This release contains the main code and data used in the manuscript:"Moving beyond morphology: Genomic insights into evolutionary histories of haplosclerid sponges".Contents:All scripts for data processing and model outputExample datasetsREADME with instructionsLicense file

This release contains the main code and data used in the manuscript:"Moving beyond morphology: Genomic insights into evolutionary histories of haplosclerid sponges".Contents:All scripts for data processing and model outputExample datasetsREADME with instructionsLicense file

Curated using this pipeline: https://github.com/bge-barcoding/bold-library-curation (release v4)result_output.tsv.gz = Processed records in BCDM TSV format with additional columns from ranking.bold.db.gz = Processed records in SQL database format.logs.tar.gz = logs from analysis.family_databases_compressed.tar.gz = manual curation package for family (database file, PDF checklist, PDF & SVG phylogeny).bold_database_statistics.pdf = summary of dataset.

Biodiversity in human-dominated landscapes is declining, but evidence-based conservation targets to guide international policies for such landscapes are lacking. We present a framework for informing habitat conservation policies based on the enhancement of habitat quantity and quality and define thresholds of habitat quantity at which it becomes effective to also prioritize habitat quality. We applied this framework to pollinators, an important part of agroecosystem biodiversity, by synthesizing 59 studies from 19 countries. Given low habitat quality, hoverflies had the lowest threshold at 6% semi-natural habitat cover, followed by solitary bees (16%), bumble bees (18%), and butterflies (37%). These figures represent minimum habitat thresholds in agricultural landscapes, but when habitat quantity is restricted, marked increases in quality are required to reach similar outcomes.

Parasites present fascinating examples of evolutionary modification that simultaneously pose challenges for systematics. This is exemplified by fully mycoheterotrophic orchids, which are completely dependent on fungi, constituting nearly half of all mycoheterotrophic plant species. A large concentration of mycoheterotrophic lineages is found among the eight tribes comprising the base of the megadiverse orchid subfamily Epidendroideae, here referred to as the early diverging Epidendroideae (EDE). To date, relationships among the EDE have been problematic. Previous analyses have suffered from sparse taxon sampling, weak support from limited loci, or long-branch attraction in plastid-based analyses. We conducted the most comprehensive nuclear phylogenomic analysis of the EDE to date, using Angiosperms353 loci, coalescent analyses, and deep exploration of support, conflict, saturation, and introgression. Our study is the first to include phylogenomic sampling from all eight EDE tribes, with 22 of 26 EDE genera represented. We took a novel approach, selecting best-fit mixture model configurations at the individual locus level, which provided significantly better fit overall and required fewer parameters than all other models, with implications for clades characterized by lineage-specific rate heterogeneity. We recovered strong support for monophyly of all EDE tribes except for Neottieae, which were inferred to be paraphyletic. Information content was generally rich for deep relationships among the EDE tribes, but overall support was weak. We found evidence of saturation and putative introgression, with two inferred reticulation events. We conclude that short internal branches associated with rapid diversification, incomplete lineage sorting, and putative introgression resulted in low concordant signal among EDE tribes, underscoring the continued difficulty in resolving their relationships. Nonetheless, we provide the first strongly supported phylogenetic hypothesis for the five genera of Gastrodieae, representing the largest known diversification of fully mycoheterotrophic plants. We discuss our findings considering recent phylogenomic studies, taxonomy, morphology, and biogeographic implications.

The island species–area relationship (ISAR) describes how larger islands support more species. Studies on oceanic archipelagos have shown that ISARs assembled over millions of years have predictable shapes. However, it remains unclear how rapidly “classic” ISARs develop, and how they are formed on much younger systems. Here, we compile a dataset for the fish communities of 79 postglacial peri-Alpine lakes, and report that an ISAR with a classical shape has formed de novo in less than 15,000 years. Despite their very young age, these lakes exhibit an ISAR mirroring older systems, with a characteristic asymptotic shape. Immigration responds primarily to area and saturates, whereas speciation is primarily driven by lake depth. This young ISAR has been reshaped by anthropogenic activities, with species introductions erasing its upper limit. We demonstrate that ISARs can develop rapidly after habitat formation in semi-isolated systems, offering insights into the assembly of ecological patterns.

