1
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Torralba Sáez M, Hofreiter M, Straube N. Shark genome size evolution and its relationship with cellular, life-history, ecological, and diversity traits. Sci Rep 2024; 14:8909. [PMID: 38632352 PMCID: PMC11024215 DOI: 10.1038/s41598-024-59202-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 04/08/2024] [Indexed: 04/19/2024] Open
Abstract
Among vertebrates, sharks exhibit both large and heterogeneous genome sizes ranging from 2.86 to 17.05 pg. Aiming for a better understanding of the patterns and causalities of shark genome size evolution, we applied phylogenetic comparative methods to published genome-size estimates for 71 species representing the main phylogenetic lineages, life-histories and ecological traits. The sixfold range of genome size variation was strongly traceable throughout the phylogeny, with a major expansion preceding shark diversification during the late Paleozoic and an ancestral state (6.33 pg) close to the present-day average (6.72 pg). Subsequent deviations from this average occurred at higher rates in squalomorph than in galeomorph sharks and were unconnected to evolutionary changes in the karyotype architecture, which were dominated by descending disploidy events. Genome size was positively correlated with cell and nucleus sizes and negatively with metabolic rate. The metabolic constraints on increasing genome size also manifested at higher phenotypic scales, with large genomes associated with slow lifestyles and purely marine waters. Moreover, large genome sizes were also linked to non-placental reproductive modes, which may entail metabolically less demanding embryological developments. Contrary to ray-finned fishes, large genome size was associated neither with the taxonomic diversity of affected clades nor with low genetic diversity.
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Affiliation(s)
- Mario Torralba Sáez
- Ichthyology Section, Bavarian State Collection of Zoology (SNSB-ZSM), 81247, Munich, Germany
- Systematic Zoology, Department Biology II, Faculty of Biology, Ludwig Maximilian University of Munich (LMU), 82152, Munich, Germany
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Nicolas Straube
- Department of Natural History, University Museum Bergen, University of Bergen (UiB), 5007, Bergen, Norway.
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2
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Fromm B, Sorger T. Rapid adaptation of cellular metabolic rate to the MicroRNA complements of mammals and its relevance to the evolution of endothermy. iScience 2024; 27:108740. [PMID: 38327773 PMCID: PMC10847693 DOI: 10.1016/j.isci.2023.108740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 09/13/2023] [Accepted: 12/12/2023] [Indexed: 02/09/2024] Open
Abstract
The metabolic efficiency of mammalian cells depends on the attenuation of intrinsic translation noise by microRNAs. We devised a metric of cellular metabolic rate (cMR), rMR/Mexp optimally fit to the number of microRNA families (mirFam), that is robust to variation in mass and sensitive to body temperature (Tb), consistent with the heat dissipation limit theory of Speakman and Król (2010). Using mirFam as predictor, an Ornstein-Uhlenbeck process of stabilizing selection, with an adaptive shift at the divergence of Boreoeutheria, accounted for 95% of the variation in cMR across mammals. Branchwise rates of evolution of cMR, mirFam and Tb concurrently increased 6- to 7-fold at the divergence of Boreoeutheria, independent of mass. Cellular MR variation across placental mammals was also predicted by the sum of model conserved microRNA-target interactions, revealing an unexpected degree of integration of the microRNA-target apparatus into the energy economy of the mammalian cell.
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Affiliation(s)
- Bastian Fromm
- The Arctic University Museum of Norway, UiT- The Arctic University of Norway, Tromsø, Norway
| | - Thomas Sorger
- Department of Biology, Roger Williams University, Bristol, RI 02809, USA
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3
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DeRaad DA, Escalona M, Benham PM, Marimuthu MPA, Sahasrabudhe RM, Nguyen O, Chumchim N, Beraut E, Fairbairn CW, Seligmann W, Bowie RCK, Cicero C, McCormack JE, Wayne RK. De novo assembly of a chromosome-level reference genome for the California Scrub-Jay, Aphelocoma californica. J Hered 2023; 114:669-680. [PMID: 37589384 PMCID: PMC10650945 DOI: 10.1093/jhered/esad047] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 07/27/2023] [Indexed: 08/18/2023] Open
Abstract
We announce the assembly of the first de novo reference genome for the California Scrub-Jay (Aphelocoma californica). The genus Aphelocoma comprises four currently recognized species including many locally adapted populations across Mesoamerica and North America. Intensive study of Aphelocoma has revealed novel insights into the evolutionary mechanisms driving diversification in natural systems. Additional insights into the evolutionary history of this group will require continued development of high-quality, publicly available genomic resources. We extracted high molecular weight genomic DNA from a female California Scrub-Jay from northern California and generated PacBio HiFi long-read data and Omni-C chromatin conformation capture data. We used these data to generate a de novo partially phased diploid genome assembly, consisting of two pseudo-haplotypes, and scaffolded them using inferred physical proximity information from the Omni-C data. The more complete pseudo-haplotype assembly (arbitrarily designated "Haplotype 1") is 1.35 Gb in total length, highly contiguous (contig N50 = 11.53 Mb), and highly complete (BUSCO completeness score = 97%), with comparable scaffold sizes to chromosome-level avian reference genomes (scaffold N50 = 66.14 Mb). Our California Scrub-Jay assembly is highly syntenic with the New Caledonian Crow reference genome despite ~10 million years of divergence, highlighting the temporal stability of the avian genome. This high-quality reference genome represents a leap forward in publicly available genomic resources for Aphelocoma, and the family Corvidae more broadly. Future work using Aphelocoma as a model for understanding the evolutionary forces generating and maintaining biodiversity across phylogenetic scales can now benefit from a highly contiguous, in-group reference genome.
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Affiliation(s)
- Devon A DeRaad
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, KS, United States
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Phred M Benham
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, United States
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Mohan P A Marimuthu
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis, Davis, CA, United States
| | - Ruta M Sahasrabudhe
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis, Davis, CA, United States
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis, Davis, CA, United States
| | - Noravit Chumchim
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis, Davis, CA, United States
| | - Eric Beraut
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Colin W Fairbairn
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - William Seligmann
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Rauri C K Bowie
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, United States
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Carla Cicero
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, United States
| | - John E McCormack
- Moore Laboratory of Zoology, Occidental College, Los Angeles, CA, United States
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, United States
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4
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Pepke ML, Ringsby TH, Eisenberg DTA. The evolution of early-life telomere length, pace-of-life and telomere-chromosome length dynamics in birds. Mol Ecol 2023; 32:2898-2912. [PMID: 36847070 DOI: 10.1111/mec.16907] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 02/09/2023] [Accepted: 02/21/2023] [Indexed: 03/01/2023]
Abstract
Telomeres, the short DNA sequences that protect chromosome ends, are an ancient molecular structure, which is highly conserved across most eukaryotes. Species differ in their telomere lengths, but the causes of this variation are not well understood. Here, we demonstrate that mean early-life telomere length is an evolutionary labile trait across 57 bird species (representing 35 families in 12 orders) with the greatest trait diversity found among passerines. Among these species, telomeres are significantly shorter in fast-lived than in slow-lived species, suggesting that telomere length may have evolved to mediate trade-offs between physiological requirements underlying the diversity of pace-of-life strategies in birds. This association was attenuated when excluding studies that may include interstitial telomeres in the estimation of mean telomere length. Curiously, within some species, larger individual chromosome size predicts longer telomere lengths on that chromosome, leading to the hypothesis that telomere length also covaries with chromosome length across species. We show that longer mean chromosome length or genome size tends to be associated with longer mean early-life telomere length (measured across all chromosomes) within a phylogenetic framework constituting up to 31 bird species. These associations were strengthened when excluding highly influential outliers. However, sensitivity analyses suggested that they were susceptible to sample size effects and not robust to the exclusion of studies that may include interstitial telomeres. Combined, our analyses generalize patterns previously found within a few species and provide potential adaptive explanations for the 10-fold variation in telomere lengths observed among birds.
