Zooplankton undergo a vertical migration which exposes them to gradients of light, temperature, oxygen and food availability on a predictable daily schedule. Anticipating and responding to these environmental conditions, which independently are known to influence metabolic rates, likely has an appreciable effect on the delivery of waste products to the distinctly different daytime (deep) and nighttime (surface) habitats. Disentangling the co-varying and potentially synergistic interactions on metabolic rates has proven difficult, despite the importance of this migration to oceanic biogeochemical cycling. This study examines the transcriptomic and proteomic profile of the circumglobal migratory copepod, Pleuromamma xiphias, over the diel cycle. The transcriptome showed a large number of up-regulated genes during the middle of the day – the period often considered to be of lowest metabolic activity. There were proteomic and transcriptomic peaks in oxidative stress response and muscle proteins after the periods of migration, suggestive of a physiological consequence of migration. There were changes in metabolic pathways over time, with increased ammonium production signals during the evening and chitin synthesis and degradation pathways during the day. Comparisons of patterns across the paired datasets suggest that 1) estimates of physiological rates made in the laboratory in steady state conditions that don’t account for time of day may not be adequate to predict in situ phenotypes 2) use of ‘omics datasets to predict organismal phenotypes must be done cautiously as highly dynamic patterns in the transcriptome and proteome are often dampened and sometimes asynchronous at the enzyme or organismal level.

Dispersal affects evolutionary processes by changing population sizes and their genetic composition, influencing the viability and persistence of populations. Investigating which mechanisms underlie variation in dispersal phenotypes and whether populations harbor adaptive potential for dispersal is crucial to understanding the eco-evolutionary dynamics of this important trait. Here, we investigate the genetic architecture of dispersal in an insular metapopulation of house sparrows. We use an extensive long-term individual-based ecological dataset and high-density single nucleotide polymorphism (SNP) genotypes for over 2500 individuals. We conducted a genome-wide association study (GWAS), finding a relationship between dispersal probability and a SNP located near genes known to regulate circadian rhythmic, glycogenesis and exercise performance, among other functions. However, this SNP only explained 3.8% of variance, suggesting that dispersal is a polygenic trait. We then used an animal model to estimate heritable genetic variation (Va), which composes 10% of the total overall variation in dispersal probability. Finally, we investigated differences in Va across populations occupying ecologically relevant habitat types (farm vs. non-farm) using a genetic-groups animal model. We found higher mean breeding value, Va, and heritability for the farm habitat, suggesting different adaptive potentials across habitats. Moreover, dispersal phenotypes may depend on genotype-by-environment interactions. Our results suggest a complex genetic architecture of dispersal, and demonstrate that adaptive potential may be environment-dependent in key eco-evolutionary traits. The eco-evolutionary implications of such environment-dependence and consequent spatial variation are likely to be ever more important with the increased fragmentation and loss of suitable habitats for many natural populations.

Early-life conditions impact fitness, but whether the combined effect of extrinsic stressors is additive or synergistic is not well known. This is a major knowledge gap, because exposure to multiple stressors is likely to be frequent. Telomere dynamics may be instrumental when testing whether combined stressor effects are additive or synergistic, because many factors affect telomere shortening, and telomere shortening predicts survival. We evaluated the effects of manipulated brood size and natural infestation by the carnid fly Carnus hemapterus on nestling growth and telomere shortening of wild jackdaws (Corvus monedula). Telomere length, measured in blood using TRF, shortened on average by 264 bp. In enlarged broods, nestlings’ telomeres shortened more when parasitized, while in reduced broods there was no effect of infestation on telomere shortening. We conclude that there is a synergistic effect of number of siblings and Carnus infestation on telomere shortening rate: blood-sucking parasites may negatively impact telomeres by increasing cell proliferation and/or physiological stress, and coping with infestation may be less successful in enlarged broods with increased sibling competition and lower per capita feeding rate. Larger nestlings had shorter telomeres independent of age, brood manipulation or infestation. Growth was independent of infestation but in enlarged broods, nestlings were lighter at fledging. Our findings indicate that (i) evaluating consequences of early-life environmental conditions in isolation may not yield a full picture due to synergistic effects, and (ii) effects of environmental conditions may be cryptic, e.g. on telomeres, with fitness consequences expressed beyond the temporal framework of the study.

