Past Population Size Research Articles

The pattern of linkage disequilibrium in German Holstein cattle

This study presents a second generation of linkage disequilibrium (LD) map statistics for the whole genome of the Holstein-Friesian population, which has a four times higher resolution compared with that of the maps available so far. We used DNA samples of 810 German Holstein-Friesian cattle genotyped by the Illumina Bovine SNP50K BeadChip to analyse LD structure. A panel of 40 854 (75.6%) markers was included in the final analysis. The pairwise r(2) statistic of SNPs up to 5 Mb apart across the genome was estimated. A mean value of r(2) = 0.30 +/- 0.32 was observed in pairwise distances of <25 kb and it dropped to 0.20 +/- 0.24 at 50-75 kb, which is nearly the average inter-marker space in this study. The proportion of SNPs in useful LD (r(2) > or = 0.25) was 26% for the distance of 50 and 75 kb between SNPs. We found a lower level of LD for SNP pairs at the distance < or =100 kb than previously thought. Analysis revealed 712 haplo-blocks spanning 4.7% of the genome and containing 8.0% of all SNPs. Mean and median block length were estimated as 164 +/- 117 kb and 144 kb respectively. Allele frequencies of the SNPs have a considerable and systematic impact on the estimate of r(2). It is shown that minimizing the allele frequency difference between SNPs reduces the influence of frequency on r(2) estimates. Analysis of past effective population size based on the direct estimates of recombination rates from SNP data showed a decline in effective population size to N(e) = 103 up to approximately 4 generations ago. Systematic effects of marker density and effective population size on observed LD and haplotype structure are discussed.

Genetic variation and evolutionary demography of Fenneropenaeus chinensis populations, as revealed by the analysis of mitochondrial control region sequences

Genetic variation and evolutionary demography of the shrimp Fenneropenaeus chinensis were investigated using sequence data of the complete mitochondrial control region (CR). Fragments of 993 bp of the CR were sequenced for 93 individuals from five localities over most of the species' range in the Yellow Sea and the Bohai Sea. There were 84 variable sites defining 68 haplotypes. Haplotype diversity levels were very high (0.95 ± 0.03-0.99 ± 0.02) in F. chinensis populations, whereas those of nucleotide diversity were moderate to low (0.66 ± 0.36%-0.84 ± 0.46%). Analysis of molecular variance and conventional population statistics (FST ) revealed no significant genetic structure throughout the range of F. chinensis. Mismatch distribution, estimates of population parameters and neutrality tests revealed that the significant fluctuations and shallow coalescence of mtDNA genealogies observed were coincident with estimated demographic parameters and neutrality tests, in implying important past-population size fluctuations or range expansion. Isolation with Migration (IM) coalescence results suggest that F. chinensis, distributed along the coasts of northern China and the Korean Peninsula (about 1000 km apart), diverged recently, the estimated time-split being 12,800 (7,400-18,600) years ago.

Towards consensus on how to measure neutral genetic diversity?

Towards consensus on how to measure neutral genetic diversity?

Archaeological Demography

Archaeological demography investigates the structure and dynamics of past human populations using evidence from traces of human activities and remnants of material culture in the archaeological record. Research in this field is interdisciplinary, incorporating findings from anthropology, paleogenetics, and human ecology but with a remit that extends beyond the primarily biological focus of paleodemography. Important questions addressed by archaeological demography include the establishment of methods for inferring past population structure, the timing of the emergence of modern human demographic systems, the relative importance of attritional and catastrophic patterns of mortality, and the search for adaptive explanations for demographic transitions, colonization events, and population extinctions. Archaeological evidence, including the extent of settlements and site catchment areas as well as measures of the exploitation, consumption, and discard of materials and artifacts, have traditionally been used as proxies for estimating past population size and density. In recent years this evidence has been supplemented by increasingly large data sets compiled from radiocarbon dating programs. These data sets have been used to investigate demographic waves of advance during continental-scale periods of colonization and cultural change and to detect episodes of population decline, extinction, and hiatuses in settlement history. By considering studies of human genetic diversity that indicate temporary but drastic reductions in effective population size, I hypothesize that catastrophic mortality may have had an important role in long-term population processes and may have limited long-term rates of growth, particularly in prehistoric populations.