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Affiliation(s)
- Michael Le Pepke
- Department of Biology, Centre for Biodiversity Dynamics (CBD), Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Thor Harald Ringsby
- Department of Biology, Centre for Biodiversity Dynamics (CBD), Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Dan T A Eisenberg
- Department of Anthropology, University of Washington, Seattle, Washington, USA
- Centre for Studies in Demography and Ecology, University of Washington, Seattle, Washington, USA
- Department of Biology, University of Washington, Seattle, Washington, USA
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5
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Liu B, Ren YS, Su CY, Abe Y, Zhu DH. Pangenomic analysis of Wolbachia provides insight into the evolution of host adaptation and cytoplasmic incompatibility factor genes. Front Microbiol 2023; 14:1084839. [PMID: 36819029 PMCID: PMC9937081 DOI: 10.3389/fmicb.2023.1084839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/13/2023] [Indexed: 02/05/2023] Open
Abstract
Introduction The genus Wolbachia provides a typical example of intracellular bacteria that infect the germline of arthropods and filarial nematodes worldwide. Their importance as biological regulators of invertebrates, so it is particularly important to study the evolution, divergence and host adaptation of these bacteria at the genome-wide level. Methods Here, we used publicly available Wolbachia genomes to reconstruct their evolutionary history and explore their adaptation under host selection. Results Our findings indicate that segmental and single-gene duplications, such as DNA methylase, bZIP transcription factor, heat shock protein 90, in single monophyletic Wolbachia lineages (including supergroups A and B) may be responsible for improving the ability to adapt to a broad host range in arthropod-infecting strains. In contrast to A strains, high genetic diversity and rapidly evolving gene families occur in B strains, which may promote the ability of supergroup B strains to adapt to new hosts and their large-scale spreading. In addition, we hypothesize that there might have been two independent horizontal transfer events of cif genes in two sublineages of supergroup A strains. Interestingly, during the independent evolution of supergroup A and B strains, the rapid evolution of cif genes in supergroup B strains resulted in the loss of their functional domain, reflected in a possible decrease in the proportion of induced cytoplasmic incompatibility (CI) strains. Discussion This present study highlights for reconstructing of evolutionary history, addressing host adaptation-related evolution and exploring the origin and divergence of CI genes in each Wolbachia supergroup. Our results thus not only provide a basis for further exploring the evolutionary history of Wolbachia adaptation under host selection but also reveal a new research direction for studying the molecular regulation of Wolbachia- induced cytoplasmic incompatibility.
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Affiliation(s)
- Bo Liu
- Laboratory of Insect Behavior and Evolutionary Ecology, College of Life Sciences, Central South University of Forestry and Technology, Changsha, China,Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Ye-Song Ren
- Laboratory of Insect Behavior and Evolutionary Ecology, College of Life Sciences, Central South University of Forestry and Technology, Changsha, China
| | - Cheng-Yuan Su
- Laboratory of Insect Behavior and Evolutionary Ecology, College of Life Sciences, Central South University of Forestry and Technology, Changsha, China
| | - Yoshihisa Abe
- Faculty of Social and Cultural Studies, Kyushu University, Fukuoka, Japan
| | - Dao-Hong Zhu
- Laboratory of Insect Behavior and Evolutionary Ecology, College of Life Sciences, Central South University of Forestry and Technology, Changsha, China,*Correspondence: Dao-Hong Zhu, ✉
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6
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Pincheira‐Donoso D, Harvey LP, Johnson JV, Hudson D, Finn C, Goodyear LEB, Guirguis J, Hyland EM, Hodgson DJ. Genome size does not influence extinction risk in the world's amphibians. Funct Ecol 2022. [DOI: 10.1111/1365-2435.14247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
| | - Lilly P. Harvey
- School of Science and Technology Nottingham Trent University Nottingham UK
| | - Jack V. Johnson
- School of Biological Sciences Queen's University Belfast Belfast UK
| | - Dave Hudson
- Centre for Ecology and Conservation, College of Life and Environmental Sciences University of Exeter Penryn UK
| | - Catherine Finn
- School of Biological Sciences Queen's University Belfast Belfast UK
| | | | - Jacinta Guirguis
- School of Biological Sciences Queen's University Belfast Belfast UK
| | - Edel M. Hyland
- School of Biological Sciences Queen's University Belfast Belfast UK
| | - Dave J. Hodgson
- Centre for Ecology and Conservation, College of Life and Environmental Sciences University of Exeter Penryn UK
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Chu JJ, Gillis DP, Riskin SH. Community science reveals links between migration arrival timing advance, migration distance, and wing shape. J Anim Ecol 2022; 91:1651-1665. [PMID: 35668666 DOI: 10.1111/1365-2656.13755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 04/11/2022] [Indexed: 11/29/2022]
Abstract
Substantial global data show that many taxa are shifting their phenologies in response to climate change. For birds, migration arrival dates in breeding regions have been shifting earlier, and there is evidence that both evolutionary adaptation and behavioural flexibility influence these shifts. As more efficient flyers may be able to demonstrate more flexibility to respond to changing conditions during migratory flight, we hypothesize that differences among passerine species in flight efficiency, as reflected by morphology, may be associated with the magnitude of shifts in arrival date in response to climate warming. We applied a logistic model to eighteen years of eBird data to estimate mean arrival date for 44 common passerines migrating to northeast North America. We then used linear mixed-effects models to estimate changes in mean arrival date and compared these changes to morphological proxies for flight efficiency and migratory distance using phylogenetic generalized least squares models. On average, passerine species shifted their arrival dates 0.120 days earlier each year, with 27 of the 44 species shifting to significantly earlier arrival times, and two shifting to significantly later ones. Of the 15 species with non-significant shifts, 13 trended toward earlier arrivals. Longer migration distances and higher wing aspect ratios were associated with greater shifts towards earlier arrivals. Migration distance and aspect ratio were also significantly correlated to each other. This suggests that changes in arrival date are affected by factors pertaining to migratory flight over long distances namely, flight efficiency and migration distance. These traits may be able predict the magnitude of arrival date shift, and by extension identify species that are most at risk to climate change due to inflexible arrival timing.
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Affiliation(s)
- J J Chu
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, Canada
| | - D P Gillis
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, Canada
| | - S H Riskin
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, Canada
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8
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Abstract
The avian pectoralis muscle demonstrates plasticity with regard to size, so that temperate birds facing winter conditions or birds enduring a migration bout tend to have significant increases in the size and mass of this tissue due to muscular hypertrophy. Myonuclear domain (MND), the volume of cytoplasm a myonuclei services, in the pectoralis muscle of birds seems to be altered during thermal stress or changing seasons. However, there is no information available regarding muscle DNA content or ploidy level within the avian pectoralis. Changes in muscle DNA content can be used in this tissue to aid in size and mass changes. Here, we hypothesized that long-distance migrants or temperate residents would use the process of endoreduplication to aid in altering muscle size. Mostly contradictory to our hypotheses, we found no differences in the mean muscle DNA content in any of the 62 species of birds examined in this study. We also found no correlations between mean muscle DNA content and other muscle structural measurements, such as the number of nuclei per millimeter of fiber, myonuclear domain, and fiber cross-sectional area. Thus, while avian muscle seems more phenotypically plastic than mammalian muscle, the biological processes surrounding myonuclear function may be more closely related to those seen in mammals.
