From 4bbfd3bfc19c51839bc342bf0bf6cd495d08bc34 Mon Sep 17 00:00:00 2001 From: Lyndon White Date: Thu, 25 Oct 2018 14:30:11 +0800 Subject: [PATCH 1/5] Delete DataOneV1 --- README.md | 13 +----- src/APIs/DataOneV1.jl | 57 ------------------------ src/DataDepsGenerators.jl | 3 +- test/DataOneV1.jl | 12 ----- test/references/DataOneV1 Drought.txt | 18 -------- test/references/DataOneV1 Ecology.txt | 18 -------- test/references/DataOneV1 Plasticity.txt | 19 -------- test/runtests.jl | 1 - 8 files changed, 3 insertions(+), 138 deletions(-) delete mode 100644 src/APIs/DataOneV1.jl delete mode 100644 test/DataOneV1.jl delete mode 100644 test/references/DataOneV1 Drought.txt delete mode 100644 test/references/DataOneV1 Ecology.txt delete mode 100644 test/references/DataOneV1 Plasticity.txt diff --git a/README.md b/README.md index a2cbf2b..380daa7 100644 --- a/README.md +++ b/README.md @@ -188,22 +188,13 @@ Example of use: ``` -### `DataOneV1()` - API Based - -https://releases.dataone.org/online/api-documentation-v1.2.0/ - -Data repositories like DataDryad, support version 1 API of the DataOne. - -Data Repositories: -* DataDryad: `generate(DataOneV1(), "https://datadryad.org/resource/doi:10.5061/dryad.74699", "Wild Crop Genomics")` - - ### `DataOneV2` https://releases.dataone.org/online/api-documentation-v2.0/apis/index.html -Supports DataOne API version 2. There are differences in the API structure in each of them, hence are accounted for, separately: +Supports DataOne API version 2. +There are differences in the API structure for each repository each of them, hence are accounted for, separately: Data Repositories: * Knowledge Network for Biocomplexity `KnowledgeNetworkforBiocomplexity()`: `generate(KnowledgeNetworkforBiocomplexity(), "https://knb.ecoinformatics.org/knb/d1/mn/v2/object/doi:10.5063/F1T43R7N")` diff --git a/src/APIs/DataOneV1.jl b/src/APIs/DataOneV1.jl deleted file mode 100644 index fd56e07..0000000 --- a/src/APIs/DataOneV1.jl +++ /dev/null @@ -1,57 +0,0 @@ -struct DataOneV1 <: DataRepo -end - -# The only APIs known to be supported by DataOne Version 1 is DataDryad -# As and when we come to know of other APIs supported by DataOne, more abstraction layers will be introduced. -# Named as DataOneV1 to make new contributors to the package aware that DataOneV1 exists. -base_url(::DataOneV1) = "https://datadryad.org/mn/object/http://dx.doi.org/" - -description(repo::DataOneV1, mainpage) = text_only(first(eachmatch(sel"dcterms\:description", mainpage.root))) - -author(::DataOneV1, mainpage) = [text_only(i) for i in eachmatch(sel"dcterms\:creator", mainpage.root)] - -license(::DataOneV1, mainpage) = "http://creativecommons.org/publicdomain/zero/1.0/" - -published_date(::DataOneV1, mainpage) = Dates.DateTime(chop(text_only(first(eachmatch(sel"dcterms\:dateSubmitted", mainpage.root))))) - -paper_cite(::DataOneV1, mainpage) = citation_text(text_only(first(eachmatch(sel"dcterms\:references", mainpage.root)))) - -dataset_cite(::DataOneV1, mainpage) = citation_text(text_only(first(eachmatch(sel"dcterms\:identifier", mainpage.root)))) - -function get_urls(repo::DataOneV1, page) - urls = [] - links = eachmatch(sel"dcterms\:hasPart", page.root) - for link in links - downloadlinks = eachmatch(sel".image-link", getpage(text_only(link)).root) - for downloadlink in downloadlinks - push!(urls, downloadlink.attributes["href"]) - end - end - urls -end - -function get_checksums(repo::DataOneV1, page) - checksums = [] - links = eachmatch(sel"dcterms\:hasPart", page.root) - for link in links - spans = eachmatch(sel".file-list span", getpage(text_only(link)).root) - for span in spans - if occursin(r"^[a-f0-9]{32}$", text_only(span)) - push!(checksums, (:md5, text_only(span))) - end - end - end - if length(checksums) > 0 - @info("The generated registration block uses md5 hash, " * - "the MD5.jl package must be loaded to run the registration") - end - checksums -end - -function data_fullname(::DataOneV1, mainpage) - text_only(first(eachmatch(sel"dcterms\:title", mainpage.root))) -end - -function website(::DataOneV1, mainpage_url, mainpage) - replace(mainpage_url, "https://datadryad.org/mn/object/" => "") -end diff --git a/src/DataDepsGenerators.jl b/src/DataDepsGenerators.jl index 6b58a5f..fb8522f 100644 --- a/src/DataDepsGenerators.jl +++ b/src/DataDepsGenerators.jl @@ -7,7 +7,7 @@ using Dates using InteractiveUtils: subtypes export generate, citation_text, remove_cite_version -export