A distinct shoulder region, defined by endoskeletal and dermal girdles and associated pectoral musculature, is a major evolutionary adaptation of jawed vertebrates. In teleost model species the large (macromeric) pectoral dermal bones can be derived from multiple embryonic tissues, identifying the shoulder of osteichthyans as a developmentally complex area at the head-trunk boundary. The absence of bone in living chondrichthyans makes Palaeozoic stem groups capable of dermal ossification key to understanding the underpinnings of skeletal growth in the shoulder of crown gnathostomes (osteichthyans and chondrichthyans). Here, using synchrotron X-ray tomography we demonstrate that individual pectoral plates in the oldest unequivocal jawed vertebrate, the Silurian (c. 439 Mya) chondrichthyan Fanjingshania renovata, develop from five separate growth centres. These centres correspond to pectoral bony spines that fuse neighbouring dermal scales into a pinnal plate and their expansion is accompanied by cyclical resorption and remodelling of bone and dentine. Our phylogenetic analyses support an interpretation of these processes as crown and stem gnathostome characters that co-occur only in the shoulder girdle of stem chondrichthyans. The systematic hard tissue remodelling in Fanjingshania reveals an unexpected growth dynamic within chondrichthyans that relates to the formation of a macromeric skeleton through integration of modular elements.

The origin of jaws and teeth represents one of the most formative episodes in our own evolutionary history. However, this event is poorly understood for a lack of detailed knowledge of key lineages, including the ‘acanthothoracid’ placoderms, which were among the earliest jawed vertebrates. Here we describe Romundina gagnieri sp. nov., a new species of ‘acanthothoracid’ from the Early Devonian of Arctic Canada based on computed and synchrotron tomographies. The new species displays anterior supragnathal plates with teeth that we have characterised using synchrotron tomography. Our study shows that teeth are arranged in a concentric manner and that the pattern of tooth addition is centrifugal, including an anterior addition. Overgrowing odontodes, present on the anterior part of the gnathal plates, are covering teeth that can display a hypermineralised layer (likely reflecting the earliest stage of teeth during the ontogeny) or be partially broken. These overgrowing odontodes develop in successive steps and without obvious organization. The presence of a pair of anterior supragnathal plates on the ethmoid part of the endocranium, as well as the growth process of these plates in R. gagnieri sp. nov. are similar to the conditions seen notably in arthrodires arguing for those as the gnathostome ancestral condition.

Ongoing declines of large-bodied frugivores limit the dispersal of large-seeded plants, contributing to their (local) demise and ‘downsizing’ of seeds across assemblages. However, the extent to which human pressure leads to contemporary seed downsizing, and whether extinct megafrugivores have left imprints on seed size, remains unclear. Here, we integrate trait and distribution data for 2,852 endozoochorous plant species, 48 extant and 15 extinct frugivore species across 361 assemblages on Madagascar. Using structural equation models, we show that assemblages with a higher human footprint, a cumulative index of human pressure, have smaller maximum seed sizes, especially through downsizing of extant frugivores. Furthermore, among assemblages with ‘mega-seeded’ plants (i.e., seeds that cannot be swallowed by any extant Malagasy frugivore), larger seed sizes are associated with larger past megafrugivores, reflecting the legacy of past interactions.  Human-driven seed downsizing highlights broader implications in the erosion of important ecosystem functions such as forest carbon storage.

Curated using this pipeline: https://github.com/bge-barcoding/bold-library-curation (release v3)result_output.tsv.gz = Processed records in BCDM TSV format with additional columns from ranking.bold.db.gz = Processed records in SQL database format.logs.tar.gz = logs from analysis.family_databases_compressed.tar.gz = manual curation package for family (database file, PDF checklist, PDF & SVG phylogeny).bold_database_statistics.pdf = summary of dataset.pipeline.zip = pipeline files as run.