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<title>bioRxiv Subject Collection: Evolutionary Biology</title>
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This feed contains articles for bioRxiv Subject Collection "Evolutionary Biology"
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<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.29.721737v1?rss=1">
<title>
<![CDATA[
Heterogeneous associations between sex ratio distorters and mitochondrial haplotypes in U.S. populations of Armadillidium vulgare 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.29.721737v1?rss=1
</link>
<description><![CDATA[
Sex ratio distorters (SRDs) are heritable elements that bias offspring sex ratios to enhance their transmission. In the terrestrial isopod Armadillidium vulgare, feminization of genetic males can occur through vertical transmission of the sex ratio distorter known as the f-element, as well as through infection by Wolbachia, a maternally inherited bacterial endosymbiont that can alter host reproduction. Previous studies have focused on the distribution of SRDs and their associations with mitochondrial haplotypes in native European populations, but these patterns are poorly understood in the United States. In this study, we sampled A. vulgare in 12 states, screening individuals for Wolbachia infection, the presence of the f-element, and mitochondrial haplotypes. We found that Wolbachia shows a heterogeneous distribution across populations and haplotypes, in contrast with stronger associations in Europe. The f-element occurred in lower overall frequencies but showed a strong association with mitochondrial haplotype VI. These results indicate that patterns associated with SRD differ from those observed in Europe and suggest that multiple introductions and population mixing have shaped these distributions.
]]></description>
<dc:creator><![CDATA[ Kansal, A., Kuhn, R. ]]></dc:creator>
<dc:date>2026-05-06</dc:date>
<dc:identifier>doi:10.64898/2026.04.29.721737</dc:identifier>
<dc:title><![CDATA[Heterogeneous associations between sex ratio distorters and mitochondrial haplotypes in U.S. populations of Armadillidium vulgare]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-05-06</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.05.04.720205v1?rss=1">
<title>
<![CDATA[
The Culicinae are Monophyletic and Ancient: A response to Pierce et al. 2025 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.05.04.720205v1?rss=1
</link>
<description><![CDATA[
Mosquitoes are classified into two subfamilies, each monophyletic, and typically considered to both be ancient, having diverged more than 100 million years ago based on previous divergence analyses. A recent publication challenged this view with phylogenomic results primarily from the third codon position and UCEs. Utilizing alternative fossil placement and these phylogenomic data, these authors find that the Culicidae and Chaoboridae diverged in the lower Cretaceous, and that one mosquito subfamily, the Anophelinae, is nested within the Culicinae. These results are in stark contrast to previous results from diverse data sources, ranging from other genomic data, to morphology, to fossils. Here, we briefly detail the substantial evidence that supports two monophyletic subfamilies of extant mosquitoes, along with fossil evidence that supports the ancient divergence of these lineages.
]]></description>
<dc:creator><![CDATA[ Soghigian, J., Morinaga, G., Yeo, H., Wilkerson, R., Linton, Y.-M., Sallum, M. A., Sharakov, I., Sharakova, M., Laurito, M., Bang, W. J., Shin, S., Snyman, L., Zavortink, T., Sither, C., Reiskind, M., Wiegmann, B. ]]></dc:creator>
<dc:date>2026-05-06</dc:date>
<dc:identifier>doi:10.64898/2026.05.04.720205</dc:identifier>
<dc:title><![CDATA[The Culicinae are Monophyletic and Ancient: A response to Pierce et al. 2025]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-05-06</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.05.05.723056v1?rss=1">
<title>
<![CDATA[
The crop pathogen Blumeria hordei exhibits genome-wide pervasive selective and neutral sweepstakes reproduction signatures. 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.05.05.723056v1?rss=1
</link>
<description><![CDATA[
The fungal crop pathogen Blumeria hordei, causal agent of powdery mildew on barley, presents life-history and epidemiological characteristics, as well as and selective pressures due to modern agriculture leading to expected sweepstakes reproduction, that is highly skewed offspring distributions. Using genome-wide polymorphism data and population genomics inferences, we aim to 1) infer the past demographic history and the strength of sweepstakes reproduction in B. hordei, and 2) quantify the contributions of these selective and neutral processes in the genome. An new inference method based on Neural Posterior Estimation and diversity and linkage disequilibrium statistics was developed and tested on simulated and B. hordei genomic data. We confirm that B. hordei exhibits a moderate sweepstakes reproduction (alpha-parameter of 1.6). We highlight that the Site Frequency Spectrum (SFS) appears sensitive to the joint occurrence of sweepstakes and recent demographic changes, which may caution on the reliability of the SFS to infer sweepstakes reproduction. We then scan the genome for selective sweeps, adjusting the significance thresholds of the methods for demographic history and sweepstakes reproduction, thereby yielding a counterintuitive result. When conditioning the significance threshold for sweep detection on simulations under sweepstakes and demography, a very large number of putatively selected regions is found (11.6% of the genome). We suggest that sweepstakes reproduction in B. hordei is due to 1) neutrality (clonal/sexual phases and Boom-and-Bust cycles) generating a genome-wide level of background noise in the coalescent genealogies, and 2) selective sweepstakes due to pervasive positive selection. Our findings have important implications for both population genomic methodology and our understanding of pathogen evolution.
]]></description>
<dc:creator><![CDATA[ Anderson, M., Wingen, L. U., Biggemann Troche, B., Liu, X., Mueller, M. C., Hueckelhoven, R., Tellier, A. ]]></dc:creator>
<dc:date>2026-05-06</dc:date>
<dc:identifier>doi:10.64898/2026.05.05.723056</dc:identifier>
<dc:title><![CDATA[The crop pathogen Blumeria hordei exhibits genome-wide pervasive selective and neutral sweepstakes reproduction signatures.]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-05-06</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.05.04.721291v1?rss=1">
<title>
<![CDATA[
Ancestral Musaceae karyotype reconstruction provides insights into chromosome evolution and bract coloration 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.05.04.721291v1?rss=1
</link>
<description><![CDATA[
The banana family (Musaceae) exhibits remarkable diversity in both karyotype structure and bract coloration, yet the evolutionary dynamics of chromosomes and the genomic and regulatory basis of color diversification remain poorly understood. Here, we present a telomere-to-telomere (T2T), gap-free genome assembly of Musa exotica, an ornamental species with brightly colored bracts occupying a basal position in sect. Callimusa (Musa L.). By integrating this high-quality genome with other Musaceae genomes, we reconstruct the ancestral Musaceae karyotype (AMK) for the first time, inferring a haploid chromosome number of n = 17. Comparative genomic analyses reveal that extant Musaceae lineages have undergone recurrent, lineage-specific inter-chromosome rearrangements, leading to stepwise reductions in chromosome number to n = 11, 10, and 9. Notably, closely related species share similar rearrangement patterns, indicating conserved evolutionary trajectories shaped by lineage-specific structural remodeling. Strikingly, rearrangement-associated regions are enriched in functionally important genes, particularly structural genes (CHS and F3H) and regulatory transcription factors (MYB and bHLH) involved in the anthocyanin biosynthesis pathway. Integrative transcriptomic and regulatory analyses demonstrate coordinated activation of anthocyanin biosynthetic genes (CHS, CHI, F3'5'H, and ANS) in bracts, with expression divergence largely decoupled from gene dosage and predominantly driven by transcriptional regulation. Co-expression analyses reveal extensive MYB- and bHLH-enzyme interactions, underscoring their central role in modulating pathway activity and bract coloration diversity. Together, our findings provide evidence linking genome structural evolution to trait diversification, offering a refined framework for understanding genome evolution and phenotypic diversification in Musaceae and other monocots.