Ecological speciation within the mormyrid genus Campylomormyrus resulted in sympatric species exhibiting divergence in their feeding apparatus and electric organ discharge (EOD). This study documents the overall diet of the genus Campylomormyrus and examines the hypothesis that Campylomormyrus radiation is caused by an adaptation to different food sources. We performed diet assessment of five sympatric Campylomormyrus species (C. alces, C. compressirostris, C. curvirostris, C. tshokwe, C. numenius) and their sister taxon Gnathonemus petersii with markedly different snout morphologies and EODs using hybrid capture/HTS DNA metabarcoding of their stomach contents. Our approach allowed for high taxonomic resolution of prey items, including benthic invertebrates, allochthonous invertebrates, and vegetation. Comparisons of the diet compositions using quantitative measures and diet overlap indices revealed that all species are able to exploit multiple food niches in their habitats, i.e., fauna at the bottom, the water surface, and the water column. Major part of the diet is larvae of aquatic insects, such as dipterans, coleopterans, and trichopterans, known to occur in holes and interstitial spaces of the substrate. The results showed that different snout morphologies and the associated divergence in the EOD translate into different prey spectra. This suggests that the diversification in EOD and the morphology of the feeding apparatus is under functional adaptation.

Phyllosphere microorganisms are essential for plant growth and health, notably through their action on nitrogen fixation and pathogens control. However, whether and how the composition of phyllosphere communities vary with plant traits and leaf age remain still unclear. We used high-throughput sequencing to explore the phyllosphere microbial diversity and composition communities in needles of different ages (i.e., originating from different cohorts) for three evergreen coniferous species (Pinus koraiensis, Picea asperata and Abies fabri). We then assessed the relationships between the composition of phyllosphere microorganisms and needle traits. The results showed that needle age explained relatively well the phyllosphere microbiome α diversity, whereas tree species identity explained the phyllosphere microorganisms β diversity. The changes in the composition of phyllosphere microbial communities between newly-formed and perennial needles were greatest in Pinus koraiensis. Overall, Cyanobacteria and Gammaproteobacteria were dominant in newly-formed needles. Plant traits such as leaf dry matter content (LDMC), leaf mass per area (LMA) and total phosphorus content (TP) were the main predictors of phyllosphere community. Our results provide new insights into the mechanisms of community assembly among different evergreen tree species and provide a better understanding of the interactions between plant traits and phyllosphere microorganisms during needle ageing.

Human conservation efforts have pros and cons for endangered animals. Metagenomic analysis of the gut microbiome provides valuable insights and tools for wildlife conservation. However, most studies only focus on changes in microbial species and potential functional genes, leaving out the assembly mechanisms and metabolic activities of wildlife gut microbiome. Herein, we investigated the gut microbiome of golden snub-nosed monkeys under varied conservation strategies (wild, captive, and food provision) using metagenome and metabolome analysis. We found that the conserved monkeys had more non-redundant genes, distinct community diversities, and less stable gut microbiota. Source-tracking analysis showed captive group has fewer wild-sourced microbes than food provision group. The captive group had more habitat specialists with narrower niche breadth compared to the provision/wild counterparts. Besides, captive group’s microbiota governed by deterministic processes more than provisioned/wild groups. Procrustes analysis revealed changes in antibiotic resistance genes and virulence factors linked to mobile genetic elements in conserved monkeys. Notably, gut microbiota and metabolomic dataset had significant co-variation and clear separation among the wild, captive and food provision groups. Weighted correlation network analysis identified co-varying modules of microbiota and metabolites with opposite variation trends between the wild and conserved animals, specifically linked to co-metabolism pathways associated with essential amino acids. This study provides new insights into the structural features, assembly mechanisms, community functions, and microbiota-metabolome associations of wildlife gut microbiome under different conservation strategies and have significant implications for advancing sustainable conservation practices.

Limited knowledge of bird microbiome in the all-body niche hinders our understanding of host–microbial relationships and animal health. Here, we characterized the microbial composition of the crested ibis from 13 body sites, representing the cloaca, oral, feather, and skin habitats, and explored assembly mechanism structuring the bacterial community of the four habitats, respectively. The bacterial community characteristics were distinct among the four habitats. The skin harbored the highest alpha diversity, most diverse functions, and more complex network, followed by feather, oral, and cloaca. Individual-specific features were observed when the skin and feathers were concentrated independently. Skin and feather samples of multiple body sites from the same individual were more similar than those from different individuals. Although a significant proportion of the microbiota in the host (3.5% to 14.5%) was not derived from the environmental microbiome, as body sites became more exposed to the environment, the relative importance of neutral processes increased. Neutral processes were the most important contributor in shaping the feather microbiome communities (R2=0.859). A higher percentage of taxa (29.3%) on the skin were selected by hosts compared to taxa on other body habitats. This study demonstrated that niche speciation and partial neutral processes, rather than environmental sources, contribute to microbiome variation in the crested ibis. These results enhance our knowledge of baseline microbial diversity in birds and will aid health management in crested ibises in the future.

