Using microsatellite diversity in wild Anegada iguanas (<Emphasis Type="Italic">Cyclura pinguis</Emphasis>) to establish relatedness in a captive breeding group of this critically endangered species

Awareness of the genealogical relationships between founder animals in captive breeding programs is essential for the selection of mating pairs that maintain genetic diversity. If captive founder relationships are unknown they can be inferred using genetic data from wild populations. Here, we report the results of such an analysis for six Cyclura pinguis (Sauria: Iguanidae) acquired as adults in 1999 by the San Diego Zoo Institute for Conservation Research to begin a captive breeding program for this critically endangered species. The six founder animals were reportedly hatched in captivity from eggs collected on Anegada in 1985. No records exist, however, as to where on Anegada the eggs were collected or from how many nests they originated. To assist determination of genealogical relationships, we genotyped the six captive founders, their first six offspring, and 33 wild adult iguanas from Anegada at 23 informative microsatellite loci. With these data, we estimated allele frequencies among the wild samples and then estimated the relatedness of the captive population. Using likelihood inference, we determined that three closely related pairs exist among the six captive founders and that each pair is not closely related to the other two. In addition, we were able to assign parentage for all six of the founders’ offspring tested, one of which had been previously misdiagnosed. Using the assigned parentage and inferred relatedness of the six founders, we calculated mean kinship for each of the six founders and their five living offspring. Finally, based on the allelic diversity of the wild iguanas sampled, we conclude that the C. pinguis population on Anegada is not excessively inbred; however, further investigation is warranted.     

Analysis of founder representation in pedigrees: Founder equivalents and founder genome equivalents

The concepts of “founder equivalent” and “founder genome equivalent” are introduced to facilitate analysis of the founding stocks of captive or other populations for which pedigrees are available. The founder equivalents of a population are the number of equally contributing founders that would be expected to produce the same genetic diversity as in the population under study. Unequal genetic contributions by founders decrease the founder equivalents, portend greater inbreeding in future generations than would be necessary, and reflect a greater loss of the genetic diversity initially present in the founders. The number of founder genome equivalents of a population is that number of equally contributing founders with no random loss of founder alleles in descendants that would be expected to produce the same genetic diversity as in the population under study. The number of founder genome equivalents is approximately that number of wild-caught animals that would be needed to obtain the same amount of genetic diversity as is in the descendant captive population. Founder equivalents and founder genome equivalents allow comparison of the genetic merits of adding new wild-caught stock vs. further equalizing founder representations in a captive population.     

Clarification of genetic terms and their use in the management of captive populations

Some of the concepts, terms, and methods used in the genetic management of captive populations have not been defined precisely in the scientific literature and consequently have been misunderstood and misused. The definitions and interrelationships among gene diversity, effective population size, founder genome equivalents, inbreeding, allelic diversity, mean kinship, and kinship value are presented here. It is important to understand what populations and generations are used as the baselines against which losses of genetic variation are measured. Gene diversity and founder genome equivalents are defined relative to a source population from which founders of the captive population were randomly sampled. Inbreeding and allelic diversity are assessed relative to the founders. The potential gene diversity that would result from an equalization of frequencies of founder alleles retained in the population can never be achieved because, among other limitations, the random process of gene transmission will prevent equalization of allele frequencies even if animals are bred optimally. The gene diversity achievable with the population can be determined by iterative production of hypothetical offspring from the pairs with lowest mean kinship. The long-term objective for offspring production from each animal is also thereby generated. Mean kinships should be recalculated with each real or hypothetical birth and death, because offspring objectives based on current mean kinships might correlate poorly with the optimal long-term offspring objectives. © 1995 Wiley-Liss, Inc.     

Management imperatives forVarecia in captivity

A review of the captive history and status ofVarecia is presented followed by specific management recommendations for bothVarecia v. variegata andVarecia v. rubra. The total living captive population for the nominate form numbers 398 animals while that for the red and black form numbers 148 individuals as of 31 December 1986.Varecia v. variegata is reported to be a rapidly growing population originating from a founder population (wildborn animals which have produced offspring) of 21 animals. Management direction for this subspecies includes equalization of founder representation and controlled reproduction.Varecia v. rubra is reported to be more highly inbred with 79.35% of the captive population originating from 3 of 8 founders. The management imperatives for this subspecies include: 1) acquisition of a small number of wildborn red ruffed lemurs to be infused into the captive population over an extended period of time; 2) increase population; 3) equalize founder representation; 4) locate space. Encouragement ofin situ research and conservation activities is strongly advocated. Formerly: International Ruffed Lemur Studbook Keeper San Diego Zoo Box 551, San Diego, California 92112     