Archaeological Demography

Archaeological demography investigates the structure and dynamics of past human populations using evidence from traces of human activities and remnants of material culture in the archaeological record. Research in this field is interdisciplinary, incorporating findings from anthropology, paleogenetics, and human ecology but with a remit that extends beyond the primarily biological focus of paleodemography. Important questions addressed by archaeological demography include the establishment of methods for inferring past population structure, the timing of the emergence of modern human demographic systems, the relative importance of attritional and catastrophic patterns of mortality, and the search for adaptive explanations for demographic transitions, colonization events, and population extinctions. Archaeological evidence, including the extent of settlements and site catchment areas as well as measures of the exploitation, consumption, and discard of materials and artifacts, have traditionally been used as proxies for estimating past population size and density. In recent years this evidence has been supplemented by increasingly large data sets compiled from radiocarbon dating programs. These data sets have been used to investigate demographic waves of advance during continental-scale periods of colonization and cultural change and to detect episodes of population decline, extinction, and hiatuses in settlement history. By considering studies of human genetic diversity that indicate temporary but drastic reductions in effective population size, I hypothesize that catastrophic mortality may have had an important role in long-term population processes and may have limited long-term rates of growth, particularly in prehistoric populations.

Fitness and survival in fragmented populations of Narthecium ossifragum at the species' range margin

Decreasing population size and increasing isolation may lead to reduced plant fitness. These effects of habitat fragmentation may especially apply to populations close to the margin of their geographical range, where populations generally are often smaller and more isolated, and the environment is less favourable than at the range centre. In this context we studied north-west German range-margin populations of Narthecium ossifragum (L.) HUDS., a clonal, perennial herb typical for acidic and nutrient-poor wet heathlands. We asked whether plant fitness and reproduction of the range-margin populations were affected by population size and habitat quality, and whether any changes in population size over the past 10–20 years were related to past population size and habitat quality. Population size varied between 60 and 100.000 individuals and was highly positively related to shoot density. Larger (and denser) populations formed more flowers and fruits, but fewer seeds. Soil water content had a strong positive effect on seed production and seed mass, and the latter also increased with increasing soil phosphorus content. Relative light intensity showed a positive impact on shoot density and, hence, population size. Compared to British range centre populations, the populations at the German range margin formed more, but smaller seeds that failed to germinate both in the field and in laboratory experiments. Despite the lack of sexual reproduction, population sizes generally had not decreased during the past two decades, most likely due to successful clonal growth. The change in population size of Narthecium, however, was negatively related to the present soil phosphorus content, indicating that an increased supply of nutrients and a decrease in light availability may have a negative effect on population dynamics. The results imply that fragmented and small range-margin populations not necessarily are doomed to extinction, provided that the habitat quality remains suitable for growth and vegetative reproduction.

Bayesian coalescent inference of major human mitochondrial DNA haplogroup expansions in Africa

Past population size can be estimated from modern genetic diversity using coalescent theory. Estimates of ancestral human population dynamics in sub-Saharan Africa can tell us about the timing and nature of our first steps towards colonizing the globe. Here, we combine Bayesian coalescent inference with a dataset of 224 complete human mitochondrial DNA (mtDNA) sequences to estimate effective population size through time for each of the four major African mtDNA haplogroups (L0-L3). We find evidence of three distinct demographic histories underlying the four haplogroups. Haplogroups L0 and L1 both show slow, steady exponential growth from 156 to 213kyr ago. By contrast, haplogroups L2 and L3 show evidence of substantial growth beginning 12-20 and 61-86kyr ago, respectively. These later expansions may be associated with contemporaneous environmental and/or cultural changes. The timing of the L3 expansion--8-12kyr prior to the emergence of the first non-African mtDNA lineages--together with high L3 diversity in eastern Africa, strongly supports the proposal that the human exodus from Africa and subsequent colonization of the globe was prefaced by a major expansion within Africa, perhaps driven by some form of cultural innovation.

