cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7976840.v1
title: Animator for the local attraction model from Asynchrony induces polarization in attraction-based models of collective motion

description: Matlab function for animating the 2D local attraction model on a periodic LxL square with N particles, of which Na update asynchronously and N-Na update synchronously, for T time steps with relative strength of local attraction c. To run the animator download the file codeS2.m, open Matlab, set current directory to where codeS2.m is located, and then run the command codeS2(L,N,Na,T,c,K) from the command line with all parameters specified. In addition to the five parameters L,N,Na,T and c specified above the parameter K specifies how often a frame will be captured for the animation. For example, if K=1 all simulation steps will be animated, if K=100 every 100th simulation step will be animated. Examples: One Swarm: codeS2(10,50,50,100,2,1) (Potentially) several swarms: codeS2(50,100,100,600,2,1) One Mill: codeS2(10,50,50,100,1,1) (Potentially) several Mills: codeS2(50,100,100,600,0.5,1) One Polarised group: codeS2(10,50,50,2000,0.15,10) (Potentially) several Polarised Groups: codeS2(50,100,100,4000,0.15,10) ! Note that K=10 here, so only every 10th frame is included in the animation, set K=1 to include every time step.
DOI: 10.6084/m9.figshare.7981637
title: Table S7 from Local ancestry analysis reveals genomic convergence in extremophile fishes.

description: Genes that were consistently differentially expressed between sulfidic and non-sulfidic populations in three drainages (Pichucalco, Puyacatengo, and Tacotalpa).
DOI: 10.6084/m9.figshare.7981631
title: Table S6 from Local ancestry analysis reveals genomic convergence in extremophile fishes.

description: Enriched Gene Ontology (GO) biological process terms in genes assigned to each cactus that clusters by ecotype, and all genes in any cacti that cluster by ecotype.
DOI: 10.6084/m9.figshare.7981637.v2
title: Table S7 from Local ancestry analysis reveals genomic convergence in extremophile fishes.

description: Genes that were consistently differentially expressed between sulfidic and non-sulfidic populations in three drainages (Pichucalco, Puyacatengo, and Tacotalpa).
DOI: 10.6084/m9.figshare.7981625
title: Table S5 from Local ancestry analysis reveals genomic convergence in extremophile fishes.

description: Genes that overlapped with structural variants (SVs) that were shared by sulfidic individuals.
DOI: 10.6084/m9.figshare.7981637.v1
title: Table S7 from Local ancestry analysis reveals genomic convergence in extremophile fishes

description: Genes that were consistently differentially expressed between sulfidic and non-sulfidic populations in three drainages (Pichucalco, Puyacatengo, and Tacotalpa).
DOI: 10.6084/m9.figshare.7981622
title: Table S2 from Local ancestry analysis reveals genomic convergence in extremophile fishes.

description: Genes that were assigned to cacti that cluster by ecotype.
DOI: 10.6084/m9.figshare.7981631.v2
title: Table S6 from Local ancestry analysis reveals genomic convergence in extremophile fishes.

description: Enriched Gene Ontology (GO) biological process terms in genes assigned to each cactus that clusters by ecotype, and all genes in any cacti that cluster by ecotype.
DOI: 10.6084/m9.figshare.7981625.v2
title: Table S5 from Local ancestry analysis reveals genomic convergence in extremophile fishes.

description: Genes that overlapped with structural variants (SVs) that were shared by sulfidic individuals.
DOI: 10.6084/m9.figshare.7981631.v1
title: Table S6 from Local ancestry analysis reveals genomic convergence in extremophile fishes

description: Enriched Gene Ontology (GO) biological process terms in genes assigned to each cactus that clusters by ecotype, and all genes in any cacti that cluster by ecotype.
DOI: 10.6084/m9.figshare.7981622.v2
title: Table S2 from Local ancestry analysis reveals genomic convergence in extremophile fishes.

