Molecular Ecology最新文献

Orthoptera provide a well-documented case of transspecies colour polymorphism, with green and brown morphs coexisting in many species. This colour polymorphism is likely under long-term balancing selection, but the genetic and molecular mechanisms underlying the variation remain poorly understood. Here, we used transcriptome data alongside a novel chromosome-level assembly to perform differential gene expression analysis in the club-legged grasshopper Gomphocerus sibiricus (Caelifera: Acrididae: Gomphocerinae), aiming to identify the specific genes involved in the differentiation between green and brown morphs. Since differential expression analyses are prone to false positives, we replicated the analysis using an independent sample of individuals of the same species. We found six genes consistently upregulated in green individuals across both datasets, all annotated as beta-carotene-binding proteins (βCBPs). βCBPs are known to play a key role in the colour regulation in both the migratory locust Locusta migratoria and the desert locust Schistocerca gregaria, although their exact role may differ in the club-legged grasshopper. The gene tree and chromosomal positions of βCBP copies in G. sibiricus, L. migratoria and S. gregaria indicate both ancestral (pre-speciation) and lineage-specific duplications. Our screening of publicly available orthopteran genomes revealed that homologues of the βCBP genes are largely absent from non-Caelifera species when using conservative homology thresholds. This restricted distribution suggests that βCBP-mediated pigmentation may represent a Caelifera-specific mechanism that is involved in the production of green body coloration, while other orthopteran lineages likely rely on distinct genetic pathways. Together, our findings provide new insights and lay the groundwork for understanding the evolutionary diversification of pigmentation mechanisms in Orthoptera.

Multigner, L. F., A. Bras, M. F. DiLeo, and M. Saastamoinen. 2025. “Relative Effects of Habitat Amount and Fragmentation Per Se on Genetic Diversity of the Glanville Fritillary Butterfly.” Molecular Ecology 34: e70037. https://doi.org/10.1111/mec.70037.

In the abstract, the line ‘[…] whereas habitat aggregation had a negative effect on genetic diversity when the available amount of habitat in the landscape was low’ was incorrect. It should have read ‘[…] whereas with the clumpiness index, fragmentation had a negative effect on genetic diversity when the available amount of habitat in the landscape was low’.

We apologise for this error.

Natal dispersal is a key life history trait determining fitness and driving population dynamics, genetic structure, and species distributions. Despite existing evidence that not all phenotypes are equally likely to successfully establish in new areas, the mechanistic underpinnings of natal dispersal remain poorly understood. The propensity to disperse into a new environment can be favoured by a high degree of phenotypic plasticity, which facilitates local adaptation and may be achieved via epigenetic mechanisms, which modify gene expression and enable rapid phenotypic changes. Epigenetic processes occur in particular genomic regions—DNA methylation on CpG sites in vertebrates—and thus individual genomes may differ in their capacity to be modified epigenetically. This ‘Epigenetic potential’ (EP) may represent the range of phenotypic plasticity attainable by an individual and be a key determinant of successful settlement in novel areas. We investigated the association between EP—quantified as the number of genome-wide CpG variants—and natal dispersal propensity in a long-term study population of Pied flycatchers (Ficedula hypoleuca) monitored since colonisation of a new habitat 35 years ago. We tested this association at three levels, comparing EP between: (i) individuals dispersing between and within habitat patches; (ii) immigrants to the population and locally born individuals; and (iii) individuals from first (comprising colonisers or their direct descendants) and later generations of the population (consisting of locally born individuals, which did not show natal dispersal between habitat patches). Results show a significant, positive association between EP and dispersal propensity in comparisons (i)—only in females—and (iii), but not (ii). Furthermore, CpG variants were non-randomly distributed across the genome, suggesting species- and/or population-specific CpGs being more frequent in promoters and exons. Our findings point to EP playing a role in dispersal propensity at spatial and temporal scales, supporting the idea that epigenetically driven phenotypic plasticity facilitates dispersal and environmental coping in free-living birds.

Cline theory has a central place in speciation studies. Cline locations delimit taxon boundaries, cline widths scale with barrier strength, and the shapes of clines (smooth or stepped) suggest whether species barriers are mono- or polygenic. How cline shapes vary along chromosomes therefore forms part of the genome's species barrier landscape. Further, asymmetric moving clines (wave fronts) can mark adaptive introgression puncturing species barriers, potentially leading to their collapse or decay. Here we review the development of cline and wavefront models and relate this to the use of dispersal kernels in epidemiology and ecology. We contrast classical results to those for a thick-tailed kernel, showing how cline shape affects the speed of spatial processes, including the widening of neutral clines and the spatial coalescent. We critique current cline models used for inference (both spatial and genomic clines) and address Barton's question: Why (after decades of cline fitting) is there so little evidence of stepped clines? We suggest evidence is weak because stepped cline models are over-parameterised, while current genomic cline models are under-parameterised. We explore goldilocks cline parameterisations and discuss non-parametric approaches that may help resolve these issues. This broadens to a discussion of the future of, and alternatives to, cline fitting.

