Severe Bottleneck Research Articles

生物活性天然有機化合物の機能解明を指向した実践的合成手法の開発

The limited supplies of biologically active natural products from natural source have been a severe bottleneck for their application to medical care or mechanistic study of their functions. Synthetic organic chemistry may become a best possible solution of this supply problem by the development of practical synthetic methods suited to the intended molecules. For right-half of halichondrin B, we established a new catalytic cycle of Cr-mediated coupling reaction, new asymmetric Ni/Cr-mediated coupling reaction, surprisingly efficient catalytic Cr-mediated coupling reaction, catalytic Ni/Cr-mediated macrocyclization without use of high-dilution techniques, and effective device for forming polycyclic ring system of halichondrin B. For mugineic acid, we established the practical synthesis of 2'-deoxy mugineic acid with minimal requirements for workup and purification procedure, efficient synthesis of mugineic acid, and synthesis of mugineic acid derivatives as molecular probes. For E-ring of palau'amine, we established Hg(OTf)2-catalyzed olefin cyclization reactions, and its application to the construction of tetra-substituted carbon center possessing nitrogen that corresponds to C16 position of palau'amine.

Population genetics ofMioscirtus wagneri, a grasshopper showing a highly fragmented distribution

The genetic consequences of population fragmentation and isolation are major issues in conservation biology. In this study we analyse the genetic variability and structure of the Iberian populations of Mioscirtus wagneri, a specialized grasshopper exclusively inhabiting highly fragmented hypersaline low grounds. For this purpose we have used seven species-specific microsatellite markers to type 478 individuals from 24 localities and obtain accurate estimates of their genetic variability. Genetic diversity was relatively low and we detected genetic signatures suggesting that certain populations of M. wagneri have probably passed through severe demographic bottlenecks. We have found that the populations of this grasshopper show a strong genetic structure even at small geographical scales, indicating that they mostly behave as isolated populations with low levels of gene flow among them. Thus, several populations can be regarded as independent and genetically differentiated units which require adequate conservation strategies to avoid eventual extinctions that in highly isolated localities are not likely to be compensated for with the arrival of immigrants from neighbouring populations. Overall, our results show that these populations probably represent the 'fragments' of a formerly more widespread population and highlight the importance of protecting Iberian hypersaline environments due to the high number of rare and endangered species they sustain.

Demographic histories of four spruce (Picea) species of the Qinghai-Tibetan Plateau and neighboring areas inferred from multiple nuclear loci

Nucleotide variation at 12-16 nuclear loci was studied in three spruce species from the Qinghai-Tibetan Plateau (QTP), Picea likiangensis, P. wilsonii, and P. purpurea, and one species from the Tian Shan mountain range, P. schrenkiana. Silent nucleotide diversity was limited in P. schrenkiana and high in the three species from the QTP, with values higher than in boreal spruce species, despite their much more restricted distributions compared with that of the boreal species. In contrast to European boreal species that have experienced severe bottlenecks in the past, coalescent-based analysis suggests that DNA polymorphism in the species from the QTP and adjacent areas is compatible with the standard neutral model (P. likiangensis, P. wilsonii, and P. schrenkiana) or with population growth (P. purpurea). In order to test if P. purpurea is a diploid hybrid of P. likiangensis and P. wilsonii, we used a combination of approaches, including model-based inference of population structure, isolation-with-migration models, and recent theoretical results on the effect of introgression on the geographic distribution of diversity. In contrast to the three other species, each of which was predominantly assigned to a single cluster in the Structure analysis, P. purpurea individuals were scattered over the three main clusters and not, as we had expected, confined to the P. likiangensis and P. wilsonii clusters. Furthermore, the contribution of P. schrenkiana was by far the largest one. In agreement with this, the divergence between P. purpurea and P. schrenkiana was lower than the divergence of either P. likiangensis or P. wilsonii from P. schrenkiana. These results, together with previous ones showing that P. purpurea and P. wilsonii share the same haplotypes at both chloroplast and mitochondrial markers, suggest that P. purpurea has a complex origin, possibly involving additional species.

