Find research datasets worth reusing

Data from: Evolution of movement rate increases the effectiveness of marine reserves for the conservation of pelagic fishes

Current debates about the efficacy of no-take marine reserves (MR) in protecting large pelagic fish such as tuna and sharks have usually not considered the evolutionary dimension of this issue, which emerges because the propensity to swim away from a given place, like any other biological trait, will probably vary in a heritable fashion among individuals. Here, based on spatially-explicit simulations, we investigated whether selection to remain in MRs to avoid higher fishing mortality can lead to the evolution of more philopatric fish. Our simulations, which covered a range of life histories among tuna species (skipjack tuna vs. Atlantic Bluefin tuna) and shark species (great white sharks vs. spiny dogfish) suggested that MRs were most effective at maintaining viable population sizes when movement distances were lowest. Decreased movement rate evolved following the establishment of marine reserves, and this evolution occurred more rapidly with higher fishing pressure. Evolutionary reductions in movement rate led to increases in within-reserve population sizes over the course of the 50 years following MR establishment, although this varied among life-histories, with skipjack responding fastest and great white sharks slowest. Our results suggest the evolution of decreased movement can augment the efficacy of marine reserves, especially for species, such as skipjack tuna, with relatively short generation times. Even when movement rates did not evolve substantially over 50 years (e.g., given long generation times or little heritable variation), marine reserves were an effective tool for the conservation of fish populations when mean movement rates were low or MRs were large.

opencc-zeroDec 2015View details →

Data from: An experimental evolution study confirms that discontinuous gas exchange does not contribute to body water conservation in locusts

The adaptive nature of discontinuous gas exchange (DGE) in insects is contentious. The classic "hygric hypothesis", which posits that DGE serves to reduce respiratory water loss (RWL), is still the best supported. We thus focused on the hygric hypothesis in this first ever experimental evolution study of any of the competing adaptive hypotheses. We compared populations of the migratory locust (Locusta migratoria) that underwent ten consecutive generations of selection for desiccation-resistance with control populations. Selected locusts survived 36% longer under desiccation stress but DGE prevalence did not differ between these and control populations (~75%). Evolved changes in DGE properties in the selected locusts included longer cycle and interburst durations. However, in contrast to predictions of the hygric hypothesis, these changes were not associated with reduced RWL rates. Other responses observed in the selected locusts were higher body water content when hydrated and lower evaporative water loss rates. Hence, our data suggest that DGE cycle properties in selected locusts are a consequence of an evolved increased ability to store water, and thus an improved capacity to buffer accumulated CO2, rather than an adaptive response to desiccation. We conclude that DGE is unlikely to be an evolutionary response to dehydration challenge in locusts.

Data from: Balancing yield with resilience and conservation objectives in harvested predator-prey communities

The global overexploitation of fish stocks is endangering many marine food webs. Scientists and managers now call for an ecosystem-based fisheries management, able to take into account the complexity of marine ecosystems and the multiple ecosystem services they provide. By contrast, many fishery management plans only focus on maximizing the productivity of harvested stocks. Such practices are suggested to affect other ecosystem services, altering the integrity and resilience of natural communities. Here we show that while yield-maximizing policies can allow for coexistence and resilience in predator-prey communities, they are not optimal in a multi-objective context. We find that although total prey and predator maximum yields are higher with a prey-oriented harvest, focusing on the predator improves species coexistence. Also, moderate harvesting of the predator can enhance resilience. Furthermore, increasing maximum yields by changing catchabilities improves resilience in predator-oriented systems, but reduces it in prey-oriented systems. In a multi-objective context, optimal harvesting strategies involve a general trade-off between yield and resilience. Resilience-maximizing strategies are however compatible with quite high yields, and should often be favored. Our results further suggest that balancing harvest between trophic levels is often best at maintaining simultaneously species coexistence, resilience and yield.