Inbreeding depression, i.e., the reduction of health and vigour in individuals with high inbreeding coefficients, is expected to increase with environmental, social, or physiological stress. Differences in the strength of sexual selection are therefore predicted to usually lead to higher inbreeding depression in males than in females. However, sex-specific differences in life history may reverse that pattern during certain developmental stages. In salmonids, for example, female juveniles start developing their gonads earlier than males who instead grow faster during that time. We tested whether the sexes are differently affected by inbreeding during that time. To study the effects of inbreeding coefficients that may be typical for natural populations of brown trout (Salmo trutta), and also to control for potentially confounding maternal or paternal effects, we sampled males and females from the wild, used their gametes in a block-wise breeding design to produce 60 full-sib families, released the offspring as yolk-sac larvae into the wild, caught them back 6 months later, identified their genetic sex, and used microsatellites to assign them to their parents. We calculated the average inbreeding coefficient per family based on a panel of >1 million SNPs. Juvenile growth could be predicted from these inbreeding coefficients and the genetic sex: Females grew slower with increasing inbreeding coefficient, while no such link could be found in males. This sex-specific inbreeding depression led to the overall pattern that females grew on average slower than males during the time of gonad formation.

Understanding the evolutionary processes that influence fitness is critical to predicting species' responses to selection. Interactions among evolutionary processes including gene flow, drift and the strength of selection can lead to either local adaptation or maladaptation especially in heterogeneous landscapes. Populations experiencing novel environments or resources are ideal for understanding the mechanisms underlying adaptation or maladaptation, specifically in locally co-evolved interactions. We used the interaction between a native herbivore that oviposits on a patchily distributed introduced plant that in turn causes significant mortality to the larvae to test for signatures of local adaptation in areas where the two co-occurred. We used whole genome sequencing to explore population structure, patterns of gene flow and signatures of local adaptation. We found signatures of local adaptation in response to the introduced plant in the absence of strong population structure with no genetic differentiation and low genetic variation. Additionally, we found localized allele frequency differences within a single population between habitats with and without the lethal plant, highlighting the effects of strong selection. Our work highlights the potential for adaptation to occur in a fine-grained landscape in the presence of gene flow and low genetic variation.

A document by Kelly Gomez-Campo. Click on the document to view its contents.

Microbial communities are complex networks of microorganisms that interact with each other and their environment. Understanding the functional roles of individual species and their interactions is challenging. High-throughput sequencing has provided valuable insights into microbial communities, but the vast amounts of data generated make deciphering mechanisms difficult. Gene regulatory networks (GRNs) provide a powerful framework for studying the functional roles of individual genes and their interactions in complex biological systems. In microbial ecology, GRNs can be used to identify key regulatory genes and their targets involved in ecological processes. By integrating genomic and transcriptomic data with environmental metadata, GRNs can reveal the genetic architecture of microbial communities. This review provides an overview of the application of GRNs in microbial ecology and discusses the challenges and opportunities of using this approach. Case studies demonstrate the potential of GRNs in uncovering novel insights into microbial community structure and function. Integration of GRNs with other omics approaches and environmental metadata holds great promise in advancing our understanding of microbial ecology and its relevance to human health and environmental sustainability.

Mesozooplankton is a key component of the ocean, regulating global processes such as the carbon pump, and ensuring energy transfer from lower to higher trophic levels. Yet, despite the importance of understanding mesozooplankton diversity, distribution and connectivity at global scale to predict the impact of climate change in marine ecosystems, there is still fragmented knowledge. To fill this gap, we applied DNA metabarcoding to mesozooplankton samples collected during the Malaspina-2010 circumnavigation expedition across temperate and tropical oceans from the surface to bathypelagic depths. By conducting a hidden diversity analysis, we highlight the still scarce knowledge on global mesozooplankton diversity and identify the Indian Ocean and the deep sea as the most understudied areas. By analysing mesozooplankton community spatial distribution, we confirm global biogeographical patterns across the temperate to tropical oceans both in the vertical and horizontal gradients. Additionally, we reveal a consistent increase in mesozooplankton beta-diversity with depth, indicating reduced connectivity at deeper layers, and identify a water mass type-mediated structuring of bathypelagic communities, instead of an oceanic basin-mediated as observed at upper layers. This suggests limited dispersal at deep ocean layers, most likely due to weaker currents and lower mixing of water mass types. Overall, our work supports the neutral theory of biodiversity and thus the importance of oceanic currents and barriers in dispersal in shaping global plankton communities, and provides key knowledge for predicting the impact of climate change in the deep-sea.