UCI, GitHub, DataDryad, DataOneV1, DataOneV2, CKAN, DataCite, Figshare, JSONLD_Web, JSONLD_DOI +export UCI, GitHub, DataDryad, DataOneV2, CKAN, DataCite, Figshare, JSONLD_Web, JSONLD_DOI @@ -38,7 +38,6 @@ include("misc_extractors.jl") include("APIs/UCI.jl") include("APIs/GitHub.jl") include("APIs/DataDryad.jl") -include("APIs/DataOneV1.jl") include("APIs/DataOneV2/DataOneV2.jl") include("APIs/CKAN.jl") include("APIs/DataCite.jl") diff --git a/test/DataOneV1.jl b/test/DataOneV1.jl deleted file mode 100644 index 88dce1a..0000000 --- a/test/DataOneV1.jl +++ /dev/null @@ -1,12 +0,0 @@ -using DataDepsGenerators -using Test - -using ReferenceTests - -@testset "DataOneV1 test" begin - @test_reference "references/DataOneV1 Ecology.txt" remove_cite_version(generate(DataOneV1(), "https://datadryad.org/mn/object/http://dx.doi.org/10.5061/dryad.74699")) - - #Checking files with multiple files available for download - @test_reference "references/DataOneV1 Plasticity.txt" remove_cite_version(generate(DataOneV1(), "https://datadryad.org/mn/object/http://dx.doi.org/10.5061/dryad.f9s4424")) - @test_reference "references/DataOneV1 Drought.txt" remove_cite_version(generate(DataOneV1(), "https://datadryad.org/mn/object/http://dx.doi.org/10.5061/dryad.cc8834s")) -end diff --git a/test/references/DataOneV1 Drought.txt b/test/references/DataOneV1 Drought.txt deleted file mode 100644 index 213b950..0000000 --- a/test/references/DataOneV1 Drought.txt +++ /dev/null @@ -1,18 +0,0 @@ -register(DataDep( - "Data from Drought intensification drives turnover of structure and function in stream invertebrate communities", - """ - Dataset: Data from: Drought intensification drives turnover of structure and function in stream invertebrate communities - Website: http://dx.doi.org/10.5061/dryad.cc8834s - Author: Aspin, Thomas W.H. et al. - Date of Publication: 2018-03-01T14:43:44 - License: http://creativecommons.org/publicdomain/zero/1.0/ - - Climatic extremes are becoming more frequent and intense across much of the globe, potentially transforming the biodiversity and functioning of affected ecosystems. In freshwaters, hydrological extremes such as drought can regulate beta diversity, acting as powerful environmental filters to dictate the complement of species and functional traits found at local and landscape scales. New methods that enable beta diversity and its functional equivalent to be partitioned into turnover (replacement of species/functions) and nestedness-resultant (gain/loss of species/functions) components may offer novel insights into the parallel impacts of drought on ecosystem structure and function. Using a series of artificial channels (mesocosms) designed to mimic perennial headwater streams, we experimentally manipulated streamflows to simulate a gradient of drought intensity. We then modelled taxonomic and functional turnover and nestedness of macroinvertebrate communities along this gradient, validating direct gradient approaches (bootstrapping, Mantel tests) against null models of nestedness. Drought intensification produced significant environmental distance decay trends (i.e. communities became increasingly taxonomically and functionally dissimilar the more differentially disturbed by drought they were). Taxonomic distance decay was primarily driven by turnover, while the functional trend reflected a combination of richness differences and turnover at different points along the gradient. Taxonomic and functional distance decay slopes were not significantly different, implying that communities were functionally vulnerable to drying. The increased frequency and intensity of droughts predicted under most climate change scenarios could thus profoundly modify not only the structure of running water invertebrate communities, but also the ecosystem functions they underpin. - - Please cite this paper: Aspin, T. W. H., Matthews, T. J., Khamis, K., Milner, A. M., Wang, Z., O’Callaghan, M. J., & Ledger, M. E. (2018). Drought intensification drives turnover of structure and function in stream invertebrate communities. Ecography. doi:10.1111/ecog.03711 - - Please cite this dataset: Aspin, T. W. H., Matthews, T. J., Khamis, K., Milner, A. M., Wang, Z., O’Callaghan, M. J., & Ledger, M. E. (2018). Data from: Drought intensification drives turnover of structure and function in stream invertebrate communities [Data set]. Dryad Digital Repository. https://doi.org/10.5061/dryad.cc8834s - """, - Any["/bitstream/handle/10255/dryad.173063/Drought%20intensities.csv?sequence=1", "/bitstream/handle/10255/dryad.173064/Presence-absence%20data.csv?sequence=1", "/bitstream/handle/10255/dryad.173075/Fuzzy%20coded%20trait%20data.xlsx?sequence=1"], - [(md5, "5f38cf6a98643ba49987eb89b02bfcb2"), (md5, "d77ccc58576b4c8fdf9c5b381baaedaa"), (md5, "d3f5faaea7cf4e70efe39fd5c0fedd24")] -)) \ No newline at end of file diff --git a/test/references/DataOneV1 Ecology.txt b/test/references/DataOneV1 Ecology.txt deleted file mode 100644 index 02036ca..0000000 --- a/test/references/DataOneV1 Ecology.txt +++ /dev/null @@ -1,18 +0,0 @@ -register(DataDep( - "Data from Ecology and genomics of an important crop wild relative as a prelude to agricultural innovation", - """ - Dataset: Data from: Ecology and genomics of an important crop wild relative as a prelude to agricultural innovation - Website: http://dx.doi.org/10.5061/dryad.74699 - Author: von Wettberg, Eric J. B. et al. - Date of Publication: 2018-02-27T21:46:38 - License: http://creativecommons.org/publicdomain/zero/1.0/ - - Domesticated species are impacted in unintended ways during domestication and breeding. Changes in the nature and intensity of selection impart genetic drift, reduce diversity, and increase the frequency of deleterious alleles. Such outcomes constrain our ability to expand the cultivation of crops into environments that differ from those under which domestication occurred. We address this need in chickpea, an important pulse legume, by harnessing the diversity of wild crop relatives. We document an extreme domestication-related genetic bottleneck and decipher the genetic history of wild populations. We provide evidence of ancestral adaptations for seed coat color crypsis, estimate the impact of environment on genetic structure and trait values, and demonstrate variation between wild and cultivated accessions for agronomic properties. A resource of genotyped, association mapping progeny functionally links the wild and cultivated gene pools and is an essential resource chickpea for improvement, while our methods inform collection of other wild crop progenitor species. - - Please cite this paper: Von Wettberg, E. J. B., Chang, P. L., Başdemir, F., Carrasquila-Garcia, N., Korbu, L. B., Moenga, S. M., … Cook, D. R. (2018). Ecology and genomics of an important crop wild relative as a prelude to agricultural innovation. Nature Communications, 9(1). doi:10.1038/s41467-018-02867-z - - Please cite this dataset: Von Wettberg, E. J. B., Chang, P. L., Başdemir, F., Carrasquila-Garcia, N., Korbu, L., Moenga, S. M., … Cook, D. R. (2018). Data from: Ecology and genomics of an important crop wild relative as a prelude to agricultural innovation [Data set]. Dryad Digital Repository. https://doi.org/10.5061/dryad.74699 - """, - Any["/bitstream/handle/10255/dryad.166590/draft_dryad_upload_dec2017.xls?sequence=1"], - [(md5, "3c837a0a41e01966a0f037beb7db43b8")] -)) \ No newline at end of file diff --git a/test/references/DataOneV1 Plasticity.txt b/test/references/DataOneV1 Plasticity.txt deleted file mode 100644 index fc43ecb..0000000 --- a/test/references/DataOneV1 Plasticity.txt +++ /dev/null @@ -1,19 +0,0 @@ -register(DataDep( - "Data from Plasticity of plant defense and its evolutionary implications in wild populations of Boechera stricta", - """ - Dataset: Data from: Plasticity of plant defense and its evolutionary implications in wild populations of Boechera stricta - Website: http://dx.doi.org/10.5061/dryad.f9s4424 - Author: Wagner, Maggie R., Mitchell-Olds, Thomas - Date of Publication: 2018-03-02T20:35:36 - License: http://creativecommons.org/publicdomain/zero/1.0/ - - Phenotypic plasticity is thought to impact evolutionary trajectories by shifting trait values in a direction that is either favored by natural selection (“adaptive plasticity”) or disfavored (“nonadaptive” plasticity). However, it is unclear how commonly each of these types of plasticity occurs in natural populations. To answer this question, we measured glucosinolate defensive chemistry and reproductive fitness in over 1,500 individuals of the wild perennial mustard Boechera stricta, planted in four common gardens across central Idaho, USA. Glucosinolate profiles—including total glucosinolate concentration as well as the relative abundances and overall diversity of different compounds—were strongly plastic both among habitats and within habitats. Patterns of glucosinolate