Mitochondrial DNA Variation and Systematics of the Guanaco (Lama guanicoe, Artiodactyla: Camelidae)

Guanacos (Lama guanicoe) are the most important native herbivorous species in the South American steppes and the dominant ungulate in a fauna rich in rodents but poor in large mammal species. Between 2 and 4 subspecies are usually recognized within Lama guanicoe, based on subtle morphological differences and geographic distribution. To evaluate whether molecular variation is consistent with the latter hypotheses, we analyzed the complete cytochrome-b and partial control region mitochondrial DNA sequences of L. guanicoe from 22 localities in Peru, Bolivia, Argentina, and Chile. Sequence analyses of both genes support the monophyly of the species but failed to distinguish the occurrence of subspecies along the geographic range. Despite that, the northernmost populations (Peru and northern Chile) showed some degree of genetic differentiation with respect to southern representatives from Argentina, Bolivia, and rest of Chile. Analysis of genetic diversity also showed a strong signal of past low population size and a recent population expansion.

The origin of selection signatures on bovine chromosome 6

The extent and pattern of linkage disequilibrium (LD) between closely spaced markers contain information about population history, including past population size and selection history. Selection signatures can be identified by comparing the LD surrounding a putative selected allele at a locus to the putative non-selected allele. In livestock populations, locations of selection signatures identified in this way should be correlated with QTL affecting production traits, as the populations have been under strong artificial selection for these traits. We used a dense SNP map of bovine chromosome 6 to characterize the pattern of LD on this chromosome in Norwegian Red cattle, a breed which has been strongly selected for milk production. The pattern of LD was generally consistent with strong selection in regions containing QTL affecting milk production traits, including a strong selection signature in a region containing a mutation known to affect milk production. The results demonstrate that in livestock populations, the origin of selection signatures will often be QTL for livestock production traits, and illustrate the value of selection signatures in uncovering new mutations with potential effects on quantitative traits.

MtDNA Variation Predicts Population Size in Humans and Reveals a Major Southern Asian Chapter in Human Prehistory

The relative timing and size of regional human population growth following our expansion from Africa remain unknown. Human mitochondrial DNA (mtDNA) diversity carries a legacy of our population history. Given a set of sequences, we can use coalescent theory to estimate past population size through time and draw inferences about human population history. However, recent work has challenged the validity of using mtDNA diversity to infer species population sizes. Here we use Bayesian coalescent inference methods, together with a global data set of 357 human mtDNA coding-region sequences, to infer human population sizes through time across 8 major geographic regions. Our estimates of relative population sizes show remarkable concordance with the contemporary regional distribution of humans across Africa, Eurasia, and the Americas, indicating that mtDNA diversity is a good predictor of population size in humans. Plots of population size through time show slow growth in sub-Saharan Africa beginning 143-193 kya, followed by a rapid expansion into Eurasia after the emergence of the first non-African mtDNA lineages 50-70 kya. Outside Africa, the earliest and fastest growth is inferred in Southern Asia approximately 52 kya, followed by a succession of growth phases in Northern and Central Asia (approximately 49 kya), Australia (approximately 48 kya), Europe (approximately 42 kya), the Middle East and North Africa (approximately 40 kya), New Guinea (approximately 39 kya), the Americas (approximately 18 kya), and a second expansion in Europe (approximately 10-15 kya). Comparisons of relative regional population sizes through time suggest that between approximately 45 and 20 kya most of humanity lived in Southern Asia. These findings not only support the use of mtDNA data for estimating human population size but also provide a unique picture of human prehistory and demonstrate the importance of Southern Asia to our recent evolutionary past.

