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.     

Modeling problems in conservation genetics using captive Drosophila populations: Rapid genetic adaptation to captivity

Long-term captive breeding programs for endangered species generally aim to preserve the option of release back into the wild. However, the success of re-release programs will be jeopardized if there is significant genetic adaptation to the captive environment. Since it is difficult to study this problem in rare and endangered species, a convenient laboratory animal model is required. The reproductive fitness of a large population of Drosophila melanogaster maintained in captivity for 12 months was compared with that of a recently caught wild population from the same locality. The competitive index measure of reproductive fitness for the captive population was twice that of the recently caught wild population, the difference being highly significant. Natural selection over approximately eight generations in captivity has caused rapid genetic adaptation. Captive breeding strategies for endangered species should minimize adaptation to captivity in populations destined for reintroduction into the wild. A framework for predicting the impact of factors on the rate of genetic adaptation to captivity is suggested. Equalization of family sizes is predicted to approximately halve the rate of genetic adaptation. Introduction of genes from the wild, increasing the generation interval, using captive environments close to those in the wild and achieving low mortality rates are all expected to slow genetic adaptation to captivity. Many of these procedures are already recommended for other reasons. © 1992 Wiley-Liss, Inc.     

Modelling problems in conservation genetics using Drosophila: consequences of fluctuating population sizes

Many natural populations fluctuate widely in population size. This is predicted to reduce effective population size, genetic variation, and reproductive fitness, and to increase inbreeding. The effects of fluctuating population size were examined in small populations of Drosophila melanogaster of the same average size, but maintained using either fluctuating ( FPS ) or equal ( EPS ) population sizes.FPS lines were maintained using seven pairs and one pair in alternate generations, and EPS lines with four pairs per generation. Ten replicates of each treatment were maintained. After eight generations, FPS had a higher inbreeding coefficient than EPS (0.60 vs. 0.38), a lower average allozyme heterozygosity (0.068 vs. 0.131), and a much lower relative fitness (0.03 vs. 0.25). Estimates of effective population sizes for FPS and EPS were 3.8 and 7.9 from pedigree inbreeding, and 4.9 vs. 7.1 from changes in average heterozygosities, as compared to theoretical expectations of 3.3 vs. 8.0. Results were generally in accordance with theoretical predictions. Management strategies for populations of rare and endangered species should aim to minimize population fluctuations over generations.     

Rapid genetic deterioration in captive populations: Causes and conservation implications

Many species require captive breeding to ensuretheir survival. The eventual aim of suchprograms is usually to reintroduce the speciesinto the wild. Populations in captivitydeteriorate due to inbreeding depression, lossof genetic diversity, accumulation of newdeleterious mutations and genetic adaptationsto captivity that are deleterious in the wild.However, there is little evidence on themagnitude of these problems. We evaluatedchanges in reproductive fitness in populationsof Drosophila maintained under benigncaptive conditions for 50 generations witheffective population sizes of 500 (2replicates), 250 (3), 100 (4), 50 (6) and 25(8). At generation 50, fitness in the benigncaptive conditions was reduced in smallpopulations due to inbreeding depression andincreased in some of the large populations dueto modest genetic adaptation. When thepopulations were moved to `wild' conditions,all 23 populations showed a marked decline(64–86%percnt;) in reproductive fitness compared tocontrols. Reproductive fitness showed acurvilinear relationship with population size,the largest and smallest population sizetreatments being the worst. Genetic analysesindicated that inbreeding depression andgenetic adaptation were responsible for thegenetic deterioration in `wild' fitness.Consequently, genetic deterioration incaptivity is likely to be a major problem whenlong-term captive bred populations ofendangered species are returned to the wild. Aregime involving fragmentation of captivepopulations of endangered species is suggestedto minimize the problems.     

Genome‐wide regulatory deterioration impedes adaptive responses to stress in inbred populations of Drosophila melanogaster*

Inbreeding depression is often intensified under environmental stress (i.e., inbreeding–stress interaction). Although the fitness consequences of this phenomenon are well‐described, underlying mechanisms such as an increased expression of deleterious alleles under stress, or a lower capacity for adaptive responses to stress with inbreeding, have rarely been investigated. We investigated a fitness component (egg‐to‐adult viability) and gene‐expression patterns using RNA‐seq analyses in noninbred control lines and in inbred lines of Drosophila melanogaster exposed to benign temperature or heat stress. We find little support for an increase in the cumulative expression of deleterious alleles under stress. Instead, inbred individuals had a reduced ability to induce an adaptive gene regulatory stress response compared to controls. The decrease in egg‐to‐adult viability due to stress was most pronounced in the lines with the largest deviation in the adaptive stress response (R² = 0.48). Thus, we find strong evidence for a lower capacity of inbred individuals to respond by gene regulation to stress and that this is the main driver of inbreeding‐stress interactions. In comparison, the altered gene expression due to inbreeding at benign temperature showed no correlation with fitness and was pronounced in genomic regions experiencing the highest increase in homozygosity.     