plasticity varied greatly among genotypes. Plasticity among sites was predicted to affect fitness in 27.1% of cases; more often than expected by chance, glucosinolate plasticity increased rather than decreased relative fitness. In contrast, we found no evidence for within-habitat selection on glucosinolate reaction norm slopes (i.e., plasticity along a continuous environmental gradient). Together, our results indicate that glucosinolate plasticity may improve the ability of B. stricta populations to persist after migration to new habitats. - - Please cite this paper: Wagner, M. R., & Mitchell-Olds, T. (2018). Plasticity of plant defense and its evolutionary implications in wild populations of Boechera stricta - . Evolution, 72(5), 1034–1049. doi:10.1111/evo.13469 - - Please cite this dataset: Wagner, M. R., & Mitchell-Olds, T. (2018). Data from: Plasticity of plant defense and its evolutionary implications in wild populations of Boechera stricta [Data set]. Dryad Digital Repository. https://doi.org/10.5061/dryad.f9s4424 - """, - Any["/bitstream/handle/10255/dryad.173251/raw_data.zip?sequence=1", "/bitstream/handle/10255/dryad.173251/README.txt?sequence=2", "/bitstream/handle/10255/dryad.173252/GSplasticity_code.R?sequence=1"], - [(md5, "aea52e9cdb6c4069720bc709415e479f"), (md5, "2abd4c62b7263eba8c74ce2bcb25790f"), (md5, "783d619e042bfe516b6ffd34dc97b5df")] -)) \ No newline at end of file diff --git a/test/runtests.jl b/test/runtests.jl index e402464..c7d9d6f 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -6,7 +6,6 @@ tests = [ "UCI", "GitHub", "DataDryad", - "DataOneV1", "DataOneV2/KNB", "DataOneV2/TERN", "CKAN", From 5f3278302d80cb7464478e10db5a0d31000b8f01 Mon Sep 17 00:00:00 2001 From: Lyndon White Date: Fri, 26 Oct 2018 13:26:32 +0800 Subject: [PATCH 2/5] update combing test now that DateOneV1 is removed --- test/references/Combining Ecology.txt | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/test/references/Combining Ecology.txt b/test/references/Combining Ecology.txt index c1689eb..6b0ea87 100644 --- a/test/references/Combining Ecology.txt +++ b/test/references/Combining Ecology.txt @@ -2,17 +2,17 @@ register(DataDep( "Data from Ecology and genomics of an important crop wild relative as a prelude to agricultural innovation", """ Dataset: Data from: Ecology and genomics of an important crop wild relative as a prelude to agricultural innovation - Website: http://dx.doi.org/10.5061/dryad.74699 - Author: von Wettberg, Eric J. B. et al. - Date of Publication: 2018-02-27T21:46:38 + Website: https://datadryad.org/resource/doi:10.5061/dryad.74699 + Author: Eric J. B. Von Wettberg et al. + Date of Publication: February 27, 2018 License: https://creativecommons.org/publicdomain/zero/1.0/ Domesticated species are impacted in unintended ways during domestication and breeding. Changes in the nature and intensity of selection impart genetic drift, reduce diversity, and increase the frequency of deleterious alleles. Such outcomes constrain our ability to expand the cultivation of crops into environments that differ from those under which domestication occurred. We address this need in chickpea, an important pulse legume, by harnessing the diversity of wild crop relatives. We document an extreme domestication-related genetic bottleneck and decipher the genetic history of wild populations. We provide evidence of ancestral adaptations for seed coat color crypsis, estimate the impact of environment on genetic structure and trait values, and demonstrate variation between wild and cultivated accessions for agronomic properties. A resource of genotyped, association mapping progeny functionally links the wild and cultivated gene pools and is an essential resource chickpea for improvement, while our methods inform collection of other wild crop progenitor species. - Please cite this paper: Von Wettberg, E. J. B., Chang, P. L., Başdemir, F., Carrasquila-Garcia, N., Korbu, L. B., Moenga, S. M., … Cook, D. R. (2018). Ecology and genomics of an important crop wild relative as a prelude to agricultural innovation. Nature Communications, 9(1). doi:10.1038/s41467-018-02867-z + Please cite this paper: von Wettberg EJB, Chang PL, Başdemir F, Carrasquila-Garcia N, Korbu L, Moenga SM, Bedada G, Greenlon A, Moriuchi KS, Suryawanshi V, Cordeiro MA, Noujdina NV, Dinegde KN, Abbas Shah Sani SG, Getahun T, Vance L, Bergmann E, Lindsay D, Mamo BE, Warschefsky EJ, Dacosta-Calheiros E, Marques