Bayesian inference of population size history from multiple loci

BackgroundEffective population size (Ne) is related to genetic variability and is a basic parameter in many models of population genetics. A number of methods for inferring current and past population sizes from genetic data have been developed since JFC Kingman introduced the n-coalescent in 1982. Here we present the Extended Bayesian Skyline Plot, a non-parametric Bayesian Markov chain Monte Carlo algorithm that extends a previous coalescent-based method in several ways, including the ability to analyze multiple loci.ResultsThrough extensive simulations we show the accuracy and limitations of inferring population size as a function of the amount of data, including recovering information about evolutionary bottlenecks. We also analyzed two real data sets to demonstrate the behavior of the new method; a single gene Hepatitis C virus data set sampled from Egypt and a 10 locus Drosophila ananassae data set representing 16 different populations.ConclusionThe results demonstrate the essential role of multiple loci in recovering population size dynamics. Multi-locus data from a small number of individuals can precisely recover past bottlenecks in population size which can not be characterized by analysis of a single locus. We also demonstrate that sequence data quality is important because even moderate levels of sequencing errors result in a considerable decrease in estimation accuracy for realistic levels of population genetic variability.

Genetic structure and evidence for recent population decline in Eurasian otter populations in the Czech and Slovak Republics: implications for conservation

AbstractOver the latter part of the 20th century, Eurasian otter Lutra lutra populations suffered dramatic declines, resulting in extinction or fragmentation of populations in many western and central European countries. Part of the Czech otter population became totally isolated while the Slovak population remained partly connected to the relatively continuous central and eastern European otter distribution range. This paper examines the genetic structure and past demographic history of otters in the Czech and Slovak Republics, using microsatellite nuclear markers amplified from DNA extracted from tissue and faecal samples. A relatively high level of genetic differentiation was found between the Czech and Slovak populations (FST=0.154, P=0.0002), supported by a perfect assignment in Bayesian cluster analysis. Both the Czech and Slovak populations showed significant heterozygosity excess (assuming an infinite allele model), indicating recent population bottlenecks. A very recent population decline was also suggested by coalescent analysis, inferring a drop to c. 25% of past effective population size in both populations. The timing of the decline was in accordance with published data from otter surveys, suggesting that the strongest decline probably occurred between the 1970s and the mid‐1990s. The results of this study confirm that otter populations remain vulnerable to any violent demographic change and, despite the claims of fish‐farmers and anglers for legal culls, it is highly desirable that they remain a strongly protected species in both countries. The spreading and re‐connection of otter populations observed recently is essential for the future health of the populations, and should be supported through habitat conservation.

Conservation management in the face of uncertainty: effectiveness of four options for managing Hector’s dolphin bycatch

ESR Endangered Species Research Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsSpecials ESR 3:169-179 (2007) - doi:10.3354/esr003169 Conservation management in the face of uncertainty: effectiveness of four options for managing Hector’s dolphin bycatch Elisabeth Slooten* Department of Zoology, University of Otago, PO Box 56, Dunedin, New Zealand *Email: liz.slooten@stonebow.otago.ac.nz ABSTRACT: New Zealand’s endemic Hector’s dolphins Cephalorhynchus hectori overlap with gillnet and trawl fisheries throughout their geographic range. The catch rate in commercial gillnets has been estimated using independent observers. No quantitative estimates are available for bycatch in recreational gillnets or trawl fisheries. The catch rate (per dolphin, per km of gillnet, per year) in commercial gillnets was used in a population viability analysis to estimate past and future population sizes. Total population size today (7873, coefficient of variation [CV] 0.16) was estimated at 27% of population size in 1970 (29316, CV 0.16), before a major expansion of commercial gillnetting. The species matches IUCN criteria for ‘endangered’. The North Island subspecies matches criteria for ‘critically endangered’. Current management, which includes 2 protected areas, is not sufficient to halt population declines. Hector’s dolphin populations are predicted to continue declining to 5475 (CV 0.20) by 2050. Creating 4 strategically placed protected areas would allow population recovery towards 1970 levels, with an estimated 47% probability of reaching 50% of 1970 population size by 2050 (proportion of 5000 model runs in which final population size was at or above this reference level). Reducing fisheries mortality to levels approaching zero shows the strongest promise of meeting national and international guidelines for managing dolphin bycatch, with a 59% probability of reaching 50% of 1970 population size by 2050. KEY WORDS: Hector’s dolphin · Fishing · Bycatch · Extinction · Risk · Population viability Full text in pdf format PreviousNextCite this article as: Slooten E (2007) Conservation management in the face of uncertainty: effectiveness of four options for managing Hector’s dolphin bycatch. Endang Species Res 3:169-179. https://doi.org/10.3354/esr003169Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in ESR Vol. 3, No. 2. Online publication date: August 02, 2007 Print ISSN: 1863-5407; Online ISSN: 1613-4796 Copyright © 2007 Inter-Research.