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Affiliation(s)
- Ana Gabriela Jimenez
- Department of Biology, Colgate University, Hamilton, NY 13346, USA.,Department of Biology, Colgate University, Hamilton, NY 13346, USA
| | - Emily Gray Lencyk
- Department of Biology, Colgate University, Hamilton, NY 13346, USA.,Department of Biology, Colgate University, Hamilton, NY 13346, USA
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9
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Bilinski T, Bylak A, Kukuła K, Zadrag-Tecza R. Senescence as a trade-off between successful land colonisation and longevity: critical review and analysis of a hypothesis. PeerJ 2021; 9:e12286. [PMID: 34760360 PMCID: PMC8570163 DOI: 10.7717/peerj.12286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 09/20/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Most common terrestrial animal clades exhibit senescence, suggesting strong adaptive value of this trait. However, there is little support for senescence correlated with specific adaptations. Nevertheless, insects, mammals, and birds, which are the most common terrestrial animal clades that show symptoms of senescence, evolved from clades that predominantly did not show symptoms of senescence. Thus, we aimed to examine senescence in the context of the ecology and life histories of the main clades of animals, including humans, and to formulate hypotheses to explain the causes and origin of senescence in the major clades of terrestrial animals. METHODOLOGY We reviewed literature from 1950 to 2020 concerning life expectancy, the existence of senescence, and the adaptive characteristics of the major groups of animals. We then proposed a relationship between senescence and environmental factors, considering the biology of these groups of animals. We constructed a model showing the phylogenetic relationships between animal clades in the context of the major stages of evolution, distinguishing between senescent and biologically 'immortal' clades of animals. Finally, we synthesised current data on senescence with the most important concepts and theories explaining the origin and mechanisms of senescence. Although this categorisation into different senescent phenotypes may be simplistic, we used this to propose a framework for understanding senescence. RESULTS We found that terrestrial mammals, insects, and birds show senescence, even though they likely evolved from non-senescent ancestors. Moreover, secondarily aquatic animals show lower rate of senescence than their terrestrial counterparts. Based on the possible life histories of these groups and the analysis of the most important factors affecting the transition from a non-senescent to senescent phenotype, we conclude that aging has evolved, not as a direct effect, but as a correlated response of selection on developmental strategies, and that this occurred separately within each clade. Adoption of specific life history strategies could thus have far-reaching effects in terms of senescence and lifespan. CONCLUSIONS Our analysis strongly suggests that senescence may have emerged as a side effect of the evolution of adaptive features that allowed the colonisation of land. Senescence in mammals may be a compromise between land colonisation and longevity. This hypothesis, is supported by palaeobiological and ecological evidence. We hope that the development of new research methodologies and the availability of more data could be used to test this hypothesis and shed greater light on the evolution of senescence.
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Affiliation(s)
- Tomasz Bilinski
- Department of Biochemistry and Cell Biology, Faculty of Biology and Agriculture, University of Rzeszów, Rzeszów, Poland
| | - Aneta Bylak
- Department of Ecology and Environmental Protection; Institute of Agricultural Sciences, Land Management and Environmental Protection, University of Rzeszów, Rzeszów, Poland
| | - Krzysztof Kukuła
- Department of Ecology and Environmental Protection; Institute of Agricultural Sciences, Land Management and Environmental Protection, University of Rzeszów, Rzeszów, Poland
| | - Renata Zadrag-Tecza
- Department of Biochemistry and Cell Biology, Institute of Biology and Biotechnology, University of Rzeszów, Rzeszów, Poland
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10
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Paule J, von Döhren J, Sagorny C, Nilsson MA. Genome Size Dynamics in Marine Ribbon Worms (Nemertea, Spiralia). Genes (Basel) 2021; 12:1347. [PMID: 34573329 PMCID: PMC8468679 DOI: 10.3390/genes12091347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/26/2021] [Accepted: 08/26/2021] [Indexed: 11/28/2022] Open
Abstract
Nemertea is a phylum consisting of 1300 mostly marine species. Nemertea is distinguished by an eversible muscular proboscis, and most of the species are venomous. Genomic resources for this phylum are scarce despite their value in understanding biodiversity. Here, we present genome size estimates of Nemertea based on flow cytometry and their relationship to different morphological and developmental traits. Ancestral genome size estimations were done across the nemertean phylogeny. The results increase the available genome size estimates for Nemertea three-fold. Our analyses show that Nemertea has a narrow genome size range (0.43-3.89 pg) compared to other phyla in Lophotrochozoa. A relationship between genome size and evolutionary rate, developmental modes, and habitat was found. Trait analyses show that the highest evolutionary rate of genome size is found in upper intertidal, viviparous species with direct development. Despite previous findings, body size in nemerteans was not correlated with genome size. A relatively small genome (1.18 pg) is assumed for the most recent common ancestor of all extant nemerteans. The results provide an important basis for future studies in nemertean genomics, which will be instrumental to understanding the evolution of this enigmatic and often neglected phylum.
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Affiliation(s)
- Juraj Paule
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany;
| | - Jörn von Döhren
- Institute of Evolutionary Biology and Ecology, University of Bonn, An der Immenburg 1, D-53121 Bonn, Germany; (J.v.D.); (C.S.)
| | - Christina Sagorny
- Institute of Evolutionary Biology and Ecology, University of Bonn, An der Immenburg 1, D-53121 Bonn, Germany; (J.v.D.); (C.S.)
| | - Maria A. Nilsson
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
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11
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Wang Q, Ren X, Liu P, Li J, Lv J, Wang J, Zhang H, Wei W, Zhou Y, He Y, Li J. Improved genome assembly of Chinese shrimp (Fenneropenaeus chinensis) suggests adaptation to the environment during evolution and domestication. Mol Ecol Resour 2021; 22:334-344. [PMID: 34240531 DOI: 10.1111/1755-0998.13463] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 06/10/2021] [Accepted: 07/05/2021] [Indexed: 11/30/2022]
Abstract
A high-quality reference genome is necessary to determine the molecular mechanisms underlying important biological phenomena; therefore, in the present study, a chromosome-level genome assembly of the Chinese shrimp Fenneropenaeus chinensis was performed. Muscle of a male shrimp was sequenced using PacBio platform, and assembled by Hi-C technology. The assembled F. chinensis genome was 1.47 Gb with contig N50 of 472.84 Kb, including 57.73% repetitive sequences, and was anchored to 43 pseudochromosomes, with scaffold N50 of 36.87 Mb. In total, 25,026 protein-coding genes were predicted. The genome size of F. chinensis showed significant contraction in comparison with that of other penaeid species, which is likely related to migration observed in this species. However, the F. chinensis genome included several expanded gene families related to cellular processes and metabolic processes, and the contracted gene families were associated with virus infection process. The findings signify the adaptation of F. chinensis to the selection pressure of migration and cold environment. Furthermore, the selection signature analysis identified genes associated with metabolism, phototransduction, and nervous system in cultured shrimps when compared with wild population, indicating targeted, artificial selection of growth, vision, and behavior during domestication. The construction of the genome of F. chinensis provided valuable information for the further genetic mechanism analysis of important biological processes, and will facilitate the research of genetic changes during evolution.
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Affiliation(s)
- Qiong Wang
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xianyun Ren
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Ping Liu
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jitao Li
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jianjian Lv
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jiajia Wang
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Haien Zhang
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Wei Wei
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Yuxin Zhou
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Yuying He
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jian Li
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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12
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Malo JE, Mata C. Web databases of feather photographs are useful tools for avian morphometry studies. Ecol Evol 2021; 11:7677-7684. [PMID: 34188843 PMCID: PMC8216968 DOI: 10.1002/ece3.7600] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/22/2021] [Accepted: 03/25/2021] [Indexed: 11/10/2022] Open
Abstract
Wing area, wing loading, and aspect ratio are key variables for studies of avian comparative ecology, despite the complexity of measuring wing characteristics in living and museum specimens. The systematic databases of feather photographs available on the Internet may offer an alternative way of obtaining such morphometric data. Here, we evaluate whether measurements of scanned feathers from web photograph databases may offer reliable estimates of avian morphometry.Published data on wing area were obtained for 317 bird species and feather measurements from web photograph databases for 225 of them. A variable termed "lift generation area," a proxy for wing area, was calculated for each species on the basis of the mean length of the five distal secondary feathers and wingspan data from literature. The fit between this proposed variable and data extracted from the literature was examined by correlation, employing linear regression to explore the lack of fit among species."Lift generation area" proved to be highly informative as a proxy for wing area for the study species as a whole (R 2 > .98). Discrepancies observed between species were strongly negatively associated with the size of the original sample used to calculate wing area (p = .001) and, to a lesser extent, with bird size (p = .023), but not with aspect ratio. It was also found that the mean value of the mismatch between "lift generation area" and wing area (13.1%) among the study species as a whole was of similar magnitude to that found between sources of bibliographic wing area data for the 64 species for which two published estimates of this variable were available (15.3%).We conclude that measurements made from feather photograph databases are reliable for use in studies of avian comparative ecology, enabling the inclusion of biomechanical parameters of many more species than featured at present.
