Effect of new founders on retention of gene diversity in captive populations: A formalization of the nucleus population concept

A nucleus population is a small captive population genetically supported by periodic importation of wild caught animals. Periodic importation will allow nucleus populations to maintain the same amount of gene diversity as larger captive populations that do not import wild caught animals. The function of nucleus populations as envisioned by the IUCN/SSC Captive Breeding Specialist Group (CBSG) is to make additional captive space available for endangered taxa not currently maintained in captivity. In this article, mathematical models are developed to assess the effectiveness of the nucleus population concept in reducing the population sizes necessary to maintain appreciable amounts of gene diversity in captive populations. It is shown that the Nucleus I population concept, as defined and promoted by the CBSG, requires an importation rate 10–20 times greater than they have indicated. Whereas nucleus populations are not appropriate for maintenance of significant amounts of gene diversity in long-term breeding programs, small populations can be valuable for research, education, and reintroduction projects with short-term goals. Decisions have to be made on which of the many endangered taxa will be maintained and for what purposes, if captive breeding is to be an effective component of species conservation. © 1993 Wiley-Liss, Inc.     

One year later: evaluation of PMC‐recommended births and transfers

To meet their exhibition, conservation, education, and scientific goals, members of the American Zoo and Aquarium Association (AZA) collaborate to manage their living collections as single species populations. These cooperative population management programs, Species Survival Plans^® (SSP) and Population Management Plans (PMP), issue specimen‐by‐specimen recommendations aimed at perpetuating captive populations by maintaining genetic diversity and demographic stability. Species Survival Plans and PMPs differ in that SSP participants agree to complete recommendations, whereas PMP participants need only take recommendations under advisement. We evaluated the effect of program type and the number of participating institutions on the success of actions recommended by the Population Management Center (PMC): transfers of specimens between institutions, breeding, and target number of offspring. We analyzed AZA studbook databases for the occurrence of recommended or unrecommended transfers and births during the 1‐year period after the distribution of standard AZA Breeding‐and‐Transfer Plans. We had three major findings: 1) on average, both SSPs and PMPs fell about 25% short of their target; however, as the number of participating institutions increased so too did the likelihood that programs met or exceeded their target; 2) SSPs exhibited significantly greater transfer success than PMPs, although transfer success for both program types was below 50%; and 3) SSPs exhibited significantly greater breeding success than PMPs, although breeding success for both program types was below 20%. Together, these results indicate that the science and sophistication behind genetic and demographic management of captive populations may be compromised by the challenges of implementation. Zoo Biol 0:1–11, 2006. © 2006 Wiley‐Liss, Inc.     

Strategic collection planning: Theory and practice

Strategic collection planning is a relatively new concept for zoos. Until recently, personal preference, availability, and competition determined which species or subspecies were acquired. In the last few years, however, there have been attempts to employ systematic criteria for taxon selection that better serve conservation objectives. Planning currently occurs at three levels: global, regional, and institutional. The current planning process is reviewed and recommendations are made for ways the process might be improved. An efficient, economical, and effective collection planning process is critical if modern, professionally managed zoological institutions are to make a significant impact on wildlife and ecosystem conservation. Rather than selecting taxa solely on the possibility of a future reintroduction, serious consideration should be given to the ability of a species or subspecies to contribute to more immediate conservation goals, including public education, fund raising to support field conservation, and scientific research. Because resources are limited, perhaps zoos should focus their long-term breeding programs primarily on flagship species—that is, those that have the potential to excite public attention and help to protect habitat and other taxa—rather than on a broad array of species that are currently endangered. © 1995 Wiley-Liss, Inc.     

