Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.64898/2026.07.26.740841

Hierarchical divergence across genomic, phenotypic, and microbiome dimensions in two annual killifish species from Malawi

Joya, T. R.·Warren, P. K.·Thompson, A. W.·Ng'oma, E.
View original source ↗Export metadata ↓

Abstract

Divergence among populations and species commonly occurs across multiple biological levels, yet the extent to which genomic, phenotypic, and ecological dimensions are coupled remains poorly understood. We integrated whole-genome sequencing, multivariate morphology, population-level phylogenetic structure, and gut microbiome composition to evaluate divergence in two allopatric annual killifish species across spatially structured populations in Malawi. Geographic and hydrological structure emerged as the primary axis of divergence, with strong differentiation between species and among populations. Genome-wide analyses revealed consistent clustering among populations in ordination and phylogenetic analyses, indicating pronounced spatial structuring of genomic variation. Although genomic divergence was widespread, exon-level enrichment analyses revealed distinct signatures across evolutionary scales. Divergence within N. kirki was associated primarily with translation-related functions, whereas divergence within N. wattersi involved ATP biosynthesis and physiological homeostasis. Interspecific divergence was enriched for transcription factor activity and transcription factor binding, implicating regulatory evolution as a major component of species differentiation. Morphological variation was likewise strongly structured among populations and aligned with drainage systems and geographic regions but was not correlated with genome-wide genetic differentiation, indicating partial decoupling between genotype and multivariate phenotype. Gut microbiome composition represented a more environmentally responsive layer of divergence, broadly reflecting host species and drainage structure while exhibiting greater overlap among populations. These results support a hierarchical model in which geographic and hydrological structure organize stable genomic divergence, whereas phenotypic and microbiome variation represent increasingly context-dependent and only partially aligned biological layers. Our findings highlight the value of integrating multiple biological levels to understand how evolutionary processes shape divergence in natural populations.

Explore related subjects

evolutionary biologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Joya, T. R., Warren, P. K., Thompson, A. W., Ng'oma, E.. 2026-07-29. Hierarchical divergence across genomic, phenotypic, and microbiome dimensions in two annual killifish species from Malawi. https://doi.org/10.64898/2026.07.26.740841

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

RELAX does not reproduce its own estimates at default settings, and its output does not show it

Selection-intensity estimates from RELAX are reported as a point value of K with a likelihood-ratio P. We report that, at default settings and on data of ordinary size, the program does not reproduce its own fits. Of 27 enzyme entries refitted under two optimiser configurations, none reproduced its log-likelihood to within 0.01 units; the median change was 103 units, the largest over 3,400, and four verdicts reversed. Eighty null orthologues reproduced none. A byte-identical command returned a distinct likelihood on every repetition, single-threaded, across three releases, and on alignments simulated under the fitted model, where 3.3 per cent of replicates reproduced. The documented random-number seed never reaches the generator when assigned on the command line, yet reads back as the value supplied. PAML localises the cause: its two-ratio model, without site classes, reproduced its log-likelihood for all 288 genes; its site-class models agreed for 27 to 67 per cent. The instability follows the mixture over sites, not the program. The output does not show it: 46 of 410 fits ended with a negative likelihood-ratio statistic, impossible under convergence, and 123 of 410 report a K re-estimated under a domain restriction rather than the unconstrained maximum. Of 234 published studies using RELAX, none reported a seed. Seeding while holding the thread count at one reproduced sixty of sixty runs on twenty genes under two releases; the seed alone reproduced none of five, and no documentation states the second condition. We recommend that fits be repeated and their dispersion published.

evolutionary biology↗
bioRxiv2026

Sequential accumulation of adaptive alleles forms an inversion supergene in deer mice

Supergenes are clusters of co-inherited loci that affect multiple or complex phenotypes. Despite the growing number of chromosomal inversions identified as supergenes in natural populations, their molecular basis and evolutionary history often remain obscure. Here, we identified two candidate genes, Slc45a2 and Npr3, within a 41-Mb inversion supergene in the deer mouse (Peromyscus maniculatus) that respectively drive darker coats and longer tails - two traits associated with forest adaptation. Mice homozygous for the inversion (inv/inv) exhibit elevated Slc45a2 expression in melanocytes relative to the congenic standard genotype (std/std), disrupting pheomelanin production. In parallel, downregulation of Npr3 in inv/inv mouse growth plates prolongs postnatal growth of caudal vertebrae, resulting in tail elongation. Population-level analyses further implicate that this supergene arose through the subsequent accumulation of the Npr3 allele within the inversion, rather than by capturing all beneficial mutations at its origin.

evolutionary biology↗
bioRxiv2026

Toxin structure shapes palatability in a chemically defended butterfly

The toxicity of chemical defences is well studied, but the potential contribution of compound structure to predator deterrence remains largely unexplored. Whether predation acts more strongly on toxicity or unpalatability remains largely untested, partly because few systems allow toxin structure to vary independently of quantity. Heliconius sara larvae provide such a system: those reared on Passiflora auriculata sequester cyclopentenyl cyanogenic glucosides (CGs), while those reared on P. biflora biosynthesise comparable quantities of aliphatic CGs. Using two invertebrate predators, Camponotus floridanus ants and Hierodula membranacea mantids, we tested whether this structural difference affects palatability independent of toxicity. Mantids rejected larvae with cyclopentenyl CGs more often than larvae with aliphatic CGs, despite no detectable difference in total CG content. This pattern was mirrored in extract-based assays with ants, independently of cyanide release: extracts with cyclopentenyl CGs remained deterrent, while extracts with aliphatic CGs did not differ in deterrence from water. Live larvae, by contrast, elicited similar responses from ants regardless of CG structure. These results show that variation in toxin structure can strongly affect palatability, with some compounds conferring greater protection than others. This demonstrates the importance of chemical structural diversity in the evolution of chemical defences.

evolutionary biology↗