Filter Results
9671 results
Transposable elements (TEs)—selfish DNA sequences that can move within the genome—comprise a large proportion of the genomes of many organisms. Although low-coverage whole genome sequencing can be used to survey TE composition, it is non-economical for species with large quantities of DNA. Here, we utilize restriction site associated DNA sequencing (RADSeq) as an alternative method to survey TE composition. First, we demonstrate in silico that double digest restriction-site associated DNA sequencing (ddRADseq) markers contain the same TE compositions as whole genome assemblies across arthropods. Next, we show empirically using eight Synalpheus snapping shrimp species with large genomes that TE compositions from ddRADseq and low-coverage whole genome sequencing are comparable within and across species. Finally, we develop a new bioinformatic pipeline, TERAD, to extract TE compositions from RADseq data. Our study expands the utility of RADseq to study the repeatome, making comparative studies of genome structure for species with large genomes more tractable and affordable.
Data Types:
  • Other
  • Tabular Data
  • Dataset
1) The construction of dams on large rivers has negative impacts on native species. Environmental flows have been proposed as a tool to mitigate these impacts, but in order for these strategies to be effective they must account for disparate temperature and flow needs of different species. 2) We applied a multi-objective approach to identify tradeoffs in dam release discharge and temperature for imperiled warm- and cold-water fishes while simultaneously meeting the needs of human water users. 3) Using the Sacramento River (California, USA) as a case study, our model suggests that current management aimed at conserving an endangered cold-water species (winter-run Chinook salmon; Oncorhynchus tshawytscha) and providing high discharge for downstream water users has detrimental impacts on a threatened warm-water species (green sturgeon; Acipenser medirostris). 4) We developed an optimal dam release scenario that can be used to meet the needs of salmon, sturgeon, and human water users. Our results show that dam releases can be managed to successfully achieve these multiple objectives in all but the most severe drought years. Synthesis and applications This study shows that managing dam releases to meet the needs of a single species can have detrimental effects on other native species with different flow and temperature requirements. We applied a multi-objective approach to balance environmental requirements of multiple species with the needs of human water users. Our findings can be used to guide management of Shasta Dam and our approach can be applied to achieve multi-object management goals in other impounded rivers beyond California’s Sacramento River.
Data Types:
  • Tabular Data
  • Dataset
1. Effects of climate change on plant community functional diversity are of interest since experiments have found functional diversity to predict ecosystem function. Functional diversity has been hypothesized to confer resilience to plant communities (as a “driver” of community change), but in unmanipulated natural communities, it might alternatively (or additionally) act as a “passenger” by responding to changes in plant diversity caused by extrinsic factors such as climate. 2. We examined trends in plant functional diversity in annual grasslands in Northern California over a 19-year period, during which a trend toward drier winters had previously been associated with the losses of drought-intolerant species. We tested whether functional diversity decreased over the period of the study (acting as a passenger), and also whether initial site functional diversity influenced the degree of community change over the study period (acting as a driver). 3. Initial community functional diversity was not related to species richness loss or community variability. We found that functional diversity declined as plant species richness and community mean specific leaf area declined over the course of the study, and all of these trends were associated with declining precipitation, indicating that functional diversity acted as a passenger of community change. 4. Synthesis. This study is among the first to demonstrate that recent climatic trends may drive loss of functional diversity. Our findings highlight that functional diversity does not necessarily confer community resilience when its variation is shaped by the environment rather than by experimental treatments.
Data Types:
  • Other
  • Tabular Data
  • Dataset
Body size correlates with most structural and functional components of an organism’s phenotype – brain size being a prime example of allometric scaling with animal size. Therefore, comparative studies of brain evolution in vertebrates rely on controlling for the scaling effects of body size variation on brain size variation by calculating brain weight/body weight ratios. Differences in the brain size-body size relationship between taxa are usually interpreted as differences in selection acting on the brain or its components, while selection pressures acting on body size, which are among the most prevalent in nature, are rarely acknowledged, leading to conflicting and confusing conclusions. We address these problems by comparing brain-body relationships from across >1,000 species of birds and non-avian reptiles. Relative brain size in birds is often assumed to be 10 times larger than in reptiles of similar body size. We examine how differences in the specific gravity of body tissues and in body design (e.g., presence/absence of a tail or a dense shell) between these two groups can affect estimates of relative brain size. Using phylogenetic comparative analyses, we show that the gap in relative brain size between birds and reptiles has been grossly exaggerated. Our results highlight the need to take into account differences between taxa arising from selection pressures affecting body size and design, and call into question the widespread misconception that reptile brains are small and incapable of supporting sophisticated behavior and cognition.
