1. Accurate differential expression of microbial metatranscriptomes based on Next Generation Sequencing depends partly on the depth of the libraries used to perform the analysis. Therefore, estimating the sequencing depth required to sample the metatranscriptome of interest using RNA-seq effectively is an essential first step to both obtain robust results in further analysis and avoiding over-expending once the information contained in the library reaches saturation. 2. Here we present a method to calculate the effort in saturation curves and a priori genes prediction using a simulated series of metatranscriptomic/metagenomic matrices. This method is based on the extrapolation rarefaction curve using a Weibull growth model to estimate the maximum number of genes/OTUs as a function of sequencing depth using a machine learning approach. This approach allows us to compute the effort at different confidence intervals and to obtain an approximate a priori effort using based on an initial fraction of sequences. 3. The accuracy of the results obtained with simulations and real samples (15 datasets of metatranscriptomes from the oral cavity, RNA sequences consist of vectors of 105-1.5x107 reads depth with a 10000 and 600000 genes size) allows one to use an initial shallowly sequenced sample (in this case 20% of the total amount of reads sampled; accuracy R2>0.99 simulated samples and 60-93% for real samples) to estimate the expected sequencing effort needed to cover the whole metatranscriptome/ metagenome from the same sample, so can be used to estimate the estimate the sample size. The algorithm containing the proposed method was saved as a function for R. 4. This proposed method of estimation of the maximum number of gene/OTUs, reads to reach 90, 95 and 99% of maximum number of gene/OTUs, is efficient to help researchers to know if the sampling is sufficient or otherwise need to be increased.
We evaluated the richness, diversity and composition of medium and large mammalian community in the Loka Abaya National Park (LANP), southern Ethiopia, and how these parametrs differ among four habitat types: wooded grassland, riverine forest, hilly scrubland and wetland) and between seasons.We recorded total of 2,573 individual animals of 28 medium and large mammal species in the park. This included three globally threatened species: the endangered African wild-dog (Lycaon pictus) and the ‘vulnerable’ Leopard (Penthra pardus) and Hippopotamus (Hippopothamus amphibus). Season had little effect on species richness, diversity and composition both across and within habitat types. However, species richness across season was significantly different among the four habitat types, in declining order of: wooded grassland > riverine forest > hilly scrubland > wetland. The strongest similarity in species composition, both across and within seasons, was found between wooded grassland and riverine forest. In terms of relative abundance, mammalia assemblage of the wooded grassland and wetland habitats had more evenly distributed number of species with different relative abundance categories. Overall, Papio anubis, Chlorocebus aethiops and Tragelephus strepsiceros were the three most abundant species across habitat types. In conclusion, findings of our study reveal that LANP plays an important role in Ethiopia’s mammal conservation. Our findings will serve as a base-line information for managers of the park to make effective conservation decisions and as a baseline for researchers wishing to conduct related ecological studies.
Fish migrations are energetically costly, especially when moving between fresh and saltwater, but are a viable strategy for Pacific salmon and trout (Oncorhynchus spp.) due to the advantageous resources available at various life stages. Anadromous steelhead (O. mykiss) migrate vast distances and exhibit variation for migration phenotypes that have a genetic basis at candidate genes known as greb1L and rock1. We examined the distribution of genetic variation at 13 candidate markers spanning greb1L, intergenic, and rock1 regions versus 246 neutral markers for 113 populations (n = 9,471) of steelhead from inland and coastal lineages in the Columbia River. Patterns of population structure with neutral markers reflected genetic similarity by geographic region as demonstrated in previous studies, but candidate markers clustered populations by predominate genetic variation associated with migration timing. Mature alleles for late migration had the highest frequency overall in steelhead populations throughout the Columbia River, with only 9 of 113 populations that had a higher frequency of premature alleles for early migration. While a single haplotype block was evident for the coastal lineage, we identified multiple haplotype blocks for the inland lineage. The inland lineage had one haplotype block that corresponded to candidate markers within the greb1L gene and immediately upstream in the intergenic region, and the second block only contained candidate markers from the intergenic region. Haplotype frequencies had similar patterns of geographic distribution as single markers, but there were distinct differences in frequency between the two haplotype blocks for the inland lineage. Redundancy analyses were used to model environmental effects on allelic frequencies of candidate markers and significant variables were migration distance, temperature, isothermality, and annual precipitation. This study improves our understanding of the spatial distribution of genetic variation underlying migration timing in steelhead as well as associated environmental factors and has direct conservation and management implications.
