INCREASED PROBABILITY OF EXTINCTION DUE TO DECREASED GENETIC EFFECTIVE POPULATION SIZE: EXPERIMENTAL POPULATIONS OF CLARKIA PULCHELLA

We established replicated experimental populations of the annual plant Clarkia pulchella to evaluate the existence of a causal relationship between loss of genetic variation and population survival probability. Two treatments differing in the relatedness of the founders, and thus in the genetic effective population size (N_e), were maintained as isolated populations in a natural environment. After three generations, the low N_e treatment had significantly lower germination and survival rates than did the high N_e treatment. These lower germination and survival rates led to decreased mean fitness in the low N_e populations: estimated mean fitness in the low N_e populations was only 21% of the estimated mean fitness in the high N_e populations. This inbreeding depression led to a reduction in population survival: at the conclusion of the experiment, 75% of the high N_e populations were still extant, whereas only 31% of the low N_e populations had survived. Decreased genetic effective population size, which leads to both inbreeding and the loss of alleles by genetic drift, increased the probability of population extinction over that expected from demographic and environmental stochasticity alone. This demonstrates that the genetic effective population size can strongly affect the probability of population persistence.     

Effects of population characteristics and structure on estimates of effective population size in a house sparrow metapopulation

Effective population size (N_e) is a key parameter to understand evolutionary processes and the viability of endangered populations as it determines the rate of genetic drift and inbreeding. Low N_e can lead to inbreeding depression and reduced population adaptability. In this study, we estimated contemporary N_e using genetic estimators (LDNE, ONeSAMP, MLNE and CoNe) as well as a demographic estimator in a natural insular house sparrow metapopulation. We investigated whether population characteristics (population size, sex ratio, immigration rate, variance in population size and population growth rate) explained variation within and among populations in the ratio of effective to census population size (N_e/N_c). In general, N_e/N_c ratios increased with immigration rates. Genetic N_e was much larger than demographic N_e, probably due to a greater effect of immigration on genetic than demographic processes in local populations. Moreover, although estimates of genetic N_e seemed to track N_c quite well, the genetic N_e‐estimates were often larger than N_c within populations. Estimates of genetic N_e for the metapopulation were however within the expected range (<N_c). Our results suggest that in fragmented populations, even low levels of gene flow may have important consequences for the interpretation of genetic estimates of N_e. Consequently, further studies are needed to understand how N_e estimated in local populations or the total metapopulation relates to actual rates of genetic drift and inbreeding.     

Pedigree analysis of the Turkish Arab horse population: structure,inbreeding and genetic variability

The aim of this study was to evaluate genetic variability in the Turkish Arab horse population using pedigree information. This study is the first detailed pedigree analysis of the breed in Turkey. Pedigree data were collected from the National Studbook. The pedigree data for 23 668 horses, born between 1904 and 2014, were used in the analysis. From this data set, a reference population (RP) of 14 838 animals symbolising the last generation was defined. Demographic parameters, the inbreeding level (F), the average relatedness (AR), the effective population size (N_e), the effective number of founders (f_e), the effective number of ancestors (f_a) and the number of founder genome equivalents (f_g) were calculated for the population. The average generation interval for the RP was 12.2±4.6 years, whereas the calculated pedigree completeness levels were 98.2%, 96.6% and 95.0% for the first, second and third known generations. The mean equivalent generations (t), the average complete generations and the mean maximum generations for the RP were 7.8, 5.4 and 12.2, respectively, whereas the meanFand AR were 4.6% and 9.5% for the RP. The rate of inbred animals was 94.2% for the RP, whereas the number of founders, the number of ancestors and thef_e,f_aandf_gwere 342, 223, 40, 22 and 9.6 for the RP. The large differences observed betweenf_e, and the number of founders demonstrates that genetic diversity decreased between the founder and the RP. Contribution of the 14 most influential founder to the RP was 50.0%, whereas just eight ancestral horses can account for 50% of the genetic variability.N_eestimated via an individual increase in inbreeding per generation (${\overline{N}}_{\text{e}}$), and paired increase in coancestry$\left(\text{}{\overline{N}}_{eC}\right)$, were 74.4±3.9 and 73.5±0.58, respectively. The inbreeding increases with the pedigree knowledge. In addition, the decrease in inbreeding in last years is more noticeable.     