opencc-zeroNov 2019View details →

Genome Data Uncover Conservation Status, Historical Relatedness and Candidate Genes under Selection in Chinese Indigenous Pigs in the Taihu Lake Region

Chinese indigenous pig breeds in the Taihu Lake region (TH) of Eastern China are well-recognized for their exceptional prolificacy. These breeds including Meishan (MS), Erhualian (EHL), Jiaxing Black (JXB), Fengjing (FJ), Shawutou (SWT), Mi (MI) and Hongdenglong (HDL). At present, these breeds are facing a great threaten of population decline, lineage admixture and inbreeding depression since Western commercial pigs have dominated Chinese pig industry. To provide better conservation schemes and identify candidate genes under selection for these breeds, we explored genome-wide SNP markers to unravel genetic variability and relatedness, population structure, historical admixture and genomic signatures of selection of 440 pigs representing the most comprehensive lineages of these breeds in TH in a context of 1228 pig from 45 Eurasian breeds. We showed that these breeds were more closely related among each other as compared to other Eurasian breeds, defining one of the main ancestral lineages of Chinese indigenous pigs. These breeds can be divided into two regional subgroups, one including JXB and FJ pigs, and the other comprising EHL, MI, HDL, MS and SWT pigs. In additional, HDL pigs were highly inbred, whereas EHL and MS pigs had more abundant genetic diversity. This is attributable to multiple conservation populations of the two breeds. Moreover, we identified a list of candidate genes for body size and prolificacy at the loci putatively under selection. our results would benefit the sustainable conservation of these valuable breeds and improve our understanding of the genetic mechanisms of body size and fecundity in pigs.

opencc-zeroDec 2017View details →

Data from: Genomewide association analyses of fitness traits in captive-reared Chinook salmon: applications in evaluating conservation strategies

A novel application of genome-wide association analyses is to use trait-associated loci to monitor the effects of conservation strategies on potentially adaptive genetic variation. Comparisons of fitness between captive- and wild-origin individuals, for example, do not reveal how captive rearing affects genetic variation underlying fitness traits or which traits are most susceptible to domestication selection. Here, we used data collected across four generations to identify loci associated with six traits in adult Chinook salmon (Oncorhynchus tshawytscha), and then determined how two alternative management approaches for captive rearing affected variation at these loci. Loci associated with date of return to freshwater spawning grounds (return timing), length and weight at return, age at maturity, spawn timing, and daily growth coefficient were identified using 9108 restriction site-associated markers and Random Forest, an approach suitable for polygenic traits. Mapping of trait-associated loci, gene annotations, and integration of results across multiple studies revealed candidate regions involved in several fitness-related traits. Genotypes at trait-associated loci were then compared between two hatchery populations that were derived from the same source but are now managed as separate lines, one integrated with and one segregated from the wild population. While no broad scale change was detected across four generations, there were numerous regions where trait-associated loci overlapped with signatures of adaptive divergence previously identified in the two lines. Many regions, primarily with loci linked to return and spawn timing, were either unique to, or more divergent in, the segregated line, suggesting that these traits may be responding to domestication selection. This study is one of the first to utilize genomic approaches to demonstrate the effectiveness of a conservation strategy, managed gene flow, on trait-associated – and potentially adaptive – loci. The results will promote the development of trait-specific tools to better monitor genetic change in captive and wild populations.

Data from: Incorporating ecological functions in conservation decision making

Systematic conservation planning has become a standard approach globally, but prioritization of conservation efforts hardly considers species traits in decision-making. This can be important for species persistence and thus adequacy of the conservation plan. Here, we developed and validated a novel approach of incorporating trophic information into a systematic conservation planning framework. We demonstrate the benefits of this approach by using fish data from Europe´s second largest river, the Danube. Our results show that adding trophic information leads to a different spatial configuration of priority areas at no additional cost. This can enhance identification of priority refugia for species in the lower position of the trophic web while simultaneously identifying areas that represent a more diverse species pool. Our methodological approach to incorporating species traits into systematic conservation planning is generally applicable, irrespective of realm, geographical area and species composition and can potentially lead to more adequate conservation plans.

