Selective recovery of founder genetic diversity in aquacultural broodstocks and captive, endangered fish populations

Hatchery broodstocks used for genetic conservation or aquaculture may represent their ancestral gene pools rather poorly. This is especially likely when the fish that found a broodstock are close relatives of each other. We re-analysed microsatellite data from a breeding experiment on red sea bream to demonstrate how lost genetic variation might be recovered when gene frequencies have been distorted by consanguineous founders in a hatchery. A minimal-kinship criterion based on a relatedness estimator was used to select subsets of breeders which represented the maximum number of founder lineages (i.e., carried the fewest identical copies of ancestral genes). UPGMA clustering of Nei's genetic distances grouped these selected subsets with the parental gene pool, rather than with the entire, highly drifted offspring generation. The selected subsets also captured much of the expected heterozygosity and allelic diversity of the parental gene pool. Independent pedigree data on the same fish showed that the selected subsets had more contributing parents and more founder equivalents than random subsets of the same size. The estimated mean coancestry was lower in the selected subsets, meaning that inbreeding in subsequent generations would be lower if they were used as breeders. The procedure appears suitable for reducing the genetic distortion due to consanguineous and over-represented founders of a hatchery gene pool.     

Prevalence of Leucocytozoon marchouxi in the endangered Pink Pigeon Columba mayeri

The prevalence and density of infection with the haematozoan parasite Leucocytozoon marchouxi was studied in captive and free-living Pink Pigeons Columba mayeri on Mauritius between 1994 and 2002. Blood smears from adults, juveniles and squabs were screened. Overall prevalence of L. marchouxi was 30% and there were age class and year differences. Younger birds (≤ 1 year) were more often infected and had a higher density of infection than did older birds. High parasite levels were found in 6% of birds, all but one of which were less than 1 year old. Leucocytozoonosis has been recorded elsewhere in 20 out of 45 Pink Pigeons post-mortem and was the primary cause of death in 15 birds. However, we detected no significant difference in the survival of infected and uninfected birds examined in this study, suggesting that only subclinical infections were detected and any mortality was probably due to additional contributing factors such as concurrent disease and food shortages. A smaller sample of smears from other columbid species was collected to examine their role as reservoir hosts. The parasite was probably introduced to Mauritius with exotic columbids, which may be partially resistant, but the Pink Pigeon has acquired sufficient immunity now to be a maintenance host for the parasite.     

Inbreeding effects in captive populations of ruffed lemurs

The two subspecies of ruffed lemurs (Vareica variegata variegata andVarecia variegata rubra) have been maintained in captivity since 1959 and all institutions which hold ruffed lemurs have contributed data to theVarecia International Studbook. Studbook data were used to analyze inbreeding effects on survival in both subspecies ofVarecia. Several variables, including offspring's inbreeding coefficient, litter size, mother's inbreeding coefficient, and mother's age, were examined for significant associations with percent survivorship per litter. Percent survivorship per litter was negatively correlated to the offspring inbreeding coefficient in the black and white ruffed lemurs (p<0.001) but no significant association was found for red ruffed lemurs. Although emphasis has been put towards the status of the red ruffed lemurs due to the small founder size, the black and white ruffed lemurs should also be managed with care due to the lower tolerance to inbreeding in captivity.     

Inbreeding and fitness in captive populations: Lessons from Drosophila

The avoidance of inbreeding is a primary goal of endangered species population management. In order to fully understand the effects of inbreeding on the fitness of natural and captive populations, it is necessary to consider fitness components which span the entire life cycle of the organism. Using Drosophila melanogaster as a model organism for conservation genetics studies, we constructed 18 experimental lines derived from wild-type stocks which were homozygous for chromosome 2 (this chromosome constitutes 38% of the genome or is equivalent to F = 0.38). For six of these lines which exhibited a reduced homozygous fitness, we estimated the relative values of fitness components operating at both the juvenile stage (pre-adult viability) and adult stage (female fecundity and male-mating ability) of the life cycle. Males in these lines showed a markedly reduced mating ability, while viability and female fecundity were much less affected. Equilibrium values of the wild-type chromosomes in these lines were accurately predicted using a model that incorporated into it these independently estimated fitness components. These results emphasize the importance of studying all fitness components directly to determine overall fitness. A reduced mating ability among inbred males of a captive population can have serious consequences for its future sustainability, and can further jeopardize reintroduction efforts; consequently, a program to carefully monitor the reproductive success of individual males, as well as other fitness components, is recommended. © 1993 Wiley-Liss, Inc.     

