Founding Population Size Research Articles

Deciphering the landscape of host barriers to Listeria monocytogenes infection

Listeria monocytogenes is a common food-borne pathogen that can disseminate from the intestine and infect multiple organs. Here, we used sequence tag-based analysis of microbial populations (STAMP) to investigate Lmonocytogenes population dynamics during infection. We created a genetically barcoded library of murinized Lmonocytogenes and then used deep sequencing to track the pathogen's dissemination routes and quantify its founding population (Nb) sizes in different organs. We found that the pathogen disseminates from the gastrointestinal tract to distal sites through multiple independent routes and that Nb sizes vary greatly among tissues, indicative of diverse host barriers to infection. Unexpectedly, comparative analyses of sequence tags revealed that fecally excreted organisms are largely derived from the very small number of L. monocytogenes cells that colonize the gallbladder. Immune depletion studies suggest that distinct innate immune cells restrict the pathogen's capacity to establish replicative niches in the spleen and liver. Finally, studies in germ-free mice suggest that the microbiota plays a critical role in the development of the splenic, but not the hepatic, barriers that prevent L. monocytogenes from seeding these organs. Collectively, these observations illustrate the potency of the STAMP approach to decipher the impact of host factors on population dynamics of pathogens during infection.

Evidence for mega‐landslides as drivers of island colonization

AbstractAimHow non‐dispersive taxa colonize islands is generalized as being by wind, or rafting, with the implicit assumption that such events involve one (wind) or a few (rafting) individuals. However, because of the evolutionary time‐scale for colonization events, the fit of individual species to a conceptual model of wind or rafting is difficult to assess. Here, we describe an alternative testable geological model for inter‐island colonization that can result in larger effective founding population sizes than traditionally accepted colonization mechanisms. We then test for the fit of genetic data to this model using weevils from the Laparocerus tessellatus species complex.LocationCanary Islands.MethodsUsing a combination of geological data for the Canary Islands, and mtDNA data from a weevil radiation within the Canary Islands, we test three species‐level predictions for mega‐landslides as drivers of oceanic rafting between islands and subsequent speciation: (1) colonization should involve multiple female lineages, (2) founding lineages should have a common geographical origin, consistent with a mega‐landslide event, and (3) colonization direction should be consistent with ocean currents.ResultsBoth individual‐level and population‐level analyses support a mega‐landslide event as the driver of colonization from the island of Tenerife to La Palma. At least four female lineages colonized La Palma from Tenerife, with the geographical range of ancestral sequences to these four lineages describing the limits of the La Orotava mega‐landslide in Tenerife.Main conclusionsIn the context of island biogeographical theory, mega‐landslides may be an important driver of colonization, and subsequent lineage diversification. They provide a framework for hypothesis testing using genetic data from species, or closely related species, with ranges that encompass landslides and potential areas of colonization.

Deep Sequencing of Influenza A Virus from a Human Challenge Study Reveals a Selective Bottleneck and Only Limited Intrahost Genetic Diversification.

ABSTRACTKnowledge of influenza virus evolution at the point of transmission and at the intrahost level remains limited, particularly for human hosts. Here, we analyze a unique viral data set of next-generation sequencing (NGS) samples generated from a human influenza challenge study wherein 17 healthy subjects were inoculated with cell- and egg-passaged virus. Nasal wash samples collected from 7 of these subjects were successfully deep sequenced. From these, we characterized changes in the subjects' viral populations during infection and identified differences between the virus in these samples and the viral stock used to inoculate the subjects. We first calculated pairwise genetic distances between the subjects' nasal wash samples, the viral stock, and the influenza virus A/Wisconsin/67/2005 (H3N2) reference strain used to generate the stock virus. These distances revealed that considerable viral evolution occurred at various points in the human challenge study. Further quantitative analyses indicated that (i) the viral stock contained genetic variants that originated and likely were selected for during the passaging process, (ii) direct intranasal inoculation with the viral stock resulted in a selective bottleneck that reduced nonsynonymous genetic diversity in the viral hemagglutinin and nucleoprotein, and (iii) intrahost viral evolution continued over the course of infection. These intrahost evolutionary dynamics were dominated by purifying selection. Our findings indicate that rapid viral evolution can occur during acute influenza infection in otherwise healthy human hosts when the founding population size of the virus is large, as is the case with direct intranasal inoculation.IMPORTANCE Influenza viruses circulating among humans are known to rapidly evolve over time. However, little is known about how influenza virus evolves across single transmission events and over the course of a single infection. To address these issues, we analyze influenza virus sequences from a human challenge experiment that initiated infection with a cell- and egg-passaged viral stock, which appeared to have adapted during its preparation. We find that the subjects' viral populations differ genetically from the viral stock, with subjects' viral populations having lower representation of the amino-acid-changing variants that arose during viral preparation. We also find that most of the viral evolution occurring over single infections is characterized by further decreases in the frequencies of these amino-acid-changing variants and that only limited intrahost genetic diversification through new mutations is apparent. Our findings indicate that influenza virus populations can undergo rapid genetic changes during acute human infections.

