Feng S, Stiller J, Deng Y, Armstrong J, Fang Q, Reeve AH, Xie D, Chen G, Guo C, Faircloth BC, et al. Author Correction: Dense sampling of bird diversity increases power of comparative genomics. Nature. 2021;592 (7856) :E24-E24. Publisher's VersionAbstract
In Supplementary Table 1 of this Article, 23 samples (B10K-DU-029-32, B10K-DU-029-33, B10K-DU-029-36 to B10K-DU-029-44, B10K-DU-029-46, B10K-DU-029-47, B10K-DU-029-49 to B10K-DU-029-53, B10K-DU-029-75 to B10K-DU-029-77, B10K-DU-029-80, and B10K-DU-030-03; styled in boldface in the revised table) were assigned to the incorrect institution. Supplementary Table 1 has been amended to reflect the correct source institution for these samples, and associated data (tissue, museum ID/source specimen ID, site, state/province, latitude, longitude, date collected and sex) have been updated accordingly. The original table is provided as Supplementary Information to this Amendment, and the original Article has been corrected online.
Sin SYW, Hoover BA, Nevitt GA, Edwards SV. Demographic history, not mating system, explains signatures of inbreeding and inbreeding depression in a large outbred population. The American Naturalist. 2021;197 (6) :658-676. Publisher's VersionAbstract
Inbreeding depression is often found in small, inbred populations, but whether it can be detected in and have evolutionary consequences for large, wide-ranging populations is poorly known. Here, we investigate the possibility of inbreeding in a large population to determine whether mild levels of inbreeding can still have genetic and phenotypic consequences and how genomically widespread these effects can be. We apply genome-wide methods to investigate whether individual and parental heterozygosity is related to morphological, growth, or life-history traits in a pelagic seabird, Leach’s storm-petrel (Oceanodroma leucorhoa). Examining 560 individuals as part of a multiyear study, we found a substantial effect of maternal heterozygosity on chick traits: chicks from less heterozygous (relatively inbred) mothers were significantly smaller than chicks from more heterozygous (noninbred) mothers. We show that these heterozygosity-fitness correlations were due to general genome-wide effects and demonstrate a correlation between heterozygosity and inbreeding, suggesting inbreeding depression. We used population genetic models to further show that the variance in inbreeding was probably due to past demographic events rather than the current mating system and ongoing mate choice. Our findings demonstrate that inbreeding depression can be observed in large populations and illustrate how the integration of genomic techniques and fieldwork can elucidate its underlying causes.
Wang P, Burley JT, Liu Y, Chang J, Chen D, Lu Q, Li S-H, Zhou X, Edwards SV, Zhang Z. Genomic Consequences of Long-Term Population Decline in Brown Eared Pheasant. Molecular Biology and Evolution. 2021;38 (1) :263-273. Publisher's VersionAbstract
Population genetic theory and empirical evidence indicate that deleterious alleles can be purged in small populations. However, this viewpoint remains controversial. It is unclear whether natural selection is powerful enough to purge deleterious mutations when wild populations continue to decline. Pheasants are terrestrial birds facing a long-term risk of extinction as a result of anthropogenic perturbations and exploitation. Nevertheless, there are scant genomics resources available for conservation management and planning. Here, we analyzed comparative population genomic data for the three extant isolated populations of Brown eared pheasant (Crossoptilon mantchuricum) in China. We showed that C. mantchuricum has low genome-wide diversity and a contracting effective population size because of persistent declines over the past 100,000 years. We compared genome-wide variation in C. mantchuricum with that of its closely related sister species, the Blue eared pheasant (C. auritum) for which the conservation concern is low. There were detrimental genetic consequences across all C. mantchuricum genomes including extended runs of homozygous sequences, slow rates of linkage disequilibrium decay, excessive loss-of-function mutations, and loss of adaptive genetic diversity at the major histocompatibility complex region. To the best of our knowledge, this study is the first to perform a comprehensive conservation genomic analysis on this threatened pheasant species. Moreover, we demonstrated that natural selection may not suffice to purge deleterious mutations in wild populations undergoing long-term decline. The findings of this study could facilitate conservation planning for threatened species and help recover their population size.
