Effective population size for culturally evolving traits

A central tenet of the so-called demographic hypothesis is that larger populations ought to be associated with more diverse and complex toolkits. Recent empirical tests of this expectation have yielded mixed results, leading some to question to what extent changes in population size might explain interesting changes in the prehistoric archaeological record. Here, I employ computer simulation as a heuristic tool to address whether these mixed results reflect deficiencies in the formal models borrowed from population genetics or problems with the generalizations archaeologists have derived from them. I show that two previously published and highly influential models highlight two different effects of demography. My results illustrate how natural selection and cultural selection weaken the relationship between census population size, cultural diversity, and mean skill level, suggesting that one should not expect population size to predict the diversity or complexity of a cultural trait under all conditions. The concept of effective population size is central to understanding why the effects of population size can vary among traits that are passed by different mechanisms of cultural transmission within the same population. In light of these findings, I suggest ways to strengthen (rather than abandon) empirical tests of the demographic hypothesis.

The last three decades have witnessed significant advances in psychotherapy. Numerous scholarly articles and books have been devoted to pertinent topics in the field, making it difficult for the practicing clinician to keep up with this rapidly growing area. The purpose of this article is to provide some guidelines on how to evaluate the empirical literature in psychotherapy and then to explore three key areas: evidence-based psychotherapies for patients with psychiatric disorders, individual variables that predict differential outcome to treatment, and the therapeutic alliance. Finally, two case examples will be presented to illustrate how knowledge of the empirical literature can facilitate an evidence-based approach to the daily practice of psychotherapy in general psychiatry.

Local Extinction and Recolonization, Species Effective Population Size, and Modern Human Origins

Data on linkage disequilibrium at unlinked loci provide an estimate of the inbreeding effective population size of the parental generation of the sampled cohort. The inbreeding effective population size, N e , is the reciprocal of the probability that two gametes, selected at random without replacement from those that produced the sampled cohort, derive from the same parent. Effective population size is an important parameter for measuring the rate of inbreeding in a population. We detail the construction of the linkage disequilibrium estimator of N e , and evaluate its performance by simulation. We simulate populations which are dioecious and non-selfing. We use the simulations to examine the effects of several types of deviation from ideal population conditions, and of sample size, genotyping errors, number of loci typed, and polymorphic loci. We find substantial bias in the N e estimator when there have been recent fluctuations in census population size, when the index of breeding variability is greater than one, and when the ratio of sample size to effective population size differs substantially from one. Due to high variability, estimators that have low bias for the reciprocal of N e can present substantial bias when used as estimators of N e itself. We consider a recent small sample size bias correction proposed for the method, and find that it improves bias in the reciprocal, but at the expense of increased bias for N e . The improvements in the bias of the reciprocal are usually small, but are substantial when sample size is much less than N e , while the increase in bias for N e is often substantial. We test the method on two exhaustively sampled rat populations, and find it performs as expected from simulation. For practitioners, we recommend that resources are spent first in ensuring that the sample size is likely to be greater than the effective population size, and only then that the number of loci is increased to improve the precision of the estimate.

BackgroundThe outcome of the arms race between hosts and pathogens depends heavily on the interactions between their genetic diversity, population size and transmission ability. Theory predicts that genetically diverse hosts will select for higher virulence and more diverse pathogens than hosts with low genetic diversity. Cultivated hosts typically have lower genetic diversity and thus small effective population sizes, but can potentially harbour large pathogen population sizes. On the other hand, hosts, such as weeds, which are genetically more diverse and thus have larger effective population sizes, usually harbour smaller pathogen population sizes. Large pathogen population sizes may lead to more opportunities for mutation and hence more diverse pathogens. Here we test the predictions that pathogen neutral genetic diversity will increase with large pathogen population sizes and host diversity, whereas diversity under selection will increase with host diversity. We assessed and compared the diversity of a fungal pathogen, Rhynchosporium commune, on weedy barley grass (which have a large effective population size) and cultivated barley (low genetic diversity) using microsatellites, effector locus nip1 diversity and pathogen aggressiveness in order to assess the importance of weeds in the evolution of the neutral and selected diversity of pathogens.ResultsThe findings indicated that the large barley acreage and low host diversity maintains higher pathogen neutral genetic diversity and lower linkage disequilibrium, while the weed maintains more pathotypes and higher virulence diversity at nip1. Strong evidence for more pathogen migration from barley grass to barley suggests transmission of virulence from barley grass to barley is common.ConclusionsPathogen census population size is a better predictor for neutral genetic diversity than host diversity. Despite maintaining a smaller pathogen census population size, barley grass acts as an important ancillary host to R. commune, harbouring highly virulent pathogen types capable of transmission to barley. Management of disease on crops must therefore include management of weedy ancillary hosts, which may harbour disproportionate supplies of virulent pathogen strains.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-016-0680-6) contains supplementary material, which is available to authorized users.

