Molecular Ecology最新文献

Gene and protein expression analyses are powerful tools to investigate the responses of cnidarians to stress, providing information on both genetic and functional variation and capturing dynamic shifts in organismal physiology. As the use of high throughput sequencing to understand responses of cnidarians to stressors is still relatively new, standard experimental protocols have not yet been established, which limits the ability to compare studies. We (1) systematically reviewed the literature of cnidarian gene and protein expression studies related to environmental stressors to determine how the laboratory experiments were designed and (2) investigated the consistency in responses of genes commonly used as biomarkers within stress experiments conducted on the five most-studied cnidarian genera. Duration of exposure to the stressor, acclimation period and intensity of stress varied greatly among experiments, and most studies did not sample during acclimation and recovery. Before designing experiments that aim to characterise molecular responses to a specific environmental stress, research efforts need to focus on understanding the plasticity of whole transcriptome responses, as gene expression can vary under different stress intensities and durations of exposure. Additionally, only seven genes that were tested in at least two different genera showed a consistent response under heat stress (CuZn-SOD, c-type lectin, FGFR1, MMP, Zn-MP, NF-κB and SLC26). These genes have the potential to standardise evaluations of temperature stress across experiments on cnidarians, and we suggest exploring their use as general cnidarian biomarkers of temperature stress (cBATS).

The carotenoid-based colours of birds are a celebrated example of biological diversity and an important system for the study of evolution. Recently, a two-step mechanism, with the enzymes cytochrome P450 2J19 (CYP2J19) and 3-hydroxybutyrate dehydrogenase 1-like (BDH1L), was described for the biosynthesis of red ketocarotenoids from yellow dietary carotenoids in the retina and plumage of birds. A common assumption has been that all birds with ketocarotenoid-based plumage coloration used this CYP2J19/BDH1L mechanism to produce red feathers. We tested this assumption in house finches (Haemorhous mexicanus) by examining the catalytic function of the house finch homologues of these enzymes and tracking their expression in birds growing new feathers. We found that CYP2J19 and BDH1L did not catalyse the production of 3-hydroxy-echinenone (3-OH-echinenone), the primary red plumage pigment of house finches, when provided with common dietary carotenoid substrates. Moreover, gene expression analyses revealed little to no expression of CYP2J19 in liver tissue or growing feather follicles, the putative sites of pigment metabolism in moulting house finches. Finally, although the hepatic mitochondria of house finches have high concentrations of 3-OH-echinenone, observations using fluorescent markers suggest that both CYP2J19 and BDH1L localise to the endomembrane system rather than the mitochondria. We propose that house finches and other birds that deposit 3-OH-echinenone as their primary red plumage pigment use an alternative enzymatic pathway to produce their characteristic red ketocarotenoid-based coloration.

Lowland and highland Peromyscus maniculatus populations display divergent, locally adapted physiological phenotypes shaped by altitudinal differences in oxygen availability. Many physiological responses to hypoxia seem to have evolved in lowland ancestors to offset episodic and localised bouts of low internal oxygen availability. However, upon chronic hypoxia exposure at high elevation, these responses can lead to physiological complications. Therefore, highland ancestry is often associated with evolved hypoxia responses, particularly traits promoting tolerance of constant hypoxia. Environmentally induced DNA methylation can dynamically alter gene expression patterns, providing a proximate basis for phenotypic plasticity. Given each population's differential reliance on plasticity for hypoxia tolerance, we hypothesised that lowland mice have a more robust epigenetic response to hypoxia exposure, driving trait plasticity, than highland mice. Using DNA methylation data of tissues from the heart's left ventricle, we show that upon hypoxia exposure, lowland mice chemically modulate the epigenetic landscape to a greater extent than highland mice, especially at key hypoxia-relevant genes such as Egln3. This gene is a regulator of the gene Epas1 that is frequently targeted for positive selection at high elevation. We find higher methylation among wild highland mice at gene Egln3 compared to wild lowland mice, suggesting a shared epigenetic ancestral response to episodic and chronic hypoxia. These findings highlight each population's distinct reliance on molecular plasticity driven by their unique evolutionary histories.

