BMC ecology and evolution最新文献

Mito-nuclear (or cytonuclear) discordance, evolutionary incongruence between the mitochondrial and nuclear genomes, is a widespread but underappreciated phenomenon that may obscure signals of introgression and hybridization important for understanding evolutionary trajectories and species boundaries. The present study explored the roles of secondary contact and introgressive hybridization in the diversification of Buthus Leach, 1815 scorpions in the Iberian Peninsula, a hotspot for mito-nuclear discordance, in which complex topography and glacial history facilitated repeated cycles of isolation and secondary contact. Patterns of mito-nuclear discordance were predicted to be consistent with overlapping distributions, similar ecological niches, and intermediate phenotypes. By integrating genomic, morphological, and ecological data, the intricate evolutionary history of Buthus, shaped by vicariance, reticulation and ecological opportunity, was revealed. The results underscore the role of introgressive hybridization in shaping patterns of biodiversity and the need to consider mito-nuclear discordance in species delimitation.

Several studies analyzed the origin of flapping birds, but only a few of them explored the scapular girdle myology in early birds and non-avian paravians. We analyze the pectoral girdle morphology in different groups of non-ornithothoracine paravians with the aim to hypothesize the anchorage sites of selected pectoral muscles and determine their main functions in forelimb movements. Notably, the pectoral girdle remained morphologically stable among non-ornithothoracine paravians since certain aspects of the coracoid and scapula are similar in non-flying taxa, such as the cursorial Buitreraptor, as well as those with the ability to fly, such as the four-winged Microraptor, the long-tailed Archaeopteryx and the pygostylians Confuciusornis and Sapeornis. The distinctions among these taxa are slightly discernible in bone morphology, but they are obvious in the forelimbs feather coverage. In this sense, main pectoral muscles (i.e., mm. supracoracoideus, pectoralis and deltoideus scapularis/major) had similar origin and insertion places, and their inferred functions were similar across a wide array of body shapes of early paravians. The most significant muscular changes occurred in the common ancestor of Pygostylia, and consisted in the displacement of the origin of the mm. biceps brachii and coracobrachialis p. cranialis, accompanying the greater development of the acrocoracoid process and the loss of the subglenoid fossa. These modifications allowed more muscles to participate in humeral protraction and in the maintenance of wing extension. Subsequently, in the Ornithothoraces node, coracoid transformations contributed to the medial reorientation of the supracoracoidal canal thus allowing the m. supracoracoideus to fulfill a wing elevation function. Our study suggests that in non-ornithothoracine paravians, the main movements of the forelimb (either fliers or not) were predominantly craniodorsal to caudoventral. The humeral movements were performed in a similar manner, in which the main elevators were the mm. deltoideus and latissimus dorsi group, while the mm. supracoracoideus and pectoralis would have acted as protractor and depressor, respectively. Therefore, the ability to maintain a continuous flapping flight present in extant volant birds may have been acquired at the Ornithothoraces node, while Archaeopterygidae, Confuciusornithidae and Omnivoropterygidae may have had functional flight, short in duration and space displacement.