A modified Wright–Fisher model that incorporates Ne: A variant of the standard model with increased biological realism and reduced computational complexity

Over three consecutive years, we surveyed the temporal variability in genetic structure of sardine populations in the Bay of Biscay and effective population size. Based on individual age, the genetic structure of year classes of the fishes was also surveyed, showing that populations of sardines have weak but significant genetic differences between sampling years and between year classes. We used two different methods to assess effective population size. The methods resulted in different values but a similar range, indicating a low effective population for Sardina pilchardus. Effective population size decreased over the 3 years, probably resulting from an abundance of fish in the Bay. Based on these results, we conclude that temporal variability in the genetic structure of the sardine population and effective size are likely related to environmental conditions in the Bay. Finally, we propose to use effective population size to estimate biomass of sardines in the Bay.

Monitoring temporal changes in population genetic diversity and effective population size can provide vital information on future viability. The dusky gopher frog, Lithobates sevosus, is a critically endangered species found only in coastal Mississippi, with low genetic variability as a consequence of isolation and population size reduction. Conservation management practices have been implemented, but their efficacy has not been addressed. We genotyped individuals collected 1997–2014 to determine temporal trends in population genetic variation, structure, and effective size. Observed and expected heterozygosity and allelic richness revealed temporally stable, but low, levels of genetic variation. Positive levels of inbreeding were found in each year. There was weak genetic structure among years, which can be attributed to increased effects of genetic drift and inbreeding in small populations. L. sevosus exhibited an increase in effective population size, and currently has an estimated effective size of 33.0–58.6 individuals, which is approximately half the census size. This large ratio could possibly be explained by genetic compensation. We found that management practices have been effective at maintaining and improving effective size and genetic diversity, but that additional strategies need to be implemented to enhance viability of the species.

Review of Intervention Effects on Activity and Participation in Adults with Brain Injury

Long‐term evolutionary history and demographic processes shape current patterns of genetic variation in natural populations. Genetic diversity is of prime importance for the long‐term survival of species, especially those threatened or endangered, which can be lost in a few generations and can take hundreds to recover. Notably, turtles are among the most endangered vertebrate taxa in the world. The Coahuilan box turtle Terrapene coahuila is the only aquatic species within the genus, microendemic to the desert‐spring ecosystem of the Cuatrociénegas Basin (CCB). The CCB has experienced significant habitat changes during recent decades, fragmenting otherwise interconnected wetlands systems. We aimed to perform a detailed evaluation of the evolutionary and genetic patterns of T. coahuila, both historical and contemporary, linked to the biogeography of the CCB and processes governing the species distribution. We assessed the contributions of historical and contemporary population demographic processes to genetic diversity and structure, by using two mitochondrial DNA genes (cytochrome b and d‐loop), one nuclear gene (GAPD), and 12 nuclear microsatellite loci. We comprehensively analysed these data to address historical patterns of demography, migration, genetic diversity, and times of divergence across the valley for T. coahuila. We also evaluated recent patterns of genetic variation and structure, inbreeding, bottleneck signals, and effective population size. Our results dated the time to the most recent common ancestor for T. coahuila in the CCB at c. 10.1 million years ago, with highest diversification during the Holocene. Structure consistently comprised two genetic clusters, Cuatrociénegas East and Cuatrociénegas West on either side of the main historical barrier, the Sierra San Marcos. Demographic results supported a divergence between western and eastern populations from 47,500 to 110,950 years ago, and colonisation of the southernmost Cuatrociénegas West distribution (Churince) 28,500–66,500 years ago, which experienced a recent bottleneck. All populations showed low values of haplotype and nuclear genetic diversity, migration, effective population size, and relatedness; significant inbreeding and bottleneck signals were also identified within genetic clusters. In accordance with the biogeographic history of the basin, our results show that T. coahuila’s diversification across the Cuatrociénegas valley continued throughout the Pleistocene, peaking during the Holocene, when the valley started to gradually dry. As predicted, T. coahuila exhibited an overall, long‐term, and probably continuing decrement in genetic variation, increased genetic differentiation, and low population sizes, as a consequence of contemporary habitat loss and fragmentation across the CCB. Changes in species demography and population connectivity have the potential to permanently alter the genetic patterns of freshwater species. Hence, given its restricted distribution, high habitat specificity and habitat loss, Terrapene coahuila is at utmost risk of extinction. Captive breeding programmes of the Coahuilan box turtle should consider our results, to prevent further loss of genetic diversity and truly expect reintroduction success. Also, it is crucial to restore connectivity among wetlands, for the conservation of species and the Cuatrociénegas valley altogether.