Toda Y, Ko M-C, Liang Q, Miller ET, Rico-Guevara A, Nakagita T, Sakakibara A, Uemura K, Sackton T, Hayakawa T, et al. Early origin of sweet perception in the songbird radiation. Science. 2021;373 (6551) :226-231. Publisher's VersionAbstract
Early events in the evolutionary history of a clade can shape the sensory systems of descendant lineages. Although the avian ancestor may not have had a sweet receptor, the widespread incidence of nectar-feeding birds suggests multiple acquisitions of sugar detection. In this study, we identify a single early sensory shift of the umami receptor (the T1R1-T1R3 heterodimer) that conferred sweet-sensing abilities in songbirds, a large evolutionary radiation containing nearly half of all living birds. We demonstrate sugar responses across species with diverse diets, uncover critical sites underlying carbohydrate detection, and identify the molecular basis of sensory convergence between songbirds and nectar-specialist hummingbirds. This early shift shaped the sensory biology of an entire radiation, emphasizing the role of contingency and providing an example of the genetic basis of convergence in avian evolution.
Lamichhaney S, Catullo R, Keogh K, Clulow S, Edwards SV. A bird-like genome from a frog: Mechanisms of genome size reduction in the ornate burrowing frog, Platyplectrum ornatum. Proceedings of the National Academy of Sciences. 2021;118 (11). Publisher's VersionAbstract
The diversity of genome sizes across the tree of life is of key interest in evolutionary biology. Various correlates of variation in genome size, such as accumulation of transposable elements (TEs) or rate of DNA gain and loss, are well known, but the underlying molecular mechanisms driving or constraining genome size are poorly understood. Here, we study one of the smallest genomes among frogs characterized thus far, that of the ornate burrowing frog (Platyplectrum ornatum) from Australia, and compare it to other published frog and vertebrate genomes to examine the forces driving reduction in genome size. At ∼1.06 gigabases (Gb), the P. ornatum genome is like that of birds, revealing four major mechanisms underlying TE dynamics: reduced abundance of all major classes of TEs; increased net deletion bias in TEs; drastic reduction in intron lengths; and expansion via gene duplication of the repertoire of TE-suppressing Piwi genes, accompanied by increased expression of Piwi-interacting RNA (piRNA)-based TE-silencing pathway genes in germline cells. Transcriptomes from multiple tissues in both sexes corroborate these results and provide insight into sex-differentiation pathways in Platyplectrum. Genome skimming of two closely related frog species (Lechriodus fletcheri and Limnodynastes fletcheri) confirms a reduction in TEs as a major driver of genome reduction in Platyplectrum and supports a macroevolutionary scenario of small genome size in frogs driven by convergence in life history, especially rapid tadpole development and tadpole diet. The P. ornatum genome offers a model for future comparative studies on mechanisms of genome size reduction in amphibians and vertebrates generally.
Edwards SV. Bicycling, Birding and #BLM across America in a Summer of Chaos. Biodiversity Information Science and Standards. 2020;4 (e59303). Publisher's VersionAbstract
From 6 June to 20 August, 2020, I undertook a 76-day, ~3800 mile bicycle trip across the United States from the Atlantic to the Pacific oceans. In this talk I will share with you some of the amazing people, landscapes and birds I encountered, mostly in rural towns and along blue highways. The gradually changing birdscape, both in sight and sound, underscored the sensitive ecological gradients to which birds respond, as well as the ability of some species to thrive in agricultural monocultures. Rivers large and small regularly benchmarked my progress, as well as the western journey of Lewis & Clark over 200 years ago. The recent incidents in the US involving African Americans as targets of white violence inexorably caused me to festoon my bicycle with #BlackLivesMatter (#BLM) signs and share my experiences on social media. I encountered a variety of reactions, often positive and occasionally sharply negative, in a sea of generosity and extraordinary kindness as I wheeled my way through towns on the brink of collapse, vast private ranches and the occasional city. Rural America exhibits an abundance of loyalty and empathy for local communities, yet it is sometimes hard for Americans – myself included – to empathize with people they have never met in person. Two imperatives I took away, with ramifications for both biodiversity and political stability, were the need to somehow bring divergent communities together and to encourage empathy at the national level, among communities that otherwise experience each other only on TV.