Recent studies have demonstrated the great advantages of marine reserves in solving bycatch problems by maintaining the persistence of endangered species without sacrificing the fisheries yields of target species. However, transient phenomena rather than equilibrium states of population dynamics still require further research. Here, with a simple and general model, the transient dynamics of strong stock fish species are investigated under the condition of weak stock persistence. A surprising and counter-intuitive finding is that fisheries yields can strongly fluctuate even if population density both inside and outside marine reserve only slightly varies, leading to transient inconsistency between the population densities and fisheries yields. This finding suggests that population density dynamics cannot be used to predict the transient phenomena of fisheries yields (or vice versa) in fisheries management. These results will deepen our understanding of the transient phenomenon in marine ecology.
Phenotypic divergence in response to divergent natural selection between environments is a common phenomenon in species of freshwater fishes. Intraspecific differentiation is often pronounced between individual inhabiting lakes versus stream habitats. The different hydrodynamic regimes in the contrasting habitats may promote a variation of body shape, but this could be intertwined with morphological adaptions to a specific foraging mode. Herein, I studied the divergence pattern of the European minnow (Phoxinus phoxinus), a common freshwater fish that has paid little attention despite its large distribution. In many Scandinavian mountain lakes, they are considered as being invasive and were found to pose threats to the native fish populations due to dietary overlap. Minnows were recently found to show phenotypic adaptions in lake versus stream habitats, but the question remained if this divergence pattern is related to trophic niche partitioning. I therefore studied the patterns of minnow divergence in morphology (i.e. using geometric morphometrics) and trophic niches (i.e. using stomach content analyses) in the lake Ånnsjön and its tributaries to link the changes in body morphology to the feeding on specific resources. Lake minnows showed a strong reliance on zooplankton and a more streamlined body shape with an upward facing snout, whereas stream minnows fed on macroinvertebrates (larvae and adults) to a higher degree and had a deeper body with a snout that was pointed down. Correlations showed a significant positive relationship of the proportion of zooplankton in the gut and morphological features present in the lake minnows. The results of this study highlight the habitat-specific divergence pattern in morphology and resource use in this ubiquitous freshwater fish, which may promote contrasting inter-specific interactions in the respective food webs.
Extensive range loss for the Golden-winged Warbler (Vermivora chrysoptera) has occurred in areas of intrusion by the Blue-winged Warbler (V. cyanoptera) potentially related to their close genetic relationship. We compiled data on social pairing from nine studies for 2,679 resident Vermivora to assess evolutionary divergence. Hybridization between pure phenotypes occurred with 1.2% of resident males for sympatric populations. Pairing success rates for Golden-winged Warblers was 83% and for Blue-winged Warblers was 77%. Pairing success for the hybrid Brewster’s Warbler was significantly lower from both species at 54%, showing sexual selection against hybrids. Backcross frequencies for Golden-winged Warblers at 4.9% was significantly higher than for Blue-winged Warblers at 1.7%. More frequent backcrossing by Golden-winged Warblers, which produces hybrid phenotypes, may contribute to the replacement of Golden-winged by Blue-winged Warblers. Reproductive isolation due to behavioral isolation plus sexual selection against hybrids was 0.966. Our analyses suggest that plumage differences are the main driving force for this strong isolation with reduced hybrid fitness contributing to a lesser degree. The major impact of plumage differences to reproductive isolation is compatible with genomic analyses (Toews et al. 2016), which showed the largest genetic difference between these phenotypes occurred with plumage genes. These phenotypes have maintained morphological, behavioral, and ecological differences during two centuries of hybridization. Our estimate of reproductive isolation supports recognition of these phenotypes as two species. The decline and extirpation of the Golden-winged Warbler in almost all areas of recent sympatry suggest that continued coexistence of both species will require eco-geographic isolation.