Application of population growth models based on cumulative size to pecan aphids

Models for aphid population growth based on cumulative (past) population size have been developed with both a deterministic formulation and a stochastic formulation. This article applies these mechanistic models to analyze a large dataset on pecan aphid. The models yield symmetric and right-skewed curves, which differ qualitatively from the observed data which tend to be left-skewed. Nevertheless this model-based analysis of data shows that the models are (1) useful representations of the data, (2) biologically reasonable descriptions of aphid population dynamics, and (3) a statistically powerful basis for the analysis of experimental data. The models also provide user-friendly predictive equations for aphid abundance. The deterministic model gives accurate point predictions of the peak and final cumulative population sizes, and the stochastic model gives, in addition, an accurate interval estimate of cumulative size. The models should be applicable to numerous other aphid abundance curves, as all aphid species have a similar reproductive mechanism.

Demography, the Population of Syria and the Census of Q. Aemilius Secundus

“In the end, demography without numbers is waffle”(Coleman and Schofield 1986, 4)“... most population figures recorded in Greek and Roman literature have been scrutinized so often that any interpretation that has not yet met with common approval will probably remain forever controversial.”(Scheidel 1996, 165)“Historical knowledge of past human population sizes is a quilt of tiny pieces of fact (archaeological remains, monuments, documents, observations of present human and nonhuman populations) patched together with large portions of conjectures and assumptions.”(Cohen 1995, 28)

Spatial and temporal mitochondrial DNA genetic homogeneity of dolphinfish populations ( Coryphaena hippurus) in the eastern central Pacific

Dolphinfish ( Coryphaena hippurus) samples were collected over four consecutive years from four locations in the eastern central Pacific to evaluate the genetic variation in a 751 bp segment of the mitochondrial NADH subunit 1 (ND1) to test for the presence of genetic population structure. Sequence analyses revealed no significant differences among collections from the same location in the different years sampled nor between locations. Mismatch distributions, estimations of population expansion parameters, and neutrality tests revealed significant fluctuations in population size in coincidence with past glacial and interglacial periods during the late Pleistocene. The low levels of nucleotide diversities and shallow coalescence of mtDNA genealogies observed were coincident with the estimated demographic parameters and neutrality tests, in suggesting the presence of important past population size fluctuations or range expansion. The prevention of the accumulation of deep lineages independently on how it was originated, probably delayed the emergence of a population divergence process which might account for the lack of genetic differences detected.

Estimation of effective population sizes from data on genetic markers.