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.     

Analysis of founders and performance test effects on an autochthonous horse population through pedigree analysis: structure,genetic variability and inbreeding

The Maremmano is an autochthonous Italian horse breed, which probably descended from the native horses of the Etruscans (VI century B.C.); the Studbook was acknowledged in 1980, and it includes 12 368 horses born from that year up to 2015. The aim of this study was to evaluate the effect of the selection program on the genetic variability of the Maremmano population; the analysis was performed using both the ‘Endog v 4.8’ program available at http://webs.ucm.es/info/prodanim/html/JP_Web.htm and in-house software on official pedigree data. Four Reference Populations were considered, and the most important one was the population of the 12 368 Maremmano horses officially registered in the National Studbook. The pedigree completeness of this population was very good because it was more than 90% at the third parental generation and more than 70% at the fifth generation; the pedigree traced back to a maximum of 10.50 generations with an average of 3.30 complete generations and 5.70 equivalent complete generations. The average generation interval was 10.65±4.72 years, with stallions used for longer periods than mares. The intervals ranged from 10.15±4.45 (mother–daughter) to 10.99±4.93 (father–daughter). The effective number of founders (f_e) was 74 and the effective number of ancestors (f_a) was 30 so that the ratio f_e/f_a was 2.47. The founder genome equivalents (f_g) was 13.72 with a ratio f_g/f_e equal to 0.18. The mean of the genetic conservation index was 5.55±3.37, and it ranged from 0.81 to 21.32. The average inbreeding coefficient was 2.94%, with an increase of 0.1%/year, and the average relatedness coefficient was 5.52%. The effective population size (N_e) computed by an individual increase in inbreeding was 68.1±13.00; the N_e on equivalent generations was 42.00, and this value slightly increased to 42.20 when computed by Log regression on equivalent generations. The analysis confirmed the presence of seven traditional male lines. The percentage of Thoroughbred blood in the foals born in 2015 was 20.30% and has increased 0.21%/year since 1980; in particular, it increased more than twice (0.51%/year) until 1993 and afterwards slightly fluctuated. The pedigree analysis confirmed the completeness of genealogical information and the traditional importance that breeders gave to the male lines; although the genetic diversity of Maremmano seemed to be not endangered by the selection program, some effects on the population structure were found and a more scientific approach to genetic conservation should be incorporated in the selection plans.     

The use of agent-based modelling of genetics in conservation genetics studies

Animal Landscape and Man Simulation System a genetically explicit agent-based model was used to obtain measures for the genetic and demographic status of simulated populations. This investigation aimed to test the applicability of this approach for assessing the effect of environmental perturbations on populations’ temporal and spatial dynamics. This was achieved by assessing how three simple scenarios with increasing degree of environmental disturbance, simulated by populations bottlenecks repeated at different intervals, affected the genetic and demographic characteristics of the simulated population. Model outputs from a simplified landscape scenario concurred with theoretical expectations validating the model in a qualitative way. Differences in medians, means and coefficient of variation of the observed (H_o) and expected heterozygosity (H_e), population census size (N), effective population size (N_e), inbreeding coefficient (F) and N_e/N ratio were observed for simulated populations. Impacts occurred rapidly after simulated bottleneck events and genetic estimates were less variable, and therefore more reliable, than demographic estimates. Precise genetic consequences of the bottlenecks repeated at different intervals, and resulting population perturbations, are a complex balance between effects on population sub-structure, size and founding events. Agent-based models are appropriate tools to simulate these interactions, being sufficiently flexible to mimic real population processes under a range of environmental conditions. Such models incorporating explicit genetics provide a promising new approach to evaluate the impact of environmental changes on genetic composition of populations.     