Recent research in island biogeography has highlighted the important role of late Quaternary sea-level fluctuations in shaping biogeographical patterns in insular systems, but largely focused on volcanic oceanic systems. Through this study we aim to extend this work by investigating the role of late Quaternary sea-level fluctuations in shaping species richness patterns in continental shelf island systems. Focusing on the Aegean archipelago, we first reconstructed the area’s geography using published data, under three sea-level stands: 1) current; 2) median over the last nine Glacial-Interglacial cycles; 3) Late Glacial Maximum (LGM). We compiled taxon-island occupancy for angiosperms (70 islands) and centipedes (56 islands). We investigated the impact of present-day and past geographical settings on chorological groups by analysing Island Species-Area Relationships (ISARs) and using Generalized Linear Mixed Models selection based on multiple metrics of goodness-of-fit. Our results confirm that the Aegean’s geography has changed dramatically since the LGM, while the median sea-level scenario only modestly differs from the present configuration. Paleogeographical changes largely shaped Aegean plant diversity patterns, and to a lesser degree centipede species richness patterns. The LGM geographic configuration affected both native and endemic species diversity through establishing connections between land-bridge islands and the mainland. Particularly on land-bridge islands we detected supersaturation of native species and stronger underrepresentation of endemics on those same islands. Unlike oceanic islands, where the longer lasting median configuration has ample effect on the current species diversity, the shorter lasting LGM configurations promoted increased connectivity with the mainland counteracting processes promoting endemism. Our study shows that in terms of processes affecting species richness patterns, continental archipelagos differ fundamentally from oceanic systems, highlighting the importance of distinguishing between them while studying biota from the perspective of historical biogeography.
Understanding the scaling between leaf size and leafing intensity is crucial for comprehending theories about light interception and leaf carbon uptake and adjustments in life history strategies. To test whether have the broad scope predictions between leaf size variation and leafing intensity on first year stem in evergreens and deciduous. A comprehensive data set of minimum (Mmin) and maximum (Mmax) leaf mass and total leaf number in twig was compiled, as well as data for the stem volume and mass. The datasets provide measurements of 123 woody species in subtropical mountain forests. Standardized major axis (SMA) analysis was used to determine the effects of the variation in leaf size (i.e., Mmin to Mmax) and the effects of different functional groups on the trade-off between leaf size and leafing intensity, i.e., the leafing intensity based on stem volume (LIV) and stem mass (LIM). Leaf size plasticity variation did not differ between evergreen and deciduous functional groups, but Mmin scaled as the 1.19 power of Mmax. Across the 123 species, the scaling exponents of the pooled data ranged between -1.14 to -0.96 for Mmin and Mmax vs. the leafing intensity based on stem volume (LIV) and from -1.24 to -1.04 for Mmin and Mmax vs. the leafing intensity based on stem mass (LIM). Across the subtropical woody species examined in this study, the results show the scaling relationship between leaf mass and leafing intensity is constrained to be ≤ -1.0. More importantly, the scopes in twig leaf size and the leafing intensity correlate with the biomass allocation to minimum and maximum leaf mass, and not sensitive to plant functional groups in subtropical mountain forests.
Ancient DNA research has developed rapidly over the past few decades due to the improvement in PCR and next-generation sequencing (NGS) technologies, but challenges still exist. One major challenge in relation to ancient DNA research is to recover genuine endogenous ancient DNA sequences from the raw sequencing data. This is often difficult due to the degradation of ancient DNA and high levels of contamination, especially homologous contamination. In this study, we collected whole genome sequencing (WGS) data from 6 ancient samples to compare different mapping algorithms. To further explore more effective methods to separate endogenous DNA from the homologous contaminations, we attempted to recover reads based on the ancient DNA specific characteristics of deamination, depurination, and DNA fragmentation with different parameters. We propose a quick and improved pipeline for separating endogenous ancient DNA while simultaneously decreasing the homologous contaminations to a very low proportion. Overall, these recommendations for ancient DNA mapping and separation of endogenous DNA in this study could facilitate future studies of ancient DNA.
