The names of meiosis-specific proteins are highlighted in green. Exact stoichiometry is not implied. In meiosis I, cohesins bind to sister chromatids (A), after which double-strand DNA breaks are made by Spo11 (accessory proteins not shown) and the axial elements (Hop1) of the synaptonemal complex are formed (B). Double strand break repair is initiated (coupled with (B) in S. cerevisiae) and Hop1 forms lateral elements of the synaptonemal complex (C). Strand exchange proteins are attracted to the double-strand break (accessory proteins not shown) (D). The resulting heteroduplex (E) may be resolved by crossovers, which utilize meiosis-specific proteins (F), or by gene conversion, which does not (G, proteins not shown). This model is based primarily upon details from S. cerevisiae, but includes details from mammals for Msh4 and Msh5, and speculates on the role of Drosophila Mei-9 (Rad1) in (F) as reviewed by [54], [97]–[100]. Table 1 gives additional details and references.

All trees shown are the consensus tree topologies determined from ≥700 best trees (i.e. those with the highest posterior probabilities) inferred by Bayesian analysis using alignments of inferred proteins. Animals are indicated in red text, fungi brown, ‘Amoebozoa’ teal, ‘Archaeplastida’ in green, Alveolates plum, ‘Chromista’ purple, ‘Excavata’ blue and prokaryotes shown in black. Branches with the best support – i.e., those with 0.95 to 1.00 Bayesian posterior probabilities – have thicker lines. Numbers at the nodes indicate Bayesian posterior probability followed by percent bootstrap support from 100 replicates of PROML. An asterisk (*) denotes topological constraints placed upon the nodes uniting Fungi and Opisthokonts for Bayesian analysis. Scale bars represent 0.1 amino acid substitutions per site. Details for each tree and the accession numbers for all sequences are provided in Figures S1.1–S1.4 in Supporting Information File S1. (A) Hop2 homologs, unrooted. 167 aligned amino acid sites were analyzed, this consensus topology derived from 900 trees, α = 3.86 (2.71<α<5.37), pI = 0.014 (0.0004<pI<0.051) and lnL = −8363.01. (B) Mnd1 homologs, unrooted. 202 aligned amino acid sites were analyzed, this consensus topology derived from 850 trees, α = 2.80 (2.18<α<3.52), pI = 0.01 (0.0005<pI<0.043) and lnL = −11589.94. (C) Spo11 homologs, rooted with the eukaryotic Top6A paralog outgroup. 148 aligned amino acid sites were analyzed, this consensus topology derived from 700 trees, α = 1.76 (1.34<α<2.23), pI = 0.10 (0.03<pI<0.17) and lnL = −10624.08. (D) Mer3 homologs unrooted. 610 aligned amino acid sites were analyzed, this consensus topology derived from 950 trees, α = 1.60 (1.39<α<1.83), pI = 0.04 (0.02<pI<0.06) and lnL = −27086.67.