Simoes, N. | Search bioRxiv

bioRxiv2026

Genomic expansion in the dark: A repeat-rich genome of a cave-dwelling remipede sheds light on the evolution of the hexapod sister group.

Remipedes are enigmatic blind, venomous crustaceans endemic to anchialine cave ecosystems (aphotic, hypoxic subterranean environments) and occupy a pivotal phylogenomic position within Pancrustacea as the sister group to Hexapoda. A high-quality genome assembly has long proven elusive for this taxon, due to accessibility challenges and the fragility of remipedes when removed from their habitat. Here we present a highly contiguous, chromosome-level genome assembly for the remipede Xibalbanus tulumensis (Xibalbanidae) spanning 8.05 Gb on 30 chromosome-scale scaffolds, placing it among the largest arthropod genomes reported to date. The protein-coding gene repertoire was highly conserved, with over 97% of arthropod orthologs recovered, and microRNA surveys showed a high level of completeness (94%) relative to pancrustacean genomes. Genome expansion appears to be driven primarily by proliferation of intronic and repetitive elements, which comprise ~71% of the genome. Comparative genomic analyses reveal extensive gene family turnover, with relatively few families showing lineage-specific expansions and contractions. Venom-associated gene families included the remipede-specific Xibalbins, while significant expansion and episodic positive selection affected other venom-associated gene families. Comparative analysis of macrosynteny revealed that the remipede genome retains the signature of ancient fusion-with-mixing events that unite Pancrustacea and Allotriocarida, with considerable similarity in the chromosome architecture of remipedes and basally branching insect orders. Our findings provide the first genomic framework for Remipedia and reveal a highly expanded, repeat-rich genome that retains deep phylogenetic signals in its architecture, despite being adapted to a highly unusual environment.

genomics↗

bioRxiv2021

Topology Testing and Demographic Modeling Illuminate a Novel Speciation Pathway in the Greater Caribbean Sea Following the Formation of the Isthmus of Panama

Recent genomic analyses have highlighted the prevalence of speciation with gene flow in many taxa and have underscored the importance of accounting for these reticulate evolutionary processes when constructing species trees and generating parameter estimates. This is especially important for deepening our understanding of speciation in the sea where fast moving ocean currents, expanses of deep water, and periodic episodes of sea level rise and fall act as soft and temporary allopatric barriers that facilitate both divergence and secondary contact. Under these conditions, gene flow is not expected to cease completely while contemporary distributions are expected to differ from historical ones. Here we conduct range-wide sampling for Pedersons cleaner shrimp (Ancylomenes pedersoni), a species complex from the Greater Caribbean that contains three clearly delimited mitochondrial lineages with both allopatric and sympatric distributions. Using mtDNA barcodes and a genomic ddRADseq approach, we combine classic phylogenetic analyses with extensive topology testing and demographic modeling (10 site frequency replicates x 45 evolutionary models x 50 model simulations/replicate = 22,500 simulations) to test species boundaries and reconstruct the evolutionary history of what was expected to be a simple case study. Instead, our results indicate a history of allopatric divergence, secondary contact, introgression, and endemic hybrid speciation driven by the final closure of the Isthmus of Panama and the strengthening of the Gulf Stream Current ~3.5 million years ago. The history of this species complex recovered by model-based methods that allow reticulation differs from that recovered by standard phylogenetic analyses and is unexpected given contemporary distributions. The geologically and biologically meaningful insights gained by our model selection analyses illuminate a novel pathway of species formation that resulted from one of the most biogeographically significant events in Earths history.

evolutionary biology↗