Interrelations between effective population size and other pedigree tools for the management of conserved populations

Genetic parameters widely used to monitor genetic variation in conservation programmes, such as effective number of founders, founder genome equivalents and effective population size, are interrelated in terms of coancestries and variances of contributions from ancestors to descendants. A new parameter, the effective number of non-founders, is introduced to describe the relation between effective number of founders and founder genome equivalents. Practical recommendations for the maintenance of genetic variation in small captive populations are discussed. To maintain genetic diversity, minimum coancestry among individuals should be sought. This minimizes the variances of contributions from ancestors to descendants in all previous generations. The method of choice of parents and the system of mating should be independent of each other because a clear-cut recommendation cannot be given on the latter.     

Breeding program for the lesser kudu (Tragelaphus imberbis) in North America

The lesser kudu (Tragelaphus imberbis) has been kept in North American zoological parks since 1930 but has never been a common species in collections. In 1987 this population totaled 28 animals: 15 males and 13 females. A pedigree evaluation in 1987 of the existing population indicated that eight effective founders and one potential founder were represented in the North American herd. Three new potential founders from European captive populations were added to the population in 1987 to increase the number of existing founder lines to 12 animals. As this species is not endangered or threatened in its native habitat, it is not a high priority to qualify for designation as an SSP species. Because of this, the institutions holding lesser kudu in North America decided to join informally and draft a breeding program to better manage this small captive population. This program was designed to minimize inbreeding and equalize genetic representation of founder animals to maximize genetic diversity. It requires a shift in management philosophy to establish stable groups of breeding females at participating institutions while rotating appropriate breeder males through these herds in a controlled manner to ensure minimization of inbreeding and maximization of genetic diversity. It is hoped that this program can serve as a model for the management of other small captive populations of non-SSP species.     

Use of animals with unknown ancestries in scientifically managed breeding programs

Whether to incorporate animals with unknown ancestries as founders into scientifically managed captive breeding programs, can be a difficult decision. If the animals are offspring of known founders, their inclusion in the breeding program will result in an increased incidence of inbreeding in the captive population. If the animals are additional founders, excluding them from the breeding program will result in the loss of valuable genetic variation. In general, the practice in scientifically managed captive breeding programs is to exclude animals with unknown ancestries to avoid possible inbreeding. A method of estimating the cost of making an incorrect decision on whether to use animals of unknown ancestry as founders both in terms of lost genetic variation and increased inbreeding is presented. It was determined that the loss of genetic variation resulting from excluding founders is always greater than the loss of genetic variation caused by unequal founder line representation resulting from including related animals, as if they were founders. In addition, the increased rate of accumulation of inbreeding resulting from excluding founders will eventually overcome the initial inbreeding resulting from including related animals. However, in some cases, it will take a substantial number of generations for this to occur, and the benefits of possible lowered future expected inbreeding may never be realized. The decision concerning whether to use animals with unknown ancestry should, therefore, be based on the estimated relative costs of making an error, in terms of both lost genetic variation and expected future inbreeding, rather than on avoiding the immediate possibility of increased inbreeding alone. Two examples using studbook data are given to show how this method can be practically applied to the management of captive populations. © 1993 Wiley-Liss, Inc.     

Analysis of relatedness and determination of the source of founders in the captive bearded vulture, Gypaetus barbatus, population

Genetic relatedness among founders is a vitalparameter in the management of captivepopulations as kin structure can have asignificant effect on subsequent populationstructure. Methods for inferring relatednessfrom microsatellite markers have all beendeveloped for natural populations; theirapplicability to captive populations withunknown founder origins needs thereforetesting. We used information derived from 14microsatellites in 177 individuals and Quellerand Goodnight's approach, to estimaterelatedness in the captive bearded vulturepopulation and to test the assumption ofunrelated founders. Mean relatedness of knownparent–offspring, full-sib and half-sib pairswithin the captive population were in agreementwith theoretical distributions. Pairwiserelatedness values among the founders had amean of –0.051 (SE ± 0.007) and theirdistribution did only differ marginally fromthe one found in the natural Pyreneanpopulation. A maximum likelihood approach wasused to determine the likelihood of founderpairs to be as closely related as full-sibs orparent–offspring. These results were combinedwith data from 268 bp mitochondrial DNA controlregion sequences and studbook information. Wecould exclude a close relationship among themajority of the 36 successfully reproducingfounders. Our study therefore removesmanagement concerns about hidden problems ofinbreeding and inbreeding depression. Itdemonstrates the applicability of relatednessestimates based on microsatellite allelefrequency data even in captive populations.Furthermore, we verified studbook informationon the origin of two founders from thePyrenees, and show the value of assignmenttests based on microsatellites for deducingfounder origins and their important role infuture monitoring projects.     