Data Types:
  • Tabular Data
  • Dataset
Most organisms are constantly adapting to pathogens and parasites that exploit their host for their own benefit. Less studied, but perhaps more ubiquitous, are intragenomic parasites or selfish genetic elements. These include transposable elements, selfish B chromosomes and meiotic drivers that promote their own replication without regard to fitness effects on hosts. Therefore, intragenomic parasites are also a constant evolutionary pressure on hosts. Gamete-killing meiotic drive elements are often associated with large chromosomal inversions that reduce recombination between the drive and wildtype chromosomes. This reduced recombination is thought to reduce the efficacy of selection on the drive chromosome and allow for the accumulation of deleterious mutations. We tested whether gamete-killing meiotic drive chromosomes were associated with reduced immune defense against two bacterial pathogens in three species of Drosophila. We found little evidence of reduced immune defense in lines with meiotic drive. One line carrying the Drosophila melanogaster autosomal Segregation Distorter did show reduced defense, but we were unable to attribute that reduced defense to either genotype or immune gene expression differences. Our results suggest that though gamete-killing meiotic drive chromosomes likely accumulate deleterious mutations, those mutations do not result in reduced capacity for immune defense.
Data Types:
  • Tabular Data
  • Dataset
In Drosophila, long sperm are favoured in sperm competition based on the length of the female’s primary sperm storage organ, the seminal receptacle (SR). This sperm-SR interaction, together with a genetic correlation between the traits, suggests that the coevolution of exaggerated sperm and SR lengths may be driven by Fisherian runaway selection. Here, we explore the costs and benefits of long sperm and SR genotypes, both in the sex that carries them and in the sex that does not. We measured male and female fitness in inbred lines of D. melanogaster derived from four populations previously selected for long sperm, short sperm, long SRs, or short SRs. We specifically asked: what are the costs and benefits of long sperm in males and long SRs in females? Furthermore, do genotypes that generate long sperm in males or long SRs in females impose a fitness cost on the opposite sex? Answers to these questions will address whether long sperm are an honest indicator of male fitness, if male post-copulatory success is associated with male pre-copulatory success, if female choice benefits females or is costly, and whether intra-genomic conflict could influence evolution of these traits. We found that both sexes have increased longevity in long sperm and long SR genotypes. Males, but not females, from long SR lines had higher fecundity. Our results suggest that sperm-SR coevolution is facilitated by both increased viability and indirect benefits of long sperm and SRs in both sexes.
Data Types:
  • Tabular Data
  • Dataset
  • Text
1. Rapid adaptation in response to novel environments can facilitate species invasions and range expansions. Understanding how invasive disease vectors rapidly evolve to novel conditions—particularly at the edge of its non-native range—has important implications for mitigating the prevalence and spread of disease. 2. Here, we evaluate the role of local adaptation in overwintering capability of the Asian tiger mosquito, Aedes albopictus. This species invaded the Southern US in the 1980s and rapidly spread northward into novel climate compared to its native range. Photoperiodically induced egg diapause is a key trait contributing to the establishment and spread of Ae. albopictus in temperate latitudes, and diapause incidence rapidly developed a cline along a latitudinal gradient in the US shortly after its initial invasion. However, variation in overwintering survival of diapause-induced eggs along this gradient is not known, but is critical to the fitness-related role of diapause evolution in the establishment and spread of Ae. albopictus in its northern US range. 3. Using reciprocal transplants, we detected local adaptation in overwinter survival of diapausing Aedes albopictus eggs. In northern range-edge winters, eggs produced by range-edge individuals survived better than those produced by range-core individuals. Diapause eggs from range-edge and range-core locations survived equally well in range-core winters, and no eggs survived a winter beyond the current northern range limit in the US. 4. Synthesis and applications. These results demonstrate rapid (~ 3 decades) local adaptation of egg diapause, a key trait facilitating overwinter survival and range expansion for the invasive Asian tiger mosquito. In light of these results, control efforts could shift from targeting satellite populations to a focus on preventing dispersal into locally adapted, range-edge locations and to aim removal efforts towards areas surrounding locally adapted populations. Adopting new approaches to target rapidly adapting populations will require large-scale collaboration among control agencies and research institutions, and should begin in the northern US range to better control Ae. albopictus mosquito populations in the face of rapid adaptation.
