Satoshi Mitarai

Taking the chaos out of genetic patchiness: seascape genetics reveals ecological and oceanographic drivers of genetic patterns in three temperate reef species

Marine species frequently show weak and/or complex genetic structuring that is commonly dismissed as ‘chaotic’ genetic patchiness and ecologically uninformative. Here, using three datasets that individually feature weak chaotic patchiness, we demonstrate that combining inferences across species and incorporating environmental data can greatly improve the predictive value of marine population genetics studies on small spatial scales. Significant correlations in genetic patterns of microsatellite markers among three species, kelp bass Paralabrax clathratus, Kellet’s whelk Kelletia kelletii and California spiny lobster Panulirus interruptus, in the Southern California Bight suggest that slight differences in diversity and pairwise differentiation across sampling sites are not simply noise or chaotic patchiness, but are ecologically meaningful. To test whether interspecies correlations potentially result from shared environmental drivers of genetic patterns, we assembled data on kelp bed size, sea surface temperature and estimates of site‐to‐site migration probability derived from a high resolution multi‐year ocean circulation model. These data served as predictor variables in linear models of genetic diversity and linear mixed models of genetic differentiation that were assessed with information–theoretic model selection. Kelp was the most informative predictor of genetics for all three species, but ocean circulation also played a minor role for kelp bass. The shared patterns suggest a single spatial marine management strategy may effectively protect genetic diversity of multiple species. This study demonstrates the power of environmental and ecological data to shed light on weak genetic patterns and highlights the need for future focus on a mechanistic understanding of the links between oceanography, ecology and genetic structure.

Comparison of the sensitivity and specificity of two whole blood interferon-gamma assays for M. tuberculosis infection

OBJECTIVES To compare the sensitivity and the specificity of the QuantiFERON-TB Gold (QFT-G) and QuantiFERON-TB Gold In Tube (QFT-GIT) diagnostic tests for Mycobacterium tuberculosis infection. METHODS One-hundred patients with culture and/or PCR confirmed M. tuberculosis infection and 168 volunteers with no risk factors for M. tuberculosis infection were tested to estimate sensitivity and specificity, respectively. RESULTS Analysis of data from the tuberculosis (TB) patients with valid results found the sensitivity of QFT-GIT (92.6%, 87/94) to be significantly higher than that for the QFT-G test (81.4%, 79/97; p=0.023). The specificity of both QFT-GIT and QFT-G was 98.8% (CI: 95.1%-99.8%) with 2 of the 160 low risk subjects with valid results for both tests being positive. Data analysis confirmed the manufacturers recommended test cut-off as being optimal, but identified higher sensitivity could be obtained by using a lower cut-off, with only a moderate decrease in specificity. CONCLUSIONS The QFT-GIT test had enhanced sensitivity for detection of M. tuberculosis infection over the QFT-G test, whilst maintaining equivalent high specificity. The logistic benefits of the QFT-GIT test format, as well as its higher sensitivity, should enable enhanced TB control.

Isolation by oceanographic distance explains genetic structure for Macrocystis pyrifera in the Santa Barbara Channel.

Ocean currents are expected to be the predominant environmental factor influencing the dispersal of planktonic larvae or spores; yet, their characterization as predictors of marine connectivity has been hindered by a lack of understanding of how best to use oceanographic data. We used a high‐resolution oceanographic model output and Lagrangian particle simulations to derive oceanographic distances (hereafter called transport times) between sites studied for Macrocystis pyrifera genetic differentiation. We build upon the classical isolation‐by‐distance regression model by asking how much additional variability in genetic differentiation is explained when adding transport time as predictor. We explored the extent to which gene flow is dependent upon seasonal changes in ocean circulation. Because oceanographic transport between two sites is inherently asymmetric, we also compare the explanatory power of models using the minimum or the mean transport times. Finally, we compare the direction of connectivity as estimated by the oceanographic model and genetic assignment tests. We show that the minimum transport time had higher explanatory power than the mean transport time, revealing the importance of considering asymmetry in ocean currents when modelling gene flow. Genetic assignment tests were much less effective in determining asymmetry in gene flow. Summer‐derived transport times, in particular for the month of June, which had the strongest current speed, greatest asymmetry and highest spore production, resulted in the best‐fit model explaining twice the variability in genetic differentiation relative to models that use geographic distance or habitat continuity. The best overall model also included habitat continuity and explained 65% of the variation in genetic differentiation among sites.

