Historical Changes In Population Size Research Articles

Congruence between microsatellite loci, SNPs, and COI gene reveals a phylogeographic break in the southern Caribbean Sea: The case of West Indian top shell Cittarium pica (Gastropoda: Tegulidae)

It has been proposed that species associated with shallow rocky bottoms in the southern Colombian Caribbean Sea are affected by two biogeographic barriers: the Magdalena River plume (MRP) and the combination of the absence of rocky bottoms and the almost permanent upwelling in the Guajira peninsula (ARB+PUG). We evaluated whether these barriers had generalized genomic effects on the phylogeographic structure of the West Indian top shell (Cittarium pica), a crucial fishery resource in many areas of the Caribbean Sea. Ten species-specific microsatellite loci, 55,112 SNPs from ddRADseq, and COI gene were used on samples of C. pica collected at five Colombian localities (Cabo de la Vela; Santa Marta; Cartagena; Isla Fuerte; and Capurganá). Genetic structure analyses performed for microsatellite and SNP loci indicated that there are three genetic groups of C. pica in Colombia (pop 1: Cabo de la Vela; pop 2: Santa Marta; pop 3: Cartagena+Isla Fuerte+Capurganá). However, both SNPs and COI gene were congruent in showing a phylogeographic break caused by only the ARB + PUG (AMOVA: ΦCT-SNP=0.224, p < 0.05; ΦCT-COI=0.722, p < 0.05), which was confirmed by the maximum-likelihood and network trees. In contrast, MRP was shown to be a permeable barrier to gene flow. Demographic history analysis indicated that C. pica experienced historical changes in population size during the last glaciation period. Cittarium pica is a biological model to demonstrate how the ARB + PUG barrier could affect marine organisms living in shallow rocky habitats, mainly those lacking larvae or having a short-lived larval phase in the southern Caribbean Sea. Finally, some recommendations for fisheries management and conservation C. pica populations are discussed.

Glacial vicariance and oceanic circulation shape population structure of the coastal legume Derris trifoliata in the Indo-West Pacific.

The phylogeography of coastal plant species is shaped by contemporary and historical biogeographic processes. In this study, we aim to decipher the phylogeography of Derris trifoliata, a woody legume of relatively recent origin and wide distribution, in coastal areas in the Indo-West Pacific (IWP) region. Genetic diversity and population structure were assessed by analyzing six nuclear and three chloroplast DNA sequences from 30 populations across the species' range. Phylogeography was inferred by estimating gene flow, divergence time, historical population size changes, and historical habitat suitability using paleoclimatic niche modeling. High genetic diversity was observed at the species level. The populations of three oceanic regions included in this study (i.e., Indian Ocean, South China Sea, and Pacific Ocean) formed distinct clades and likely diverged during the late Pleistocene. Potential barriers to gene flow were identified, including the Sunda and Sahul shelves, geographic distance, and current patterns of oceanic circulation. Analysis of changes in population size supported the bottleneck model, which was strengthened by estimates of habitat suitability across paleoclimatic conditions. The once widespread distribution of D. trifoliata was fragmented by changes in climatic suitability and biogeographic barriers that arose following sea-level changes during the Pleistocene. In addition, contemporary patterns of oceanic circulation and geographic distance between populations appear to maintain genetic differentiation across its distribution in the IWP.

Inferring the demographic history of Japanese eel (Anguilla japonica) from genomic data: Insights for conservation and fisheries management

Abstract Assessing the status or population size of species is a key task for wildlife conservation and the sustainable management of harvested species. In particular, assessing historical changes in population size provides an evolutionary perspective on current population dynamics. Japanese eel (Anguilla japonica) is an endangered yet commercially important catadromous fish species. This article assesses the demographic history of Japanese eel using the pairwise and multiple sequentially Markovian coalescent methods. The analyses indicate a reduction in effective population size Ne from 38,000 to 10,000 individuals between 4 and 1 Mya, followed by an increase to 80,000 individuals between 1 Mya and 22–30 kya. Approximately 22–30 kya there is evidence for a reduction in Ne to approximately 60,000 individuals. These events may be related to changes in environmental conditions, especially around the last glacial maximum (19–33 kya). The results of this study suggest that Japanese eel has experienced at least two population bottlenecks, interspersed by a period of population growth. The overall level of genetic diversity is relatively low, although there is no evidence for inbreeding. Data from this study will be used to help model the extinction risk of Japanese eel.

