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      The relevance of pedigrees in the conservation genomics era

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          Abstract

          Over the past 50 years conservation genetics has developed a substantive toolbox to inform species management. One of the most long‐standing tools available to manage genetics—the pedigree—has been widely used to characterize diversity and maximize evolutionary potential in threatened populations. Now, with the ability to use high throughput sequencing to estimate relatedness, inbreeding, and genome‐wide functional diversity, some have asked whether it is warranted for conservation biologists to continue collecting and collating pedigrees for species management. In this perspective, we argue that pedigrees remain a relevant tool, and when combined with genomic data, create an invaluable resource for conservation genomic management. Genomic data can address pedigree pitfalls (e.g., founder relatedness, missing data, uncertainty), and in return robust pedigrees allow for more nuanced research design, including well‐informed sampling strategies and quantitative analyses (e.g., heritability, linkage) to better inform genomic inquiry. We further contend that building and maintaining pedigrees provides an opportunity to strengthen trusted relationships among conservation researchers, practitioners, Indigenous Peoples, and Local Communities.

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          Towards complete and error-free genome assemblies of all vertebrate species

          High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species 1 – 4 . To address this issue, the international Genome 10K (G10K) consortium 5 , 6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences. The Vertebrate Genome Project has used an optimized pipeline to generate high-quality genome assemblies for sixteen species (representing all major vertebrate classes), which have led to new biological insights.
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            Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome".

            The development of efficient and inexpensive genome sequencing methods has revolutionized the study of human bacterial pathogens and improved vaccine design. Unfortunately, the sequence of a single genome does not reflect how genetic variability drives pathogenesis within a bacterial species and also limits genome-wide screens for vaccine candidates or for antimicrobial targets. We have generated the genomic sequence of six strains representing the five major disease-causing serotypes of Streptococcus agalactiae, the main cause of neonatal infection in humans. Analysis of these genomes and those available in databases showed that the S. agalactiae species can be described by a pan-genome consisting of a core genome shared by all isolates, accounting for approximately 80% of any single genome, plus a dispensable genome consisting of partially shared and strain-specific genes. Mathematical extrapolation of the data suggests that the gene reservoir available for inclusion in the S. agalactiae pan-genome is vast and that unique genes will continue to be identified even after sequencing hundreds of genomes.
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              Coefficients of Inbreeding and Relationship

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                Author and article information

                Contributors
                sgalla32@gmail.com
                Journal
                Mol Ecol
                Mol Ecol
                10.1111/(ISSN)1365-294X
                MEC
                Molecular Ecology
                John Wiley and Sons Inc. (Hoboken )
                0962-1083
                1365-294X
                22 October 2021
                January 2022
                : 31
                : 1 ( doiID: 10.1111/mec.v31.1 )
                : 41-54
                Affiliations
                [ 1 ] Department of Biological Sciences Boise State University Boise Idaho USA
                [ 2 ] School of Biological Sciences University of Canterbury Christchurch Canterbury New Zealand
                [ 3 ] New Zealand Department of Conservation Twizel Canterbury New Zealand
                [ 4 ] Te Rūnanga o Ngāi Tahu Te Whare o Te Waipounamu Christchurch Canterbury New Zealand
                [ 5 ] New Zealand Department of Conservation Invercargill Southland New Zealand
                [ 6 ] Smithsonian‐Mason School of Conservation Front Royal Maryland USA
                [ 7 ] Center for Species Survival Smithsonian Conservation Biology Institute National Zoological Park Washington District of Columbia USA
                [ 8 ] Department of Biological Sciences North Dakota State University Fargo North Dakota USA
                [ 9 ] Department of Biological Sciences University of Wisconsin‐Milwaukee Milwaukee Wisconsin USA
                [ 10 ] Department of Natural Resources and Environmental Science Program in Ecology, Evolution and Conservation Biology University of Nevada Reno Reno Nevada USA
                [ 11 ] The Isaac Conservation and Wildlife Trust Christchurch Canterbury New Zealand
                [ 12 ] School of Life and Environmental Sciences University of Sydney Sydney NSW Australia
                [ 13 ] School of Biological Sciences University of Auckland Auckland Auckland New Zealand
                Author notes
                [*] [* ] Correspondence

                Stephanie J. Galla, Department of Biological Sciences, Boise State University, Boise, ID, USA.

                Email: sgalla32@ 123456gmail.com

                Author information
                https://orcid.org/0000-0002-4650-8067
                https://orcid.org/0000-0002-4245-3900
                https://orcid.org/0000-0002-7872-6296
                https://orcid.org/0000-0002-3041-0508
                https://orcid.org/0000-0002-9606-1689
                https://orcid.org/0000-0002-3404-5253
                https://orcid.org/0000-0002-9892-1056
                https://orcid.org/0000-0003-4829-3749
                https://orcid.org/0000-0001-8095-4282
                https://orcid.org/0000-0002-6328-398X
                https://orcid.org/0000-0001-8965-1042
                https://orcid.org/0000-0003-2112-5761
                Article
                MEC16192
                10.1111/mec.16192
                9298073
                34553796
                edb12896-a0f5-4516-9314-79121baaae7b
                © 2021 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 12 September 2021
                : 05 July 2021
                : 17 September 2021
                Page count
                Figures: 4, Tables: 0, Pages: 0, Words: 12141
                Funding
                Funded by: National Science Foundation Track 2 EPSCoR Program
                Award ID: OIA‐1826801
                Funded by: Ministry of Business, Innovation and Employment (MBIE) Endeavour Fund
                Award ID: UOCX1602
                Funded by: Strategic Environmental Research and Development Program
                Award ID: RC‐2702
                Categories
                News and Views
                News and Views
                Opinion
                Custom metadata
                2.0
                January 2022
                Converter:WILEY_ML3GV2_TO_JATSPMC version:6.1.7 mode:remove_FC converted:20.07.2022

                Ecology
                conservation genomics,ex situ,in situ,kinship,pedigree,quantitative genetics
                Ecology
                conservation genomics, ex situ, in situ, kinship, pedigree, quantitative genetics

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