]]></description>
<dc:creator><![CDATA[ Fu, N., Sun, P., Liu, X., Liu, T.-J., Wang, Y.-B., Li, W.-M., Xiao, T.-W., Li, X.-N., Mi, Y.-Y., Wang, Z.-F., Rouard, M., Ge, X.-J., Huang, H.-R., Wang, X. ]]></dc:creator>
<dc:date>2026-05-06</dc:date>
<dc:identifier>doi:10.64898/2026.05.04.721291</dc:identifier>
<dc:title><![CDATA[Ancestral Musaceae karyotype reconstruction provides insights into chromosome evolution and bract coloration]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-05-06</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.05.04.722624v1?rss=1">
<title>
<![CDATA[
Assessing the Efficacy of Computational Workshops and Participatory Live Coding in Evolutionary Biology 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.05.04.722624v1?rss=1
</link>
<description><![CDATA[
Computational workshops are common in evolutionary biology and are used to share discipline-specific tools and skills with researchers. Despite the perceived importance of these workshops, there is no common set of criteria for workshop success, and there are few peer-reviewed studies investigating the efficacy of workshops or assessing the value of particular instructional techniques in this context. Here, we focused on one key element of a successful workshop: its ability to increase participants' motivation to use the methods and tools presented during the workshop. We analyzed the goals, perceptions, and future plans of research practitioners engaging in a workshop on phylogenetic methods of historical biogeography using pre- and post-workshop surveys. Overall, the workshop was successful at motivating participants, and survey responses provided insights into participants' perceptions of different activities, including "participatory live coding". Apart from this case study, we aim to highlight the importance of developing a common set of workshop goals in collaboration with other workshop stakeholders and the need for specialized, validated tools for assessing the efficacy of computational workshops for researchers.
]]></description>
<dc:creator><![CDATA[ Swiston, S. K., Kuehne, L., Moore, R., Landis, M. J. ]]></dc:creator>
<dc:date>2026-05-06</dc:date>
<dc:identifier>doi:10.64898/2026.05.04.722624</dc:identifier>
<dc:title><![CDATA[Assessing the Efficacy of Computational Workshops and Participatory Live Coding in Evolutionary Biology]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-05-06</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.05.04.722668v1?rss=1">
<title>
<![CDATA[
Morphological integration of the avian beak facilitates evolution along lines of least resistance 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.05.04.722668v1?rss=1
</link>
<description><![CDATA[
Innovation of the avian beak has facilitated a grand radiation of >11,000 species, with vast morphological disparity suggesting limited developmental constraints on beak diversification. We assess four macroevolutionary currencies: integration, disparity, phenotypic evolutionary rates, and ecological specialization, using 3D beak landmarks for 8,627 species mapped to a complete avian supertree with a resolved genomic backbone. We introduce a Gini coefficient-based metric of ecological specialization, measuring evolutionary time spent across trophic niches. Phylogenetic regressions show that lineages with faster phenotypic rates exhibit stronger beak integration (landmark covariation) and more generalised diets, while beak disparity declines with greater trophic specialization. These results suggest that integration facilitates, rather than constrains, phenotypic evolution, by channeling variation along lines of least resistance. Future work should explore modular structure of the bird beak, which arises from multiple genetic and developmental factors.
]]></description>
<dc:creator><![CDATA[ Ely, R., Sommer, S., Hipsley, C. ]]></dc:creator>
<dc:date>2026-05-06</dc:date>
<dc:identifier>doi:10.64898/2026.05.04.722668</dc:identifier>
<dc:title><![CDATA[Morphological integration of the avian beak facilitates evolution along lines of least resistance]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-05-06</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.05.03.722549v1?rss=1">
<title>
<![CDATA[
The Longest 3D-preserved Plumage Reveals Stepwise Pennaceous Feather Evolution 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.05.03.722549v1?rss=1
</link>
<description><![CDATA[
Powered flight is a critical innovation associated with the evolutionary transition from non-avialan theropods to birds, yet how early feathers gave rise to modern pennaceous feather structures with optimized aerodynamic performance remains unclear. Here we report a three-dimensionally preserved pennaceous feather from the Burmese amber (~99 Ma) that exceeds 105 mm in preserved length, representing the longest known feather preserved in amber. It shows symmetrical vanes with densely packed barbs, indicating a derived pennaceous branching architecture, but lacks interlocking barbules and exhibits incompletely differentiated rachis and barbs, implying limited aerodynamic performance. This combination of advanced branching organization and incomplete tissue differentiation indicates asynchronous evolution of pennaceous feathers, in which branching organization, elongation and vane organization preceded the acquisition of interlocking barbules and fully differentiated cortical and medullary tissues required for aerodynamic function. These findings provide direct fossil evidence for stepwise, modular evolution of pennaceous feathers. They suggest that aerodynamic optimization of flight-related feather structures may not have been the primary driver of pennaceous feather branching.
]]></description>
<dc:creator><![CDATA[ Zhang, Y., Tang, J., Jagielska, N., WANG, S. ]]></dc:creator>
<dc:date>2026-05-06</dc:date>
<dc:identifier>doi:10.64898/2026.05.03.722549</dc:identifier>
<dc:title><![CDATA[The Longest 3D-preserved Plumage Reveals Stepwise Pennaceous Feather Evolution]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-05-06</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.05.03.722455v1?rss=1">
<title>
<![CDATA[
Emergence of meniscus-guided movement in drosophilid larvae through posture-dependent capillary forces 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.05.03.722455v1?rss=1
</link>
<description><![CDATA[
Freshwater habitats cover only ~1% of the Earth surface yet harbor approximately 10% of all animal species, of which ~60% are insects, making them hotspots of biodiversity. However, tractable model systems to investigate how insects transition to aquatic environments remain limited. Here, we show that larvae of Scaptodrosophila dorsocentralis, but not related species including Drosophila melanogaster, move along the water meniscus by exploiting surface tension, enabling them to reach nearby objects. This movement is achieved through a sequence of actions: larvae adopt an S shaped body posture by extending the posterior body, anchor at the air water interface, and generate propulsive forces by elevating the anterior end while depressing the posterior end. Larvae successfully reach and land on nearby objects via meniscus guided movement even under flowing conditions, whereas other species fail to do so, indicating ecological relevance. A biomimetic PDMS (polydimethylsiloxane) model recapitulates this movement without external actuation, demonstrating that body configuration alone is sufficient to generate capillary driven motion. We further show that posterior elongation is mediated by a folding and unfolding mechanism driven by hydrostatic pressure. These results establish a tractable system for studying water surface locomotion and provide mechanistic insight into how terrestrial insects may acquire the capacity to exploit water surface environments.