The effective population size (Ne) is an important parameter in ecology, evolutionary biology and conservation biology. It is, however, notoriously difficult to estimate, mainly because of the highly stochastic nature of the processes of inbreeding and genetic drift for which Ne is usually defined and measured, and because of the many factors (such as time and spatial scales, systematic forces) confounding such processes. Many methods have been developed in the past three decades to estimate the current, past and ancient effective population sizes using different information extracted from some genetic markers in a sample of individuals. This paper reviews the methodologies proposed for estimating Ne from genetic data using information on heterozygosity excess, linkage disequilibrium, temporal changes in allele frequency, and pattern and amount of genetic variation within and between populations. For each methodology, I describe mainly the logic and genetic model on which it is based, the data required and information used, the interpretation of the estimate obtained, some results from applications to simulated or empirical datasets and future developments that are needed.

Sibship within samples of brown trout (Salmo trutta) and implications for supportive breeding

We analysed family relationships among brown trout from two small tributary populations that have been suggested as a source of individuals for supportive breeding, using variation at eight microsatellite loci. As a control, we analysed a sample of supposedly unrelated individuals representing a large anadromous population, and we simulated unrelated individuals based on the allelic distributions in all three samples. Two different approaches were used: (1) pairwise estimates of relatedness between individuals and (2) a method for partitioning individuals into half-sib and full-sib families. The anadromous population did not show evidence of a significant number of closely related individuals. In both tributary populations, however, the distributions of pairwise relatedness estimates suggested the presence of several related individuals, and sibship reconstruction suggested fewer families consisting of more individuals than were observed for the simulated individuals. The expected increase of inbreeding coefficient in the two samples due to family structure was 0.026 and 0.030 respectively. Moreover, tests for recent bottlenecks yielded significant outcomes in both populations suggesting a history of low effective population sizes. Depending on the effective population size of captive spawners and past effective population sizes in the populations it could be beneficial to conduct sib-avoidance matings, though this cannot eliminate inbreeding but only delay it. Alternatively, individuals from different populations could be crossed. Sibship reconstruction provided the clearest evidence for family structure, but pairwise relatedness is the best measure for designing mating schemes, as it allows for mating as unrelated individuals as possible rather than just avoiding mating between sibs.

GENETIC VARIABILITY AND DRIFT LOAD IN POPULATIONS OF AN AQUATIC SNAIL

Population genetic theory predicts that in small populations, random genetic drift will fix and accumulate slightly deleterious mutations, resulting in reduced reproductive output. This genetic load due to random drift (i.e., drift load) can increase the extinction risk of small populations. We studied the relationship between genetic variability (indicator of past population size) and reproductive output in eight isolated, natural populations of the hermaphroditic snail Lymnaea stagnalis. In a common laboratory environment, snails from populations with the lowest genetic variability mature slower and have lower fecundity than snails from genetically more variable populations. This result suggests that past small population size has resulted in increased drift load, as predicted. The relationship between genetic variability and reproductive output is independent of the amount of nonrandom mating within populations. However, reproductive output and the current density of snails in the populations were not correlated. Instead, data from the natural populations suggest that trematode parasites may determine, at least in part, population densities of the snails.

A long-term perspective on ungulate–vegetation interactions

The fossil record of vegetation and ungulates places present conditions and trends in a temporal perspective. Ungulate–vegetation interactions during the last 500 000 years were primarily driven by the climatic variation of the glacial–interglacial cycle. There were distinctive faunas associated with each temperate period and a loss of species diversity only in the present interglacial. Climate change and human activities have interacted during the most recent glacial cycle, accelerating extinction rates. This unique course of events has the consequence that no stable, ‘base-line’ conditions can be recognised. A review of the full-glacial ‘mammoth-steppe’ debate suggests that ungulate populations were limited by available forage, but a mosaic of habitat supported a diverse fauna in Beringia. In the debate over early–mid Holocene ‘wood pasture’, past ungulate populations are one of a range of disturbance factors, including burning, that influenced regional vegetation composition and structure in northern Europe. These debates concerning the scale and impacts of past ungulate–vegetation interactions will not be fully resolved until more is known about past ungulate population sizes. Modelling past scenarios would enhance the value of retrospective studies and help provide goals for management of near-natural ecosystems.