opencc-zeroDec 2012View details →

Data from: High lability of sexual system over 250 million years of evolution in morphologically conservative tadpole shrimps

Background: Sexual system is a key factor affecting the genetic diversity, population structure, genome structure and the evolutionary potential of species. The sexual system androdioecy -- where males and hermaphrodites coexist in populations -- is extremely rare, yet is found in three crustacean groups, barnacles, a genus of clam shrimps Eulimnadia, and in the order Notostraca, the tadpole shrimps. In the ancient crustacean order Notostraca, high morphological conservatism contrasts with a wide diversity of sexual systems, including androdioecy. An understanding of the evolution of sexual systems in this group has been hampered by poor phylogenetic resolution and confounded by the widespread occurrence of cryptic species. Here we use a multigene supermatrix for 30 taxa to produce a comprehensive phylogenetic reconstruction of Notostraca. Based on this phylogenetic reconstruction we use character mapping techniques to investigate the evolution of sexual systems. We also tested the hypothesis that reproductive assurance has driven the evolution of androdioecy in Notostraca. Results: Character mapping analysis showed that sexual system is an extremely flexible trait within Notostraca, with repeated shifts between gonochorism and androdioecy, the latter having evolved a minimum of five times. In agreement with the reproductive assurance hypothesis androdioecious notostracans are found at significantly higher latitudes than gonochoric ones indicating that post glacial re-colonisation may have selected for the higher colonisation ability conferred by androdioecy. Conclusions: In contrast to their conserved morphology, sexual system in Notostraca is highly labile and the rare reproductive mode androdioecy has evolved repeatedly within the order. Furthermore, we conclude that this lability of sexual system has been maintained for at least 250 million years and may have contributed to the long term evolutionary persistence of Notostraca. Our results further our understanding of the evolution of androdioecy and indicate that reproductive assurance is a recurrent theme involved in the evolution of this sexual system.

opencc-zeroDec 2014View details →

Data from: Conservation tillage mitigates the negative effect of landscape simplification on biological control

Biological pest control is a key ecosystem service, and it depends on multiple factors acting from the local to the landscape scale. However, the effects of soil management on biological control and its potential interaction with landscape are still poorly understood. In a field exclusion experiment, we explored the relative effect of tillage system (conservation vs. conventional tillage) on aphid biological control in 15 pairs of winter cereal fields (barley and wheat) selected along a gradient of landscape complexity. We sampled the abundance of the main natural enemy guilds, and we evaluated their relative contribution to aphid predation and parasitism. Conservation tillage was found to support more abundant predator communities and higher aphid predation (16% higher than in the fields managed under conventional tillage). In particular, both the abundance and the aphid predation of vegetation- and ground-dwelling arthropods were increased under conservation tillage conditions. Conservation tillage also increased the parasitism rate of aphids. A high proportion of semi-natural habitats in the landscape enhanced both aphid parasitism and predation by vegetation-dwelling organisms but only in the fields managed under conventional tillage. The better local habitat quality provided by conservation tillage may compensate for a low-quality landscape. Synthesis and applications. Our study stresses the importance of considering both soil management and landscape composition when planning strategies to maximize biological control services in agro-ecosystems, highlighting the role played by conservation tillage in supporting natural enemy communities. In simple landscapes, the adoption of conservation tillage will locally improve biological control provided by both predators and parasitoids mitigating the negative effects of landscape simplification. Moreover, considering the small scale at which both predation and parasitism responded to landscape composition, a successful strategy to improve biological control would be to establish a fine mosaic of crop and non-crop areas such as hedgerows, tree lines and small semi-natural habitat patches.

opencc-zeroMay 2019View details →

Data from: Conservation of the threatened species Pulsatilla vulgaris Mill. (pasqueflower) is aided by reproductive system and polyploidy