1. Trees are characterised by the large number of seeds they produce. Although most of those seeds will never germinate, plenty will. Of those which germinate, many die young, and eventually only a minute fraction will grow to adult stage and reproduce. Is this just a random process? Do variations in germination and survival at very young stages rely on variations in adaptations to microgeographic heterogeneity? and do these processes matter at all in determining tree species distribution and abundance? 2. We have studied these questions with the Neotropical Symphonia syngameon. In the Guiana shield, Symphonia are represented by at least two sympatric taxa or ecotypes, Symphonia globulifera found almost exclusively in bottomlands, and a yet undescribed more generalist taxon/ecotype, Symphonia sp1. A reciprocal transplantation experiment (510 seeds, 16 conditions) was set-up and followed over the course of 6 years to evaluate the survival and performance of individuals from different ecotypes and provenances. 3. Germination, survival, growth, and herbivory showed signs of local adaptation, with some combinations of ecotypes and provenances growing faster and surviving better in their own habitat or provenance region. S. globulifera was strongly penalised when planted outside its home habitat but showed the fastest growth rates when planted in its home habitat, suggesting it’s a specialist of a high-risk high-gain strategy. Conversely, S. sp1 behaved as a generalist, performing well in a variety of environments. 4. Synthesis: The differential performance of seeds and seedlings in the different habitats matches the known distribution of both ecotypes, indicating that environmental filtering at the very early stages can be a key determinant of tree species distributions, even at the microgeographic level and among very closely related taxa. Furthermore, such differential performance also contributes to explain, in part, the maintenance of the different ecotypes in the Symphonia syngameon living in intimate sympatry despite occasional gene flow.
1. The role of interspecific interactions in structuring low-diversity helminth communities is a controversial topic in parasite ecology research. Most parasitic communities of fish are species poor; thus, interspecific interactions are believed to be unimportant in structuring these communities. 2. We explored the factors that might contribute to the richness and coexistence of helminth parasites of a poecilid fish in a neotropical river. 3. Repeatability of community structure was examined in parasitic communities among 11 populations of Pseudoxiphophorus bimaculatus in the La Antigua River Basin, Veracruz, Mexico. We examined the species saturation of parasitic communities and explored the patterns of species co-occurrence. We also quantified the associations between parasitic species pairs and analysed the correlations between helminth species abundance to look for repeated patterns among the study populations. 4. Our results suggested that interspecific competition could occur in species-poor communities, aggregation played a role in determining local richness, and intraspecific aggregation allowed the coexistence of species by reducing the overall intensity of interspecific competition.
Aim Kelp forests worldwide are important marine ecosystems that foster high primary to secondary productivity and multiple ecosystem services. These ecosystems are increasingly under threat from extreme storms, changing ocean temperatures, harvesting, and greater herbivore pressure at regional and global scales, necessitating urgent documentation of their historical to present day distributions. Species range shifts to higher latitudes have already been documented in some species that dominate subtidal habitats within Europe. Very little is known about kelp forest ecosystems in Ireland, where rocky coastlines are dominated by Laminaria hyperborea. In order to rectify this substantial knowledge gap, we compiled historical records from an array of sources to present historical distribution, kelp and kelp forest recording effort over time, and present rational for the monitoring of kelp habitats to better understand ecosystem resilience. Location Ireland (Northern Ireland and Éire). Methods Herbaria, literature from the Linnaean society dating back to late 1700s, journal articles, government reports, and online databases were scoured for information on L. hyperborea. Information about kelp ecosystems was solicited from dive clubs and citizen science groups that are active along Ireland’s coastlines. Results Data were used to create distribution maps, analyse methodology and technology used to record L. hyperborea presence and kelp ecosystems within Ireland. We discuss the recent surge in studies on Irish kelp ecosystems and fauna associated with kelp ecosystems that may be used as indicators of ecosystem health and suggest methodologies for continued monitoring. Main Conclusions While there has been a steady increase in recording effort of the dominant subtidal kelp forest species, L. hyperborea, only recently have studies begun to address other important eco-evolutionary processes at work in kelp forests including connectivity among kelp populations in Ireland. Further monitoring, using suggested methodologies, is required to better understand the resilience of kelp ecosystems in Ireland.
