Caudata macrogenetics: Species range size predicts intraspecific genetic variation in global salamanders

Amador, L.; Wiley, D. L. F.; Arroyo-Torres, I.; McDaniels, C. X.; Rosario-Sanchez, E. O.; Farmer, H.; Bradley, H.; Erdmann, J.; Pelletier, T. A.; Barrow, L. N.

doi:10.1101/2025.01.24.634750

bioRxiv · 10.1101/2025.01.24.634750

Caudata macrogenetics: Species range size predicts intraspecific genetic variation in global salamanders

Amador, L.·Wiley, D. L. F.·Arroyo-Torres, I.·McDaniels, C. X.·Rosario-Sanchez, E. O.·Farmer, H.·Bradley, H.·Erdmann, J.·Pelletier, T. A.·Barrow, L. N.

View original source ↗Export metadata ↓

Abstract

AimGenetic diversity contains valuable information about ecological and evolutionary aspects of species. Intraspecific genetic variation is shaped by species natural history traits and by characteristics of geography and climate within their ranges. Amphibians are of ecological and conservation interest because of their global distribution, deep history, trait diversity, and roles within ecological communities. Here, we studied genetic variation within salamanders to investigate predictors of nucleotide diversity and spatial patterns of genetic differentiation. LocationGlobal. Time PeriodPresent. Major Taxa StudiedSalamanders. MethodsWe repurposed mitochondrial DNA sequences and ecological data from open-access databases for 220 salamander species. We calculated nucleotide diversity ({pi}) and tested for isolation by distance (IBD) and isolation by environment (IBE). We analyzed these three variables with random forest and phylogenetic comparative methods using 28 predictors expected to be associated with genetic variation. ResultsWe recovered 8,108 Cytb sequences with their associated geographic coordinates, of which 7,007 sequences were manually curated by us. Range size, lineage age, and sample size were important predictors of genetic variation. We found higher diversity in regions including the Neotropics and central-eastern Europe. The absence of phylogenetic signal in {pi}, IBD, and IBE suggests that genetic variation is shaped by local ecological and geographical factors rather than by shared ancestry. Main ConclusionsOur finding of range size as an important predictor aligns with theoretical expectations that species with larger ranges tend to harbor more genetic diversity. Furthermore, lineage age being an important predictor is in line with the clade-age hypothesis, in which species with longer divergence times have higher genetic diversity because they have had more time to accumulate genetic variation. Our results underscore the importance of integrating spatial data into macrogenetic studies, providing valuable information for future studies and conservation strategies targeting regions with high or low genetic diversity.

Explore related subjects

evolutionary biology Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Amador, L., Wiley, D. L. F., Arroyo-Torres, I., McDaniels, C. X., Rosario-Sanchez, E. O., Farmer, H., Bradley, H., Erdmann, J., Pelletier, T. A., Barrow, L. N.. 2025-01-27. Caudata macrogenetics: Species range size predicts intraspecific genetic variation in global salamanders. https://doi.org/10.1101/2025.01.24.634750

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

KEEP EXPLORING

Related preprints

bioRxiv2026

Isoform inflation and annotation heterogeneity can confound Kunitz-repertoire comparisons in blood-feeding animals: a gene-level reappraisal

Hematophagy has arisen independently many times across Metazoa, and recurrent anticoagulant protein families in blood-feeders are often read as convergent recruitment - the Kunitz/BPTI domain a paradigm case, with the leech an oft-cited low-Kunitz exception. We re-examine this at the gene level and ask whether a confirmatory cross-phylum test of this blood-feeding/anticoagulant association is feasible with public genomes. Applying an auditable gene-level protocol (one longest-isoform representative per gene; conservation-checked protein to gene mapping) to eight metazoan lineages, we find no consistent, universal elevation of whole-genome gene-level Kunitz-repertoire size in these blood-feeders (blood-feeder median 18 genes vs non-blood-feeder median 39; a descriptive comparison of non-independent taxa, not a formal test). Protein-entry counts inflate gene-level Kunitz counts by up to ~4.6x (mosquito 23 to 5), and neither this inflation nor proteome-wide isoform density (1.0-2.7x) tracks diet, so protein-entry comparisons are an unreliable basis for repertoire claims. Separately, deterministic bookkeeping under a fixed topology and a no-reversal rule counts 12 independent blood-feeding origins (11 if the ancestral lamprey is treated as parasitic with two losses); a non-exhaustive screen of annotated public genomes yielded only one candidate blood/non-blood pair (bedbug), and, under the pre-registered simulation scenario, only a cross-origin heterogeneity endpoint is attainable within a realistic origin ceiling, and only under strong heterogeneity (among-origin SD >= 3-4). An exploratory, feasibility-grade secretome-composition estimate did not meet the pre-registered criterion. We offer a gene-level, annotation-aware re-analysis, a caution about isoform/annotation bias in cross-phylum comparisons, and an account of what current data can and cannot support.

evolutionary biology↗

bioRxiv2026

Denisovan introgression left differential selection regimes in Humans and Neanderthals on the SLC30A9 gene

Signals of positive selection around the SLC30A9 gene have been reported in human populations outside Africa. Selection likely acted on a highly differentiated single-nucleotide polymorphism, rs1047626, leading to a non-synonymous substitution in the encoded zinc transporter. Because of the striking similarity between the putatively selected SLC30A9 haplotype observed in several current human populations and the Denisovan individual, previous work has proposed adaptive introgression. Yet alternative explanations, including ancient human variation, and the precise archaic source -Neanderthal or Denisovan- remained unresolved. Considering the potentially complex evolution of SLC30A9, we applied Approximate Bayesian Computation (ABC) algorithms coupled to machine learning to investigate the most plausible evolutionary origin of this substitution. After modelling different evolutionary scenarios with forward-in-time simulations, our results highlight that the most probable scenario is a Denisovan origin of the rs1047626 polymorphism. However, the allele likely introgressed into Neanderthals first and was then passed into non-African modern humans. Moreover, the derived allele frequency for rs1047626 across several African populations is consistent with back-to-Africa migrations. Finally, our ABC analyses indicate strong positive selection in East Asian populations and other out-of-Africa populations, whereas in Neanderthal populations, the selection coefficient was probably neutral or slightly deleterious.

evolutionary biology↗

bioRxiv2026

Distinct associative learning abilities for colour and odour in the flower-feeding Drosophila elegans and the fruit-feeding Drosophila melanogaster

Animal behaviour is both innately constrained and shaped by learning. This mosaic organization has evolved in response to species-specific ecological demands and may differ between sensory modalities. Flower-visiting animals are a particularly useful system for investigating the relationship between sensory ecology and learning because they rely on multiple floral cues, particularly odour and colour, to locate food sources. However, it remains largely unexplored whether specialization on floral resources entails divergence in learning abilities across sensory modalities. Drosophila elegans is a flower-feeding species that depends heavily on floral resources throughout its life; adults spend much of their time on flowers and larvae develop on fallen flower leaves. Here, we compared odour-reward and colour-reward associative learning between the flower-feeding D. elegans and the fruit-feeding D. melanogaster. We found that, under conditions of equilibrated motivation, odour- and colour-preference, and using the same sugar reward, D. elegans exhibited poorer odour-reward learning performance but better colour-reward learning performance than D. melanogaster. These results suggest that the modality-specific eligibility of sensory information to enter into associations, known as the 'Garcia-effect' in experimental psychology, can evolve oppositely between species. This highlights the relationship between ecological specialization and mnemonic processing, and shows that biological 'intelligence' is not general.

evolutionary biology↗