Mitochondrial DNA structure and colony expansion dynamics of New Zealand fur seals (Arctocephalus forsteri) around Banks Peninsula

ABSTRACTNew Zealand fur seals are one of many pinniped species that survived the commercial sealing of the eighteenth and nineteenth centuries in dangerously low numbers. After the enforcement of a series of protection measures in the early twentieth century, New Zealand fur seals began to recover from the brink of extinction. We examined the New Zealand fur seal populations of Banks Peninsula, South Island, New Zealand using the mitochondrial DNA control region. We identified a panmictic population structure around Banks Peninsula. The most abundant haplotype in the area showed a slight significant aggregated structure. The Horseshoe Bay colony showed the least number of shared haplotypes with other colonies, suggesting a different origin of re-colonisation of this specific colony. The effective population size of the New Zealand fur seal population at Banks Peninsula was estimated at approximately 2500 individuals. The exponential population growth rate parameter for the area was 35, which corresponds to an expanding population. In general, samples from adjacent colonies shared 4.4 haplotypes while samples collected from colonies separated by between five and eight bays shared 1.9 haplotypes. The genetic data support the spill-over dynamics of colony expansion already suggested for this species. Approximate Bayesian computations analysis suggests re-colonisation of the area from two main clades identified across New Zealand with a most likely admixture coefficient of 0.41 to form the Banks Peninsula population. Approximate Bayesian computations analysis estimated a founder population size of approximately 372 breeding individuals for the area, which then rapidly increased in size with successive waves of external recruitment. The population of fur seals in the area is probably in the late phase of maturity in the colony expansion dynamic.

Interpretation of findings of founder population genetics studies applying lineage extinction theory

Population genetic investigation of founder events produce intriguing results and this work discusses how branching processes help the cross-examination of such results. For example one reads that 40% of the current Ashkenazi population carry the mtDNA of four founding mothers, (Behar et al., 2006) half of the Ashkenazi Levites descend from one founder (Behar et al., 2003), and 22% of the Malagasy population are descendants of a Polynesian ancestor, (Cox et al., 2012). Probability distributions obtained using a Galton–Watson lineage extinction model yield statistical relations between current population and founder population data. These relations lead to most likely estimates and 90% confidence intervals of the founder population size. The investigation compares the Galton–Watson methodology with the Wright–Fisher model adopted by coalescent theory and a back-to-back analysis of the Malagasy founder event produces matching results. The results reconcile the previous knowledge about the roots of Ashkenazi Jewry with published population genetic findings. They also confirm that random drift is sufficient to explain the genetic findings of the examined examples.

The minimum founding population in dispersing organisms subject to strong Allee effects

Summary Dispersal can push population density below strong Allee thresholds ensuring the demise of small founding populations. As a result, for isolated populations of dispersing organisms, the minimum founding population size that enables establishment can be quite different from the Allee threshold. We derive an expression for the minimum founding population size for a general integrodifference equation model of a dispersing population with a strong Allee effect. We demonstrate the utility of the general model by using it to approximate minimum founding populations for the mountain pine beetle. The minimum founding population of the general model increases linearly with the mean squared displacement of the dispersing organism. Transient dynamics of the general model suggest that population density at the point of introduction will often decrease before increasing, even when the minimum founding population size is exceeded. Calculation of minimum founding population sizes may prove useful for predicting invasion success based on propagule size and for maximizing the success of species reintroductions when strong Allee effects exist.

