Severe Bottleneck Effects Research Articles

MtDNA <italic>COⅠ</italic> sequence diversity of <italic>Gerres limbatus</italic> in coastal waters of China

In order to contribute information on genetic background of <italic>Gerres limbatus</italic> in coastal waters of China, 652 bp mtDNA <italic>COⅠ</italic> sequences of 140 individuals from 9 geographic populations were analyzed. 14 mutation sites were found and 13 haplotypes were identified, of which 9 were unique haplotypes and 4 were shared haplotypes. The overall haplotype and nucleotide diversity were low ( <italic>H</italic>_d=0.276±0.050, π =0.000 5±0.000 1 ), of which genetic diversity of populations from the east part of the Qiongzhou Strait ( <italic>H</italic>_d = 0.338-0.456, π = 0.000 6-0.001 1 ) was higher than those in the western Beibu Gulf ( <italic>H</italic>_d =0-0.295, π =0-0.000 5 ). Haplotype network diagrams did not show obvious genealogical and geographic structure. Genetic differentiation coefficicent(<italic>F</italic>_st) showed that there was indistinctively low-middle genetic differentiation between Naozhou population and other populations ( <italic>F</italic>_st= 0.0773-0.1696). No obvious differentiation was found among other populations ( <italic>F</italic>_st=-0.041 5-0.061 2). AMOVA analysis also showed that 95% population variation originated from within the group. The negative overall value of the neutrality test (Tajima’s <italic>D</italic>=-2.254 9; Fu’s <italic>F</italic>_s=-16.472 5 ) and a significant single peak in the nucleotide mismatch distribution were consistent with demographic expansion in the past, and deduced expansion time ranged from about 0.130 4 to 0.043 5 million years ago. Since the overall genetic diversity of the population was less than 0.5 and nucleotide diversity was less than 0.005, it was speculated that <italic>Gerres limbatus</italic> population in coastal waters of China had recently encountered a severe bottleneck effect. The nucleotide diversity of the Ningde and Naozhou populations was relatively high and had a conservation priority. As genetic diversity of populations in the Beibu Gulf was extremely low, measures should be taken to avoid further decline in genetic diversity.

Fine-scale genetic structure of the overwintering Chilo suppressalis in the typical bivoltine areas of northern China.

The rice stem borer (RSB), Chilo suppressalis (Lepidoptera: Pyralidae), is an important agricultural pest that has caused serious economic losses in the major rice-producing areas of China. To effectively control this pest, we investigated the genetic diversity, genetic differentiation and genetic structure of 16 overwintering populations in the typical bivoltine areas of northern China based on 12 nuclear microsatellite loci. Moderate levels of genetic diversity and genetic differentiation among the studied populations were detected. Neighbour-joining dendrograms, Bayesian clustering and principal coordinate analysis (PCoA) consistently divided these populations into three genetic clades: western, eastern and northern/central. Isolation by distance (IBD) and spatial autocorrelation analyses demonstrated no correlation between genetic distance and geographic distance. Bottleneck analysis illustrated that RSB populations had not undergone severe bottleneck effects in these regions. Accordingly, our results provide new insights into the genetic relationships of overwintering RSB populations and thus contribute to developing effective management strategies for this pest.

Genetic variation and phylogeographic structure of Laodelphax striatellus in China based on microsatellite markers

AbstractThe small brown planthopper (SBPH), Laodelphax striatellus (Fallén) (Hemiptera: Delphacidae), is an important agricultural pest that has caused serious economic losses in the major rice‐producing areas of China. To effectively manage this insect pest, we analysed its genetic variation, genetic structure and population demographic history. We used nine nuclear microsatellite loci to investigate the genetic diversity and population genetic structure of SBPH at 43 sampling sites in China. High levels of genetic diversity and genetic differentiation among most populations were detected. Overall, neighbour‐joining dendrograms, STRUCTURE and principal coordinate analysis (PCoA) revealed no genetically distinct groups and exhibited an admixed phylogeographic structure in China. Isolation by distance (IBD) and spatial autocorrelation analyses demonstrated no correlation between genetic distance and geographic distance. On the other hand, bottleneck analysis indicated that SBPH populations had not undergone severe bottleneck effects in these regions. This study provides useful data for resolving the genetic relationships and migration patterns of SBPH and thus contributes to developing effective management strategies for this pest.

