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Structural genomic variation leads to unexpected genetic differentiation in Lake Tanganyika’s sardines

https://doi.org/10.1101/800904
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Limnological annual cycle inferred from physical-chemical fluctuations at three stations of Lake Tanganyika
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Avian sex, sex chromosomes, and dosage compensation in the age of genomics
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Turnover of sex chromosomes and speciation in fishes
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Limnological variability and pelagic fish abundance (Stolothrissa tanganicae and Lates stappersii) in Lake Tanganyika
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Seismic records of late Pleistocene aridity in Lake Tanganyika, tropical East Africa
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Spatio-temporal dynamics of phytoplankton and primary production in Lake Tanganyika using a MODIS based bio-optical time series
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Sex chromosomes and speciation in Drosophila
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Eco-Evolutionary Genomics of Chromosomal Inversions
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Effects of inter-annual variability, seasonality and persistence on the perception of long-term trends in catch rates of the industrial pelagic purse-seine fishery of northern Lake Tanganyika (Burundi)
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Wind Patterns, Evaporation, and Related Physical Variables in Lake Tanganyika, East Africa
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10.1016/s0967-0653(98)81767-5
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Ecosystem Based Management for Marine Fisheries
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Fisheries research towards resource management on Lake Tanganyika
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Macrozooplankton communities in Lake Tanganyika indicate food chain differences between the northern part and the main basins
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Limnological annual cycle inferred from physical-chemical fluctuations at three stations of Lake Tanganyika
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Speciation through evolution of sex-linked genes
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Trans-oceanic genomic divergence of Atlantic cod ecotypes is associated with large inversions
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Climate change decreases aquatic ecosystem productivity of Lake Tanganyika, Africa
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The genomic basis of adaptive evolution in threespine sticklebacks
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Origins and functional evolution of Y chromosomes across mammals
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How to make a sex chromosome
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The genomics of ecological vicariance in threespine stickleback fish
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Fast gapped-read alignment with Bowtie 2
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Sex-specific evolution during the diversification of live-bearing fishes
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Characterization of a male specific region containing a candidate sex determining gene in Atlantic cod
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Steps in the evolution of heteromorphic sex chromosomes
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Climate warming reduces fish production and benthic habitat in Lake Tanganyika, one of the most biodiverse freshwater ecosystems
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Extraordinarily rapid speciation in a marine fish
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Parallel adaptive evolution of geographically distant herring populations on both sides of the North Atlantic Ocean
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A Case of Rearrangement of Genes in Drosophila
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Ecosystem monitoring in the development of sustainable fisheries in Lake Tanganyika
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Pelagic food web as the basis of fisheries in Lake Tanganyika: A bioenergetic modeling analysis
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Changes in species composition and abundance of commercially important pelagic fish species in Kigoma area, Lake Tanganyika, Tanzania
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Comparative analysis of fisheries restoration and public participation in Lake Victoria and Lake Tanganyika
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Lake Tanganyika fisheries frame survey analysis: Assessment of the options for management of the fisheries of Lake Tanganyika
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Seasonal changes in the pelagic catch of two clupeid zooplanktivores in relation to the abundance of copepod zooplankton in the northern end of Lake Tanganyika
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Linkage Disequilibrium in Humans: Models and Data
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PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses
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Fast and accurate short read alignment with Burrows–Wheeler transform
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The Sequence Alignment/Map format and SAMtools
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The variant call format and VCFtools
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A high-performance computing toolset for relatedness and principal component analysis of SNP data
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Versatile genome assembly evaluation with QUAST-LG
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The ecology of sexual dimorphism in size and shape of the freshwater blenny Salaria fluviatilis
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Novel Sex Chromosomes in 3 Cichlid Fishes from Lake Tanganyika
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DNA polymorphisms amplified by arbitrary primers are useful as genetic markers
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The dangers of ignoring stock complexity in fishery management: the case of the North Sea cod
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Sexual dimorphism in a top predator ( Notophthalmus viridescens ) drives aquatic prey community assembly
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Local adaptation and the evolution of inversions on sex chromosomes and autosomes
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A chromosome-level assembly of the Atlantic herring genome—detection of a supergene and other signals of selection
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Rates of karyotypic evolution in Estrildid finches differ between island and continental clades
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Genes located in a chromosomal inversion are correlated with territorial song in white‐throated sparrows
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The biology of Lates species (Nile perch) in Lake Tanganyika, and the status of the pelagic fishery for Lates species and Luciolates stappersii (Blgr.)