The Iberian desman (Galemys pyrenaicus), a semiaquatic mammal endemic to southwestern Europe, is listed as Endangered by the IUCN due to substantial range and population decline in recent years, with its populations now largely limited to river headwaters. This restriction to upstream locations highlights the importance of documenting genetic variation and population connectivity in Iberian desmans for effective conservation strategies. While previous studies have revealed phylogeographic structure across the range of the species, gaps remain in our understanding of the microgeographic dynamics that shape genetic exchange within specific geographic regions. This study first combined our newly generated SNP data with previous datasets to further explore genetic structure across the entire Iberian desman distribution using the 115 individuals now available. Due to differences in methodology between our study and previous studies, only 110 SNPs were available for comparison across all individuals. Nevertheless, the analysis with these SNPs confirmed the presence of the five major phylogeographic units previously described and validated the assignment of our newly generated dataset to the Occidental phylogeographic unit. Focusing on our newly generated data, we explored the microgeographic dynamics of this Occidental phylogeographic unit with a higher-resolution genomic dataset (7,604 SNPs, 14 individuals). This analysis provided evidence of isolation-by-distance (IBD), suggesting that gene flow decreases with increasing geographic distance and that dispersal occurs primarily over short distances. Focussing on the Douro river system, our genomic clustering results showed both connectivity along the best-sampled river (Sabor) and between headwaters of this and headwaters from a closely located river (Tua). Our IBD results were consistent with this, indicating riverine dispersal as well as a combination of riverine and overland dispersal at headwaters. These results highlight the importance of both aquatic and terrestrial corridors in upstream areas for maintaining connectivity. Thus, conservation efforts should prioritize the protection and restoration of riparian and terrestrial corridors, particularly in fragmented landscapes, to mitigate isolation and preserve genetic diversity in the Iberian desman. This study underscores the value of genomic approaches in conservation and contributes to a deeper understanding of the ecological and evolutionary processes that maintain population connectivity in an endangered species.

Background: The evolutionary relationships within Stomiiformes, a diverse order of deep-sea fishes dominating the mesopelagic and bathypelagic zones, remain contentious due to conflicting morphological and molecular evidence. These fishes, comprising 464 species across four traditionally recognized families (Gonostomatidae, Sternoptychidae, Phosichthyidae, and Stomiidae), exhibit remarkable adaptations such as bioluminescence, ultra-black pigmentation, and extreme jaw morphologies. Their global abundance and ecological significance, including contributions to the biological carbon pump, underscores the need to resolve their phylogeny amid escalating threats from climate change and human activities.

Results: We conducted the most comprehensive phylogenomic analysis of Stomiiformes to date, integrating 936 nuclear loci from 60 species and an expanded dataset of 135 species with mitochondrial sequences from publicly available repositories such as the Barcode of Life Data Systems (BOLD) database. We used maximum likelihood and coalescent-based approaches to assess family monophyly and relationships, including extensive quality control to address contamination in public databases. Our analyses reveal unstable tree topologies and complex evolutionary histories that challenge traditional classifications, while our quality control analyses identified 29% of BOLD sequences as misidentified or contaminated, emphasizing rigorous curation for deep-sea taxa. Congruent with a recent taxonomic treatment of Stomiiformes, the families Phosichthyidae and Gonostomatidae exhibit polyphyly and paraphyly, respectively, while subfamilies within Stomiidae are extensively non-monophyletic, leading us to recommend their abandonment. We propose the recognition of eight monophyletic families: Vinciguerriidae, Diplophidae, Gonostomatidae, Yarrellidae, Ichthyococcidae, Phosichthyidae, Sternoptychidae, and Stomiidae, supported by robust molecular and morphological evidence.

Conclusions: This revised classification reflects the morphological and ecological diversity of Stomiiformes, aligning with their evolutionary diversification in the deep sea. Our phylogenomic framework resolves longstanding systematic uncertainties and highlights the power of genome-wide data in tackling taxonomically challenging clades. These findings provide a foundation for understanding deep-sea fish diversification and assessing the potential ecological drivers for their evolutionary diversity.