Cooling and freezing of sperm from captive,free-living and endangered squirrel monkey species

Germoplasm banking is an important tool for the preservation of genetic material from Neotropical primates in captivity, and from free living species, especially the endangered ones like Saimiri vanzolinii (Black-headed squirrel monkey), a primate with a low incidence area (870 km² of floodplains) in the southern part of the Mamirauá Sustainable Development Reserve, Brazil. Therefore, in the present study we aimed to develop a sperm cryopreservation protocol comparing sperm cooling in presence (T1) and absence (T2) of egg yolk, and to test freezing protocols to preserve semen from captive (Saimiri collinsi), and free-living (Saimiri vanzolinii, Saimiri cassiquiarensis and Saimiri macrodon) New World primates. Cooling preserved sperm of S. collinsi in all evaluated microscopic parameters, except for sperm motility. No differences were observed among the treatments, indicating that semen of this species can be cooled without egg yolk. Freezing did not affect sperm quality of S. collinsi, except plasma membrane integrity that was negatively affected. Generally, a good maintenance rate was observed between cooling and thawing of semen for the four species, showing the positive translational application of protocols from S. collinsi to the free-living species. Developed freezing protocol proved to be useful for sperm cryopreservation of S. collinsi and in field conditions.     

Clinical and pathological studies on the Mauritian Pink Pigeon Columba mayeri

Six Pink Pigeons Columba = Nesoenas mayeri from the captive breeding project on Mauritius which showed a range of physical abnormalities were examined clinically and post mortem. Significant findings included a pedal deformity in several birds and cerebellar hypoplasia/aplasia in another. Parasites were not detected and none of the birds showed serum antibodies to Newcastle disease virus, Paramyxovirus or Chlamydia psittaci. The results are of relevance to the captive breeding and management of this endangered species.     

Inbreeding trends and genetic diversity in purebred sheep populations

Monitoring the rate of change in inbreeding and genetic diversity within a population is important to guide breeding programmes. Such interest stems from the impact of loss in genetic diversity on sustainable genetic gain but also the impact on performance (i.e. inbreeding depression). The objective of the present study was to evaluate trends in inbreeding and genetic diversity in 43 066 Belclare, 120 753 Charollais, 22 652 Galway, 78 925 Suffolk, 187 395 Texel, and 19 821 Vendeen purebred sheep. The effective population size for each of the six breeds was between 116.0 (Belclare population) and 314.8 (Charollais population). The Charollais population was the most genetically diverse with the greatest number of effective founders, effective ancestors, and effective founder genomes; conversely, the Belclare was the least genetically diverse population with the fewest number of effective founders, effective ancestors, and effective founder genomes for each of the six breeds investigated. Overall, the effective population sizes and the total genetic diversity within each of the six breeds were above the minimum thresholds generally considered to be required for the long-term viability of a population.     

Inbreeding depression in insular and central populations of Peromyscus mice

We tested the hypothesis that small, isolated populations would show less depression in fitness when inbred than would large, central populations. Laboratory stocks of Peromyscus leucopus and P. polionotus were established from insular, peninsular, and central populations. The isolated populations had one-third to one-half the genic diversity of central populations. Responses to inbreeding were highly varied: some populations had smaller litters, others experienced higher mortality, some showed slower growth rates, and one displayed no measurable effects when inbred. These results suggest that inbreeding depression is controlled by a small number of genes and that the size of the genetic load depends on which alleles are present in the founders of a population. The severity of fitness depression in inbred litters did not correlate with initial genic diversity of the stocks nor, therefore, with the size of the wild populations. Fitness measures appeared linearly related to the inbreeding coefficient of the liters, with no diminution of deleterious effects through subsequent generations of inbreeding. Thus overdominance of fitness traits probably contributed as much to the genetic load as did deleterious recessive alleles. The inbreeding level of the dam negatively affected the size, growth, and survival of litters only in genetically diverse populations, indicating that the load of recessive alleles negatively impacting maternal care may have been reduced by selection in the more peripheral populations during past bottlenecks.     