Urbanisation is rapidly altering ecosystems, leading to profound biodiversity loss. To mitigate these effects, we need a better understanding of how urbanisation impacts dispersal and reproduction. Two contrasting population demographic models have been proposed which predict that urbanisation either promotes (facilitation model) or constrains (fragmentation model) gene flow and genetic diversity. Which of these models prevails likely depends on the strength of selection on specific phenotypic traits that influence dispersal, survival or reproduction. Here, we examine the genomic impact of urbanisation on the Neotropical túngara frog (Engystomops pustulosus), a species known to adapt its reproductive traits to urban selective pressures. Using whole-genome resequencing for multiple paired urban and forest populations we examined genomic diversity, population connectivity and demographic history. Contrary to both the fragmentation and facilitation models, urban populations did not exhibit substantial changes in genomic diversity or differentiation compared to forest populations and genomic variation was best explained by geographic distance rather than environmental factors. Moreover, both urban and forest populations appear to have undergone population declines which are coincident with extensive human-activity around the Panama Canal during the last few centuries rather than recent urbanisation. Overall, our study underscores the importance of considering the historical context in urban evolution studies as anthropogenic effects may be extensive and impact non-urban areas on both recent and older timescales. Failure to take this into account when interpreting comparisons between urban and non-urban areas may underestimate the impact of urbanisation.

According to prevailing theory, sexually reproducing animals adapt to different environments by the production of phenotypic variation from the standing genetic variation and selection of the most suited phenotypes. Contrary to all expectations, asexually reproducing animals can also inhabit broad ranges of geographical latitudes, altitudes and habitats, despite virtual genetic identity. Recent whole genome analyses of differently adapted clonal populations and genetically impoverished invaders revealed that they can use epigenetic variation instead of genetic variation to stably adapt to different environments. The required phenotypes are produced from the same DNA sequence via changes in gene expression, which is trigged by strong environmental cues and mediated by environment-sensitive epigenetic mechanisms like DNA methylation. Habitat-specific epigenetic fingerprints were maintained over subsequent years, pointing at the existence of epigenetic ecotypes. Obviously, all animals can produce different phenotypes from the same DNA sequence, but in asexually reproducing populations, genetically impoverished invaders, sessile taxa and species with long generation times it is apparently of prime importance. In contrast to beneficial genetic mutations and meiotic gene combinations that require many generations to be established in a population, environmentally-induced epigenetic changes and subsequent alterations in gene and phenotype expression affect population members synchronously in the first exposed generation, providing an ideal means for fast, directional adaptation to changing conditions. The production of different phenotypes from the same genome in response to different environmental cues via epigenetic mechanisms is also suitable to explain the “general-purpose genotype” and the “genetic paradox of invasion”.

Increasing evidence suggests that fungal communities are key components of biogeochemical cycles in coastal ecosystems. While several studies highlighted strong spatial patterns in fungal abundance and diversity, there are very few studies using a more integrative approach to study the spatio-temporal distribution of fungi, taking also the active part of the community into account. To better understand the consequences of anthropogenic activities, e.g. marine aquaculture, for fungal community composition and activities, we simultaneously evaluated the temporal (four different seasons) and spatial dynamics in total (DNA) and active (RNA) fungal communities in relation to several major physicochemical properties. Fungal communities were highly diverse, but showed the ubiquitous dominance of Dikarya and the occasional predominance of Glomeromycota, Mucoromycota, Mortierellomycota, Chytridiomycota, Mortierellomycota, Olpidiomycota, and Rozellomycota. Thereby, fungal diversity indices showed a much higher seasonal variation than with the degree of aquaculture activity, for both total and active communities. This notion is supported by co-occurrence networks exhibiting a clear seasonal pattern. Furthermore, fungal community structure in coastal waters showed distinct relationships with environmental factors varying both with season and in space. For both, total and active fungal communities, a combination of environmental variables such as temperature, DO and NO2- exhibited the greatest impact on community structure. Our study demonstrates a distinct spatio-temporal dynamics of both, total and active fungi and provides a foundation to better understand the ecological roles of marine fungi in coastal ecosystems in relation to mariculture activities.