]]></description>
<dc:creator><![CDATA[ Matsunaga, T., Nose, A. ]]></dc:creator>
<dc:date>2026-05-06</dc:date>
<dc:identifier>doi:10.64898/2026.05.03.722455</dc:identifier>
<dc:title><![CDATA[Emergence of meniscus-guided movement in drosophilid larvae through posture-dependent capillary forces]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-05-06</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.05.01.722204v1?rss=1">
<title>
<![CDATA[
Weber's law of proportional processing influences coevolution of ornaments and preferences in models of sexual selection 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.05.01.722204v1?rss=1
</link>
<description><![CDATA[
Mate preferences are often influenced by the magnitude of sexual signals, which are presumed to indicate underlying aspects of signaller quality. Although the perception of these signals depends on sensory processes, the role of perceptual adaptations and constraints in mate assessment is frequently overlooked. Many sensory systems follow Weber's law of proportional processing, where discrimination between signals is based upon their proportional, or relative, difference rather than their absolute difference. Because preference strength varies with relative trait magnitude, Weber's law could strongly influence sexual selection, changing the coevolution of traits and preferences. Here, we explore the consequences of Weber's law for sexual selection using individual-based models, applying Scalar Utility Theory to mate choice. We investigate the coevolution of male ornaments and female preferences under both Fisherian and good genes scenarios, as well as scrutinizing the sexual selection of multiple ornaments and preferences. Including Weber's law in these models either reduced ornament exaggeration, or promoted exaggeration and diversification of ornaments and preferences, depending on the costs of choice and how rapidly female survival decreases when preferences evolve away from the naturally selected optimum. These results highlight the importance of perception and cognitive processing in shaping sexual selection and its evolutionary impacts.
]]></description>
<dc:creator><![CDATA[ Bullough, K., Kelley, L., Kuijper, B. ]]></dc:creator>
<dc:date>2026-05-05</dc:date>
<dc:identifier>doi:10.64898/2026.05.01.722204</dc:identifier>
<dc:title><![CDATA[Weber's law of proportional processing influences coevolution of ornaments and preferences in models of sexual selection]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-05-05</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.05.01.722148v1?rss=1">
<title>
<![CDATA[
Evolutionary divergence and adaptive potential of scototaxis in juvenile Trinidadian Guppies 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.05.01.722148v1?rss=1
</link>
<description><![CDATA[
Matching habitat choice provides a mechanism for individuals to maximise their expected fitness by selecting an environment that better fits their phenotype. Many animals choose their local environment by evaluating levels of perceived predation risk against possible resource gain. To test if predation risk is a major driver of habitat choice, we quantify scototaxis, or preference for dark versus light backgrounds, in juvenile guppies. As light backgrounds increase visibility to predators, this aspect of habitat choice captures variation in boldness in small fishes. By rearing and testing 586 fish descended from ten natural populations from Trinidad under common garden conditions, we first quantify (broad sense) heritable variation, i.e. evolutionary potential, within populations. Next, we test for evolutionary divergence among populations in mean preference, and if present, whether ancestral predation regime is a mediator of divergence. Finally, we ask whether families and/or populations differ in the amount of behavioural variation they contain. Habitat choice varied among families (12% of total variance), consistent with heritable variation (0.2). We also found mean preference varies among populations (11% of total variance explained). Evolutionary divergence among-populations is partly explained by ancestral predation regime, with populations from low-predation sites showing a stronger average preference for dark backgrounds than high-predation populations from the same river. Additionally, we find that within-population behavioural variation is greater in high-predation populations. We conclude that guppy populations contain heritable variation that could facilitate adaptive evolution if scototaxis is subject to natural selection. Furthermore, while genetic drift may also contribute to evolutionary divergence among-populations, observed patterns are qualitatively consistent with local adaption to predation regime. Our results suggests that high predation sites favour 'bolder' habitat choice on average, but also that local predation regime shape the evolutionary dynamics of variation, perhaps by maintaining shy-bold variation among-individuals or by favouring individuals with less-predicable behaviour.
]]></description>
<dc:creator><![CDATA[ Phelps, E. C., Yong, L., Prentice, P., Fraser, B. A., Postma, E., Wilson, A. J. ]]></dc:creator>
<dc:date>2026-05-05</dc:date>
<dc:identifier>doi:10.64898/2026.05.01.722148</dc:identifier>
<dc:title><![CDATA[Evolutionary divergence and adaptive potential of scototaxis in juvenile Trinidadian Guppies]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-05-05</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.30.722031v1?rss=1">
<title>
<![CDATA[
The lack of simplicity in sequence-fitness relationships 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.30.722031v1?rss=1
</link>
<description><![CDATA[
Gene interactions play an important role in the development of antimicrobial drug resistance and other evolutionary processes of medical importance. Empirical studies have revealed multiple peaks, inaccessible trajectories, and constraints on mutation order. Higher order epistasis is associated with obstacles in fitness landscapes. However, its importance has been debated in recent years, sometimes through reinterpretations of data from previous publications. We suggest that local higher order interactions may help reconcile these seemingly contradictory findings. Rank order based methods can be informative when other methods fail to detect consequential interactions. In addition to conventional rank order methods, including sign epistasis, we introduce signed bipyramids as indicators of interactions.
]]></description>
<dc:creator><![CDATA[ Crona, K., Greene, D. ]]></dc:creator>
<dc:date>2026-05-05</dc:date>
<dc:identifier>doi:10.64898/2026.04.30.722031</dc:identifier>
<dc:title><![CDATA[The lack of simplicity in sequence-fitness relationships]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-05-05</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.30.721997v1?rss=1">
<title>
<![CDATA[
Misleading inference of schistosome epidemiology from ribosomal internal transcribed spacer (ITS) and mitochondrial DNA 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.30.721997v1?rss=1
</link>
<description><![CDATA[
The nuclear, internal transcribed spacer (ITS) and mitochondrial cox1 markers are widely used to differentiate Schistosoma haematobium from its livestock counterparts, S. bovis and S. curassoni. Schistosoma isolated from humans that have ITS and cox1 markers from livestock schistosomes are typically inferred as zoonotic infections, those with mixed species, heterozygous ITS are classified as F1s or recent hybrids, while those with discordant ITS and cox1 markers are considered to reflect older hybridization events. We evaluated the reliability of this classification scheme by genotyping ITS and cox1 from 132 parasites isolated from human urine, and from 37 adult schistosomes collected from cattle at 14 Nigerian locations. We also genome sequenced each sample to empirically determine livestock schistosome ancestry. ITS/cox1 genotyping suggested extensive recent hybridization and zoonotic infection. Among parasites from humans, 10.1% carried both S. curassoni and S. haematobium ITS, consistent with F1 or early generation hybrids, 21% had livestock schistosome markers at both cox1 and ITS suggesting zoonotic infection, while 13.7% carried S. bovis cox1 alongside mixed S. curassoni and S. haematobium ITS, suggesting more complex ancestry. Genome sequencing revealed a very different picture. All parasites from humans formed a tight cluster regardless of ITS or cox1 genotype, while all worms from cattle were well differentiated. We found no schistosomes containing 50% livestock parasite ancestry consistent with F1s. Instead, we observed regionally varying levels of S. bovis introgression, with modest levels in southern Nigeria (mean = 4.9%) and low levels in northern Nigeria (mean = 0.06%). These results demonstrate that: (i) two-locus genotyping is uninformative for detecting zoonotic infection or recent hybridization between S. haematobium and livestock schistosomes and (ii) previous data generated using this approach requires reinterpretation. These findings reveal the limitations of widely-used approaches for documenting zoonotic infection and hybridization between S. haematobium and livestock schistosome species.