Genetic differentiation in red‐bellied piranha populations (Pygocentrus nattereri,Kner, 1858) from the Solimões‐Amazonas River

Red‐bellied piranhas (Pygocentrus nattereri) are widely caught with different intensities throughout the region of Solimões‐Amazonas River by local fishermen. Thus, the management of this resource is performed in the absence of any information on its genetic stock. P. nattereri is a voracious predator and widely distributed in the Neotropical region, and it is found in other regions of American continent. However, information about genetic variability and structure of wild populations of red‐bellied piranha is unavailable. Here, we describe the levels of genetic diversity and genetic structure of red‐bellied piranha populations collected at different locations of Solimões‐Amazonas River system. We collected 234 red‐bellied piranhas and analyzed throughout eight microsatellite markers. We identified high genetic diversity within populations, although the populations of lakes ANA, ARA, and MAR have shown some decrease in their genetic variability, indicating overfishing at these communities. Was identified the existence of two biological populations when the analysis was taken altogether at the lakes of Solimões‐Amazonas River system, with significant genetic differentiation between them. The red‐bellied piranha populations presented limited gene flow between two groups of populations, which were explained by geographical distance between these lakes. However, high level of gene flow was observed between the lakes within of the biological populations. We have identified high divergence between the Catalão subpopulation and all other subpopulations. We suggest the creation of sustainable reserve for lakes near the city of Manaus to better manage and protect this species, whose populations suffer from both extractive and sport fishing.     

Unexpected genetic differentiation between recently recolonized populations of a long‐lived and highly vagile marine mammal

Many species have been heavily exploited by man leading to local extirpations, yet few studies have attempted to unravel subsequent recolonization histories. This has led to a significant gap in our knowledge of the long‐term effects of exploitation on the amount and structure of contemporary genetic variation, with important implications for conservation. The Antarctic fur seal provides an interesting case in point, having been virtually exterminated in the nineteenth century but subsequently staged a dramatic recovery to recolonize much of its original range. Consequently, we evaluated the hypothesis that South Georgia (SG), where a few million seals currently breed, was the main source of immigrants to other locations including Livingston Island (LI), by genotyping 366 individuals from these two populations at 17 microsatellite loci and sequencing a 263 bp fragment of the mitochondrial hypervariable region 1. Contrary to expectations, we found highly significant genetic differences at both types of marker, with 51% of LI individuals carrying haplotypes that were not observed in 246 animals from SG. Moreover, the youngest of three sequentially founded colonies at LI showed greater similarity to SG at mitochondrial DNA than microsatellites, implying temporal and sex‐specific variation in recolonization. Our findings emphasize the importance of relict populations and provide insights into the mechanisms by which severely depleted populations can recover while maintaining surprisingly high levels of genetic diversity.     

Genome‐wide assessment of diversity and differentiation between original and modern Brown cattle populations

Identifying genomic regions involved in the differences between breeds can provide information on genes that are under the influence of both artificial and natural selection. The aim of this study was to assess the genetic diversity and differentiation among four different Brown cattle populations (two original vs. two modern populations) and to characterize the distribution of runs of homozygosity (ROH) islands using the Illumina Bovine SNP50 BeadChip genotyping data. After quality control, 34 735 SNPs and 106 animals were retained for the analyses. Larger heterogeneity was highlighted for the original populations. Patterns of genetic differentiation, multidimensional scaling, and the neighboring joining tree distinguished the modern from the original populations. The F_ST‐outlier identified several genes putatively involved in the genetic differentiation between the two groups, such as stature and growth, behavior, and adaptability to local environments. The ROH islands within both the original and the modern populations overlapped with QTL associated with relevant traits. In modern Brown (Brown Swiss and Italian Brown), ROH islands harbored candidate genes associated with milk production traits, in evident agreement with the artificial selection conducted to improve this trait in these populations. In original Brown (Original Braunvieh and Braunvieh), we identified candidate genes related with fat deposition, confirming that breeding strategies for the original Brown populations aimed to produce dual‐purpose animals. Our study highlighted the presence of several genomic regions that vary between Brown populations, in line with their different breeding histories.     