description: Genes that were assigned to cacti that cluster by ecotype.
DOI: 10.6084/m9.figshare.7981625.v1
title: Table S5 from Local ancestry analysis reveals genomic convergence in extremophile fishes

description: Genes that overlapped with structural variants (SVs) that were shared by sulfidic individuals.
DOI: 10.6084/m9.figshare.7981622.v1
title: Table S2 from Local ancestry analysis reveals genomic convergence in extremophile fishes

description: Genes that were assigned to cacti that cluster by ecotype.
DOI: 10.6084/m9.figshare.7987115
title: Supplementary tables from Rate variation in the evolution of non-coding DNA associated with social evolution in bees.

description: The evolutionary origins of eusociality represent increases in complexity from individual to caste-based, group reproduction. These behavioural transitions have been hypothesized to go hand in hand with an increased ability to regulate when and where genes are expressed. Bees have convergently evolved eusociality up to five times, providing a framework to test this hypothesis. To examine potential links between putative gene regulatory elements and social evolution, we compare alignable, non-coding sequences in 11 diverse bee species, encompassing three independent origins of reproductive division of labour and two elaborations of eusocial complexity. We find that rates of evolution in a number of non-coding sequences correlate with key social transitions in bees. Interestingly, while we find little evidence for convergent rate changes associated with independent origins of social behaviour, a number of molecular pathways exhibit convergent rate changes in conjunction with subsequent elaborations of social organization. We also present evidence that many novel non-coding regions may have been recruited alongside the origin of sociality in corbiculate bees; these loci could represent gene regulatory elements associated with division of labour within this group. Thus, our findings are consistent with the hypothesis that gene regulatory innovations are associated with the evolution of eusociality and illustrate how a thorough examination of both coding and non-coding sequence can provide a more complete understanding of the molecular mechanisms underlying behavioural evolution.This article is part of the theme issue ‘Convergent evolution in the genomics era: new insights and directions’.
DOI: 10.6084/m9.figshare.7987115.v2
title: Supplementary tables from Rate variation in the evolution of non-coding DNA associated with social evolution in bees.

description: The evolutionary origins of eusociality represent increases in complexity from individual to caste-based, group reproduction. These behavioural transitions have been hypothesized to go hand in hand with an increased ability to regulate when and where genes are expressed. Bees have convergently evolved eusociality up to five times, providing a framework to test this hypothesis. To examine potential links between putative gene regulatory elements and social evolution, we compare alignable, non-coding sequences in 11 diverse bee species, encompassing three independent origins of reproductive division of labour and two elaborations of eusocial complexity. We find that rates of evolution in a number of non-coding sequences correlate with key social transitions in bees. Interestingly, while we find little evidence for convergent rate changes associated with independent origins of social behaviour, a number of molecular pathways exhibit convergent rate changes in conjunction with subsequent elaborations of social organization. We also present evidence that many novel non-coding regions may have been recruited alongside the origin of sociality in corbiculate bees; these loci could represent gene regulatory elements associated with division of labour within this group. Thus, our findings are consistent with the hypothesis that gene regulatory innovations are associated with the evolution of eusociality and illustrate how a thorough examination of both coding and non-coding sequence can provide a more complete understanding of the molecular mechanisms underlying behavioural evolution.This article is part of the theme issue ‘Convergent evolution in the genomics era: new insights and directions’.
DOI: 10.6084/m9.figshare.7987115.v1
title: Supplementary tables from Rate variation in the evolution of non-coding DNA associated with social evolution in bees

description: The evolutionary origins of eusociality represent increases in complexity from individual to caste-based, group reproduction. These behavioural transitions have been hypothesized to go hand in hand with an increased ability to regulate when and where genes are expressed. Bees have convergently evolved eusociality up to five times, providing a framework to test this hypothesis. To examine potential links between putative gene regulatory elements and social evolution, we compare alignable, non-coding sequences in 11 diverse bee species, encompassing three independent origins of reproductive division of labour and two elaborations of eusocial complexity. We find that rates of evolution in a number of non-coding sequences correlate with key social transitions in bees. Interestingly, while we find little evidence for convergent rate changes associated with independent origins of social behaviour, a number of molecular pathways exhibit convergent rate changes in conjunction with subsequent elaborations of social organization. We also present evidence that many novel non-coding regions may have been recruited alongside the origin of sociality in corbiculate bees; these loci could represent gene regulatory elements associated with division of labour within this group. Thus, our findings are consistent with the hypothesis that gene regulatory innovations are associated with the evolution of eusociality and illustrate how a thorough examination of both coding and non-coding sequence can provide a more complete understanding of the molecular mechanisms underlying behavioural evolution.This article is part of the theme issue ‘Convergent evolution in the genomics era: new insights and directions’.
DOI: 10.6084/m9.figshare.7987271
title: Dataset S2 from Convergent evolution in <i>Arabidopsis halleri</i> and <i>Arabidopsis arenosa</i> on calamine metalliferous soils.