]]></description>
<dc:creator><![CDATA[ Enabuele, E. E., Platt, R. N., Adeyemi, E. E., Aisien, M. S. O., Ajakaye, O. G., Ali, M. U., Amaechi, E. C., Atalabi, T. E., Auta, T., Awosolu, O. B., Dagona, A. G., Edo-Taiwo, O., Ejikeugwu, C. P., Igbeneghu, C., Njom, V. S., Onwude-Agbugui, M., Orji, M.-K. N., Oyinloye, F. O., Oyemade, E., Ozemoka, H. J., Pam, C. R., Ugah, U. I., Hulke, J. M., Arya, G. A., Anderson, T. J. ]]></dc:creator>
<dc:date>2026-05-05</dc:date>
<dc:identifier>doi:10.64898/2026.04.30.721997</dc:identifier>
<dc:title><![CDATA[Misleading inference of schistosome epidemiology from ribosomal internal transcribed spacer (ITS) and mitochondrial DNA]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-05-05</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.05.01.722137v1?rss=1">
<title>
<![CDATA[
Genome-wide architecture of prolonged starvation adaptation in experimentally evolved Drosophila and comparative enrichment in human orthologs 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.05.01.722137v1?rss=1
</link>
<description><![CDATA[
Long-term starvation stress represents a strong evolutionary constraint across taxa, yet the genetic architecture underlying adaptation to sustained nutrient deprivation remains poorly resolved. We experimentally evolved Drosophila melanogaster under starvation stress for 60 generations, maintaining four starvation-selected populations and four matched controls, and then performed whole-genome resequencing. Starvation-selected populations exhibited extended survival and pronounced genome-wide restructuring, including the expansion of low-heterozygosity regions, reduced nucleotide diversity, and recurrent sweep signatures across replicates. Drift-aware allele-frequency modeling identified 3,578 single-nucleotide polymorphisms (SNPs) whose shifts exceeded neutral expectations, indicating widespread, parallel responses to sustained starvation. Mitochondrial pathways emerged as prominent targets: nuclear-encoded mitochondrial genes were significantly enriched among low-diversity, sweep-associated, and drift-exceeding loci, and the mitochondrial origin of replication harbored a sharply differentiated variant, suggesting a mito-nuclear component of starvation adaptation. Comparative analyses further showed that human orthologs of starvation-responsive fly genes were enriched for highly differentiated variants in selected 1000 Genomes populations, with regulators of TOR/S6K signaling recurring among loci in the extreme tails of population differentiation. Together, these results define a replicate-convergent and functionally coherent genomic response to prolonged starvation in Drosophila, comprising regional signatures of linked selection and distributed allele-frequency shifts exceeding neutral expectations, and connect laboratory selection in flies to population differentiation in human orthologs.
]]></description>
<dc:creator><![CDATA[ Yadav, G., Mishra, P., Sahu, R. K., Sharma, V., Michalak, P., Aggarwal, D. D. ]]></dc:creator>
<dc:date>2026-05-05</dc:date>
<dc:identifier>doi:10.64898/2026.05.01.722137</dc:identifier>
<dc:title><![CDATA[Genome-wide architecture of prolonged starvation adaptation in experimentally evolved Drosophila and comparative enrichment in human orthologs]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-05-05</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.30.722098v1?rss=1">
<title>
<![CDATA[
Fixed human pangenome sequences reveal origins of common human traits 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.30.722098v1?rss=1
</link>
<description><![CDATA[
Humans possess human-specific traits such as spoken language and lineage-specific traits such as ape-specific taillessness. Previous efforts to identify the DNA sequences responsible for such human traits were limited by necessary accommodations for poor genome assembly quality and lack of population genomic sampling. Here, we implement new algorithms that combine the near-complete human reference pangenome alignment with a new near-complete simian cross-species alignment to define human- and lineage-specific DNA sequences fixed across human haplotypes. Previously reported FOXP2/NOVA1 amino acid substitutions linked to human spoken language and TBXT transposable element insertion contributing to ape taillessness were unique to their respective clades and fixed in sampled humans. In contrast, widely used sets of candidate human-mutated loci showed limited enrichment for either human specificity or fixation. Integration with candidate cis-regulatory elements identified putative regulatory sequences specific to humans and linked to human-specific traits like hair reduction and brain transcriptome patterning. Although brain-associated fixed regulatory changes were present in all lineages, enrichment for spoken language was human-specific and enrichment for receptive language was ape-specific. This study provides a new pangenome-aware comparative framework and catalogs of candidate genomic loci to trace the evolutionary origins of common human traits and disease risks.
]]></description>
<dc:creator><![CDATA[ Goh, C.-s., Davenport, M., Lee, C., Jarvis, E. ]]></dc:creator>
<dc:date>2026-05-05</dc:date>
<dc:identifier>doi:10.64898/2026.04.30.722098</dc:identifier>
<dc:title><![CDATA[Fixed human pangenome sequences reveal origins of common human traits]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-05-05</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.30.721964v1?rss=1">
<title>
<![CDATA[
Ecological diversification without genomic reorganization: repeat dynamics and regulatory evolution in Metarhizium robertsii 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.30.721964v1?rss=1
</link>
<description><![CDATA[
How can closely related organisms occupy distinct ecological niches without extensive genomic reorganization? We addressed this question by comparing eight strains of the entomopathogenic fungus Metarhizium robertsii that span a shallow phylogenetic gradient yet exhibit striking differences in virulence, plant associations, and metabolic capabilities. Despite nucleotide identity exceeding 98.5% and extensive macrosynteny, these strains showed pronounced variation in repeat-rich genomic regions: synteny gaps were twofold enriched near chromosome ends, transposable element loads varied from less than 3% to over 13% across strains diverging within ~0.3 million years, and repeat-induced point mutation signatures tracked TE activity rather than phylogenetic distance. Notably, repeat expansion occurs through diverse spatial mechanisms rather than being uniformly concentrated in chromosome-terminal regions. In contrast, core functional repertoires, proteases, carbohydrate-active enzymes, developmental regulators, and most secondary metabolite biosynthetic genes, were highly conserved, with phenotypic differences in virulence and secondary metabolism arising primarily from regulatory divergence and local structural variation rather than gene presence or absence. Metabolic specialization similarly reflected functional repurposing within a conserved enzymatic framework: loss of processive cellulases alongside enrichment of oxidative auxiliary activity enzymes produced a profile convergent with brown-rot fungi but adapted for insect-associated and rhizosphere niches. These results support a hierarchical model of ecological diversification in which diverse repeat expansion mechanisms, TE dynamics, and regulatory innovation operate as coupled axes of localized genomic change within an otherwise constrained genomic framework, reconciling rapid niche differentiation with strong structural conservation and suggesting a general mechanism for intraspecific adaptation in complex eukaryotic microbes.
]]></description>
<dc:creator><![CDATA[ Sheng, H., St. Leger, R. J. ]]></dc:creator>
<dc:date>2026-05-04</dc:date>
<dc:identifier>doi:10.64898/2026.04.30.721964</dc:identifier>
<dc:title><![CDATA[Ecological diversification without genomic reorganization: repeat dynamics and regulatory evolution in Metarhizium robertsii]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-05-04</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.30.721865v1?rss=1">
<title>
<![CDATA[
Modeling Site-Specific Mutation Patterns in Pandemic-Scale Phylogenetics 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.30.721865v1?rss=1
</link>
<description><![CDATA[
Models of genome evolution often account for different evolutionary rates at different genome positions due to, e.g., varying selective pressures or mutation rates. Recent evidence from millions of publicly shared SARS-CoV-2 genomes has revealed a more complex mutational landscape than can be modeled with existing approaches. Here, mutation rates are in fact not only highly position-specific, as currently modeled, but also nucleotide-specific; for example, specific mutations can occur very often at certain determined genome positions, while at the same positions other mutations might not be highly recurrent. Here, we propose and investigate a general model of genome evolution where each genome position is allowed to evolve under an independent, non-normalized substitution rate matrix describing site-specific rates of all mutation types ("Site-Specific Matrix" model, or SSM). We implement SSM in the efficient pandemic-scale phylogenetic inference software CMAPLE. Large-scale genomic epidemiological simulations suggest that, given enough data, SSM can accurately infer position- and nucleotide-specific substitution rates for more frequently observed nucleotides (typically the reference nucleotide), while other rates require higher levels of divergence. Simulations also show that SSM has a modest impact on the accuracy of phylogenetic tree estimation. We use SSM to analyze the evolution of millions of SARS-CoV-2 genomes and observe substantial mismatches between the substitution rates of classical rate variation models and our SSM estimates. These results suggest that classical models of rate variation are inadequate for modeling site-specific mutation patterns and that SSM is a useful alternative for large-scale genome analyses.