Genetic management of captive prosimian populations,a report of experience withLoris tardigradus

Extinction of small, closed populations in captivity as well as in the wild is believed to be nearly inevitable, because inbreeding will adversely effect reproductive success, mortality, sex ratio and also the susceptibility to epidemic diseases and environmental stress. An ever increasing number of primate species exist only in small isolated populations, which contain only a part of the original genetic variability. In captive breeding programs research about genetic management strategies is, therefore, of essential importance. In 1980 we imported 9Loris tardigrdus nordicus (4 females, 5 males) from NE-Sri Lanka. The founders came from one natural breeding population. All sexual mature females are breeding. Up to now the colony contains 36 living individuals. The main goal of our long-term genetic management plan was to minimize inbreeding and to preserve the genetic diversity. Therefore, we try to pass the founder bottleneck rapidly by enlarging the population to a desired minimum population size of 25 pairs and to equalize the founder representation within any generation. The need to control the spread of sublethal genes, introduced by one of the founders, conflicts directly with the aim of equalizing the founder representation. A solution of this problem is discussed. To produce a sufficiently large population we intend to give animals to other institutions and to build up an exchange-system for offspring individuals, which should lead to an international studbook.     

Evaluating ex situ conservation projects: Genetic structure of the captive population of the Arabian sand cat

Ex situ conservation plays an increasingly important role in the conservation of endangered species. Molecular genetic markers can be helpful to assess the status of captive breeding programmes. We present the first molecular genetic analysis of the captive population of the Arabian sand cat (Felis margarita harrisoni) using microsatellites. Our data indicates that the captive population of F. m. harrisoni comprises three genetic clusters, which are based on different founder lineages. Genetic diversity was relatively high, the effective population size even exceeded the number of founders. This was presumably caused by subsequently integrating unrelated, genetically diverse founders into the captive population and a careful management based on minimizing kinship. However, we detected an error in the studbook records, which might have led to incestuous matings and underlines the usefulness of molecular evaluations in captive breeding programmes for endangered species.     

Ex situ conservation genetics: a review of molecular studies on the genetic consequences of captive breeding programmes for endangered animal species

Captive breeding has become an important tool in species conservation programmes. Current management strategies for ex situ populations are based on theoretical models, which have mainly been tested in model species or assessed using studbook data. During recent years an increasing number of molecular genetic studies have been published on captive populations of several endangered species. However, a comprehensive analysis of these studies is still outstanding. Here, we present a review of the published literature on ex situ conservation genetics with a focus on molecular studies. We analysed 188 publications which either presented empirical studies using molecular markers (105), studbook analyses (26), theoretical work (38), or tested the genetic effects of management strategies using model species (19). The results show that inbreeding can be minimized by a thorough management of captive populations. There seems to be a minimum number of founders (15) and a minimum size of a captive population (100) necessary in order to minimize a loss of genetic diversity. Optimally, the founders should be unrelated and new founders should be integrated into the captive population successively. We recommend that genetic analyses should generally precede and accompany ex situ conservation projects in order to avoid inbreeding and outbreeding depression. Furthermore, many of the published studies do not provide all the relevant parameters (founder size, captive population size, H_o, H_e, inbreeding coefficients). We, therefore, propose that a general standard for the presentation of genetic studies should be established, which would allow integration of the data into a global database.     

Genome-Wide SNP and STR Discovery in the Japanese Crested Ibis and Genetic Diversity among Founders of the Japanese Population

The Japanese crested ibis is an internationally conserved, critically threatened bird. Captive-breeding programs have been established to conserve this species in Japan. Since the current Japanese population of crested ibis originates only from 5 founders donated by the Chinese government, understanding the genetic diversity between them is critical for an effective population management. To discover genome-wide single nucleotide polymorphisms (SNPs) and short tandem repeats (STRs) while obtaining genotype data of these polymorphic markers in each founder, reduced representation libraries were independently prepared from each of the founder genomes and sequenced on an Illumina HiSeq2000. This yielded 316 million 101-bp reads. Consensus sequences were created by clustering sequence reads, and then sequence reads from each founder were mapped to the consensus sequences, resulting in the detection of 52,512 putative SNPs and 162 putative STRs. The numbers of haplotypes and STR alleles and the investigation of genetic similarities suggested that the total genetic diversity between the founders was lower, although we could not identify a pair with closely related genome sequences. This study provided important insight into protocols for genetic management of the captive breeding population of Japanese crested ibis in Japan and towards the national project for reintroduction of captive-bred individuals into the wild. We proposed a simple, efficient, and cost-effective approach for simultaneous detection of genome-wide polymorphic markers and their genotypes for species currently lacking a reference genome sequence.     

