Divergence-time estimation

We should be worried that different molecular dating analyses can give dramatically different answers, even when applied to similar -or even identical- data sets .” (L. Bromham, 2020, p.59) 


The future prospects of chronotaxonomics are critically dependent on advances in divergence-times estimation comprising the following principal steps: 

  1. Selection of orthologous genes. 
  2. Evaluation of genetic differences.
  3. Transformation into divergence-time estimates. 

Selection of genes

Today, divergence-time estimates are mostly based on a limited number of mitochondrial genes. In the future, long UCEs or universal single-copy orthologs (USCOs) might serve as nuclear markers for species delimitation and higher-level zoological classification (Dietz et al. 2023a,b; Musher et al. 2024). 

Evaluation of genetic differences

Molecular sequence data only provide information on genetic distances. The absolute time of divergence however cannot be inferred because nucleotide substitution rates vary. 

Transformation into divergence times

The fact that the average rate of molecular evolution differs from gene to gene and from taxon to taxon makes inference of evolutionary time from genetic differences challenging. 

References

Ahrens D (2023), Species diagnosis and DNA taxonomy, In: DNA barcoding: methods and protocols, Desalle R (ed.), preprint (free pdf) 

Berv JS, and Field DJ (2017), Genomic signature of an avian Lilliput effect across the K-Pg extinction, Syst. Biol. 67, 1-13. (free pdf)

Bromham L (2020) Causes of variation in the rate of molecular evolution, In: The Molecular Evolutionary Clock, Ho SYW (ed.), chapter 4, p. 45-64. Springer, Cham. (abstract)

Dietz L, Eberle J, Mayer C, Kukowka S, Bohacz C, Baur H, Espeland M, Huber BA, Hutter C, Mengual X, Peters RS, Vences M, Wesener T, Willmott K, Misof B, Niehuis O, and Ahrens D (2023a), Standardized nuclear markers improve and homogenize species delimitation in Metazoa, Methods Ecol. Evol. 14, 543-555. (pdf)

Dietz L, Mayer C, Stolle E, Eberle J, Misof B, Posiadlowski L, Niehuis O, and Ahrens D (2023b), Metazoa-level USCOs as markers in species delimitation and classification, Mol. Ecol. Resour. 00, e:13921. (pdf) 

Ericson PGP, Klopfstein S, Irestedt M, Nguyen JMT, and Nylander JAA (2014), Dating the divergences of the major lineages of Passeriformes (Aves), BMCEvol. Biol. 14, e:8. (free pdf)

Lovette IJ (2004), Mitochondrial dating and mixed support for the “2% rule” in birds, Auk 121, 1-6. (free pdf) 

Musher LJ, Catanach TA, Valqui T, Brumfield RT, Aleixo A, Johnson KP, and Weckstein JD (2024), Whole-genome phylogenomics of the tinamous (Aves: Tinamidae): comparing gene tree estimation error between BUSCOs and UCEs illuminates rapid divergence with introgression, bioRxiv (pdf)