Effect of population bottlenecks on the egg morphology of introduced birds in New Zealand

Hatching failure is inversely correlated with population bottleneck size among exotic birds introduced to New Zealand, but the mechanism for this is unclear. We assess whether the bottlenecks these species experienced during their introduction have affected hatching failure through deleterious changes in egg morphology. We measured egg size and shape of 13 species that passed through bottlenecks of 11–800 individuals during their establishment in the 19th century. Eggs were also measured in the source populations (‘pre‐bottleneck’) of each species to compare pre‐ and post‐bottleneck egg morphology directly. Significant changes in egg volume were found in six of 13 species, with most laying smaller eggs in New Zealand. Egg shape changed in four of 13 species but there was no directional bias; two species developed more elongated eggs and two species broader eggs. There was no relationship between bottleneck size and change in egg volume, but species passing through severe bottlenecks had greater variability in egg volume and were more likely to have eggs that deviated in shape from their source populations. There was no relationship between changes in either egg volume or shape and rates of hatching failure. Further work is needed to assess whether changes in egg morphology have negative consequences on offspring fitness and whether the observed changes are the result of differing environmental conditions in the introduced range.

Unexpectedly high genetic diversity of mtDNA control region through severe bottleneck in vulnerable albatross Phoebastria albatrus

In the late part of the nineteenth century and the early part of the last century, the short-tailed albatross Phoebastria albatrus was in danger of extinction owing to feather hunting. In the middle of the last century, the total number of this species was inferred to be approximately 50-60 with breeding occurring only on Torishima Island of the Izu Islands. Recently, the number of individuals has increased to more than 2,000 and that of their breeding islands to three, namely, Torishima Island, and Minami- and Kita-kojima Islands of the Senkaku Islands. Here, we show that the 44 short-tailed albatrosses we examined represent 29 haplotypes in the control region of mitochondrial DNA, and have a considerably higher genetic diversity than most avian species, but not very high in albatross species; the h and π were 0.96 and 0.013, respectively. However, the parsimony network clearly showed that many intermediate haplotypes were lost. It was concluded that the majority of the haplotypes in the founder population have been maintained. Judging from these findings and the exponential increase in the number of individuals, the present population of the short-tailed albatross seems not to be affected by inbreeding depression through a severe bottleneck. The conservation and expansion of their breeding grounds, and effective protection from bycatch mortality in foraging areas are important for the future survival of this species.

Contrasting genetic structures of two parasitic nematodes, determined on the basis of neutral microsatellite markers and selected anthelmintic resistance markers

For the first time, the neutral genetic relatedness of natural populations of Trichostrongylid nematodes was investigated in relation to polymorphism of the beta-tubulin gene, which is selected for anthelminthic treatments. The aim of the study was to assess the contribution of several evolutionary processes: migration and genetic drift by neutral genetic markers and selection by anthelminthic treatments on the presence of resistance alleles at beta-tubulin. We studied two nematode species (Teladorsagia circumcincta and Haemonchus contortus) common in temperate climatic zones; these species are characterized by contrasting life history traits. We studied 10 isolated populations of goat nematode parasites: no infected adult goat had been exchanged after the herds were established. Beta-tubulin polymorphism was similar in these two species. One and two beta-tubulin alleles from T. circumcincta and H. contortus respectively were shared by several populations. Most of the beta-tubulin alleles were 'private' alleles. No recombination between alleles was detected in BZ-resistant alleles from T. circumcincta and H. contortus. The T. circumcincta populations have not diverged much since their isolation (F(ST) <0.08), whereas H. contortus displayed marked local genetic differentiation (F(ST) ranging from 0.08 to 0.18). These findings suggest that there are severe bottlenecks in the H. contortus populations, possibly because of their reduced abundance during unfavourable periods and their high reproductive rate, which allows the species to persist even after severe population reduction. Overall, the data reported contradict the hypothesis of the origin of beta-tubulin resistance alleles in these populations from a single mutational event, but two other hypotheses (recurrent mutation generating new alleles in isolated populations and the introduction of existing alleles) emerge as equally likely.

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.

Uncertainty and Operational Considerations in Mass Prophylaxis Workforce Planning