Genetic and reproductive characterization of distylous Primula reinii in the Hakone volcano, Japan: implications for conservation of the rare and endangered plant

Genetic and ecological evaluation are crucial in effective management of rare and endangered species, including those exhibiting complex breeding systems such as distyly. We studied a threatened distylous herb Primula reinii in the Hakone volcano, central Japan, to obtain baseline information of reproductive and genetic status towards conservation. In two representative populations inhabiting a central cone and somma of the volcano, population size, floral morph ratio, stigmatic pollen deposition, and fruit-set were measured. Using microsatellite markers, we evaluated genetic diversity, structure and differentiation of populations. Population bottlenecks and historical changes in population size were also estimated from genotype data. We found significant deviation from equal morph ratios in the central cone population, which also exhibited skewed mating success together with a high frequency of pollination within the same morph. These trends were not detected in the somma population. From genetic insights, the central cone population showed slightly lower genetic diversity, whereas no significant deviation from Hardy-Weinberg equilibrium was found in either population. The estimated moderate genetic differentiation and admixed genetic structure suggest recent lineage divergence and/or gene flow between populations. While robust evidence for a recent bottleneck was not obtained in our analyses, a clear signature of historical population contraction was detected in the central cone population. Our findings suggest that the skewed morph ratio strongly influenced the reproduction of small and isolated populations in the short-term, highlighting the vulnerability of distylous plant populations under ongoing anthropogenic pressure.

Inference of Historical Population-Size Changes with Allele-Frequency Data.

With up to millions of nearly neutral polymorphisms now being routinely sampled in population-genomic surveys, it is possible to estimate the site-frequency spectrum of such sites with high precision. Each frequency class reflects a mixture of potentially unique demographic histories, which can be revealed using theory for the probability distributions of the starting and ending points of branch segments over all possible coalescence trees. Such distributions are completely independent of past population history, which only influences the segment lengths, providing the basis for estimating average population sizes separating tree-wide coalescence events. The history of population-size change experienced by a sample of polymorphisms can then be dissected in a model-flexible fashion, and extension of this theory allows estimation of the mean and full distribution of long-term effective population sizes and ages of alleles of specific frequencies. Here, we outline the basic theory underlying the conceptual approach, develop and test an efficient statistical procedure for parameter estimation, and apply this to multiple population-genomic datasets for the microcrustacean Daphnia pulex.

Green sea turtle (Chelonia mydas) population history indicates important demographic changes near the mid-Pleistocene transition

The increased availability of genome sequences has provided remarkable advances in our understanding of the evolutionary history of non-model species. One important consideration in evolutionary studies is the role of demographic history in shaping contemporary levels and distribution of genetic variation. In green sea turtles (Chelonia mydas), a draft genome sequence has recently been made available, yet little is known regarding how past demographic events have shaped genomic variation in populations of this species. In this study, single nucleotide polymorphisms were identified in the green sea turtle’s genome and used to reconstruct past demographic events. It was found that this green sea turtle population, from the South China Sea, experienced a marked expansion ca. 0.8 million years ago near the mid-Pleistocene transition (MPT). Simulations revealed that the past demographic history can at least partially be explained by changes in population structure and gene flow; possibly associated with the climatic and geomagnetic events occurring since the MPT. The results demonstrate the importance in considering the effects of gene flow when reconstructing historical changes in population size and provide an extensive set of genomic resources for future evolutionary studies of green sea turtles.

Computing the joint distribution of the total tree length across loci in populations with variable size

In recent years, a number of methods have been developed to infer complex demographic histories, especially historical population size changes, from genomic sequence data. Coalescent Hidden Markov Models have proven to be particularly useful for this type of inference. Due to the Markovian structure of these models, an essential building block is the joint distribution of local genealogical trees, or statistics of these genealogies, at two neighboring loci in populations of variable size. Here, we present a novel method to compute the marginal and the joint distribution of the total length of the genealogical trees at two loci separated by at most one recombination event for samples of arbitrary size. To our knowledge, no method to compute these distributions has been presented in the literature to date. We show that they can be obtained from the solution of certain hyperbolic systems of partial differential equations. We present a numerical algorithm, based on the method of characteristics, that can be used to efficiently and accurately solve these systems and compute the marginal and the joint distributions. We demonstrate its utility to study the properties of the joint distribution. Our flexible method can be straightforwardly extended to handle an arbitrary fixed number of recombination events, to include the distributions of other statistics of the genealogies as well, and can also be applied in structured populations.