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Affiliation(s)
- Juan E. Malo
- Terrestrial Ecology Group (TEG‐UAM)Departamento de EcologíaFacultad de CienciasUniversidad Autónoma de MadridMadridSpain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC‐UAM)Universidad Autónoma de MadridMadridSpain
| | - Cristina Mata
- Terrestrial Ecology Group (TEG‐UAM)Departamento de EcologíaFacultad de CienciasUniversidad Autónoma de MadridMadridSpain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC‐UAM)Universidad Autónoma de MadridMadridSpain
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13
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Lamichhaney S, Catullo R, Keogh JS, Clulow S, Edwards SV, Ezaz T. A bird-like genome from a frog: Mechanisms of genome size reduction in the ornate burrowing frog, Platyplectrum ornatum. Proc Natl Acad Sci U S A 2021; 118:e2011649118. [PMID: 33836564 PMCID: PMC7980411 DOI: 10.1073/pnas.2011649118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
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.
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Affiliation(s)
- Sangeet Lamichhaney
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138
| | - Renee Catullo
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, ACT, Australia 2601
- Australian National Insect Collection and Future Science Platform Environomics, Commonwealth Scientific and Industrial Research Organization, Acton, ACT, Australia 2601
| | - J Scott Keogh
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, ACT, Australia 2601
| | - Simon Clulow
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia 2109
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138;
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138
| | - Tariq Ezaz
- Institute for Applied Ecology, Faculty of Science and Technology, University of Canberra, Canberra, ACT, Australia 2617
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14
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Grzywacz B, Skórka P. Genome size versus geographic range size in birds. PeerJ 2021; 9:e10868. [PMID: 33614292 PMCID: PMC7881720 DOI: 10.7717/peerj.10868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 01/10/2021] [Indexed: 11/20/2022] Open
Abstract
Why do some species occur in small, restricted areas, while others are distributed globally? Environmental heterogeneity increases with area and so does the number of species. Hence, diverse biotic and abiotic conditions across large ranges may lead to specific adaptations that are often linked to a species' genome size and chromosome number. Therefore, a positive association between genome size and geographic range is anticipated. Moreover, high cognitive ability in organisms would be favored by natural selection to cope with the dynamic conditions within large geographic ranges. Here, we tested these hypotheses in birds-the most mobile terrestrial vertebrates-and accounted for the effects of various confounding variables, such as body mass, relative brain mass, and geographic latitude. Using phylogenetic generalized least squares and phylogenetic confirmatory path analysis, we demonstrated that range size is positively associated with bird genome size but probably not with chromosome number. Moreover, relative brain mass had no effect on range size, whereas body mass had a possible weak and negative effect, and range size was larger at higher geographic latitudes. However, our models did not fully explain the overall variation in range size. Hence, natural selection may impose larger genomes in birds with larger geographic ranges, although there may be additional explanations for this phenomenon.
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Affiliation(s)
- Beata Grzywacz
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Kraków, Poland
| | - Piotr Skórka
- Institute of Nature Conservation, Polish Academy of Sciences, Kraków, Poland
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15
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Louha S, Ray DA, Winker K, Glenn TC. A High-Quality Genome Assembly of the North American Song Sparrow, Melospiza melodia. G3 (BETHESDA, MD.) 2020; 10:1159-1166. [PMID: 32075855 PMCID: PMC7144075 DOI: 10.1534/g3.119.400929] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 02/13/2020] [Indexed: 01/25/2023]
Abstract
The song sparrow, Melospiza melodia, is one of the most widely distributed species of songbirds found in North America. It has been used in a wide range of behavioral and ecological studies. This species' pronounced morphological and behavioral diversity across populations makes it a favorable candidate in several areas of biomedical research. We have generated a high-quality de novo genome assembly of M. melodia using Illumina short read sequences from genomic and in vitro proximity-ligation libraries. The assembled genome is 978.3 Mb, with a physical coverage of 24.9×, N50 scaffold size of 5.6 Mb and N50 contig size of 31.7 Kb. Our genome assembly is highly complete, with 87.5% full-length genes present out of a set of 4,915 universal single-copy orthologs present in most avian genomes. We annotated our genome assembly and constructed 15,086 gene models, a majority of which have high homology to related birds, Taeniopygia guttata and Junco hyemalis In total, 83% of the annotated genes are assigned with putative functions. Furthermore, only ∼7% of the genome is found to be repetitive; these regions and other non-coding functional regions are also identified. The high-quality M. melodia genome assembly and annotations we report will serve as a valuable resource for facilitating studies on genome structure and evolution that can contribute to biomedical research and serve as a reference in population genomic and comparative genomic studies of closely related species.
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Affiliation(s)
- Swarnali Louha
- Institute of Bioinformatics, University of Georgia, Athens, GA
| | - David A Ray
- Department of Biological Science, Texas Tech University, Lubbock, TX
| | | | - Travis C Glenn
- Institute of Bioinformatics, University of Georgia, Athens, GA
- Department of Environmental Health Science, University of Georgia, Athens, GA
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16
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Gardner JD, Laurin M, Organ CL. The relationship between genome size and metabolic rate in extant vertebrates. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190146. [PMID: 31928192 PMCID: PMC7017434 DOI: 10.1098/rstb.2019.0146] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/10/2019] [Indexed: 12/13/2022] Open
Abstract
Genome size has long been hypothesized to affect the metabolic rate in various groups of animals. The mechanism behind this proposed association is the nucleotypic effect, in which large nucleus and cell sizes influence cellular metabolism through surface area-to-volume ratios. Here, we provide a review of the recent literature on the relationship between genome size and metabolic rate. We also conduct an analysis using phylogenetic comparative methods and a large sample of extant vertebrates. We find no evidence that the effect of genome size improves upon models in explaining metabolic rate variation. Not surprisingly, our results show a strong positive relationship between metabolic rate and body mass, as well as a substantial difference in metabolic rate between endothermic and ectothermic vertebrates, controlling for body mass. The presence of endothermy can also explain elevated rate shifts in metabolic rate whereas genome size cannot. We further find no evidence for a punctuated model of evolution for metabolic rate. Our results do not rule out the possibility that genome size affects cellular physiology in some tissues, but they are consistent with previous research suggesting little support for a direct functional connection between genome size and basal metabolic rate in extant vertebrates. This article is part of the theme issue 'Vertebrate palaeophysiology'.
