no compelling genetic evidence for color being under divergent selection. A time-calibrated mtDNA tree suggests that the present distribution of dorsal coloration resulted from processes occurring during the Pleistocene. Separate phylogenies based on SNPs and mtDNA resolved the same well supported clades, each containing different colored populations. Ancestral character state analysis provided some evidence for evolutionary transitions in color type. Genetic structure was more strongly associated with geographic features, than color category, suggesting that the distribution of color is explained by localized processes. Evidence for geographic isolation together with estimates of low effective population size implicates drift as playing a key role in color diversification. Our results highlight the relevance of considering the neutral processes involved with the evolution of traits with important fitness consequences.

Estimating effective population size using RADseq: Effects of SNP selection and sample size

Effective population size (Ne ) is a key parameter of population genetics. However, N e remains challenging to estimate for natural populations as several factors are likely to bias estimates. These factors include sampling design, sequencing method, and data filtering. One issue inherent to the restriction site-associated DNA sequencing (RADseq) protocol is missing data and SNP selection criteria (e.g., minimum minor allele frequency, number of SNPs). To evaluate the potential impact of SNP selection criteria on Ne estimates (Linkage Disequilibrium method) we used RADseq data for a nonmodel species, the thornback ray. In this data set, the inbreeding coefficient F IS was positively correlated with the amount of missing data, implying data were missing nonrandomly. The precision of Ne estimates decreased with the number of SNPs. Mean Ne estimates (averaged across 50 random data sets with2000 SNPs) ranged between 237 and 1784. Increasing the percentage of missing data from 25% to 50% increased Ne estimates between 82% and 120%, while increasing the minor allele frequency (MAF) threshold from 0.01 to 0.1 decreased estimates between 71% and 75%. Considering these effects is important when interpreting RADseq data-derived estimates of effective population size in empirical studies.

Decomposing demographic contributions to the effective population size with moose as a case study

Levels of random genetic drift are influenced by demographic factors, such as mating system, sex ratio and age structure. The effective population size (N_e ) is a useful measure for quantifying genetic drift. Evaluating relative contributions of different demographic factors to N_e is therefore important to identify what makes a population vulnerable to loss of genetic variation. Until recently, models for estimating N_e have required many simplifying assumptions, making them unsuitable for this task. Here, using data from a small, harvested moose population, we demonstrate the use of a stochastic demographic framework allowing for fluctuations in both population size and age distribution to estimate and decompose the total demographic variance and hence the ratio of effective to total population size (N_e /N) into components originating from sex, age, survival and reproduction. We not only show which components contribute most to N_e /N currently, but also which components have the greatest potential for changing N_e /N. In this relatively long-lived polygynous system we show that N_e /N is most sensitive to the demographic variance of older males, and that both reproductive autocorrelations (i.e., a tendency for the same individuals to be successful several years in a row) and covariance between survival and reproduction contribute to decreasing N_e /N (increasing genetic drift). These conditions are common in nature and can be caused by common hunting strategies. Thus, the framework presented here has great potential to increase our understanding of the demographic processes that contribute to genetic drift and viability of populations, and to inform management decisions.

Towards a predictive conservation biology: the devil is in the behaviour

One of the most important challenges in conservation biology is to predict the viability of populations of vulnerable and threatened species. This requires that the demographic stochasticity strongly affecting the ecological and evolutionary dynamics of especially small populations is correctly estimated and modelled. Here, we summarize theoretical evidence showing that the demographic variance in population dynamics is a key parameter determining the probability of extinction and also is directly linked to the magnitude of the genetic drift in the population. The demographic variance is dependent on the mating system, being larger in a polygynous than in monogamous populations. Understanding factors affecting intersexual differences in mating success is therefore essential in explaining variation in the demographic variance. We hypothesize that the strength of sexual selection, for example, quantified by the Bateman gradient, may be a useful predictor of the magnitude of the demographic stochasticity and hence the genetic drift in the population. We provide results from a field study of moose that support this claim. Thus, including central principles from behavioural ecology may increase the reliability of population viability analyses through an improvement of our understanding of factors affecting stochastic influences on population dynamics and evolutionary processes. This article is part of the theme issue 'Linking behaviour to dynamics of populations and communities: application of novel approaches in behavioural ecology to conservation'.

Low Genetic Diversity and Low Gene Flow Corresponded to a Weak Genetic Structure of Ruddy-Breasted Crake (Porzana fusca) in China

The Ruddy-breasted Crake (Porzana fusca) is an extremely poorly known species. Although it is not listed as globally endangered, in recent years, with the interference of climate change and human activities, its habitat is rapidly disappearing and its populations have been shrinking. There are two different life history traits for Ruddy-breasted Crake in China, i.e., non-migratory population in the south and migratory population in the north of China. In this study, mitochondrial control sequences and microsatellite datasets of 88 individuals sampled from 8 sites were applied to analyze their genetic diversity, genetic differentiation, and genetic structure. Our results indicated that low genetic diversity and genetic differentiation exit in most populations. The neutrality test suggested significantly negative Fu's Fs value, which, in combination with detection of the mismatch distribution, indicated that population expansion occurred in the interglacier approximately 98,000 years ago, and the time of the most recent common ancestor (TMRCA) was estimated to about 202,705 years ago. Gene flow analysis implied that the gene flow was low, but gene exchange was frequent among adjacent populations. Both phylogenetic and STRUCTURE analyses implied weak genetic structure. In general, the genetic diversity, gene flow, and genetic structure of Ruddy-breasted Crake were low.