Birds have been observed to have dietary preferences for unsaturated fatty acids (FAs) during migration. Polyunsaturated fatty acids (PUFAs) increase the exercise performance of migrant birds; however, PUFAs are also peroxidation prone and might therefore incur increased costs in terms of enhanced oxidative stress in migratory individuals. To shed light on this potential constraint, we analysed plasma FA composition and estimated the susceptibility to peroxidation of migrants and residents of the partially migratory common blackbird (Turdus merula) at a stop-over site during autumn migration. As predicted, migrant birds had higher relative and absolute levels of PUFAs compared to resident birds. This included the strictly dietary ω-3 PUFA α-linoleic acid, suggesting a dietary preference for these fatty acids in migrants. Interestingly, the FA unsaturation index, which is an index of lipid peroxidation susceptibility, did not differ between migrants and residents. These findings suggest a mechanism where birds alter their levels of metabolic substrate to increase exercise performance without simultaneously increasing the risk of lipid peroxidation and oxidative stress. In summary, our results are in line with the hypothesis of increased exercise performance being constrained by oxidative stress during migration, which is manifested in changes in the composition of key FAs to retain the unsaturation index constant despite the increased levels of peroxidizable PUFAs.
Leaf soluble sugars and starch are important components of nonstructural carbohydrates (NSCs), which are crucial for plant growth, development, and reproduction. Although there is a large body of research focusing on the regulation of plant NSC (soluble sugars and starch) concentrations, the response of foliar NSC concentrations to continuous nitrogen (N) and phosphorus (P) addition is still unclear, especially in tropical forests. Here, we used a long-term manipulative field experiment to investigate the response of leaf NSC concentrations to continuous N and P addition (3-, 5-, and 8-year fertilization) in a tropical forest in southern China. We found significant species-specific variation in leaf NSC concentrations in this tropical forest. Phosphorus addition dramatically decreased both leaf soluble sugar and starch concentrations, while N addition had no significant effects on leaf soluble sugar and starch concentrations. These results suggest that, in plants growing in P-limiting tropical soil, leaf NSC concentrations are regulated by soil P availability rather than N availability. Moreover, the negative relationships between NSC concentrations and leaf mass per area (LMA) revealed that NSCs could supply excess carbon (C) for leaf expansion under P addition. This was further supported by the increased structural P fraction after P fertilization in our previous study at the same site. We conclude that soil P availability strongly regulates leaf starch and soluble sugar concentrations in the tropical tree species included in this study. The response of leaf NSC concentrations to long-term N and P addition can reflect the close relationships between plant C dynamics and soil nutrient availability in tropical forests. Maintaining relatively higher leaf NSC concentrations in tropical plants can be a potential mechanism for adapting to P-deficient conditions.
1. Previous macrophysiological studies suggested that temperature-driven colour lightness and body size variations strongly influence biogeographical patterns in ectotherms, but whether these trait-environment relationships scale to local assemblages and the extent to which they can be modified by dispersal remains largely unexplored. We test whether the predictions of the thermal melanism hypothesis and the Bergmann’s rule hold for local assemblages. We also assess whether these trait-environment relationships are more important for species adapted to less stable (lentic) habitats, due to their greater dispersal propensity compared to those adapted to stable (lotic) habitats. 2. We quantified the colour lightness and body volume of 99 European dragon- and damselflies (Odonata) and combined these trait information with survey data for 518 local assemblages across Europe. Based on this continent-wide yet spatially explicit dataset, we tested for effects temperature and precipitation on the colour lightness and body volume of local assemblages and assessed differences in their relative importance and strength between lentic and lotic assemblages, while accounting for spatial and phylogenetic autocorrelation. 3. The colour lightness of assemblages of odonates increased and body size decreased with increasing temperature. Trait-environment relationships in the average and phylogenetic predicted component were equally important for assemblages of both habitat types but were stronger in lentic assemblages when accounting for phylogenetic autocorrelation. 4. Our results show that the mechanism underlying colour lightness and body size variations scale to local assemblages, indicating their general importance. These mechanisms were of equal evolutionary significance for lentic and lotic species, but higher dispersal ability seems to enable lentic species to cope better with historical climatic changes. The documented differences between lentic and lotic assemblages also highlight the importance of integrating interactions of thermal adaptations with proxies of the dispersal ability of species into trait-based models, for improving our understanding of climate-driven biological responses.