description: It is a plausible hypothesis that parallel adaptation events to the same environmental challenge should result in genetic changes of similar or identical effects, depending on the underlying fitness landscapes. However, systematic testing of this is scarce. Here we examine this hypothesis in two closely related plant species, <i>Arabidopsis halleri</i> and <i>Arabidopsis arenosa</i>, which co-occur at two calamine metalliferous (M) sites harbouring toxic levels of the heavy metals zinc and cadmium. We conduct individual genome resequencing alongside soil elemental analysis for 64 plants from eight populations on M and non-metalliferous (NM) soils, and identify genomic footprints of selection and local adaptation. Selective sweep and environmental association analyses indicate a modest degree of gene as well as functional network convergence, whereby the proximal molecular factors mediating this convergence mostly differ between site pairs and species. Notably, we observe repeated selection on identical single nucleotide poly-morphisms in several <i>A. halleri</i> genes at two independently colonized M sites. Our data suggest that species-specific metal handling and other biological features could explain a low degree of convergence between species. The parallel establishment of plant populations on calamine M soils involves convergent evolution, which will probably be more pervasive across sites purposely chosen for maximal similarity in soil composition.This article is part of the theme issue ‘Convergent evolution in the genomics era: new insights and directions’.
DOI: 10.6084/m9.figshare.7987292
title: Dataset S1 from Convergent evolution in <i>Arabidopsis halleri</i> and <i>Arabidopsis arenosa</i> on calamine metalliferous soils.

description: It is a plausible hypothesis that parallel adaptation events to the same environmental challenge should result in genetic changes of similar or identical effects, depending on the underlying fitness landscapes. However, systematic testing of this is scarce. Here we examine this hypothesis in two closely related plant species, <i>Arabidopsis halleri</i> and <i>Arabidopsis arenosa</i>, which co-occur at two calamine metalliferous (M) sites harbouring toxic levels of the heavy metals zinc and cadmium. We conduct individual genome resequencing alongside soil elemental analysis for 64 plants from eight populations on M and non-metalliferous (NM) soils, and identify genomic footprints of selection and local adaptation. Selective sweep and environmental association analyses indicate a modest degree of gene as well as functional network convergence, whereby the proximal molecular factors mediating this convergence mostly differ between site pairs and species. Notably, we observe repeated selection on identical single nucleotide poly-morphisms in several <i>A. halleri</i> genes at two independently colonized M sites. Our data suggest that species-specific metal handling and other biological features could explain a low degree of convergence between species. The parallel establishment of plant populations on calamine M soils involves convergent evolution, which will probably be more pervasive across sites purposely chosen for maximal similarity in soil composition.This article is part of the theme issue ‘Convergent evolution in the genomics era: new insights and directions’.
DOI: 10.6084/m9.figshare.7987271.v2
title: Dataset S2 from Convergent evolution in <i>Arabidopsis halleri</i> and <i>Arabidopsis arenosa</i> on calamine metalliferous soils.