Identifying critical regions in small-world marine metapopulations

The precarious state of many nearshore marine ecosystems has prompted the use of marine protected areas as a tool for management and conservation. However, there remains substantial debate over their design and, in particular, how to best account for the spatial dynamics of nearshore marine species. Many commercially important nearshore marine species are sedentary as adults, with limited home ranges. It is as larvae that they disperse greater distances, traveling with ocean currents sometimes hundreds of kilometers. As a result, these species exist in spatially complex systems of connected subpopulations. Here, we explicitly account for the mutual dependence of subpopulations and approach protected area design in terms of network robustness. Our goal is to characterize the topology of nearshore metapopulation networks and their response to perturbation, and to identify critical subpopulations whose protection would reduce the risk for stock collapse. We define metapopulation networks using realistic estimates of larval dispersal generated from ocean circulation simulations and spatially explicit metapopulation models, and we then explore their robustness using node-removal simulation experiments. Nearshore metapopulations show small-world network properties, and we identify a set of highly connected hub subpopulations whose removal maximally disrupts the metapopulation network. Protecting these subpopulations reduces the risk for systemic failure and stock collapse. Our focus on catastrophe avoidance provides a unique perspective for spatial marine planning and the design of marine protected areas.

Promising loci of variable numbers of tandem repeats for typing Beijing family Mycobacterium tuberculosis

We analysed the genotypes of 325 Mycobacterium tuberculosis clinical isolates obtained during 2002 throughout Japan. The genotyping methods included insertion sequence IS6110 RFLP, spoligotyping and variable number of tandem repeat (VNTR) analyses. Clustered isolates revealed by IS6110 RFLP analysis accounted for 18.5 % (60/325) of the isolates. Beijing genotype tuberculosis (TB) accounted for 73.8 % (240/325) of the isolates. Using VNTR, we analysed 35 loci, including 12 standard mycobacterial interspersed repetitive units and 4 exact tandem repeats. The discriminatory power of these 16 loci was low. Using VNTR analyses of the 35 loci, 12 loci (VNTRs 0424, 0960, 1955, 2074, 2163b, 2372, 2996, 3155, 3192, 3336, 4052 and 4156) were selected for the genotyping of Beijing genotype strains. Comparison of the discriminatory power of the 12-locus VNTR [Japan Anti-Tuberculosis Association (JATA)] to that of the 15-locus and 24-locus VNTRs proposed by Supply et al. (2006) showed that our established VNTR system was superior to the reported 15-locus VNTR and had almost equal discriminatory power to the 24-locus VNTR. This 12-locus VNTR (JATA) can therefore be used for TB genotyping in areas where Beijing family strains are dominant.

Changing Seascapes, Stochastic Connectivity, and Marine Metapopulation Dynamics

The probability of dispersal from one habitat patch to another is a key quantity in our efforts to understand and predict the dynamics of natural populations. Unfortunately, an often overlooked property of this potential connectivity is that it may change with time. In the marine realm, transient landscape features, such as mesoscale eddies and alongshore jets, produce potential connectivity that is highly variable in time. We assess the impact of this temporal variability by comparing simulations of nearshore metapopulation dynamics when potential connectivity is constant through time (i.e., when it is deterministic) and when it varies in time (i.e., when it is stochastic). We use mathematical analysis to reach general conclusions and realistic biophysical modeling to determine the actual magnitude of these changes for a specific system: nearshore marine species in the Southern California Bight. We find that in general the temporal variability of potential connectivity affects two important quantities: metapopulation growth rates when the species is rare and equilibrium abundances. Our biophysical models reveal that stochastic outcomes are almost always lower than their deterministic counterparts, sometimes by up to 40%. This has implications for how we use spatial information, such as connectivity, to manage nearshore (and other) systems.