CD8+ T cells specific to a single Yersinia pseudotuberculosis epitope restrict bacterial replication in the liver but fail to provide sterilizing immunity

CD8+ T cells use contact-dependent cytolysis of target cells to protect the host against intracellular pathogens. We have previously shown that CD8+ T cells and perforin are required to protect against the extracellular pathogen Yersinia pseudotuberculosis. Here we establish an experimental system where CD8+ T cells specific to a single model antigen are the only memory response present at time of challenge. Using mice immunized with a vaccine strain of Listeria monocytogenes that expresses secreted ovalbumin (Lm-OVA), we show that OVA-specific CD8+ T cells are generated and provide limited protection against challenge with virulent OVA+Y. pseudotuberculosis. Perforin expression by OVA-specific CD8+ T cells was required, as Lm-OVA-immunized perforin-deficient mice showed higher bacterial burden as compared to Lm-OVA-immunized perforin-sufficient mice. Surprisingly, antigen-specific T cell protection waned over time, as Lm-OVA-immune mice eventually succumbed to Yersinia infection. Kinetic analysis of infection in mice with and without OVA-specific CD8+ T cells revealed that bacterial numbers increased sharply in OVA-naïve mice until death, while OVA-immune mice held bacterial burden to a lower level throughout the duration of illness until death. Clonal analysis of bacterial populations in OVA-naïve and OVA-immune mice at distinct time points revealed equivalent and severe bottle-neck effects for bacteria in both sets of mice immediately after intravenous challenge, demonstrating a dominant role for other aspects of the immune system regardless of CD8+ T cell status. These studies indicate that CD8+ T cells against a single antigen can restrict Y. pseudotuberculosis colonization in a perforin-dependent manner, but ultimately are insufficient in their ability to provide sterilizing immunity and protect against death.

On the Mass-Transfer Properties of Partially-Saturated Carbon-Paper Gas Diffusion Layers: Global Vs. Local Effective Diffusivity

Understanding the impact of liquid water on reactant transport in Gas Diffusion Layers (GDLs) is of paramount importance to achieving an increased performance in Proton Exchange Membrane Fuel Cells (PEMFCs). In the present work, X-ray Computed Tomography (XCT) was combined with the Lattice Boltzmann Method (LBM) to determine the gas-phase effective diffusivity of partially-saturated carbon-fiber GDLs. Ex-situ invasion experiments were conducted on a PTFE–treated Toray® TGP-H 120 GDL (10% b.w.) at Lawrence Berkeley National Lab’s (LBNL) Advanced Light Source (ALS) synchrotron (Beamline 8.3.2). Water was injected into the sample at different applied capillary pressures varying the static head of water at the bottom face, while tomographic images were acquired at a resolution of 1.33 μm/voxel. A hydrophobic membrane located at the top of the sample prevented liquid water from leaving the system. The reconstructed image stacks were then segmented into fiber, air and liquid phases, and used as computational meshes for the LB simulations. A single relaxation time D3Q7 model was implemented in the open-source LB code Palabos, using the supercomputers Gullimin and Colosse, managed by Calcul Québec and Compute Canada, to run the calculations. The diffusivities in both the in- and through-plane directions were examined due to the anisotropic nature of carbon-paper materials (see Figure 1). It was found that the effective diffusivity in thin GDLs is strongly dependent upon the actual saturation distribution across the material. Unlike the notable number of connected pathways existing in the in-plane direction, the influence of water configuration was higher on through-plane diffusion. A severe bottleneck effect, preventing almost any flux through the medium, was observed for the full-thickness sample due to the high-gradient saturation profiles in the invasion experiments. In contrast, a pronounced increase of the global effective diffusivity was observed in calculations performed on GDL domains progressively excluding a thicker portion of the flooded region near the inlet. The relative resistance of water in these domains was in the range of that reported in previous works [1,2], even though it didn’t stabilize at a well-defined value. The diffusion flux across the medium continuously increases as the saturation profile in the examined portion of GDL was flatter. The hypersensitivity of the effective diffusivity on the through-plane water distribution shows the impossibility to describe uniquely the transport properties in thin GDLs just considering the overall saturation level. Moreover, continuum models explicitly solving transport processes inside the GDL should incorporate local constitutive relations obtained under conditions of no saturation gradient. It is contradictory to use global correlations extracted from an inhomogeneous porous medium to characterize the numerical nodes composing the same medium. Local and global effective properties can only be equal if the porous medium is fully homogeneous, but this is not the case of partially-saturated finite-size GDLs. This modeling inconsistency was explored by performing a massive computational campaign including more than 2000 calculations on dry and wet subsamples with nearly flat saturation profiles. The computed average relative resistances in the in- and through-plane directions were similar to those proposed in Ref. [3]. Further, the ability of the computed correlations for the local effective diffusivity, using harmonic and arithmetic averaging techniques, to recover the results obtained on global heterogeneous domains was confirmed. A similar constitutive relationship for the local effective diffusivity was also determined by combining the aforementioned upscaling/downscaling techniques and the global pore network results by Gostick [4]. Nevertheless, a detailed comparison with the in-situ numerical results presented in [2] showed that a more restrictive dependence of the local effective diffusivity on local saturation may be expected for the region under the rib due to the more tortuous transport paths resulting from condensation of water and interface effects with the rib in addition to capillary transport.