]]></description>
<dc:creator><![CDATA[ Martin, S., Ly-Trong, N., Minh, B. Q., Goldman, N., De Maio, N. ]]></dc:creator>
<dc:date>2026-05-04</dc:date>
<dc:identifier>doi:10.64898/2026.04.30.721865</dc:identifier>
<dc:title><![CDATA[Modeling Site-Specific Mutation Patterns in Pandemic-Scale Phylogenetics]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-05-04</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.30.721928v1?rss=1">
<title>
<![CDATA[
Diversity and divergence of two sympatric, sibling octopus species 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.30.721928v1?rss=1
</link>
<description><![CDATA[
Coleoid cephalopods have convergently evolved many traits shared with vertebrates, including camera-type eyes, large brain-to-body size ratios, and complex behaviors. Most evolutionary studies of cephalopods have compared individual genomes of taxa that diverged tens to hundreds of millions of years ago, yet very few have examined more recent evolution from a population genetics perspective. Here we present a comparative population genomic analysis of the sympatric sister species Octopus bimaculatus and Octopus bimaculoides using whole-genome resequencing. Despite similar morphologies, these species differ substantially in their life histories, ecologies, and geographic distributions. Using demographic inference, we estimated that the two species diverged approximately one million years ago and that O. bimaculatus has maintained a consistently larger effective population size since divergence. Consistent with these demographic histories, we found stronger signatures of positive selection in O. bimaculatus, including a positive correlation between recombination rate and nucleotide diversity, more selective sweeps, and a higher proportion of mutations fixed by adaptation---all consistent with more efficient natural selection in larger populations. Protein-coding genes overlapping with selective sweeps were enriched for various functions that included many related to brain and eye development, suggesting that traits characteristic of coleoid cephalopods continue to be shaped by positive selection on recent timescales in these species. Comparing coding-sequence divergence on the Z chromosome to the autosomes, we also find evidence for a female-biased mutation rate, consistent with an independent estimate from a deeper-timescale cephalopod comparison.
]]></description>
<dc:creator><![CDATA[ Coffing, G., Tittes, S., Small, S. T., Kern, A. D. ]]></dc:creator>
<dc:date>2026-05-04</dc:date>
<dc:identifier>doi:10.64898/2026.04.30.721928</dc:identifier>
<dc:title><![CDATA[Diversity and divergence of two sympatric, sibling octopus species]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-05-04</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.29.721543v1?rss=1">
<title>
<![CDATA[
South Asian Maternal Lineage haplogroup R30 Provides Phylogenetic Evidence of human dispersal across South Asia 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.29.721543v1?rss=1
</link>
<description><![CDATA[
South Asia is central to debates on early human dispersals, particularly the Out of Africa model and Eurasian colonization. Studies of M haplogroups have been used to support both Northern and Southern route hypotheses, but current archaeological and genetic evidence in the region remains contradictory. In the present work, we find that in addition to haplogroup M lineages, a few R lineages exhibit ancient, locally rooted variation, with R30 being one of the widespread haplogroup of R lineages across South Asia. To better understand South Asian demographic history, we investigated the phylogeographic distribution of haplogroup R30, an indigenous lineage. We used 190 complete modern and ancient sequences from diverse mainland and island populations including incorporation of 44 newly generated sequences which enabled the refinement of the R30 phylogeny and the identification of a novel basal lineage, R30c. Bayesian and {rho}-based age estimates suggest that R30 originated in the Indian subcontinent ~50 kya. Early diversification likely occurred in Northern India, giving rise to R30b (~44 kya), while R30a and R30c differentiated primarily in Southern India. Several subclades of haplogroup R30 exhibit strong signatures of founder effects, particularly among the language isolate Vedda of Sri Lanka, Uru Kurumban of Southern India, and the populations of the Lakshadweep archipelago. Bayesian skyline analyses indicate long-term demographic stability followed by rapid lineage expansion ~20 kya and more recent declines consistent with localised drift and relatively recent founder events. The presence of early-diverging R30 lineages in Thailand and Indonesia further supports long-term connections between South and Southeast Asia. Overall, archaeological and genetic evidence point towards the multiple migrations for South Asia colonizations.
]]></description>
<dc:creator><![CDATA[ Desai, S., Adhikary, V., Bhattacharyya, M., Tharu, M. K., Sharma, A., Sequeira, J. J., Pandey, R. k., Pandey, P., Shendre, S. S., Tayyeh, A. M., S, S. L., Mustak, M. S., Petraglia, M., Chaubey, G. ]]></dc:creator>
<dc:date>2026-05-04</dc:date>
<dc:identifier>doi:10.64898/2026.04.29.721543</dc:identifier>
<dc:title><![CDATA[South Asian Maternal Lineage haplogroup R30 Provides Phylogenetic Evidence of human dispersal across South Asia]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-05-04</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.29.721584v1?rss=1">
<title>
<![CDATA[
Evolutionary and epidemiological considerations for anthelmintic treatments in ruminant livestock 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.29.721584v1?rss=1
</link>
<description><![CDATA[
Anthelmintic drug resistance is a concern for the sustained control of gastrointestinal nematodes (GINs) in ruminant livestock globally. Evolutionary-epidemiological modelling, which considers both parasite dynamics and resistance dynamics in response to interventions, can be useful in determining which anthelmintic resistance management (ARM) strategies may be effective without compromising parasite control. We address two key questions in ARM. First, how to improve the measurement of AR in populations. Second, identifying effective ARM strategies to slow the spread of AR while maintaining effective parasite control. We developed a simulation framework which tracks the weather-dependent epidemiology of GINs and AR evolution, providing a highly flexible methodology to evaluate multiple ARM strategy options in a single modelling framework, allowing for novel insights due to direct comparisons between strategies. Simulations to refine our understanding of anthelmintic resistance management evaluated the impact of key areas of uncertainty, including transmission intensity, resistance intensity, resistance frequency, drug decay and linking faecal egg count reduction tests (FECRT) to resistance allele frequency. Large-scale simulations present a methodologically thorough evaluation of how treatment choices simultaneously impact epidemiological and evolutionary outcomes. Phenotypic classifications of resistance status using FECRT failed to capture fine scale changes in resistance allele frequency. The pharmacokinetics of drug decay strongly influenced ARM outcomes, and trade-offs between ARM and effective parasite control depends on genetic factors underpinning resistance. Combination therapies appear to be the most effective resistance management strategy evaluated. Our findings suggest practical implementations to manage anthelmintic resistance must simultaneously consider parasite transmission, pharmacology and parasite genetics to be robust and sustainable. We provide a rigorous simulation framework to enable such discussions allowing for a refinement into our understanding of parasite control in the presence of resistance evolution.