Relative abundance of Mycobacterium bovis molecular types in cattle: a simulation study of potential epidemiological drivers

BackgroundThe patterns of relative species abundance are commonly studied in ecology and epidemiology to provide insights into underlying dynamical processes. Molecular types (MVLA-types) of Mycobacterium bovis, the causal agent of bovine tuberculosis, are now routinely recorded in culture-confirmed bovine tuberculosis cases in Northern Ireland. In this study, we use ecological approaches and simulation modelling to investigate the distribution of relative abundances of MVLA-types and its potential drivers. We explore four biologically plausible hypotheses regarding the processes driving molecular type relative abundances: sampling and speciation; structuring of the pathogen population; historical changes in population size; and transmission heterogeneity (superspreading).ResultsNorthern Irish herd-level MVLA-type surveillance shows a right-skewed distribution of MVLA-types, with a small number of types present at very high frequencies and the majority of types very rare. We demonstrate that this skew is too extreme to be accounted for by simple neutral ecological processes. Simulation results indicate that the process of MVLA-type speciation and the manner in which the MVLA-typing loci were chosen in Northern Ireland cannot account for the observed skew. Similarly, we find that pathogen population structure, assuming for example a reservoir of infection in a separate host, would drive the relative abundance distribution in the opposite direction to that observed, generating more even abundances of molecular types. However, we find that historical increases in bovine tuberculosis prevalence and/or transmission heterogeneity (superspreading) are both capable of generating the skewed MVLA-type distribution, consistent with findings of previous work examining the distribution of molecular types in human tuberculosis.ConclusionAlthough the distribution of MVLA-type abundances does not fit classical neutral predictions, our simulations show that increases in pathogen population size and/or superspreading are consistent with the pattern observed, even in the absence of selective pressures acting on the system.

The greater snow goose Anser caerulescens atlanticus: Managing an overabundant population

Between the early 1900s and the 1990s, the greater snow goose Anser caerulescens atlanticus population grew from 3000 individuals to more than 700 000. Because of concerns about Arctic degradation of natural habitats through overgrazing, a working group recommended the stabilization of the population. Declared overabundant in 1998, special management actions were then implemented in Canada and the United States. Meanwhile, a cost–benefit socioeconomic analysis was performed to set a target population size. Discussions aiming towards attaining a common vision were undertaken with stakeholders at multiple levels. The implemented measures have had varying success; but population size has been generally stable since 1999. To be effective and meet social acceptance, management actions must have a scientific basis, result from a consensus among stakeholders, and include an efficient monitoring programme. In this paper, historical changes in population size and management decisions along with past and current challenges encountered are discussed.

Genetic variability, local selection and demographic history: genomic evidence of evolving towards allopatric speciation in Asian seabass.

Genomewide analysis of genetic divergence is critically important in understanding the genetic processes of allopatric speciation. We sequenced RAD tags of 131 Asian seabass individuals of six populations from South-East Asia and Australia/Papua New Guinea. Using 32433 SNPs, we examined the genetic diversity and patterns of population differentiation across all the populations. We found significant evidence of genetic heterogeneity between South-East Asian and Australian/Papua New Guinean populations. The Australian/Papua New Guinean populations showed a rather lower level of genetic diversity. FST and principal components analysis revealed striking divergence between South-East Asian and Australian/Papua New Guinean populations. Interestingly, no evidence of contemporary gene flow was observed. The demographic history was further tested based on the folded joint site frequency spectrum. The scenario of ancient migration with historical population size changes was suggested to be the best fit model to explain the genetic divergence of Asian seabass between South-East Asia and Australia/Papua New Guinea. This scenario also revealed that Australian/Papua New Guinean populations were founded by ancestors from South-East Asia during mid-Pleistocene and were completely isolated from the ancestral population after the last glacial retreat. We also detected footprints of local selection, which might be related to differential ecological adaptation. The ancient gene flow was examined and deemed likely insufficient to counteract the genetic differentiation caused by genetic drift. The observed genomic pattern of divergence conflicted with the 'genomic islands' scenario. Altogether, Asian seabass have likely been evolving towards allopatric speciation since the split from the ancestral population during mid-Pleistocene.