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Affiliation(s)
- Jacob D. Gardner
- Department of Earth Sciences, Montana State University, Bozeman, MT 59717, USA
| | - Michel Laurin
- Centre de Recherches sur la Paléobiologie et les Paléoenvironnements (CR2P), Centre National de la Recherche Scientifique (CNRS)/Muséum National d'Histoire Naturelle (MNHN)/Sorbonne Université, Paris, France
| | - Chris L. Organ
- Department of Earth Sciences, Montana State University, Bozeman, MT 59717, USA
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Hjelmen CE, Parrott JJ, Srivastav SP, McGuane AS, Ellis LL, Stewart AD, Johnston JS, Tarone AM. Effect of Phenotype Selection on Genome Size Variation in Two Species of Diptera. Genes (Basel) 2020; 11:genes11020218. [PMID: 32093067 PMCID: PMC7074110 DOI: 10.3390/genes11020218] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 02/11/2020] [Accepted: 02/15/2020] [Indexed: 11/16/2022] Open
Abstract
Genome size varies widely across organisms yet has not been found to be related to organismal complexity in eukaryotes. While there is no evidence for a relationship with complexity, there is evidence to suggest that other phenotypic characteristics, such as nucleus size and cell-cycle time, are associated with genome size, body size, and development rate. However, what is unknown is how the selection for divergent phenotypic traits may indirectly affect genome size. Drosophila melanogaster were selected for small and large body size for up to 220 generations, while Cochliomyia macellaria were selected for 32 generations for fast and slow development. Size in D. melanogaster significantly changed in terms of both cell-count and genome size in isolines, but only the cell-count changed in lines which were maintained at larger effective population sizes. Larger genome sizes only occurred in a subset of D. melanogaster isolines originated from flies selected for their large body size. Selection for development time did not change average genome size yet decreased the within-population variation in genome size with increasing generations of selection. This decrease in variation and convergence on a similar mean genome size was not in correspondence with phenotypic variation and suggests stabilizing selection on genome size in laboratory conditions.
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Affiliation(s)
- Carl E. Hjelmen
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA; (J.J.P.); (S.P.S.); (A.S.M.); (L.L.E.); (J.S.J.); (A.M.T.)
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
- Correspondence: or
| | - Jonathan J. Parrott
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA; (J.J.P.); (S.P.S.); (A.S.M.); (L.L.E.); (J.S.J.); (A.M.T.)
- School of Mathematical and Natural Sciences, Arizona State University, Glendale, AZ 85306, USA
| | - Satyam P. Srivastav
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA; (J.J.P.); (S.P.S.); (A.S.M.); (L.L.E.); (J.S.J.); (A.M.T.)
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Alexander S. McGuane
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA; (J.J.P.); (S.P.S.); (A.S.M.); (L.L.E.); (J.S.J.); (A.M.T.)
- Harris County Institute of Forensic Sciences, 1861 Old Spanish Trail, Houston, TX 77054, USA
| | - Lisa L. Ellis
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA; (J.J.P.); (S.P.S.); (A.S.M.); (L.L.E.); (J.S.J.); (A.M.T.)
- Department of Biology, Houston Baptist University, Houston, TX 77074, USA
| | | | - J. Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA; (J.J.P.); (S.P.S.); (A.S.M.); (L.L.E.); (J.S.J.); (A.M.T.)
| | - Aaron M. Tarone
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA; (J.J.P.); (S.P.S.); (A.S.M.); (L.L.E.); (J.S.J.); (A.M.T.)
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18
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Evolution and diversity of transposable elements in fish genomes. Sci Rep 2019; 9:15399. [PMID: 31659260 PMCID: PMC6817897 DOI: 10.1038/s41598-019-51888-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 10/09/2019] [Indexed: 12/22/2022] Open
Abstract
Transposable elements (TEs) are genomic sequences that can move, multiply, and often form sizable fractions of vertebrate genomes. Fish belong to a unique group of vertebrates, since their karyotypes and genome sizes are more diverse and complex, with probably higher diversity and evolution specificity of TE. To investigate the characteristics of fish TEs, we compared the mobilomes of 39 species, and observed significant variation of TE content in fish (from 5% in pufferfish to 56% in zebrafish), along with a positive correlation between fish genome size and TE content. In different classification hierarchies, retrotransposons (class), long terminal repeat (order), as well as Helitron, Maverick, Kolobok, CMC, DIRS, P, I, L1, L2, and 5S (superfamily) were all positively correlated with fish genome size. Consistent with previous studies, our data suggested fish genomes to not always be dominated by DNA transposons; long interspersed nuclear elements are also prominent in many species. This study suggests CR1 distribution in fish genomes to be obviously regular, and provides new clues concerning important events in vertebrate evolution. Altogether, our results highlight the importance of TEs in the structure and evolution of fish genomes and suggest fish species diversity to parallel transposon content diversification.
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19
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Furness EN, Robinson RA. Long-term declines in winter body mass of tits throughout Britain and Ireland correlate with climate change. Ecol Evol 2019; 9:1202-1210. [PMID: 30805153 PMCID: PMC6374658 DOI: 10.1002/ece3.4812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 11/18/2018] [Accepted: 11/22/2018] [Indexed: 11/24/2022] Open
Abstract
The optimum body mass of passerine birds typically represents a trade-off between starvation risk, which promotes fat gain, and predation pressure, which promotes fat loss to maintain maneuvrability. Changes in ecological factors that affect either of these variables will therefore change the optimum body masses of populations of passerine birds. This study sought to identify and quantify the effects of changing temperatures and predation pressures on the body masses and wing lengths of populations of passerine birds throughout Britain and Ireland over the last 50 years. We analyzed over 900,000 individual measurements of body mass and wing length of blue tits Cyanistes caeruleus, coal tits Periparus ater, and great tits Parus major collected by licenced bird ringers throughout Britain and Ireland from 1965 to 2017 and correlated these with publicly available temperature data and published, UK-wide data on the abundance of a key predator, the sparrowhawk Accipiter nisus. We found highly significant, long-term, UK-wide decreases in winter body masses of adults and juveniles of all three species. We also found highly significant negative correlations between winter body mass and winter temperature, and between winter body mass and sparrowhawk abundance. Independent of these effects, body mass further correlated negatively with calendar year, suggesting that less well understood dynamic factors, such as supplementary feeding levels, may play a major role in determining population optimum body masses. Wing lengths of these birds also decreased, suggesting a hitherto unobserved large-scale evolutionary adjustment of wing loading to the lower body mass. These findings provide crucial evidence of the ways in which species are adapting to climate change and other anthropogenic factors throughout Britain and Ireland. Such processes are likely to have widespread implications as the equilibria controlling evolutionary optima in species worldwide are upset by rapid, anthropogenic ecological changes.
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Formenti G, Chiara M, Poveda L, Francoijs KJ, Bonisoli-Alquati A, Canova L, Gianfranceschi L, Horner DS, Saino N. SMRT long reads and Direct Label and Stain optical maps allow the generation of a high-quality genome assembly for the European barn swallow (Hirundo rustica rustica). Gigascience 2019; 8:5202456. [PMID: 30496513 PMCID: PMC6324554 DOI: 10.1093/gigascience/giy142] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 11/14/2018] [Indexed: 11/12/2022] Open
Abstract
Background The barn swallow (Hirundo rustica) is a migratory bird that has been the focus of a large number of ecological, behavioral, and genetic studies. To facilitate further population genetics and genomic studies, we present a reference genome assembly for the European subspecies (H. r. rustica). Findings As part of the Genome10K effort on generating high-quality vertebrate genomes (Vertebrate Genomes Project), we have assembled a highly contiguous genome assembly using single molecule real-time (SMRT) DNA sequencing and several Bionano optical map technologies. We compared and integrated optical maps derived from both the Nick, Label, Repair, and Stain technology and from the Direct Label and Stain (DLS) technology. As proposed by Bionano, DLS more than doubled the scaffold N50 with respect to the nickase. The dual enzyme hybrid scaffold led to a further marginal increase in scaffold N50 and an overall increase of confidence in the scaffolds. After removal of haplotigs, the final assembly is approximately 1.21 Gbp in size, with a scaffold N50 value of more than 25.95 Mbp. Conclusions This high-quality genome assembly represents a valuable resource for future studies of population genetics and genomics in the barn swallow and for studies concerning the evolution of avian genomes. It also represents one of the very first genomes assembled by combining SMRT long-read sequencing with the new Bionano DLS technology for scaffolding. The quality of this assembly demonstrates the potential of this methodology to substantially increase the contiguity of genome assemblies.
