Molecular Ecology最新文献

The lucinid clam Lucinoma capensis thrives at the oxygen minimum zone margins in the Benguela Upwelling System, where oxygen levels fluctuate dramatically. Understanding its adaptation to such extreme conditions provides key insights into survival strategies under fluctuating oxygen availability. We investigated the transcriptomic and metabolomic responses of L. capensis under normoxia, hypoxia, and recovery, focusing on the gills and digestive gland. Our findings highlight distinct organ-specific responses, with the gills showing strong transcriptional changes to oxygen fluctuations, in contrast to the more stable profile observed in the digestive gland. Under hypoxic conditions, the gills exhibited coordinated downregulation of protein synthesis, transposable element activity, and immune function, suggesting a tightly regulated energy conservation strategy and mechanisms to preserve symbiont stability and genomic integrity. Activation of prokaryotic metabolism in the gills supports the symbionts' role in host energy acquisition and sulfide detoxification during hypoxia. In contrast, the digestive gland showed minimal transcriptional shifts during anoxia, with upregulation of pathways supporting structural maintenance. Upon reoxygenation, the gills displayed an active and asymmetric recovery, characterised by rapid restoration of protein synthesis and gradual normalisation of protein degradation and immune functions. Despite significant transcriptomic changes, the metabolome remained largely stable, reflecting L. capensis's resilience to oxygen fluctuations. However, an overshoot in TCA cycle intermediates and derepression of previously downregulated pathways indicate that reoxygenation involves active metabolic reprogramming, not merely a return to baseline. This study highlights the specialised tissue responses and symbiotic contributions that enable L. capensis to thrive in one of the ocean's most challenging environments.

Adaptation to the environment plays an essential role in yeast evolution as a consequence of selective pressures. Lachancea thermotolerans, a yeast related to fermentation and one of the current trends in wine technology research, has undergone an anthropisation process, leading to a notable genomic and phenomic differentiation. Using whole-genome sequencing, of 145 L. thermotolerans strains, we identified six well-defined groups primarily delineated by their ecological origin and exhibiting high levels of genetic diversity. Anthropised strains showed lower genetic diversity due to the selective pressure imposed by the winemaking environment. Strong evidence of anthropisation and adaptation to the wine environment through modification of gene content was also found. Differences in genes involved in the assimilation of alternative carbon and nitrogen sources, such as the MAL31 and DAL5 genes, which confer greater fitness in the winemaking environment, were observed. Additionally, we found that phenotypic traits considered domestication hallmarks are present in anthropised strains. Among these, increased fitness in the presence of ethanol and sulphites, assimilation of non-fermentable carbon sources, and lower levels of residual fructose under fermentative conditions highlight. We hypothesise that lactic acid production in the Saccharomyces-Lachancea lineage is an anthropisation signature linked to winemaking, resulting from the loss of respiratory chain complex I and the evolutionary preference for fermentation over respiration, even in the presence of oxygen. Overall, the results of this work provide valuable insight into the anthropisation process in L. thermotolerans and demonstrate how fermentation environments give rise to similar adaptations in different yeast species.

Networks of alpine lakes and ponds support unique assemblages of aquatic organisms and provide an ideal biogeographical setting for studying the evolutionary, ecological and demographic outcomes of population fragmentation. In this study, we integrate genomic, morphological and community-level data within a comparative multi-taxon framework to investigate genetic connectivity, demographic trajectories and eco-evolutionary dynamics in four diving beetles (Coleoptera: Dytiscidae) representative of the macroinvertebrate assemblages inhabiting high altitude lakes in the Sierra Nevada massif, southeastern Iberia. Although the focal taxa share similar ecological requirements, primarily occupy lentic habitats and disperse by flight, our results reveal substantial heterogeneity in their demographic responses to the naturally fragmented distribution of alpine lakes. Taxa with higher wing loading exhibited stronger genetic differentiation among populations, probably due to their reduced capacity to disperse across the direct geographic distances separating lakes. Populations located at the range periphery tended to exhibit lower genetic diversity than central populations in all taxa. Demographic reconstructions showed a general decline in effective population size from the last glacial maximum (LGM) to the present. However, some populations of genetically more structured taxa went through brief bottlenecks that coincided with periods of warmer climate and lower lake levels, as inferred from local paleoclimatic reconstructions. Finally, the composition of macroinvertebrate assemblages (α-diversity and β-diversity) was not associated with intra-specific genetic diversity or differentiation, suggesting that species-level demographic trajectories and community-level dynamics are decoupled. Our findings indicate that interspecific differences in dispersal capacity outweigh shared environmental constraints in determining the contrasting demographic trajectories of the studied taxa. Collectively, these results emphasise the importance of multi-taxon approaches for understanding the dynamics of species assemblages in alpine ecosystems that are highly vulnerable to climate warming.

