Strategies for establishing and using genome resource banks to protect genetic diversity in conservation breeding programs

Genome resource banks (GRBs) have the potential to preserve the genetic diversity of a species over time, yet they are rarely utilized as effective components of conservation breeding programs. Advances have been made in reproductive biology, collection and storage techniques, and use of stored gametes for achieving successful reproduction, but there are few guidelines for integrating GRBs into established breeding programs. Here we present basic guidelines, focusing on strategies for the collection, maintenance, and use of semen GRBs for protecting genetic diversity. These guidelines should be applied in the context of the specific purposes and roles of a breeding program's GRB, which will differ among species depending on vulnerability to loss and the status of rescue and conservation efforts. We recommend establishing up to three types of collections: (1) a National Reserve to preserve a species' genetic diversity, to be used only as a last resort; (2) a Savings Account to be used periodically to invigorate a genetically depauperate population; and (3) a Checking Account to be used as a regular part of the breeding program. We present methods for identifying donors to maximize genetic diversity in a GRB, as well as strategies for maintaining and optimally using GRBs.

Applying the zoo model to conservation of threatened exceptional plant species

Maintaining a living plant collection is the most common method of ex situ conservation for plant species that cannot be seed banked (i.e., exceptional species). Viability of living collections, and their value for future conservation efforts, can be limited without coordinated efforts to track and manage individuals across institutions. Using a pedigree-focused approach, the zoological community has established an inter-institutional infrastructure to support long-term viability of captive animal populations. We assessed the ability of this coordinated metacollection infrastructure to support the conservation of 4 plant species curated in living collections at multiple botanic gardens around the world. Limitations in current practices include the inability to compile, share, and analyze plant collections data at the individual level, as well as difficulty in tracking original provenance of ex situ material. The coordinated metacollection framework used by zoos can be adopted by the botanical community to improve conservation outcomes by minimizing the loss of genetic diversity in collections. We suggest actions to improve ex situ conservation of exceptional plant species, including developing a central database to aggregate data and track unique individuals of priority threatened species among institutions and adapting a pedigree-based population management tool that incorporates life-history aspects unique to plants. If approached collaboratively across regional, national, and global scales, these actions could transform ex situ conservation of threatened plant species.

Conservation and Genetics

Humans are responsible for a cataclysm of species extinction that will change the world as we see it, and will adversely affect human health and wellbeing. We need to understand at individual and societal levels why species conservation is important. Accepting the premise that species have value, we need to next consider the mechanisms underlying species extinction and what we can do to reverse the process. One of the last stages of species extinction is the reduction of a species to a few populations of relatively few individuals, a scenario that leads invariably to inbreeding and its adverse consequences, inbreeding depression. Inbreeding depression can be so severe that populations become at risk of extinction not only because of the expression of harmful recessive alleles (alleles having no phenotypic effect when in the heterozygous condition, e.g., Aa, where a is the recessive allele), but also because of their inability to respond genetically with sufficient speed to adapt to changing environmental conditions. However, new conservation approaches based on foundational quantitative and population genetic theory advocate for active genetic management of fragmented populations by facilitating gene movements between populations, i.e., admixture, or genetic rescue. Why species conservation is critical, the genetic consequences of small population size that often lead to extinction, and possible solutions to the problem of small population size are discussed and presented.

A father effect explains sex-ratio bias

Sex ratio allocation has important fitness consequences, and theory predicts that parents should adjust offspring sex ratio in cases where the fitness returns of producing male and female offspring vary. The ability of fathers to bias offspring sex ratios has traditionally been dismissed given the expectation of an equal proportion of X- and Y-chromosome-bearing sperm (CBS) in ejaculates due to segregation of sex chromosomes at meiosis. This expectation has been recently refuted. Here we used Peromyscus leucopus to demonstrate that sex ratio is explained by an exclusive effect of the father, and suggest a likely mechanism by which male-driven sex-ratio bias is attained. We identified a male sperm morphological marker that is associated with the mechanism leading to sex ratio bias; differences among males in the sperm nucleus area (a proxy for the sex chromosome that the sperm contains) explain 22% variation in litter sex ratio. We further show the role played by the sperm nucleus area as a mediator in the relationship between individual genetic variation and sex-ratio bias. Fathers with high levels of genetic variation had ejaculates with a higher proportion of sperm with small nuclei area. This, in turn, led to siring a higher proportion of sons (25% increase in sons per 0.1 decrease in the inbreeding coefficient). Our results reveal a plausible mechanism underlying unexplored male-driven sex-ratio biases. We also discuss why this pattern of paternal bias can be adaptive. This research puts to rest the idea that father contribution to sex ratio variation should be disregarded in vertebrates, and will stimulate research on evolutionary constraints to sex ratios-for example, whether fathers and mothers have divergent, coinciding, or neutral sex allocation interests. Finally, these results offer a potential explanation for those intriguing cases in which there are sex ratio biases, such as in humans.

