Hays, D. | Search bioRxiv

bioRxiv2026

Whole-genome phylogenomics and synteny resolve a single origin of body-plan asymmetry in flatfishes

Flatfishes display the most dramatic asymmetric body plan in vertebrates, yet whether this rare innovation evolved once (flatfish monophyly, FM) or multiple times (flatfish polyphyly, FP) has remained contentious. A recent genome-wide study supported FP by placing Psettodes, the earliest-diverging flatfish lineage, among symmetric relatives within Carangaria, the clade that also includes billfishes, jacks, mahi-mahi, and barracudas. Subsequent work traced this to base-composition artifacts and inadequate substitution modeling. Here we revisit the question using whole-genome phylogenomic and synteny data from 17 carangarian species spanning flatfishes and carangarian relatives. We contribute three new chromosome-level assemblies, including the first for Psettodes. Nucleotide-based coalescent analyses (e.g., ROADIES, CASTER) yield strong support for FM, with Psettodes sister to all other flatfishes. Microsynteny analyses built from conserved gene-order blocks corroborate this result: topology tests, cluster-profile counts, and rearrangement-based trees favor FM over two competing FP topologies. Macrosynteny, based on chromosome-scale rearrangements, yields a more mixed signal, with support for FM depending on the metric and taxon-sampling scheme. We interpret this scale-dependent pattern in the context of the explosive post-Cretaceous radiation of Carangaria. The short intervals between speciation events that characterize rapid radiations appear to have left sufficient signal in fine-grained microsyntenic rearrangements, while chromosome-scale rearrangements were too rare to consistently resolve these closely spaced splits. When integrated with evidence from conserved developmental mechanisms active during metamorphosis, the stage at which flatfish asymmetry first emerges, and from the exceptionally complete fossil record, our multi-scale genomic evidence supports a single evolutionary origin of flatfish asymmetry.

evolutionary biology↗

bioRxiv2026

Competition among freshwater clades explains cave colonization in blind cavefishes

Flatfishes display the most dramatic asymmetric body plan in vertebrates, yet whether this rare innovation evolved once (flatfish monophyly, FM) or multiple times (flatfish polyphyly, FP) has remained contentious. A recent genome-wide study supported FP by placing Psettodes, the earliest-diverging flatfish lineage, among symmetric relatives within Carangaria, the clade that also includes billfishes, jacks, mahi-mahi, and barracudas. Subsequent work traced this to base-composition artifacts and inadequate substitution modeling. Here we revisit the question using whole-genome phylogenomic and synteny data from 17 carangarian species spanning flatfishes and carangarian relatives. We contribute three new chromosome-level assemblies, including the first for Psettodes. Nucleotide-based coalescent analyses (e.g., ROADIES, CASTER) yield strong support for FM, with Psettodes sister to all other flatfishes. Microsynteny analyses built from conserved gene-order blocks corroborate this result: topology tests, cluster-profile counts, and rearrangement-based trees favor FM over two competing FP topologies. Macrosynteny, based on chromosome-scale rearrangements, yields a more mixed signal, with support for FM depending on the metric and taxon-sampling scheme. We interpret this scale-dependent pattern in the context of the explosive post-Cretaceous radiation of Carangaria. The short intervals between speciation events that characterize rapid radiations appear to have left sufficient signal in fine-grained microsyntenic rearrangements, while chromosome-scale rearrangements were too rare to consistently resolve these closely spaced splits. When integrated with evidence from conserved developmental mechanisms active during metamorphosis, the stage at which flatfish asymmetry first emerges, and from the exceptionally complete fossil record, our multi-scale genomic evidence supports a single evolutionary origin of flatfish asymmetry.

evolutionary biology↗

bioRxiv2026

High specificity meets genomic flexibility in the Siphamia-Photobacterium symbiosis

Host-microbe symbioses must balance partner specificity with enough flexibility to remain adaptable to environmental change. The Siphamia-Photobacterium symbiosis exemplifies this balance, as tropical siphonfish (Siphamia spp.) form a highly specific association with the bioluminescent bacterium Photobacterium mandapamensis, though it is unknown whether this specificity extends to temperate species of siphonfish. Here, we use long-read genome sequencing and functional assays to characterize the strain-level diversity of symbionts isolated from two temperate siphonfish hosts, Siphamia cephalotes and Siphamia roseigaster, and compare them to tropical isolates. We found that both hosts exclusively associate with P. mandapamensis in their light organs and that temperate strains form host-specific clades despite being collected in close proximity (< 5km). This is consistent with selective host filtering, microhabitat-driven adaptation, or conspecific host seeding. Pangenome analyses showed notable differences in accessory gene content, variation in the lux-rib operon, and a dramatic expansion of mobile genetic element (MGE) content in a subset of strains. We also identified the first host-derived P. mandapamensis isolate that is non-luminescent under laboratory conditions despite an intact lux-rib operon. Luminescence varied across strains, salinities, and temperature but was not correlated with the presence of luxF, with the majority of high-MGE strains exhibiting reduced light output. Together, these results extend the specificity of the Siphamia-Photobacterium symbiosis into temperate hosts and show that animals can maintain tight symbiont specificity despite the symbiont harboring substantial genomic and phenotypic flexibility at the strain level.

microbiology↗