Inbreeding depression in self-incompatible and self-compatible populations of Leavenworthia alabamica

Inbreeding depression is one of the leading factors preventing the evolution of self-fertilization in plants. In populations where self-fertilization evolves, theory suggests that natural selection against partially recessive deleterious alleles will reduce inbreeding depression. The purpose of this study was to evaluate this hypothesis by comparing the magnitude of inbreeding depression in self-incompatible and self-compatible populations of Leavenworthia alabamica. Within-population crosses were conducted to compare the quantity and quality of offspring produced by outcrossing and self-fertilization. These progeny were grown in a common greenhouse and inbreeding depression was measured in germination, survival, biomass, transition rate to flowering, flower number, petal length, pollen grains/anther, pollen viability, and ovule number. In comparison to outcrossing, self-fertilization led to the production of fewer and smaller seeds within self-incompatible populations. Moreover, inbreeding depression was observed in eight of 11 offspring traits within self-incompatible populations of L. alabamica. In contrast, there was significant inbreeding depression only in flower number within self-compatible populations. The results of this study are consistent with the idea that self-fertilization selectively removes partially recessive deleterious alleles causing inbreeding depression in natural plant populations. However, in plant species such as L. alabamica where self-compatibility may evolve in small populations following long-distance dispersal, declines in inbreeding depression may also be facilitated by genetic drift.     

Phylogeography of the endangered Otago skink, Oligosoma otagense: population structure, hybridisation and genetic diversity in captive populations

Climatic cooling and substantial tectonic activity since the late Miocene have had a pronounced influence on the evolutionary history of the fauna of New Zealand's South Island. However, many species have recently experienced dramatic range reductions due to habitat fragmentation and the introduction of mammalian predators and competitors. These anthropogenic impacts have been particularly severe in the tussock grasslands of the Otago region. The Otago skink (Oligosoma otagense), endemic to the region, is one of the most critically endangered vertebrates in New Zealand. We use mitochondrial DNA sequence data to investigate the evolutionary history of the Otago skink, examine its population genetic structure, and assess the level of genetic diversity in the individuals in the captive breeding program. Our data indicate that the Otago skink diverged from its closest relatives in the Miocene, consistent with the commencement of tectonic uplift of the Southern Alps. However, there is evidence for past introgression with the scree skink (O. waimatense) in the northern Otago-southern Canterbury region. The remnant populations in eastern Otago and western Otago are estimated to have diverged in the mid-Pliocene, with no haplotypes shared between these two regions. This divergence accounts for 95% of the genetic diversity in the species. Within both regions there is strong genetic structure among populations, although shared haplotypes are generally evident between adjacent localities. Although substantial genetic diversity is present in the captive population, all individuals originate from the eastern region and the majority had haplotypes that were not evident in the intensively managed populations at Macraes Flat. Our data indicate that eastern and western populations should continue to be regarded as separate management units. Knowledge of the genetic diversity of the breeding stock will act to inform the captive management of the Otago skink and contribute to a key recovery action for the species.     

Inbreeding and inbreeding depression in endangered red wolves (Canis rufus)

In natural populations, the expression and severity of inbreeding depression can vary widely across taxa. Describing processes that influence the extent of inbreeding and inbreeding depression aid in our understanding of the evolutionary history of mating systems such as cooperative breeding and nonrandom mate selection. Such findings also help shape wildlife conservation theory because inbreeding depression reduces the viability of small populations. We evaluated the extent of inbreeding and inbreeding depression in a small, re‐introduced population of red wolves (Canis rufus) in North Carolina. Since red wolves were first re‐introduced in 1987, pedigree inbreeding coefficients (f) increased considerably and almost every wild born wolf was inbred (average f = 0.154 and max f = 0.383). The large inbreeding coefficients were due to both background relatedness associated with few founders and numerous close relative matings. Inbreeding depression was most evident for adult body size and generally absent for direct fitness measures such as reproductive success and survival; no lethal equivalents (LE = 0.00) were detected in juvenile survival. The lack of strong inbreeding depression in direct measures of fitness could be due to a founder effect or because there were no outbred individuals for comparison. Our results highlight the variable expression of inbreeding depression across traits and the need to measure a number of different traits when evaluating inbreeding depression in a wild population.     

Inbreeding depression in small populations of self-incompatible plants.