The public health response to an influenza pandemic or other large-scale health emergency may include mass prophylaxis using multiple points of dispensing (PODs) to deliver countermeasures rapidly to affected populations. Computer models created to date to determine "optimal" staffing levels at PODs typically assume stable patient demand for service. The authors investigated POD function under dynamic and uncertain operational environments. The authors constructed a Monte Carlo simulation model of mass prophylaxis (the Dynamic POD Simulator, or D-PODS) to assess the consequences of nonstationary patient arrival patterns on POD function under a variety of POD layouts and staffing plans. Compared are the performance of a standard POD layout under steady-state and variable patient arrival rates that may mimic real-life variation in patient demand. To achieve similar performance, PODs functioning under nonstationary patient arrival rates require higher staffing levels than would be predicted using the assumption of stationary arrival rates. Furthermore, PODs may develop severe bottlenecks unless staffing levels vary over time to meet changing patient arrival patterns. Efficient POD networks therefore require command and control systems capable of dynamically adjusting intra- and inter-POD staff levels to meet demand. In addition, under real-world operating conditions of heightened uncertainty, fewer large PODs will require a smaller total staff than many small PODs to achieve comparable performance. Modeling environments that capture the effects of fundamental uncertainties in public health disasters are essential for the realistic evaluation of response mechanisms and policies. D-PODS quantifies POD operational efficiency under more realistic conditions than have been modeled previously. The authors' experiments demonstrate that effective POD staffing plans must be responsive to variation and uncertainty in POD arrival patterns. These experiments highlight the need for command and control systems to be created to manage emergency response successfully.

Quantitative Genetic Effects of Bottlenecks: Experimental Evidence from a Wild Plant Species, Nigella degenii

Understanding the genetic consequences of changes in population size is fundamental in a variety of contexts, such as adaptation and conservation biology. In the study presented here, we have performed a replicated experiment with the plant Nigella degenii to explore the quantitative genetic effects of a single-founder bottleneck. In agreement with additive theory, the bottleneck reduced the mean (co)variance within lines and caused stochastic, line-specific changes in the genetic (co)variance structure. However, a significant portion of the (co)variance structure was conserved, and 2 characters-leaf and flower (sepal) size-turned out to be positively correlated in all data sets, indicating a potential for correlated evolution in these characters, even after a severe bottleneck. The hierarchical partitioning of genetic variance for flower size was in good agreement with predictions from additive theory, whereas the remaining characters showed an excess of within-line variance and a deficiency of among-line variance. The latter discrepancies were most likely a result of selection, given the small proportion of lines (23%) that remained viable until the end of the experiment. Our results suggest that bottlenecked populations of N. degenii generally have a lower adaptive potential than the ancestral population but also highlight the idiosyncratic nature of bottleneck effects.

Founder effect and bottleneck signatures in an introduced, insular population of elk

The population of elk (Cervus elaphus roosevelti) inhabiting Afognak Island, Alaska, USA arose from an introduction of 8 individuals from an established population in Washington, USA in 1929, and recently peaked at approximately 1,400 individuals. We examined indices of diversity for 15 microsatellite loci in the Afognak population and compared them to levels in the parent population to determine effects of translocation and demography on genetic variation. The Afognak population differed significantly (P < 0.0001) from the source population in both allele and genotype frequencies. Allelic richness, number of private alleles and multilocus heterozygosity, but not percent loci polymorphic, were significantly lower in Afognak elk. Mean inbreeding coefficients within Afognak (f = 0.019) and source (f = −0.006) populations did not differ significantly from zero. Despite the demographic bottleneck, no evidence of a genetic bottleneck in the Afognak population was detected using a test for heterozygosity excess or mode shift of allele frequencies. Simulations indicated that rapid population growth after the translocation resulted in heterozygosity excess for only 8 years. Conversely, a statistic testing for a bottleneck signature in the ratio of allele number to allele size range (M-ratio) was significant for both the Afognak and source populations, suggesting that the Afognak population had effectively undergone serial bottlenecks. Nonetheless, Afognak failed to show a smaller M-ratio than the parent population, suggesting a failure of that statistic to detect the bottleneck associated with introduction. We show that a severe bottleneck followed by rapid population growth may be undetectable using available tests.

Pseudo-cryptic species Arenicola defodiens and Arenicola marina (Polychaeta: Arenicolidae) in Wadden Sea, North Sea and Skagerrak: Morphological and molecular variation

The polychaete Arenicola defodiens, or black lug, was recently described as a morphologically highly similar species alongside the blow lug Arenicola marina. So far it was only known from the British Isles. A double spawning peak was observed earlier in lugworms of the western Wadden Sea. Here, we test the hypothesis that the two spawning peaks represent the two species in sympatry. This hypothesis is refuted on the basis of both morphological and mitochondrial DNA data; both spawning peaks are attributed to A. marina. In spite of this, we confirm, on the basis of new collections as well as re-examination of museum collections, the presence of A. defodiens in the western Wadden Sea, North Sea and also the Skagerrak; its distribution is restricted to habitats which are either submerged or have short emersion times, have relatively coarse sediments and high and stable salinities. Sympatry is common. The species differ strongly in the mitochondrial DNA fragment examined; the observed 14% uncorrected minimum difference amounts to an estimated 33–63 million years since sequence divergence. The amount of intraspecific molecular variation is larger for A. defodiens than for A. marina. This is evidence to suggest that A. marina may have undergone more recent and/or more severe population size bottlenecks.

