cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14371350
title: Table S7.xlsx from Species-specific but not phylosymbiotic gut microbiomes of New Guinean passerines birds are shaped by diet and flight-associated gut modifications

description: Animal hosts have evolved intricate associations with microbial symbionts, where both depend on each other for particular functions. In many cases, these associations lead to phylosymbiosis, where phylogenetically related species harbour compositionally more similar microbiomes than distantly related species. However, evidence for phylosymbiosis is either weak or lacking in gut microbiomes of flying vertebrates, particularly in birds. To shed more light on this phenomenon, we compared cloacal microbiomes of 37 tropical passerine bird species from New Guinea using 16S rRNA bacterial gene sequencing. We show a lack of phylosymbiosis and document highly variable microbiomes. Furthermore, we find that gut bacterial community compositions are species-specific and tend to be shaped by host diet but not sampling locality, potentially driven by the similarities in habitats used by individual species. We further show that flight-associated gut modifications, coupled with individual dietary differences, shape gut microbiome structure and variation, contributing to the lack of phylosymbiosis. These patterns indicate that the stability of symbiosis may depend on microbial functional diversity rather than taxonomic composition. Furthermore, the more variable and fluid host–microbe associations suggest probable disparities in the potential for coevolution between bird host species and microbial symbionts.
DOI: 10.6084/m9.figshare.14371350.v1
title: Table S7.xlsx from Species-specific but not phylosymbiotic gut microbiomes of New Guinean passerines birds are shaped by diet and flight-associated gut modifications

description: Animal hosts have evolved intricate associations with microbial symbionts, where both depend on each other for particular functions. In many cases, these associations lead to phylosymbiosis, where phylogenetically related species harbour compositionally more similar microbiomes than distantly related species. However, evidence for phylosymbiosis is either weak or lacking in gut microbiomes of flying vertebrates, particularly in birds. To shed more light on this phenomenon, we compared cloacal microbiomes of 37 tropical passerine bird species from New Guinea using 16S rRNA bacterial gene sequencing. We show a lack of phylosymbiosis and document highly variable microbiomes. Furthermore, we find that gut bacterial community compositions are species-specific and tend to be shaped by host diet but not sampling locality, potentially driven by the similarities in habitats used by individual species. We further show that flight-associated gut modifications, coupled with individual dietary differences, shape gut microbiome structure and variation, contributing to the lack of phylosymbiosis. These patterns indicate that the stability of symbiosis may depend on microbial functional diversity rather than taxonomic composition. Furthermore, the more variable and fluid host–microbe associations suggest probable disparities in the potential for coevolution between bird host species and microbial symbionts.
DOI: 10.6084/m9.figshare.14371347
title: Table S1.xlsx from Species-specific but not phylosymbiotic gut microbiomes of New Guinean passerines birds are shaped by diet and flight-associated gut modifications

description: Animal hosts have evolved intricate associations with microbial symbionts, where both depend on each other for particular functions. In many cases, these associations lead to phylosymbiosis, where phylogenetically related species harbour compositionally more similar microbiomes than distantly related species. However, evidence for phylosymbiosis is either weak or lacking in gut microbiomes of flying vertebrates, particularly in birds. To shed more light on this phenomenon, we compared cloacal microbiomes of 37 tropical passerine bird species from New Guinea using 16S rRNA bacterial gene sequencing. We show a lack of phylosymbiosis and document highly variable microbiomes. Furthermore, we find that gut bacterial community compositions are species-specific and tend to be shaped by host diet but not sampling locality, potentially driven by the similarities in habitats used by individual species. We further show that flight-associated gut modifications, coupled with individual dietary differences, shape gut microbiome structure and variation, contributing to the lack of phylosymbiosis. These patterns indicate that the stability of symbiosis may depend on microbial functional diversity rather than taxonomic composition. Furthermore, the more variable and fluid host–microbe associations suggest probable disparities in the potential for coevolution between bird host species and microbial symbionts.
DOI: 10.6084/m9.figshare.14371353
title: Table S3.xlsx from Species-specific but not phylosymbiotic gut microbiomes of New Guinean passerines birds are shaped by diet and flight-associated gut modifications

description: Animal hosts have evolved intricate associations with microbial symbionts, where both depend on each other for particular functions. In many cases, these associations lead to phylosymbiosis, where phylogenetically related species harbour compositionally more similar microbiomes than distantly related species. However, evidence for phylosymbiosis is either weak or lacking in gut microbiomes of flying vertebrates, particularly in birds. To shed more light on this phenomenon, we compared cloacal microbiomes of 37 tropical passerine bird species from New Guinea using 16S rRNA bacterial gene sequencing. We show a lack of phylosymbiosis and document highly variable microbiomes. Furthermore, we find that gut bacterial community compositions are species-specific and tend to be shaped by host diet but not sampling locality, potentially driven by the similarities in habitats used by individual species. We further show that flight-associated gut modifications, coupled with individual dietary differences, shape gut microbiome structure and variation, contributing to the lack of phylosymbiosis. These patterns indicate that the stability of symbiosis may depend on microbial functional diversity rather than taxonomic composition. Furthermore, the more variable and fluid host–microbe associations suggest probable disparities in the potential for coevolution between bird host species and microbial symbionts.
DOI: 10.6084/m9.figshare.14371353.v1
title: Table S3.xlsx from Species-specific but not phylosymbiotic gut microbiomes of New Guinean passerines birds are shaped by diet and flight-associated gut modifications

