Severe Bottleneck Research Articles

Population history, genetic variation and conservation status of the endangered birch species Betula nana L. in Poland

The effective conservation of species requires data on the levels and distribution of genetic diversity within and among populations. In this study, we estimated the genetic variation in three isolated populations of Betula nana in Poland. An analysis of 11 nuclear microsatellites revealed moderate mean heterozygosities (H=0.556, H=0.562), low mean number of alleles per locus (A=4.57) and no inbreeding in the total sample. An M-ratio test indicated that each population had experienced a severe bottleneck in the past. Tests for heterozygosity excess revealed that a significant decrease in the numbers of individuals in two populations had occurred quite recently. The large number of private alleles and very restricted number of migrants between populations (Nm=0.35) strongly suggest that genetic drift and geographic isolation are the primary factors responsible for the reduction of genetic variation in the Polish populations of B. nana. We detected two cpDNA haplotypes in the study populations, which can be explained in terms of either the genetic drift acting on the relict localities or a postglacial recolonisation from distinct refugia. Palynological data indicated that one refugium could be located in the Carpathians and their northern foreland. The primary threat to B. nana in Poland is the overgrowth of its habitats by competing species, which has likely resulted in a lack of generative reproduction in the mountain populations.OE

Production of UCP1 a membrane protein from the inner mitochondrial membrane using the cell free expression system in the presence of a fluorinated surfactant

Structural studies of membrane protein are still challenging due to several severe bottlenecks, the first being the overproduction of well-folded proteins. Several expression systems are often explored in parallel to fulfil this task, or alternately prokaryotic analogues are considered. Although, mitochondrial carriers play key roles in several metabolic pathways, only the structure of the ADP/ATP carrier purified from bovine heart mitochondria was determined so far. More generally, characterisations at the molecular level are restricted to ADP/ATP carrier or the uncoupling protein UCP1, another member of the mitochondrial carrier family, which is abundant in brown adipose tissues. Indeed, mitochondrial carriers have no prokaryotic homologues and very few efficient expression systems were described so far for these proteins. We succeeded in producing UCP1 using a cell free expression system based on E. coli extracts, in quantities that are compatible with structural approaches. The protein was synthesised in the presence of a fluorinated surfactant, which maintains the protein in a soluble form. Further biochemical and biophysical analysis such as size exclusion chromatography, circular dichroism and thermal stability, of the purified protein showed that the protein is non-aggregated, monodisperse and well-folded.

Catastrophic Floods May Pave the Way for Increased Genetic Diversity in Endemic Artesian Spring Snail Populations

The role of disturbance in the promotion of biological heterogeneity is widely recognised and occurs at a variety of ecological and evolutionary scales. However, within species, the impact of disturbances that decimate populations are neither predicted nor known to result in conditions that promote genetic diversity. Directly examining the population genetic consequences of catastrophic disturbances however, is rarely possible, as it requires both longitudinal genetic data sets and serendipitous timing. Our long-term study of the endemic aquatic invertebrates of the artesian spring ecosystem of arid central Australia has presented such an opportunity. Here we show a catastrophic flood event, which caused a near total population crash in an aquatic snail species (Fonscochlea accepta) endemic to this ecosystem, may have led to enhanced levels of within species genetic diversity. Analyses of individuals sampled and genotyped from the same springs sampled both pre (1988–1990) and post (1995, 2002–2006) a devastating flood event in 1992, revealed significantly higher allelic richness, reduced temporal population structuring and greater effective population sizes in nearly all post flood populations. Our results suggest that the response of individual species to disturbance and severe population bottlenecks is likely to be highly idiosyncratic and may depend on both their ecology (whether they are resilient or resistant to disturbance) and the stability of the environmental conditions (i.e. frequency and intensity of disturbances) in which they have evolved.

