Meta-analysis data of skeletal muscle slow fiber content across mammalian species.

Herein, the dataset generated for Queeno et al. [1] is presented and described. Mammalian skeletal muscle slow (MyHC-I) fiber composition data was collated from 269 eligible studies identified via a systematic literature search and meta-analysis, following a structure similar to PRISMA [2]. Academic search systems were queried with terms relating to mammalian skeletal muscle fiber content and reference lists of selected articles were thoroughly investigated for additional studies. Eligible studies were those that provided skeletal muscle fiber composition data from mammalian species that were not subjected to experimental manipulations. Taxonomic information, sex, age, number of individuals sampled, average body mass (kg), average slow fiber content (%) of each skeletal muscle under investigation and fiber-typing methodology were collated from eligible studies when available. Muscle fiber composition data was collected from more than 200 skeletal muscles across 174 mammalian species, which will be of value to those interested in muscle physiology, interspecific muscle comparisons, and connections between muscle physiology, taxonomy, body mass, ecomorphology and locomotor strategy (among others).

Human and African ape myosin heavy chain content and the evolution of hominin skeletal muscle.

Humans are unique among terrestrial mammals in our manner of walking and running, reflecting 7 to 8 Ma of musculoskeletal evolution since diverging with the genus Pan. One component of this is a shift in our skeletal muscle biology towards a predominance of myosin heavy chain (MyHC) I isoforms (i.e. slow fibers) across our pelvis and lower limbs, which distinguishes us from chimpanzees. Here, new MyHC data from 35 pelvis and hind limb muscles of a Western gorilla (Gorilla gorilla) are presented. These data are combined with a similar chimpanzee dataset to assess the MyHC I content of humans in comparison to African apes (chimpanzees and gorillas) and other terrestrial mammals. The responsiveness of human skeletal muscle to behavioral interventions is also compared to the human-African ape differential. Humans are distinct from African apes and among a small group of terrestrial mammals whose pelvis and lower limb muscle is slow fiber dominant, on average. Behavioral interventions, including immobilization, bed rest, spaceflight and exercise, can induce modest decreases and increases in human MyHC I content (i.e. -9.3% to 2.3%, n = 2033 subjects), but these shifts are much smaller than the mean human-African ape differential (i.e. 31%). Taken together, these results indicate muscle fiber content is likely an evolvable trait under selection in the hominin lineage. As such, we highlight potential targets of selection in the genome (e.g. regions that regulate MyHC content) that may play an important role in hominin skeletal muscle evolution.

Importance of timely metadata curation to the global surveillance of genetic diversity.

Genetic diversity within species represents a fundamental yet underappreciated level of biodiversity. Because genetic diversity can indicate species resilience to changing climate, its measurement is relevant to many national and global conservation policy targets. Many studies produce large amounts of genome-scale genetic diversity data for wild populations, but most (87%) do not include the associated spatial and temporal metadata necessary for them to be reused in monitoring programs or for acknowledging the sovereignty of nations or Indigenous peoples. We undertook a distributed datathon to quantify the availability of these missing metadata and to test the hypothesis that their availability decays with time. We also worked to remediate missing metadata by extracting them from associated published papers, online repositories, and direct communication with authors. Starting with 848 candidate genomic data sets (reduced representation and whole genome) from the International Nucleotide Sequence Database Collaboration, we determined that 561 contained mostly samples from wild populations. We successfully restored spatiotemporal metadata for 78% of these 561 data sets (n = 440 data sets with data on 45,105 individuals from 762 species in 17 phyla). Examining papers and online repositories was much more fruitful than contacting 351 authors, who replied to our email requests 45% of the time. Overall, 23% of our email queries to authors unearthed useful metadata. The probability of retrieving spatiotemporal metadata declined significantly as age of the data set increased. There was a 13.5% yearly decrease in metadata associated with published papers or online repositories and up to a 22% yearly decrease in metadata that were only available from authors. This rapid decay in metadata availability, mirrored in studies of other types of biological data, should motivate swift updates to data-sharing policies and researcher practices to ensure that the valuable context provided by metadata is not lost to conservation science forever.

Importancia de la curación oportuna de metadatos para la vigilancia mundial de la diversidad genética Resumen La diversidad genética intraespecífica representa un nivel fundamental, pero a la vez subvalorado de la biodiversidad. La diversidad genética puede indicar la resiliencia de una especie ante el clima cambiante, por lo que su medición es relevante para muchos objetivos de la política de conservación mundial y nacional. Muchos estudios producen una gran cantidad de datos sobre la diversidad a nivel genético de las poblaciones silvestres, aunque la mayoría (87%) no incluye los metadatos espaciales y temporales asociados para que sean reutilizados en los programas de monitoreo o para reconocer la soberanía de las naciones o los pueblos indígenas. Realizamos un "datatón" distribuido para cuantificar la disponibilidad de estos metadatos faltantes y para probar la hipótesis que supone que esta disponibilidad se deteriora con el tiempo. También trabajamos para reparar los metadatos faltantes al extraerlos de los artículos asociados publicados, los repositorios en línea y la comunicación directa con los autores. Iniciamos con 838 candidatos de conjuntos de datos genómicos (representación reducida y genoma completo) tomados de la colaboración internacional para la base de datos de secuencias de nucleótidos y determinamos que 561 incluían en su mayoría muestras tomadas de poblaciones silvestres. Restauramos con éxito los metadatos espaciotemporales en el 78% de estos 561 conjuntos de datos (n = 440 conjuntos de datos con información sobre 45,105 individuos de 762 especies en 17 filos). El análisis de los artículos y los repositorios virtuales fue mucho más productivo que contactar a los 351 autores, quienes tuvieron un 45% de respuesta a nuestros correos. En general, el 23% de nuestras consultas descubrieron metadatos útiles. La probabilidad de recuperar metadatos espaciotemporales declinó de manera significativa conforme incrementó la antigüedad del conjunto de datos. Hubo una disminución anual del 13.5% en los metadatos asociados con los artículos publicados y los repositorios virtuales y hasta una disminución anual del 22% en los metadatos que sólo estaban disponibles mediante la comunicación con los autores. Este rápido deterioro en la disponibilidad de los metadatos, duplicado en estudios de otros tipos de datos biológicos, debería motivar la pronta actualización de las políticas del intercambio de datos y las prácticas de los investigadores para asegurar que en las ciencias de la conservación no se pierda para siempre el contexto valioso proporcionado por los metadatos.

Poor data stewardship will hinder global genetic diversity surveillance.

Genomic data are being produced and archived at a prodigious rate, and current studies could become historical baselines for future global genetic diversity analyses and monitoring programs. However, when we evaluated the potential utility of genomic data from wild and domesticated eukaryote species in the world's largest genomic data repository, we found that most archived genomic datasets (86%) lacked the spatiotemporal metadata necessary for genetic biodiversity surveillance. Labor-intensive scouring of a subset of published papers yielded geospatial coordinates and collection years for only 33% (39% if place names were considered) of these genomic datasets. Streamlined data input processes, updated metadata deposition policies, and enhanced scientific community awareness are urgently needed to preserve these irreplaceable records of today's genetic biodiversity and to plug the growing metadata gap.