Conventional coalescent inferences of population history make the critical assumption that the population under examination is panmictic.However,most populations are structured.This complicates the prevailing coalesce...Conventional coalescent inferences of population history make the critical assumption that the population under examination is panmictic.However,most populations are structured.This complicates the prevailing coalescent analyses and sometimes leads to inaccurate estimates.To develop a coalescent method unhampered by population structure,we perform two analyses.First,we demonstrate that the coalescent probability of two randomly sampled alleles from the immediate preceding generation(one generation back)is independent of population structure.Second,motivated by this finding,we propose a new coalescent method:i-coalescent analysis.The i-coalescent analysis computes the instantaneous coalescent rate by using a phylogenetic tree of sampled alleles.Using simulated data,we broadly demonstrate the capability of i-coalescent analysis to accurately reconstruct population size dynamics of highly structured populations,although we find this method often requires larger sample sizes for structured populations than for panmictic populations.Overall,our results indicate i-coalescent analysis to be a useful tool,especially for the inference of population histories with intractable structure such as the developmental history of cell populations in the organs of complex organisms.展开更多
Unraveling the lineage relationships of all descendants from a zygote is fundamental to advancing our understanding of developmental and stem cell biology.However,existing cell barcoding technologies in zebrafish lack...Unraveling the lineage relationships of all descendants from a zygote is fundamental to advancing our understanding of developmental and stem cell biology.However,existing cell barcoding technologies in zebrafish lack the resolution to capture the majority of cell divisions during embryogenesis.A recently developed method,a substitution mutation-aided lineage-tracing system(SMALT),successfully reconstructed high-resolution cell phylogenetic trees for Drosophila melanogaster.Here,we implement the SMALT system in zebrafish,recording a median of 14 substitution mutations on a one-kilobase-pair barcoding sequence for one-day post-fertilization embryos.Leveraging this system,we reconstruct four cell lineage trees for zebrafish fin cells,encompassing both original and regenerated fin.Each tree consists of hundreds of internal nodes with a median bootstrap support of 99%.Analysis of the obtained cell lineage trees reveals that regenerated fin cells mainly originate from cells in the same part of the fins.Through multiple times sampling germ cells from the same individual,we show the stability of the germ cell pool and the early separation of germ cell and somatic cell progenitors.Our system offers the potential for reconstructing high-quality cell phylogenies across diverse tissues,providing valuable insights into development and disease in zebrafish.展开更多
All species on the Earth can trace their origins back to a common ancestor,and their evolutionary history can be illustrated as a tree-like structure.The root of the tree represents the shared ancestor,while the bifur...All species on the Earth can trace their origins back to a common ancestor,and their evolutionary history can be illustrated as a tree-like structure.The root of the tree represents the shared ancestor,while the bifurcations signify past speciation events,and the leaves indicate present-day species(Fig.1a).展开更多
基金supported by National Natural Science Foundation of China(31630042 and 31970570)Guangdong Special Support Program。
文摘Conventional coalescent inferences of population history make the critical assumption that the population under examination is panmictic.However,most populations are structured.This complicates the prevailing coalescent analyses and sometimes leads to inaccurate estimates.To develop a coalescent method unhampered by population structure,we perform two analyses.First,we demonstrate that the coalescent probability of two randomly sampled alleles from the immediate preceding generation(one generation back)is independent of population structure.Second,motivated by this finding,we propose a new coalescent method:i-coalescent analysis.The i-coalescent analysis computes the instantaneous coalescent rate by using a phylogenetic tree of sampled alleles.Using simulated data,we broadly demonstrate the capability of i-coalescent analysis to accurately reconstruct population size dynamics of highly structured populations,although we find this method often requires larger sample sizes for structured populations than for panmictic populations.Overall,our results indicate i-coalescent analysis to be a useful tool,especially for the inference of population histories with intractable structure such as the developmental history of cell populations in the organs of complex organisms.
基金supported by the National Key R&D Program of China(2021YFA1302500 and 2021YFA1302501)the National Natural Science Foundation of China(32293190,32293191,31970570,and 32200492).
文摘Unraveling the lineage relationships of all descendants from a zygote is fundamental to advancing our understanding of developmental and stem cell biology.However,existing cell barcoding technologies in zebrafish lack the resolution to capture the majority of cell divisions during embryogenesis.A recently developed method,a substitution mutation-aided lineage-tracing system(SMALT),successfully reconstructed high-resolution cell phylogenetic trees for Drosophila melanogaster.Here,we implement the SMALT system in zebrafish,recording a median of 14 substitution mutations on a one-kilobase-pair barcoding sequence for one-day post-fertilization embryos.Leveraging this system,we reconstruct four cell lineage trees for zebrafish fin cells,encompassing both original and regenerated fin.Each tree consists of hundreds of internal nodes with a median bootstrap support of 99%.Analysis of the obtained cell lineage trees reveals that regenerated fin cells mainly originate from cells in the same part of the fins.Through multiple times sampling germ cells from the same individual,we show the stability of the germ cell pool and the early separation of germ cell and somatic cell progenitors.Our system offers the potential for reconstructing high-quality cell phylogenies across diverse tissues,providing valuable insights into development and disease in zebrafish.
基金supported by the National Key R&D Program of China(2021YFA1302500 and 2021YFA1302501)the National Natural Science Foundation of China(32293190,32293191,31970570+1 种基金32200492)the Fundamental Research Funds for the Central Universities,Sun Yat-sen University(33000-31620269)。
文摘All species on the Earth can trace their origins back to a common ancestor,and their evolutionary history can be illustrated as a tree-like structure.The root of the tree represents the shared ancestor,while the bifurcations signify past speciation events,and the leaves indicate present-day species(Fig.1a).