Self-incompatibility (SI) is a widespread mechanism that prevents inbreeding in flowering plants. In many species, SI is controlled by a single locus (the S locus) where numerous alleles are maintained by negative frequency-dependent selection. Inbreeding depression, the decline in fitness of selfed individuals compared to outcrossed ones, is an essential factor in the evolution of SI systems. Conversely, breeding systems influence levels of inbreeding depression. Little is known about the joint effect of SI and drift on inbreeding depression. Here we studied, using a two-locus model, the effect of SI (frequency-dependent selection) on a locus subject to recurrent deleterious mutations causing inbreeding depression. Simulations were performed to assess the effect of population size and linkage between the two loci on the level of inbreeding depression and genetic load. We show that the sheltering of deleterious alleles linked to the S locus strengthens inbreeding depression in small populations. We discuss the implications of our results for the evolution of SI systems.     

Genetic diversity among endangered Uruguayan populations of Butia Becc. species based on ISSR

The genus Butia Becc. (Arecaceae) comprises 18 species distributed exclusively in South America, four of them in Uruguay: Butia lallemantii, B. paraguayensis, B. yatay and B. capitata. All species show serious regeneration problems which jeopardise their continuity in the near future. Butia lallemantii and B. paraguayensis are in the most critical situation, with restricted distributions (fragmented and reduced by cattle grazing and forestation) and populations with few individuals. Taxonomy in the genus is complex, and species delimitation remains unclear. The aim of this study was to examine the genetic variability of natural populations of B. paraguayensis, B. lallemantii and B. yatay, based on inter?Csimple sequence repeat markers, in view of long term conservation plans and to assist the taxonomic resolution of these closely related species. Twenty individuals from each population were sampled including four populations of B. lallemantii, three of B. yatay and the only B. paraguayensis population reported for Uruguay. Syagrus romanzoffiana was used as outgroup. Five primers were selected based on amplification profiles. Relationships among species were evaluated by constructing dendrograms and principal coordinates analysis. Genetic distance analyses indicate the existence of low variability among Butia species. Variability within populations was high, possibly due to gene flow, past hybridisation or life history traits. This variability provides great potential for recovery. Results do not allow us to suggest changes to the present taxonomic status of these species. We propose management recommendations involving restoration of recruitment and augmentation via stocks from within populations.     

Patterns of genetic diversity of mitochondrial DNA within captive populations of the endangered itasenpara bitterling: implications for a reintroduction program

In this study, the level of genetic diversity of captive populations of the itasenpara bitterling (Acheilognathus longipinnis) was assessed to obtain information useful for successful captive breeding and reintroduction; this analysis was performed using mitochondrial DNA (mtDNA) sequence data. Comparison of the captive and wild populations showed low levels of genetic diversity within the captive population and significant genetic differentiation among the captive populations and also between the wild and captive populations, suggesting at chance effect during the founding process for the captive population and a subsequent genetic drift. Therefore, for successful reintroduction, it is important that the reintroduced population reflects all the genetic diversity available from the captive populations, and that releasing a large number of individuals that consist of all captive 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.     

Patterns of differentiation among endangered pondberry populations

Pondberry, Lindera melissifolia, is an endangered and partially clonally reproducing shrub species found in isolated populations that inhabit seasonally wet depressions in forested areas of the lower Mississippi River alluvial valley and southeastern regions of the United States. With eleven microsatellite loci, we quantified population genetic differentiation and diversity among 450 genets in 10 locations distributed across pondberry’s range. We used estimates of F _st and Jost’s D _est to measure genetic differences between populations and between geographic regions. The largest pairwise regional difference was found between eastern and western regional population groups (F _st = 0.23, D _est = 0.67), with the northern-most population groups in each region exhibiting larger divergence from each other than the southern-most population groups. Genetic diversity was lowest in the Sand Pond Conservation Area (A _e = 1.9, H _e = 0.36), which was the northern-most pondberry population, and highest in the Francis Marion National Forest (A _e = 4.1, H _e = 0.69), although we identified only 17 genets in that admixed population. Following adjustments for estimated null allele frequencies, we identified heterozygote excess in four eastern populations and found no evidence for inbreeding in any population. The observed patterns of differentiation indicate a phylogeography that exhibits an Appalachian Mountain discontinuity coupled with northward migrations along the Southern Atlantic Coastal Plain and into the Mississippi Alluvial Plain. The genetic consequences of this proposed phylogeographical structure may affect selection of germplasm sources for population reestablishment programs across pondberry’s range.     