Genetic diversity of the endangered Chinese endemic herb Dayaoshania cotinifolia (Gesneriaceae) revealed by simple sequence repeat (SSR) markers

Abstract Dayaoshania cotinifolia W.T. Wang is a critically endangered perennial herb endemic to southern China. Simple sequence repeat (SSR) markers were employed to assess genetic diversity in two populations of D. cotinifolia . Eight primer pairs generated a total of 36 alleles, with a mean of 4.5 alleles per locus. The expected heterozygosity ( H e = 0.416) and observed heterozygosity ( H o = 0.508) indicated a moderate level of genetic diversity, though the genetic differentiation between the populations was low ( F st = 0.014), a result that was supported by a higher gene flow ( N m = 18.000). No severe bottleneck effect was detected in the two populations. Thus, the endangered status of this species is most likely due to anthropologic effects rather than a lack of genetic diversity. In situ conservation strategies should be promoted, and the sizes of the populations should be increased through artificial breeding.

Analytical framework for identifying and differentiating recent hitchhiking and severe bottleneck effects from multi-locus DNA sequence data.

Hitchhiking and severe bottleneck effects have impact on the dynamics of genetic diversity of a population by inducing homogenization at a single locus and at the genome-wide scale, respectively. As a result, identification and differentiation of the signatures of such events from DNA sequence data at a single locus is challenging. This paper develops an analytical framework for identifying and differentiating recent homogenization events at multiple neutral loci in low recombination regions. The dynamics of genetic diversity at a locus after a recent homogenization event is modeled according to the infinite-sites mutation model and the Wright-Fisher model of reproduction with constant population size. In this setting, I derive analytical expressions for the distribution, mean, and variance of the number of polymorphic sites in a random sample of DNA sequences from a locus affected by a recent homogenization event. Based on this framework, three likelihood-ratio based tests are presented for identifying and differentiating recent homogenization events at multiple loci. Lastly, I apply the framework to two data sets. First, I consider human DNA sequences from four non-coding loci on different chromosomes for inferring evolutionary history of modern human populations. The results suggest, in particular, that recent homogenization events at the loci are identifiable when the effective human population size is 50000 or greater in contrast to 10000, and the estimates of the recent homogenization events are agree with the “Out of Africa” hypothesis. Second, I use HIV DNA sequences from HIV-1-infected patients to infer the times of HIV seroconversions. The estimates are contrasted with other estimates derived as the mid-time point between the last HIV-negative and first HIV-positive screening tests. The results show that significant discrepancies can exist between the estimates.