description: It is a plausible hypothesis that parallel adaptation events to the same environmental challenge should result in genetic changes of similar or identical effects, depending on the underlying fitness landscapes. However, systematic testing of this is scarce. Here we examine this hypothesis in two closely related plant species, <i>Arabidopsis halleri</i> and <i>Arabidopsis arenosa</i>, which co-occur at two calamine metalliferous (M) sites harbouring toxic levels of the heavy metals zinc and cadmium. We conduct individual genome resequencing alongside soil elemental analysis for 64 plants from eight populations on M and non-metalliferous (NM) soils, and identify genomic footprints of selection and local adaptation. Selective sweep and environmental association analyses indicate a modest degree of gene as well as functional network convergence, whereby the proximal molecular factors mediating this convergence mostly differ between site pairs and species. Notably, we observe repeated selection on identical single nucleotide poly-morphisms in several <i>A. halleri</i> genes at two independently colonized M sites. Our data suggest that species-specific metal handling and other biological features could explain a low degree of convergence between species. The parallel establishment of plant populations on calamine M soils involves convergent evolution, which will probably be more pervasive across sites purposely chosen for maximal similarity in soil composition.This article is part of the theme issue ‘Convergent evolution in the genomics era: new insights and directions’.
DOI: 10.6084/m9.figshare.7987250
title: Dataset S4 from Convergent evolution in <i>Arabidopsis halleri</i> and <i>Arabidopsis arenosa</i> on calamine metalliferous soils.

description: It is a plausible hypothesis that parallel adaptation events to the same environmental challenge should result in genetic changes of similar or identical effects, depending on the underlying fitness landscapes. However, systematic testing of this is scarce. Here we examine this hypothesis in two closely related plant species, <i>Arabidopsis halleri</i> and <i>Arabidopsis arenosa</i>, which co-occur at two calamine metalliferous (M) sites harbouring toxic levels of the heavy metals zinc and cadmium. We conduct individual genome resequencing alongside soil elemental analysis for 64 plants from eight populations on M and non-metalliferous (NM) soils, and identify genomic footprints of selection and local adaptation. Selective sweep and environmental association analyses indicate a modest degree of gene as well as functional network convergence, whereby the proximal molecular factors mediating this convergence mostly differ between site pairs and species. Notably, we observe repeated selection on identical single nucleotide poly-morphisms in several <i>A. halleri</i> genes at two independently colonized M sites. Our data suggest that species-specific metal handling and other biological features could explain a low degree of convergence between species. The parallel establishment of plant populations on calamine M soils involves convergent evolution, which will probably be more pervasive across sites purposely chosen for maximal similarity in soil composition.This article is part of the theme issue ‘Convergent evolution in the genomics era: new insights and directions’.
DOI: 10.6084/m9.figshare.7987271.v1
title: Dataset S2 from Convergent evolution in <i>Arabidopsis halleri</i> and <i>Arabidopsis arenosa</i> on calamine metalliferous soils

description: It is a plausible hypothesis that parallel adaptation events to the same environmental challenge should result in genetic changes of similar or identical effects, depending on the underlying fitness landscapes. However, systematic testing of this is scarce. Here we examine this hypothesis in two closely related plant species, <i>Arabidopsis halleri</i> and <i>Arabidopsis arenosa</i>, which co-occur at two calamine metalliferous sites harbouring toxic levels of the heavy metals zinc and cadmium. We conduct individual genome resequencing alongside soil elemental analysis for 64 plants from eight populations on metalliferous and non-metalliferous soils, and identify genomic footprints of selection and local adaptation. Selective sweep and environmental association analyses indicate a modest degree of gene as well as functional network convergence, whereby the proximal molecular factors mediating this convergence mostly differ between site pairs and species. Notably, we observe repeated selection on identical SNPs in several <i>A. halleri</i> genes at two independently colonized metalliferous sites. Our data suggest that species-specific metal handling and other biological features could explain a low degree of convergence between species. The parallel establishment of plant populations on calamine metalliferous soils involves convergent evolution, which will likely be more pervasive across sites purposely chosen for maximal similarity in soil composition.This article is part of the theme issue ‘Convergent evolution in the genomics era: new insights and directions’.
DOI: 10.6084/m9.figshare.7987286
title: Dataset S3 from Convergent evolution in <i>Arabidopsis halleri</i> and <i>Arabidopsis arenosa</i> on calamine metalliferous soils.