Translocation strategies for multiple species depend on interspecific interaction type.

Conservation translocations, anthropogenic movements of species to prevent their extinction, have increased substantially over the last few decades. Although multiple species are frequently moved to the same location, current translocation guidelines consider species in isolation. This practice ignores important interspecific interactions and thereby risks translocation failure. We model three different two-species systems to illustrate the inherent complexity of multispecies translocations and to assess the influence of different interaction types (consumer-resource, mutualism, and competition) on translocation strategies. We focus on how these different interaction types influence the optimal founder population sizes for successful translocations and the order in which the species are moved (simultaneous or sequential). Further, we assess the effect of interaction strength in simultaneous translocations and the time delay between translocations when moving two species sequentially. Our results show that translocation decisions need to reflect the type of interaction. While all translocations of interacting species require a minimum founder population size, which is demarked by an extinction boundary, consumer-resource translocations also have a maximum founder population limit. Above the minimum founder size, increasing the number of translocated individuals leads to a substantial increase in the extinction boundary of competitors and consumers, but not of mutualists. Competitive and consumer-resource systems benefit from sequential translocations, but the order of translocations does not change the outcomes for mutualistic interaction partners noticeably. Interspecific interactions are important processes that shape population dynamics and should therefore be incorporated into the quantitative planning of multispecies translocations. Our findings apply whenever interacting species are moved, for example, in reintroductions, conservation introductions, biological control, or ecosystem restoration.

How propagule size and environmental suitability jointly determine establishment success: a test using dung beetle introductions

Both the size of founding populations (propagule size) and environmental suitability are known to influence whether a species newly introduced to a location will establish a self-sustaining population. However, these two factors do not operate independently: it is the interaction between propagule size and environmental suitability that determines the probability an introduced population will establish. Here I use the example of dung beetle introductions to Australia to illustrate the importance of this interaction. I first describe equations that model establishment success jointly as a function of propagule size and environmental suitability. I then show how these equations provide insight into the different outcomes observed in two dung beetle species widely introduced to Australia. In one species, variation in propagule size had relatively little influence on establishment success due to large variation in environmental suitability, leading to an essentially bimodal outcome: sites were either very suitable for establishment and introductions succeeded, or sites were unsuitable and introductions failed regardless of propagule size. For the second species, there was much less variation among locations in environmental suitability, leading to propagule size having a strong influence on establishment success. These examples highlight how the interplay between environmental suitability and founding population size is central to determining the probability an introduced species will establish.

Saving wild ungulate diversity through enhanced management and sperm cryopreservation.

Wild ungulates throughout the world face the impending risk of extinction. Small founding population size, lack of interest in exhibiting wild ungulates and declining space in zoos are not sustaining ex situ populations. Animals managed in ex situ collections continue to experience >20% neonate loss globally. To ensure population sustainability there is a critical need to: (1) manage ungulates in large herds, increasing mate choice and reproductive efficiency; (2) improve husbandry and genetic management; and (3) develop consistent assisted reproductive technologies, including sperm cryopreservation and AI. Recently, new models in the management of ungulates have begun to emerge. Animal managers and researchers are also beginning to exploit advances in genomics to improve genetic management of their collections. Furthermore, the past decade has witnessed significant advances particularly in semen collection and cryopreservation in numerous species. Advances in gonadal tissue cryopreservation now offer additional opportunities to preserve male genomes. The new knowledge generated is enabling the creation of genetic (sperm) banks to rescue and enhance reproductive management of wild ungulates. The present paper reviews the threats to ungulate populations, the status and relevance of animal management and biomaterial banking efforts to ensure long-term survival of these charismatic species.

Historical Invasion Records Can Be Misleading: Genetic Evidence for Multiple Introductions of Invasive Raccoons (Procyon lotor) in Germany.