Estimating Inbreeding Rates in Natural Populations: Addressing the Problem of Incomplete Pedigrees

Understanding and estimating inbreeding is essential for managing threatened and endangered wildlife populations. However, determination of inbreeding rates in natural populations is confounded by incomplete parentage information. We present an approach for quantifying inbreeding rates for populations with incomplete parentage information. The approach exploits knowledge of pedigree configurations that lead to inbreeding coefficients of F = 0.25 and F = 0.125, allowing for quantification of Pr(I|k): the probability of observing pedigree I given the fraction of known parents (k). We developed analytical expressions under simplifying assumptions that define properties and behavior of inbreeding rate estimators for varying values of k. We demonstrated that inbreeding is overestimated if Pr(I|k) is not taken into consideration and that bias is primarily influenced by k. By contrast, our new estimator, incorporating Pr(I|k), is unbiased over a wide range of values of k that may be observed in empirical studies. Stochastic computer simulations that allowed complex inter- and intragenerational inbreeding produced similar results. We illustrate the effects that accounting for Pr(I|k) can have in empirical data by revisiting published analyses of Arabian oryx (Oryx leucoryx) and Red deer (Cervus elaphus). Our results demonstrate that incomplete pedigrees are not barriers for quantifying inbreeding in wild populations. Application of our approach will permit a better understanding of the role that inbreeding plays in the dynamics of populations of threatened and endangered species and may help refine our understanding of inbreeding avoidance mechanisms in the wild.

EFFECTIVENESS OF SELECTION IN REDUCING THE GENETIC LOAD IN POPULATIONS OF PEROMYSCUS POLIONOTUS DURING GENERATIONS OF INBREEDING

It has been hypothesized that natural selection reduces the "genetic load" of deleterious alleles from populations that inbreed during bottlenecks, thereby ameliorating impacts of future inbreeding. We tested the efficiency with which natural selection purges deleterious alleles from three subspecies of Peromyscus polionotus during 10 generations of laboratory inbreeding by monitoring pairing success, litter size, viability, and growth in 3604 litters produced from 3058 pairs. In P. p. subgriseus, there was no reduction across generations in inbreeding depression in any of the fitness components. Strongly deleterious recessive alleles may have been removed previously during episodes of local inbreeding in the wild, and the residual genetic load in this population was not further reduced by selection in the lab. In P. p. rhoadsi, four of seven fitness components did show a reduction of the genetic load with continued inbreeding. The average reduction in the genetic load was as expected if inbreeding depression in this population is caused by highly deleterious recessive alleles that are efficiently removed by selection. For P. p. leucocephalus a population that experiences periodic bottlenecks in the wild, the effect of further inbreeding in the laboratory was to exacerbate rather than reduce the genetic load. Recessive deleterious alleles may have been removed from this population during repeated bottlenecks in the wild; the population may be close to a threshold level of heterozygosity below which fitness declines rapidly. Thus, the effects of selection on inbreeding depression varied substantially among populations, perhaps due to different histories of inbreeding and selection.