Phylogeography of Cycas revoluta Thunb. (Cycadaceae) on the Ryukyu Islands: very low genetic diversity and geographical structure

Variations in the chloroplast and mitochondrial DNA of Cycas revoluta Thunb. (Cycadaceae) were examined in 22 populations distributed across the Ryukyu Islands and southern Kyushu. Among the 14,130 bp of sequence examined, only one site mutation and one indel were polymorphic. The identified polymorphisms were located in the spacers between trnS (UGA) and trnfM (CAU) of the chloroplast DNA and between nad1 exon B and exon C of the mitochondrial DNA, respectively. Three haplotypes were identified from the Ryukyu Islands and southern Kyushu. The areas of distribution of the three haplotypes were highly geographically structured. The boundaries of two of the three haplotypes were demarcated by Okinoerabujima Island in the middle Ryukyus. The northern type and southern types lay north and south of the island, respectively. The third haplotype was almost sympatrically distributed with the southern type. The genetic variation within C. revoluta was estimated to be very low (h = 0.641, π = 0.00071) in comparison to its relative in Taiwan, C. taitungensis, which possesses 97 cpDNA haplotypes and 55 mtDNA haplotypes from two relic populations. A reasonable explanation for the low genetic diversity of the cycad on the Ryukyu Islands could be severe bottleneck effects, resulting from the submersion of low islands and the diminished landmass of islands in the interglacial age in the Quaternary period. The geographically restricted nature of the haplotypes could be attributed to vicariance resulting from the land configuration of the Ryukyu Islands, including changes in geography during the interglacial age in the Quaternary.

Characterization of Coffea chloroplast microsatellites and evidence for the recent divergence of C. arabica and C. eugenioides chloroplast genomes

Comparative sequencing of >7 kb of highly variable chloroplast genome regions (atpB-rbcL, trnS-trnG, rpl22-rps19, and rps19-rpl2 spacers; introns in atpF, trnG, trnK, and rpl16) with microsatellites known from other angiosperms was carried out in Coffea. Samples comprised 8 diploid species of Coffea, 5 individuals of tetraploid C. arabica representing geographically distant wild populations from Ethiopia, 2 commercial cultivars of C. arabica, and Psilanthus leroyi and Ixora coccinea as outgroups. Phylogeny reconstruction using maximum parsimony and Bayesian inference resulted in congruent topologies with high support for C. arabica and C. eugenioides being sisters. Partitioned analyses showed that all regions except the atpB-rbcL spacer resolved this sister-group, although this was often unsupported. The large sequence data set further shows that chloroplast genomes of C. arabica and C. eugenioides each possess apomorphies, indicating that not C. eugenioides but an ancestor or close relative of C. eugenioides is the maternal parent of C. arabica. Seven variable chloroplast microsatellites were characterized in Coffea. Most microsatellites are poly(A/T) stretches, whereas one in the trnS-trnG spacer has an (AT)n motif. Most strikingly, all individuals of C. arabica possess identical sequences, suggesting a single chloroplast haplotype. This can be explained by a recent origin of C. arabica in a unique allopolyploidization event, or by severe bottleneck effects in the evolutionary history of the species. Reconstruction of the evolution of microstructural mutations shows much higher levels of homoplasy in microsatellite loci than in other parts of spacers and introns. Microsatellites are inferred to evolve by insertion and deletion of 1 to 3 motif copies in one step.