Translocating individuals into existing populations of conspecifics can support threatened species by increasing population size, maintaining genetic diversity and reducing the risk of inbreeding. However, for species whose adaptive potential is compromised due to ongoing threats, like disease, the outcome of such management interventions becomes more complex. The Tasmanian devil (Sarcophilus harrisii) is a prime example, where the emergence of Devil Facial Tumour Disease (DFTD) has led to significant population declines, raising concerns about their long-term survival. It is therefore critical to understand if the introduction of new functional genetic variants through supplementation actions enhances, or potentially hinders, their long-term persistence. We investigated changes in functional gene diversity at both the population- and individual-levels, pre- and post-supplementation, across multiple wild devil sites (four supplemented and four not supplemented). We found that functional diversity increased post-supplementation. Though the magnitude of change was varied among sites, a similar site-specific pattern was also evident in genome-wide diversity. Importantly, we saw no evidence of swamping of local alleles or those putatively associated with DFTD regressions. This is likely due to the source population representing the broad wild genetic diversity and supplementations facilitating gene flow across the current fragmented landscape. Continued and long-term monitoring at multiple wild sites will be necessary to determine whether future generations retain this introduced genetic variation.

The kākāpō is a critically endangered flightless parrot which suffers from exudative cloacitis, a debilitating disease resulting in inflammation of the vent margin or cloaca. Despite this disease emerging over 20 years ago, the cause of exudative cloacitis remains elusive. We used total RNA sequencing and metatranscriptomic analysis to characterise the infectome of lesions and cloacal swabs from nine kākāpō affected with exudative cloacitis, and compared this to cloacal swabs from 45 non-diseased kākāpō. We identified three bacterial species-Streptococcus gallolyticus, Enterococcus faecalis and Escherichia coli-as significantly more abundant in diseased kākāpō compared to healthy individuals. The genetic diversity observed in both S. gallolyticus and E. faecalis among diseased kākāpō suggests that these bacteria originate from exogenous sources rather than from kākāpō-to-kākāpō transmission. The presence of extraintestinal pathogenic E. coli (ExPEC)-associated virulence factors in the diseased kākāpō population suggests that E. coli may play a critical role in disease progression by facilitating iron acquisition and causing DNA damage in host cells, possibly in association with E. faecalis. No avian viral, fungal nor other parasitic species were identified. These results, combined with the consistent presence of one E. coli gnd sequence type across multiple diseased birds, suggest that this species may be the primary cause of exudative cloacitis. These findings shed light on possible causative agents of exudative cloacitis, and offer insights into the interplay of microbial factors influencing the disease.

Cameroon Blackbelly sheep are a domestic breed of hair sheep from West/Central Africa. They are popular with small-holder farmers in Cameroon as they are highly resilient to local environmental challenges and are prolific a-seasonal breeders. The aim of this study was to characterise the genetics of Cameroon Blackbelly sheep in relation to global sheep populations and to investigate their relationship to Caribbean hair sheep. We first examined the genetic diversity of the Cameroon Blackbelly breed relative to global sheep populations using 50K SNP data. We also used whole genome sequence data to further investigate relationships between Cameroon Blackbelly and breeds from Africa and Europe, as well as the Barbados Blackbelly breed from the Caribbean, which is phenotypically similar to Cameroon Blackbelly. ADMIXTURE results based on 50K and WGS data demonstrated both West/Central African and European ancestries for the Barbados Blackbelly sheep. Results from f₄-statistics-based qpAdm analyses supported these findings. Local ancestry inference identified several genomic regions in Barbados Blackbelly with high proportions of West/Central African ancestry. One of these, on OAR3, includes various keratin genes, suggesting that these genes may play a role in the shared coat phenotypes of the Barbados Blackbelly and Cameroon Blackbelly. This result is consistent with previous reports of adaptive introgression of coat characteristics in both wild and domesticated species. The findings of our study support the view that sheep were transported from West/Central Africa to the Caribbean as part of the transatlantic slave trade and European colonisation, similar to introductions proposed for cattle and goats.