]]></description>
<dc:creator><![CDATA[ Hobbs, N. P., Graham-Brown, J., Morgan, E. R., Rose Vineer, H. ]]></dc:creator>
<dc:date>2026-05-01</dc:date>
<dc:identifier>doi:10.64898/2026.04.29.721584</dc:identifier>
<dc:title><![CDATA[Evolutionary and epidemiological considerations for anthelmintic treatments in ruminant livestock]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-05-01</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.29.721739v1?rss=1">
<title>
<![CDATA[
Flower color locus resists introgression due to correlational selection with other floral traits in Ipomoea cordatotriloba 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.29.721739v1?rss=1
</link>
<description><![CDATA[
O_LIWhen species hybridize, resistance to introgression is presumably due to selection against hybridizing alleles. While many studies have characterized direct selection at these sites, alleles may resist introgression through correlational selection. Here we investigate the role of direct and correlational selection in reducing introgression at the color locus in Ipomoea cordatotriloba.
C_LIO_LIWe used recombinant inbred lines that varied in limb color, flower size and sugar concentration to estimate the fitness advantage of the flower color allele via direct and correlational selection. To assess the effect of correlational selection on fitness, we ask if floral size or nectar sugar concentration is correlated with fecundity in pink- but not white-limbed lines.
C_LIO_LIWe find no evidence for direct selection on flower color across four fitness components - germination, survival, fecundity, and siring success. Instead, both flower size and sugar concentration significantly correlate with fecundity in pink, but not white limbed lines. As a result, correlational selection on the color allele opposes introgression when recurrent migration is low (<3%).
C_LIO_LIThese results demonstrate that correlational, rather than direct, selection is sufficient to resist introgression via hybridization and suggest that correlational selection is an underexplored mechanism to generate resistance to introgression across multiple loci.
C_LI
]]></description>
<dc:creator><![CDATA[ Colen, J. Z., Rausher, M. D. ]]></dc:creator>
<dc:date>2026-05-01</dc:date>
<dc:identifier>doi:10.64898/2026.04.29.721739</dc:identifier>
<dc:title><![CDATA[Flower color locus resists introgression due to correlational selection with other floral traits in Ipomoea cordatotriloba]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-05-01</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.29.721752v1?rss=1">
<title>
<![CDATA[
Insights from sourdough redefine the domestication landscape of baker's yeast 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.29.721752v1?rss=1
</link>
<description><![CDATA[
While the domestication of plants and animals is widely recognized for its role in the rise of human civilization, humans have also cultivated microbes over millennia to produce food and beverages. One microbe in particular, Saccharomyces cerevisiae, is associated with a wide variety of human-fermentation environments, including wine, beer, and notably bread, such that it is often referred to as "bakers yeast." To better illuminate the domestication history of baking associated yeast, we isolated 38 Saccharomyces cerevisiae strains from sourdough starters donated by bakers throughout North America and compared them to thousands of S. cerevisiae isolates from a variety of wild and human-fermentation environments. We identified 6 major clades with two primary domestication hubs, Mediterranean liquid-state fermentation and Asian solid-state fermentation, diverging across Eurasia that gave rise to human-associated lineages. Population genomic analyses demonstrate that S. cerevisiae strains found in sourdough starters are genetically distinct from commercial baking strains and do not come from the surrounding wild environment. Our results show that sourdough yeast strains are closely related to each other and have shared ancestry with strains isolated from various Asian solid state grain fermentations such Japanese sake, Asian rice wines, Chinese distilled spirits (baijiu), and Chinese steamed bread (mantou). We found evidence of significant admixture throughout S. cerevisiae populations, including baking-associated lineages, likely facilitated by human activity. Pangenome gene content largely captures S. cerevisiae traditional genomic sequence-based population structure and reflects human cultural practices, with differences in gene content and copy number between baking associated strains and other groups. Overall, we show that many generalized hallmarks of domestication, such as genome contraction, loss of genetic diversity, and lack of niche expansion, are not universal features of S. cerevisiae domestication, and that baking-associated yeasts have a complex evolutionary history heavily shaped by human culture.
]]></description>
<dc:creator><![CDATA[ Ruffieux, M., Brandt, N., Gutierrez, A., Wolfe, B. E., Dunn, R. R., Smukowski Heil, C. ]]></dc:creator>
<dc:date>2026-05-01</dc:date>
<dc:identifier>doi:10.64898/2026.04.29.721752</dc:identifier>
<dc:title><![CDATA[Insights from sourdough redefine the domestication landscape of baker's yeast]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-05-01</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.29.721748v1?rss=1">
<title>
<![CDATA[
Ovipositor morphology and mechanosensory divergence drive niche breadth expansion in Drosophila 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.29.721748v1?rss=1
</link>
<description><![CDATA[
For most Drosophila species, the firm surface of intact ripe fruit acts as a physical barrier to oviposition, effectively restricting them to the saprophagous niche. How species overcome such mechanical constraints at the behavioral and sensory levels, and whether doing so leads to niche breadth expansion or niche specialization, remain poorly understood. Here we show across ten Drosophila species that substrate physical hardness is a critical barrier preventing most species from exploiting ripe fruit. Unlike saprophagous species, the pest D. suzukii and the widely distributed D. immigrans have evolved a tolerance for high substrate stiffness to perform puncture oviposition. This behavioral shift is enabled by distinct morphology of saw-like and needle-like ovipositors respectively, which are critical for breaching intact fruit. To uncover the neural basis for this mechanical adaptation, we screened mechanosensory mutants in D. melanogaster and identified the Inactive (IAV) channel as a key sensory gene mediating this behavior. Functional rescue experiments reveal that IAV has diverged in D. suzukii and D. immigrans, mediating a sensory relaxation that permits oviposition on stiff substrates. This mechanical breach confers a direct fitness advantage, allowing only the offspring of these two species to successfully complete larval development in fresh fruit. Finally, field surveys in the wild demonstrate that this modular adaptation facilitates niche overlap and resource partitioning in natural habitats. Overall, this work reveals how the divergence of mechanosensory channels and morphological innovations can overcome physical constraints to drive broad ecological niche expansion.
]]></description>
<dc:creator><![CDATA[ He, S., Wang, T., Yu, Y.-j., Yang, X.-n., Zhang, W., Lu, B., Luo, Y.-b. ]]></dc:creator>
<dc:date>2026-05-01</dc:date>
<dc:identifier>doi:10.64898/2026.04.29.721748</dc:identifier>
<dc:title><![CDATA[Ovipositor morphology and mechanosensory divergence drive niche breadth expansion in Drosophila]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-05-01</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.29.721599v1?rss=1">
<title>
<![CDATA[
Secondary structure distances reveal a new dimension of protein evolution 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.29.721599v1?rss=1
</link>
<description><![CDATA[
Molecular phylogenetics based on primary sequence comparisons has been central to reconstructing protein evolution. However, structural evolution does not necessarily parallel sequence divergence, particularly in proteins combining ordered domains with intrinsically disordered regions (IDRs). Here, we introduce a quantitative secondary structure distance (S2D) metric that enables systematic comparison of protein secondary structure, including both ordered elements and IDRs. Using the MADS-box transcription factor family as a model, we show that structural divergence is domain-specific and only partially coupled to sequence-based phylogeny. Domain-resolved analyses reveal that the DNA-binding M domain remains structurally constrained, whereas the I and C domains exhibit extensive sequence divergence while retaining conserved intrinsic disorder. In contrast, the K domain contributes disproportionately to global structural variability. Integrating S2D with phylogenetic distance uncovers both convergent structural architectures among distantly related proteins and pronounced structural remodelling within closely related paralogs--patterns not evident from primary sequence comparisons alone. Residue-level analyses further demonstrate that the structural impact of mutation depends strongly on amino acid identity and does not scale directly with substitution frequency or conservation metrics. Together, these findings indicate that secondary structural evolution provides an additional dimension of protein diversification beyond sequence divergence. By integrating phylogenetic and structural distances, this framework offers a complementary approach to interpreting protein evolution, particularly in families containing mixtures of ordered domains and intrinsically disordered regions.