Origin of Gymnocypris przewalskii and phylogenetic history of Gymnocypris eckloni (Teleostei: Cyprinidae)

The origins and phylogenetic patterns were assessed for G. przewalskii and G. eckloni by analyzing the complete mtDNA cytochrome b gene sequence (1140bp). Phylogenetic analyses further supported that there were three mtDNA lineages (A-C) identified in G. przewalskii and G. eckloni, demonstrating that outer rakers of the first gill have little significance in the phylogeny of the Gymnocypris fishes. The network established showed that G. eckloni of the Yellow River specific haplotype A1 was a founder and it radiated all haplotypes of G. przewalskii which suggested G. przewalskii might only originate from one of two maternals of G. eckloni from the Yellow River. Fs test and mismatch analysis showed at least two expansion events in the population of G. przewalskii about 0.2734 Ma and 0.0658 Ma, while G. eckloni from Qaidam Basin could have experienced severe bottleneck effect about 0.0693 Ma. The population expansion was detected in subclades A1 and A21 with the most recent common ancestor (TMRCA) about 0.2308 +/- 0.01 Ma and 0.1319 +/- 0.015 Ma, respectively, which were within the geological age range of Gonghe Movement event that caused the separation of Lake Qinghai from the upper Yellow River. These results suggested the effect of the fish diversification by rapid uplift of the Qinghai-Tibetan Plateau in the Late Pleistocene.

Efficient repeated low-dose intravaginal infection with X4 and R5 SHIVs in rhesus macaque: Implications for HIV-1 transmission in humans

We examined the effect of inoculum dose on SHIV transmission and infection. We found that repeated low-dose intravaginal exposure with either R5-SHIV SF162P3 or X4-SHIV SF33A results in infections that are blunted and rapidly controlled. Interestingly, although the transmission rate after all repeated exposures is comparable for the two viruses, the probability of low-dose vaginal transmission is greater for the X4 than R5 virus. Furthermore, X4-SHIV SF33A replication predominates in low-dose dually-exposed macaques, suggesting that it is better at establishing a systemic infection following transmission. However, X4-SHIV SF33A advantage in transmission and infection is not observed in macaques inoculated intravenously with low-dose mixed inoculum. The finding that although matched in tissue culture infectious dose, the X4 inoculum is more complex leads us to hypothesize that the greater genetic heterogeneity of the X4 virus population may have rendered it less susceptible to the severe bottleneck effects imposed by IVAG inoculation with small doses, allowing for greater probability of transmission and establishment of a generalized infection. These data have implications for HIV-1 transmission and infection in humans.

Genetic diversity and geographic pattern of wild lotus (Nelumbo nucifera) in Heilongjiang Province

Based on 47 accessions from Ussuri River Valley, Songhua River Valley and Heilong River Valley together with 2 accessions from Russia and 27 accessions of cultivated lotus from other provinces in China, genetic diversity of wild lotus (Nelumbo nucifera) were revealed using RAPD and ISSR markers. Twenty RAPD primers generated 113 loci, of which 71.68% were polymorphic across all samples. The expected heterozygosity was 0.1583. The percentage of polymorphic loci and expected heterozygosity in the wild lotus were 50.44% and 0.1241, respectively. The parameters of the cultivated lotus were slightly higher, 53.98% and 0.1651 correspondingly. Sixteen ISSR primers produced 90 loci. The percentages of polymorphic loci and expected heterozygosity were 41.11% and 0.0851 at species level, 28.89% and 0.0661 for the wild lotus, and 32.22% and 0.0963 for the cultivated lotus. AMOVA analysis of the wild lotus showed that a small number of variances exist among the 3 river valleys (21.68% for RAPD with Gst=0.1312 and 15.11% for ISSR with Gst=0.1352). The molecular variances of both the wild and the cultivated lotuses came predominantly from within the 3 river valleys and the cultivated samples (73.25% for RAPD and 81.11% for ISSR). Variance components from the wild and the cultivated lotus accounted for 19.17% for RAPD and 13.17% for ISSR, and variations among the valleys and the culta seemed the least important (7.585 for RAPD and 5.725 for ISSR). Neighbor-joining analysis demonstrated that considerable differentiation happened between the wild and the cultivated lotus. The wild lotus at middle reaches of the Songhua River Valley seemed to be the centre of remnants, from which it spread to the Ussuri River Valley and the Heilong River Valley. The very limited genetic diversity suggests that the wild lotus has experienced severe bottleneck effect, founder effect and rebirth effect. Considering its long evolutionary history, scarcity of genetic variations and importance in wetland ecosystems, we appeal to take lawful measures to protect the wild lotus. For conservation purpose, special attention should be paid to the lotus at the middle reaches of the Songhua River Valley.