Analysis of a stochastic predator–prey model with applications to intrahost HIV genetic diversity

During an infection, HIV experiences strong selection by immune system T cells. Recent experimental work has shown that MHC escape mutations form an important pathway for HIV to avoid such selection. In this paper, we study a model of MHC escape mutation. The model is a predator-prey model with two prey, composed of two HIV variants, and one predator, the immune system CD8 cells. We assume that one HIV variant is visible to CD8 cells and one is not. The model takes the form of a system of stochastic differential equations. Motivated by well-known results concerning the short life-cycle of HIV intrahost, we assume that HIV population dynamics occur on a faster time scale then CD8 population dynamics. This separation of time scales allows us to analyze our model using an asymptotic approach. Using this model we study the impact of an MHC escape mutation on the population dynamics and genetic evolution of the intrahost HIV population. From the perspective of population dynamics, we show that the competition between the visible and invisible HIV variants can reach steady states in which either a single variant exists or in which coexistence occurs depending on the parameter regime. We show that in some parameter regimes the end state of the system is stochastic. From a genetics perspective, we study the impact of the population dynamics on the lineages of an HIV sample taken after an escape mutation occurs. We show that the lineages go through severe bottlenecks and that in certain parameter regimes the lineage distribution can be characterized by a Kingman coalescent. Our results depend on methods from diffusion theory and coalescent theory.

Genetic consequences of subtropical rainforest fragmentation onMacadamia tetraphylla(Proteaceae)

AbstractHabitat fragmentation can bring about a variety of gene-flow alterations in plant populations, potentially threatening adaptive potential and local persistence. It is expected that following habitat fragmentation an increased level of inbreeding will be evident. In addition, a reduction in genetic diversity and increased genetic differentiation is expected following severe or long term population bottlenecks. We examined population genetic parameters for the subtropical rainforest treeMacadamia tetraphylla(Proteaceae) at six field sites throughout its recently fragmented range, using four microsatellite loci. Genetic diversity (HE) of the juvenile cohort was significantly correlated with estimated population size. No significant difference was observed for genetic diversity between adult and juvenile cohorts, but juveniles, and not adults, exhibited significant population differentiation (θ =0.061;P<0.0001 and θ =0.016;P=0.23, respectively). A second, standardised measure of differentiation, ×′, yielded similarly large differences between the two cohorts, though higher estimates of differentiation overall (adults – θ′=0.034, juveniles – θ′=0.116). The coefficient of population inbreeding (f) was significant and positive in all juvenile, and four out of six adult, populations, and was significantly positively correlated with adult tree density, but not adult population size. Since fragmentation is relatively recent for this species, the population bottleneck must have been quite severe to have produced the observed patterns of population differentiation and genetic diversity. Fragmentation of forest across the study area over the last 100+ years has led to the genetic isolation ofM. tetraphyllapopulations resulting in increased population divergence and likely eventual loss of genetic variation in future generations.

Genetic Diversity in Watermelon Cultivars and Related Species Based on AFLPs and EST-SSRs

The genetic relationships among 27 watermelon cultigens (Citrullus lanatus var. lanatus) from different countries of origin and with different horticultural characteristics and 5 related wild-type species and subspecies (Citrullus colocynthis, Citrullus lanatus var. citroides, and Citrullus rehmii) were assessed using amplified fragment length polymorphism (AFLP) and expressed sequence tag-simple sequence repeat (EST-SSR) markers. AFLPs were evaluated using 16 EcoRI-MseI primer combinations, and 862 alleles (an average of 53.8 alleles per primer combination) were scored. Polymorphisms were found in 806 (93.4%) alleles, whereas 56 monomorphic alleles were identified. Using 16 EST-SSR primer sets, 103 alleles were scored, and all 103 alleles were polymorphic among the 32 genotypes with an average of 6.4 polymorphic alleles per primer pair. However, the high polymorphic ratio among the AFLPs and EST-SSRs was largely due to the wild-type species, while little diversity was observed among the adapted cultivars. Genetic similarity coefficients were calculated based on the 965 polymorphic AFLP and EST-SSR alleles, and a phenetic tree was constructed. The dendrogram contained 2 major clusters. Cluster I included all adapted watermelon cultivars, and the similarity among these cultigens was very high (0.94-0.98), demonstrating cross relationships and a narrow genetic background. Cluster II was composed of 4 wild-type species. The genetic distance between the nodes that comprise these 2 clusters was approximately 0.63, indicating a high level of genetic dissimilarity between the adapted watermelon species and the other related species. The low level of marker polymorphism among the adapted cultivars implies that a severe bottleneck in genetic diversity existed in watermelon during the initial breeding practices.