Biological invasions provide excellent study systems to understand evolutionary, genetic and ecological processes during range expansions. There is strong evidence for positive effects of high propagule pressure and the associated higher genetic diversity on invasion success, but some species have become invasive despite small founder numbers. The raccoon (Procyon lotor) is often considered as a typical example for such a successful invasion resulting from a small number of founders. The species’ largest non-native population in Germany is commonly assumed to stem from a small number of founders and two separate founding events in the 1930s and 1940s. In the present study we analyzed 407 raccoons at 20 microsatellite loci sampled from the invasive range in Western Europe to test if these assumptions are correct. Contrary to the expectations, different genetic clustering methods detected evidence for at least four independent introduction events that gave rise to genetically differentiated subpopulations. Further smaller clusters were either artifacts or resulted from founder events at the range margin and recent release of captive individuals. We also found genetic evidence for on-going introductions of individuals. Furthermore a novel randomization process was used to determine the potential range of founder population size that would suffice to capture all the alleles present in a cluster. Our results falsify the assumption that this species has become widespread and abundant despite being genetically depauperate and show that historical records of species introductions may be misleading.

Transposable elements as agents of rapid adaptation may explain the genetic paradox of invasive species.

Rapid adaptation of invasive species to novel habitats has puzzled evolutionary biologists for decades, especially as this often occurs in the face of limited genetic variability. Although some ecological traits common to invasive species have been identified, little is known about the possible genomic/genetic mechanisms that may underlie their success. A common scenario in many introductions is that small founder population sizes will often lead to reduced genetic diversity, but that invading populations experience large environmental perturbations, such as changes in habitat and environmental stress. Although sudden and intense stress is usually considered in a negative context, these perturbations may actually facilitate rapid adaptation by affecting genome structure, organization and function via interactions with transposable elements (TEs), especially in populations with low genetic diversity. Stress-induced changes in TE activity can alter gene action and can promote structural variation that may facilitate the rapid adaptation observed in new environments. We focus here on the adaptive potential of TEs in relation to invasive species and highlight their role as powerful mutational forces that can rapidly create genetic diversity. We hypothesize that activity of transposable elements can explain rapid adaptation despite low genetic variation (the genetic paradox of invasive species), and provide a framework under which this hypothesis can be tested using recently developed and emerging genomic technologies.

Sequence tag-based analysis of microbial population dynamics.

We describe a new method (STAMP) for characterization of pathogen population dynamics during infection. STAMP analyzes the frequency changes of genetically “barcoded” organisms to quantify population bottlenecks and infer the founding population size. Analyses of intra-intestinal Vibrio cholerae revealed infection-stage and region-specific host barriers to infection, and unexpectedly showed V. cholerae migration counter to intestinal flow. STAMP provides a robust, widely applicable analytical framework for high confidence characterization of in vivo microbial dissemination.

Quantifying invasion risk: the relationship between establishment probability and founding population size

Summary Invasive species usually start out as small colonizing populations that are prone to extinction through demographic stochasticity and Allee effects, leading to a positive relationship between establishment probability and founding population size. However, establishment success also depends on the environment to which species are introduced: for a given species, some locations will be more favourable for establishment than others. We present equations for modelling the expected relationship between establishment probability and founding population size when demographic stochasticity, Allee effects and, for the first time, environmental heterogeneity are operating. We show that heterogeneity in environmental conditions can change the shape of the relationship between establishment probability and founding population size through a disproportionate decline in the probability of establishment in larger populations, the opposite of an Allee effect. This outcome is likely in most empirical data sets relating founding population size to establishment probability, and highlights that unfavourable environments are often the major cause of establishment failures. It also emphasizes the insights that can be gained from applying models with a theoretical underpinning.

A Century of Elk Restoration in Eastern North America

AbstractOver a century has passed since elk were extirpated in eastern North America. During that time, numerous attempts to reintroduce elk into eastern North America have resulted in varying degrees of success and failure. An overview of restoration efforts during the last 100 years is presented here with emphasis on the differences in rates of population change among regions and differences in major causes of elk mortality during both the pre‐ and post‐acclimation periods. Approximately 40% of recorded elk reintroduction attempts in eastern North America resulted in failure, with the majority of these having occurred in the first half of the 20th century. Although rates of population change in elk were highly variable, they were not related to founding population size. Major causes of mortality varied among regions and should be considered in future reintroduction attempts.

