Deep-time reticulation and ancient mitochondrial genome capture during the radiation of Jamaican Anolis lizards (Squamata; Iguanidae)

Gene flow and reticulation are increasingly recognized as important
processes in the diversification of many taxonomic groups. With the
increasing ease of collecting genomic data and the development of
multispecies coalescent network approaches, such reticulations can be
accounted for when inferring phylogeny and diversification. Caribbean
Anolis lizards are a classic example of an adaptive radiation in which
species have independently radiated on the islands of the Greater Antilles
into the same ecomorph classes. Within the Jamaican radiation at least one
species, A. opalinus, has been documented to be polyphyletic in its
mitochondrial DNA, which could be the result of an ancient reticulation
event or incomplete lineage sorting. Here we generate mtDNA and
genotyping-by-sequencing (GBS) data and implement gene-tree, species-tree,
and multispecies coalescent network methods to infer the diversification
of this group. Our mtDNA gene-tree recovers the same relationships
previously inferred for this group, which is strikingly different from the
species-tree inferred from our GBS data. Posterior predictive simulations
suggest that our genomic data violate commonly adopted assumptions of the
multispecies coalescent model, so we use network approaches to infer
phylogenetic relationships. The inferred network topology contains a
reticulation event but does not explain the mtDNA polyphyly observed in
this group, however coalescent simulations suggest that the observed mtDNA
topology is likely the result of past introgression. How common a
signature of gene flow and reticulation is across the radiation of Anolis
is unknown; however, the reticulation events that we demonstrate here may
have allowed for adaptive evolution, as has been suggested in other, more
recent adaptive radiations.