Speciation, i.e., the formation of new species, implies that diverging populations evolve genetic, phenotypic or ecological factors that promote reproductive isolation (RI), but the relative contributions of these factors remain elusive. Here we test which of genomic, bioacoustic, morphological, and environmental differences best predicts RI across a continuum of divergence in the midwife toads (genus Alytes), a group of Western Mediterranean amphibians, using a total evidence approach. We found that, without strong geographic barriers to dispersal, the extent of introgression across hybrid zones between phylogeographic lineages, which should reflect the strength of RI, predominantly covaries with genomic divergence. Overall phenotypic differentiation becomes substantial only between well established, fully isolated species. These results suggest that speciation in midwife toads initially involve cryptic lineages, which probably evolve RI through intrinsic (genetic) hybrid incompatibilities. As they continue to diverge, these nascent species eventually differentiate externally, which potentially enforces pre-mating barriers and facilitates sympatry. This speciation scenario has practical implications for species delimitation, notably when using hybrid zones and divergence thresholds as proxies for reproductive isolation.

Biological invasions offer a valuable 'natural experiment' to investigate survival mechanisms, as invaders successfully endure substantial environmental changes during their geographical spread and settlement. Phenotypic plasticity enhances fitness by enabling rapid responses without requiring new genetic variations. Among numerous mechanisms involved in phenotypic plasticity, microRNAs (miRNAs) and their regulatory networks are believed to enable rapid responses by fine-tuning gene expression, though their roles remain poorly understood. By integrating miRNAomic and transcriptomic analyses in the model invasive ascidian Ciona robusta, we simulated recurring salinity stresses encountered during invasions to investigate the molecular mechanisms of miRNA-mediated gene regulation in response to recurrent environmental challenges. Multiple analyses demonstrated that miRNAs exhibited rapid, dynamic and reversible responses to recurrent stresses, displaying duration-dependent and stage-specific profiles. The upregulation of genes in the miRNA biogenesis process, rather than the decay pathway, primarily accounted for the increased expression abundance of miRNAs. Responsive miRNAs regulated target genes through an intricate regulatory network, demonstrated by both up and downregulatory relationships and diverse binding sites. Interestingly, miRNAs and their target genes exhibited a 'stress memory' effect, where miRNAs 'remembered' previous challenges and further mediated the enhanced response of target genes at later stresses. Functionally, miRNA-mediated salinity coping strategies and associated genes exhibited temporal variations depending on challenge duration and stage, and these strategies primarily involved the modulation and alternation of free amino acid metabolism and ion transport to maintain osmotic homeostasis. These findings highlight the importance of miRNA-mediated regulatory networks in shaping short-term phenotypic plasticity in response to environmental changes.

Loss of genetic diversity threatens a species' adaptive potential and long-term resilience. Predicted to be extinct by 2038, the orange-bellied parrot (Neophema chrysogaster) is a critically endangered migratory bird threatened by numerous viral, bacterial and fungal diseases. The species has undergone multiple population crashes, reaching a low of three wild-born females and 13 males in 2016, and is now represented by only a single wild population and individuals in the captive breeding program. Here we used our high-quality long-read reference genome, and contemporary (N = 19) and historical (N = 16) resequenced genomes from as early as 1829, to track the long-term genomic erosion and immunogenetic diversity decline in this species. 62% of genomic diversity was lost between historical (mean autosomal heterozygosity = 0.00149 ± 0.000699 SD) and contemporary (0.00057 ± 0.000026) parrots. A greater number and length of runs of homozygosity in contemporary samples were also observed. A temporal reduction in the number of alleles at Toll-like receptor genes was found (historical average alleles = 5.78 ± 2.73; contemporary = 3.89 ± 2.10), potentially exacerbating disease susceptibility in the contemporary population. Of particular concern is the new threat of avian influenza strain (HPAI) to Australia. We discuss the conservation implications of our findings and propose that hybridisation and synthetic biology may be required to address the catastrophic loss of genetic diversity that has occurred in this species in order to prevent extinction.