Data Types:
  • Tabular Data
  • Dataset
Whilst movements of organisms have been studied across a myriad of environments, information is often lacking regarding spatio-seasonal patterning in complex temperate coastal systems. Highly mobile fish form an integral part of marine food webs providing linkages within habitats, between patches of habitats and at different life stages. We investigated how movement, activity and connectivity patterns of Atlantic cod (Gadus morhua) are influenced by dynamic environmental conditions. Movement patterns of 39 juvenile and subadult Atlantic cod were assessed in two coastal sites in the Swedish Skagerrak for 5 months. We used passive acoustic telemetry and network analysis to assess seasonal and spatial movement patterns of cod and their relationships to different environmental factors, using statistical correlations, analysis of recurrent spatial motifs and generalised linear mixed models. Temperature, in combination with physical barriers, precludes significant connectivity (complex motifs) within the system. Sea surface temperature had a strong influence on connectivity (node strength, degree and motif frequency), where changes from warmer summer waters to colder winter waters significantly reduced movement activity of fish. As the seasons changed, movement of fish gradually decreased from large-scale (km) linkages in the summer to more localised movement patterns in the winter (limited to 100s m). Certain localised areas, however, were identified as important for connectivity throughout the whole study period, likely due to these multiple-habitat areas fulfilling functions required for foraging and shelter. This study provides new knowledge regarding inshore movement dynamics of juvenile and subadult Atlantic cod that use complex, coastal fjord systems. The findings show that connectivity, seasonal patterns in particular, should be carefully considered when selecting conservation areas to promote marine stewardship.
Data Types:
  • Other
  • Tabular Data
  • Dataset
1. Plant traits can provide unique insights into plant performance at the community scale. Functional composition, defined by both functional diversity and community-weighted trait means (CWMs), can affect the stability of aboveground net primary production (ANPP) in response to climate extremes. Further complexity arises, however, when functional composition itself responds to environmental change. The duration of climate extremes, such as drought, is expected to increase with rising global temperatures; thus, understanding the impacts of long-term drought on functional composition and the corresponding effect that has on ecosystem function could improve predictions of ecosystem sensitivity to climate change. 2. We experimentally reduced growing season precipitation by 66% across six temperate grasslands for four years and measured changes in three indices of functional diversity (functional dispersion, richness, and evenness), community-weighted trait means, and phylogenetic diversity (PD). Specific leaf area (SLA), leaf nitrogen content (LNC) and (at most sites) leaf turgor loss point (πTLP) were measured for species cumulatively representing ~90% plant cover at each site. 3. Long-term drought led to increased community functional dispersion in three sites, with negligible effects on the remaining sites. Species re-ordering following the mortality/senescence of dominant species was the main driver of increased functional dispersion. The response of functional diversity was not consistently matched by changes in phylogenetic diversity. Community-level drought strategies (assessed as CWMs) largely shifted from drought tolerance to drought avoidance and/or escape strategies, as evidenced by higher community-weighted πTLP, SLA, and LNC. Lastly, ecosystem drought sensitivity (i.e. relative reduction in ANPP) was positively correlated with community-weighted SLA and negatively correlated with functional diversity. 4. Synthesis: Increased functional diversity following long-term drought may stabilize ecosystem functioning in response to future drought. However, shifts in community-scale drought strategies may increase ecosystem drought sensitivity, depending on the nature and timing of drought. Thus, our results highlight the importance of considering both functional diversity and abundance-weighted traits means of plant communities as their collective effect may either stabilize or enhance ecosystem sensitivity to drought.
Data Types:
  • Other
  • Tabular Data
  • Dataset
1. Phenotypic plasticity has become a key-concept to enhance our ability to understand the adaptive potential of species to track the pace of climate change by allowing a relatively rapid adjustment of life history traits. 2. Recently, population-level trends of an earlier timing of reproduction to climate change have been highlighted in many taxa but only few studies have explicitly taken into consideration between-individual heterogeneity in phenotypic plasticity. 3. Using a long-term data of a semi-domesticated reindeer (Rangifer tarandus) population, we demonstrated that females differed greatly in their mean calving date but only slightly in the magnitude of their plastic response to the amount of precipitation in April. We also showed that despite the absence of a population trend, females individually responded to the amount of precipitation in April by delaying their calving dates. 4. Females’ calving date under average climatic conditions was best predicted by their birthdate, their physical condition in March-April-May before their first calving season and by their first calving date. The degree of their phenotypic plasticity was not dependent on any of the females’ attributes early in life tested in this study. However, females who delayed their calving dates in response to a higher amount of precipitation in April slightly produced less calves over their reproductive life. 5. These findings confirmed that early life conditions of female reindeer can shape their phenotypic value during reproductive life, supporting the importance of maternal effects in shaping individuals’ lifetime reproductive success. Whether females differed in the magnitude of their plastic response to climatic changes has received contrasted responses for various ungulate species. This calls for more research to enhance our understanding of the underlying mechanisms leading to the complexity of plastic responses among populations to cope with current climate change.
Data Types:
  • Tabular Data
  • Dataset
8