Inbreeding depression and drift load in small populations at demographic disequilibrium

Inbreeding depression is a major driver of mating system evolution and has critical implications for population viability. Theoretical and empirical attention has been paid to predicting how inbreeding depression varies with population size. Lower inbreeding depression is predicted in small populations at equilibrium, primarily due to higher inbreeding rates facilitating purging and/or fixation of deleterious alleles (drift load), but predictions at demographic and genetic disequilibrium are less clear. In this study, we experimentally evaluate how lifetime inbreeding depression and drift load, estimated by heterosis, vary with census (N_c) and effective (estimated as genetic diversity, H_e) population size across six populations of the biennial Sabatia angularis as well as present novel models of inbreeding depression and heterosis under varying demographic scenarios at disequilibrium (fragmentation, bottlenecks, disturbances). Our experimental study reveals high average inbreeding depression and heterosis across populations. Across our small sample, heterosis declined with H_e, as predicted, whereas inbreeding depression did not vary with H_e and actually decreased with N_c. Our theoretical results demonstrate that inbreeding depression and heterosis levels can vary widely across populations at disequilibrium despite similar H_e and highlight that joint demographic and genetic dynamics are key to predicting patterns of genetic load in nonequilibrium systems.     

A comparison of pedigree‐ and DNA‐based measures for identifying inbreeding depression in the critically endangered Attwater's Prairie‐chicken

The primary goal of captive breeding programmes for endangered species is to prevent extinction, a component of which includes the preservation of genetic diversity and avoidance of inbreeding. This is typically accomplished by minimizing mean kinship in the population, thereby maintaining equal representation of the genetic founders used to initiate the captive population. If errors in the pedigree do exist, such an approach becomes less effective for minimizing inbreeding depression. In this study, both pedigree‐ and DNA‐based methods were used to assess whether inbreeding depression existed in the captive population of the critically endangered Attwater's Prairie‐chicken (Tympanuchus cupido attwateri), a subspecies of prairie grouse that has experienced a significant decline in abundance and concurrent reduction in neutral genetic diversity. When examining the captive population for signs of inbreeding, variation in pedigree‐based inbreeding coefficients (f_pedigree) was less than that obtained from DNA‐based methods (f_DNA). Mortality of chicks and adults in captivity were also positively correlated with parental relatedness (r_DNA) and f_DNA, respectively, while no correlation was observed with pedigree‐based measures when controlling for additional variables such as age, breeding facility, gender and captive/release status. Further, individual homozygosity by loci (HL) and parental r_DNA values were positively correlated with adult mortality in captivity and the occurrence of a lethal congenital defect in chicks, respectively, suggesting that inbreeding may be a contributing factor increasing the frequency of this condition among Attwater's Prairie‐chickens. This study highlights the importance of using DNA‐based methods to better inform management decisions when pedigrees are incomplete or errors may exist due to uncertainty in pairings.     

Do estimates of contemporary effective population size tell us what we want to know?

Estimation of effective population size (N_e) from genetic marker data is a major focus for biodiversity conservation because it is essential to know at what rates inbreeding is increasing and additive genetic variation is lost. But are these the rates assessed when applying commonly used N_e estimation techniques? Here we use recently developed analytical tools and demonstrate that in the case of substructured populations the answer is no. This is because the following: Genetic change can be quantified in several ways reflecting different types of N_e such as inbreeding (N_eI), variance (N_eV), additive genetic variance (N_eAV), linkage disequilibrium equilibrium (N_eLD), eigenvalue (N_eE) and coalescence (N_eCo) effective size. They are all the same for an isolated population of constant size, but the realized values of these effective sizes can differ dramatically in populations under migration. Commonly applied N_e‐estimators target N_eV or N_eLD of individual subpopulations. While such estimates are safe proxies for the rates of inbreeding and loss of additive genetic variation under isolation, we show that they are poor indicators of these rates in populations affected by migration. In fact, both the local and global inbreeding (N_eI) and additive genetic variance (N_eAV) effective sizes are consistently underestimated in a subdivided population. This is serious because these are the effective sizes that are relevant to the widely accepted 50/500 rule for short and long term genetic conservation.  The bias can be infinitely large and is due to inappropriate parameters being estimated when applying theory for isolated populations to subdivided ones.     