Foreword. Preface. Contributors. Part I Concepts and Methods in Bacterial Population Genetics. 1 The Coalescent of Bacterial Populations. 1.1 Background and Motivation. 1.2 Population Reproduction Models. 1.3 Time and the Effective Population Size. 1.4 The Genealogy of a Sample of Size n. 1.5 From Coalescent Time to Real Time. 1.6 Mutations. 1.7 Demography. 1.8 Recombination and Gene Conversion. 1.9 Summary. 2 Linkage, Selection, and the Clonal Complex. 2.1 Introduction Historical Overview. 2.2 Recombination, Linkage, and Substructure. 2.3 Neutrality versus Selection. 2.4 Clustering Techniques. 3 Sequence-Based Analysis of Bacterial Population Structures. 3.1 Introduction. 3.2 Alignments. 3.3 Phylogenetic Methods. 3.4 Measures of Uncertainty. 3.5 Beyond the Tree Model. 4 Genetic Recombination and Bacterial Population Structure. 4.1 Introduction. 4.2 Constraints on LGT. 4.3 Infl uences of LGT on Sequence Analyses. 4.4 The Detection of Individual LGT Events. 4.5 The Estimation of Homologous Recombination Rates. 4.6 Properly Accounting for LGT During Sequence Analyses. 4.7 Questions Relating Directly to LGT. 5 Statistical Methods for Detecting the Presence of Natural Selection in Bacterial Populations. 5.1 Introduction. 5.2 Natural Selection. 5.3 Statistical Methods for Detecting the Presence of Natural Selection. 5.4 Statistical Methods for Bacterial Populations. 5.5 An Example. 5.6 Discussion and Perspective. 6 Demographic Infl uences on Bacterial Population Structure. 6.1 Bacterial Population Size. 6.2 Measures of Genetic Diversity. 6.3 The Concept of Effective Population Size. 6.4 Inferring Past Demography from Genetic Sequence Data. 6.5 Population Subdivision. 6.6 What is a Bacterial Population? 6.7 Conclusion. 7 Population Genomics of Bacteria. 7.1 Introduction. 7.2 Classical Bacterial Population Genetics. 7.3 The Genomics Era. 7.4 Bacterial Population Genomics. 7.5 Next-Gen Bacterial Population Genomics. 7.6 Next-Gen Genomics Technology. 7.7 Next-Gen Genomic Data Analysis. 7.8 Conclusions/Future Prospects. 8 The Use of MLVA and SNP Analysis to Study the Population Genetics of Pathogenic Bacteria. 8.1 Introduction. 8.2 MLVA and Other DNA Fragment-Based Methods. 8.3 SNP and DNA Sequence-Based Methods. 8.4 Conclusion. Part II Population Genetics of Select Bacterial Pathogens. 9 Population Genetics of Bacillus: Phylogeography of Anthrax in North America. 9.1 Introduction. 9.2 History of Anthrax in North America. 9.3 The Anthrax Districts after 1944. 9.4 Molecular Genotyping of B. anthracis. 9.5 Genotypes within the Anthrax Districts in North America. 9.6 Phylogenetic Resolution within the WNA Lineage. 9.7 Phylogeographic Resolution within the Ames Lineage. 9.8 Additional B. anthracis Genotypes in North America. 9.9 Conclusions. 10 Population Genetics of Campylobacter. 10.1 Introduction. 10.2 Human Infection. 10.3 Genetic Structure. 10.4 Models of Campylobacter Evolution. 10.5 Clades and Species. 10.6 Conclusion. 11 Population Genetics of Enterococcus. 11.1 Introduction. 11.2 Antibiotic Resistance. 11.3 Vancomycin Resistance. 11.4 VRE: A Zoonosis or Not? 11.5 Population Structure and Genetic Evolution: Similarities and Differences Between E. faecium and E. faecalis. 11.6 What Is Driving GD in E. faecium and E. faecalis? 11.7 The Accessory Genome of E. faecium and E. faecalis. 11.8 Summary, Conclusions, and Future Perspectives. 12 Population Biology of Lyme Borreliosis Spirochetes. 12.1 Introduction. 12.2 Genome Organization of LB Spirochetes. 12.3 Genotyping of LB Spirochetes and Phylogenetic Tools. 12.4 Population Biology and Evolution of LB Spirochetes. 12.5 Do LB Species Exist? 12.6 Future Research Avenues. 13 Population Genetics of Neisseria meningitidis. 13.1 Introduction. 13.2 A Brief History of Typing of Meningococci. 13.3 Species Separation. 13.4 Sampling Strategies. 13.5 The Clonal Complexes of Meningococci. 13.6 Forces Shaping the Meningococcal Metalineage. 13.7 Virulence, a Mysterious Trait. 13.8 Population Effect of Meningococcal Vaccines. 13.9 Antibiotic Resistance and Meningococcal Lineages. 13.10 Concluding Remarks. 14 Population Genetics of Pathogenic Escherichia coli. 14.1 Introduction. 14.2 E. coli Population Genetics: Clonal or not Clonal? 14.3 The E. coli Phylogenetic Structure. 14.4 The Evolutionary History of a Host-Specifi c Obligate Pathogen: The Shigella and EIEC Case Study. 14.5 What Makes You an Opportunistic Pathogen? 14.6 The Virulence Resistance Trade-off. 14.7 Concluding Remarks. 15 Population Genetics of Salmonella: Selection for Antigenic Diversity. 15.1 Introduction. 15.2 Generation Timescale Diversifi cation. 15.3 Antigenic Diversity in Salmonella. 15.4 Why Are Diverse H and O Antigens Maintained in Salmonella? 15.5 Conclusions. 16 Population Genetics of Staphylococcus. 16.1 Introduction. 16.2 Overview of The Staphylococcal Population Structure. 16.3 Staphylococcal Population Structure in Specific Disease Contexts. 16.4 Origin and Maintenance of Staphylococcal Genetic Variation. 16.5 Macroevolutionary Considerations and Concluding Remarks. Appendix 1 Diversity and Differentiation. 17 Population Genetics of Streptococcus. 17.1 Habitats, Transmission, and Disease. 17.2 Classical Strain Typing. 17.3 Multilocus Sequence Typing (MLST) Based on Housekeeping Genes. 17.4 Species Boundaries and Gene Flow. 17.5 Niche-driving Genes. 17.6 Bacterial Population Dynamics and Selection. 17.7 Machinery of Genetic Change, Revisited. 18 Population Genetics of Vibrios. 18.1 Introduction. 18.2 V. cholerae. 18.3 V. parahaemolyticus . 18.4 V. vulnificus. 18.5 Conclusions. References. Index.