Loss of genetic diversity and increased embryonic mortality in non‐native lizard populations

Many populations are small and isolated with limited genetic variation and high risk of mating with close relatives. Inbreeding depression is suspected to contribute to extinction of wild populations, but the historical and demographic factors that contribute to reduced population viability are often difficult to tease apart. Replicated introduction events in non‐native species can offer insights into this problem because they allow us to study how genetic variation and inbreeding depression are affected by demographic events (e.g. bottlenecks), genetic admixture and the extent and duration of isolation. Using detailed knowledge about the introduction history of 21 non‐native populations of the wall lizard Podarcis muralis in England, we show greater loss of genetic diversity (estimated from microsatellite loci) in older populations and in populations from native regions of high diversity. Loss of genetic diversity was accompanied by higher embryonic mortality in non‐native populations, suggesting that introduced populations are sufficiently inbred to jeopardize long‐term viability. However, there was no statistical correlation between population‐level genetic diversity and average embryonic mortality. Similarly, at the individual level, there was no correlation between female heterozygosity and clutch size, infertility or hatching success, or between embryo heterozygosity and mortality. We discuss these results in the context of human‐mediated introductions and how the history of introductions can play a fundamental role in influencing individual and population fitness in non‐native species.     

Fewer S‐alleles are maintained in plant populations with sporophytic as opposed to gametophytic self‐incompatibility

Plants use self‐incompatibility to reject pollen bearing alleles in common at the S‐locus. These systems are classified as gametophytic (GSI) if recognition involves haploid pollen or sporophytic (SSI) if recognition involves diploid paternal genotypes. Dominance in SSI systems reduces the number of S‐alleles, but it has not been clear which system should maintain greater diversity when all else is equal. We simulated finite populations to compare the equilibrium number of S‐alleles in populations with either GSI or a co‐dominant SSI system. When population size was constant, SSI systems maintained more S‐alleles than GSI systems. When populations fluctuated in response to an S‐Allee effect, fewer S‐alleles were observed in SSI systems when S‐allele diversity was low, and SSI populations were vulnerable to extinction over a broader range of parameters. Turnover rates at the S‐locus were also faster in SSI populations experiencing strong S‐Allee effects. Given the variable expectations concerning S‐allele diversity in these systems, we reviewed published estimates of S‐allele diversity. GSI populations have significantly more S‐alleles on average than SSI populations (GSI = 25.70 and SSI = 16.80). Dominance likely contributes to this pattern, although the demographic consequences of the S‐Allee effect may be important in populations with fewer than 10 S‐alleles.     

Short-term effects of nitrogen enrichment, litter removal and cutting on a Mediterranean grassland

Semi-natural grassland communities are of great interest in conservation because of their high species richness. These communities are being threatened by both land abandonment and nitrogen eutrophication, and their continued existence will depend upon correct management. However, there is a distinct lack of studies of the ecological mechanisms that regulate species diversity and productivity in Mediterranean grasslands. We have conducted a 3-year field experiment in a species-poor grassland in central Italy to investigate the effects of nitrogen fertilization coupled with removal of plant litter and artificial cutting on species diversity and community productivity. Vegetation cutting reduced living biomass but increased species diversity. In fact, cutting had positive effects on the cover of almost all of the annual and biennial species, while it had a negative effect on the dominant perennial grasses Brachypodium rupestre and Dactylis glomerata. Litter removal had similar effects to cutting, although it was far less effective in increasing species diversity. In contrast, nitrogen enrichment strongly increased the living biomass while maintaining very low species diversity. Our results have indicated that semi-natural Mediterranean grasslands need specific management regimes for maintenance and restoration of species diversity. In the management of these grasslands, attention should be paid to the potential threat from nitrogen enrichment, especially when coupled with land abandonment.     

栖息地片断化对动物种群间基因流的影响及其测定方法

栖息地片断化指在人为活动和自然干扰下,大面积连续分布的自然栖息地被其它非适宜栖息地分隔成许多面积较小的斑块(岛屿)的过程。栖息地片断化是导致生物多样性丧失和物种绝灭的主要因素,也是威胁自然界生物生存的重要因素之一。栖息地片断化将影响基因在种群间和种群内的运动(基因流),开展栖息地片断化研究对保持物种间遗传多样性具有重要意义。本文介绍了片断化程度和基因流的测定方法。回顾了国内外的研究现状,并探讨了片断化对种群间基因流的影响和对濒危物种保护的意义。     

SNP‐based genetic characterization of the Tulane National Primate Research Center's conventional and specific pathogen‐free rhesus macaque (Macaca mulatta) populations

Background

The rhesus macaque is an important biomedical model organism, and the Tulane National Primate Research Center (TNPRC) has one of the largest rhesus macaque breeding colonies in the United States.

