ABSTRACT Copy number variation (CNV) constitutes a major source of adaptive genetic variation, yet its relative contribution to climate adaptation compared to non‐CNV (single‐copy) variants remains unresolved. Using whole‐genome sequencing of 125 Nelumbo nucifera (sacred lotus, a common aquatic vegetable) wild accessions spanning tropical‐temperate gradients, we distinguished 388,600 CNV‐derived SNPs from 485,982 SNPs of single‐copy regions. Latent factor mixed models (LFMM) revealed that CNV‐SNPs appear to drive adaptation to temperature extremes and precipitation seasonality, whereas non‐CNV SNPs dominate humid thermal adaptation. NnPAL2 , a homologue of a drought‐related gene in Arabidopsis, shows a recent selective sweep in temperate N. nucifera , with reduced copy number and expression associated with lower precipitation in the warmest quarter. Our results suggest that CNV SNPs and non‐CNV SNPs contribute to distinct environmental axes, but the heterogeneous CNV effects across bioclimatic variables largely reflect ecotype‐specific copy number backgrounds rather than intrinsic differences in selective pressures. CNV therefore plays a disproportionate role in coping with abiotic extremes. Discriminating CNV‐derived SNPs from those derived from single‐copy genomic regions is essential for accurately understanding the genetic basis of climate adaptation, with potential applications for crop improvement.
ABSTRACT Over 14,900 COI DNA sequences of drosophilids were used to build a character‐based diagnostic system for the identification of genera and species in the group. This approach uses aligned COI sequence characters, k‐mer characters and applies a hybrid approach that combines the two. To assess the efficacy of the diagnostics, accuracy versus coverage plots were used and resulted in the observation that practical rules (allowing 5% leakage [misidentified assignments]) perform much better than strict rules (no leakage). In addition, k = 10 was determined as the optimal k value for k‐mer character analysis. Hybrid methods incorporating both k‐mer characters and aligned DNA sequence characters outperform the individual approaches. Finally, unnamed drosophilid accessions were compiled and tentatively assigned taxonomy based on the diagnostic system developed here.
ABSTRACT Understanding how phenotypic plasticity and local specialization are shaped by gene flow and environmental heterogeneity requires natural systems that vary in both spatial isolation and environmental conditions across the landscape, yet such systems are uncommon. Naturally discontinuous inselbergs may provide this opportunity. Here, using populations of the inselberg‐specialist frog Leptodactylus lithonaetes , we evaluated whether habitat discontinuity translates into restricted gene flow and genetic structure and then tested how variation in connectivity and environmental heterogeneity shapes the balance between phenotypic plasticity and local specialization. We predicted that populations with higher environmental heterogeneity and higher gene flow would evolve plasticity in growth and development, whereas populations in more homogeneous environments and more genetically isolated would exhibit reduced plasticity and increased specialization. Using > 11,000 SNPs, we showed that the apparent habitat discontinuity among nine inselbergs spanning 300 km was reflected in a strong population structure and varying levels of gene flow among inselbergs, in an isolation‐by‐distance pattern. We then tested whether tadpoles alter their size or timing at metamorphosis to pond‐drying risk, and whether these plastic responses vary among populations with environmental heterogeneity (seasonality). Although tadpoles did not plastically accelerate metamorphosis under pond‐drying risk, the magnitude of body mass reduction under desiccation stress differed among populations, indicating developmental plasticity in body mass. Northern localities, exposed to greater environmental heterogeneity, showed greater survival and less body weight loss, resulting in higher tolerance to environmental stress than southern localities. Even in the absence of developmental acceleration, population‐level variation in responses to environmental stress is congruent with reduced plasticity, or increased specialization, in isolated populations exposed to less heterogeneous environments.
ABSTRACT To understand the effects of climate change and other disturbances on ecosystems, methodologies capable of unravelling the complexity of biotic interactions are vital. Here, we present a dietary study on five passerines nesting in boreal forests: the crested tit Lophophanes cristatus , willow tit Poecile montanus , blue tit Cyanistes caeruleus , great tit Parus major , and pied flycatcher Ficedula hypoleuca . We used metabarcoding to describe their arthropod prey during the breeding season, and linked diets' properties with breeding success to understand birds' dependence on particular prey. The birds' diets contained hundreds of arthropod taxa, showing considerable richness and interannual variation. Most prey identities were resolved to species level. The most common prey were Lepidoptera, followed by Diptera, Coleoptera and Araneae. Dietary overlap was low to middling, conformed to temporal overlap, and fluctuated across the three studied years. Higher consumption of lepidopterans and their larvae was strongly associated with higher breeding success in blue tits and, to a lesser extent, great tits. In contrast, crested tits, willow tits and pied flycatchers had a more constant breeding success without relying on specific prey. The results suggest that the more recently settled blue tits and great tits are less capable of optimally utilizing the comparatively resource‐poor boreal environments. The apparent good adaptation to local foraging conditions contrasts to declining population trends in the Red‐Listed crested tits and willow tits. Our study highlights the complexity of arthropod communities and insectivore food webs, and showcase how molecular methods can be used to study ecological interactions.
ABSTRACT The Antarctic region, a centre of biodiversity origin, influences deep‐sea ecosystems by supplying species to distant regions. Understanding the influence of Antarctic Upper Circumpolar Deep Water (UCDW) on deep‐sea eukaryotic diversity is therefore essential for outlining global biodiversity patterns. Our results showed the UCDW community exhibited ~1.5‐fold higher taxonomic and phylogenetic diversity than the Caroline Basin control community and contained a substantial proportion of unique taxa across multiple eukaryotic lineages. Source tracking using the available Southern Ocean surface‐water reference detected a 4.42% Antarctic‐associated contribution to the UCDW community. Indicators and generalists of the UCDW community shared > 97% sequence identity with Southern Ocean samples. The community analyses suggested that the Yap‐Mariana Junction choke point did not constitute a strong barrier to connectivity between adjacent basins, consistent with UCDW‐mediated dispersal into the Philippine Basin. The UCDW microbial dispersal into the Philippine Basin occurs through two potential routes: directly through the YMJ at 2000–3000 m and via upwelling across seamounts at 500–750 m. Governed mainly by neutral, dispersal‐driven processes, the UCDW community showed strong genetic exchange and connectivity. These findings suggest a role for deep‐water circulation in shaping the diversity and distribution of eukaryotes detected in western Pacific deep‐water samples.