Modeling problems in conservation genetics using captive Drosophila populations: Consequences of equalizing founder representation

Equalizing founder representation is a recommended practice for maintaining captive populations. However, this procedure has not been subject to controlled experimental evaluation. The effects on inbreeding, genetic variation, and reproductive fitness of maintaining small captive populations by equalizing founder representation (EFR) versus randomly choosing parents (RC) were compared. Ten replicate lines were created with unequal founder representations, split into EFR and RC lines, and maintained for a further eight generations. Founder representations computed from pedigrees were closer to equality in the EFR lines than in the RC lines or the base population, most of the changes being evident after one generation. Significant benefits of EFR were found in lowered inbreeding (mean inbreeding coefficients of 0.35 and 0.41, respectively, for EFR and RC lines) and average heterozygosity (0.141 for EFR, 0.084 for RC, compared with 0.216 in the base population). However, EFR was not significantly better than RC in moving allele frequencies towards equalized founder representation. No significant difference was found in reproductive fitness between EFR and RC (relative fitnesses compared to the base population were 0.179 for EFR and 0.182 for RC). The use of equalization of founder representation for a few generations can be recommended in the genetic management of captive populations derived from a small number of founders that contribute unequally. © 1992 Wiley-Liss, Inc.     

Integrating microsatellite and pedigree analyses to facilitate the captive management of the endangered Mississippi sandhill crane (Grus canadensis pulla)

The minimization of kinship in captive populations is usually achieved through the use of pedigree information. However, pedigree knowledge alone is not sufficient if pedigree information is missing, questionable, or when the founders of the captive population are related to one another. If this is the case, higher levels of inbreeding and lower levels of genetic diversity may be present in a captive population than those calculated by pedigree analyses alone. In this study, the genetic status of the critically endangered Mississippi sandhill crane (MSC) (Grus canadensis pulla) was analyzed using studbook data from the U.S. Fish and Wildlife Service managed captive breeding program as well as microsatellite DNA data. These analyses provided information on shared founder genotypes, allowing for refined analysis of genetic variation in the population, and the development of a new DNA-based studbook pedigree that will assist in the genetic management of the MSC population.     

Incorporation of new founders into captive populations

This report describes preliminary studies intended to develop generalizations for the optimal incorporation of newcomers into breeding pools. Small populations, which grow from four to a stable size of 16 animals per generation, were simulated on a computer. New founders were introduced and various breeding schemes tried and evaluated for their effect on inbreeding coefficients and founder representation. Two variables were examined for their effects on inbreeding and founder representation: number of progeny produced by crossing new founders with the established population, and number of mates the new founder had from the established population. Increasing the value of these variables to the point at which new-founder representation was equal to the original founders' representations decreased inbreeding. Beyond this point, inbreeding increased.     

Conservation of population structure and genetic diversity under captive breeding of remnant coaster brook trout (<Emphasis Type="Italic">Salvelinus fontinalis</Emphasis>) populations

Rebuilding wild populations often involves captive broodstocks derived from small, remnant populations. We measured a hatchery program’s ability to conserve genetic diversity when founding captive broodstocks from such populations. Migratory coaster brook trout were extirpated from most of their historic range in US waters of Lake Superior and were proposed for listing under the Endangered Species Act. Two captive broodstocks, one with 19 founders and another with 99 founders, were established to rebuild US populations. We used microsatellite markers to examine genetic variation in source populations and early hatchery generations. Broodstocks retained the strong differentiation found between source populations; however, one founder, with a low probability of belonging to either source population, sired 5.7% of F₁ progeny. We found small changes in within-population genetic variation across successive wild and hatchery generations of broodstocks. Evaluation of stage-specific survivorship indicated that equalizing family sizes of embryos produced modest gains in the effective number of breeders, and that survival in the hatchery was nearly random across families. Our study demonstrates the value of genetic monitoring during initial stages of hatchery programs for small and declining populations.     