Methods

SNP profiles from 3266 rhesus macaques were used to examine the TNPRC colony genetic composition over time and across conventional or SPF animals of Chinese and Indian ancestry.

Results

Chinese origin animals were the least genetically diverse and the most inbred; however, since their derivation from their conventional forebearers, neither the Chinese nor the Indian SPF animals exhibit any significant loss of genetic diversity or differentiation.

Conclusions

The TNPRC colony managers have successfully minimized loss in genetic variation across generations. Although founder effects and bottlenecks among the Indian animals have been successfully curtailed, the Chinese subpopulation still show some influences from these events.     

Genomewide patterns of variation in genetic diversity are shared among populations,species and higher‐order taxa

Genomewide screens of genetic variation within and between populations can reveal signatures of selection implicated in adaptation and speciation. Genomic regions with low genetic diversity and elevated differentiation reflective of locally reduced effective population sizes (N_e) are candidates for barrier loci contributing to population divergence. Yet, such candidate genomic regions need not arise as a result of selection promoting adaptation or advancing reproductive isolation. Linked selection unrelated to lineage‐specific adaptation or population divergence can generate comparable signatures. It is challenging to distinguish between these processes, particularly when diverging populations share ancestral genetic variation. In this study, we took a comparative approach using population assemblages from distant clades assessing genomic parallelism of variation in N_e. Utilizing population‐level polymorphism data from 444 resequenced genomes of three avian clades spanning 50 million years of evolution, we tested whether population genetic summary statistics reflecting genomewide variation in N_e would covary among populations within clades, and importantly, also among clades where lineage sorting has been completed. All statistics including population‐scaled recombination rate (ρ), nucleotide diversity (π) and measures of genetic differentiation between populations (F_ST, PBS, d_xy) were significantly correlated across all phylogenetic distances. Moreover, genomic regions with elevated levels of genetic differentiation were associated with inferred pericentromeric and subtelomeric regions. The phylogenetic stability of diversity landscapes and stable association with genomic features support a role of linked selection not necessarily associated with adaptation and speciation in shaping patterns of genomewide heterogeneity in genetic diversity.     

Spatio‐temporal patterns of genetic variations in populations of yellowtail kingfish Seriola lalandi from the south‐eastern Pacific Ocean and potential implications for its fishery management

The genetic population structure and genetic diversity of yellowtail kingfish Seriola lalandi from the coastal south‐eastern Pacific Ocean (SEP) were evaluated at spatiotemporal scale in order to understand the ecology of this species. Between 2012 and 2015, temporal and spatial population genetic structure and a low genetic diversity were detected in S. lalandi from SEP. These results suggest that S. lalandi specimens arriving annually from offshore to the SEP coast could come from at least two genetically distinct populations, revealing a particular life strategy (i.e. reproductive or habitat segregation) for this fish species. Therefore, the SEP coast might constitute a point of population mixing for this species. Additionally, the low genetic diversity of S. lalandi in the SEP could be a result of a founder effect or overfishing. Regardless of the process explaining the genetic diversity and structure of S. lalandi in this geographical area, this new information should be considered in order to implement successful fishery management of this resource in the South Pacific.     

Interactions of target population size,population parameters,and program management on viability of captive populations

When established conservation programs expand and evolve, management practices may become inconsistent with program goals. In the past decade, the American Zoo and Aquarium Association expanded species conservation programs by increasing the number of Species Survival Plans (SSP) and establishing more than 300 new Population Management Plan (PMP) programs. However, limited space in captive breeding facilities forces a competition among SSPs and less intensively managed PMPs. Regional Collection Plans establish priorities and allocate space accordingly by setting target population size for each species; species of high conservation priority (SSPs) are allocated space at the expense of lower priority species (PMPs). Because population size and genetic composition interact to impact population viability, target population size is a significant factor to a population’s prospects for long‐term survival. We examined four population parameters (current population size, target population size, current gene diversity, and mean generation time) for 46 mammalian SSPs and 17 PMPs. Relative to SSPs, PMPs combine smaller current and target population sizes, lower levels of current gene diversity, and shorter mean generation times than SSPs. Thus, the average PMP population can expect to lose gene diversity more rapidly than the average SSP population. PMPs are projected to lose 10% or more of their founding gene diversity, within only 2 years. In contrast, the average SSP population is projected to lose 10% in 40 years. Populations with small current or target population sizes require intensive management to avoid extinction. More intensive genetic management of populations typically designated as PMPs, through recruitment of potential founders and equalization of founder representation, could increase gene diversity and improve viability. Less rigorous population management should be reserved for populations whose long‐term survival is either secure or that can be readily replenished from the wild. Because PMP populations need intense genetic management similar to that currently in effect for SSPs, there should be neither a management‐level distinction between programs nor an arbitrary difference in space allocated to programs. Zoo Biol 20:169–183, 2001. © 2001 Wiley‐Liss, Inc.     