Significance StatementEvolutionary relationships are typically inferred from primary sequence comparisons, yet structural evolution may follow different trajectories. By developing a quantitative measure of secondary structural divergence, we show that structural change within the MADS-box transcription factor family can both converge and diverge independently of sequence-based phylogeny. Intrinsically disordered regions exhibit extensive sequence divergence while retaining conserved disorder, whereas specific amino acid substitutions disproportionately reshape secondary structure. These findings demonstrate that evolutionary diversification operates through domain-specific structural modulation rather than uniform sequence divergence. Integrating structural and phylogenetic distances provides a complementary framework for interpreting protein evolution and reveals evolutionary patterns that remain hidden when relying on sequence comparisons alone.
]]></description>
<dc:creator><![CDATA[ Bastida, A., Mun oz Morales, A. M., Egea-Cortines, M. ]]></dc:creator>
<dc:date>2026-05-01</dc:date>
<dc:identifier>doi:10.64898/2026.04.29.721599</dc:identifier>
<dc:title><![CDATA[Secondary structure distances reveal a new dimension of protein evolution]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-05-01</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.28.721371v1?rss=1">
<title>
<![CDATA[
Disassortative mating in replicated secondary contact experiments in nature 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.28.721371v1?rss=1
</link>
<description><![CDATA[
Ecological speciation is now regarded as one of the primary processes by which new species are generated. Adaptive divergence in allopatry begins this process, but it is often unclear when and how mechanisms that promote reproductive isolation, such as assortative mating and selection against hybrids, evolve. Here, we test for evidence of these mechanisms across replicated secondary contact experiments in natural settings. We introduced four to eight allopatric populations of threespine stickleback (Gasterosteus aculeatus), in both single-ecotype and mixed-ecotype treatments, into nine natural lakes, after which we inferred mating patterns by genotyping the resulting F1 generation. Contrary to expectations from the literature, we found no evidence of assortative mating or partial reproductive isolation among the introduced source populations. Instead, we detected evidence of disassortative mating by source population in three lakes and some evidence of disassortative mating by ecotype in one lake. These mating patterns were both context-dependent and population-dependent, varying substantially across lakes receiving the same source populations, and with some source populations generally displaying greater tendencies for disassortment. The absence of positive assortative mating in any replicate demonstrates that adaptive divergence in allopatry alone might be insufficient to generateassortative mating in many cases, while the possibility of disassortative mating in these contexts poses an additional hurdle on the path toward speciation.
]]></description>
<dc:creator><![CDATA[ Eckert, L., Bolnick, D. I., Peichel, C. L., Hendry, A. P., Barrett, R. D. H. ]]></dc:creator>
<dc:date>2026-05-01</dc:date>
<dc:identifier>doi:10.64898/2026.04.28.721371</dc:identifier>
<dc:title><![CDATA[Disassortative mating in replicated secondary contact experiments in nature]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-05-01</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.29.721577v1?rss=1">
<title>
<![CDATA[
Social microbiome transmission predicts microbial specialization and host lifespan in a wild primate 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.29.721577v1?rss=1
</link>
<description><![CDATA[
Social interactions are proposed to provide reliable routes for microbial transmission between animals, facilitating animal-microbiome co-evolution. However, microbiome transmission remains challenging to measure in wild populations. Here we combine behavioral observations of wild baboons with repeated strain-resolved metagenomic profiling to identify individual gut microbial species that follow a dominant mode of social transmission. In an 18-year metagenomic time series from the same population, baboons with higher levels of socially transmitted species lived longer than those with lower levels of socially transmitted species. Socially transmitted species were also more stable and persistent within baboons, yet had narrower host ranges outside of baboons. Thus, social transmission is not only detectable in free-living primates, but may play a special role in both host and microbial fitness.
]]></description>
<dc:creator><![CDATA[ Debray, R., Dickson, C. C., Webb, S. E., Ferretti, P., Meloimet, A., Gilbert, J., Alberts, S. C., Blekhman, R., Archie, E. A., Tung, J. ]]></dc:creator>
<dc:date>2026-04-30</dc:date>
<dc:identifier>doi:10.64898/2026.04.29.721577</dc:identifier>
<dc:title><![CDATA[Social microbiome transmission predicts microbial specialization and host lifespan in a wild primate]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-30</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.27.721019v1?rss=1">
<title>
<![CDATA[
Eco-evolutionary dynamics and environmental detoxification jointly shape bacterial community response to antibiotic perturbation 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.27.721019v1?rss=1
</link>
<description><![CDATA[
Microbial communities frequently encounter recurrent antibiotic disturbance, yet how ecological, evolutionary, and environmental processes jointly shape the response remains unresolved. Here we experimentally disentangle these mechanisms using a 23-species bacterial community exposed to ampicillin pulses with pre-pulse and resistance priming. Pre-pulse priming preconditioned composition toward resistant taxa, reducing compositional change during the main pulse. Resistance priming was the dominant determinant of community response, buffering change, relaxing selection, and altering gene expression. This buffering arose from both evolution of higher resistance and accelerated ampicillin detoxification by a dominant degrader, which transiently reduced antibiotic effects and favored non-degrading taxa. Yet buffering did not translate into better recovery: because resistance was coupled to competitive dominance, diversity remained comparable to or below ancestral communities and dominance was reinforced. Together, we show that antibiotic history reshapes microbial disturbance response through coupled eco-evolutionary and environmental feedbacks, generating a trade-off between resistance and recovery.
]]></description>
<dc:creator><![CDATA[ Cairns, J., Smolander, N., Pausio, S., Pitkänen, O., Lindqvist, M., Tamminen, M., Das Roy, R., Friman, V.-P., Becks, L., Mustonen, V., Hiltunen, T. ]]></dc:creator>
<dc:date>2026-04-29</dc:date>
<dc:identifier>doi:10.64898/2026.04.27.721019</dc:identifier>
<dc:title><![CDATA[Eco-evolutionary dynamics and environmental detoxification jointly shape bacterial community response to antibiotic perturbation]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-29</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.27.721057v1?rss=1">
<title>
<![CDATA[
Do sex differences in autosomal recombination rates facilitate divergence? 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.27.721057v1?rss=1
</link>
<description><![CDATA[
Recombination rate varies within and between individuals. One form of such variations is seen between sexes in dioecious populations, with males typically exhibiting a smaller recombination rate than females. This is true both for sex chromosomes and autosomes (so-called heterochiasmy). Although a large body of theory exists on the role of sex chromosomes in adaptation and population divergence, much less is known about the role of heterochiasmy. Recently, it has been suggested that heterochiasmy can facilitate local adaptation and divergence, but if, and when this is true has not been systematically studied theoretically to date. Here we use Individual-based simulations to assess the effect of sex differences in autosomal recombination rates on the process of divergence and adaptation in populations subject to divergent selection and migration. We found evidence supporting that sex differences in autosomal recombination rate between adaptive loci can facilitate, and especially maintain, divergence, but this is true only under very limited conditions, involving strong selection, high sex-averaged effective recombination rates and relatively high rates of migration compared to the strength of selection. We further found that this effect, when present, is typically weak but is amplified in cases of highly polygenic adaptation in comparison to cases with a few adaptive loci of strong effect. We conclude that, in most cases, sex differences in autosomal recombination rate alone are unlikely to noticeably contribute to the process of adaptation and divergence. Further studies are needed to evaluate their effect in combination with other processes not considered in the present study, such as assortative mating between the alike mates, or recombination suppression in heterozygotes.