Two-Locus Likelihoods Under Variable Population Size and Fine-Scale Recombination Rate Estimation.

Two-locus sampling probabilities have played a central role in devising an efficient composite-likelihood method for estimating fine-scale recombination rates. Due to mathematical and computational challenges, these sampling probabilities are typically computed under the unrealistic assumption of a constant population size, and simulation studies have shown that resulting recombination rate estimates can be severely biased in certain cases of historical population size changes. To alleviate this problem, we develop here new methods to compute the sampling probability for variable population size functions that are piecewise constant. Our main theoretical result, implemented in a new software package called LDpop, is a novel formula for the sampling probability that can be evaluated by numerically exponentiating a large but sparse matrix. This formula can handle moderate sample sizes ([Formula: see text]) and demographic size histories with a large number of epochs ([Formula: see text]). In addition, LDpop implements an approximate formula for the sampling probability that is reasonably accurate and scales to hundreds in sample size ([Formula: see text]). Finally, LDpop includes an importance sampler for the posterior distribution of two-locus genealogies, based on a new result for the optimal proposal distribution in the variable-size setting. Using our methods, we study how a sharp population bottleneck followed by rapid growth affects the correlation between partially linked sites. Then, through an extensive simulation study, we show that accounting for population size changes under such a demographic model leads to substantial improvements in fine-scale recombination rate estimation.

Signatures of Demography and Recombination at Coding Genes in Naturally-Distributed Populations of Arabidopsis Lyrata Subsp. Petraea

Demography impacts the observed standing level of genetic diversity present in populations. Distinguishing the relative impacts of demography from selection requires a baseline of expressed gene variation in naturally occurring populations. Six nuclear genes were sequenced to estimate the patterns and levels of genetic diversity in natural Arabidopsis lyrata subsp. petraea populations that differ in demographic histories since the Pleistocene. As expected, northern European populations have genetic signatures of a strong population bottleneck likely due to glaciation during the Pleistocene. Levels of diversity in the northern populations are about half of that in central European populations. Bayesian estimates of historical population size changes indicate that central European populations also have signatures of population size change since the last glacial maxima, suggesting that these populations are not as stable as previously thought. Time since divergence amongst northern European populations is higher than amongst central European populations, suggesting that the northern European populations were established before the Pleistocene and survived glaciation in small separated refugia. Estimates of demography based on expressed genes are complementary to estimates based on microsatellites and transposable elements, elucidating temporal shifts in population dynamics and confirming the importance of marker selection for tests of demography.

Evaluating the Effects of Population Management on a Herbivore Grazing Conflict

Abundant herbivores can damage plants and so cause conflict with conservation, agricultural, and fisheries interests. Management of herbivore populations is a potential tool to alleviate such conflicts but may raise concerns about the economic and ethical costs of implementation, especially if the herbivores are ‘charismatic’ and popular with the public. Thus it is critical to evaluate the probability of achieving the desired ecological outcomes before proceeding to a field trial. Here we assessed the potential for population control to resolve a conflict of non-breeding swans grazing in river catchments. We used a mathematical model to evaluate the consequences of three population management strategies; (a) reductions in reproductive success, (b) removal of individuals, and (c) reduced reproductive success and removal of individuals combined. This model gave accurate projections of historical changes in population size for the two rivers for which data were available. Our model projected that the River Frome swan population would increase by 54%, from 257 to 397 individuals, over 17 years in the absence of population control. Removal of ≥60% of non-breeding individuals each year was projected to reduce the catchment population below the level for which grazing conflicts have been previously reported. Reducing reproductive success, even to 0 eggs per nest, failed to achieve the population reduction required. High adult and juvenile survival probabilities (>0.7) and immigration from outside of the catchment limited the effects of management on population size. Given the high, sustained effort required, population control does not represent an effective management option for preventing the grazing conflicts in river catchments. Our study highlights the need to evaluate the effects of different management techniques, both alone and in combination, prior to field trials. Population models, such as the one presented here, can provide a cost-effective and ethical means of such evaluations.