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Affiliation(s)
- Giulio Formenti
- Department of Environmental Science and Policy, University of Milan, via celoria 2, Milan, 20133, Italy
| | - Matteo Chiara
- Department of Biosciences, University of Milan, via celoria 26, Milan, 20133, Italy
| | - Lucy Poveda
- Functional Genomics Center of Zurich, University of Zurich, Winterthurerstrasse 190, Zürich, 8057, Switzerland
| | | | - Andrea Bonisoli-Alquati
- Department of Biological Sciences, California State Polytechnic University, 3801 West Temple Avenue, Pomona, California, 91768, USA
| | - Luca Canova
- Department of Biochemistry, University of Pavia, Via Taramelli 12, Pavia, 27100, Italy
| | - Luca Gianfranceschi
- Department of Biosciences, University of Milan, via celoria 26, Milan, 20133, Italy
| | - David Stephen Horner
- Department of Biosciences, University of Milan, via celoria 26, Milan, 20133, Italy
| | - Nicola Saino
- Department of Environmental Science and Policy, University of Milan, via celoria 2, Milan, 20133, Italy
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21
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Smith CCR, Flaxman SM, Scordato ESC, Kane NC, Hund AK, Sheta BM, Safran RJ. Demographic inference in barn swallows using whole-genome data shows signal for bottleneck and subspecies differentiation during the Holocene. Mol Ecol 2018; 27:4200-4212. [PMID: 30176075 DOI: 10.1111/mec.14854] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 08/27/2018] [Indexed: 12/20/2022]
Abstract
Accounting for historical demographic features is vital for many types of evolutionary inferences, including the estimation of divergence times between closely related populations. In barn swallow, Hirundo rustica, inferring historical population sizes and subspecies divergence times can shed light on the recent co-evolution of this species with humans. Pairwise sequentially Markovian coalescent uncovered population growth beginning on the order of one million years ago-which may reflect the radiation of the broader Hirundo genus-and a more recent population decline. Additionally, we used approximate Bayesian computation to evaluate hypotheses about recent timescale barn swallow demography, including population growth due to human commensalism, and a potential founder event associated with the onset of nesting on human structures. We found signal for a bottleneck event approximately 7,700 years ago, near the time that humans began building substantial structures, although there was considerable uncertainty associated with this estimate. Subspecies differentiation and subsequent growth occurred after the bottleneck in the best-supported model, an order of magnitude more recently than previous estimates in this system. We also compared results obtained from whole-genome sequencing versus reduced representation sequencing, finding many similar results despite substantial allelic dropout in the reduced representation data, which may have affected estimates of some parameters. This study presents the first genetic evidence of a potential barn swallow founder effect and subspecies divergence coinciding with the Holocene, which is an important step in analysing the biogeographical history of a well-known human commensal species.
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Affiliation(s)
- Chris C R Smith
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado
| | - Samuel M Flaxman
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado
| | - Elizabeth S C Scordato
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado.,Biological Sciences Department, California State Polytechnic University, Pomona, California
| | - Nolan C Kane
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado
| | - Amanda K Hund
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado
| | - Basma M Sheta
- Zoology Department, Faculty of Science, Damietta University, Damietta, Egypt
| | - Rebecca J Safran
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado
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22
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Sohn JI, Nam K, Hong H, Kim JM, Lim D, Lee KT, Do YJ, Cho CY, Kim N, Chai HH, Nam JW. Whole genome and transcriptome maps of the entirely black native Korean chicken breed Yeonsan Ogye. Gigascience 2018; 7:5052204. [PMID: 30010758 PMCID: PMC6065499 DOI: 10.1093/gigascience/giy086] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 05/19/2018] [Accepted: 07/04/2018] [Indexed: 12/30/2022] Open
Abstract
Background Yeonsan Ogye (YO), an indigenous Korean chicken breed (Gallus gallus domesticus), has entirely black external features and internal organs. In this study, the draft genome of YO was assembled using a hybrid de novo assembly method that takes advantage of high-depth Illumina short reads (376.6X) and low-depth Pacific Biosciences (PacBio) long reads (9.7X). Findings The contig and scaffold NG50s of the hybrid de novo assembly were 362.3 Kbp and 16.8 Mbp, respectively. The completeness (97.6%) of the draft genome (Ogye_1.1) was evaluated with single-copy orthologous genes using Benchmarking Universal Single-Copy Orthologs and found to be comparable to the current chicken reference genome (galGal5; 97.4%; contigs were assembled with high-depth PacBio long reads (50X) and scaffolded with short reads) and superior to other avian genomes (92%-93%; assembled with short read-only or hybrid methods). Compared to galGal4 and galGal5, the draft genome included 551 structural variations including the fibromelanosis (FM) locus duplication, related to hyperpigmentation. To comprehensively reconstruct transcriptome maps, RNA sequencing and reduced representation bisulfite sequencing data were analyzed from 20 tissues, including 4 black tissues (skin, shank, comb, and fascia). The maps included 15,766 protein-coding and 6,900 long noncoding RNA genes, many of which were tissue-specifically expressed and displayed tissue-specific DNA methylation patterns in the promoter regions. Conclusions We expect that the resulting genome sequence and transcriptome maps will be valuable resources for studying domestic chicken breeds, including black-skinned chickens, as well as for understanding genomic differences between breeds and the evolution of hyperpigmented chickens and functional elements related to hyperpigmentation.
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Affiliation(s)
- Jang-il Sohn
- Department of Life Science, Hanyang University, Seoul, 133-791, Republic of Korea
- Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, 133-791, Republic of Korea
| | - Kyoungwoo Nam
- Department of Life Science, Hanyang University, Seoul, 133-791, Republic of Korea
| | - Hyosun Hong
- Department of Life Science, Hanyang University, Seoul, 133-791, Republic of Korea
| | - Jun-Mo Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea
| | - Dajeong Lim
- Department of Animal Biotechnology & Environment, National Institute of Animal Science, RDA, Wanju, 55365, Republic of Korea
| | - Kyung-Tai Lee
- Department of Animal Biotechnology & Environment, National Institute of Animal Science, RDA, Wanju, 55365, Republic of Korea
| | - Yoon Jung Do
- Department of Animal Biotechnology & Environment, National Institute of Animal Science, RDA, Wanju, 55365, Republic of Korea
| | - Chang Yeon Cho
- Animal Genetic Resource Research Center, National Institute of Animal Science, RDA, Namwon, 55717, Republic of Korea
| | - Namshin Kim
- Personalized Genomic Medicine Research Center, KRIBB, Daejeon, 34141, Republic of Korea
| | - Han-Ha Chai
- Department of Animal Biotechnology & Environment, National Institute of Animal Science, RDA, Wanju, 55365, Republic of Korea
- College of Pharmacy, Chonnam National University, Kwangju, 61186, Republic of Korea
| | - Jin-Wu Nam
- Department of Life Science, Hanyang University, Seoul, 133-791, Republic of Korea
- Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, 133-791, Republic of Korea
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23
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Abstract
Birds exhibit small, constrained genome sizes relative to many other vertebrates. This has often been attributed to the metabolic constraints of powered flight, which requires small cells for efficient gas exchange. Small cells, in turn, are achieved in part by limiting nucleus size and thus DNA content. However, metabolism is not the only organismal trait that correlates with genome size in birds; relationships have also been reported with body size (positive) and relative brain size (inverse). In this study, a recent data set on cell numbers in the brains of birds was combined with available data on genome sizes to demonstrate a relationship between genome size and density of cells per gram of brain tissue. This suggests that small genomes are relevant not only in the evolution of avian flight but may also be associated with the extraordinary behavioural complexity shown by birds.