Molecular phylogenetics of Gymnocypris (Teleostei: Cy-prinidae) in Lake Qinghai and adjacent drainages

149 complete mitochondrial DNA (mtDNA) cytochrome b (Cyt b) genes (1140 bp) of Gymnocypris przewalskii, Gymnocypris eckloni and Gymnocyptis scolistomus from the Lake Qinghai, Yellow River and Qaidam Basin were sequenced and analyzed. Consistent dendrogram indicated that the samples collected from the same species do not constitute a separate monophyletic group and all the samples were grouped into three highly divergent lineages (A, B and C). Among them, Lineage A contained all samples of G. przewalskii from the Lake Qinghai and partial samples of the G. eckloni from the Yellow River. Lineage B contained the remaining samples of G. eckloni from the Yellow River. Lineage C was composed of a monophyletic group by G. eckloni from the Qaidam Basin. Analysis of molecular variance (AMOVA) indicated that most of genetic variations were detected within these three mtDNA lineages (93.12%), suggesting that there are three different lineages of Gymnocypris in this region. Our Cyt b sequence data showed that G. przewalskii was not a polytypic species, and G. scolistomus was neither an independent species nor a subspecies of G. eckloni. The divergent mtDNA lineages of G. eckloni from the Yellow River suggested that gene flow between the different populations was restricted to a certain extent by several gorges on the upper reach of the Yellow River. Lineage B of G. eckloni might be the genetic effect from the ancestor which was incorporated with the endemic schizothoracine fishes when the headward erosion of the Yellow River reached to its current headwaters of late. The G. eckloni from Basin Qaidam was a monophyletic group (lineage C) and F-st values within G. eckloni from the Yellow River were higher than 0.98, suggesting that the gene flow has been interrupted for a long time and the G. eckloni from Basin Qaidam might have been evolved into different species by ecology segregation. The correlation between the rakers number of Gymnocypris and population genetic variation was not significant. All Gymnocypris populations exhibited a low nucleotide diversity (pi = 0.00096-0.00485). Therefore the Gymnocyptis populations from Basin Qaidam could have experienced severe bottleneck effect in history. Our result suggested Gym-nocypris populations of Basin Qaidam should give a high priority in conservation programs.

Fixation of translocation 2A·4B infers the monophyletic origin of Ethiopian tetraploid wheat

Analysis of structural chromosomal polymorphism revealed the presence of a previously reported 2A·4B translocation common to all 15 strains of Ethiopian tetraploid wheat examined. Using the C-banding technique, we found two new translocations,T1B·6B and T5B·6B, and a pericentric inversion of chromosome 5A. The C-banding pattern indicated that in all three translocations the breakpoint was located in the centromeric region. Sequential N-banding and genomic in situ hybridization (GISH) confirmed the location of the breakpoint of translocation 2A·4B, and revealed that the breakpoint of another known translocation, 2A-2B, was in the proximal region of 2BL. The fixation of the 2A·4B translocation indicates the monophyletic origin of Ethiopian tetraploid wheat and the presence of a very severe bottleneck effect during its dispersal.

Allozyme Variation in a Natural Population of the Nile Crocodile

Synopsis. Blood samples were collected for allozyme studies from 92 Crocodylus niloticus from the Runde River in Gonarezhou National Park, southern Zimbabwe. Two (glucose phosphate isomerase and erythrocyte acid phosphatase) of 27 protein coding loci were polymorphic when examined by starch-gel electrophoresis. This amount of variability is similar to that found in another crocodilian, Alligator mississippiensis and is not unusually low as has been found in a number of large vertebrates. In a single semi-isolated population, allele frequencies at both polymorphic loci were in Hardy-Weinberg equilibrium suggesting a random mating pattern with no severe bottleneck effect in the founding of this population. Population F-statistics suggest that panmixia exists within and among the three main breeding sites studied.