description: Animal hosts have evolved intricate associations with microbial symbionts, where both depend on each other for particular functions. In many cases, these associations lead to phylosymbiosis, where phylogenetically related species harbour compositionally more similar microbiomes than distantly related species. However, evidence for phylosymbiosis is either weak or lacking in gut microbiomes of flying vertebrates, particularly in birds. To shed more light on this phenomenon, we compared cloacal microbiomes of 37 tropical passerine bird species from New Guinea using 16S rRNA bacterial gene sequencing. We show a lack of phylosymbiosis and document highly variable microbiomes. Furthermore, we find that gut bacterial community compositions are species-specific and tend to be shaped by host diet but not sampling locality, potentially driven by the similarities in habitats used by individual species. We further show that flight-associated gut modifications, coupled with individual dietary differences, shape gut microbiome structure and variation, contributing to the lack of phylosymbiosis. These patterns indicate that the stability of symbiosis may depend on microbial functional diversity rather than taxonomic composition. Furthermore, the more variable and fluid host–microbe associations suggest probable disparities in the potential for coevolution between bird host species and microbial symbionts.
DOI: 10.6084/m9.figshare.14371359.v1
title: Table S6.xlsx from Species-specific but not phylosymbiotic gut microbiomes of New Guinean passerines birds are shaped by diet and flight-associated gut modifications

description: Animal hosts have evolved intricate associations with microbial symbionts, where both depend on each other for particular functions. In many cases, these associations lead to phylosymbiosis, where phylogenetically related species harbour compositionally more similar microbiomes than distantly related species. However, evidence for phylosymbiosis is either weak or lacking in gut microbiomes of flying vertebrates, particularly in birds. To shed more light on this phenomenon, we compared cloacal microbiomes of 37 tropical passerine bird species from New Guinea using 16S rRNA bacterial gene sequencing. We show a lack of phylosymbiosis and document highly variable microbiomes. Furthermore, we find that gut bacterial community compositions are species-specific and tend to be shaped by host diet but not sampling locality, potentially driven by the similarities in habitats used by individual species. We further show that flight-associated gut modifications, coupled with individual dietary differences, shape gut microbiome structure and variation, contributing to the lack of phylosymbiosis. These patterns indicate that the stability of symbiosis may depend on microbial functional diversity rather than taxonomic composition. Furthermore, the more variable and fluid host–microbe associations suggest probable disparities in the potential for coevolution between bird host species and microbial symbionts.
DOI: 10.6084/m9.figshare.14371362
title: Table S2.xlsx from Species-specific but not phylosymbiotic gut microbiomes of New Guinean passerines birds are shaped by diet and flight-associated gut modifications

description: Animal hosts have evolved intricate associations with microbial symbionts, where both depend on each other for particular functions. In many cases, these associations lead to phylosymbiosis, where phylogenetically related species harbour compositionally more similar microbiomes than distantly related species. However, evidence for phylosymbiosis is either weak or lacking in gut microbiomes of flying vertebrates, particularly in birds. To shed more light on this phenomenon, we compared cloacal microbiomes of 37 tropical passerine bird species from New Guinea using 16S rRNA bacterial gene sequencing. We show a lack of phylosymbiosis and document highly variable microbiomes. Furthermore, we find that gut bacterial community compositions are species-specific and tend to be shaped by host diet but not sampling locality, potentially driven by the similarities in habitats used by individual species. We further show that flight-associated gut modifications, coupled with individual dietary differences, shape gut microbiome structure and variation, contributing to the lack of phylosymbiosis. These patterns indicate that the stability of symbiosis may depend on microbial functional diversity rather than taxonomic composition. Furthermore, the more variable and fluid host–microbe associations suggest probable disparities in the potential for coevolution between bird host species and microbial symbionts.
DOI: 10.6084/m9.figshare.14371362.v1
title: Table S2.xlsx from Species-specific but not phylosymbiotic gut microbiomes of New Guinean passerines birds are shaped by diet and flight-associated gut modifications