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Affiliation(s)
- T. Ryan Gregory
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
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24
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Fernández-Juricic E, Brand J, Blackwell BF, Seamans TW, DeVault TL. Species With Greater Aerial Maneuverability Have Higher Frequency of Collisions With Aircraft: A Comparative Study. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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25
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Kretschmer R, de Oliveira TD, de Oliveira Furo I, Oliveira Silva FA, Gunski RJ, Del Valle Garnero A, de Bello Cioffi M, de Oliveira EHC, de Freitas TRO. Repetitive DNAs and shrink genomes: A chromosomal analysis in nine Columbidae species (Aves, Columbiformes). Genet Mol Biol 2018; 41:98-106. [PMID: 29473932 PMCID: PMC5901494 DOI: 10.1590/1678-4685-gmb-2017-0048] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 08/16/2017] [Indexed: 12/02/2022] Open
Abstract
An extensive karyotype variation is found among species belonging to the
Columbidae family of birds (Columbiformes), both in diploid number and
chromosomal morphology. Although clusters of repetitive DNA sequences play an
important role in chromosomal instability, and therefore in chromosomal
rearrangements, little is known about their distribution and amount in avian
genomes. The aim of this study was to analyze the distribution of 11 distinct
microsatellite sequences, as well as clusters of 18S rDNA, in nine different
Columbidae species, correlating their distribution with the occurrence of
chromosomal rearrangements. We found 2n values ranging from 76 to 86 and nine
out of 11 microsatellite sequences showed distinct hybridization signals among
the analyzed species. The accumulation of microsatellite repeats was found
preferentially in the centromeric region of macro and microchromosomes, and in
the W chromosome. Additionally, pair 2 showed the accumulation of several
microsatellites in different combinations and locations in the distinct species,
suggesting the occurrence of intrachromosomal rearrangements, as well as a
possible fission of this pair in Geotrygon species. Therefore,
although birds have a smaller amount of repetitive sequences when compared to
other Tetrapoda, these seem to play an important role in the karyotype evolution
of these species.
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Affiliation(s)
- Rafael Kretschmer
- Programa de Pós-Graduação em Genética e Biologia Molecular, PPGBM, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, RS, Brazil
| | - Thays Duarte de Oliveira
- Programa de Pós-Graduação em Ciências Biológicas, PPGCB, Universidade Federal do Pampa, São Gabriel, Rio Grande do Sul, RS, Brazil
| | - Ivanete de Oliveira Furo
- Programa de Pós-Graduação em Genética e Biologia Molecular, PPGBM, Universidade Federal do Pará, Belém, PA, Brazil
| | | | - Ricardo José Gunski
- Programa de Pós-Graduação em Ciências Biológicas, PPGCB, Universidade Federal do Pampa, São Gabriel, Rio Grande do Sul, RS, Brazil
| | - Analía Del Valle Garnero
- Programa de Pós-Graduação em Ciências Biológicas, PPGCB, Universidade Federal do Pampa, São Gabriel, Rio Grande do Sul, RS, Brazil
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Edivaldo Herculano Corrêa de Oliveira
- Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, PA, Brazil.,Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua, PA, Brazil
| | - Thales Renato Ochotorena de Freitas
- Programa de Pós-Graduação em Genética e Biologia Molecular, PPGBM, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, RS, Brazil
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26
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Termignoni-García F, Jaramillo-Correa JP, Chablé-Santos J, Liu M, Shultz AJ, Edwards SV, Escalante-Pliego P. Genomic footprints of adaptation in a cooperatively breeding tropical bird across a vegetation gradient. Mol Ecol 2017; 26:4483-4496. [DOI: 10.1111/mec.14224] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Revised: 05/06/2017] [Accepted: 06/12/2017] [Indexed: 12/30/2022]
Affiliation(s)
- Flavia Termignoni-García
- Department of Zoology; National Collection of Birds (CNAV); Institute of Biology; Universidad Nacional Autónoma de México; CdMx México
| | - Juan P. Jaramillo-Correa
- Department of Evolutionary Ecology; Institute of Ecology; Universidad Nacional Autónoma de México; CdMx México
| | - Juan Chablé-Santos
- Department of Zoology; Facultad de Medicina Veterinaria y Zootecnia; Universidad Autónoma de Yucatán; Yucatán México
| | - Mark Liu
- Biodiversity Research Center; Academia Sinica; Taipei Nankang Taiwan
| | - Allison J. Shultz
- Department of Organismic and Evolutionary Biology (OEB); Harvard University; Cambridge MA USA
| | - Scott V. Edwards
- Department of Organismic and Evolutionary Biology (OEB); Harvard University; Cambridge MA USA
| | - Patricia Escalante-Pliego
- Department of Zoology; National Collection of Birds (CNAV); Institute of Biology; Universidad Nacional Autónoma de México; CdMx México
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27
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Abstract
Genome size in mammals and birds shows remarkably little interspecific variation compared with other taxa. However, genome sequencing has revealed that many mammal and bird lineages have experienced differential rates of transposable element (TE) accumulation, which would be predicted to cause substantial variation in genome size between species. Thus, we hypothesize that there has been covariation between the amount of DNA gained by transposition and lost by deletion during mammal and avian evolution, resulting in genome size equilibrium. To test this model, we develop computational methods to quantify the amount of DNA gained by TE expansion and lost by deletion over the last 100 My in the lineages of 10 species of eutherian mammals and 24 species of birds. The results reveal extensive variation in the amount of DNA gained via lineage-specific transposition, but that DNA loss counteracted this expansion to various extents across lineages. Our analysis of the rate and size spectrum of deletion events implies that DNA removal in both mammals and birds has proceeded mostly through large segmental deletions (>10 kb). These findings support a unified "accordion" model of genome size evolution in eukaryotes whereby DNA loss counteracting TE expansion is a major determinant of genome size. Furthermore, we propose that extensive DNA loss, and not necessarily a dearth of TE activity, has been the primary force maintaining the greater genomic compaction of flying birds and bats relative to their flightless relatives.
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28
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de Oliveira TD, Kretschmer R, Bertocchi NA, Degrandi TM, de Oliveira EHC, Cioffi MDB, Garnero ADV, Gunski RJ. Genomic Organization of Repetitive DNA in Woodpeckers (Aves, Piciformes): Implications for Karyotype and ZW Sex Chromosome Differentiation. PLoS One 2017; 12:e0169987. [PMID: 28081238 PMCID: PMC5230766 DOI: 10.1371/journal.pone.0169987] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 12/27/2016] [Indexed: 11/24/2022] Open
Abstract
Birds are characterized by a low proportion of repetitive DNA in their genome when compared to other vertebrates. Among birds, species belonging to Piciformes order, such as woodpeckers, show a relatively higher amount of these sequences. The aim of this study was to analyze the distribution of different classes of repetitive DNA—including microsatellites, telomere sequences and 18S rDNA—in the karyotype of three Picidae species (Aves, Piciformes)—Colaptes melanochloros (2n = 84), Colaptes campestris (2n = 84) and Melanerpes candidus (2n = 64)–by means of fluorescence in situ hybridization. Clusters of 18S rDNA were found in one microchromosome pair in each of the three species, coinciding to a region of (CGG)10 sequence accumulation. Interstitial telomeric sequences were found in some macrochromosomes pairs, indicating possible regions of fusions, which can be related to variation of diploid number in the family. Only one, from the 11 different microsatellite sequences used, did not produce any signals. Both species of genus Colaptes showed a similar distribution of microsatellite sequences, with some difference when compared to M. candidus. Microsatellites were found preferentially in the centromeric and telomeric regions of micro and macrochromosomes. However, some sequences produced patterns of interstitial bands in the Z chromosome, which corresponds to the largest element of the karyotype in all three species. This was not observed in the W chromosome of Colaptes melanochloros, which is heterochromatic in most of its length, but was not hybridized by any of the sequences used. These results highlight the importance of microsatellite sequences in differentiation of sex chromosomes, and the accumulation of these sequences is probably responsible for the enlargement of the Z chromosome.