E, Yilmaz MA, Cakmak AM, Rose J, Migneault A, Krieg CP, Saylak S, Temel H, Friesen ML, Silor E, Akhmetov Z, Ozelik H, Kholova J, Can C, Gaur P, Yildirim M, Sharma H, Vadez V, Tesfaye K, Woldemedhin AF, Tar'an B, Aydogan A, Bukun B, Penmetsa RV, Berger J, Kahraman A, Nuzhdin SV, Cook DR (2018) Ecology and genomics of an important crop wild relative as a prelude to agricultural innovation. Nature Communications 9: 649. https://doi.org/10.1038/s41467-018-02867-z Please cite this dataset: Von Wettberg, E. J. B., Chang, P. L., Başdemir, F., Carrasquila-Garcia, N., Korbu, L., Moenga, S. M., … Cook, D. R. (2018). Data from: Ecology and genomics of an important crop wild relative as a prelude to agricultural innovation [Data set]. Dryad Digital Repository. https://doi.org/10.5061/dryad.74699 """, - Any["/bitstream/handle/10255/dryad.166590/draft_dryad_upload_dec2017.xls?sequence=1"], - [(md5, "3c837a0a41e01966a0f037beb7db43b8")] + Any["https://datadryad.org/bitstream/handle/10255/dryad.166590/draft_dryad_upload_dec2017.xls?sequence=1"], + [(md5, "efc75490db3444d3708b3e9ccd030d38")] )) \ No newline at end of file From 95756833d48b16eaa2d5b2da140d0b0bb5d223eb Mon Sep 17 00:00:00 2001 From: Lyndon White Date: Sat, 27 Oct 2018 17:11:45 +0800 Subject: [PATCH 3/5] =make DataDryad work with DOIs --- src/APIs/Figshare.jl | 5 ++++- src/APIs/GitHub.jl | 2 +- src/generate.jl | 2 +- test/DataDryad.jl | 3 +++ 4 files changed, 9 insertions(+), 3 deletions(-) diff --git a/src/APIs/Figshare.jl b/src/APIs/Figshare.jl index 202aebb..502016e 100644 --- a/src/APIs/Figshare.jl +++ b/src/APIs/Figshare.jl @@ -2,6 +2,9 @@ struct Figshare <: DataRepo end base_url(::Figshare) = "https://api.figshare.com/v2/articles" +# Note: Unlike other generators, FigShare base_url is sometimes a "directory" and sometimes a file +# But it is OK, because Figshare also overloads all the functions that use `base_url` +# Most importantly `mainpage_url` description(repo::Figshare, mainpage) = mainpage["description"] @@ -49,7 +52,7 @@ function mainpage_url(repo::Figshare, dataname) return JSON.parse(text_only(getpage(url).root)), url elseif match_figshare(dataname)!= nothing identifier = match_figshare(dataname) - url = base_url(repo) * "/" *identifier + url = joinpath(base_url(repo), identifier) return JSON.parse(text_only(getpage(url).root)), url else throw(GeneratorError(repo)) diff --git a/src/APIs/GitHub.jl b/src/APIs/GitHub.jl index efd1378..90969c9 100644 --- a/src/APIs/GitHub.jl +++ b/src/APIs/GitHub.jl @@ -1,7 +1,7 @@ struct GitHub <: DataRepo end -base_url(::GitHub) = "https://github.com" +base_url(::GitHub) = "https://github.com/" git_repo_page_url(page) = base_url(GitHub()) * getattr(first(eachmatch(sel"strong[itemprop=\"name\"] a", page.root)), "href") diff --git a/src/generate.jl b/src/generate.jl index 87ea149..3dbaee8 100644 --- a/src/generate.jl +++ b/src/generate.jl @@ -116,7 +116,7 @@ function mainpage_url(repo::DataRepo, dataname) if startswith(dataname, "http") url = dataname else # not a URL - url = joinpath(base_url(repo), dataname) + url = base_url(repo) * dataname end getpage(url), url end diff --git a/test/DataDryad.jl b/test/DataDryad.jl index 0edcd26..ff7b908 100644 --- a/test/DataDryad.jl +++ b/test/DataDryad.jl @@ -4,6 +4,9 @@ using Test using ReferenceTests @testset "DataDryad test" begin + # Via URL + @test_reference "references/DataDryad Ecology.txt" generate(DataDryad(), "https://datadryad.org/resource/doi:10.5061/dryad.74699") + #Via DOI @test_reference "references/DataDryad Ecology.txt" generate(DataDryad(), "https://datadryad.org/resource/doi:10.5061/dryad.74699") #Checking files with multiple files available for download From 3d097e6e93d6cc19596db0b06c30f6966a5f8c2e Mon Sep 17 00:00:00 2001 From: Lyndon White Date: Sat, 27 Oct 2018 17:30:30 +0800 Subject: [PATCH 4/5] =sanitize some test urls and update references --- test/combine.jl | 2 +- test/references/Combining Ecology.txt | 4 ++-- test/references/Combining Plasticity.txt | 17 ++++++++--------- 3 files changed, 11 insertions(+), 12 deletions(-) diff --git a/test/combine.jl b/test/combine.jl index 2858fd4..6db369e 100644 --- a/test/combine.jl +++ b/test/combine.jl @@ -6,7 +6,7 @@ using ReferenceTests @testset "Combining test" begin @test_reference "references/Combining Ecology.txt" remove_cite_version(generate("10.5061/dryad.74699")) - @test_reference "references/Combining