Pattern of genetic differentiation in Gentiana pannonica Scop.: did subalpine plants survive glacial events at low altitudes in Central Europe?

The molecular population structure of 20 populations of the subalpine plant Gentiana pannonica was studied by use of amplified fragment length polymorphism (AFLP) and sequencing of non-coding regions of plastid DNA. Of the populations sampled, 18 were native (11 were from the Eastern Alps, which is the distribution centre of the species, and seven were from the Bohemian Forest, which is on the margin of the distribution range), and two were from the Giant Mts and of unclear status. No plastid DNA polymorphisms were found within the entire 6,185 bp investigated. The AFLP data revealed grouping of populations at the regional level. However, differentiation at the regional level (10.3 %) and at the interpopulation level (14.2 %) was low. Even though current populations are isolated and contain small numbers of individuals, the within-population variation (75.511 %) was high. Genetic variation was higher for alpine populations than for Bohemian Forest populations, probably because of fundamental differences in historical changes in population size between these regions. Within-population variation was intermediate for populations in the Giant Mts. The results indicate the possibility of a large distribution of species in the unglaciated areas of Central Europe, irrespective of altitude, during the late Pleistocene and early Holocene. Our results do not confirm that G.pannonica was introduced in the Giant Mts, and native status in the Giant Mts is possible.

Recent population decline and selection shape diversity of taxol‐related genes

Taxanes are defensive metabolites produced by Taxus species (yews) and used in anticancer therapies. Despite their medical interest, patterns of natural diversity in taxane-related genes are unknown. We examined variation at five main genes of Taxus baccata in the Iberian Peninsula, a region where unique yew genetic resources are endangered. We looked at several gene features and applied complementary neutrality tests, including diversity/divergence tests, tests solely based on site frequency spectrum (SFS) and Zeng's compound tests. To account for specific demography, microsatellite data were used to infer historical changes in population size based on an Approximate Bayesian Computation (ABC) approach. Polymorphism-divergence tests pointed to positive selection for genes TBT and TAT and balancing selection for DBAT. In addition, neutrality tests based on SFS found that while a recent reduction in population size may explain most statistics' values, selection may still be in action in genes TBT and DBAT, at least in some populations. Molecular signatures on taxol genes suggest the action of frequent selective waves with different direction or intensity, possibly related to varying adaptive pressures produced by the host-enemy co-evolution on defence-related genes. Such natural selection processes may have produced taxane variants still undiscovered.

A novel predictor of multilocus haplotype homozygosity: comparison with existing predictors

The patterns of linkage disequilibrium (LD) between dense polymorphic markers are shaped by the ancestral population history. It is therefore possible to use multilocus predictors of LD to infer past population history and to infer sharing of identical alleles in quantitative trait locus (QTL) studies. We develop a multilocus predictor of LD for pairs of haplotypes, which we term haplotype homozygosity (HHn): the probability that any two haplotypes share a given number of n adjacent identical markers or 'runs of homozygosity'. Our method, based on simplified coalescence theory, accounts for recombination and mutation. We compare our HHn predictions, with HHn in simulated populations and with two published predictors of HHn. Our method performs consistently better across a range of population parameters, including populations with a severe bottleneck followed by expansion, compared to two published methods. We demonstrate that we can predict the pattern of HHn observed in dense single nucleotide polymorphisms (SNPs) genotyped in a cattle population, given appropriate historical changes in population size. Our method is practical for use with very large numbers of individuals and dense genome wide polymorphic DNA data. It has potential applications in inferring ancestral population history and QTL mapping studies.

