Details on the molecular clock analysis.

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+++ b/biblio/36867684.mdwn
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 [[!meta title="Three amphioxus reference genomes reveal gene and chromosome evolution of chordates. "]]
-[[!tag genome]]
+[[!tag genome clock]]
 
 Huang Z, Xu L, Cai C, Zhou Y, Liu J, Xu Z, Zhu Z, Kang W, Cen W, Pei S, Chen D, Shi C, Wu X, Huang Y, Xu C, Yan Y, Yang Y, Xue T, He W, Hu X, Zhang Y, Chen Y, Bi C, He C, Xue L, Xiao S, Yue Z, Jiang Y, Yu JK, Jarvis ED, Li G, Lin G, Zhang Q, Zhou Q. 
 
@@ -7,4 +7,28 @@ Proc Natl Acad Sci U S A. 2023 Mar 7;120(10):e2201504120. doi:10.1073/pnas.22015
 
 Three amphioxus reference genomes reveal gene and chromosome evolution of chordates. 
 
-[[!pmid 36867684 desc="Chromosomal assembly of _Branchiostoma floridae_ (Bf), _Branchiostoma belcheri_ (Bb) and _Branchiostoma japonicum_ (Bj).  ”we devised an interspecific trio sequencing strategy [...] for the F1 hybrids derived from Bf-Bb or Bf-Bj crosses. [...] the hybrids contain two haploid parental genomes that have become too diverged in sequences to form cross-species chimeric assembly”  “The three amphioxus genomes show a highly conserved chromosomal synteny to each other, with  most  chromosomes  showing  a  one-to-one  homologous  relationship except for a few chromosome fusions.”  ”genome-wide heterozygosity [estimated to] range from 3.2 to 4.2%”  ”Based on 3,653 single-copy orthologous genes, we estimated that different chordate lineages diverged about 592.5 Mya, and three amphioxus  species  diverged  about  99.9  Mya”.  “Using whole-genome resequencing data of between 10 and 48 individuals per sex per species, we identified the sexually differentiated regions (SDR) that harbor [...] excessive  female heterozygotes, and are not shared between the three amphioxus species.  In particular, the SDR of Bf is located on Chr16 and harbors 194 genes; and those of Bj and Bb are located at two different genomic loci of Chr3, harboring 35 genes and one gene with unknown function respectively. Bf Chr16 is not homologous with Chr3 of Bj or Bb.”"]]
+[[!pmid 36867684 desc="Chromosomal assembly of _Branchiostoma floridae_ (Bf),
+_Branchiostoma belcheri_ (Bb) and _Branchiostoma japonicum_ (Bj).  ”we devised
+an interspecific trio sequencing strategy [...] for the F1 hybrids derived from
+Bf-Bb or Bf-Bj crosses. [...] the hybrids contain two haploid parental genomes
+that have become too diverged in sequences to form cross-species chimeric
+assembly”  “The three amphioxus genomes show a highly conserved chromosomal
+synteny to each other, with most chromosomes showing a one-to-one homologous
+relationship except for a few chromosome fusions.”  ”genome-wide heterozygosity
+[estimated to] range from 3.2 to 4.2%”  ”Based on 3,653 single-copy orthologous
+genes, we estimated that different chordate lineages diverged about 592.5 Mya,
+and three amphioxus species diverged about 99.9 Mya”.  “Using whole-genome
+resequencing data of between 10 and 48 individuals per sex per species, we
+identified the sexually differentiated regions (SDR) that harbor [...]
+excessive female heterozygotes, and are not shared between the three amphioxus
+species.  In particular, the SDR of Bf is located on Chr16 and harbors 194
+genes; and those of Bj and Bb are located at two different genomic loci of
+Chr3, harboring 35 genes and one gene with unknown function respectively. Bf
+Chr16 is not homologous with Chr3 of Bj or Bb.”"]]
+
+Mean and confidence interval for divergence times given in Table S2:
+
+ - _B. belcheri_ and _B. japonicum_: 59.3 [12.2, 132.0].
+ - all _Branchiostoma_: 99.9 [22.1, 211.7].
+ - all chordates: 592.5 [530.8, 640.3].  Prior: [514, 636.1].
+ - Euarchontoglires: 116.1 [72.1, 163.1].  Prior: [65.6, 164.6].