The purplish bifurcate mussel Mytilisepta virgata is widely distributed and represents one of the major components of the intertidal community in the northwestern Pacific (NWP). Here, we characterized population genetic structure of NWP populations throughout their whole distribution range using both mitochondrial (mtDNA cox1) and nuclear (ITS1) markers. Population genetic analyses for mtDNA cox 1 sequences revealed two monophyletic lineages (i.e., southern and northern lineages) geographically distributed according to the two different surface water temperature zones in the NWP. The timing of the lineage split is estimated at the Pliocene- mid-Pleistocene (5.49-1.61 Mya), which is consistent with the timing of the historical isolation of the East Sea/Sea of Japan from the South and East China Seas caused by sea level decline during glacial cycles. Historical sea level fluctuation during the Pliocene-Pleistocene and subsequent adaptation of mussels to different surface water temperature zones may have contributed to shaping the contemporary genetic diversity and deep divergence of the two mitochondrial lineages. Unlike mtDNA sequences, a clear lineage splitting between the two mitochondrial lineages was not found in ITS1 sequences, showing a star-like structure that is composed of a mixture of southern and northern mitochondrial lineages. Possible scenarios are proposed to explain this type of mito-nuclear discordance: stochastic divergence in the coalescent processes of the two molecular markers, or balancing selection under different marine environments. Future work is required to address whether the thermal physiology of these mussels correlates with the deep divergence of their mitochondrial genes.

Despite the success of the United States (US) Boll Weevil Eradication Program, the boll weevil, Anthonomus grandis Boheman (Coleoptera: Curculionidae), remains a threat to cotton production in the southern US and is arguably the most important cotton pest in Central and South America. Management of this species is complicated by the existence of morphologically similar variants and re-infestations of areas where eradication had been successful. To date, no study has applied a high-throughput sequencing approach to better understand the population genetic structure of the boll weevil. Furthermore, only a single study has investigated genetic relationships between populations in North and South America. Here, we used double digest restriction site-associated DNA sequencing (ddRADseq) to resolve the population genomic structure of the boll weevil in the southern US, northern Mexico, and Argentina, test the two-form and three-form hypotheses of boll weevil variation in North America using a phylogeographic approach, and determine the relationship of the South American populations to the North. Our results supported the two-form hypothesis of boll weevil variation in North America wherein there are two major genetic lineages – one consisting of populations found geographically west of the Sierra Madre Occidental mountain range and the second consisting of populations found to the east – both are highly sub-structured across space and time. Boll weevil populations from Argentina were more closely related to the eastern lineage, suggesting a range expansion by the eastern lineage, but additional sampling across Central and South America is needed to determine a probable origin.

The rapid stem elongation of the invasive weed Mikania micrantha in the forest understory is of vital significance for its successful invasion. To understand the physiological and molecular mechanisms for this process, here we comparatively investigated the physiological characteristics and transcriptome patterns of M. micrantha stem under low light (30%) and full light (100%) conditions. The results showed that M. micrantha stem had photosynthetic capacity, which was highly plastic to light intensities, constituting of an indispensable part of the plastic response of M. micrantha to shading. M. micrantha had longer internodes, epidermal cells, and consequently longer stems under low light than full light conditions, which could be attributed to the reduced photoprotective substances (flavonoid and anthocyanin) and increased synthesis of phytohormones (gibberellin, GA and Auxin) as observed under shading treatment. The transcriptome sequencing and qPCR verified the results from physiological investigation, and showed that under low light condition the expression levels of genes involving in photosynthesis (e.g. MmPsaA, MmPsbO1 and MmFd3) were generally down-regulated in comparison to full light condition, so were the genes related to the photoprotective substances synthesis (e.g. MmCHS, and MmF3H1) and the negative regulators of phytohormone (e.g. MmAUX1, MmRR1 and MmGAI). It was concluded that the regulation of phytohormones and photoprotective substances are the important material basis for the rapid elongation of M. micrantha stems with high plasticity, which really matters to the vine to have high invasiveness in the forest understory.