Fragmentation of the Québec population genetic pool (Canada): evidence from the genetic contribution of founders per region in the 17th and 18th centuries

The 6 million French-Canadians of Québec derive from a relatively small number of founders. Consequently, some hereditary diseases, which may or may not present a worldwide distribution, have been detected in high frequency in this population. Several studies, however, indicate a nonuniform distribution of these diseases through the population, suggesting that the French-Canadian founder effect has been geographically stratified. Here we explore this stratification by using a demographic database, the Population Register of Early Québec, that contains almost all birth, marriage, and death certificates (>712,000) recorded in parish registers between 1608-1800. In this database, every genealogical link has been traced back to the founders of the population, so that we can compute the genetic contribution of founder per region, and then account for the early events that have shaped the distribution of diseases. Ten regions, comprising varying numbers of parishes, have been selected. We first describe each region in terms of homogeneity and concentration of its gene pool. For this purpose, a new concept is introduced, the founders' uniform contribution number (FUN), i.e., the number of founders a population would have if all its founders had an equal contribution. Second, we estimate genetic similarity between regions on the basis of differential genetic contribution. To classify the regions, we use principal component and cluster analysis. Our results show a tripartite clustering of the population, and invite us to reconsider the results obtained from biomolecular and clinical studies, which show a bipartite clustering.     

The cryptic genetic structure of the North American captive gorilla population

Western lowland gorillas (Gorilla gorilla gorilla) were imported from across their geographical range to North American zoos from the late 1800s through 1974. The majority of these gorillas were imported with little or no information regarding their original provenance and no information on their genetic relatedness. Here, we analyze 32 microsatellite loci in 144 individuals using a Bayesian clustering method to delineate clusters of individuals among a sample of founders of the captive North American zoo gorilla collection. We infer that the majority of North American zoo founders sampled are distributed into two distinct clusters, and that some individuals are of admixed ancestry. This new information regarding the existence of ancestral genetic population structure in the North American zoo population lays the groundwork for enhanced efforts to conserve the evolutionary units of the western lowland gorilla gene pool. Our data also show that the genetic diversity estimates in the founder population were comparable to those in wild gorilla populations (Mondika and Cross River), and that pairwise relatedness among the founders is no different from that expected for a random mating population. However, the relatively high level of relatedness (R = 0.54) we discovered in a pair of known breeding pairs reveals the need for incorporating genetic relatedness estimates in the captive management of western lowland gorillas.     

Serial founder effects during range expansion: a spatial analog of genetic drift

Range expansions cause a series of founder events. We show that, in a one-dimensional habitat, these founder events are the spatial analog of genetic drift in a randomly mating population. The spatial series of allele frequencies created by successive founder events is equivalent to the time series of allele frequencies in a population of effective size ke, the effective number of founders. We derive an expression for ke in a discrete-population model that allows for local population growth and migration among established populations. If there is selection, the net effect is determined approximately by the product of the selection coefficients and the number of generations between successive founding events. We use the model of a single population to compute analytically several quantities for an allele present in the source population: (i) the probability that it survives the series of colonization events, (ii) the probability that it reaches a specified threshold frequency in the last population, and (iii) the mean and variance of the frequencies in each population. We show that the analytic theory provides a good approximation to simulation results. A consequence of our approximation is that the average heterozygosity of neutral alleles decreases by a factor of 1-1/(2ke) in each new population. Therefore, the population genetic consequences of surfing can be predicted approximately by the effective number of founders and the effective selection coefficients, even in the presence of migration among populations. We also show that our analytic results are applicable to a model of range expansion in a continuously distributed population.     

Founder effect and genetic disease in Sottunga, Finland

Pedigree data are analyzed in order to determine the factors responsible for the high frequencies of certain genetic disorders in an isolated Swedish-speaking population of Finland's A land archipelago. The founders of Sottunga are identified, and the genetic contributions of each founder to descending birth cohorts are estimated. Founders born before 1700 have far more descendants in the contemporary gene pool than do more recent founders. However, because of migration and depopulation since 1900, the expected genetic contributions of the early founders to the present-day population are similar to those of later founders. A descendant in the contemporary population has a 2% chance of having inherited a particular gene from the founder who makes the largest single contribution to the gene pool. This corresponds approximately to a 2% probability of inheriting an autosomal dominant disease gene from this founder. Given an average inbreeding coefficient of 0.0016, the probability of inheriting two recessive disease genes from this founder is 0.000032. The incidence of autosomal dominant von Willebrand disease in Sottunga is greater than 10% while that of autosomal recessive tapetoretinal disease is 1.5%. We conclude, therefore, that the high frequencies of these diseases are not due to the disproportionate genetic contribution of one or a few particular founders. It is more likely that these disease genes occurred in high frequency in the initial population or were introduced repeatedly through time.