Population loss due to habitat disturbance is a major concern in biodiversity conservation. Here we investigate the genetic causes of the demographic decline observed in English populations of Pulsatilla vulgaris and the consequences for conservation. Using ten nuclear microsatellite markers, we compare genetic variation in wild populations with restored and seed-regenerated populations (674 samples). Emergence of genetic structure and loss of allelic variation in natural populations is not as evident as expected from demographic trends. Restored populations show genetic variation comparable to their source populations and, in general, to the wild ones. Genetic homogeneity is observed in regeneration trials, although some alleles not captured in source populations are detected. We infer that polyploidy, longevity and clonal reproduction have provided P. vulgaris with the standing genetic variation necessary to make the species resilient to the effects of demographic decline, suggesting that the use of multiple sources for reintroduction may be beneficial to mimic natural gene flow and the availability of multiple allele copies typical of polyploid species.

opencc-zeroMay 2019View details →

Data from: Towards more effective integration of tropical forest restoration and conservation

Conservation and restoration interventions can be mutually reinforcing and are converging through an increased focus on social dimensions. This paper examines how to more effectively integrate the complementary goals of conservation and restoration of tropical forests. Forest conservation and restoration interventions are integral components of a broad approach to forest ecosystem and landscape management that aims to maintain and restore key ecological processes and enhance human well-being, while minimizing biodiversity loss. The forest transition model provides a useful framework for understanding the relative importance of forest conservation and restoration interventions in different regions. Harmonizing conservation and restoration presents serious challenges for forest policy in tropical countries, particularly regarding the use and management of secondary forests, fallow vegetation, and forests degraded by logging and fire. Research to implement restoration more effectively in tropical regions can be stimulated by transforming questions that initially focused on conservation issues. Examination of papers published in Biotropica from 2000–2018 shows that most studies relevant to tropical forest conservation do not address forest restoration issues. Forest restoration studies, on the other hand, show a consistent association with conservation issues. There is much scope for further integration of conservation and restoration in research, practice, and policy. Securing a sustainable future for tropical forests requires developing and applying integrated approaches to landscape management that effectively combine knowledge and tools from multiple disciplines with practical experience and engagement of local stakeholders.

Data from: Inbreeding and selection shape genomic diversity in captive populations: implications for the conservation of endangered species

Captive breeding programs are often initiated to prevent species extinction until reintroduction into the wild can occur. However, the evolution of captive populations via inbreeding, drift, and selection can impair fitness, compromising reintroduction programs. To better understand the evolutionary response of species bred in captivity, we used nearly 5500 single nucleotide polymorphisms (SNPs) in populations of white-footed mice (Peromyscus leucopus) to measure the impact of breeding regimes on genomic diversity. We bred mice in captivity for 20 generations using two replicates of three protocols: random mating (RAN), selection for docile behaviors (DOC), and minimizing mean kinship (MK). The MK protocol most effectively retained genomic diversity and reduced the effects of selection. Additionally, genomic diversity was significantly related to fitness, as assessed with pedigrees and SNPs supported with genomic sequence data. Because captive-born individuals are often less fit in wild settings compared to wild-born individuals, captive-estimated fitness correlations likely underestimate the effects in wild populations. Therefore, minimizing inbreeding and selection in captive populations is critical to increasing the probability of releasing fit individuals into the wild.

opencc-zeroDec 2015View details →

Data from: Conserved genetic architecture underlying recombination rate variation in a wild population of Soay sheep (Ovis aries)