Sin SYW, Lu L, Edwards SV. De Novo Assembly of the Northern Cardinal (Cardinalis cardinalis) Genome Reveals Candidate Regulatory Regions for Sexually Dichromatic Red Plumage Coloration. G3: Genes, Genomes, Genetics. 2020;10 (10) :3541–3548.
Feng S, Stiller J, Deng Y, Armstrong J, Fang Q, Reeve AH, Xie D, Chen G, Guo C, Faircloth BC, et al. Dense sampling of bird diversity increases power of comparative genomics. Nature. 2020;587 (7833) :252–257.
Hedrick BP, Heberling MJ, Meineke EK, Turner KG, Grassa CJ, Park DS, Kennedy J, Clarke JA, Cook JA, Blackburn DC, et al. Digitization and the future of natural history collections. BioScience. 2020;70 (3) :243–251.
Corbett EC, Bravo GA, Schunck F, Naka LN, Silveira L{\'ısF, Edwards SV. Evidence for the Pleistocene Arc Hypothesis from genome-wide SNPs in a Neotropical dry forest specialist, the Rufous-fronted Thornbird (Furnariidae: Phacellodomus rufifrons). Molecular Ecology. 2020;29 (22) :4457–4472.
Harvey MG, Bravo GA, Claramunt S, Cuervo AM, Derryberry GE, Battilana J, Seeholzer GF, McKay JS, O’Meara BC, Faircloth BC, et al. The evolution of a tropical biodiversity hotspot. Science. 2020;370 (6522) :1343–1348.
Dierickx EG, Sin SYW, van Veelen PHJ, de Brooke ML, Liu Y, Edwards SV, Martin SH. Genetic diversity, demographic history and neo-sex chromosomes in the Critically Endangered Raso lark. Proceedings of the Royal Society B. 2020;287 (1922) :20192613.
Edwards SV. Genomics of adaptation and acclimation: from field to lab and back. National Science Review. 2020;7 (1) :128–128.
Bakker FT, Antonelli A, Clarke JA, Cook JA, Edwards SV, Ericson PGP, Faurby S, Ferrand N, Gelang M, Gillespie RG, et al. The Global Museum: natural history collections and the future of evolutionary science and public education. PeerJ. 2020;8 :e8225.
Rannala B, Edwards SV, Leaché A, Yang Z. The multi-species coalescent model and species tree inference. Phylogenetics in the Genomic Era. 2020 :3–3.
Jiang X, Edwards SV, Liu L. The Multispecies Coalescent Model Outperforms Concatenation across Diverse Phylogenomic Data Sets. Systematic Biology. 2020.
Smith SD, Pennell MW, Dunn CW, Edwards SV. Phylogenetics is the New Genetics (for Most of Biodiversity). Trends in Ecology & Evolution. 2020.
Termignoni-Garcia F, Louder MIM, Balakrishnan CN, O’Connell L, Edwards SV. Prospects for sociogenomics in avian cooperative breeding and parental care. Current Zoology. 2020;66 (3) :293–306.
Edwards SV, Hopkins R, Mallet J. Speciation. In: The Theory of Evolution: Principles, Concepts, and Assumptions. University of Chicago Press ; 2020. pp. 296.
Gemmell NJ, Rutherford K, Prost S, Tollis M, Winter D, Macey RJ, Adelson DL, Suh A, Bertozzi T, Grau JH, et al. The tuatara genome reveals ancient features of amniote evolution. Nature. 2020;584 :403–409.