The beta-globin gene cluster distribution revisited-patterns in Native American populations

New frequencies for the beta-globin gene cluster haplotypes are presented for the Aché (N = 82 individuals), Guarani (N = 76), and Kaingang (N = 54), three Native South American populations that live in an area between parallels 20 degrees S and 30 degrees S not covered by previous studies at this locus. The haplotype frequencies obtained for the three populations are within the interval observed for 28 other Native American populations. The Aché show much less haplotypes (five) than the other two populations (9-10), the haplotype prevalences being more similar to those of the Guarani than to the Kaingang. The Native American total heterozygosity was about half (0.41) that obtained for the African populations (0.71), but was not much different from those obtained for other continents. A geographical pattern was disclosed in South America by mapping the frequencies of the most common haplotype (haplotype 2), and by means of spatial correlation analysis. The analysis of molecular variance (AMOVA) and pairwise F(ST) data suggest three distinct sectors for the genetic landscape of Native South America: the Andes, the Center/Southeast region, and the Amazon.     

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.     

Genetic variation at twentythree microsatellite loci in sixteen human populations

We have analysed genetic variation at 23 microsatellite loci in a global sample of 16 ethnically and geographically diverse human populations. On the basis of their ancestral heritage and geographic locations, the studied populations can be divided into five major groups, viz. African, Caucasian, Asian Mongoloid, American Indian and Pacific Islander. With respect to the distribution of alleles at the 23 loci, large variability exists among the examined populations. However, with the exception of the American Indians and the Pacific Islanders, populations within a continental group show a greater degree of similarity. Phylogenetic analyses based on allele frequencies at the examined loci show that the first split of the present-day human populations had occurred between the Africans and all of the non-African populations, lending support to an African origin of modern human populations. Gene diversity analyses show that the coefficient of gene diversity estimated from the 23 loci is, in general, larger for populations that have remained isolated and probably of smaller effective sizes, such as the American Indians and the Pacific Islanders. These analyses also demonstrate that the component of total gene diversity, which is attributed to variation between groups of populations, is significantly larger than that among populations within each group. The empirical data presented in this work and their analyses reaffirm that evolutionary histories and the extent of genetic variation among human populations can be studied using microsatellite loci.     

Fine‐scale population structure of Collichtys lucidus populations inferred from microsatellite markers

The spinyhead croaker Collichthys lucidus (Richardson) is a small sciaenid species distributed along the inshore waters of northwestern Pacific Ocean, and now has been listed as Key Protected Commercial Sources of Aquatic Animals and Plants in China. To delineate stock boundaries and inform conservation policy for its management, samples were collected from eight locations across the Chinese coastal waters and analyzed at nine microsatellite loci. C. lucidus populations showed low genetic diversity (expected heterozygosity = 0.445–0.542; observed heterozygosity = 0.392–0.539; Polymorphism Information Content = 0.268–0.684). Strong genetic fdifferentiation (F_st = 0.065–0.510, all significant after Bonferroni correction) among all populations and high levels of self‐recruitment (89.2%–91.5%) were observed, which suggested limited genetic exchange for this species. Clustering results of discriminant analysis of principal components and STRUCTURE found strong support for obvious genetic clusters (populations FZ, XM and SZ vs. populations SH, YRE, ZS, WZ and ND). The results of the present study not only supported the phylogeographic pattern of north‐south differentiation, but also suggested that C. lucidus populations may be predominantly sustained by self‐replenishment rather than by recruitment from distant populations.