Does reduced MHC diversity decrease viability of vertebrate populations?

Loss of genetic variation may render populations more vulnerable to pathogens due to inbreeding depression and depletion of variation in genes responsible for immunity against parasites. Here we review the evidence for the significance of variation in genes of the Major Histocompatibility Complex (MHC) for conservation efforts. MHC molecules present pathogen-derived antigens to the effector cells of the immune system and thus trigger the adaptive immune response. Some MHC genes are the most variable functional genes in the vertebrate genome. Their variation is clearly of adaptive significance and there is considerable evidence that its maintenance is mainly due to balancing selection imposed by pathogens. However, while the evidence for selection shaping MHC variation on the historical timescale is compelling, a correlation between levels of MHC variation and variation at neutral loci is often observed, indicating that on a shorter timescale drift also substantially affects MHC, leading to depletion of MHC diversity. The evidence that the loss of MHC variation negatively affects population survival is so far equivocal and difficult to separate from effects of general inbreeding. Some species with depleted MHC variation seem to be particularly susceptible to infection, but other species thrive and expand following severe bottlenecks that have drastically limited their MHC variation. However, while the latter demonstrate that MHC variation is not always critical for population survival, these species may in fact represent rare examples of survival despite of the loss of MHC variation. There is clearly a compelling need for data that would disclose the possible consequences of MHC diversity for population viability. In particular, we need more data on the impact of MHC allelic richness on the abundance of parasites or prevalence of disease in populations, while controlling for the role of general inbreeding. Before such evidence accumulates, captive breeding programs and other conservation measures aimed at inbreeding avoidance should be favoured over those protecting only MHC variation, especially since inbreeding avoidance programs would usually conserve both types of genetic diversity simultaneously.

Vulnerability to eutrophication of a semi-annual life history: A lesson learnt from an extinct eelgrass ( Zostera marina) population

A semi-annual eelgrass ( Zostera marina L.) population became extinct in 2004. It had flourished for many decades at Terschelling in the western Wadden Sea, one of the most eutrophied locations where seagrass growth has been recorded. Semi-annual populations survive the winter season by seed (annual), and by incidental plant survival (semi-annual). We compared seed bank dynamics and fate of plants between this impacted site and a reference site in the winter of 1990–1991. Seed bank density at Terschelling was extremely low (5–35 seeds m −2) in comparison to the reference site (>60 seeds m −2) and also in comparison to seed bank densities of (semi-)annual eelgrass populations in other parts of the world. Plant survival during winter was nil. Nevertheless, the population more than doubled its area in 1991, implying maximum germination and seedling survival rates. However, from 1992 onwards the decline set in and continued – while the nutrient levels decreased. To establish the cause of the low seed bank density, we conducted a transplantation experiment in 2004 to study the relationship between seed production and macro-algal cover. The transplantation experiment showed a negative relationship between the survival of seed producing shoots and suffocation by macro-algae, which is associated with light limitation and unfavourable biogeochemical conditions. The plants died before they had started to produce seeds. Thus, it is likely that macro-algal cover was responsible for the low seed bank density found in Terschelling in 1990–1991. Both the recorded low seed bank density and absence of incidental plant survival during winter were related to eutrophication. These parameters must have been a severe bottleneck in the life history of the extinct population at the impacted site, particularly as Z. marina seed banks are transient. Therefore we deduce that this population had survived at the edge of collapse, and became extinct after a small, haphazard environmental change. We argue that its resilience during these years must have been due to (i) maximum germination and seedling survival rates and (ii) spatial spreading of risks: parts of the population may have survived at locally macro-algae-free spots from where the area could be recolonised. As a consequence, the timing of the collapse was unpredictable and did not synchronise with the eutrophication process. The lesson learnt for conservation is to recognise that eutrophication may be a cause for seagrass population collapse and its eventual extinction, even years after nutrient levels stabilised, or even decreased.