description: Animal hosts have evolved intricate associations with microbial symbionts, where both depend on each other for particular functions. In many cases, these associations lead to phylosymbiosis, where phylogenetically related species harbour compositionally more similar microbiomes than distantly related species. However, evidence for phylosymbiosis is either weak or lacking in gut microbiomes of flying vertebrates, particularly in birds. To shed more light on this phenomenon, we compared cloacal microbiomes of 37 tropical passerine bird species from New Guinea using 16S rRNA bacterial gene sequencing. We show a lack of phylosymbiosis and document highly variable microbiomes. Furthermore, we find that gut bacterial community compositions are species-specific and tend to be shaped by host diet but not sampling locality, potentially driven by the similarities in habitats used by individual species. We further show that flight-associated gut modifications, coupled with individual dietary differences, shape gut microbiome structure and variation, contributing to the lack of phylosymbiosis. These patterns indicate that the stability of symbiosis may depend on microbial functional diversity rather than taxonomic composition. Furthermore, the more variable and fluid host–microbe associations suggest probable disparities in the potential for coevolution between bird host species and microbial symbionts.
DOI: 10.6084/m9.figshare.14371359
title: Table S6.xlsx from Species-specific but not phylosymbiotic gut microbiomes of New Guinean passerines birds are shaped by diet and flight-associated gut modifications

description: Animal hosts have evolved intricate associations with microbial symbionts, where both depend on each other for particular functions. In many cases, these associations lead to phylosymbiosis, where phylogenetically related species harbour compositionally more similar microbiomes than distantly related species. However, evidence for phylosymbiosis is either weak or lacking in gut microbiomes of flying vertebrates, particularly in birds. To shed more light on this phenomenon, we compared cloacal microbiomes of 37 tropical passerine bird species from New Guinea using 16S rRNA bacterial gene sequencing. We show a lack of phylosymbiosis and document highly variable microbiomes. Furthermore, we find that gut bacterial community compositions are species-specific and tend to be shaped by host diet but not sampling locality, potentially driven by the similarities in habitats used by individual species. We further show that flight-associated gut modifications, coupled with individual dietary differences, shape gut microbiome structure and variation, contributing to the lack of phylosymbiosis. These patterns indicate that the stability of symbiosis may depend on microbial functional diversity rather than taxonomic composition. Furthermore, the more variable and fluid host–microbe associations suggest probable disparities in the potential for coevolution between bird host species and microbial symbionts.
DOI: 10.6084/m9.figshare.14371368.v1
title: Table S4.xlsx from Species-specific but not phylosymbiotic gut microbiomes of New Guinean passerines birds are shaped by diet and flight-associated gut modifications

description: Animal hosts have evolved intricate associations with microbial symbionts, where both depend on each other for particular functions. In many cases, these associations lead to phylosymbiosis, where phylogenetically related species harbour compositionally more similar microbiomes than distantly related species. However, evidence for phylosymbiosis is either weak or lacking in gut microbiomes of flying vertebrates, particularly in birds. To shed more light on this phenomenon, we compared cloacal microbiomes of 37 tropical passerine bird species from New Guinea using 16S rRNA bacterial gene sequencing. We show a lack of phylosymbiosis and document highly variable microbiomes. Furthermore, we find that gut bacterial community compositions are species-specific and tend to be shaped by host diet but not sampling locality, potentially driven by the similarities in habitats used by individual species. We further show that flight-associated gut modifications, coupled with individual dietary differences, shape gut microbiome structure and variation, contributing to the lack of phylosymbiosis. These patterns indicate that the stability of symbiosis may depend on microbial functional diversity rather than taxonomic composition. Furthermore, the more variable and fluid host–microbe associations suggest probable disparities in the potential for coevolution between bird host species and microbial symbionts.
DOI: 10.6084/m9.figshare.14371368
title: Table S4.xlsx from Species-specific but not phylosymbiotic gut microbiomes of New Guinean passerines birds are shaped by diet and flight-associated gut modifications

description: Animal hosts have evolved intricate associations with microbial symbionts, where both depend on each other for particular functions. In many cases, these associations lead to phylosymbiosis, where phylogenetically related species harbour compositionally more similar microbiomes than distantly related species. However, evidence for phylosymbiosis is either weak or lacking in gut microbiomes of flying vertebrates, particularly in birds. To shed more light on this phenomenon, we compared cloacal microbiomes of 37 tropical passerine bird species from New Guinea using 16S rRNA bacterial gene sequencing. We show a lack of phylosymbiosis and document highly variable microbiomes. Furthermore, we find that gut bacterial community compositions are species-specific and tend to be shaped by host diet but not sampling locality, potentially driven by the similarities in habitats used by individual species. We further show that flight-associated gut modifications, coupled with individual dietary differences, shape gut microbiome structure and variation, contributing to the lack of phylosymbiosis. These patterns indicate that the stability of symbiosis may depend on microbial functional diversity rather than taxonomic composition. Furthermore, the more variable and fluid host–microbe associations suggest probable disparities in the potential for coevolution between bird host species and microbial symbionts.
DOI: 10.6084/m9.figshare.14371386
title: ESM_Descriptions.txt from Incorporating domain growth into hybrid methods for reaction–diffusion systems