Genetic Diversity and Population Structure of Reddish Egrets Along the Texas Coast

Little is known about the ecology and population structure of the Reddish Egret (Egretta rufescens). Furthermore, the effects of the near extirpation on genetic variation of Reddish Egrets are unknown. A 223-basepair region of the mitochondrial DNA (mtDNA) control region was sequenced in 149 Reddish Egret samples from sixteen breeding colonies along the Texas Coast to investigate genetic diversity and population structure. Despite experiencing a severe reduction in population size, Reddish Egrets retained a moderate amount of haplotype (0.705) and nucleotide diversity (0.005). A mismatch distribution among haplotypes and non-equilibrium relationship between the number and similarity of haplotypes (Fu's Fs) are consistent with historical population size changes. No evidence of genetic structuring was found among either colonies or color morphs. Reddish Egrets along the Texas Coast appear to form a single panmictic population. The results of this first conservation genetic study of Reddish Egrets serve as a foundation for management and additional research.

Genetic structure of an isolated population of mantled howler monkeys (Alouatta palliata) on Barro Colorado Island, Panama

Habitat fragmentation may influence genetic variability through reductions in population size and the physical isolation of conspecifics. We explored the effects of these factors on genetic diversity in a population of mantled howler monkeys (Alouatta palliata) on Barro Colorado Island (BCI), Panama. The study population was established in 1914 when an unknown number of resident individuals were isolated from the surrounding mainland by damming of the Rio Chagres to create the Panama Canal. Analyses of 10 microsatellite loci indicated that, despite this isolation, the howler monkeys on BCI exhibit levels of genetic diversity (H S = 0.584 ± 0.063) among the highest reported for any species of Alouatta. These data also revealed that although relatedness among adults in a social group was significantly greater than zero, the BCI population is not highly genetically structured. Tests for genetic bottlenecks based on departures from equilibrium expectations failed to reveal evidence of a recent reduction in population size. In contrast, coalescent modeling indicated that this population has likely experienced a marked decline within the last few 100 years. These findings generate new insights into the genetic structure of A. palliata and suggest that while the formation of BCI may not have substantially reduced genetic variation in these animals, genetic diversity has been influenced by historical changes in population size.

INTRASPECIFIC VARIATION IN EFFECTIVE POPULATION SIZE IN TALAR TUCO-TUCOS (CTENOMYS TALARUM): THE ROLE OF DEMOGRAPHY

Abstract Effective population size (Ne) is a fundamental concept that links population structure to the evolutionary processes that shape genetic variation. Demographic estimates of Ne may be influenced by a number of factors, including adult sex ratio and variance in individual reproductive success. Genetic estimates of Ne are influenced not only by these variables but also by neighborhood size, degree of population substructure, and historical changes in population size. Hence, comparisons of demographic and genetic estimates of Ne may yield important insights into the parameters that determine effective size. To explore interactions between demography and Ne, we compared estimates of effective population size/census size (Ne/N) for 2 demographically distinct populations of the talar tuco-tuco (Ctenomys talarum), a subterranean rodent from Buenos Aires Province, Argentina. Examination of data on adult sex ratios and reproductive success obtained from long-term field studies of C. talarum at Mar de Cobo ...

The fall and rise of bison populations in Wood Buffalo National Park: 1971 to 2003

Two hypotheses have been proposed to explain the decline of bison (Bison bison (L., 1758)) abundance in Wood Buffalo National Park (WBNP). The "disease–predation" hypothesis proposes that tuberculosis (Mycobacterium bovis (Karlson and Lessel 1970)) and brucellosis (Brucella abortus (Schmidt 1901)) reduce bison survival and reproduction, resulting in a low-density, predator-regulated equilibrium. The "habitat dispersion hypothesis" proposes that bison in one area of WBNP, the Peace–Athabasca Delta (Delta), have an increased risk of predation because they are concentrated in large meadows with high temporal and spatial predictability. We incorporate bison census data, calf and yearling segregation counts, reproductive rates, adult survival rates, and adult disease incidence in a stochastic population model to show that the historical decline of bison in WBNP would have occurred regardless of disease prevalence. Our model shows that survival of juveniles, the age class that is least susceptible to disease effects, was likely an important determinant of historical changes in population size. We also demonstrate that the population decline was most pronounced in the Delta and that juvenile survival was lower in the Delta, despite evidence that disease incidence was lower in the Delta than in the rest of WBNP. Lastly, the current population trend in WBNP is one of rapid increase, even in the presence of disease.