Genetic diversity within and among populations of the endangered and endemic species Primula merrilliana in China

Primula merrilliana Schltr. is an endangered and narrowly-distributed endemic species of southern Anhui Province in China. In this study, the level of genetic variation and the pattern of genetic structure in six natural populations of P. merrilliana were assessed by using ISSR (inter-simple sequence repeats) markers. Based on ten primers, 137 clear and reproducible DNA fragments were generated, of which 109 were polymorphic. The statistical results indicated that there was a relatively low genetic diversity within populations, and a high genetic differentiation among populations (G_ST = 0.53, Φ_ST = 0.49). The level of population genetic diversity was correlated to habitat type and the gene flow (N_m) was low with only 0.45. The unexpected genetic structure of P. merrilliana may be explained by limited gene flow that was caused by habitat fragmentation and limited seeds and pollen dispersal ability, self-compatible breeding system and biennial life form.     

Inbreeding and promiscuity in the endangered grand skink

The inbreeding avoidance hypothesis predicts that organisms that often encounter relatives as potential mates should evolve behaviours to avoid incestuous matings. Avoidance behaviours have practical importance for small populations because deleterious genetic processes may be less imminent than otherwise expected from genetic models that assume random mating. I used genetic techniques to investigate the extent of inbreeding and inbreeding avoidance behaviours in rare lizards from southern New Zealand. Grand skinks, Oligosoma grande, live in small patchily distributed groups, and have low rates of inter-group dispersal (ca. 3–20% disperse). I used data from 15 microsatellite loci to test the hypothesis that adults are likely to encounter kin as potential mates and will inbreed. These data showed that adult skinks usually inhabited rock outcrops with adult relatives of the opposite sex – up to 35% of potential mates were of equivalent relatedness as half-sibs and 17% were equivalent to full sibs. However, skinks did not preferentially breed with less related mates, and 18.2% of matings were between individuals of equivalent relatedness as full-sibs. Instead, skinks mated with partners of all levels of relatedness, and were promiscuous – almost half of adult females and nearly three quarters of adult males reproduced with multiple partners. In addition, inbreeding had no effect on survival of offspring in their first year. Two other putative mechanisms of inbreeding avoidance, sex-biased and natal dispersal, were not pronounced in this species. This study adds to a growing list of species that inbreed despite the risks.     

An investigation of inbreeding depression and purging in captive pedigreed populations

We use regression models to investigate the effects of inbreeding in 119 zoo populations, encompassing 88 species of mammals, birds, reptiles and amphibians. Meta-analyses show that inbreeding depression for neonatal survival was significant across the 119 populations although the severity of inbreeding depression appears to vary among taxa. However, few predictors of a population's response to inbreeding are found reliable. The models are most likely to detect inbreeding depression in large populations, that is, in populations in which their statistical power is maximised. Purging was found to be significant in 14 populations and a significant trend of purging was found across populations. The change in inbreeding depression due to purging averaged across the 119 populations is <1%, however, suggesting that the fitness benefits of purging are rarely appreciable. The study re-emphasises the necessity to avoid inbreeding in captive breeding programmes and shows that purging cannot be relied upon to remove deleterious alleles from zoo populations.     

濒危植物资源冷杉遗传多样性研究

资源冷杉(Abies ziyuanensis)属松科(Pinaceae)冷杉属(Abies),是国家一级保护的濒危植物。利用RAPD分子标记对分布于广西资源县银竹老山和湖南省炎陵县大院的2个资源冷杉种群共54株进行了遗传多样性分析。用20个随机引物共扩增到126个位点,其中66个位点是多态性的,总的多态位点百分率为52.4％,在两个种群分别为33.6％和31。2％。Nei's基因多样性为0.312,Shannon信息指数为0.475,两个种群的遗传分化系数Gst为0.455。基于Nei's遗传距离进行了UPGMA聚类分析,结果两种群的样品彼此明显区分开来。分析结果表明资源冷杉种群内的遗传多样性较低,但两种群间的遗传分化明显。需要同时重视两分布地的资源冷杉的保护工作。