Effective Population Size,Extended Linkage Disequilibrium and Signatures of Selection in the Rare Dog Breed Lundehund

The Lundehund is an old dog breed with remarkable anatomical features including polydactyly in all four limbs and extraordinary flexibility of the spine. We genotyped 28 Lundehund using the canine Illumina high density beadchip to estimate the effective population size (N_e) and inbreeding coefficients as well as to identify potential regions of positive selection. The decay of linkage disequilibrium was slow with r² = 0.95 in 50 kb distance. The last 7-200 generations ago, Ne was at 10-13. An increase of N_e was noted in the very recent generations with a peak value of 19 for N_e at generation 4. The FROH estimated for 50-, 65- and 358-SNP windows were 0.87, 087 and 0.81, respectively. The most likely estimates for F_ROH after removing identical-by-state segments due to linkage disequilibria were at 0.80-0.81. The extreme loss of heterozygosity has been accumulated through continued inbreeding over 200 generations within a probably closed population with a small effective population size. The mean inbreeding coefficient based on pedigree data for the last 11 generations (F_Ped = 0.10) was strongly biased downwards due to the unknown coancestry of the founders in this pedigree data. The long-range haplotype test identified regions with genes involved in processes of immunity, olfaction, woundhealing and neuronal development as potential targets of selection. The genes QSOX2, BMPR1B and PRRX2 as well as MYOM1 are candidates for selection on the Lundehund characteristics small body size, increased number of digits per paw and extraordinary mobility, respectively.     

Relationship between effective population size,inbreeding and adult fitness‐related traits in a steelhead (Oncorhynchus mykiss) population released in the wild

Inbreeding is of concern in supportive breeding programmes in Pacific salmonids, Oncorhynchus spp, where the number of breeding adults is limited by rearing space or poor survival to adulthood, and large numbers are released to supplement wild stocks and fisheries. We reconstructed the pedigree of 6602 migratory hatchery steelhead (Oncorhynchus mykiss) over four generations, to determine the incidence and fitness consequences of inbreeding in a northwest USA programme. The hatchery maintained an effective population size,  = 107.9 from F₀ to F₂, despite an increasing census size (N), which resulted in a decreasing N_e/N ratio (0.35 in F₀ to 0.08 in F₂). The reduced ratio was attributed to a small broodstock size, nonrandom transfers and high variance in reproductive success (particularly in males). We observed accumulation of inbreeding from the founder generation (in F₄, percentage individuals with inbreeding coefficients Δf > 0 = 15.7%). Generalized linear mixed models showed that body length and weight decreased significantly with increasing Δf, and inbred fish returned later to spawn in a model that included father identity. However, there was no significant correlation between Δf and age at return, female fecundity or gonad weight. Similarly, there was no relationship between Δf and reproductive success of F₂ and F₃ individuals, which might be explained by the fact that reproductive success is partially controlled by hatchery mating protocols. This study is one of the first to show that small changes in inbreeding coefficient can affect some fitness‐related traits in a monitored population propagated and released to the wild.     

Inbreeding and extinction: Effects of rate of inbreeding

Deleterious alleles may be removed (purged) bynatural selection in populations undergoinginbreeding. However, there is controversyregarding the effectiveness of selection inreducing the risk of extinction due toinbreeding, especially in relation to the rateof inbreeding. We evaluated the effect of therate of inbreeding on reducing extinction risk,in populations of Drosophila melanogastermaintained using full-sib mating (160replicates), or at effective population sizes(N _e) of 10 (80) or 20 (80).Extinction rates in the populations maintainedusing full-sib mating occurred at lower levelsof inbreeding than in the larger populations,whereas the two larger populations did notdiffer significantly from each other.Inbreeding coefficients at 50% extinction were0.62, 0.79 and 0.77 for the full-sib (N _e = 2.6), N _e = 10 and N _e = 20 treatments, respectively. Populations of N _e = 20 that remained extant after 60 generations, showed inbreeding depression, with the mean fitness of these populations being only 45% of the outbredcontrols. There was considerable variationamong the 31 inbred populations in fitness, butnone of the N _e = 20 populations hadfitness that was higher than the outbredcontrol. We conclude that purging may slow therate of extinction slightly, but it cannot berelied on to eliminate the deleterious effectsof inbreeding.     