Turbulent dispersal promotes species coexistence

Several recent advances in coexistence theory emphasize the importance of space and dispersal, but focus on average dispersal rates and require spatial heterogeneity, spatio-temporal variability or dispersal-competition tradeoffs to allow coexistence. We analyse a model with stochastic juvenile dispersal (driven by turbulent flow in the coastal ocean) and show that a low-productivity species can coexist with a high-productivity species by having dispersal patterns sufficiently uncorrelated from those of its competitor, even though, on average, dispersal statistics are identical and subsequent demography and competition is spatially homogeneous. This produces a spatial storage effect, with an ephemeral partitioning of a ‘spatial niche’, and is the first demonstration of a physical mechanism for a pure spatiotemporal environmental response. ‘Turbulent coexistence’ is widely applicable to marine species with pelagic larval dispersal and relatively sessile adult life stages (and perhaps some wind-dispersed species) and complements other spatial and temporal storage effects previously documented for such species.

Biological and Molecular Characteristics of Mycobacterium tuberculosis Clinical Isolates with Low-Level Resistance to Isoniazid in Japan

ABSTRACT We reevaluated the BACTEC MGIT 960 antimicrobial susceptibility testing system (MGIT 960 AST) by using 1,112 isolates of Mycobacterium tuberculosis. When the results of MGIT 960 AST were compared with that of the proportion method using Ogawa medium (Ogawa PM), discrepant results were obtained for 30 strains with isoniazid, all resistant by MGIT 960 AST but susceptible by Ogawa PM. For 93% of the strains that produced discrepant results, the MIC was 0.4 or 0.8 μg/ml, showing resistance by the proportion method using Middlebrook agar plates. Furthermore, it was also established by analyses of the katG and inhA genes that strains resistant only by MGIT 960 AST have a low level of isoniazid (INH) resistance, indicating that MGIT 960 AST is a reliable method. Ninety-six strains were resistant to 0.1 μg/ml INH by MGIT 960 AST. When they were divided into three groups, Low-S (susceptible at 0.2 μg/ml), Low-R (resistant at 0.2 μg/ml), and High-R (resistant at 1.0 μg/ml), by Ogawa PM, 43.3% of the Low-S strains had mutations in the promoter region of inhA and no mutations were detected in katG codon 315, while 61.7% of the High-R strains had katG codon 315 mutations or a gross deletion of katG. These results suggest that mutations in inhA are associated with low-level resistance to INH and katG codon 315 mutations are associated with high-level resistance to INH. In addition, the analyses demonstrated some relationship of mutations in the inhA gene with ethionamide resistance for the Low-S strains, but not for the High-R strains.

Clonal Expansion of Multidrug- Resistant and Extensively Drug- Resistant Tuberculosis, Japan

Strain clustering suggests community transmission plays a critical role in incidence.

TGS-TB: Total Genotyping Solution for Mycobacterium tuberculosis Using Short-Read Whole-Genome Sequencing

Whole-genome sequencing (WGS) with next-generation DNA sequencing (NGS) is an increasingly accessible and affordable method for genotyping hundreds of Mycobacterium tuberculosis (Mtb) isolates, leading to more effective epidemiological studies involving single nucleotide variations (SNVs) in core genomic sequences based on molecular evolution. We developed an all-in-one web-based tool for genotyping Mtb, referred to as the Total Genotyping Solution for TB (TGS-TB), to facilitate multiple genotyping platforms using NGS for spoligotyping and the detection of phylogenies with core genomic SNVs, IS6110 insertion sites, and 43 customized loci for variable number tandem repeat (VNTR) through a user-friendly, simple click interface. This methodology is implemented with a KvarQ script to predict MTBC lineages/sublineages and potential antimicrobial resistance. Seven Mtb isolates (JP01 to JP07) in this study showing the same VNTR profile were accurately discriminated through median-joining network analysis using SNVs unique to those isolates. An additional IS6110 insertion was detected in one of those isolates as supportive genetic information in addition to core genomic SNVs. The results of in silico analyses using TGS-TB are consistent with those obtained using conventional molecular genotyping methods, suggesting that NGS short reads could provide multiple genotypes to discriminate multiple strains of Mtb, although longer NGS reads (≥300-mer) will be required for full genotyping on the TGS-TB web site. Most available short reads (~100-mer) can be utilized to discriminate the isolates based on the core genome phylogeny. TGS-TB provides a more accurate and discriminative strain typing for clinical and epidemiological investigations; NGS strain typing offers a total genotyping solution for Mtb outbreak and surveillance. TGS-TB web site: https://gph.niid.go.jp/tgs-tb/.