Oceanic islands are not sinks of biodiversity in spore-producing plants.

Islands have traditionally been considered as migratory and evolutionary dead ends for two main reasons: island colonizers are typically assumed to lose their dispersal power, and continental back colonization has been regarded as unlikely because of niche preemption. The hypothesis that islands might actually represent dynamic refugia and migratory stepping stones for species that are effective dispersers, and in particular, for spore-producing plants, is formally tested here, using the archipelagos of the Azores, Canary Islands, and Madeira, as a model. Population genetic analyses based on nuclear microsatellite variation indicate that dispersal ability of the moss Platyhypnidium riparioides does not decrease in the island setting. The analyses further show that, unlike island populations, mainland (southwestern Europe and North Africa) populations underwent a severe bottleneck during the last glacial maximum (LGM). Our results thus refute the traditional view of islands as the end of the colonization road and point to a different perception of North Atlantic archipelagos as major sources of biodiversity for the postglacial recolonization of Europe by spore-producing plants.

Climate‐induced changes to the ancestral population size of two Patagonian galaxiids: the influence of glacial cycling

Patagonia is one of the few areas in the Southern Hemisphere to have been directly influenced by Quaternary glaciers. In this study, we evaluate the influence that Quaternary glacial ice had on the genetic diversity of two congeneric fish species, the diadromous Galaxias maculatus and the nondiadromous Galaxias platei, using multilocus estimates of effective population size through time. Mid-Quaternary glaciations had far-reaching consequences for both species. Galaxias maculatus and G. platei each experienced severe genetic bottlenecks during the period when Patagonia ice sheet advance reached its maximum positions c. 1.1-0.6 Ma. Concordant drops in effective size during this time suggest that range sizes were under similar constraints. It is therefore unlikely that coastal (brackish/marine) environments served as a significant refuge for G. maculatus during glacial periods. An earlier onset of population declines for G. platei suggests that this species was vulnerable to modest glacial advances. Declines in effective sizes were continuous for both species and lasted into the late-Pleistocene. However, G. maculatus exhibited a strong population recovery during the late-Quaternary (c. 400,000 bp). Unusually long and warm interglacials associated with the late-Quaternary may have helped to facilitate a strong population rebound in this primarily coastal species.

Health care reform and the primary care workforce bottleneck.

To establish and sustain the high-performing health care system envisioned in the Affordable Care Act (ACA), current provisions in the law to strengthen the primary care workforce must be funded, implemented, and tested. However, the United States is heading towards a severe primary care workforce bottleneck due to ballooning demand and vanishing supply. Demand will be fueled by the "silver tsunami" of 80 million Americans retiring over the next 20years and the expanded insurance coverage for 32 million Americans in the ACA. The primary care workforce is declining because of decreased production and accelerated attrition. To mitigate the looming primary care bottleneck, even bolder policies will be needed to attract, train, and sustain a sufficient number of primary care professionals. General internists must continue their vital leadership in this effort.

Dates of HIV infection can be estimated for seroprevalent patients by coalescent analysis of serial next-generation sequencing data

To reconstruct dates of HIV infection by the coalescent analysis of longitudinal next-generation sequencing (NGS) data. The coalescent predicts the time that has elapsed since the most recent common ancestor (MRCA) of a population. Because HIV tends to undergo severe bottlenecks upon transmission, the MRCA may be a good predictor of the time of infection. NGS provides an efficient means for performing large-scale clonal sequencing of HIV populations within patients, and the ideal raw material for coalescent analysis. Baseline and follow-up plasma samples were obtained from 19 individuals enrolled into the Montréal Primary HIV Infection cohort. Dates of infection were initially estimated at baseline from nongenetic data (clinical and serological markers and patient questionnaires). HIV RNA was extracted and seven regions of the genome were amplified, subjected to parallel-tagged 454 pyrosequencing, and analyzed using the software package BEAST. Mean estimates of the time to the MRCA per patient were significantly correlated with nongenetic estimates (Spearman's ρ = 0.65, P = 4.4 × 10(-3)). The median absolute difference between coalescent and nongenetic date estimates was smallest (median 29.4 days) for highly variable regions of the HIV genome such as env V3, and greater (median 114.9 days) for more conserved regions such as pol. This application of NGS represents an important advancement, not only because accurate estimates of dates of infection can be derived retrospectively from archived specimens, but also because each analysis is patient-specific and, therefore, robust to variation in rates of HIV evolution.