The roles of demography and genetics in the early stages of colonization.

Colonization success increases with the size of the founding group. Both demographic and genetic factors underlie this relationship, yet because genetic diversity normally increases with numbers of individuals, their relative importance remains unclear. Furthermore, their influence may depend on the environment and may change as colonization progresses from establishment through population growth and then dispersal. We tested the roles of genetics, demography and environment in the founding of Tribolium castaneum populations. Using three genetic backgrounds (inbred to outbred), we released individuals of four founding sizes (2-32) into two environments (natal and novel), and measured establishment success, initial population growth and dispersal. Establishment increased with founding size, whereas population growth was shaped by founding size, genetic background and environment. Population growth was depressed by inbreeding at small founding sizes, but growth rates were similar across genetic backgrounds at large founding size, an interaction indicating that the magnitude of the genetic effects depends upon founding population size. Dispersal rates increased with genetic diversity. These results suggest that numbers of individuals may drive initial establishment, but that subsequent population growth and spread, even in the first generation of colonization, can be driven by genetic processes, including both reduced growth owing to inbreeding depression, and increased dispersal with increased genetic diversity.

Genetic Diversity in Introduced Populations with an Allee Effect

A phenomenon that strongly influences the demography of small introduced populations and thereby potentially their genetic diversity is the demographic Allee effect, a reduction in population growth rates at small population sizes. We take a stochastic modeling approach to investigate levels of genetic diversity in populations that successfully overcame either a strong Allee effect, in which populations smaller than a certain critical size are expected to decline, or a weak Allee effect, in which the population growth rate is reduced at small sizes but not negative. Our results indicate that compared to successful populations without an Allee effect, successful populations with a strong Allee effect tend to (1) derive from larger founder population sizes and thus have a higher initial amount of genetic variation, (2) spend fewer generations at small population sizes where genetic drift is particularly strong, and (3) spend more time around the critical population size and thus experience more genetic drift there. In the case of multiple introduction events, there is an additional increase in diversity because Allee-effect populations tend to derive from a larger number of introduction events than other populations. Altogether, a strong Allee effect can either increase or decrease genetic diversity, depending on the average founder population size. By contrast, a weak Allee effect tends to decrease genetic diversity across the entire range of founder population sizes. Finally, we show that it is possible in principle to infer critical population sizes from genetic data, although this would require information from many independently introduced populations.

The invisible cliff: abrupt imposition of Malthusian equilibrium in a natural-fertility, agrarian society.

Analysis of a natural fertility agrarian society with a multi-variate model of population ecology isolates three distinct phases of population growth following settlement of a new habitat: (1) a sometimes lengthy copial phase of surplus food production and constant vital rates; (2) a brief transition phase in which food shortages rapidly cause increased mortality and lessened fertility; and (3) a Malthusian phase of indefinite length in which vital rates and quality of life are depressed, sometimes strikingly so. Copial phase duration declines with increases in the size of the founding group, maximum life expectancy and fertility; it increases with habitat area and yield per hectare; and, it is unaffected by the sensitivity of vital rates to hunger. Transition phase duration is unaffected by size of founding population and area of settlement; it declines with yield, life expectancy, fertility and the sensitivity of vital rates to hunger. We characterize the transition phase as the Malthusian transition interval (MTI), in order to highlight how little time populations generally have to adjust. Under food-limited density dependence, the copial phase passes quickly to an equilibrium of grim Malthusian constraints, in the manner of a runner dashing over an invisible cliff. The three-phase pattern diverges from widely held intuitions based on standard Lotka-Verhulst approaches to population regulation, with implications for the analysis of socio-cultural evolution, agricultural intensification, bioarchaeological interpretation of food stress in prehistoric societies, and state-level collapse.