Modeling the adaptive potential of isolated populations: experimental simulations using Drosophila

The genetic variability underlying many morphological and stress resistance traits may largely depend on the effects of genetic drift balanced by polygenic mutation. This model of adaptive potential has played a central role in the minimum viable population size concept and has been used to predict the effective population size necessary to prevent extinction within changing environments. However, there have been few long-term experimental studies of adaptive potential within isolated populations, and no study has thus far provided an experimental test of the drift-mutation model of quantitative genetic variation. Using the sternopleural bristle number of Drosophila melanogaster as a model quantitative trait, we performed repeated measurements of adaptive potential on 15 replicate populations of two and 10 male-female pairs over 30 and 77 generations, respectively. Declines in adaptive potential were analyzed by comparing observed and expected changes in realized heritability over time. The only significant model deviation occurred immediately after bottlenecks of two pairs, in which greater than expected declines in realized heritability were observed. This result suggests that changes in allelic diversity during bottleneck events may be as important as changes in heterozygosity in determining adaptive potential. Drift-mutation model expectations were otherwise realized over all generations. Our results validate the use of the drift-mutation model as a tool for understanding the dynamics of adaptive potential for peripheral fitness characters, but suggest caution in applying this model to recently bottlenecked populations.     

AlleleRetain: a program to assess management options for conserving allelic diversity in small,isolated populations

Preserving genetic health is an important aspect of species conservation. Allelic diversity is particularly important to conserve, as it provides capacity for adaptation and thus enables long‐term population viability. Allele retention is difficult to predict beyond one generation for real populations with complex demography and life‐history traits, so we developed a computer model to simulate allele retention in small populations. AlleleRetain is an individual‐based model implemented in r and can be applied to assess management options for conserving allelic diversity in small populations of animals with overlapping generations. AlleleRetain remedies the limitations of similar existing software, and its source code is freely available for further modification. AlleleRetain and its supporting materials can be downloaded from https://sites.google.com/site/alleleretain/ or CRAN ( http://cran.r-project.org ).     

Population genetics of Drosophila ananassae: inversion polymorphism and body size in Indian geographical populations

Twelve Indian natural populations of Drosophila ananassae, a cosmopolitan and domestic species, were sampled and laboratory populations (mass cultures) were established from naturally impregnated females. These populations were maintained in the laboratory for some generations and were analysed chromosomally to know the frequency of different inversions. The chromosomal analysis revealed the presence of three cosmopolitan inversions. The data on the whole show that there are significant differences in the frequencies of different chromosome arrangements in these populations. Body size (wing length and thorax length) was measured in both sexes (50 females and 50 males), in all the 12 geographical populations of D. ananassae. There are statistically significant differences in wing length as well as in thorax length of both sexes among different geographical populations. Five geographical strains were crossed reciprocally and body size (wing length and thorax length) was measured in F₁ and F₂ progeny. The comparison of body size (both traits) between mid‐parent, F₁ and F₂ shows that there is an increase in body size in F₁ and F₂ progeny as compared with parents. Thus, there is no break down of heterosis in F₂, which suggests absence of coadaptation in geographical populations of D. ananassae. Scaling test statistical analysis showed additive, dominance and epistatic effects in certain crosses involving geographical strains of D. ananassae. Correlation between chromosome arrangement frequency and body size has also been tested and significant negative correlation has been found between 2L – ST chromosome arrangement and male thorax.     

Assessing losses of genetic diversity due to translocation: long-term case histories in Merriam's turkey (<Emphasis Type="Italic">Meleagris gallopavo merriami</Emphasis>)

Translocation is a widely used tool in wildlife management, but populations established as a result of translocations may be subject to a range of genetic problems, including loss of genetic diversity and founder effects. The genetic impact of single translocation events can be difficult to assess because of complex management histories in translocated or source populations. Here we use molecular markers to assess the genetic impact of three well-documented translocation events, each occurring between 42 and 53 years ago and each originating from a native, extant source population that we also included in our study. Comparing translocated populations to their sources, we found genetic evidence of a recent bottleneck in all three translocated populations, including one which is now a very large, productive population. Based on our results, we recommend caution in (1) using short term census data to assess the long term success of a translocation and (2) conducting serial translocations (i.e., using translocated populations as the source for other translocations), which could exacerbate a genetic bottleneck. We also used the data on translocated populations to investigate the relative utility of three bottleneck detection methods. With this dataset, only assessment of the modal allele frequency distribution, described by Luikart etal. [Journal of Heredity, 89, 238–247 (1998)], provided evidence of a bottleneck in the absence of source population data.     

