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PubMed2002

Perceptions of genetics research as harmful to society: differences among samples of African-Americans and European-Americans.

Genetics has the potential not only to find cures for diseases, but to possess the mechanisms to change the bio-social make-up of populations. A specific question that has arisen on this issue is how developments in genetic technology may intersect with existing race and ethnic relations. Evidence of the racialization of some genetic disorders has been demonstrated elsewhere. The purpose of this study is to compare and contrast African-American and European-American attitudes on the benefits of genetics research for society. Findings show that African-Americans were more likely to say genetics research is harmful for society. This relationship remained statistically significant after controls were introduced in a regression model. Demographic characteristics and self-rated knowledge of genetics had no effect on attitudes among African-Americans. A willingness to use genetic services correlated with favorable attitudes. Differences in social position may lead some groups to opposing interpretations and symbolic meanings of genetics. This may be true in the context of this study because the social meanings of genetics may be tainted by racialization, historical attempts at eugenics, and the potential abuse of genetics targeting groups partially defined by superficial genetic characteristics.

Black or African American↗

PubMed1997

The probability of fixation in populations of changing size.

The rate of adaptive evolution of a population ultimately depends on the rate of incorporation of beneficial mutations. Even beneficial mutations may, however, be lost from a population since mutant individuals may, by chance, fail to reproduce. In this paper, we calculate the probability of fixation of beneficial mutations that occur in populations of changing size. We examine a number of demographic models, including a population whose size changes once, a population experiencing exponential growth or decline, one that is experiencing logistic growth or decline, and a population that fluctuates in size. The results are based on a branching process model but are shown to be approximate solutions to the diffusion equation describing changes in the probability of fixation over time. Using the diffusion equation, the probability of fixation of deleterious alleles can also be determined for populations that are changing in size. The results developed in this paper can be used to estimate the fixation flux, defined as the rate at which beneficial alleles fix within a population. The fixation flux measures the rate of adaptive evolution of a population and, as we shall see, depends strongly on changes that occur in population size.

Alleles↗

PubMed1997

Population dynamics inferred from temporal variation at microsatellite loci in the selfing snail Bulinus truncatus.

We analyzed short-term forces acting on the genetics of subdivided populations based on a temporal survey of the microsatellite variability in the hermaphrodite freshwater snail Bulinus truncatus. This species inhabits temporary habitats, has a short generation time and exhibits variable rates of selfing. We studied the variability over three sampling dates in 12 Sahelian populations (1161 individuals). Classical genetic parameters (estimators of Ho, He, f, selfing rate and Fst) showed limited change over time whereas important temporal changes of allelic frequencies were detected for 10 of the ponds studied. These variations are not easily explained by selection, sampling drift and genetic drift alone and may be due to periodic migration. Indeed the habitats occupied by the populations studied are subject to large temporal fluctuations owing to annual cycles of drought and flood. In such ponds our results support a demographic model of population expansions and contractions under which available habitats, after the rainy season, are colonized by individuals originating from a smaller number of refuges (areas that never dry out in the deepest parts of the ponds). In contrast, selfing appeared to be an important force affecting the genetic structure in permanent ponds.

Animals↗

PubMed2001

Immigration and the regional demographics of the elderly population in the United States.

OBJECTIVES: This research examined the impacts of past international and interregional migration flows on regional elderly population growth and distribution patterns. METHODS: The authors used 1960, 1970, 1980, and 1990 Census data and multiregional demographic models to analyze changes in the sources of regional elderly population growth rates, age compositions, and spatial distributions over time. RESULTS: Past elderly interregional migration patterns have exhibited considerable stability and have contributed less than aging-in-place in shaping regional elderly population geographies. Also the effects of immigration on elderly dependency ratios have been very modest. DISCUSSION: Little evidence exists of any significant breaks with past trends in internal elderly migration patterns. Reconstruction of elderly population changes between 1950 and 1990 reveals that the driving force behind the changes was net aging-in-place and not net migration. Finally, analysis of the possible population rejuvenating effects of immigration suggests that although its impact has contributed to lower elderly-to-worker dependency ratios, its level over the past decades has been insufficient to counteract the much stronger countervailing impact of population aging.

Aged↗

PubMed2026

Targeted population genomics uncovers demographic history and genetic divergence in north American wild cranberry.

