Extended Data Fig. 4: Pairwise chromosomal dotplots for halictid species.

Dotplots showing alignment of chromosome-length scaffolds from 16 bee assemblies against the N. melanderi (NMEL) chromosome-length genome assembly. The NMEL reference (generated as part of this study) is shown on the y-axis. The x-axis shows the chromosome-length scaffolds in the respective bee assemblies that have been ordered and oriented to best match the NMEL chromosomes in order to facilitate comparison. The vertical and horizontal lines outline the boundaries of chromosomes in respective species, and the numbers on the axes mark the relevant chromosome name and orientation, with ‘-’ in front of the chromosome name representing a reverse complement to the chromosome sequence as reported in the assembly. Each dot represents the position of a 1000 bp syntenic stretch between the two genomes identified by Progressive Cactus alignments. The colour of the dots reflects the orientation of individual alignments with respect to NMEL (red indicates collinearity, whereas blue indicates inverted orientation). The dotplots illustrate that, with the exception of a few species, highly conserved regions belonging to the same chromosome in one species tend to lie on the same chromosome in other bee species, even though their relative position within a chromosome may change dramatically. This rearrangement pattern accounts for the characteristic appearance of the dotplots with large diffuse blocks of scrambled chromosome-to-chromosome alignments appearing along the diagonal. The pattern is visibly different from those characteristic of mammalian chromosome evolution (for example, see Extended Data Fig. 3). The few exceptions are species with multiple fissions (L. marginatum, L. albipes) and fusions (Augochlora pura, L. vierecki, L. pauxillum, L. malachurum) events. In the fission species, the syntenic regions that belonged to two different chromosomes in one bee species tend to belong to different chromosomes after the fission. The analysis of the fusion species suggests that the regions corresponding to separate chromosomes in the closely related species (and likely the ancestral species) remain separate in the new genome, possibly corresponding to the two chromosome arms. The alignments have been extracted from the hal file using the cactus hal2maf utility with the following parameters: –maxRefGap 500 –maxBlockLen 1000 –refGenome NMEL.