Predicting the probability of outbreeding depression

Fragmentation of animal and plant populations typically leads to genetic erosion and increased probability of extirpation. Although these effects can usually be reversed by re-establishing gene flow between population fragments, managers sometimes fail to do so due to fears of outbreeding depression (OD). Rapid development of OD is due primarily to adaptive differentiation from selection or fixation of chromosomal variants. Fixed chromosomal variants can be detected empirically. We used an extended form of the breeders' equation to predict the probability of OD due to adaptive differentiation between recently isolated population fragments as a function of intensity of selection, genetic diversity, effective population sizes, and generations of isolation. Empirical data indicated that populations in similar environments had not developed OD even after thousands of generations of isolation. To predict the probability of OD, we developed a decision tree that was based on the four variables from the breeders' equation, taxonomic status, and gene flow within the last 500 years. The predicted probability of OD in crosses between two populations is elevated when the populations have at least one of the following characteristics: are distinct species, have fixed chromosomal differences, exchanged no genes in the last 500 years, or inhabit different environments. Conversely, the predicted probability of OD in crosses between two populations of the same species is low for populations with the same karyotype, isolated for <500 years, and that occupy similar environments. In the former case, we recommend crossing be avoided or tried on a limited, experimental basis. In the latter case, crossing can be carried out with low probability of OD. We used crosses with known results to test the decision tree and found that it correctly identified cases where OD occurred. Current concerns about OD in recently fragmented populations are almost certainly excessive.

Survivorship patterns in captive mammalian populations: implications for estimating population growth rates

For species of conservation concern, ecologists often need to estimate potential population growth rates with minimal life history data. We use a survivorship database for captive mammals to show that, although survivorship scale (i.e., longevity) varies widely across mammals, survivorship shape (i.e., the age-specific pattern of mortality once survivorship has been scaled to maximum longevity) varies little. Consequently, reasonable estimates of population growth rate can be achieved for diverse taxa using a model of survivorship shape along with an estimate of longevity. In addition, we find that the parameters of survivorship shape are related to taxonomic group, a fact that may be used to further improve estimates of survivorship when full life history data are unavailable. Finally, we compare survivorship shape in captive and wild populations of the same species and find higher adult survivorship in captive populations but no corresponding increase in juvenile survivorship. These differences likely reflect a convolution of true differences in captive vs. wild survivorship and the difficulty of observing juvenile mortality in field studies.

Simulation model for contraceptive management of the Assateague Island feral horse population using individual-based data

The National Park Service (NPS) manages a culturally significant population of feral horses (Equus caballus) inhabiting the Maryland portion of Assateague Island, a barrier island in the eastern United States. Rapid growth of this population over the past few decades from 28 to 166 horses negatively impacts native species and ecological processes on the island. Since 1994, contraception via porcine zona pellucida vaccine has been used to control horse numbers, although herd reduction has been slower than initially expected, leading NPS to consider other management options. An individual-based stochastic simulation model was developed using the Vortex software program to examine the effects of different management strategies on the population. Data from the managed population were used to populate the model parameters. Model projections over the next 50 years using current management practices show an average rate of population decline of 13% per year, suggesting that the population will reach the management target of 80–100 horses in 5–8 years. The effectiveness of contraception to reduce the herd and maintain it at various target sizes of 20–100 horses was also assessed. The accumulation of inbreeding at each target population size was also modelled.

Computer simulations to determine the efficacy of different genome resource banking strategies for maintaining genetic diversity

Genome resource banks (GRBs) and assisted reproductive techniques are increasingly recognized as useful tools for the management and conservation of biodiversity, including endangered species. Cryotechnology permits long-term storage of valuable genetic material. Although, the actual application to endangered species management requires technical knowledge about sperm freezing and thawing, a systematic understanding of the quantitative impacts of various germ plasm storage and use scenarios is also mandatory. In this study, various GRB strategies were analyzed using the historical data from three managed populations of endangered species with varied pedigrees (Eld's deer, Przewalski's horse, and Sumatran tiger). The following types of sperm banks were assessed: (1) a "Wild Bank" consisting of sperm (i.e., genes) from 5 to 10 males unrelated to the managed population and to each other; and (2) a "Best Male" bank containing sperm from only the most genetically valuable males alive in the ex situ population at the time the bank was established. These different bank types were then used to evaluate the effectiveness of different bank usage frequencies. The efficiency of each scenario was assessed by examining the level of inbreeding and gene diversity in the population. Overall, a sperm usage frequency of five times per year was determined to be the most efficient and "wild banks" were highly successful at enhancing genetic diversity. The value of a GRB established from the ex situ population depends on how closely related the banked males are to future generations. A GRB will have significantly less benefit when banked males also produce many successful offspring, or when donors are already genetically over-represented in the population at the time of establishing the GRB.