Sensitivity to larval density in populations of Drosophila mojavensis: Influences of host plant variation on components of fitness

Summary Chromosomally polymorphic populations of Drosophila mojavensis from Baja California feed and breed on agria cactus, Stenocereus gummosus; whereas, monomorphic Arizona populations are associated exclusively with organ pipe cactus, S. thurberi. The effects of this host plant shift in expanding the kinds of feeding and breeding sites were assessed by manipulating larval density and recording differences in egg to adult development time and viability, and adult thorax size in both populations on artificially rotted substrates of both cactus species. Older agria rots increased development time but had no effect on viability. Organ pipe rots were qualitatively poorer substrates than agria rots for both monomorphic and polymorphic populations of D. mojavensis, especially at higher larval densities causing longer egg to adult development times, lower viabilities, and smaller thorax sizes than agria.The Baja population expressed shorter development times, higher viabilities, and smaller thorax sizes than the Arizona population on both cactus substrates. No evidence for cactus host race formation was found. The Baja population was less sensitive to increasing larval densities for all fitness characters studied on both cactus substrates indicating greater developmental homeostasis than in the monomorphic Arizona population. These data support the hypothesized central-marginal population structure within this species coincident with the distribution of host plants and lend insight into the process of adaptive divergence at different life history stages caused by host plant shifts.     

Usher syndrome in the Samaritans: Strengths and limitations of using inbred isolated populations to identify genes causing recessive disorders

We have previously reported significant linkage between markers on 11q13.5 and Usher syndrome type 1 (USH1B) in a large Samaritan kindred. USH1B is an autosomal recessive disease characterized by profound congenital sensorineural deafness, vestibular dysfunction and progressive visual loss. A unique haplotype found only in all USH1B carriers and affected individuals implied that the disease-causing mutation probably entered the community from a single founder. Screening for mutations in a gene called GARP, which was mapped to the same genetic interval as USH1B, revealed a base substitution in the coding region of the gene, in a homozygous state in all affected individuals. This base substitution, which results in an arginine to tryptophane change, is not found in control individuals and occurs at an amino acid residue that is conserved across species, including mouse, gorilla, chimpanzee and macaque. This study emphasizes the strength of using an isolated inbred population for efficient identification of the primary linkage and for narrowing the disease interval, but also demonstrates its limitations in distinguishing between mutations causing the disease and those representing unique and private polymorphisms. Am J Phys Anthropol 104:193–200, 1997. © 1997 Wiley-Liss, Inc.     

Modeling senescence changes of the pubic symphysis in historic Italian populations: A comparison of the Rostock and forensic approaches to aging using transition analysis

Age‐related anatomical changes to the surface of the pubic symphysis are well‐documented in the literature. However, aligning these morphological changes with chronological age has proven problematic, often resulting in biased age estimates. Statistical modeling provides an avenue for forensic anthropologists and bioarchaeologists to increase the accuracy of traditional aging methods. Locating appropriate samples to use as a basis for modeling age estimations can be challenging due to differing sample age distributions and potentially varying patterns of senescence. We compared two approaches, Rostock and Forensic, coupled with a Bayesian methodology, to address these issues. Transition analysis was run specific to each method (which differ by sample selection). A Gompertz model was derived from an informative prior that yielded the mortality and senescence parameters for constructing highest posterior density ranges, i.e., coverages, which are analogous to age ranges. These age ranges were generated from both approaches and are presented as reference tables useful for historic male and female Italian samples. The age ranges produced from each approach were tested on an historic Italian sample, using cumulative binomial tests. These two approaches performed similarly, with the Forensic approach showing a slight advantage. However, the Forensic approach is unable to identify varying senescence patterns between populations, thus preference for one approach over the other will depend on research design. Finally, we demonstrate that while populations exhibit similar morphological changes with advancing age, there are no significant sex differences in these samples, and the timing of these changes varies from population to population. Am J Phys Anthropol 156:466–473, 2015. © 2014 Wiley Periodicals, Inc.