scholarly journals Integrated Population Genomic Analysis and Numerical Simulation to Estimate Larval Dispersal of Acanthaster cf. solaris Between Ogasawara and Other Japanese Regions

2022 ◽  
Vol 8 ◽  
Author(s):  
Mizuki Horoiwa ◽  
Takashi Nakamura ◽  
Hideaki Yuasa ◽  
Rei Kajitani ◽  
Yosuke Ameda ◽  
...  
Keyword(s):  
Larval Dispersal ◽  
Large Scale ◽  
Genomic Analysis ◽  
Connectivity Matrix ◽  
Larval Recruitment ◽  
Population Genomic ◽  
Population Outbreak ◽  
Japanese Regions ◽  
The Kuroshio ◽  
Kuroshio Region

The estimation of larval dispersal on an ecological timescale is significant for conservation of marine species. In 2018, a semi-population outbreak of crown-of-thorns sea star, Acanthaster cf. solaris, was observed on a relatively isolated oceanic island, Ogasawara. The aim of this study was to assess whether this population outbreak was caused by large-scale larval recruitment (termed secondary outbreak) from the Kuroshio region. We estimated larval dispersal of the coral predator A. cf. solaris between the Kuroshio and Ogasawara regions using both population genomic analysis and simulation of oceanographic dispersal. Population genomic analysis revealed overall genetically homogenized patterns among Ogasawara and other Japanese populations, suggesting that the origin of the populations in the two regions is the same. In contrast, a simulation of 26-year oceanographic dispersal indicated that larvae are mostly self-seeded in Ogasawara populations and have difficulty reaching Ogasawara from the Kuroshio region within one generation. However, a connectivity matrix produced by the larval dispersal simulation assuming a Markov chain indicated gradual larval dispersal migration from the Kuroshio region to Ogasawara in a stepping-stone manner over multiple years. These results suggest that the 2018 outbreak was likely the result of self-seeding, including possible inbreeding (as evidenced by clonemate analysis), as large-scale larval dispersal from the Kurishio population to the Ogasawara population within one generation is unlikely. Instead, the population in Ogasawara is basically sustained by self-seedings, and the outbreak in 2018 was also most likely caused by successful self-seedings including possible inbreeding, as evidenced by clonemate analysis. This study also highlighted the importance of using both genomic and oceanographic methods to estimate larval dispersal, which provides significant insight into larval dispersal that occurs on ecological and evolutionary timescales.

scholarly journals Integrated population genomic analysis and numerical simulation to estimate larval dispersal of Acanthaster cf. solaris between Ogasawara and other Japanese regions

2021 ◽  
Author(s):  
Mizuki Horoiwa ◽  
Takashi Nakamura ◽  
Hideaki Yuasa ◽  
Rei Kajitani ◽  
Yosuke Ameda ◽  
...  
Keyword(s):  
Larval Dispersal ◽  
Large Scale ◽  
Genomic Analysis ◽  
Connectivity Matrix ◽  
Larval Recruitment ◽  
Population Genomic ◽  
Population Outbreak ◽  
Japanese Regions ◽  
The Kuroshio ◽  
Kuroshio Region

AbstractThe estimation of larval dispersal of marine species occurring on an ecological timescale is significant for conservation. In 2018, a semi-population outbreak of crown of thorns starfish, Acanthaster cf. solaris was observed on a relatively isolated oceanic island, Ogasawara. The aim of this study was to assess whether this population outbreak was caused by large-scale larval recruitment (termed secondary outbreak) from the Kuroshio region. We estimated larval dispersal of the coral predator A. cf. solaris between the Kuroshio and Ogasawara regions using both population genomic analysis and oceanographic dispersal simulation. Population genomic analysis revealed overall genetically homogenized patterns among Ogasawara and other Japanese populations, suggesting that the origin of the populations in the two regions is the same. In contrast, a simulation of 26-year oceanographic dispersal indicated that larvae are mostly self-seeded in Ogasawara populations and have difficulty reaching Ogasawara from the Kuroshio region within one generation. However, a connectivity matrix produced by the larval dispersal simulation assuming a Markov chain indicated gradual larval dispersal migration from the Kuroshio region to Ogasawara in a stepping-stone manner over multiple years. These results suggest that, while large-scale larval dispersal from an outbreak of the Kuroshio population spreading to the Ogasawara population within one generation is unlikely. This study also highlighted the importance of using both genomic and oceanographic methods to estimate larval dispersal, which provides significant insight into larval dispersal that occurs on ecological and evolutionary timescales.