Meiotic recombination breaks down linkage disequilibrium and forms new haplotypes, meaning that it is an important driver of diversity in eukaryotic genomes. Understanding the causes of variation in recombination rate is important in interpreting and predicting evolutionary phenomena and for understanding the potential of a population to respond to selection. However, despite attention in model systems, there remains little data on how recombination rate varies at the individual level in natural populations. Here, we used extensive pedigree and high-density SNP information in a wild population of Soay sheep (Ovis aries) to investigate the genetic architecture of individual autosomal recombination rate. Individual rates were high relative to other mammal systems, and were higher in males than in females (autosomal map lengths of 3748 cM and 2860 cM, respectively). The heritability of autosomal recombination rate was low but significant in both sexes (h2 = 0.16 & 0.12 in females and males, respectively). In females, 46.7% of the heritable variation was explained by a sub-telomeric region on chromosome 6; a genome-wide association study showed the strongest associations at the locus RNF212, with further associations observed at a nearby ~374kb region of complete linkage disequilibrium containing three additional candidate loci, CPLX1, GAK and PCGF3. A second region on chromosome 7 containing REC8 and RNF212B explained 26.2% of the heritable variation in recombination rate in both sexes. Comparative analyses with 40 other sheep breeds showed that haplotypes associated with recombination rates are both old and globally distributed. Both regions have been implicated in rate variation in mice, cattle and humans, suggesting a common genetic architecture of recombination rate variation in mammals.

opencc-zeroDec 2015View details →

Data from: Are heritability and selection related to population size in nature? Meta-analysis and conservation implications

It is widely thought that small populations should have less additive genetic variance and respond less efficiently to natural selection than large populations. Across taxa, we meta-analytically quantified the relationship between adult census population size (N) and additive genetic variance (proxy: h2) and found no reduction in h2 with decreasing N; surveyed populations ranged from four to one million individuals (1735 h2estimates, 146 populations, 83 species). In terms of adaptation, ecological conditions may systematically differ between populations of varying N; the magnitude of selection these populations experience may therefore also differ. We thus also meta-analytically tested whether selection changes with N, and found little evidence for systematic differences in the strength, direction, or form of selection with N across different trait types and taxa (7344 selection estimates, 172 populations, 80 species). Collectively, our results (i) indirectly suggest that genetic drift neither overwhelms selection more in small than in large natural populations, nor weakens adaptive potential/h2 in small populations, and (ii) imply that natural populations of varying sizes experience a variety of environmental conditions, without consistently differing habitat quality at small N. However, we caution that the data are currently insufficient to determine whether some small populations may retain adaptive potential definitively. Further study is required into (i) selection and genetic variation in completely isolated populations of known N, underrepresented taxonomic groups, and non-generalist species, (ii) adaptive potential using multidimensional approaches, and (iii) the nature of selective pressures for specific traits.

Data from: Identifying conserved genomic elements and designing universal bait sets to enrich them

Targeted enrichment of conserved genomic regions is a popular method for collecting large amounts of sequence data from non-model taxa for phylogenetic, phylogeographic and population genetic studies. For example, two available bait sets each allow enrichment of thousands of orthologous loci from >20 000 species (Faircloth et al. Systematic Biology, 61, 717–726, 2012; Molecular Ecology Resources, 15, 489–501, 2015). Unfortunately, few open-source workflows are available to identify conserved genomic elements shared among divergent taxa and to design enrichment baits targeting these regions. Those that do exist require extensive bioinformatics expertise and significant amounts of time to use. These shortcomings limit the application of targeted enrichment methods to additional organismal groups. Here, I describe a universal workflow for identifying conserved genomic regions in available genomic data and for designing targeted enrichment baits to collect data from these conserved regions. These methods require less expertise, less time and better use commonly available information to identify conserved loci and design baits to capture them. I apply this computational approach to the understudied arthropod groups Arachnida, Coleoptera, Diptera, Hemiptera or Lepidoptera to identify thousands of conserved loci in each group and design target enrichment baits to capture these loci. I then use in silico analyses to demonstrate that targeted enrichment of the conserved loci can be used to reconstruct the accepted relationships among genome sequences from the focal arthropod orders. The software workflow I created allowed me to identify thousands of conserved loci in five diverse arthropod groups and design sequence capture baits to target them. This suite of capture bait designs should enable collection of phylogenomic data from >900 000 arthropod species. Although the examples in this manuscript focus on understudied arthropod groups, the approach I describe is applicable to all organismal groups having some form of pre-existing genomic information (e.g. other invertebrates, plants, fungi and microbes). Finally, the documentation, design steps, software code and bait sets developed here are available under an open-source license for restriction-free testing, use, and additional modification by any research group.