Plasticity.txt" remove_cite_version(generate("https://datadryad.org/mn/object/http://dx.doi.org/10.5061/dryad.f9s4424")) + @test_reference "references/Combining Plasticity.txt" remove_cite_version(generate("http://dx.doi.org/10.5061/dryad.f9s4424")) @test_reference "references/Combining Stack Overflow.txt" generate("https://www.kaggle.com/stackoverflow/stack-overflow-2018-developer-survey") diff --git a/test/references/Combining Ecology.txt b/test/references/Combining Ecology.txt index 6b0ea87..5ac12fb 100644 --- a/test/references/Combining Ecology.txt +++ b/test/references/Combining Ecology.txt @@ -5,13 +5,13 @@ register(DataDep( Website: https://datadryad.org/resource/doi:10.5061/dryad.74699 Author: Eric J. B. Von Wettberg et al. Date of Publication: February 27, 2018 - License: https://creativecommons.org/publicdomain/zero/1.0/ + License: http://creativecommons.org/publicdomain/zero/1.0/ Domesticated species are impacted in unintended ways during domestication and breeding. Changes in the nature and intensity of selection impart genetic drift, reduce diversity, and increase the frequency of deleterious alleles. Such outcomes constrain our ability to expand the cultivation of crops into environments that differ from those under which domestication occurred. We address this need in chickpea, an important pulse legume, by harnessing the diversity of wild crop relatives. We document an extreme domestication-related genetic bottleneck and decipher the genetic history of wild populations. We provide evidence of ancestral adaptations for seed coat color crypsis, estimate the impact of environment on genetic structure and trait values, and demonstrate variation between wild and cultivated accessions for agronomic properties. A resource of genotyped, association mapping progeny functionally links the wild and cultivated gene pools and is an essential resource chickpea for improvement, while our methods inform collection of other wild crop progenitor species. Please cite this paper: von Wettberg EJB, Chang PL, Başdemir F, Carrasquila-Garcia N, Korbu L, Moenga SM, Bedada G, Greenlon A, Moriuchi KS, Suryawanshi V, Cordeiro MA, Noujdina NV, Dinegde KN, Abbas Shah Sani SG, Getahun T, Vance L, Bergmann E, Lindsay D, Mamo BE, Warschefsky EJ, Dacosta-Calheiros E, Marques E, Yilmaz MA, Cakmak AM, Rose J, Migneault A, Krieg CP, Saylak S, Temel H, Friesen ML, Silor E, Akhmetov Z, Ozelik H, Kholova J, Can C, Gaur P, Yildirim M, Sharma H, Vadez V, Tesfaye K, Woldemedhin AF, Tar'an B, Aydogan A, Bukun B, Penmetsa RV, Berger J, Kahraman A, Nuzhdin SV, Cook DR (2018) Ecology and genomics of an important crop wild relative as a prelude to agricultural innovation. Nature Communications 9: 649. https://doi.org/10.1038/s41467-018-02867-z - Please cite this dataset: Von Wettberg, E. J. B., Chang, P. L., Başdemir, F., Carrasquila-Garcia, N., Korbu, L., Moenga, S. M., … Cook, D. R. (2018). Data from: Ecology and genomics of an important crop wild relative as a prelude to agricultural innovation [Data set]. Dryad Digital Repository. https://doi.org/10.5061/dryad.74699 + Please cite this dataset: https://doi.org/10.5061/dryad.74699 """, Any["https://datadryad.org/bitstream/handle/10255/dryad.166590/draft_dryad_upload_dec2017.xls?sequence=1"], [(md5, "efc75490db3444d3708b3e9ccd030d38")] diff --git a/test/references/Combining Plasticity.txt b/test/references/Combining Plasticity.txt index 0cea3b9..18efa99 100644 --- a/test/references/Combining Plasticity.txt +++ b/test/references/Combining Plasticity.txt @@ -2,18 +2,17 @@ register(DataDep( "Data from Plasticity of plant defense and its evolutionary implications in wild populations of Boechera stricta", """ Dataset: Data from: Plasticity of plant defense and its evolutionary implications in wild populations of Boechera stricta - Website: https://datadryad.org/mn/object/http://dx.doi.org/10.5061/dryad.f9s4424 - Author: Wagner, Maggie R., Mitchell-Olds, Thomas - Date of Publication: 2018-03-02T20:35:36 - License: https://creativecommons.org/publicdomain/zero/1.0/ + Website: http://dx.doi.org/10.5061/dryad.f9s4424 + Author: Wagner MR + Date of Publication: March 2, 2018 + License: http://creativecommons.org/publicdomain/zero/1.0/ Phenotypic plasticity is thought to impact evolutionary trajectories by shifting trait values in a direction that is either favored by natural selection (“adaptive plasticity”) or disfavored (“nonadaptive” plasticity). However, it is unclear how commonly each of these types of plasticity occurs