Conservation genomics of the endangered Seychelles Magpie‐Robin (Copsychus sechellarum):a unique insight into the history of a precious endemic bird

The Seychelles Magpie-Robin Copsychus sechellarum is an IUCN Red-List Endangered species endemic to the Seychelles, whose population was reduced to eight individuals on a single island in the 1960s. Translocations from the remaining population to four additional islands have been an integral factor in their recovery, but the potential genetic consequences of their translocation history have not previously been explored. We resequenced the genomes of 141 individuals sampled across the five current island populations and analysed the data to characterize their population structure, as well as to explore suspected inbreeding. Overall, very low levels of heterozygosity were observed, all coupled with long homozygous segments that suggest recent inbreeding, probably the consequence of a population bottleneck in the 1960s. Three of the four translocated populations displayed less genetic diversity than the founder population from which they were taken, a familiar pattern observed as a result of the evolutionary force of genetic drift following founder events. Furthermore, and perhaps surprising given the recent time since the new populations were established, population structure was observed within these same three populations. New awareness of inbreeding in the Seychelles Magpie-Robin populations, and continued genetic monitoring, will allow for genetically informed management decisions. This is particularly prudent in maximizing the success of the future conservation translocation planned for this species

Dense sampling of bird diversity increases power of comparative genomics

© 2020, The Author(s). Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1–4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families—including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species

When birds of a feather flock together: Severe genomic erosion and the implications for genetic rescue in an endangered island passerine

Publication status: PublishedAbstractThe Seychelles magpie‐robin's (SMR) five island populations exhibit some of the lowest recorded levels of genetic diversity among endangered birds, and high levels of inbreeding. These populations collapsed during the 20th century, and the species was listed as Critically Endangered in the IUCN Red List in 1994. An assisted translocation‐for‐recovery program initiated in the 1990s increased the number of mature individuals, resulting in its downlisting to Endangered in 2005. Here, we explore the temporal genomic erosion of the SMR based on a dataset of 201 re‐sequenced whole genomes that span the past ~150 years. Our sample set includes individuals that predate the bottleneck by up to 100 years, as well as individuals from contemporary populations established during the species recovery program. Despite the SMR's recent demographic recovery, our data reveal a marked increase in both the genetic load and realized load in the extant populations when compared to the historical samples. Conservation management may have reduced the intensity of selection by increasing juvenile survival and relaxing intraspecific competition between individuals, resulting in the accumulation of loss‐of‐function mutations (i.e. severely deleterious variants) in the rapidly recovering population. In addition, we found a 3‐fold decrease in genetic diversity between temporal samples. While the low genetic diversity in modern populations may limit the species' adaptability to future environmental changes, future conservation efforts (including IUCN assessments) may also need to assess the threats posed by their high genetic load. Our computer simulations highlight the value of translocations for genetic rescue and show how this could halt genomic erosion in threatened species such as the SMR.</jats:p

Conservation genomics of the endangered Seychelles Magpie-Robin (Copsychus sechellarum): a unique insight into the history of a precious endemic bird

The Seychelles Magpie-Robin Copsychus sechellarum is an IUCN Red-List Endangered species endemic to the Seychelles, whose population was reduced to eight individuals on a single island in the 1960s. Translocations from the remaining population to four additional islands have been an integral factor in their recovery, but the potential genetic consequences of their translocation history have not previously been explored. We resequenced the genomes of 141 individuals sampled across the five current island populations and analysed the data to characterize their population structure, as well as to explore suspected inbreeding. Overall, very low levels of heterozygosity were observed, all coupled with long homozygous segments that suggest recent inbreeding, probably the consequence of a population bottleneck in the 1960s. Three of the four translocated populations displayed less genetic diversity than the founder population from which they were taken, a familiar pattern observed as a result of the evolutionary force of genetic drift following founder events. Furthermore, and perhaps surprising given the recent time since the new populations were established, population structure was observed within these same three populations. New awareness of inbreeding in the Seychelles Magpie-Robin populations, and continued genetic monitoring, will allow for genetically informed management decisions. This is particularly prudent in maximizing the success of the future conservation translocation planned for this species

Dense sampling of bird diversity increases power of comparative genomics

Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1,2,3,4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families—including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species

The Physical Activity Messaging Framework (PAMF) and Checklist (PAMC): International consensus statement and user guide

Effective physical activity messaging plays an important role in the pathway towards changing physical activity behaviour at a population level. The Physical Activity Messaging Framework (PAMF) and Checklist (PAMC) are outputs from a recent modified Delphi study. This sought consensus from an international expert panel on how to aid the creation and evaluation of physical activity messages. In this paper, we (1) present an overview of the various concepts within the PAMF and PAMC, (2) discuss in detail how the PAMF and PAMC can be used to create physical activity messages, plan evaluation of messages, and aid understanding and categorisation of existing messages, and (3) highlight areas for future development and research. If adopted, we propose that the PAMF and PAMC could improve physical activity messaging practice by encouraging evidence-based and target population-focused messages with clearly stated aims and consideration of potential working pathways. They could also enhance the physical activity messaging research base by harmonising key messaging terminologies, improving quality of reporting, and aiding collation and synthesis of the evidence.Education, Faculty ofOther UBCNon UBCKinesiology, School ofReviewedFacultyResearcherOthe

Dense sampling of bird diversity increases power of comparative genomics

Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity(1-4). Sparse taxon sampling has previously been proposed to confound phylogenetic inference(5), and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species. A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.Peer reviewe