Molecular Ecology最新文献

The vast tropical rainforests of the Guiana Shield in Northern South America play a vital role in maintaining the region's ecological balance and economy. Increasing pressure from selective logging, gold mining and climate variability threatens these ecosystems. Sustainable rainforest management requires understanding the genetic diversity and local adaptation of key tree species to inform conservation. This study focuses on Dicorynia guianensis (Fabaceae), a widespread and economically important tree species in French Guiana. We performed genome resequencing on 87 individuals sampled in 11 sites across French Guiana to investigate the genetic structure, diversity and genetic basis of local adaptation. Genetic structure analysis identified three distinct groups: western, central and eastern, with similar levels of genetic diversity distributed in areas with different environmental conditions. Six methods applied to detect genomic signatures of selection revealed region-specific selective sweeps and a weak overlap between single nucleotide polymorphisms (SNPs) identified through outlier analysis or genome-environment association analyses. The strongest associations between environmental variables and genomic constitution were observed for potential evapotranspiration of the wettest quarter and for precipitation of the coldest quarter, suggesting that environmental variables related to high rainfall during the wet season are stronger drivers of local adaptation of D. guianensis populations than drought. Sites located in central and western French Guiana had higher risks of climatic maladaptation. These findings advance our understanding of local adaptation and climatic vulnerability in tropical trees and emphasise the need for targeted, area-specific management strategies for conservation and sustainable timber extraction under climate change.

Niche specialisation is a double-edged sword as it aids species in adapting to a particular environment but makes them more susceptible to environmental change, which may result in species extinction. Although it has long been debated whether niche specialisation necessarily falls into an 'evolutionary dead end', empirical evidence from a population genetics perspective remains scant, especially when comparing both ecological generalists and specialists simultaneously. In this study, we scrutinised two Taiwan endemic gingers (Zingiber pleiostachyum and Z. shuanglongense) to evaluate how their contrasting patterns in niche breadth evolution have shaped their evolutionary trajectories. We utilised a genome-wide sequencing approach to investigate the demographic histories of each species, assess their maladaptation to future climate change, and estimate their mutational loads. Our results revealed distinct demographic histories between these two gingers. Z. shuanglongense, as the specialist, despite an initial increase during the Last Glacial Maximum (~22 Kya), has been subjected to a long-term decrease in effective population size (Ne), while Z. pleiostachyum is on the contrary increasing, leading to a significantly larger current Ne. Furthermore, ecological specialists are much more vulnerable to future climate change and exhibit greater drift-associated deleterious mutations compared to generalists, directly affecting species' fitness. This study strongly supports the idea that the transition in niche breadth towards specialisation will push Z. shuanglongense perilously close to extinction and also sheds light on species conservation within limited migratory space.

Coastal seawater hypoxia is increasing in temperate estuaries under global climate change, yet it is unknown how low oxygen conditions affect most estuarine species. We found that hypoxia has increased since the 1990s in an estuary hosting the sea anemone Nematostella vectensis (Jacques Cousteau National Estuarine Research Reserve, New Jersey, USA). Adult N. vectensis bred from anemones collected in this estuary exposed to three consecutive nights of hypoxia (dissolved oxygen = 0.5–1.5 mg L⁻¹ for ~12 h night⁻¹) during gametogenesis displayed decreased aerobic respiration rates and biomass, indicating metabolic disruption. Physiological declines were correlated with changes in the expression of genes related to oxygen-dependent metabolic processes, many of which are targets of hypoxia-inducible factor 1α (HIF1α), demonstrating the activity of this transcription factor for the first time in this early-diverging metazoan. The upregulation of genes involved in the unfolded protein response and endoplasmic reticulum and Golgi apparatus homeostasis suggested that misfolded proteins contributed to disrupted physiology. Notably, these responses were more pronounced in females, demonstrating sex-specific sensitivity that was also observed in reproductive outcomes, with declines in female but not male fecundity following hypoxia exposure. However, sperm from exposed males had higher mitochondrial membrane potential, indicating altered spermatogenesis. Further, crosses performed with gametes from hypoxia-exposed adults yielded strikingly low developmental success (~2%), yet larvae that did develop displayed similar respiration rates and accelerated settlement compared to controls. Overall, hypoxia depressed fitness in N. vectensis by over 95%, suggesting that even stress-tolerant estuarine species may be threatened by coastal deoxygenation.

Caloric restriction (CR) studies have traditionally focused on species with conventional reproductive roles, emphasising female's greater investment in costly gametes and parental care. While the divergent impact of CR on males and females is evident across species, the factors driving this variation, that is, resource allocation to reproductive elements as part of distinct life history strategies, remain unclear. To address this, we investigated the effects of CR on development, gene expression and intestinal microbiota in the lined seahorse Hippocampus erectus, a species with male pregnancy, where fathers invest in offspring through gestation. Juvenile seahorses were subjected to ad libitum (AL) or CR feeding for 5 months. CR stunted male growth and brood pouch development, reflecting the energy demands of this crucial parental care trait. However, condition index declined in CR females but not males, while ovarian weight remained unchanged. Transcriptome analysis demonstrated organ- and sex-specific responses to CR with distinct lipid and energy-related pathways activated in male and female livers, indicative of survival enhancement strategies. CR had minimal impact on genes associated with spermatogenesis, but downregulated lipid metabolic and inflammatory genes in ovaries, emphasising the importance of pre-copulatory resource allocation in female gametes. CR strongly shaped gut microbial composition, creating distinct communities from AL seahorses while also driving sex-specific taxonomic differences. Our research indicates that nutrient limitation's impact on males and females is influenced by their allocation of resources to reproduction and parental investment. We underscore the significance of studying species with diverse reproductive strategies, sex roles and life-history strategies.

