Genomics of Neotropical biodiversity indicators: Two butterfly radiations with rampant chromosomal rearrangements and hybridization

Abstract

A central question in evolutionary biology is what drives the diversification of lineages. Rapid, recent radiations are ideal systems for this question because they still show key morphological and ecological adaptations associated with speciation. While most research on recent radiations focuses on those occurring in insular environments, less attention has been given to continental radiations with complex species interactions. Here, we study the drivers of continental radiations of Melinaea and Mechanitis butterflies (Nymphalidae: Ithomiini), which have rapidly radiated in the continental Neotropics. They are classical models for Amazonian biogeography and color pattern mimicry and have been proposed as biodiversity indicators. We generated reference genomes for five species of each genus and whole-genome resequencing data of most species and subspecies covering a wide geographic range to assess phylogeographic relationships, hybridization patterns, and chromosomal rearrangements. Our data help resolve the classification of these taxonomically challenging butterflies and reveal very high diversification rates. We find rampant evidence of historical hybridization and putative hybrid species in both radiations, which may have facilitated their rapid diversification by enriching the genetic diversity. Moreover, we identified dozens of chromosomal fusions and fissions between congeneric species that have likely expedited reproductive isolation. We conclude that interactions between geography, hybridization and chromosomal rearrangements have contributed to these rapid radiations in the highly diverse Neotropical region. We hypothesize that rapid radiations may be spurred if repeated periods of geographic isolation are combined with lineage-specific rapid accumulation of incompatibilities, followed by secondary contact with some gene exchange.

Keywords: Neotropics; biodiversity; butterflies; genomics; speciation.

Fig. 1.

Rampant cytonuclear discordance and a need for taxonomic revision. Cophyloplot showing the nuclear and mitochondrial phylogenies of 135 Mechanitis and 109 Melinaea individuals. Nuclear phylogeny (Left) based on 537,500 sites for Mechanitis (A) and 784,526 sites for Melinaea (B) and full mitochondrial genome phylogeny (Right). The colored circles and connecting lines indicate the currently classified species (25, 28). Br = Brazil; FG = French Guiana; E-Co = eastern Colombia; W-Co = western Colombia; E-Ec = eastern Ecuador; W-Ec = western Ecuador; E-Pe = eastern Peru; Pa = Panama, Su = Suriname. The colored boxes highlight key findings. The node labels show concordance factors, indicating the percentage of trees produced for windows across the genome that contain that node. Full trees (with root) can be found in SI Appendix, Figs. S1–S4.

Fig. 2.

Calibrated phylogeny with evidence of introgression and biogeographic patterns. Time-calibrated BEAST2 phylogenies of Mechanitis (A) and Melinaea (B) with the newly proposed species classification and secondary calibrations from ref. (the asterisk indicates which node was used to calibrate). The node labels indicate the age as obtained by the calibration. One individual was included at the species level, or subspecies-level if they were very divergent. Arrows between clades indicate potential hybridization events (based on AIM, Fbranch, and BPP). “Core” in the Melinaea phylogeny indicates the core clade of fast diverging Melinaea, and “ingroup” is a clade referred to in the text. For each clade, cartoon wings based on representative color patterns are shown, and pink stars exemplify one mimicry ring. The collection location of our individuals is indicated by colored dots and rings on a distribution map based on ref. ; map from USGS, Esri, TANA, DeLorme, and NPS (SI Appendix, Figs. S6 and S7). The region names in the overview map are adapted from ref. . Chromosome numbers are based on ref. or our reference genomes (asterisk). The last column contains boxplots of the altitudinal ranges.

Fig. 3.

Three ancestrally admixed species, with a focus on Mechanitis nesaea. A multispecies coalescent-with-introgression model explored the relation and timing of introgression relative to the divergence times, in (A) Mel. lilis, Mel. idae, and Mel. marsaeus; (B) Mec. menapis, Mec. messenoides, and Mec. polymnia; and (C) the Brazilian Mec. lysimnia lysimnia, Mec. nesaea, and Mec. polymnia casabranca. In (A and B), several replicates produced different outcomes, indicated with “scen1” and “scen2.” Note that estimated divergence time T_T in both second scenarios is more recent than T_S, contrasting with scenario 1 (indicated in red). (D) Overlaid chromatograms of androconial extracts of representative individuals of Mec. nesaea (yellow line), Mec. l. lysimnia (blue), and Mec. polymnia casabranca (orange). Peaks: (1) 4-Hydroxy-3,5,5-trimethylcyclohex-2-enone, (2) Hydroxydanaidal, (3) Methyl hydroxydanaidoate, (4) Methyl farnesoate isomer, (5) Methyl (E,E)-farnesoate, (6) m/z 57, 43, 55, 56, 85, (7) Octadecatrienoic acid (cf.), (8) Octadecanoic acid, (9) Ethyl linolenate, (10) (E)-Phytyl acetate (11) Hexacosene, (12) Heptacosene, (13) Nonacosene (not all compounds of SI Appendix, Table S3 are found in these three individuals). (E) NMDS shows that the androconial chemical bouquet of Mec. nesaea is clearly distinct from sympatric lineages, most similar to Mec. polymnia. (F) A closer look into the restored species Mec. nesaea: phylogenetic relationships, chromosome numbers (50), representative adult and early fifth instar larva (60, 61). The photo of Mec. lysimnia lysimnia is courtesy of Augusto Rosa. (G) f_dM across the genome (20 kb windows) reveals that regions with strong signatures of introgression (f_dM) between Mec. nesaea and Mec. lysimnia (P1 = allopatric polymnia, P2 = nesaea, P3 = lysimnia, P4 = Forbestra) overlap with regions of high differentiation (F_ST) between Mec. nesaea and its sister species Mec. polymnia (orange vertical lines—high F_ST; red dots—high f_dM and high F_ST). Chromosomal breakpoints between Mec. polymnia and the four other reference genomes are shown with blue bars on top.

Fig. 4.

Chromosomal rearrangements. (A) Synteny between Melinaea and Mechanitis chromosomes based on whole genome alignments. Horizontal bars represent individual chromosomes, with sex chromosomes (black bar) and chromosomes involved in within-species fusion–fission polymorphisms (purple bar) highlighted. The cladogram is based on Fig. 2 and shows haploid chromosome numbers in parentheses. (B) Example of differentiation (F_ST) and breakpoints (blue vertical lines) between Mec. mazaeus and Mec. menapis along the genome. The red dots indicate windows coinciding with breakpoints. (C) Examples of HiC-contact maps. Top panel: sex chromosomes in Mec. mazaeus. Lower panel: autosomal fission-fusion heterozygote in Mel. mothone. (D) Matrix displaying the number of fusion–fission rearrangements between species in each genus.