Does isolation affect phenotypic variability and fluctuating asymmetry in the endangered Red Apollo?

Isolated populations represent one of the main focuses in conservation biology. Long-term isolation often causes losses of genetic diversity and as a consequence might reduce individual fitness. Morphometric characters can be used as suitable markers to analyse ecological stress and individual fitness of local populations. Asymmetry in bilateral symmetry is used as a measure for developmental instability of populations and is often negatively correlated with population size and low genetic diversity. As a study system, we selected the endangered butterfly Parnassius apollo, which occurs in small and isolated remnant populations in Central Europe, but also in fairly large metapopulations in the Alps. We analysed wing morphometrics (shape and size characters) of 812 individuals representing (1) already extinct, (2) highly isolated and (3) still interconnected populations. Seventeen landmarks on veins were used to analyse morphological variances in the wing shape. Our data show significant deviations between landmarks on the left and right wing side within individuals and strong morphological variance among individuals. The highest morphological variability could be found for individuals in the Alps, however, the level of asymmetry was very similar for all populations analysed. The higher morphological variability found in the Alps can be interpreted as a consequence of the higher level of the genetic diversity detectable for this region. Analysis on morphological variance of P. apollo individuals of the Mosel valley using time series ranging from 1895 until today showed no significant rise in asymmetry and no decline of morphological variability over time, although, anthropogenic habitat destruction has caused severe bottlenecks in this population.

Rescue of HIV-1 long-time archived X4 strains to escape maraviroc

Entry of Human Immunodeficiency Virus type 1 (HIV-1) into target cells is mediated by the CD4 receptor and a coreceptor, CCR5 or CXCR4. Maraviroc interferes with HIV entry by binding the CCR5 coreceptor. Virological failure to maraviroc-containing regimens can occur through the emergence of resistance, or through tropism evolution and broadened coreceptor usage. In the latter case, the physiological relevance of minority strains is a major concern.Here we report a retrospective analysis of coreceptor-usage and evolution based on 454-ultra-deep-sequencing of plasma and Peripheral Blood Mononuclear Cell (PBMC)-derived envelope V3-loops, accounting for coreceptor usage, from a patient who failed a maraviroc-containing regimen through the emergence of X4 strains. The X4 maraviroc-escape variant resulted from recombination between a long time archived proviral sequence from 2003 (5′-portion, including the V3-loop) and the dominant R5 strains circulating in plasma at the time of maraviroc-treatment initiation (3′-portion). Phylogenetic analyses and BEAST modeling highlighted that an early diverse viral quasispecies underwent a severe bottleneck following reinitiation of HAART and repeated IL-2 cycles between 1999 and 2001, leading to the transient outgrowth and archiving of one highly homogeneous X4 population from plasma, and to the expansion in plasma of one PBMC-derived R5 strain. Under maraviroc selective pressure, the early, no longer detectable X4 strains archived in PBMC were partially rescued to provide X4-determinants to the main circulating strain.

Increased genetic differentiation in house sparrows after a strong population decline: From panmixia towards structure in a common bird

A drastic decline in abundance prompts conservation measures, even though a species may still be common, partly because such a decline may be associated with loss of genetic variability. Longitudinal evidence (i.e. repeated measures across time) for loss of genetic diversity is scarce and mostly concerns organisms that have experienced a severe bottleneck. Here, we study the house sparrow in Finland, where a strong (50–86%) reduction in abundance occurred in four decades, starting earlier and resulting steeper decline in the south than in the north. Based on thirteen polymorphic microsatellites, we compared 12 Finnish populations both prior (mid-1980s) and after (2009) the major population decline. There was no evidence of bottlenecks and only little loss of genetic variation, but we found a significant threefold increase in genetic differentiation (FST) across the populations. This may reflect a non-equilibrium situation between the rates of change in the genetic diversity and differentiation and indicate future loss of genetic diversity. Our findings indicate that a strong decline in population size in a relatively common species still leaves a noticeable population-genetic imprint and warrants conservation concern.