scholarly journals Phylogeographic separation and formation of sexually discrete lineages in a global population of Yersinia pseudotuberculosis

2017 ◽  
Author(s):  
Tristan Seecharran ◽  
Laura Kalin-Mänttäri ◽  
Katja A. Koskela ◽  
Simo Nikkari ◽  
Benjamin Dickins ◽  
...  
Keyword(s):  
Large Scale ◽  
Yersinia Pseudotuberculosis ◽  
Genomic Analysis ◽  
Genetic Exchange ◽  
Evolutionary Trajectory ◽  
Population Genomic ◽  
The World ◽  
Genomic Studies ◽  
Lineage Structure ◽  
Global Population

AbstractYersinia pseudotuberculosis is a Gram negative intestinal pathogen of humans and has been responsible for several nation-wide gastro-intestinal outbreaks. Large-scale population genomic studies have been performed on the other human pathogenic Yersinia, Y. pestis and Y. enterocolitica allowing a high-resolution understanding of the ecology, evolution and dissemination of these pathogens. However, to date no large-scale global population genomic analysis of Y. pseudotuberculosis has been performed. Here we present analyses of the genomes of 134 strains of Y. pseudotuberculosis isolated from around the world, from multiple ecosystems since 1960’s. Our data display a phylogeographic split within the population, with an Asian ancestry and subsequent dispersal of successful clonal lineages into Europe and the rest of the world. These lineages can be differentiated by CRISPR cluster arrays, and we show that the lineages are limited with respect to inter-lineage genetic exchange. This restriction of genetic exchange maintains the discrete lineage structure in the population despite co-existence of lineages for thousands of years in multiple countries. Our data highlights how CRISPR can be informative of the evolutionary trajectory of bacterial lineages, and merits further study across bacteria.

scholarly journals Large scale enterohemorrhagic E coli population genomic analysis using whole genome typing reveals recombination clusters and potential drug target

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 33
Author(s):  
DJ Darwin Bandoy
Keyword(s):  
Drug Discovery ◽  
Drug Target ◽  
Large Scale ◽  
Genomic Analysis ◽  
Wide Distribution ◽  
Whole Genome ◽  
Potential Drug Target ◽  
Potential Drug ◽  
New Paradigm ◽  
Population Genomic

Enterohemorrhagic Escherichia coli continues to be a significant public health risk. With the onset of next generation sequencing, whole genome sequences require a new paradigm of analysis relevant for epidemiology and drug discovery. A large-scale bacterial population genomic analysis was applied to 702 isolates of serotypes associated with EHEC resulting in five pangenome clusters. Serotype incongruence with pangenome types suggests recombination clusters. Core genome analysis was performed to determine the population wide distribution of sdiA as potential drug target. Protein modelling revealed nonsynonymous variants are notably absent in the ligand binding site for quorum sensing, indicating that population wide conservation of the sdiA ligand site can be targeted for potential prophylactic purposes. Applying pathotype-wide pangenomics as a guide for determining evolution of pharmacophore sites is a potential approach in drug discovery.

scholarly journals Large scale enterohemorrhagic E coli population genomic analysis using whole genome typing reveals recombination clusters and potential drug target

F1000Research ◽  
2020 ◽  
Vol 8 ◽  
pp. 33
Author(s):  
DJ Darwin Bandoy
Keyword(s):  
Drug Discovery ◽  
Drug Target ◽  
Large Scale ◽  
Genomic Analysis ◽  
Wide Distribution ◽  
Whole Genome ◽  
Potential Drug Target ◽  
Potential Drug ◽  
New Paradigm ◽  
Population Genomic