Restoration of reproductive potential following expiration or removal of melengestrol acetate contraceptive implants in golden lion tamarins (Leontopithecus rosalia)

Although reversible contraception is important to successful management of small populations, there are concerns about the reversibility of melengestrol acetate (MGA), the most commonly used implant in captive animals. Female golden lion tamarins (Leontopithecus rosalia) placed in potential breeding situations after surgical MGA implant removal showed a 75% return to reproduction within 2 yr, unlike golden-headed tamarins (Leontopithecus chrysomelas), which have had a 29% return to reproduction following implant removal. This rate was indistinguishable from the breeding probability for newly formed pairs involving nonimplanted females. Litter size, stillbirth rate, and infant survival rate were not significantly different between nonimplanted and implant-removed female golden lion tamarins. However, females with implants left in (and assumed to have expired) showed higher stillbirth and infant mortality rates than did females with implants removed. For seven female golden lion tamarins for which reproductive histories before and after MGA implantation were available, litter size was unaffected by MGA implantation and subsequent removal. Infant survival rate for these females appeared to be lower after removal but was indistinguishable from rates in the nonimplanted females. Prior reproductive experience, length of time with an implant, and age of the females did not affect the probability of breeding for females after removal of the implants. Overall, breeding probability of nonimplanted females declined with age. Although the results of this study confirm the reversibility of MGA implants in golden lion tamarins, there appear to be some effects on viability of offspring, particularly offspring born to females with implants left in and presumed expired.

Ancestral inbreeding only minimally affects inbreeding depression in mammalian populations

Inbreeding depression can be reduced, or purged, by selection against deleterious alleles. This prediction is the basis of the recommendation that captive wildlife populations suffering from inbreeding depression be intentionally bred from healthy inbred animals. Yet data on the effectiveness of purging inbreeding depression are few. In this study I present and use two different regression models (an ancestral inbreeding model and a lethal recessive model) to test for the presence of purging effects in 25 captive mammalian populations. Fitness components examined were neonatal survival, survival from neonate to weaning, and litter size. In only one species was purging statistically significant. However, 15 of 17 species that showed inbreeding depression exhibited a slight decline in inbreeding depression in neonatal survival among descendants of inbred animals. These results show a small but highly significant trend of purging on neonatal survival. No trends in purging effects were observed in weaning survival or litter size. The effects were not likely to be strong enough to be of practical use in eliminating inbreeding depression.

Desmethionine-bombesin receptor antagonist blocks bombesin-induced inhibition of alcohol intake

[D-Phe6,Des-Met14]bombesin(6-14), ethyl amide (D-BN) is a specific, competitive receptor antagonist of bombesin, a neuropeptide that inhibits alcohol and food intake. We tested the effects of IP injected D-BN (4-400 micrograms/kg) on bombesin-induced (4 micrograms/kg) reduction of caloric intake. In the first experiment, ad lib-fed female and male rats (Ns = 18) were deprived of water for 23 h, injected with peptides or saline in randomized sequences of doses, and immediately given access to 5% w/v ethanol for 30 min, followed by 30 min of water. In a second experiment, male rats (N = 10) were injected with the antagonist at 10 or 20 min prior to bombesin injection and alcohol access, and behaviors were observed and quantified once a minute with an instantaneous time-sampling technique. D-BN injection blocked the bombesin-induced reduction in alcohol intake (> or = 40 micrograms/kg) and food intake (> or = 200 micrograms/kg). When injected 20 min prior to access, D-BN alone (200 micrograms/kg) initially elevated alcohol drinking and later increased feeding behaviors and decreased resting, relative to saline injection. Results indicate bombesin-induced reduction of alcohol intake depends on a specific peptidergic receptor process, and endogenous bombesin-like peptide could act physiologically to elicit satiation with ethanol and food.

Dubin-Johnson-like syndrome in golden lion tamarins (Leontopithecus rosalia rosalia)