Inferring the ancient population structure of the vulnerable albatross Phoebastria albatrus, combining ancient DNA, stable isotope, and morphometric analyses of archaeological samples

The history of population structure is a key to effective wildlife management and conservation. However, inferring the history of population structure using present genetic structures is problematic when the method is applied to species that have experienced severe population bottlenecks. Ancient DNA analysis seemed to be a promising, direct method for inferring ancient population structures. However, the usual methods for inferring modern population structure, i.e. the phylogeographic approach using mitochondrial DNA and the Bayesian approach using microsatellite DNA, are often unsuitable for ancient samples. In this study, we combined ancient DNA obtained from zooarchaeological bones with carbon/nitrogen stable isotope ratios and morphological variations to infer ancient population structure of the short-tailed albatross Phoebastria albatrus. The results showed that the bird existed in two populations, between which the genetic distance was greater than that of distinct sister albatross species, although no subspecies of P. albatrus have been proposed. Our results suggest that the birds at the present two breeding regions (Torishima in the Izu Islands and two islets of the Senkaku Islands) are descended from these two ancient populations, and that reevaluation of the status and conservation strategy for the species is required. Our results also indicate that lineage breeding on the Senkaku Islands has drastically reduced genetic diversity, while that on Torishima has not. The approach proposed in this study would be useful for inferring ancient population structure, using samples of highly mobile animals and/or samples from archaeological sites, and the reconstructed ancient population structure would be useful for conservation and management recommendations.

Deciphering the genetic basis of animal domestication

Genomic technologies for livestock and companion animal species have revolutionized the study of animal domestication, allowing an increasingly detailed description of the genetic changes accompanying domestication and breed development. This review describes important recent results derived from the application of population and quantitative genetic approaches to the study of genetic changes in the major domesticated species. These include findings of regions of the genome that show between-breed differentiation, evidence of selective sweeps within individual genomes and signatures of demographic events. Particular attention is focused on the study of the genetics of behavioural traits and the implications for domestication. Despite the operation of severe bottlenecks, high levels of inbreeding and intensive selection during the history of domestication, most domestic animal species are genetically diverse. Possible explanations for this phenomenon are discussed. The major insights from the surveyed studies are highlighted and directions for future study are suggested.

Passive Network Performance Estimation for Large-Scale, Data-Intensive Computing

Distributed computing applications are increasingly utilizing distributed data sources. However, the unpredictable cost of data access in large-scale computing infrastructures can lead to severe performance bottlenecks. Providing predictability in data access is, thus, essential to accommodate the large set of newly emerging large-scale, data-intensive computing applications. In this regard, accurate estimation of network performance is crucial to meeting the performance goals of such applications. Passive estimation based on past measurements is attractive for its relatively small overhead compared to relying on explicit probing. In this paper, we take a passive approach for network performance estimation. Our approach is different from existing passive techniques that rely either on past direct measurements of pairs of nodes or on topological similarities. Instead, we exploit secondhand measurements collected by other nodes without any topological restrictions. In this paper, we present Overlay Passive Estimation of Network performance (OPEN), a scalable framework providing end-to-end network performance estimation based on secondhand measurements, and discuss how OPEN achieves cost-effective estimation in a large-scale infrastructure. Our extensive experimental results show that OPEN estimation can be applicable for replica and resource selections commonly used in distributed computing.

