Units of species and speciation.

<p>The Neo-Darwinian view of the Modern Synthesis is that "speciation genes" are the units driving speciation across the genome. Alternatively, if gene sets (including consortia of genes like plasmids or other mobile genetic elements) are sufficiently decoupled from their host genomes, this will lead to "gene ecology," in which gene sets, not species, determine reproductive isolation and/or adapt to ecological niches. Speciation could also be maintained (or potentially driven) by microbial symbionts or by host genes that select for particular symbionts, resulting in hologenome species. All of these speciation mechanisms can potentially be driven by selection or drift, and the list of units and mechanisms (arrows) is not exhaustive.</p

Models of speciation under different regimes of selection and recombination.

<p>In all models, a single population of chromosomes (circles) splits into two nascent species, distinguishable by sets of genetic differences. At each time point, the most frequent multilocus genotype is shown, but other chromosomes could be segregating in the population at lower frequencies. Different haplotypes (or clonal frames) are shown as black or white circles. The ancestral niche is shown in blue and a new niche in orange. Gene flow (recombination) between species is indicated by horizontal connections between branches. (<b>A</b>) In the simplest model of speciation with gene flow, a single mutation controlling sexual isolation (but not under selection) is the only divergent locus (yellow square), with other loci experiencing gene flow between incipient species. (<b>B</b>) Selection during speciation can produce a pattern of genetic diversity across the genome very similar to (A), but species are expected to be longer-lived. Mutations under selection at early and later stages of speciation are shown as orange stars. (<b>C</b>) Allopatric speciation with a population bottleneck and neutral divergence of species. As in (A), competitive exclusion should lead to the extinction of one species if they come back into contact. (<b>D</b>) Without gene flow, the mutation under selection between species (orange star) will purge diversity genome-wide as it sweeps through one population, resulting in genome-wide divergence from the other population.</p

Transcript of talk by Michael Majerus, Uppsala, 2007

This is Michael Majerus' transcript of the talk he gave at Uppsala, Sweden, on 22 Aug 2007. This is the original PDF format he published on his website

Transcript of talk by Michael Majerus, Uppsala, 2007 (raw ANSI text version)

This is Michael Majerus' transcript of the talk he gave at Uppsala, Sweden, on 22 Aug 2007. This is a raw text version of the PDF file he originally made publi

Slides of talk by Michael Majerus, Uppsala, 2007

Describes the data from the peppered moth that he had collected 2001-2006, including the results from his new experiment and the observations of natural resting sites of the moth

Additional file 1: Figure S1. of Genome-wide introgression among distantly related Heliconius butterfly species

A maximum-likelihood phylogeny of 32 samples combined with dating of the nodes. Divergence times were calibrated using a fast Bayesian approach based on the separation time of melpomene and cydno-timareta clades (1.3 ± 0.1 Mya) and the separation time of H. pachinus from the cydno clade (0.4 ± 0.1 Mya). Samples from H. besckei and H. m. nanna are highlighted in red. Numbers are in million years and blue bars stand for 95 % confidence intervals. Figures S2-S9. Maximum-likelihood phylogenetic trees were constructed for all candidate introgression loci using original windows (5 kb, 10 kb and 50 kb), expanded windows (original 5 kb + 5 kb on either side, original 10 kb + 10 kb on either side) and multiple 10 kb windows within original 50 kb windows. The window size (as shown in each figure) may vary due to actual scaffold length and position. Figure S10. A maximum-likelihood phylogeny of Heliconius butterflies based on the SNP data from the Z chromosome. The cydno-timareta-melpomene clade is grouped with a subset of silvaniform species (highlighted in blue). (PDF 715 kb

Additional file 2: Table S1. of Genome-wide introgression among distantly related Heliconius butterfly species

Sample information and sequencing statistics. Table S2. Results of chromosomal D-statistics. Table S3. D-statistics and f d -statistics for all the predicted candidate introgression loci. Table S4. Results of chromosomal dxy. Table S5. Results of dxy for all the candidate introgression loci. Table S6. Read depth analyses for all the predicted candidate introgression loci among four focal species. Table S7. Results of D-statistics to examine gene flow between other species and H. m. nanna. Table S8. Gene annotations of 41 candidate introgression loci. Table S9. Autosome versus Z chromosome population genetic statistics. (DOCX 123 kb

Supplementary Information

Supplementary data (Tables and Figures) for Kozak et al. 2015

Online Appendix 2 Partitions

Partitions selected by PartitionFinder

Online Appendix 4 starBEAST

Online Appendix 4 starBEAS