Aim Describing the landscape variables that accurately reflect how environmental and topographic variations affect population connectivity and demography is a major goal of landscape genetics and conservation biology. However, few landscape genetics studies have quantified the relationships between landscape variables and effective population size (Ne), although Ne is a key conservation and population genetics parameter. In this study, I estimated genetic structure and effective population sizes in the Yosemite toad (Bufo canorus) and tested for associations with environmental and geographic variables.Location Yosemite National Park, California, USA.Methods I estimated FST, Dps and Ne using 10 microsatellite loci amplified from 781 individuals from 24 populations. I used three landscape variables (environmental variation, topography and slope) to generate geographic distance models and a series of regression analyses to identify the variables that contributed to genetic structure in this species. I also tested for correlations between Ne and a suite of variables, including geographic and genetic isolation, habitat suitability, elevation, temperature and precipitation.Results I found substantial variation in genetic distances between populations (FST = 0.004–0.396, Dps = 0.045–0.839) and in effective population sizes (Ne = 9–52). Environmental variation and slope played important roles in explaining variation in genetic distances, and precipitation variables were significantly correlated with Ne.Main conclusions These results show that environmental and topographic variables are both important for understanding population connectivity in B. canorus and provide some of the first evidence, in any species, for a link between environmental variables and effective population size.