Origin and taxonomic status of the Palearctic population of the stem borer Sesamia nonagrioides (Lefèbvre) (Lepidoptera: Noctuidae)

The major pest of maize in Mediterranean Europe, the stem borer Sesamia nonagrioides (Lefèbvre) (Lepidoptera: Noctuidae), has a fragmented distribution, north and south of the Sahara. The present study aimed: (1) to clarify the uncertain taxonomic status of the Palearctic and sub-Saharan populations which were first considered as different species and later on as subspecies (Sesamia nonagrioides nonagrioides and Sesamia nonagrioides botanephaga) and (2) to investigate the origin of the Palearctic population which extends from Spain to Iran, outside what is considered typical for this mainly tropical genus. We reconstructed the evolutionary history of both populations using one nuclear and two mitochondrial genes. The sub-Saharan taxon was fragmented in two isolated populations (West and East) whose mitochondrial genes were distant by 2.3%. The Palearctic population was included in the East African clade and its genes were close or identical to those of a population from Central Ethiopia, where the species was discovered for the first time. Similarly, in Africa, the alleles of the nuclear gene were distributed mainly in two West and East clades, whereas some Palearctic alleles belonged to the West clade. The Palearctic population originated therefore from East and West Africa and is the progeny of the cross between these two African populations. The main species concepts were in agreement, leading to the conclusion that the three populations are still conspecific. In the surveyed regions, the species therefore does not include two subspecies but three isolated populations. The Palearctic population suffered from severe bottlenecks that resulted in the fixation of one East African mitochondrial genome and the large reduction in its genetic diversity compared to the African populations. The data suggest that natural colonization of the Palearctic region was more plausible than human introduction. The allelic distribution of the Palearctic population was similar to that of species that survived the last glaciation. It is concluded that the African populations expanded during the last interglacial, crossed the Sahara and mixed in North Africa where fixation of the East mitochondrial genome occurred. The species then colonized Europe westward through only one eastern entrance. The coalescent-based estimate of the time to the ancestor of the Palearctic population was 108 000 years, which is consistent with this scenario.

ChemInform Abstract: Development of Practical Synthetic Method Toward Mechanistic Elucidation of Biologically Active Natural Products

AbstractReview: ca. 50 refs.

Inference of human population history from individual whole-genome sequences.

The history of human population size is important to understanding human evolution. Various studies1-5 have found evidence for a founder event (bottleneck) in East Asian and European populations associated with the human dispersal out-of-Africa event around 60 thousand years ago (kya) before present. However, these studies have to assume simplified demographic models with few parameters and do not precisely date the start and stop times of the bottleneck. Here, with fewer assumptions on population size changes, we present a more detailed history of human population sizes between approximately ten thousand to a million years ago, using the pairwise sequentially Markovian coalescent (PSMC) model applied to the complete diploid genome sequences of a Chinese male (YH)6, a Korean male (SJK)7, three European individuals (Venter8, NA12891 and NA128789) and two Yoruba males (NA1850710 and NA19239). We infer that European and Chinese populations had very similar population size histories before 10–20kya. Both populations experienced a severe bottleneck between 10–60kya while African populations experienced a milder bottleneck from which they recovered earlier. All three populations have an elevated effective population size between 60–250kya, possibly due to a population structure11. We also infer that the differentiation of genetically modern humans may have started as early as 100–120kya12, but considerable genetic exchanges may still have occurred until 20–40kya.

Genetic analysis of farmed and wild stocks of large yellow croaker Larimichthys crocea by using microsatellite markers

locus ranged from 5.57 to 7.93, with an average of 6.75; the observed and expected heterozygosity ranged from 0.572 to 0.665 and from 0.649 to 0.751, with an average of 0.621 and 0.694, respectively; the Shannon’s diversity index ranged from 1.34 to 1.64, with an average of 1.48. The selectively bred strain had the lowest genetic diversity; all farmed stocks showed a slight reduction of genetic variability contrasted with wild stock. All stocks suffered severe bottleneck. The pair-wise FST , the phylogenetic tree, the factor correspondence analysis and the model based clustering analysis revealed that, the Ningbo stock, which was from Zhejiang province, was different from the remaining stocks from Fujian province. This study suggested that (1) the farmed stocks were at relatively low level of genetic diversity compared with the wild stock; (2) samples from Ningbo investigated in this study have a distinct divergence with those from Fujian province; (3) there had emerged significant differentiation among farmed stocks.