in natural populations. To answer this question, we measured glucosinolate defensive chemistry and reproductive fitness in over 1,500 individuals of the wild perennial mustard Boechera stricta, planted in four common gardens across central Idaho, USA. Glucosinolate profiles—including total glucosinolate concentration as well as the relative abundances and overall diversity of different compounds—were strongly plastic both among habitats and within habitats. Patterns of glucosinolate plasticity varied greatly among genotypes. Plasticity among sites was predicted to affect fitness in 27.1% of cases; more often than expected by chance, glucosinolate plasticity increased rather than decreased relative fitness. In contrast, we found no evidence for within-habitat selection on glucosinolate reaction norm slopes (i.e., plasticity along a continuous environmental gradient). Together, our results indicate that glucosinolate plasticity may improve the ability of B. stricta populations to persist after migration to new habitats. - Please cite this paper: Wagner, M. R., & Mitchell-Olds, T. (2018). Plasticity of plant defense and its evolutionary implications in wild populations of Boechera stricta - . Evolution, 72(5), 1034–1049. doi:10.1111/evo.13469 + Please cite this paper: Wagner MR, Mitchell-Olds T (2018) Plasticity of plant defense and its evolutionary implications in wild populations of Boechera stricta. Evolution 72(5): 1034-1049. https://doi.org/10.1111/evo.13469 - Please cite this dataset: Wagner, M. R., & Mitchell-Olds, T. (2018). Data from: Plasticity of plant defense and its evolutionary implications in wild populations of Boechera stricta [Data set]. Dryad Digital Repository. https://doi.org/10.5061/dryad.f9s4424 + Please cite this dataset: https://doi.org/10.5061/dryad.f9s4424 """, - Any["/bitstream/handle/10255/dryad.173251/raw_data.zip?sequence=1", "/bitstream/handle/10255/dryad.173251/README.txt?sequence=2", "/bitstream/handle/10255/dryad.173252/GSplasticity_code.R?sequence=1"], - [(md5, "aea52e9cdb6c4069720bc709415e479f"), (md5, "2abd4c62b7263eba8c74ce2bcb25790f"), (md5, "783d619e042bfe516b6ffd34dc97b5df")] + Any["https://datadryad.org/bitstream/handle/10255/dryad.173251/raw_data.zip?sequence=1", "https://datadryad.org/bitstream/handle/10255/dryad.173251/README.txt?sequence=2", "https://datadryad.org/bitstream/handle/10255/dryad.173252/GSplasticity_code.R?sequence=1"], + [(md5, "898237b1dd8306be586ffc036ebda768"), (md5, "af502ff7111868c548cc7923a9193673")] )) \ No newline at end of file From 50198a1be92ea60e167be4babd489696900f1fce Mon Sep 17 00:00:00 2001 From: Lyndon White Date: Sat, 27 Oct 2018 22:42:15 +0800 Subject: [PATCH 5/5] =update references --- test/references/Combining Ecology.txt | 4 ++-- test/references/Combining Plasticity.txt | 9 +++++---- 2 files changed, 7 insertions(+), 6 deletions(-) diff --git a/test/references/Combining Ecology.txt b/test/references/Combining Ecology.txt index 5ac12fb..6b0ea87 100644 --- a/test/references/Combining Ecology.txt +++ b/test/references/Combining Ecology.txt @@ -5,13 +5,13 @@ register(DataDep( Website: https://datadryad.org/resource/doi:10.5061/dryad.74699 Author: Eric J. B. Von Wettberg et al. Date of Publication: February 27, 2018 - License: http://creativecommons.org/publicdomain/zero/1.0/ + License: https://creativecommons.org/publicdomain/zero/1.0/ Domesticated species are impacted in unintended ways during domestication and breeding. Changes in the nature and intensity of selection impart genetic drift, reduce diversity, and increase the frequency of deleterious alleles. Such outcomes constrain our ability to expand the cultivation of crops into environments that differ from those under which domestication occurred. We address this need in chickpea, an important pulse legume, by harnessing the diversity of wild crop relatives. We document an extreme domestication-related genetic bottleneck and decipher the genetic history of wild populations. We provide evidence of ancestral adaptations for seed coat color crypsis, estimate the impact of environment on genetic structure and trait values, and demonstrate variation between wild and cultivated accessions for agronomic properties. A resource of genotyped, association mapping progeny functionally links the wild and cultivated gene pools and is an essential resource chickpea for improvement, while our methods inform collection of other wild crop progenitor