The diversity and the motor performance of birdsongs can both be sexually selected. In wood warblers, most species with high motor performance sing a greater proportion of trills, presumably to advertise performance, and thus have lower syllable diversity. We tested if this trade‐off between motor performance and syllable diversity extends to canaries, goldfinches and allies, a clade with much longer and more varied songs. We assembled a molecular phylogeny and inferred song motor performance based on the speed of frequency modulation either in trills or in within‐song intervals. The two metrics of performance were positively, but only mildly, related across species. While performance evaluated in intervals had high phylogenetic signal, performance evaluated in trills changed independently of phylogeny and was constrained by body size. Species in densely vegetated habitats sang fewer trills, but did not differ in motor performance. Contrary to wood warblers, song motor performance did not predict the proportion of trilled syllables nor within‐song syllable diversity, perhaps because large differences in the song duration of canaries, goldfinches and allies prevent trills from severely compromising syllable diversity. Opposed results in wood warblers and in these finches indicate the existence of clade‐specific trade‐offs in the evolution of birdsong.
Abstract Phylogenetic diversity is an increasingly applied metric used to maximize the representation of evolutionary history in spatial conservation planning. When following this approach, researchers commonly overlook sites with a relatively higher proportion of recently diverged endemic species, also known as centers of neo-endemism. Here we aim to demonstrate how targeting the conservation of different facets of diversity (taxonomic diversity, phylogenetic diversity and centers of endemism) can provide more cost-effective solutions to the conservation of the all evolutionary spectrum of biodiversity. We do so by using the mantellid frogs of Madagascar as a case study. Our results confirm that areas with high concentrations of neo-endemism can be effectively identified as conservation planning priorities only if we specifically target them. Neglecting areas that are poor in phylogenetic diversity may therefore compromise the maintenance of diversification processes, particularly when lesser proportions of the landscape are protected. This approach can be of particular interest to island ecosystems, since they often harbor unique and restricted evolutionary radiations.
This research received support from the SYNTHESYS Project http://www.synthesys.info, which is financed by the European Community Research Infrastructure Action under the FP7 “Capacities” programme.
The Paroedura bastardi clade, a subgroup of the Madagascan gecko genus Paroedura , currently comprises four nominal species: P. bastardi , supposedly widely distributed in southern and western Madagascar, P. ibityensis , a montane endemic, and P. tanjaka and P. neglecta , both restricted to the central west region of the island. Previous work has shown that Paroedura bastardi is a species complex with several strongly divergent mitochondrial lineages. Based on one mitochondrial and two nuclear markers, plus detailed morphological data, we undertake an integrative revision of this species complex. Using a representative sampling for seven nuclear and five mitochondrial genes we furthermore propose a phylogenetic hypothesis of relationships among the species in this clade. Our analyses reveal at least three distinct and independent evolutionary lineages currently referred to P. bastardi . Conclusive evidence for the species status of these lineages comes from multiple cases of syntopic occurrence without genetic admixture or morphological intermediates, suggesting reproductive isolation. We discuss the relevance of this line of evidence and the conditions under which concordant differentiation in unlinked loci under sympatry provides a powerful approach to species delimitation, and taxonomically implement our findings by (1) designating a lectotype for Paroedura bastardi , now restricted to the extreme South-East of Madagascar, (2) resurrecting of the binomen Paroedura guibeae Dixon & Kroll, 1974, which is applied to the species predominantly distributed in the South-West, and (3) describing a third species, Paroedura rennerae sp. nov., which has the northernmost distribution within the species complex.
CatalogueOfPlantsOfMadagascar.csv -- Comma-separated table with comprehensive taxonomic database of plants of Madagascar, from the “Catalogue of the Plants of Madagascar” project. Contact: Peter Phillipson - peter.phillipson@mobot.org and Marina Rabarimanarivo - marina.rabarimanarivo@mobot.mg Ex_situ_plants.xlsx -- Excel spreadsheet with numbers of ex situ conserved plant species, per family, from BGCI’s PlantSearch database and collections of Jardin Botanique Educatif and Parc Ivoloina. Contact: Malin Rivers - malin.rivers@bgci.org Ex_situ_vertebrates.xlsx -- Excel spreadsheet with the list of extant native Malagasy vertebrates with information on their presence in at least one international zoo holding and whether they have been bred successfully over the last 12 months. Data from the Zoological Information Management (ZIM) Software performed in February 2021. Contact: Angelica Crottini - tiliquait@yahoo.it