opencc-by-4.0May 2020View details →

Figure 3 from: Karam-Gemael M, Decker P, Stoev P, Marques MI, Chagas Jr A (2020) Conservation of terrestrial invertebrates: a review of IUCN and regional Red Lists for Myriapoda. In: Korsós Z, Dányi L (Eds) Proceedings of the 18th International Congress of Myriapodology, Budapest, Hungary. ZooKeys 930: 221-229. https://doi.org/10.3897/zookeys.930.48943

Figure 3 Proportion of extinction risk categories of the Worldwide Myriapoda Red List presented here. Includes data from regional Red Lists from eleven countries and from IUCN Red List of Threatened Species. Threatened categories are within dashed red lines.

opencc-by-4.0May 2020View details →

Figure 1 from: Karam-Gemael M, Decker P, Stoev P, Marques MI, Chagas Jr A (2020) Conservation of terrestrial invertebrates: a review of IUCN and regional Red Lists for Myriapoda. In: Korsós Z, Dányi L (Eds) Proceedings of the 18th International Congress of Myriapodology, Budapest, Hungary. ZooKeys 930: 221-229. https://doi.org/10.3897/zookeys.930.48943

Figure 1 IUCN extinction risks categories for global assessments. Threatened categories are within dashed red line. (Modified from IUCN 2019).

opencc-by-4.0May 2020View details →

Figure 2 from: Karam-Gemael M, Decker P, Stoev P, Marques MI, Chagas Jr A (2020) Conservation of terrestrial invertebrates: a review of IUCN and regional Red Lists for Myriapoda. In: Korsós Z, Dányi L (Eds) Proceedings of the 18th International Congress of Myriapodology, Budapest, Hungary. ZooKeys 930: 221-229. https://doi.org/10.3897/zookeys.930.48943

Figure 2 Countries included in this study. In orange, countries consulted that have their own local lists and myriapods are listed: Brazil, Bulgaria, Czech Republic, Finland, Germany, Greece, Norway, Slovenia, Russia, Sweden, UK. In green, countries consulted that have their own local lists, but there are not myriapods listed: Albania, Argentina, Australia, Austria, Belgium, Bolivia, Canada, Chile, Colombia, Cuba, Dominican Republic, Ecuador, Estonia, France, French Guiana, Guatemala, Guiana, India, Italy, Ireland, Mexico, Madagascar, Mongolia, Netherlands, Peru, Republic of Korea, South Africa, Spain, Sri Lanka, Suriname, Switzerland, Taiwan, Uganda, Uruguay, USA, Venezuela, Vietnam.

opencc-zeroMay 2020View details →

Supplementary material 1 from: Karam-Gemael M, Decker P, Stoev P, Marques MI, Chagas Jr A (2020) Conservation of terrestrial invertebrates: a review of IUCN and regional Red Lists for Myriapoda. In: Korsós Z, Dányi L (Eds) Proceedings of the 18th International Congress of Myriapodology, Budapest, Hungary. ZooKeys 930: 221-229. https://doi.org/10.3897/zookeys.930.48943

Worlwide Myriapoda assessments

opencc-by-4.0Jun 2016View details →

Conservative Interpolation Between Control-Volume Meshes: Application to Advection & Multiphase Flow

Numerical Raw Data pertaining to the Publication linked to the DOI above. Uploaded as per Open Access requirements. The paper itself presents a general, higher order conservative and bounded interpolation for the dynamic and adaptive meshing of continuous and discontinuous control-volume fields. The method is discussed in detail and its robustness and applicability demonstrated through several examples, including advection dominated inertial flow as well multiphase porous media flow.