Genome variability in European and American bison detected using the BovineSNP50 BeadChip

The remaining wild populations of bison have all been through severe bottlenecks. The genomic consequences of these bottlenecks present an interesting area to study. Using a very large panel of SNPs developed in Bos taurus we have carried out a genome-wide screening on the European bison (Bison bonasus; EB) and on two subspecies of American bison: the plains bison (B. bison bison; PB) and the wood bison (B. bison athabascae; WB). One hundred bison samples were genotyped for 52,978 SNPs along with seven breeds of domestic bovine Bos taurus. Only 2,209 of the SNPs were polymorphic in the bison when EB, PB and WB were pooled and only 929 SNPs were polymorphic in EB. Larger numbers of polymorphic SNPs were found in PB (1,403 SNPs) and WB (1,524 SNPs). Also the expected heterozygosity was lower in EB (HE = 0.135) than in WB (HE = 0.197) and PB (HE = 0.199). The polymorphic SNPs were not randomly distributed in the bison, but were aggregated and separated from each other by regions with low haplotype diversity (haplotype blocks). Based on our results we suggest that the utilization of genome-wide screening technologies holds large potential to radically change the breeding practices in captive or managed populations of threatened populations and advocate for developing marker assisted selected strategies in such populations.

Life cycle and population dynamics of a protective insect symbiont reveal severe bottlenecks during vertical transmission

Insects engage in mutualistic relationships with a wide variety of microorganisms that are usually transmitted vertically to the next generation. During transmission, the symbiont populations often suffer significant bottlenecks that may entail major genetic and genomic consequences. Here we investigated the life-cycle and the severity of transmission bottlenecks in a symbiotic system with an unusual way of post-hatch vertical transmission by using quantitative PCRs and morphological 3D-reconstructions. European beewolves (Philanthus triangulum, Hymenoptera: Crabronidae) harbor symbiotic bacteria (‘Candidatus Streptomyces philanthi’) in specialized antennal gland reservoirs and secrete them into their subterranean brood cells. The symbionts are later taken up by the beewolf larva and incorporated into the cocoon material to provide protection against pathogenic microorganisms. Even after months of hibernation, the symbiont population on the cocoon is estimated to encompass around 1.4 × 105 cells. However, our results indicate that only few of these bacterial cells (about 9.7 × 102) are taken up from the cocoon by the emerging female. The symbiont population subsequently undergoes logistic growth within the antennal gland reservoirs and reaches a maximum of about 1.5 × 107 cells 3–4 days after emergence. The maximum specific growth rate is estimated to be 0.084–0.105 h−1. With a total reduction in cell numbers of about 6.7 × 10−5 during vertical transmission, the symbiont population experiences one of the most severe bottlenecks known for any symbiotic system to date. This extreme bottleneck may have significantly affected the evolution of the beewolf-Streptomyces symbiosis by increased genetic drift, an accumulation of mildly deleterious mutations and genome erosion.

Effectiveness of microsatellite and SNP markers for parentage and identity analysis in species with low genetic diversity: the case of European bison

The European bison (Bison bonasus) has recovered successfully after a severe bottleneck about 90 years ago but has been left with low genetic variability that may substantially hinder parentage and identity analysis. According to pedigree analysis, over 80% of the genes in the contemporary population descend from just two founder animals and inbreeding coefficients averaged almost 0.5, whereas microsatellite heterozygosity does not exceed 0.3. We present a comparison of the effectiveness of 17 microsatellite and 960 single nucleotide polymorphism (SNP) markers for paternity and identity analysis in the European bison. Microsatellite-based paternity and identity analysis was unsuccessful because of low marker heterozygosity and is not a practical approach in this species. Simulations using SNP markers suggest that 80-90 randomly selected loci, or just 50-60 of the most heterozygous loci, would be sufficient to ensure successful paternity and identity analysis in this species. For the purpose of standardizing future analysis, a panel of 50-60 bovine SNPs characterized by high heterozygosity and an even distribution in the genome could be selected. This panel of markers could be typed using VeraCode (Illumina) or similar SNP genotyping systems. The low cost of these SNP genotyping methods compared with a 16 locus microsatellite survey means that off-the-shelf SNP genotyping systems developed for domestic species represent powerful tools for genetic analysis in related species, and can be effective even in bottlenecked species in which heterozygosity of other markers such as microsatellites may be very low.