Wild populations of North American cranberry (Vaccinium macrocarpon Aiton) are reservoirs of genetic variation that may contribute to the improvement of breeding-relevant traits. However, the extent to which wild genetic variation is geographically structured and represented in elite germplasm remains unclear. We analysed 179 wild cranberry accessions from the upper Midwest and Eastern North America to estimate nucleotide diversity (π), population structure, and loci associated with genetic differentiation and environmental variables using a genome-informed targeted genotyping panel. Additionally, 14 demographic scenarios were evaluated using site-frequency-spectrum-based inference to identify historical events that could explain current genetic diversity. We observed extremely low nucleotide diversity within the targeted panel (π = 5 × 10-6). Rare allele distributions strongly influenced π and Tajima's D values, suggesting constrained diversity in the genomic regions assayed that is not captured by heterozygosity-based estimates alone. However, we interpreted these results as conservative lower bounds on genome-wide neutral diversity because the targeted panel is enriched for genic and conserved regions. A clear separation between the Midwest and East populations was observed, with inbreeding coefficients ranging from -0.13 to 0.15. Furthermore, site frequency spectrum inference from the targeted panel supported a demographic scenario consistent with a significant population reduction ≈15-14 thousand years ago (kya), followed by a divergence between the two regions ≈12 kya, and an asymmetric gene flow ≈1.3 kya. We detected 254 candidate loci showing regional allele-frequency differentiation. Several of these loci colocalized with candidate genes linked to stress response, development, and metabolic processes. To evaluate the representation of geographically differentiated wild alleles in a breeding context, we analysed Rutgers breeding materials (n = 484) and found that this panel is enriched for common alleles in Eastern wild populations. These findings indicate regionally structured allele-frequency variation in wild cranberry, with potential relevance to environmental response and breeding. This study extends prior wild cranberry population-genetic research by providing targeted-panel estimates of diversity, comparisons of demographic models, and breeding insights on geographically differentiated alleles, while highlighting the importance of conserving wild cranberry germplasm for use in modern breeding programs.

Journal Article↗

PubMedDate not supplied

Determinants of effective population size for loci with different modes of inheritance.

Here we report an assessment of the determinants of effective population size (N(e)) in species with overlapping generations. Specifically, we used a stochastic demographic model to investigate the influence of different life-history variables on N(e)/N (where N = population census number) and the influence of sex differences in life-history variables on N(e) for loci with different modes of inheritance. We applied an individual-based modeling approach to two datasets: one from a natural population of savannah baboons (Papio cynocephalus) in the Amboseli basin of southern Kenya and one from a human tribal population (the Gainj of Papua New Guinea). Simulation-based estimates of N(e)/N averaged 0.329 for the Amboseli baboon population (SD = 0.116, 95% CI = 0.172 - 0.537) and 0.786 for the Gainj (SD = 0.184, 95% CI = 0.498 - 1.115). Although variance in male fitness had a substantial impact on N(e)/N in each of the two primate populations, ratios of N(e) values for autosomal and sex-linked loci exhibited no significant departures from Poisson-expected values. In each case, similarities in sex-specific N(e) values were attributable to the unexpectedly high variance in female fitness. Variance in male fitness resulted primarily from age-dependent variance in reproductive success, whereas variance in female fitness resulted primarily from stochastic variance in survival during the reproductive phase.

Alleles↗

PubMed2026

Past genomes guide future conservation: insights from extinct populations of the endangered Pacific pocket mouse.

Efforts to recover endangered species often rely on restoring populations to their historical range, yet reestablishing lost genetic variation is challenging when the ancestral genetic landscape is poorly understood. The Pacific pocket mouse (Perognathus longimembris pacificus), a federally endangered heteromyid rodent, has been extirpated from most of its range in coastal southern California. Recovery efforts call for establishing new populations in their historic range through translocation, but the extent to which historical patterns of genetic variation can be recapitulated is unknown. To inform conservation planning, we sequenced whole genomes of historical samples, including individuals from populations that went extinct in the mid-1900s. Phylogenetic analyses revealed that mice from the southernmost extirpated population form a clade with a different subspecies, while populations to the north form a sister clade. These findings support morphological evidence calling for a taxonomic revision, which would modify the definition of the historic range and complicate the interpretation of suitable reintroduction sites. Despite this divergence, D-statistics and demographic models indicate historical gene flow among coastal populations, suggesting that alleles reintroduced to the southern coast may echo ancestral connectivity. Thus, management efforts should consider potential receiver sites that contain suitable habitat within this range as viable for population creation. These results highlight the value of historical genomics in guiding conservation decisions, particularly when taxonomic uncertainty, extirpation, and limited genetic diversity constrain modern management. Although historical baselines often cannot be restored, conservation strategies can leverage genomic insights to enhance future adaptive potential and long-term resilience of threatened species.