Leaf shape is a defining feature of how we recognise and classify plant species. Although there is extensive variation in leaf shape within many species, few studies have disentangled the underlying genetic architecture. We characterised the genetic architecture of leaf shape variation in Eurasian aspen (Populus tremula L.) by performing a genome wide association studies (GWAS) for physiognomy traits. To ascertain the roles of identified GWAS candidate genes within the leaf development transcriptional program, we performed gene co-expression network analyses from a developmental series, which is publicly available at http://aspleaf.plantgenie.org. We additionally used gene expression measurements across the population to analyse GWAS candidate genes in the context of a population-wide co-expression network and to identify genes that were differentially expressed between groups of individuals with contrasting leaf shapes. These data were integrated with expression GWAS (eQTL) results to define a set of candidate genes associated with leaf shape variation. Our results identified no clear adaptive link to leaf shape variation and indicate that leaf shape traits are genetically complex, likely determined by numerous small-effect variations in gene expression. Genes associated with shape variation were peripheral within the population-wide co-expression network, were not highly connected within the leaf development co-expression network and exhibited signatures of relaxed selection. As such, our results are consistent with the omnigenic model.
Predator-prey interactions are critical to understand how communities function. However, we need to describe intraspecific variation in diet to accurately depict those interactions. Harbor seals (Phoca vitulina, Linnaeus 1758) are an abundant marine predator that prey on species of conservation concern. We estimated intrapopulation feeding diversity of harbor seals in the Salish Sea relative to sex, time, and location with a novel approach that combined molecular techniques, repeated cross-sectional sampling of scat, and a specialization metric (within-individual consistency in diet). Based on 1,083 scat samples collected from five haul-out sites during four non-sequential years, we quantified diet using metabarcoding techniques, and determined the sex of the scat depositor using a molecular assay. Results suggest that intrapopulation feeding diversity was pervasive. Specialization was high over short periods (24 - 48 hours,〖PS〗_i = 0.392, 95% CI = 0.013, R = 100,000) and variable in time and space. Females showed more specialization than males, particularly during summer and fall, and demersal and benthic prey species were correlated with more specialized diets. The latter finding suggests that this type of prey likely require specific foraging strategies and that there are trade-offs between pelagic and benthic foraging styles for harbor seals. This differential feeding on prey species, as well as between sexes of harbor seals, indicate that predator-prey interactions in harbor seals are complex and that each sex may have a different impact on species of conservation concern. As such, describing intraspecific variation in diet may unravel hitherto unknown complex predator-prey interactions in the community.
1) The more demanding requirements of DNA preservation for genomic research can be difficult to meet when field conditions limit the methodological approaches that can be used, or cause samples to be stored in suboptimal conditions. Such limitations may increase rates of DNA degradation, potentially rendering samples unusable for applications such as genome-wide sequencing. Nonetheless, little is known about the impact of suboptimal sampling conditions. 2) We evaluated the performance of two widely used preservation solutions (1. DESS: 20% DMSO, 0.25M EDTA, NaCl saturated solution, and 2. ethanol) under a range of storage conditions over a three-month period (sampling at 1 day, 1 week, 2 weeks, 1 month, and 3 months) to provide practical guidelines for DNA preservation. DNA degradation was quantified as the reduction in average DNA fragment size over time (DNA fragmentation) because the size distribution of DNA segments plays a key role in generating genomic datasets. Tissues were collected from a marine teleost species, the Australasian snapper, Chrysophrys auratus. 3) We found that the storage solution has a dramatic effect on DNA preservation. In DESS, DNA was only moderately degraded after three months of storage while DNA stored in ethanol showed high levels of DNA degradation already within 24 hours, making samples unsuitable for next-generation-sequencing. 4) We recommend DESS as the most promising solution to improve DNA preservation. These results provide practical and economical advice to improve DNA preservation when sampling for genome-wide applications. Keywords: DMSO, DNA preservation, ethanol, fish, next-generation-sequencing, NGS, snapper