On routine blood screens, persistent conjugated hyperbilirubinemia was discovered in two groups of closely related adult female golden lion tamarins (Leontopithecus rosalia rosalia, n = 8). Bromosulfophthalein (BSP) retention tests were performed on four hyperbilirubinemic and three control tamarins. BSP excretion was delayed in hyperbilirubinemic tamarins as compared with controls. Grossly, liver of affected tamarins was dark brown to black, with a prominent reticulated pattern. Histologic examination revealed abundant intrahepatic pigment, primarily in a centrilobular and midzonal distribution. Most of the pigment did not react with Perls' Prussian blue method for iron, Hall's method for bilirubin, or the Armed Forces Institute of Pathology acid-fast method for lipofuscin but was positive with Fontana and lipofuscin-ferric ferricyanide reduction techniques. Liver from control golden lion tamarins had intrahepatocellular Perls' iron-positive pigment diffusely throughout the lobule with a small amount of Fontana method-positive pigment. Ultrastructurally, hepatocytes from a hyperbilirubinemic tamarin contained pleomorphic electron-dense structures within lysosomes. Transport studies demonstrated secretion of fluorescein isothiocyanate-labeled glycocholic acid, a fluorescent bile acid analog, into bile canaliculi and no secretion of carboxydichlorofluorescein diacetate, a non-bile acid organic anion, by liver from a hyperbilirubinemic tamarin. In contrast, control liver secreted carboxydichlorofluorescein diacetate readily into bile canaliculi. The clinicopathologic presentation of this syndrome in golden lion tamarins is similar to that described for Dubin-Johnson syndrome of human beings.

MK-329 blocks the inhibition of alcohol intake by CCK-8

Peripheral administration of sulfated cholecystokinin octapeptide (CCK-8) potently reduces alcohol intake, preference, and blood levels in rats. MK-329 (L-364,718 or Devazepide) acts at peripheral cholecystokinin (CCKA) receptors to antagonize CCK-8's physiological and behavioral effects, such as pancreatic stimulation and inhibition of feeding. We determined whether CCKA receptor blockade would also prevent CCK-8's alcohol satiety effect. Water-deprived female and male rats (n = 7 for each) received randomized combinations of intraperitoneal injections of MK-329 (0, 100, 200, or 400 micrograms/kg) followed by CCK-8 (0 or 4 micrograms/kg). Rats were then given access to 5% w/v ethanol for 30 min, followed by 30-min access to water, with food ad lib. MK-329 at all doses significantly (p < 0.05) reduced the suppression of alcohol intake and food intake by CCK-8. MK-329 alone increased alcohol intake at 400 micrograms/kg, and increased food intake, in females and males at 100 and 200 micrograms/kg, respectively. We concluded that CCK-8's alcohol and food satiation effects depend on specific, peripheral CCKA receptors, and satiation of alcohol consumption and drinking-associated feeding reflect an endogenous functional interaction of CCK-8 with CCKA receptors.

Potential contribution of cryopreserved germ plasm to the preservation of genetic diversity and conservation of endangered species in captivity

Demographic and genetic objectives of captive propagation programs for endangered species focus on establishing demographically secure populations that maintain adequate levels of genetic diversity. Long-term storage and utilization of cryopreserved germ plasm could extend the population's generation length and allow higher levels of genetic variation to be maintained in smaller populations. Since fewer breeding animals would be needed, more species would be "rescued" from extinction using the cage facilities currently available at existing institutions. Doubling generation lengths for callitrichid primates through use of cryopreservation could almost triple the number of species that could be rescued in world zoos. Additionally, long-term cryopreservation would allow for a third population, that of the frozen zoo. Three-way exchange of germ from germ plasm banks to captive and wild populations would increase genetic diversity at reduced risk and expense. Advances in reproductive technology and better understanding of the reproductive physiology of these animal populations are necessary to permit routine application of artificial insemination and embryo transfer using frozen-stored germ plasm.

Genetic variation within and among lion tamarins

The golden lion tamarin Leontopithecus rosalia rosalia, one of the rarest and most endangered of New World primates, has been the focus of an intensive research and conservation effort for two decades. During that period, managed breeding from 44 founders has brought the captive population to over 400 individuals, a number that equals or exceeds the estimated number of free-ranging golden lion tamarins. The extent of genetic variation among golden lion tamarins was estimated with an electrophoretic survey of 47 allozyme loci from 67 captive and 73 free-ranging individuals. The amount of variation was low, compared to 15 other primate species, with 4% of the loci being polymorphic (P), and with an average heterozygosity H estimate of 0.01 in these callitrichids. Electrophoretic analyses of captive and free-ranging animals (N = 31) of two allopatric morphotypes, Leontopithecus rosalia chrysopygus and L. r. chrysomelas, were similar to the L. r. rosalia findings insofar as they also revealed limited genetic polymorphism. Computation of the Nei-genetic distance measurements showed that the three morphotypes were genetically very similar, although discernible differentiation had occurred at two loci. These data are consistent with the occurrence of recent reproductive isolations of these subspecies.