Endangered Species↗

PubMed2025

Host-Associated Genetic Differentiation in the Face of Ongoing Gene Flow: Ecological Speciation in a Pathogenic Parasite of Freshwater Fish.

Adaptive evolution in response to varying environments, leading to population divergence, is among the most intriguing processes of speciation. However, the extent to which these adaptive processes effectively drive population divergence amidst ongoing gene flow remains controversial. Our study addresses this by analyzing population genetic structure, gene flow, and genomic divergence between lineages of a tapeworm parasite (Ligula intestinalis) isolated from sympatric fish hosts. This parasite, which must overcome host immunological defenses for successful infection, significantly impacts host health. Utilizing genome-wide Single Nucleotide Polymorphisms (SNPs) and transcriptome data, we investigated whether host species impose distinct selection pressures on parasite populations. Genetic clustering analyses revealed clear divergence, with parasites from bream (Abramis brama) forming a distinct genetic cluster separate from those infecting roach (Rutilus rutilus), rudd (Scardinius erythrophthalmus), and bleak (Alburnus alburnus). Demographic modeling indicated isolation with continuous gene flow as the most plausible scenario for this divergence. Selection analyses identified 896 SNPs under selection, displaying low to moderate nucleotide diversity and genetic divergence compared with neutral loci. Transcriptome profiling supported these findings, revealing distinct gene expression profiles between parasite populations. Examination of selected SNPs and differentially expressed genes identified candidate genes linked to immune evasion mechanisms, potentially driving ecological speciation. This research highlights the interplay of host specificity, population demography, and disruptive selection in ecological speciation. By dissecting genomic factors, our study improves the understanding of mechanisms facilitating population divergence despite ongoing gene flow.

Animals↗

PubMed2026

Deep learning reveals genomic regions introgressed between two recurrently hybridizing lynx species.

Recently, diverged species with overlapping distributional ranges have high chances of hybridizing and if hybrids are viable, genomic material can be transferred between species in a process called introgression. To characterize the patterns and consequences of introgression in species with historically low population sizes and recent steep declines resulting in genetic erosion, we analyze the Iberian and Eurasian lynx (EL) as an illustrative and relevant case study. While genome-wide introgression was already detected, here we apply a method using a deep convolutional neural network to detect specific regions of the genome with signals of introgression in three populations of these two species. Over 6% of the genome of both Iberian lynx and ELw shows introgression from the other species, compared with only 2% in the ELs. This observation, along with the results from demographic modeling, suggests that the ELw population is genetically closest to the source of EL introgression, a probably now extinct group that coexisted with the Iberian lynx in Southern Europe and Northern Iberia until recently. As predicted by theory, introgression was generally higher in populations with smaller effective sizes and in genomic regions of high recombination. However, the Iberian lynx did not show higher overall introgression than the more abundant ELw, and coding regions introgressed as frequently as intergenic regions. Local genetic diversity is boosted approximately 3-fold in genomic windows where introgression occurs, potentially including the adaptively relevant and highly diverse MHC region of the Iberian lynx.

Animals↗

PubMed2003

Population differences in the human functional olfactory repertoire.

Olfactory receptors (OR) constitute the molecular basis for the sense of smell. They are encoded by a large multigene family that in humans includes approximately 400 functional genes and approximately 600 putative pseudogenes, distributed on all but two chromosomes. To examine the ethnogeographic variability in the functional chemosensory repertoire, we resequenced 32 OR loci reported to contain a single coding region disruption in seven Caucasians and seven Pygmies. Thirteen of the 32 OR loci were found to have an interrupted coding region in all 28 alleles sampled, seven had an intact form in all the individuals examined, and 12 were polymorphic, segregating both the intact and the null variants. Among the latter loci, the frequency of the null allele was higher in Caucasians than in Pygmies, suggesting that African populations may have a larger repertoire of functional OR genes. Interestingly, when analyzing the entire OR coding regions, we find an excess of high-frequency derived alleles at many loci in the Caucasian sample but less so in the Pygmy sample. Our observations are unlikely to be accounted for by simple demographic models but may be explained by positive selection acting on OR loci in Caucasians.

Animals↗

PubMed2004

Testing the accuracy of demographic estimates in countries with generalized epidemics.