Temporal-method estimates of Ne from highly polymorphic loci

The temporal method is used widely to estimategenetic effective population size (N _e), a parameter of fundamental interestto studies of evolutionary and conservationbiology. The statistical properties oftemporal-method estimates have not beenexplored for highly polymorphic DNA markersthat often contain many alleles occurring invery low frequencies. We used a Monte Carlosimulation approach to assess accuracy andprecision of the temporal method whenimplemented with haplotypic/allelic data atmitochondrial (mt)DNA and nuclear-encodedmicrosatellite DNA loci. Estimates of N _e were between 2%–106% greater thantheir true values in 48 simulationsparameterized using different demographicscenarios, models of mutation, and samplesizes. Overestimation of N _e resultsfrom a bias in the approximation used by Waples(1989) to derive the relationship between theexpected temporal variance (F) and N _e when allele frequencies are very closeto 0 or 1. Our results show that one commonlyapplied solution to this problem, binning oflow-frequency alleles, results in a trade-offof accuracy and precision in some cases. Weshow that both chi-square and normalapproximations are appropriate for estimating95% confidence intervals of N _e andwe develop a power analysis based on thechi-square distribution to estimate samplesizes and allelic diversity required toevaluate specific hypotheses. For highlypolymorphic loci like mtDNA andmicrosatellites, the increased precisionafforded by the presence of rare allelesoutweighs the upward bias in temporal-methodestimates of N _e.     

Small localized breeding populations in a widely distributed coastal shark species

Identifying the geographical scale at which natural populations structure themselves is essential for conservation. One way to gauge this structure is by estimating local effective population size (N_e) and the associated measure of effective number of breeders (N_b), as the smaller and more isolated natural populations are, the smaller N_e and N_b they will present. However, as N_e and N_b are greatly influenced by demographic events and by both species’ behavior and biology, assessing the effectiveness of sample design is necessary to ensure the reliability of said estimates. Here, we first test the sample size effect on yearly N_b and generational N_e estimates from a lemon shark Negaprion brevirostris nursery in Bimini (The Bahamas) and subsequently compare these parameters to estimates of the minimal number of breeders based on pedigree reconstruction. We found that yearly estimates of N_b are positively correlated to annual variations in number of breeders estimated via pedigree reconstructions. Moreover, we measured that 30 individuals from a single cohort were sufficient to obtain reliable yearly estimates of N_b in Bimini’s lemon sharks. We then estimated generational N_e in 10 lemon shark nurseries across the Western Atlantic. Almost every nursery sampled represents an independent population on a generational time scale, with N_e rarely higher than 100 individuals. Our study reveals strong local population structure in lemon sharks, and thus their exposure to localized depletion or extirpation, suggesting that studies of coastal shark nursery areas could routinely estimate N_e and N_b to obtain management-relevant information on adult populations.

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INBREEDING INFLUENCES WITHIN‐BROOD HETEROZYGOSITY‐FITNESS CORRELATIONS (HFCS) IN AN ISOLATED PASSERINE POPULATION