TeaserIn dioecious populations, recombination rate typically differs between males and females. This is true both for sex chromosomes and autosomes. While much theoretical research has focused on understanding how recombination rate differences in sex chromosomes shape local adaptation and divergence, we lack theoretical knowledge of the potential role of sex differences in autosomal recombination rates. Recombination has a dual role in local adaptation. Strong recombination can effectively purge deleterious alleles, but it can also break apart beneficial allele complexes (and vice versa for weak recombination). Thus, one may expect that in the presence of both strong and weak recombination exhibited by females, and males, respectively, population divergence can be efficiently facilitated. But is this true? Here, we study this question theoretically using computer simulations. Our main finding is that sex differences in autosomal recombination can facilitate divergence, but this effect is typically weak and present only under very stringent conditions.
]]></description>
<dc:creator><![CDATA[ Hansson, A., Rafajlovic, M. ]]></dc:creator>
<dc:date>2026-04-29</dc:date>
<dc:identifier>doi:10.64898/2026.04.27.721057</dc:identifier>
<dc:title><![CDATA[Do sex differences in autosomal recombination rates facilitate divergence?]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-29</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.28.721375v1?rss=1">
<title>
<![CDATA[
Domestication and deep lineage divergence define two discrete trajectories in Kluyveromyces marxianus 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.28.721375v1?rss=1
</link>
<description><![CDATA[
Although genomics has greatly improved our ability to detect population structure and genetic divergence, it remains difficult to determine when diversity within a recognized species reflects continuous variation and when it marks the emergence of discrete evolutionary lineages. In yeasts, population-genomic studies often reveal overlapping signatures of environmental association, admixture, and domestication, making this distinction especially challenging. By analyzing 178 globally sampled genomes from Kluyveromyces marxianus, an emerging yeast of biotechnological interest, we show that diversity within this species resolves into two contrasting evolutionary trajectories that do not map onto broad geographic origin. Most industrial and clinical isolates belong to a lineage marked by gene loss, aneuploidy, and reduced fertility, consistent with genomic hallmarks of domestication. In contrast, isolates confined to traditional agave fermentations in Mexico and South Africa form a highly distinct lineage, separated from the other lineages by up to 4.8% genome-wide nucleotide divergence, widespread reciprocal monophyly, no detectable recent gene flow, and reduced mating compatibility despite co-occurrence with other lineages. Together, these results show that within a single yeast species, domestication-associated genome remodeling and deep lineage divergence can define distinct trajectories, with implications for strain selection in biotechnology.
]]></description>
<dc:creator><![CDATA[ Moreno-Hernandez, J. M., Smets, J., Torres-Machorro, A. L., Garcia-Ortega, L. F., Avelar-Rivas, J. A., Ortiz- Merino, R. A., Kirchmayr, M. R., Muszewska, A., Morales, L., Verstrepen, K., DeLuna, A., Mancera, E. ]]></dc:creator>
<dc:date>2026-04-29</dc:date>
<dc:identifier>doi:10.64898/2026.04.28.721375</dc:identifier>
<dc:title><![CDATA[Domestication and deep lineage divergence define two discrete trajectories in Kluyveromyces marxianus]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-29</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.27.721060v1?rss=1">
<title>
<![CDATA[
Plastome convergence across heterotrophic plant lineages: genome reduction, extreme AT bias, high substitution rates, and functional persistence in the endoparasitic Mitrastemonaceae 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.27.721060v1?rss=1
</link>
<description><![CDATA[
The loss of photosynthesis triggers extreme plastid genome (ptDNA) decay, including complete genome loss. Of the multiple transitions to heterotrophy among angiosperms, the ptDNA status remains poorly defined in lineages such as the endophytic Mitrastemonaceae (Ericales). Adopting a panplastome perspective, we characterized genomic variation across Mitrastemon yamamotoi individuals, assembling two complete circular ptDNAs and re-evaluating all available genomic resources for the genus. Our results reveal a highly minimized ptDNA (18-26 kb) with extreme AT content (>77%) and loss of the typical quadripartite architecture. Despite the absence of the stabilizing inverted repeats, the Mitrastemon panplastome exhibits remarkable structural stability and collinearity among individuals. The reduced suite of 26 genes, which includes accD, infA, clpP, ycf1, ycf2, and the essential tetrapyrrole precursor trnE-UUC, exhibit elevated substitution rates. Evolutionary rate analyses (dN/dS) demonstrate that the core ribosomal suite remains under strong purifying selection ({omega}<1), confirming the organelles functional status. Furthermore, transcriptomic analysis identified a nearly complete set of nuclear-encoded DNA-RRR genes, with the notable exception of the MUTS2 surveillance system. The convergent loss of these homologs in Mitrastemon and another holoparasitic lineage may be linked to the shared structural instability and mutational bias. Our findings demonstrate that despite extreme genome compaction, accelerated substitution rates, and severe AT-bias, the Mitrastemon panplastome remains quite stable, providing a definitive genomic framework for understanding plastid evolution within the endoparasitic Mitrastemonaceae.
]]></description>
<dc:creator><![CDATA[ Roulet, M. E., Gatica-Soria, L., Garcia, L. E., Yu, R., Wang, C., Zhou, R., Sanchez-Puerta, M. V. ]]></dc:creator>
<dc:date>2026-04-29</dc:date>
<dc:identifier>doi:10.64898/2026.04.27.721060</dc:identifier>
<dc:title><![CDATA[Plastome convergence across heterotrophic plant lineages: genome reduction, extreme AT bias, high substitution rates, and functional persistence in the endoparasitic Mitrastemonaceae]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-29</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.27.721161v1?rss=1">
<title>
<![CDATA[
Convergent evolution of parrotfish beaks enables stress redistribution during high-force feeding 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.27.721161v1?rss=1
</link>
<description><![CDATA[
Convergent evolution is often interpreted as evidence that similar ecological challenges select for optimal functional solutions, yet the biomechanical mechanisms underlying such convergence remain poorly resolved. Parrotfishes independently evolved fused, beak-like dentition multiple times, a trait associated with feeding on hard substrates such as coral, but its advantage has not been quantified. Here, we combine finite element analysis with shockwave modeling to evaluate the performance of the beak during feeding. Across five species spanning independent evolutionary origins of beaked and non-beaked dentitions, we find that jaw opening is governed primarily by geometric scaling, with minimal influence from dentition morphology. In contrast, under stabilized biting, fused dentition reduces the rate of stress accumulation relative to discrete teeth, indicating a functional advantage under constrained loading. Shockwave modeling further shows that tooth geometry and stacking regulate stress propagation: smooth profiles reduce stress concentration, while stacked architectures localize stresses within the tooth material and limit transmission into the surrounding bone. These results suggest that convergent beak evolution in parrotfish reflects repeated optimization for stress management under constrained and impact loading, and reveals a general principle by which biological structures control internal force transmission during high-force feeding rather than maximize strength alone.
]]></description>
<dc:creator><![CDATA[ Menghani, R. R., Trainor, S. A., Evans, K. M., Avila, R. ]]></dc:creator>
<dc:date>2026-04-29</dc:date>
<dc:identifier>doi:10.64898/2026.04.27.721161</dc:identifier>
<dc:title><![CDATA[Convergent evolution of parrotfish beaks enables stress redistribution during high-force feeding]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-29</prism:publicationDate>
<prism:section></prism:section>
</item>
</rdf:RDF>