Extinct_Animals_madagascar.csv -- Comma-separated table of all known anthropogenic extinctions before 1500 CE in Madagascar. Contact: Ferran Sayol - fsayol@gmail.com features_predict210325_predictions.txt -- Tab-separated table with results of the conservation status prediction from a Bayesian Neural Network for 5,887 species of vascular plants from Madagascar. Values are the mean posterior probabilities for each IUCN Red List category. Contact: Daniele Silvestro - daniele.silvestro@unifr.ch Fossils_Madagascar.csv -- Comma-separated table with Malagasy fossil records, downloaded from the PaleoBiology Database. Contact: Juan Carillo - juan.carrillo@mnhn.fr Fungi_supplementary_material.zip -- Zipped archive containing: R script to get fungal endemism estimates from GBIF/UNITE and process data; comma-separated tables from GBIF, PlutoF, Goodman lichen checklist and Index Fungorum (as of 02/12/20): comma-separated table listing Madagascan taxa with endemism status. Contact: Rowena Hill - r.hill @kew.org Genera_records_world.csv -- Comma-separated table with worldwide fossil records for Malagasy species, downloaded from the PaleoBiology Database. -- Juan Carillo - juan.carrillo@mnhn.fr lineage_data_clean_v4.csv -- Comma-separated table with crown and stem ages, number of species, and geographic origin or distribution of sister clade of Malagasy endemic lineages, extracted from the literature. Contact: Jan Hackel - j.hackel@kew.org and Angelica Crottini - tiliquait@yahoo.it Madagascar Protected Areas - Sources.csv -- Comma-separated table with comments and sources for columns in the protected area data in the csv and shapefile. Contact: Maria S. Vorontsova - m.vorontsova@kew.org Madagascar_terrestrial_protected_areas.csv -- Comma-separated values matching the data within the Protected Area Shapefile except the shapes. Contact: Daniel Edler - daniel.edler@umu.se and Henintsoa Razanajatovo - H.Razanajatovo@kew.org Madagascar_terrestrial_protected_areas.zip -- ESRI Shapefile for the synthesized protected areas of Madagascar, including Key Biodiversity Areas and attributes. Contact: Daniel Edler - daniel.edler@umu.se and Rasolohery Andriambolantsoa - arasolohery@ileiry.com moatsmith_1km_extended.zip -- Raster geotiff with new expanded vegetation types based on Moat & Smith (2007). Contact: Justin Moat - j.moat@kew.org Observed_and_predicted_threats.csv -- Comma-separated table with the number of species with each listed threat, as defined by the IUCN or predicted by our model, across taxonomic groups. Contact: Rob Cooke - 03rcooke@gmail.com PhylogeneticDiversityMethods.zip -- Zipped archive containing community matrices, species range shapefiles, and R script used to estimate phylogenetic diversity for amphibians, mammals, and reptiles. Contact: Weston Testo - westontesto@gmail.com SpeciesRichnessModelingOccurrences.csv -- Comma-separated table with specimen-based occurrence data for Malagasy amphibians, grasses, lemurs, palms, reptiles, and Sarcolaenaceae. Contact: Weston Testo - westontesto@gmail.com TaxonDescriptionByYear.csv -- Comma-separated table with years of basionym publication for Malagasy amphibians, reptiles, vascular plants, and ants. Contact: Weston Testo - westontesto@gmail.com VertebrateSpeciesList.csv -- Comma-separated table with species list of amphibians, birds, mammals, and reptiles of Madagascar (curated list based on IUCN data). Contact: Weston Testo - westontesto@gmail.com
Data repository for the double review on Madagascar's biodiversity [ADD FULL CITATIONS + DOI WHEN ACCEPTED] REVIEW I: EVOLUTION, DISTRIBUTION AND USE CatalogueOfVascularPlantsOfMadagascar.csv -- Comma-separated table with comprehensive taxonomic database of vascular plants of Madagascar, from the “Catalogue of the Vascular Plants of Madagascar” project. Contact: Peter Phillipson - peter.phillipson@mobot.org and Marina Rabarimanarivo - marina.rabarimanarivo@mobot.mg Fossils_Madagascar.csv -- Comma-separated table with Malagasy fossil records, downloaded from the PaleoBiology Database. Contact: Juan Carillo - juan.carrillo@mnhn.fr [REMOVE - NOT USED] Fungi_supplementary_material.zip -- Zipped archive containing: R script to get fungal endemism estimates from GBIF/UNITE and process data; comma-separated tables from GBIF, PlutoF, Goodman lichen checklist and Index Fungorum (as of 02/12/20): comma-separated table listing Madagascan taxa with endemism status. Contact: Rowena Hill - r.hill@kew.org Genera_records_world.csv -- Comma-separated table with worldwide fossil records for Malagasy species, downloaded from the PaleoBiology Database. -- Juan Carillo - juan.carrillo@mnhn.fr [ADD FILE AND RENAME AS Malagasy_fossil_genera_occurrences.csv] lineage_data_clean_v4.csv -- Comma-separated table with crown and stem ages, number of species, and geographic origin or distribution of sister clade of Malagasy endemic lineages, extracted from the literature. Contact: Jan Hackel - j.hackel@kew.org and Angelica Crottini - tiliquait@yahoo.it moatsmith_1km_extended.zip -- Raster geotiff with new expanded vegetation types based on Moat & Smith (2007). Contact: Justin Moat - j.moat@kew.org SpeciesRichnessModelingOccurrences.csv -- Comma-separated table with specimen-based occurrence data for Malagasy amphibians, grasses, lemurs, palms, reptiles, and Sarcolaenaceae. Contact: Weston Testo - westontesto@gmail.com TaxonDescriptionByYear.csv -- Comma-separated