OBJECTIVE: To assess the accuracy of demographic estimates that include the effects of HIV/AIDS on adult mortality. DESIGN: To compare estimates of demographic indicators based on UNAIDS/WHO estimates and projections with newly available estimates based on cohort studies, hospital records, national surveys and other sources of data. METHODS: New information has become available recently from a number of sites in Africa on the ratio of mortality among the HIV-positive and HIV-negative population, the proportion of all adult deaths attributable to AIDS, and the number of orphans. These data are compared with the same indicators calculated from UNAIDS/WHO estimates to assess the accuracy of those estimates. RESULTS: Differences between demographic indicators based on UNAIDS/WHO estimates and study-based estimates are generally within the uncertainty range of the UNAIDS/WHO figures. CONCLUSION: Demographic estimates based on surveillance data and demographic models are close enough to study-based estimates to be useful for advocacy and medium-term planning. However, significant differences do exist that should be taken into account for short-term planning.

Acquired Immunodeficiency Syndrome↗

PubMed2001

HIV incidence estimates among women of childbearing age in the area around Paris, France: no evidence for any effect of age or time.

OBJECTIVE: To explore whether there are any age or time effects on the HIV incidence rate among women of childbearing age in the area around Paris (France). DESIGN: Three seroprevalence surveys were conducted among pregnant women in the Paris area (PREVAGEST) during three periods (1990-1991, 1992-1993, 1994-1995); their data were used to derive HIV incidence estimates with Ades and Medley's method. To assess the power of our study, data were also simulated with a demographic model under different assumptions for HIV-incidence rates. RESULTS: No age or time effect was detected on HIV incidence in the Paris area during the period from 1990 to 1995. Analysis of simulated surveys showed that with the sample size of the PREVAGEST surveys, the method was able to detect an age or time effect with a relative risk of about 2.5 between age groups or periods. CONCLUSION: We conclude that the method is applicable to our data. If any existed, age or time effect was quite likely no higher than 2.5. As we previously reported using another method, incidence of HIV infection among women of childbearing age in the Paris area can be estimated at 0.74/1,000 per year (95% confidence interval, 0.62-0.87) from 1990 through 1995.

Adolescent↗

PubMed2004

Rapid population decline in red knots: fitness consequences of decreased refuelling rates and late arrival in Delaware Bay.

Most populations of migrant shorebirds around the world are in serious decline, suggesting that vital condition-dependent rates such as fecundity and annual survival are being affected globally. A striking example is the red knot (Calidris canutus rufa) population wintering in Tierra del Fuego, which undertakes marathon 30,000 km hemispheric migrations annually. In spring, migrant birds forage voraciously on horseshoe crab eggs in Delaware Bay in the eastern USA before departing to breed in Arctic polar deserts. From 1997 to 2002 an increasing proportion of knots failed to reach threshold departure masses of 180-200 g, possibly because of later arrival in the Bay and food shortage from concurrent over-harvesting of crabs. Reduced nutrient storage, especially in late-arriving birds, possibly combined with reduced sizes of intestine and liver during refuelling, had severe fitness consequences for adult survival and recruitment of young in 2000-2002. From 1997 to 2002 known survivors in Delaware Bay were heavier at initial capture than birds never seen again, annual survival of adults decreased by 37% between May 2000 and May 2001, and the number of second-year birds in wintering flocks declined by 47%. Population size in Tierra del Fuego declined alarmingly from 51,000 to 27,000 in 2000-2002, seriously threatening the viability of this subspecies. Demographic modelling predicts imminent endangerment and an increased risk of extinction of the subspecies without urgent risk-averse management.

Age Factors↗

PubMed2002

Genetic effective size of a wild primate population: influence of current and historical demography.

A comprehensive assessment of the determinants of effective population size (N(e)) requires estimates of variance in lifetime reproductive success and past changes in census numbers. For natural populations, such information can be best obtained by combining longitudinal data on individual life histories and genetic marker-based inferences of demographic history. Independent estimates of the variance effective size (N(ev), obtained from life-history data) and the inbreeding effective size (N((eI), obtained from genetic data) provide a means of disentangling the effects of current and historical demography. The purpose of this study was to assess the demographic determinants of N(e) in one of the most intensively studied natural populations of a vertebrate species: the population of savannah baboons (Papio cynocephalus) in the Amboseli Basin, southern Kenya. We tested the hypotheses that N(eV) < N < N(eI) (where N = population census number) due to a recent demographic bottleneck. N(eV) was estimated using a stochastic demographic model based on detailed life-history data spanning a 28-year period. Using empirical estimates of age-specific rates of survival and fertility for both sexes, individual-based simulations were used to estimate the variance in lifetime reproductive success. The resultant values translated into an N(eV)/N estimate of 0.329 (SD = 0.116, 95% CI = 0.172-0.537). Historical N(eI), was estimated from 14-locus microsatellite genotypes using a coalescent-based simulation model. Estimates of N(eI) were 2.2 to 7.2 times higher than the contemporary census number of the Amboseli baboon population. In addition to the effects of immigration, the disparity between historical N(eI) and contemporary N is likely attributable to the time lag between the recent drop in census numbers and the rate of increase in the average probability of allelic identity-by-descent. Thus, observed levels of genetic diversity may primarily reflect the population's prebottleneck history rather than its current demography.