description: Reaction–diffusion mechanism are a robust paradigm that can be used to represent many biological and physical phenomena over multiple spatial scales. Applications include intracellular dynamics, the migration of cells and the patterns formed by vegetation in semi-arid landscapes. Moreover, domain growth is an important process for embryonic growth and wound healing. There are many numerical modelling frameworks capable of simulating such systems on growing domains; however, each of these may be well suited to different spatial scales and particle numbers. Recently, spatially extended hybrid methods on static domains have been produced in order to bridge the gap between these different modelling paradigms in order to represent multiscale phenomena. However, such methods have not been developed with domain growth in mind. In this paper, we develop three hybrid methods on growing domains, extending three of the prominent static domain hybrid methods. We also provide detailed algorithms to allow others to employ them. We demonstrate that the methods are able to accurately model three representative reaction–diffusion systems accurately and without bias.
DOI: 10.6084/m9.figshare.14371386.v1
title: ESM_Descriptions.txt from Incorporating domain growth into hybrid methods for reaction–diffusion systems

description: Reaction–diffusion mechanism are a robust paradigm that can be used to represent many biological and physical phenomena over multiple spatial scales. Applications include intracellular dynamics, the migration of cells and the patterns formed by vegetation in semi-arid landscapes. Moreover, domain growth is an important process for embryonic growth and wound healing. There are many numerical modelling frameworks capable of simulating such systems on growing domains; however, each of these may be well suited to different spatial scales and particle numbers. Recently, spatially extended hybrid methods on static domains have been produced in order to bridge the gap between these different modelling paradigms in order to represent multiscale phenomena. However, such methods have not been developed with domain growth in mind. In this paper, we develop three hybrid methods on growing domains, extending three of the prominent static domain hybrid methods. We also provide detailed algorithms to allow others to employ them. We demonstrate that the methods are able to accurately model three representative reaction–diffusion systems accurately and without bias.
DOI: 10.6084/m9.figshare.14371394
title: Results table from Natural history collections recapitulate 200 years of faunal change

description: ESM file 2 is a large table containing results for each species, including the number of records, the year of the first and last record, the proportion of records prior and past 1912 and their significance, and the relative records tool results.
DOI: 10.6084/m9.figshare.14371394.v1
title: Results table from Natural history collections recapitulate 200 years of faunal change

description: ESM file 2 is a large table containing results for each species, including the number of records, the year of the first and last record, the proportion of records prior and past 1912 and their significance, and the relative records tool results.
DOI: 10.6084/m9.figshare.14371409
title: OpenSees Code 1 from A Markov chain-based model for structural vulnerability assessment of corrosion-damaged reinforced concrete bridges

description: FE Model
DOI: 10.6084/m9.figshare.14371409.v1
title: OpenSees Code 1 from A Markov chain-based model for structural vulnerability assessment of corrosion-damaged reinforced concrete bridges

description: FE Model
DOI: 10.6084/m9.figshare.14371412
title: OpenSees Code 3 from A Markov chain-based model for structural vulnerability assessment of corrosion-damaged reinforced concrete bridges

description: Material Models
DOI: 10.6084/m9.figshare.14371413.v1
title: Supplementary Materials for Appendix A from Explicit transformation between non-adhesive and adhesive contact problems by means of the classical Johnson–Kendall–Roberts formalism

description: The scripts provided as supplementary materials can be used to recreate in full the calculations presented in Appendix A of the paper.
DOI: 10.6084/m9.figshare.14371412.v1
title: OpenSees Code 3 from A Markov chain-based model for structural vulnerability assessment of corrosion-damaged reinforced concrete bridges

description: Material Models
DOI: 10.6084/m9.figshare.14371413
title: Supplementary Materials for Appendix A from Explicit transformation between non-adhesive and adhesive contact problems by means of the classical Johnson–Kendall–Roberts formalism

description: The scripts provided as supplementary materials can be used to recreate in full the calculations presented in Appendix A of the paper.
DOI: 10.6084/m9.figshare.14371415
title: OpenSees Code 2 from A Markov chain-based model for structural vulnerability assessment of corrosion-damaged reinforced concrete bridges

description: Column Section
DOI: 10.6084/m9.figshare.14371418
title: MATLAB Code from A Markov chain-based model for structural vulnerability assessment of corrosion-damaged reinforced concrete bridges

description: Markov State Probabilities
DOI: 10.6084/m9.figshare.14371418.v1
title: MATLAB Code from A Markov chain-based model for structural vulnerability assessment of corrosion-damaged reinforced concrete bridges

description: Markov State Probabilities