Molecular estimates of inbreeding may be made using genetic markers such as microsatellites, however the interpretation of resulting heterozygosity‐fitness correlations (HFCs) with respect to inbreeding depression is not straightforward. We investigated the relationship between pedigree‐determined inbreeding coefficients (f) and HFCs in a closely monitored, reintroduced population of Stewart Island robins (Petroica australis rakiura) on Ulva Island, New Zealand. Using a full sibling design, we focused on differences in juvenile survival associated specifically with individual sibling variation in standardized multilocus heterozygosity (SH) when expected f was identical. We found that within broods, siblings with higher SH at microsatellite loci experienced a higher probability of juvenile survival. This effect, however, was detected primarily within broods that experienced inbreeding or when inbreeding had occurred in their pedigree histories (i.e., at the parents’ level). Thus we show, for the first time in a wild population, that the strength of an HFC is partially dependent on the presence of inbreeding events in the recent pedigree history. Our results illustrate the importance of realized effects of inbreeding on genetic variation and fitness and the value of full‐sibling designs for the study of HFCs in the context of small, inbred populations.     

Comparative Analysis of Genome Diversity in Bullmastiff Dogs

Management and preservation of genomic diversity in dog breeds is a major objective for maintaining health. The present study was undertaken to characterise genomic diversity in Bullmastiff dogs using both genealogical and molecular analysis. Genealogical analysis of diversity was conducted using a database consisting of 16,378 Bullmastiff pedigrees from year 1980 to 2013. Additionally, a total of 188 Bullmastiff dogs were genotyped using the 170,000 SNP Illumina CanineHD Beadchip. Genealogical parameters revealed a mean inbreeding coefficient of 0.047; 142 total founders (f); an effective number of founders (f_e) of 79; an effective number of ancestors (f_a) of 62; and an effective population size of the reference population of 41. Genetic diversity and the degree of genome-wide homogeneity within the breed were also investigated using molecular data. Multiple-locus heterozygosity (MLH) was equal to 0.206; runs of homozygosity (ROH) as proportion of the genome, averaged 16.44%; effective population size was 29.1, with an average inbreeding coefficient of 0.035, all estimated using SNP Data. Fine-scale population structure was analysed using NETVIEW, a population analysis pipeline. Visualisation of the high definition network captured relationships among individuals within and between subpopulations. Effects of unequal founder use, and ancestral inbreeding and selection, were evident. While current levels of Bullmastiff heterozygosity, inbreeding and homozygosity are not unusual, a relatively small effective population size indicates that a breeding strategy to reduce the inbreeding rate may be beneficial.     

Breeding without breeding: minimum fingerprinting effort with respect to the effective population size

We present a probabilistic model to minimize the fingerprinting effort associated with the implementation of the “breeding without breeding” scheme under partial pedigree reconstruction. Our approach is directed at achieving a declared target population’s minimum effective population size (N _e ), following the pedigree reconstruction and genotypic selection and is based on the graph theory algorithm. The primary advantage of the proposed method is to reduce the cost associated with fingerprinting before the implementation of the pedigree reconstruction for seed parent–offspring derived from breeding arboreta and production or natural populations. Stochastic simulation was conducted to test the method’s efficiency assuming a simple polygenic model and a single trait. Hypothetical population consisted of 30 parental trees that were paired at random (selfing excluded), resulting in 600 individuals (potential candidates for forwards selection). The male parentage was assumed initially unknown. The model was used to estimate the minimum genotyping sample size needed to reaching the prescribed N _e . Results were compared with the known pedigree data. The model was successful in revealing the true relationship pattern over the whole range of N _e . Two to three offspring entered genotyping to meet the N _e  = 2 while 41 to 43 were required to satisfy the N _e  = 14. Importantly, genetic gain was affected at the lower limits of the genotyping effort. Doubling the number of parents resulted in considerable reduction of the genotyping effort at higher N _e values.     

Can Genetic Estimators Provide Robust Estimates of the Effective Number of Breeders in Small Populations?