Enterohemorrhagic Escherichia coli continues to be a significant public health risk. With the onset of next generation sequencing, whole genome sequences require a new paradigm of analysis relevant for epidemiology and drug discovery. A large-scale bacterial population genomic analysis was applied to 702 isolates of serotypes associated with EHEC resulting in five pangenome clusters. Serotype incongruence with pangenome types suggests recombination clusters. Core genome analysis was performed to determine the population wide distribution of sdiA as potential drug target. Protein modelling revealed nonsynonymous variants are notably absent in the ligand binding site for quorum sensing, indicating that population wide conservation of the sdiA ligand site can be targeted for potential prophylactic purposes. Applying pathotype-wide pangenomics as a guide for determining evolution of pharmacophore sites is a potential approach in drug discovery.

scholarly journals Population Genomic Analysis of ALMS1 in Humans Reveals a Surprisingly Complex Evolutionary History

2009 ◽  
Vol 26 (6) ◽  
pp. 1357-1367 ◽  
Author(s):  
Laura B. Scheinfeldt ◽  
Shameek Biswas ◽  
Jennifer Madeoy ◽  
Caitlin F. Connelly ◽  
Eric E. Schadt ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Genomic Analysis ◽  
Population Genomic ◽  
Complex Evolutionary History

scholarly journals Distribution of ultraphytoplankton in the western part of the North Pacific subtropical gyre during a strong La Niña condition: relationship with the hydrological conditions

2013 ◽  
Vol 10 (9) ◽  
pp. 5947-5965 ◽  
Author(s):  
M. Girault ◽  
H. Arakawa ◽  
A. Barani ◽  
H. J. Ceccaldi ◽  
F. Hashihama ◽  
...  
Keyword(s):  
El Niño ◽  
North Pacific ◽  
El Nino ◽  
Subtropical Gyre ◽  
La Niña ◽  
North Pacific Subtropical Gyre ◽  
Heterogeneous Distribution ◽  
La Nina ◽  
The Kuroshio ◽  
Kuroshio Region

Abstract. The distribution of ultraphytoplankton was investigated in the western North Pacific Subtropical Gyre (NPSG) during La Niña, a cold phase of El Niño Southern Oscillation (ENSO). Observations were conducted in a north-south transect (33.6–13.25° N) along the 141.5° E meridian in order to study the ultraplankton assemblages in various oligotrophic conditions. Analyses were performed at the single cell level by analytical flow cytometry. Five ultraphytoplankton groups (Prochlorococcus, Synechococcus, picoeukaryotes, nanoeukaryotes and nanocyanobacteria-like) defined by their optical properties were enumerated in three different areas visited during the cruise: the Kuroshio region, the subtropical Pacific gyre and a transition zone between the subtropical Pacific gyre and the Warm pool. Prochlorococcus outnumbered the other photoautotrophs in all the investigated areas. However, in terms of carbon biomass, an increase in the relative contribution of Synechococcus, picoeukaryotes and nanoeukaryotes was observed from the centre of the subtropical gyre to the Kuroshio area. In the Kuroshio region, a peak of abundance of nanoeukaryotes observed at the surface suggested an increase in nutrients likely due to the vicinity of a cold cyclonic eddy. In contrast, in the salinity front along the isohaline 35 and anticyclonic eddy located around 22.83° N, the mainly constant distribution of Prochlorococcus from the surface down to 150 m characterised the dominance by these microorganisms in high salinity and temperature zone. Results suggested that the distribution of nanocyanobacteria-like is also closely linked to the salinity front rather than low phosphate concentration. The maximum abundance of ultraphytoplankton was located above the SubTropical Counter Current (STCC) at depths > 100 m where higher nutrient concentrations were measured. Finally, comparison of the ultraphytoplankton concentrations during El Niño (from the literature) and La Niña (this study) conditions seems to demonstrate that La Niña conditions lead to higher concentrations of Synechococcus in the Subtropical gyre and a lower abundance of Synechococcus in the Kuroshio region. Our results suggest that the west part of NPSG is a complex area, where different water masses, salinity fronts and eddies lead to a heterogeneous distribution of ultraphytoplankton assemblages in the upper layer of the water column.

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