Parental genetic characteristics and hatching success in a recovering population of Lesser Kestrels

Decreased hatchability is a common consequence of inbreeding in oviparous organisms and it has been generally considered a useful measure of the effects of reduced genetic diversity on embryological development. Here, we examined the pattern of hatching failure in a wild population of the endangered Lesser Kestrel (Falco naumanni). Particularly, we first analyzed long-term changes of hatching failure over a 16-year study period (1991-2006), in which the study population experienced a concurrent demographic and genetic recovery, and then we determined the consequences of parental genetic characteristics on hatching success. Long-term data analyses revealed a significant decline of hatching failure over time, with annual average hatching failure decreasing from rates characterizing species that have passed a severe population bottleneck to levels generally reported for outbred bird populations. Partial purging of deleterious recessive alleles after the species population decline, the increase of heterozygosity over time reported in a previous study and/or the selection for efficient mechanisms of inbreeding avoidance could be responsible of the observed temporal pattern. In contrast to previous studies, we found no effect of parental genetic characteristics on hatching success. Even though we analyzed an extensive dataset, the 11 neutral markers typed may have had low power to detect such an association. Further, this analysis was limited to the last 5 years (2002-2006) of the whole study period, when DNA samples for genetic analyses were available. During these years, hatching rates were like those typically reported for non-inbred populations, suggesting that the absence of association could be explained by a reduction of the genetic load or consequence of the genetic recover reported in the study population in recent years.

Intron-Dominated Genomes of Early Ancestors of Eukaryotes

Evolutionary reconstructions using maximum likelihood methods point to unexpectedly high densities of introns in protein-coding genes of ancestral eukaryotic forms including the last common ancestor of all extant eukaryotes. Combined with the evidence of the origin of spliceosomal introns from invading Group II self-splicing introns, these results suggest that early ancestral eukaryotic genomes consisted of up to 80% sequences derived from Group II introns, a much greater contribution of introns than that seen in any extant genome. An organism with such an unusual genome architecture could survive only under conditions of a severe population bottleneck.

Brief communication: Restricted geographic distribution for Y‐Q* paragroup in South America

We analyzed 21 paragroup Q* Y chromosomes from South American aboriginal and urban populations. Our aims were to evaluate the phylogenetic status, geographic distribution, and genetic diversity in these groups of chromosomes and compare the degree of genetic variation in relation to Q1a3a haplotypes. All Q* chromosomes from our series and five samples from North American Q* presented the derivate state for M346, that is present upstream to M3, and determined Q1a3* paragroup. We found a restrictive geographic distribution and low frequency of Q1a3* in South America. We assumed that this low frequency could be reflecting extreme drift effects. However, several estimates of gene diversity do not support the existence of a severe bottleneck. The mean haplotype diversity expected was similar to that for South American Q1a3* and Q1a3a (0.478 and 0.501, respectively). The analysis of previous reports from other research groups and this study shows the highest frequencies of Q* for the West Corner and the Grand Chaco regions of South America. At present, there is no information on whether the phylogenetic status of Q* paragoup described in previous reports is similar to that of Q1a3* paragroup though our results support this possibility.

Genetic diversity in Chinese sorghum landraces revealed by chloroplast simple sequence repeats

A collection of sorghum, including more than 12,000 Chinese landraces, has been constructed and maintained in China. However, the genetic diversity of Chinese sorghum landraces has not been fully investigated, and the origin of Chinese sorghum is still in dispute. In this study, the complete chloroplast genome sequence of sorghum line Tx623B was searched for simple sequence repeats (SSRs). 31 SSR loci with at least 10 mononucleotide repeats or five dinucleotide repeats were identified, and primer pairs for 27 loci were designed. Chloroplast DNA variation in cultivated sorghum was investigated by using these primer pairs on 185 Chinese sorghum landraces and 70 cultivated sorghum accessions from other countries. Among the 27 loci, 14 were polymorphic. The number of alleles per polymorphic locus ranged from 2 to 5 with an average of 2.79. Allelic data at 14 polymorphic loci were combined to give 12 haplotypes. The average allelic diversity index across the 14 polymorphic loci and corresponding haplotype diversity were markedly lower for Chinese sorghum landraces than were those for accessions from other countries. However, Chinese sorghum landraces shared a predominant allele at each polymorphic locus and a predominant haplotype with foreign accessions. Our results indicate that Chinese landraces experienced a severe maternal bottleneck during the introduction process with a predominant haplotype being present in 171 of 185 accessions analyzed. Except for one rare exception, haplotypes found in Chinese landraces were either identical or closely related to those found in foreign accessions and could not be separated clearly from them by cluster analysis. Our results are consistent with the hypothesis of African origin of Chinese sorghum.