description: It is a plausible hypothesis that parallel adaptation events to the same environmental challenge should result in genetic changes of similar or identical effects, depending on the underlying fitness landscapes. However, systematic testing of this is scarce. Here we examine this hypothesis in two closely related plant species, <i>Arabidopsis halleri</i> and <i>Arabidopsis arenosa</i>, which co-occur at two calamine metalliferous (M) sites harbouring toxic levels of the heavy metals zinc and cadmium. We conduct individual genome resequencing alongside soil elemental analysis for 64 plants from eight populations on M and non-metalliferous (NM) soils, and identify genomic footprints of selection and local adaptation. Selective sweep and environmental association analyses indicate a modest degree of gene as well as functional network convergence, whereby the proximal molecular factors mediating this convergence mostly differ between site pairs and species. Notably, we observe repeated selection on identical single nucleotide poly-morphisms in several <i>A. halleri</i> genes at two independently colonized M sites. Our data suggest that species-specific metal handling and other biological features could explain a low degree of convergence between species. The parallel establishment of plant populations on calamine M soils involves convergent evolution, which will probably be more pervasive across sites purposely chosen for maximal similarity in soil composition.This article is part of the theme issue ‘Convergent evolution in the genomics era: new insights and directions’.
DOI: 10.6084/m9.figshare.7987256
title: Dataset S6 from Convergent evolution in <i>Arabidopsis halleri</i> and <i>Arabidopsis arenosa</i> on calamine metalliferous soils.

description: It is a plausible hypothesis that parallel adaptation events to the same environmental challenge should result in genetic changes of similar or identical effects, depending on the underlying fitness landscapes. However, systematic testing of this is scarce. Here we examine this hypothesis in two closely related plant species, <i>Arabidopsis halleri</i> and <i>Arabidopsis arenosa</i>, which co-occur at two calamine metalliferous (M) sites harbouring toxic levels of the heavy metals zinc and cadmium. We conduct individual genome resequencing alongside soil elemental analysis for 64 plants from eight populations on M and non-metalliferous (NM) soils, and identify genomic footprints of selection and local adaptation. Selective sweep and environmental association analyses indicate a modest degree of gene as well as functional network convergence, whereby the proximal molecular factors mediating this convergence mostly differ between site pairs and species. Notably, we observe repeated selection on identical single nucleotide poly-morphisms in several <i>A. halleri</i> genes at two independently colonized M sites. Our data suggest that species-specific metal handling and other biological features could explain a low degree of convergence between species. The parallel establishment of plant populations on calamine M soils involves convergent evolution, which will probably be more pervasive across sites purposely chosen for maximal similarity in soil composition.This article is part of the theme issue ‘Convergent evolution in the genomics era: new insights and directions’.
DOI: 10.6084/m9.figshare.7987292.v1
title: Dataset S1 from Convergent evolution in <i>Arabidopsis halleri</i> and <i>Arabidopsis arenosa</i> on calamine metalliferous soils

description: It is a plausible hypothesis that parallel adaptation events to the same environmental challenge should result in genetic changes of similar or identical effects, depending on the underlying fitness landscapes. However, systematic testing of this is scarce. Here we examine this hypothesis in two closely related plant species, <i>Arabidopsis halleri</i> and <i>Arabidopsis arenosa</i>, which co-occur at two calamine metalliferous sites harbouring toxic levels of the heavy metals zinc and cadmium. We conduct individual genome resequencing alongside soil elemental analysis for 64 plants from eight populations on metalliferous and non-metalliferous soils, and identify genomic footprints of selection and local adaptation. Selective sweep and environmental association analyses indicate a modest degree of gene as well as functional network convergence, whereby the proximal molecular factors mediating this convergence mostly differ between site pairs and species. Notably, we observe repeated selection on identical SNPs in several <i>A. halleri</i> genes at two independently colonized metalliferous sites. Our data suggest that species-specific metal handling and other biological features could explain a low degree of convergence between species. The parallel establishment of plant populations on calamine metalliferous soils involves convergent evolution, which will likely be more pervasive across sites purposely chosen for maximal similarity in soil composition.This article is part of the theme issue ‘Convergent evolution in the genomics era: new insights and directions’.