In vascular plants, heterosporous lineages typically have fewer chromosomes than homosporous lineages. The underlying mechanism causing this disparity has been debated for over half a century. Although reproductive mode has been identified as critical to these patterns, the symmetry of meiosis during sporogenesis has been overlooked as a potential cause of the difference in chromosome numbers. In most heterosporous plants, meiosis during megasporogenesis is asymmetric, meaning one of the four meiotic products survives to become the egg. Comparatively, meiosis is symmetric in homosporous megasporogenesis and all meiotic products survive. The symmetry of meiosis is important because asymmetric meiosis enables meiotic drive and associated genomic changes, while symmetric meiosis cannot lead to meiotic drive. Meiotic drive is a deviation from Mendelian inheritance where genetic elements are preferentially inherited by the surviving egg cell, and can profoundly impact chromosome (and genome) size, structure, and number. Here we review how meiotic drive impacts chromosome number evolution in heterosporous plants, how the lack of meiotic drive in homosporous plants impacts their genomes, and explore future approaches to understand the role of meiotic drive on chromosome number across land plants.

Fire is a common ecological disturbance that structures terrestrial ecosystems and biological communities. The ability of fires to contribute to ecosystem heterogeneity has been termed pyrodiversity and has been directly linked to biodiversity (i.e., the pyrodiversity-biodiversity hypothesis). Since climate change models predict increases in fire frequency, understanding how fire pyrodiversity influences soil microbes is important for predicting how ecosystems will respond to fire regime changes. Here we tested how fire frequency-driven changes in burn patterns (i.e., pyrodiversity) influenced soil microbial communities and diversity. We assessed pyrodiversity effects on soil microbes by manipulating fire frequency (annual vs. biennial fires) in a tallgrass prairie restoration and evaluating how changes in burn patterns influenced microbial communities (bacteria and fungi). Annual burns produced more heterogeneous burn patterns (higher pyrodiversity) that were linked to shifts in fungal and bacterial community composition. While fire frequency did not influence microbial (bacteria and fungi) alpha diversity, beta diversity did increase with pyrodiversity. Changes in fungal community composition were not linked to burn patterns, suggesting that pyrodiversity effects on other ecosystem components (e.g., plants and soil characteristics) influenced fungal community dynamics and the greater beta diversity observed in the annually burned plots. Shifts in bacterial community composition were linked to variation in higher severity burn pattern components (grey and white ash), suggesting that thermotolerance contributed to the observed changes in bacterial community composition and lower beta diversity in the biennially burned plots. This demonstrates that fire frequency-driven increases in pyrodiversity augment biodiversity and may influence productivity in fire-prone ecosystems.

Geographically widespread species tend to have more opportunities to hybridise with different related species. However, the evolutionary consequences of such multi-species hybridisation are still poorly understood. In the Hengduan Mountains of southwest China, Quercus aquifolioides and its closely related species form two types of elevational hybrid zone in different geographical areas (i.e., Q. aquifolioides-Q. guyavaefolia-Q. longispica and Q. aquifolioides-Q. spinosa). Here, we investigated genome-wide patterns of introgression between Q. aquifolioides and its sympatric relatives to assess the evolutionary consequences of multi-species hybridisation. A new assembled genome of Q. longispica as a reference genome and whole-genome resequencing data of these focal oaks were used in this study. Our results showed that bidirectional gene flow occurred between Q. aquifolioides and its sympatric relatives, and candidate genomic regions derived from introgression were broadly distributed across the oak genome. Local introgression with different sympatric relatives has fuelled the intraspecific divergence of Q. aquifolioides between two regions with different species compositions. We found genomic signatures of positive selection in some candidate introgressed regions. Putative adaptation signals were detected in candidate introgressed genes with diverse functions, including stress response and organism development and growth. In addition, we identified the genomic targets of environment-associated selection in Q. aquifolioides, some of which were located in candidate introgressed regions. In sum, this study demonstrates that local introgression with relatives is a non-negligible mechanism facilitating intraspecific divergence and reveals putative adaptive introgression between Q. aquifolioides and its sympatric relatives.

Many island archipelagos sit on shallow continental shelves, and during the Pleistocene, these islands were often connected as global sea levels dropped following glaciation. Given a continental shelf only 30–60 m below sea level, the terrestrial biota of the Seychelles Archipelago likely dispersed amongst now isolated islands during the Pleistocene. Hypogeophis rostratus is an egg-laying, direct-developing caecilian amphibian found on 10 islands in the granitic Seychelles. Despite the seemingly limited dispersal abilities of this salt-intolerant amphibian, its distribution on multiple islands suggests likely historic dispersal across now submerged continental shelf corridors. We tested for the genetic signature of these historic corridors using fine-scale genomic data (ddRADseq). We found that genomic clusters often did not correspond to islands in the archipelago and that isolation-by-distance patterns were more consistent with gene flow across a continuous landscape than with isolated island populations. Using effective migration surfaces and ancestral range expansion prediction, we found support for contemporary populations originating near the large southern island of Mahé and dispersing to northern islands via the isolated Frégate island, with additional historic migration across the flat expanse of the Seychelles bank. Collectively, our results suggest that biogeographic patterns can retain signals from Pleistocene ‘palaeo-islands’ and that present-day islands can be thought of as hosting bottlenecks or transient refugia rather than discrete genetic units. Thus, the signatures of gene flow associated with palaeo-islands may be stronger than the isolating effects of contemporary islands in terrestrial species distributed on continental shelf islands.