Amphibians are the most threatened vertebrates on Earth, and one of the main factors involved in their decline is the loss and fragmentation of their natural habitats. Contemporary urban development is a major cause of habitat fragmentation, and populations trapped within urban environments offer a unique opportunity to study effects of fragmentation. Here, we compared, for the first time in fire salamanders (Salamandra salamandra), estimates of census (N) and effective population size (N e ) in a small urban population in the city of Oviedo (Spain). We performed a 4 year capture-mark-recapture study and used three single-sample N e estimators based on 58 individuals genotyped for 15 polymorphic microsatellite loci. Our study showed a small ( $$\hat{N} = 113$$ salamanders; 95 % CI 100–142) but dense population (mean 0.45 individuals per m2), while single-sample estimators provided congruent N e estimates. A high N e /N population size ratio (range 0.50–0.84) obtained in this small and isolated population suggests the existence of mechanisms of genetic compensation (low reproductive variance and multiple paternity) in fire salamanders.

ABSTRACTEstimating and understanding the ratio between effective population size (Ne) and census population size (Nc) are pivotal in the conservation of large marine pelagic fish species, including bony fish such as tunas and cartilaginous fish such as sharks, given the challenges associated with obtaining accurate estimates of their abundance. The difficulties inherent in capturing and monitoring these species in vast and dynamic marine environments often make direct estimation of their population size challenging. By focusing on Ne, it is conceivable in certain cases to approximate census size once the Ne/Nc ratio is known, although this ratio can vary and does not always increase linearly, as it is influenced by various ecological and evolutionary factors. Thus, this ratio presents challenges and complexities in the context of pelagic species conservation. To delve deeper into these challenges, firstly, we recall the diverse types of effective population sizes, including contemporary and historical sizes, and their implications in conservation biology. Secondly, we outline current knowledge about the influence of life history traits on the Ne/Nc ratio in the light of examples drawn from large and abundant pelagic fish species. Despite efforts to document an increasing number of marine species using recent technologies and statistical methods, establishing general rules to predict Ne/Nc remains elusive, necessitating further research and investment. Finally, we recall statistical challenges in relating Ne and Nc emphasizing the necessity of aligning temporal and spatial scales. This last part discusses the roles of generation and reproductive cycle effective population sizes to predict genetic erosion and guiding management strategies. Collectively, these sections underscore the multifaceted nature of effective population size estimation, crucial for preserving genetic diversity and ensuring the long‐term viability of populations. By navigating statistical and theoretical complexities, and addressing methodological challenges, scientists should be able to advance our understanding of the Ne/Nc ratio.

Effective population size is a fundamental parameter in population genetics, and factors that alter effective population size will shape the genetic characteristics of populations. Habitat disturbance may have a large effect on genetic characteristics of populations by influencing immigration and gene flow, particularly in fragmented habitats. We used the Florida Sand Skink (Plestiodon reynoldsi) to investigate the effect of fire-based habitat disturbances on the effective population size in the highly threatened, severely fragmented, and fire dependent Florida scrub habitat. We screened 7 microsatellite loci in 604 individuals collected from 12 locations at Archbold Biological Station. Archbold Biological Station has an active fire management plan and detailed records of fires dating to 1967. Our objective was to determine how the timing, number, and intervals between fires affect effective population size, focusing on multiple fires in the same location. Effective population size was higher in areas that had not been burned for more than 10 years and decreased with number of fires and shorter time between fires. A similar pattern was observed in abundance: increasing abundance with time-since-fire and decreasing abundance with number of fires. The ratio of effective population size to census size was higher at sites with more recent fires and tended to decrease with time-since-last-fire. These results suggest that habitat disturbances, such as fire, may have a large effect in the genetic characteristics of local populations and that Florida Sand Skinks are well adapted to the natural fire dynamics required to maintain Florida scrub.