species. Please cite this paper: von Wettberg EJB, Chang PL, Başdemir F, Carrasquila-Garcia N, Korbu L, Moenga SM, Bedada G, Greenlon A, Moriuchi KS, Suryawanshi V, Cordeiro MA, Noujdina NV, Dinegde KN, Abbas Shah Sani SG, Getahun T, Vance L, Bergmann E, Lindsay D, Mamo BE, Warschefsky EJ, Dacosta-Calheiros E, Marques E, Yilmaz MA, Cakmak AM, Rose J, Migneault A, Krieg CP, Saylak S, Temel H, Friesen ML, Silor E, Akhmetov Z, Ozelik H, Kholova J, Can C, Gaur P, Yildirim M, Sharma H, Vadez V, Tesfaye K, Woldemedhin AF, Tar'an B, Aydogan A, Bukun B, Penmetsa RV, Berger J, Kahraman A, Nuzhdin SV, Cook DR (2018) Ecology and genomics of an important crop wild relative as a prelude to agricultural innovation. Nature Communications 9: 649. https://doi.org/10.1038/s41467-018-02867-z - Please cite this dataset: https://doi.org/10.5061/dryad.74699 + Please cite this dataset: Von Wettberg, E. J. B., Chang, P. L., Başdemir, F., Carrasquila-Garcia, N., Korbu, L., Moenga, S. M., … Cook, D. R. (2018). Data from: Ecology and genomics of an important crop wild relative as a prelude to agricultural innovation [Data set]. Dryad Digital Repository. https://doi.org/10.5061/dryad.74699 """, Any["https://datadryad.org/bitstream/handle/10255/dryad.166590/draft_dryad_upload_dec2017.xls?sequence=1"], [(md5, "efc75490db3444d3708b3e9ccd030d38")] diff --git a/test/references/Combining Plasticity.txt b/test/references/Combining Plasticity.txt index 18efa99..03c5092 100644 --- a/test/references/Combining Plasticity.txt +++ b/test/references/Combining Plasticity.txt @@ -3,15 +3,16 @@ register(DataDep( """ Dataset: Data from: Plasticity of plant defense and its evolutionary implications in wild populations of Boechera stricta Website: http://dx.doi.org/10.5061/dryad.f9s4424 - Author: Wagner MR + Author: Maggie R. Wagner, Thomas Mitchell-Olds Date of Publication: March 2, 2018 - License: http://creativecommons.org/publicdomain/zero/1.0/ + License: https://creativecommons.org/publicdomain/zero/1.0/ Phenotypic plasticity is thought to impact evolutionary trajectories by shifting trait values in a direction that is either favored by natural selection (“adaptive plasticity”) or disfavored (“nonadaptive” plasticity). However, it is unclear how commonly each of these types of plasticity occurs in natural populations. To answer this question, we measured glucosinolate defensive chemistry and reproductive fitness in over 1,500 individuals of the wild perennial mustard Boechera stricta, planted in four common gardens across central Idaho, USA. Glucosinolate profiles—including total glucosinolate concentration as well as the relative abundances and overall diversity of different compounds—were strongly plastic both among habitats and within habitats. Patterns of glucosinolate plasticity varied greatly among genotypes. Plasticity among sites was predicted to affect fitness in 27.1% of cases; more often than expected by chance, glucosinolate plasticity increased rather than decreased relative fitness. In contrast, we found no evidence for within-habitat selection on glucosinolate reaction norm slopes (i.e., plasticity along a continuous environmental gradient). Together, our results indicate that glucosinolate plasticity may improve the ability of B. stricta populations to persist after migration to new habitats. - Please cite this paper: Wagner MR, Mitchell-Olds T (2018) Plasticity of plant defense and its evolutionary implications in wild populations of Boechera stricta. Evolution 72(5): 1034-1049. https://doi.org/10.1111/evo.13469 + Please cite this paper: Wagner, M. R., & Mitchell-Olds, T. (2018). Plasticity of plant defense and its evolutionary implications in wild populations of Boechera stricta + . Evolution, 72(5), 1034–1049. doi:10.1111/evo.13469 - Please cite this dataset: https://doi.org/10.5061/dryad.f9s4424 + Please cite this dataset: Wagner, M. R., & Mitchell-Olds, T. (2018). Data from: Plasticity of plant defense and its evolutionary implications in wild populations of Boechera stricta [Data set]. Dryad Digital Repository. https://doi.org/10.5061/dryad.f9s4424 """, Any["https://datadryad.org/bitstream/handle/10255/dryad.173251/raw_data.zip?sequence=1", "https://datadryad.org/bitstream/handle/10255/dryad.173251/README.txt?sequence=2", "https://datadryad.org/bitstream/handle/10255/dryad.173252/GSplasticity_code.R?sequence=1"], [(md5, "898237b1dd8306be586ffc036ebda768"), (md5, "af502ff7111868c548cc7923a9193673")]