Effects of founder population size on the performance of Orius laevigatus (Hemiptera: Anthocoridae) colonies

Orius laevigatus (Hemiptera: Anthocoridae) is a key predator of thrips and is mass reared in large numbers for use in biological control. The aim of this study was to evaluate the effect of founder population size on the biological and behavioral performance of O. laevigatus over time. Laboratory lines were started from 1, 10 and 50 founder couples from 750 adults collected in the field and their performance was evaluated at the 5th–6th and 10th–11th generations. Adaptation to the captive rearing situation occurred in the 10 and 50 founder couples lines while it failed in the 1 founder couple line. The intrinsic rate of natural increase (rm) increased and the period for doubling the population (D) decreased over the generations in the 10 and 50 founder couples lines, while (rm) decreased and (D) increase in the 1 founder couple line. Also, consumption of Frankliniella occidentalis prey was significantly lower for females from the 1 founder couple line at the 5th generation compared to females from the 10 and 50 founder couples lines. Females of laboratory lines of all founder couples did not respond to odours from thrips infested plants during the 5th and 10th generations, whereas wild females strongly reacted to these odours. We suggest that the lack of reaction to infested plant volatiles may be due to the artificial rearing method where mass reared predators do not experience an infested crop. The results showed that the 1 founder couple line differed from the 10 and 50 founder couples lines, suggesting that bottlenecking had an effect at that level. However, no difference was found between the 10 and 50 founder couples lines which suggest that these founder numbers can be used to start laboratory-reared O. laevigatus lines without a significant loss in quality of its relevant biological characteristics.

Reconstructing the Population Genetic History of the Caribbean

The Caribbean basin is home to some of the most complex interactions in recent history among previously diverged human populations. Here, we investigate the population genetic history of this region by characterizing patterns of genome-wide variation among 330 individuals from three of the Greater Antilles (Cuba, Puerto Rico, Hispaniola), two mainland (Honduras, Colombia), and three Native South American (Yukpa, Bari, and Warao) populations. We combine these data with a unique database of genomic variation in over 3,000 individuals from diverse European, African, and Native American populations. We use local ancestry inference and tract length distributions to test different demographic scenarios for the pre- and post-colonial history of the region. We develop a novel ancestry-specific PCA (ASPCA) method to reconstruct the sub-continental origin of Native American, European, and African haplotypes from admixed genomes. We find that the most likely source of the indigenous ancestry in Caribbean islanders is a Native South American component shared among inland Amazonian tribes, Central America, and the Yucatan peninsula, suggesting extensive gene flow across the Caribbean in pre-Columbian times. We find evidence of two pulses of African migration. The first pulse—which today is reflected by shorter, older ancestry tracts—consists of a genetic component more similar to coastal West African regions involved in early stages of the trans-Atlantic slave trade. The second pulse—reflected by longer, younger tracts—is more similar to present-day West-Central African populations, supporting historical records of later transatlantic deportation. Surprisingly, we also identify a Latino-specific European component that has significantly diverged from its parental Iberian source populations, presumably as a result of small European founder population size. We demonstrate that the ancestral components in admixed genomes can be traced back to distinct sub-continental source populations with far greater resolution than previously thought, even when limited pre-Columbian Caribbean haplotypes have survived.

Approximate Bayesian estimation of extinction rate in the Finnish Daphnia magna metapopulation

Approximate Bayesian computation (ABC) is useful for parameterizing complex models in population genetics. In this study, ABC was applied to simultaneously estimate parameter values for a model of metapopulation coalescence and test two alternatives to a strict metapopulation model in the well-studied network of Daphnia magna populations in Finland. The models shared four free parameters: the subpopulation genetic diversity (θS), the rate of gene flow among patches (4Nm), the founding population size (N0) and the metapopulation extinction rate (e) but differed in the distribution of extinction rates across habitat patches in the system. The three models had either a constant extinction rate in all populations (strict metapopulation), one population that was protected from local extinction (i.e. a persistent source), or habitat-specific extinction rates drawn from a distribution with specified mean and variance. Our model selection analysis favoured the model including a persistent source population over the two alternative models. Of the closest 750,000 data sets in Euclidean space, 78% were simulated under the persistent source model (estimated posterior probability = 0.769). This fraction increased to more than 85% when only the closest 150,000 data sets were considered (estimated posterior probability = 0.774). Approximate Bayesian computation was then used to estimate parameter values that might produce the observed set of summary statistics. Our analysis provided posterior distributions for e that included the point estimate obtained from previous data from the Finnish D. magna metapopulation. Our results support the use of ABC and population genetic data for testing the strict metapopulation model and parameterizing complex models of demography.