Species as units of biological diversity Molecular Ecology, MUNI, 7. 11. 2024 The concept of species Dobzhansky 1958, Pereira & SInghal Mol. Ecol. 2022 oreproductive communities •colonization, survival ofunctional groups •ecosystems, coexistence ospecies = independent evolutionary lineages ✕evolutionary lineages are: •fractal •possibly ephemeral A diagram of a structure Description automatically generated Dufresnes et al. PNAS 2021 ospecies = independent & persistent evolutionary lineages oevidence: •experimental – in present •statistical – from the past The concept of species African striped mice: Lemniscomys A mouse eating in the dirt Description automatically generated A mouse on a branch Description automatically generated A mouse on a log Description automatically generated A mouse next to a map Description automatically generated Hánová et al. Mol. Phyl. Evol. 2021 Single-locus methods: genetic distances •Matrix of genetic distances •Barcode gap rule of thumb 2% - 11% (Bradley & Baker 2001) → ASAP (Puillandre et al. 2021) Single-locus methods: tree structure •mPTP = multi-rate Poisson tree processes •branchcutting mPTP tree = interspecific backbone + intraspecific crowns exponential distributions of branch lengths Kapli et al. Bioinformatics 2017 branchcutting tree = interspecific backbone + intraspecific crowns backbone = structurally important branches Multi-locus methods reciprocal monophyly? gene tree incongruence! Multi-species coalescent model Rannala et al. 2020, Fig. 2 gene trees vs. species tree Multi-species coalescent model Unended quest •fusions and fissions •post-divergence gene flow •migration •introgression •genealogical distinctiveness •rule of thumb < 0.2, > 0.7 •genomic distribution of introgressed loci? •back to experiments? A diagram of a body with blue lines Description automatically generated Flouri et al. Mol. Biol. Evol. 2020, Fig.2 Software & literature •ASAP •https://bioinfo.mnhn.fr/abi/public/asap/ •mPTP •https://mptp.h-its.org/#/tree •https://github.com/Pas-Kapli/mptp •branchcutting •https://github.com/onmikula/branchcutting •BPP •https://github.com/bpp/bpp •https://github.com/abacus-gene/hhsd •Open Access Book: Phylogenetics in the Genomic Era • https://inria.hal.science/PGE/