The effective population size (N_e) is proportional to the loss of genetic diversity and the rate of inbreeding, and its accurate estimation is crucial for the monitoring of small populations. Here, we integrate temporal studies of the gecko Oedura reticulata, to compare genetic and demographic estimators of N_e. Because geckos have overlapping generations, our goal was to demographically estimate N_bI, the inbreeding effective number of breeders and to calculate the N_bI/N_a ratio (N_a = number of adults) for four populations. Demographically estimated N_bI ranged from 1 to 65 individuals. The mean reduction in the effective number of breeders relative to census size (N_bI/N_a) was 0.1 to 1.1. We identified the variance in reproductive success as the most important variable contributing to reduction of this ratio. We used four methods to estimate the genetic based inbreeding effective number of breeders N_bI(gen) and the variance effective populations size N_eV(gen) estimates from the genotype data. Two of these methods - a temporal moment-based (MBT) and a likelihood-based approach (TM3) require at least two samples in time, while the other two were single-sample estimators - the linkage disequilibrium method with bias correction LDNe and the program ONeSAMP. The genetic based estimates were fairly similar across methods and also similar to the demographic estimates excluding those estimates, in which upper confidence interval boundaries were uninformative. For example, LDNe and ONeSAMP estimates ranged from 14–55 and 24–48 individuals, respectively. However, temporal methods suffered from a large variation in confidence intervals and concerns about the prior information. We conclude that the single-sample estimators are an acceptable short-cut to estimate N_bI for species such as geckos and will be of great importance for the monitoring of species in fragmented landscapes.     

Effects of inbreeding on fitness‐related traits in a small isolated moose population

Inbreeding can affect fitness‐related traits at different life history stages and may interact with environmental variation to induce even larger effects. We used genetic parentage assignment based on 22 microsatellite loci to determine a 25 year long pedigree for a newly established island population of moose with 20–40 reproducing individuals annually. We used the pedigree to calculate individual inbreeding coefficients and examined for effects of individual inbreeding (f) and heterozygosity on fitness‐related traits. We found negative effects of f on birth date, calf body mass and twinning rate. The relationship between f and calf body mass and twinning rate were found to be separate but weaker after accounting for birth date. We found no support for an inbreeding effect on the age‐specific lifetime reproductive success of females. The influence of f on birth date was related to climatic conditions during the spring prior to birth, indicating that calves with a low f were born earlier after a cold spring than calves with high f. In years with a warm spring, calf f did not affect birth date. The results suggest that severe inbreeding in moose has both indirect effects on fitness through delayed birth and lower juvenile body mass, as well as separate direct effects, as there still was a significant relationship between f and twinning rate after accounting for birth date and body mass as calf. Consequently, severe inbreeding as found in the study population may have consequences for population growth and extinction risk.     

Migration and inbreeding: the importance of recipient population size for genetic management

Sewall Wright demonstrated 70 years ago thatthe number of migrants required to maintainspecified levels of gene flow (i.e. avoidexcessive inbreeding) is virtually independentof the size of the recipient population. According to conventional wisdom, this idea isvalid provided population size exceeds 20. Itis well known that this independence implicitlyassumes that a population's effective size(N _e) is equal to its census size(N). However, it is not obvious whetherindependence between the required number ofmigrants (to avoid excessive inbreeding) andpopulation size constitutes a reasonableassumption for real populations of conservationconcern. Relying on empirical data, wedemonstrate that for real populations, theassumption (i.e. N _e = N) isroutinely violated to a degree such that therequired number of migrants is stronglydependent on the size of the recipientpopulation. Because a population's effectivesize (N _e) is typically much smallerthan its census size (N), the number ofmigrants required to avoid inbreeding isactually dependent on N even when it isconsiderably greater than 20. For example,when N _e/N = 0.1, the number ofmigrants required to maintain the inbreedingcoefficient (F) at 0.2 doubles (from 4 to8) as N increases from 9 to 60. Similarly, when N _e/N = 0.05, thenumber of migrants required increases by 50%as N increases from 18 to 45, andincreases again by 50% as N increasesfrom 45 to 260. Thus, for populations muchlarger than 20, the required number of migrantsincreases asymptotically with N, anddramatically so when N _e/N1. Simple conventions regarding the requisitenumber of migrants may not apply to manypopulations of conservation concern. Geneticmanagement should routinely rely on models thatexplicitly account for this and other recentconsiderations. Failure to do so mayjeopardize the viability of populations thatare sensitive to altered levels of inbreeding.