Our understanding of speciation processes is constantly changing. Two important concepts that have influenced thinking over the long term are the isolation and the genic views of speciation. However, neither of these views is fully compatible with our current understanding of speciation processes. The fact that many species with overlapping ranges remain distinct despite hybridisation and introgression suggests that species are not co-adapted gene pools that have evolved in allopatry and are protected from merging by reproductive isolation, as the isolation view of speciation assumes. Speciation can occur without geographic isolation, and alleles of some genes may be exchanged between species, while others may not, as suggested by the genic view of speciation. However, in contrast to the genic view, the alleles of genes underlying differential adaptation may not have opposite fitness effects. Rather, the traits under selection may be determined by effects of many genes. The facts that individual genes have usually only small effects on adaptive traits, the same trait can be achieved by different combinations of alleles, homologous traits may be determined by different gene regulatory underpinnings, new traits resulting from transgressive segregation may be essential for differential adaptation, and that non-genic traits can cause speciation, indicate that traits rather than individual genes are the most relevant units of speciation. The development of strong barriers that allow diverging populations to coexist may require a coupling of barrier effects, which can be facilitated by several factors, such as the pleiotropic effects of many genes or structural variants that reduce recombination, which are not considered in the genic view. Considering traits rather than single genes as units of speciation, and considering factors above the level of genes that contribute to the coupling of barrier effects, distinguishes the trait view of speciation from the genic view.

Global change is accelerating biological invasions, making it crucial to understand how species adapt in new environments to improve management strategies. Genomic data provide valuable insights into adaptation through genotype-environment association (GEA) studies, which identify genes and biological processes tied to invasion success, and through geometric genomic offset (gGO) statistics, which estimate genetic (mal)adaptation to new environments. Here, we investigate genetic adaptation in the invasive pest Drosophila suzukii using novel genomic resources and statistical methods. We use a new chromosome-level genome assembly and data from 37 populations, combining publicly available and newly generated pooled and individual sequencing data, analysed with an enhanced version of BayPass software, tailored for such hybrid datasets. First, we identify genomic regions showing genetic differentiation between native and invasive populations. Then, using a GEA with 29 environmental covariates, we estimate the gGO between the source environments and the invaded areas, shedding light on the potential adaptive challenges D. suzukii faced during previous invasions. In addition, we estimate gGO for geographical areas not yet invaded to predict future invasion risks, and identify regions from which preadapted populations may originate. Our results reveal numerous genomic regions associated with the invasive status from genome scans. However, when considering broader patterns of adaptation to specific environmental variables through gGO analyses, we find that D. suzukii populations likely faced only limited adaptive challenges across their major invasion range, while certain uninvaded regions still remain at high risk of future invasion. Our study offers significant insights into D. suzukii adaptation and provides a practical population genomics framework to predict biological invasions, applicable to various species.

The marine environment comprises vast regions without physical barriers to movement, making the understanding of population isolation and the evolution of diversity challenging. This is especially the case for highly mobile marine species. Here we investigate populations of the common bottlenose dolphin (Tursiops truncatus) across the Mediterranean Sea and adjacent North Atlantic using high-resolution genomic markers (RADseq) and stable isotope analyses to better understand the evolution of population structure in this system. High-resolution genomic data and broad geographic sampling revealed patterns of structure not previously identified, and integration with stable isotope data suggests that prey choice varies across this region. Unexpected patterns included genetic and isotopic similarity between the North Atlantic and the region around Sicily (but not including the medially located Gulf of Cádiz and surrounding regions). The regional habitat within and beyond the Mediterranean Sea is structured with ocean frontal systems including thermal and halocline transitions, several of which show alignment with genetic transitions within our data. Our data help to distinguish among possible drivers of population differentiation for a marine predator that has the potential for long-distance dispersion.

Dispersal of marine benthic invertebrates is typically dependent on the developmental mode of their pelagic larvae, which can be prolonged and based on plankton feeding (planktotrophic), or short and rely on the nutrients from the egg (non-planktotrophic). The uncommon poecilogonic species can commit to both developmental modes, with remarkable implications for their population genetics, not yet fully investigated. In this study, we obtained reduced-representation genome-wide SNP data for three species of the neogastropod genus Raphitoma Bellardi, 1847 from the Mediterranean, including the putatively poecilogonic species Raphitoma philberti (Michaud, 1829) and R. laviae (R. A. Philippi, 1844). A total of 80 samples were sequenced to test the poecilogony and analyse the population genetics of R. laviae. Although a certain degree of segregation was highlighted between the planktotrophic and non-planktotrophic samples in both species, they were ultimately found within conspecific bounds, confirming poecilogony. A set of loci that split samples with different development was identified, suggesting that a genetic component may be involved in poecilogony in both species. The population genetics of R. laviae fit patterns of both long- and short-dispersal species: in Corsica, with only planktotrophic developers, no geographic structure was detected, whereas in Croatia, with only non-planktotrophic developers, the geographic structure was present among localities 15-40 km apart. Notably, the species delimitation based on genome-wide SNP data was contrasting with the one assessed in past studies, reiterating that a solid taxonomy (still not achieved) is paramount to correctly interpret the evolution of larval development in this group.