Comparative biology seeks to unlock the power of cross-species trait variation to learn the rules of life. In this venture, modern studies increasingly leverage large datasets spanning many traits and levels of biological organization and complexity. To analyze these complex data in a statistically-sound manner, researchers must choose a phylogeny that is assumed to model the mean trait values across species-an assumption that may be tenuous depending on the true evolutionary architecture of the traits. Yet the consequences of this decision remain poorly understood, particularly for modern studies seeking to analyze multiple, distinct traits within the same framework. Here, we conduct a comprehensive simulation study to examine how tree choice impacts phylogenetic regression in large-scale analyses of many traits and species. We find that regression outcomes are highly sensitive to the assumed tree, sometimes yielding alarmingly high false positive rates as the number of traits and species increase together. Counterintuitively, adding more data exacerbates rather than mitigates this issue, highlighting the risks inherent for high-throughput analyses typical of modern comparative research. Experimental manipulations of tree topology in an empirical case study of gene expression and longevity traits further reveal extreme sensitivity to tree choice. While significant challenges remain in aligning traits with appropriate trees, we find compelling promise with robust estimators, which can mitigate the effects of tree misspecification under realistic evolutionary scenarios. Collectively, our findings underscore the critical need for careful tree selection in comparative studies while pointing to robust regression as a powerful tool for navigating phylogenetic uncertainty in modern evolutionary research.

Background: The Asian elephant, a keystone species of immense ecological and evolutionary significance, is under intensifying threat from habitat fragmentation and human-elephant conflict. Reliable population estimates are critical for effective conservation planning and understanding demographic processes, yet traditional methods like dung counts can be skewed by detectability issues and environmental variability. Here, we compared conventional line-transect dung counts with a non-invasive genetic spatially explicit capture-recapture (genetic SECR) approach in Kodagu, Karnataka, using high-throughput microsatellite sequencing (SSR-Seq). Our study area harbours a known population of 34 elephants (0.21 elephants/km²), providing a rare opportunity to evaluate the accuracy and bias of estimation methods against a field-validated reference point.

Results: Dung counts yielded an elephant density of 1.27(±0.32) elephants/km², overestimating the true population by 6 times. In contrast, genetic SECR based on genotypes from 131 fecal samples estimated a density of 0.23 elephants (±0.03)/km² individuals), closely aligning with the known density. Genetic analysis also revealed substantial allelic richness and potential population substructure.

Conclusions: These results demonstrate that genetic SECR not only reduces estimation bias but also reveals evolutionary relevant insights into genetic diversity and population structure. While genetic methods require greater per-unit investment compared to dung counts, a hybrid strategy may be most practical: periodic genetic SECR surveys to calibrate and validate easier methods (like dung counts or camera traps) used more frequently. As technology advances, costs of fecal DNA analysis are likely to decrease further. This hybrid framework optimizes resource allocation while maintaining scientific rigor, particularly important for large-scale monitoring programs across diverse landscapes.

Background: Ecological niche models (ENMs) and analyses of niche overlap/divergence have become popular methods in ecology and evolutionary biology. These analyses rely on environmental data available from several databases. However, the influence of data sources on these analyses is rarely tested. Here, we test the impact of climatic data choice on the prediction of current and Plio-Pleistocene suitable habitats for two distantly related, but broadly sympatric, salamanders endemic to the Korean Peninsula. We ran MaxEnt separately on WorldClim and CHELSA climate data. We then hindcasted ENMs to five time periods of the Plio-Pleistocene, bracketing the estimated intraspecific divergence times for these species. We then quantified the differences in predictions between WorldClim- and CHELSA-based models. Also, given the sympatry and similar habitat requirements of the two species, we tested for niche overlaps using niche identity and background tests and tested the sensitivity of the results to climatic data choice.

Results: The ENMs successfully predicted contemporary suitable habitats for the two species. However, the predictions were highly sensitive to climatic data choice as well as variable combinations. The hindcasted ENMs produced contrasting predictions depending on the choice of climatic dataset and failed to predict suitable habitats for some Pleistocene time periods regardless of the climatic data choice. The niche analyses were also sensitive to climatic data choice, with results suggesting either niche overlaps or divergence depending on the climatic dataset used for the analyses.

Conclusions: Our study highlights the influence of climatic data choice on the outcomes of ENMs and niche analyses. Our results also underscore the limitations of macroclimate-based ENMs, especially when the species is likely buffered from macroclimatic changes by microhabitat. We argue for the need for additional ecological, ecophysiological, and population genomic studies to better understand the range formation of these enigmatic species.