table with years of basionym publication for Malagasy amphibians, reptiles, vascular plants, and ants. Contact: Weston Testo - westontesto@gmail.com VertebrateSpeciesList.csv -- Comma-separated table with species list of freshwater fish, amphibians, reptiles, birds and mammals of Madagascar (curated list based on IUCN data). Contact: Weston Testo - westontesto@gmail.com [FILE TO UPDATE] REVIEW II: THREATS AND OPPORTUNITIES CatalogueOfVascularPlantsOfMadagascar.csv -- Comma-separated table with comprehensive taxonomic database of vascular plants of Madagascar, from the “Catalogue of the Vascular Plants of Madagascar” project. Contact: Peter Phillipson - peter.phillipson@mobot.org and Marina Rabarimanarivo - marina.rabarimanarivo@mobot.mg Ex_situ_plants.xlsx -- Excel spreadsheet with numbers of ex situ conserved plant species, per family, from BGCI’s PlantSearch database and collections of Jardin Botanique Educatif and Parc Ivoloina. Contact: Malin Rivers - malin.rivers@bgci.org Ex_situ_vertebrates.xlsx -- Excel spreadsheet with the list of extant native Malagasy vertebrates with information on their presence in at least one international zoo holding and whether they have been bred successfully over the last 12 months. Data from the Zoological Information Management (ZIM) Software performed in February 2021. Contact: Angelica Crottini - tiliquait@yahoo.it [FILE TO UPDATE] Extinct_Animals_madagascar.csv -- Comma-separated table of all known anthropogenic extinctions before 1500 CE in Madagascar. Contact: Ferran Sayol - fsayol@gmail.com features_predict210325_predictions.txt -- Tab-separated table with results of the conservation status prediction from a Bayesian Neural Network for 5,887 species of vascular plants from Madagascar. Values are the mean posterior probabilities for each IUCN Red List category. Contact: Daniele Silvestro - daniele.silvestro@unifr.ch Madagascar Protected Areas - Sources.csv -- Comma-separated table with comments and sources for columns in the protected area data in the csv and shapefile. Contact: Maria S. Vorontsova - m.vorontsova@kew.org Madagascar_terrestrial_protected_areas.csv -- Comma-separated values with description of the pretected areas, matching the Protected Area Shapefile. Contact: Daniel Edler - daniel.edler@umu.se and Henintsoa Razanajatovo - H.Razanajatovo@kew.org Madagascar_terrestrial_protected_areas.zip -- ESRI Shapefile for the synthesized protected areas of Madagascar, including Key Biodiversity Areas and attributes. Contact: Daniel Edler - daniel.edler@umu.se and Rasolohery Andriambolantsoa - arasolohery@ileiry.com Observed_and_predicted_threats.csv -- Comma-separated table with the number of species with each listed threat, as defined by the IUCN or predicted by our model, across taxonomic groups. Contact: Rob Cooke - 03rcooke@gmail.com PhylogeneticDiversityMethods.zip -- Zipped archive containing community matrices, species range shapefiles, and R script used to estimate phylogenetic diversity for amphibians, mammals, and reptiles. Contact: Weston Testo - westontesto@gmail.com predicting_species_IUCN_status.zip -- Zipped archive containing data, scripts and an Rstudio project to: (1) prepare features for using IUCNN v1.0 to predict the conservation status for Not Evaluated species (01_feature_preparation); (2) predict species IUCN status assessment using neural networks (02_predicting_species_IUCN_status); (3) predict species’ threat status using neural networks (03_predicting_species_threats). Contact: Alexander Zizka - alexander.zizka@idiv.de and Daniele Silvestro - daniele.silvestro@unifr.ch
A global genome database of all of Earth's species diversity could be a treasure trove of scientific discoveries. However, regardless of the major advances in genome sequencing technologies, only a tiny fraction of species have genomic information available. To contribute to a more complete planetary genomic database, scientists and institutions across the world have united under the Earth BioGenome Project (EBP), which plans to sequence and assemble high-quality reference genomes for all ~1.5 million recognized eukaryotic species through a stepwise phased approach. As the initiative transitions into Phase II, where 150,000 species are to be sequenced in just four years, worldwide participation in the project will be fundamental to success. As the European node of the EBP, the European Reference Genome Atlas (ERGA) seeks to implement a new decentralised, accessible, equitable and inclusive model for producing high-quality reference genomes, which will inform EBP as it scales. To embark on this mission, ERGA launched a Pilot Project to establish a network across Europe to develop and test the first infrastructure of its kind for the coordinated and distributed reference genome production on 98 European eukaryotic species from sample providers across 34 European countries. Here we outline the process and challenges faced during the development of a pilot infrastructure for the production of reference genome resources, and explore the effectiveness of this approach in terms of high-quality reference genome production, considering also equity and inclusion. The outcomes and lessons learned during this pilot provide a solid foundation for ERGA while offering key learnings to other transnational and national genomic resource projects.
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