Animals↗

PubMed2005

Bayesian inference of evolutionary history from chloroplast microsatellites in the cosmopolitan weed Capsella bursa-pastoris (Brassicaceae).

Besides showing an extraordinary degree of phenotypic variability, Capsella bursa-pastoris (Brassicaceae) is also one of the world's most common plant species and a serious weed in many countries. We have employed a coalescent-based Bayesian analysis of chloroplast microsatellite data to infer demographic and evolutionary parameters of this species. Two different demographic models applied to data from seven chloroplast microsatellite loci among 59 accessions show that the effective population size of C. bursa-pastoris is very small indicating a rapid expansion of the species, a result that is in accordance with fossil and historical data. Against this background, analysis of flowering time variation among accessions suggests that ecotypic differentiation in flowering time has occurred recently in the species' history. Finally, our results also indicate that mononucleotide repeat loci in the chloroplast genome can deteriorate in relatively short periods of evolutionary time.

Base Sequence↗

PubMed2006

The role of roadsides in plant invasions: a demographic approach.

Non-native plant species are common along roadsides, but presence does not necessarily indicate spread along the road axis. Roadsides may serve merely as habitat for a species spreading independently of roads. The potential conduit function of roads depends on the habitat specificity of the spreading species, its dispersal range relative to the spacing of roads in the landscape, and the relative importance of long- and short-range dispersal. We describe a demographic model of the road x species interaction and suggest methods of assessing conduit function in the field based on the model results. A species limited to roadside habitat will be constrained to spread along the road axis unless its long-range dispersal is sufficient to carry it across the intervening unfavorable area to another road. It will propagate along a road corridor at a rate determined by the scale of short-range dispersal. Effective management of an invasion requires distinguishing between the habitat and conduit functions, a distinction difficult to make with only snapshot data. Invasions can be reconstructed by several methods, but none is totally satisfactory. We suggest comparing stem distributions on transects parallel and perpendicular to the road axis, and beside the road, and away from it, with an idealized Gaussian curve. Such comparisons would allow discrimination between pattern determined by habitat suitability and pattern reflecting random and facilitated dispersal.

Conservation of Natural Resources↗

PubMed2006

Conservation of the marbled murrelet under the Northwest Forest Plan.

The Marbled Murrelet (Brachyramphus marmoratus) was listed as threatened in 1992, primarily because of loss of its old-forest nesting habitat. Monitoring conducted over the first 10 years following implementation of the Northwest Forest Plan shows at-sea murrelet populations appear to be stationary, but recruitment is very low and demographic models project a 4-6% annual rate of decline. Monitoring of nesting habitat indicated there were about 1.6 million ha of higher-suitability nesting habitat on all lands at the start of the plan, about half of which occurred on federal lands. Most (88%) of higher-suitability habitat on federal lands was protected within reserves. Over the past 10 years, losses of habitat due primarily to fire have totaled about 2% on federal lands. Losses have been much greater (12%) on nonfederal lands, due primarily to timber harvest. Habitat is expected to accrue within reserves as younger forest matures and attains sufficient diameter to support nesting sites. At-sea estimates of population size are strongly and positively correlated with amounts of adjacent nesting habitat at a broad scale, supporting the idea that amounts of nesting habitat are a primary driver in wide-scale murrelet population distribution. Conditions at sea, however such as temperature regimes, prey availability, and pollutants, continue to affect murrelet populations. The system of large reserves seems to have achieved the short-term objective of conserving much of the remaining nesting habitat on federal lands. These reserves are also likely to contribute to the long-term objective of creating large, contiguous blocks of nesting habitat. The plan has a primary role in conserving and restoring nesting habitat on federal land but will succeed in this role only if land allocations calling for such protection are in place for many decades.

Animals↗

PubMed1997

Chaotic Dynamics in an Insect Population

A nonlinear demographic model was used to predict the population dynamics of the flour beetle Tribolium under laboratory conditions and to establish the experimental protocol that would reveal chaotic behavior. With the adult mortality rate experimentally set high, the dynamics of animal abundance changed from equilibrium to quasiperiodic cycles to chaos as adult-stage recruitment rates were experimentally manipulated. These transitions in dynamics corresponded to those predicted by the mathematical model. Phase-space graphs of the data together with the deterministic model attractors provide convincing evidence of transitions to chaos.

Journal Article↗