Ambu, J., S. N. Litvinchuk, C. Caballero-Díaz, et al. 2025. “Genomic, Phenotypic, and Environmental Correlates of Speciation in the Midwife Toads (Alytes).” Molecular Ecology 34: e17736.

In a recent article on the evolution of midwife toads (Alytes) published in March 2025 in Molecular Ecology (Ambu et al. 2025), we performed multivariate analyses of mating calls, based on a dataset of four bioacoustic variables, namely the dominant frequency (DF), the rising time (RT), the note duration (ND), and a fourth variable dubbed pulse rate (PR).

However, midwife toads do not have pulsed calls, and the fourth variable PR actually consists of the number of oscillations (not pulses) per time unit, thus being a manual calculation of DF. In effect, our multivariate analysis technically included three (not four) variables, with one variable (DF) being pseudo-replicated.

The results of the study are, nevertheless, not affected by this confusion. Pairwise call distances computed with or without PR are almost perfectly correlated (r = 0.99, p < 0.001; Mantel test on log-transformed distance matrices). Accordingly, restricting analyses to the three independent variables (DF, RT, and ND) yielded exactly the same patterns, with nearly identical statistics (Figure 1, Table 1). Specifically, and as emphasized in our original article, (1) calls are far more different between species that have achieved complete reproductive isolation than between the hybridizing lineages of the subgenus Alytes (Figure 1A); (2) pairwise call differences in the subgenus Alytes are not related to the level of introgression between lineages (Figure 1B); (3) pairwise call differences significantly increase with genomic divergence at the level of the genus but not among the lineages of the subgenus Alytes (Figure 1C).

The conclusions of our article thus stand strong, namely that reproductive isolation predominantly starts with genetic rather than phenotypic (including bioacoustic) barriers in midwife toads, the latter arising at later stages of speciation.

We apologize for this error.

Environmental and climatic changes have shaped the evolutionary trajectories of natural populations, leaving genomic signatures that reflect how species respond to these shifts and their impacts on genetic health. While these insights are essential for unravelling evolutionary histories and informing conservation strategies, studies on Neotropical species remain largely underrepresented. Maned Three-Toed Sloths, endemic to the fragmented Atlantic Forest of Brazil, were recently reclassified into two distinct species: the Northern and Southern Maned Sloths. Our study investigates the genomic imprints left by ancient and recent environmental changes in the Atlantic Forest in these two sloth lineages, using whole-genome resequencing data. Our analysis reveals that the Southern Maned Sloth exhibits a smaller historical population size than the Northern Maned Sloth. This disparity likely stems from differing climatic changes along the Atlantic Forest distribution during the Pleistocene, characterised by greater climatic stability and larger refugia areas in the north. Consequently, the southern lineage presents a lower genetic diversity and higher overall inbreeding level. Nonetheless, the northern population has experienced a fast increase in inbreeding levels in the last few decades, likely associated with extensive recent deforestation in the northeast region of Bahia State. The distinct demographic trajectories also resulted in the northern lineage carrying a higher genetic load, implying higher fitness costs for this lineage if inbreeding persists. Together, our findings confirm the independent evolutionary paths of these two lineages and underscore the unique conservation challenges posed by both historical climatic changes and ongoing deforestation of the Atlantic Forest.

Cichlids are a textbook model system of adaptive radiation and a fascinating example of rapid sex chromosome evolution. Yet in these fish, as in most other taxa, the mechanisms causing sex chromosome turnover and the subsequent impact thereof are unknown. Sexual antagonism was long thought to be a driver of sex chromosome emergence, but experimental support remains scarce. Here, we show that sex-biased genes, often used as indicators of sexual antagonism, are enriched in three different sex chromosome systems of Lake Tanganyika cichlid species that diverged less than 4 million years ago. Moreover, gene expression is feminised in species that transitioned from an XY to a ZW system on the same chromosome. This is achieved by gain of female-biased genes, increase of female sex-bias as well as decrease of male-bias depending on the tissue investigated. We further show that XY sex chromosomes have more male-biased genes but without higher intensity of sex-biased expression. A large fraction of sex-bias in gene expression evolved adaptively, with a stronger signature in females than males. While we find that sex-bias in gene expression clearly depends on the heterogametic system, we find only weak support for sex-biased expression priming chromosomes to become sex chromosomes. Overall, we conclude that there is little evidence that sexual antagonism drives sex chromosome emergence but that it likely plays a role during sex chromosome differentiation. We see rapid emergence of antagonistic expression in sex-linked genes.