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The evolution of sexual size dimorphism in fish*
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Morphological and genetic differentiation of the African clupeidLimnothrissa miodon34 years after its introduction to Lake Kivu
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Genetic population structure in the Lake Tanganyika sardineLimnothrissa miodon
inferredcites →https://doi.org/10.1111/j.1365-2109.1983.tb00050.xopenalex-snapshot
Success of the Introduction of the Fresh Water Clupeid Limnothrissa miodon (Boulenger) in Lake Kivu
inferredcites →https://doi.org/10.1111/mec.12354openalex-snapshot
Stacks: an analysis tool set for population genomics
inferredcites →https://doi.org/10.1111/mec.13592openalex-snapshot
Two adjacent inversions maintain genomic differentiation between migratory and stationary ecotypes of Atlantic cod
inferredcites →https://doi.org/10.1111/mec.14217openalex-snapshot
Sex matters in massive parallel sequencing: Evidence for biases in genetic parameter estimation and investigation of sex determination systems
inferredcites →https://doi.org/10.1111/mec.14280openalex-snapshot
Long‐term balancing selection on chromosomal variants associated with crypsis in a stick insect
inferredcites →https://doi.org/10.1111/mec.14874openalex-snapshot
Sex chromosome inversions enforce reproductive isolation across an avian hybrid zone
inferredcites →https://doi.org/10.1111/mec.14944openalex-snapshot
Chromosomal inversions associated with environmental adaptation in honeybees
inferredcites →https://doi.org/10.1126/science.1084846openalex-snapshot
Ecological Consequences of a Century of Warming in Lake Tanganyika
inferredcites →https://doi.org/10.1126/science.1174705openalex-snapshot
Sexual Conflict Resolved by Invasion of a Novel Sex Determiner in Lake Malawi Cichlid Fishes
inferredcites →https://doi.org/10.1126/science.277.5325.509openalex-snapshot
The Management of Fisheries and Marine Ecosystems
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Estimating the age of formation of lakes: An example from Lake Tanganyika, East African Rift system
inferredcites →https://doi.org/10.1186/1471-2105-14-289openalex-snapshot
Calculation of Tajima’s D and other neutrality test statistics from low depth next-generation sequencing data
inferredcites →https://doi.org/10.1186/1471-2156-11-94openalex-snapshot
Discriminant analysis of principal components: a new method for the analysis of genetically structured populations
inferredcites →https://doi.org/10.1186/s12859-014-0356-4openalex-snapshot
ANGSD: Analysis of Next Generation Sequencing Data
inferredcites →https://doi.org/10.1186/s12862-018-1325-8openalex-snapshot
First genomic study on Lake Tanganyika sprat Stolothrissa tanganicae: a lack of population structure calls for integrated management of this important fisheries target species
inferredcites →https://doi.org/10.1371/journal.pbio.1000501openalex-snapshot
How and Why Chromosome Inversions Evolve
inferredcites →https://doi.org/10.1371/journal.pbio.2006062openalex-snapshot
Repeated translocation of a gene cassette drives sex-chromosome turnover in strawberries
inferredcites →https://doi.org/10.1371/journal.pgen.1000391openalex-snapshot
Turnover of Sex Chromosomes in the Stickleback Fishes (Gasterosteidae)
inferredcites →https://doi.org/10.1371/journal.pgen.1004223openalex-snapshot
Sex Chromosome Turnover Contributes to Genomic Divergence between Incipient Stickleback Species
inferredcites →https://doi.org/10.1371/journal.pgen.1005237openalex-snapshot
Y Fuse? Sex Chromosome Fusions in Fishes and Reptiles
inferredcites →https://doi.org/10.1371/journal.pgen.1005887openalex-snapshot
Genomics of Rapid Incipient Speciation in Sympatric Threespine Stickleback
inferredcites →https://doi.org/10.1371/journal.pone.0001979openalex-snapshot
Marine Incursion: The Freshwater Herring of Lake Tanganyika Are the Product of a Marine Invasion into West Africa
inferredcites →https://doi.org/10.1371/journal.pone.0003376openalex-snapshot
Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers
inferredcites →https://doi.org/10.1371/journal.pone.0093656openalex-snapshot
Decadal Trends and Common Dynamics of the Bio-Optical and Thermal Characteristics of the African Great Lakes
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Century-Long Warming Trends in the Upper Water Column of Lake Tanganyika
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Genetic Structure in a Small Pelagic Fish Coincides with a Marine Protected Area: Seascape Genetics in Patagonian Fjords
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A Dense Linkage Map of Lake Victoria Cichlids Improved the Pundamilia Genome Assembly and Revealed a Major QTL for Sex-Determination
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Growth and Mortality of Stolothrissa tanganicae
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Reproductive activities of two zooplanktivorous clupeid fish in relation to the seasonal abundance of copepod prey in the northern end of Lake Tanganyika
inferredcites →https://doi.org/10.3354/meps223251openalex-snapshot
Marked genetic structuring in localised spawning populations of cod Gadus morhua in the North Sea and adjoining waters, as revealed by microsatellites
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Unusual Diversity of Sex Chromosomes in African Cichlid Fishes
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Differential cooling drives large‐scale convective circulation in Lake Tanganyika
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The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing

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inferred← citeshttps://doi.org/10.1016/j.ijpara.2020.02.002openalex-snapshot
Weak population structure and recent demographic expansion of the monogenean parasite Kapentagyrus spp. infecting clupeid fishes of Lake Tanganyika, East Africa
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