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Affiliation(s)
- Thays Duarte de Oliveira
- Programa de Pós-graduação em Ciências Biológicas, Universidade Federal do Pampa, São Gabriel, Rio Grande do Sul, Brazil
- * E-mail:
| | - Rafael Kretschmer
- Programa de Pós-graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Natasha Avila Bertocchi
- Programa de Pós-graduação em Ciências Biológicas, Universidade Federal do Pampa, São Gabriel, Rio Grande do Sul, Brazil
| | - Tiago Marafiga Degrandi
- Programa de Pós-graduação em Genética, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Edivaldo Herculano Corrêa de Oliveira
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua, Pará, Brazil
- Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, São Paulo, Brazil
| | - Analía del Valle Garnero
- Programa de Pós-graduação em Ciências Biológicas, Universidade Federal do Pampa, São Gabriel, Rio Grande do Sul, Brazil
| | - Ricardo José Gunski
- Programa de Pós-graduação em Ciências Biológicas, Universidade Federal do Pampa, São Gabriel, Rio Grande do Sul, Brazil
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29
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Sun YF, Ren ZP, Wu YF, Lei FM, Dudley R, Li DM. Flying high: limits to flight performance by sparrows on the Qinghai-Tibet Plateau. ACTA ACUST UNITED AC 2016; 219:3642-3648. [PMID: 27609759 DOI: 10.1242/jeb.142216] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 09/01/2016] [Indexed: 01/18/2023]
Abstract
Limits to flight performance at high altitude potentially reflect variable constraints deriving from the simultaneous challenges of hypobaric, hypodense and cold air. Differences in flight-related morphology and maximum lifting capacity have been well characterized for different hummingbird species across elevational gradients, but relevant within-species variation has not yet been identified in any bird species. Here we evaluate load-lifting capacity for Eurasian tree sparrow (Passer montanus) populations at three different elevations in China, and correlate maximum lifted loads with relevant anatomical features including wing shape, wing size, and heart and lung masses. Sparrows were heavier and possessed more rounded and longer wings at higher elevations; relative heart and lung masses were also greater with altitude, although relative flight muscle mass remained constant. By contrast, maximum lifting capacity relative to body weight declined over the same elevational range, while the effective wing loading in flight (i.e. the ratio of body weight and maximum lifted weight to total wing area) remained constant, suggesting aerodynamic constraints on performance in parallel with enhanced heart and lung masses to offset hypoxic challenge. Mechanical limits to take-off performance may thus be exacerbated at higher elevations, which may in turn result in behavioral differences in escape responses among populations.
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Affiliation(s)
- Yan-Feng Sun
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, People's Republic of China.,Ocean College, Agricultural University of Hebei, Qinhuangdao 066003, People's Republic of China
| | - Zhi-Peng Ren
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, People's Republic of China
| | - Yue-Feng Wu
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, People's Republic of China
| | - Fu-Min Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
| | - Robert Dudley
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Dong-Ming Li
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, People's Republic of China
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30
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Safran RJ, Scordato ESC, Wilkins MR, Hubbard JK, Jenkins BR, Albrecht T, Flaxman SM, Karaardıç H, Vortman Y, Lotem A, Nosil P, Pap P, Shen S, Chan S, Parchman T, Kane NC. Genome‐wide differentiation in closely related populations: the roles of selection and geographic isolation. Mol Ecol 2016; 25:3865-83. [DOI: 10.1111/mec.13740] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 06/08/2016] [Accepted: 06/15/2016] [Indexed: 12/19/2022]
Affiliation(s)
- R. J. Safran
- Department of Ecology and Evolutionary Biology University of Colorado Boulder CO USA
| | - E. S. C. Scordato
- Department of Ecology and Evolutionary Biology University of Colorado Boulder CO USA
| | - M. R. Wilkins
- Department of Ecology and Evolutionary Biology University of Colorado Boulder CO USA
- School of Biological Sciences University of Nebraska‐Lincoln Lincoln NE USA
| | - J. K. Hubbard
- Department of Ecology and Evolutionary Biology University of Colorado Boulder CO USA
- School of Biological Sciences University of Nebraska‐Lincoln Lincoln NE USA
| | - B. R. Jenkins
- Department of Ecology and Evolutionary Biology University of Colorado Boulder CO USA
| | - T. Albrecht
- Department of Zoology Charles University in Prague and Institute of Vertebrate Biology Academy of Sciences of the Czech Republic Prague Czech Republic
| | - S. M. Flaxman
- Department of Ecology and Evolutionary Biology University of Colorado Boulder CO USA
| | - H. Karaardıç
- Elementary Science Education Department Education Faculty Alanya Alaaddin Keykubat University Alanya Turkey
| | - Y. Vortman
- Department of Zoology Tel‐Aviv University Tel‐Aviv Israel
- Hula Research Center Department of Animal Sciences Tel‐Hai College Israel
| | - A. Lotem
- Department of Zoology Tel‐Aviv University Tel‐Aviv Israel
| | - P. Nosil
- Department of Animal and Plant Sciences University of Sheffield Sheffield UK
| | - P. Pap
- Department of Taxonomy and Ecology Babeş‐Bolyai University Cluj‐Napoca Romania
| | - S. Shen
- Biodiversity Research Center Academia Sinica Taipei Taiwan
| | - S.‐F. Chan
- Biodiversity Research Center Academia Sinica Taipei Taiwan
| | - T.L. Parchman
- Department of Biology University of Nevada Reno NV USA
| | - N. C. Kane
- Department of Ecology and Evolutionary Biology University of Colorado Boulder CO USA
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31
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von Rönn JA, Shafer AB, Wolf JB. Disruptive selection without genome-wide evolution across a migratory divide. Mol Ecol 2016; 25:2529-41. [DOI: 10.1111/mec.13521] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 12/01/2015] [Accepted: 12/18/2015] [Indexed: 01/15/2023]
Affiliation(s)
- Jan A.C. von Rönn
- Department of Evolutionary Genetics; Max Planck Institute of Evolutionary Biology; August-Thienemann-Str. 2 24306 Plön Germany
| | - Aaron B.A. Shafer
- Department of Evolutionary Biology and Science for Life Laboratory; Uppsala University; Norbyvägen 18D 75236 Uppsala Sweden
| | - Jochen B.W. Wolf
- Department of Evolutionary Genetics; Max Planck Institute of Evolutionary Biology; August-Thienemann-Str. 2 24306 Plön Germany
- Department of Evolutionary Biology and Science for Life Laboratory; Uppsala University; Norbyvägen 18D 75236 Uppsala Sweden
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32
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Deppe JL, Ward MP, Bolus RT, Diehl RH, Celis-Murillo A, Zenzal TJ, Moore FR, Benson TJ, Smolinsky JA, Schofield LN, Enstrom DA, Paxton EH, Bohrer G, Beveroth TA, Raim A, Obringer RL, Delaney D, Cochran WW. Fat, weather, and date affect migratory songbirds' departure decisions, routes, and time it takes to cross the Gulf of Mexico. Proc Natl Acad Sci U S A 2015; 112:E6331-8. [PMID: 26578793 PMCID: PMC4655507 DOI: 10.1073/pnas.1503381112] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Approximately two thirds of migratory songbirds in eastern North America negotiate the Gulf of Mexico (GOM), where inclement weather coupled with no refueling or resting opportunities can be lethal. However, decisions made when navigating such features and their consequences remain largely unknown due to technological limitations of tracking small animals over large areas. We used automated radio telemetry to track three songbird species (Red-eyed Vireo, Swainson's Thrush, Wood Thrush) from coastal Alabama to the northern Yucatan Peninsula (YP) during fall migration. Detecting songbirds after crossing ∼1,000 km of open water allowed us to examine intrinsic (age, wing length, fat) and extrinsic (weather, date) variables shaping departure decisions, arrival at the YP, and crossing times. Large fat reserves and low humidity, indicative of beneficial synoptic weather patterns, favored southward departure across the Gulf. Individuals detected in the YP departed with large fat reserves and later in the fall with profitable winds, and flight durations (mean = 22.4 h) were positively related to wind profit. Age was not related to departure behavior, arrival, or travel time. However, vireos negotiated the GOM differently than thrushes, including different departure decisions, lower probability of detection in the YP, and longer crossing times. Defense of winter territories by thrushes but not vireos and species-specific foraging habits may explain the divergent migratory behaviors. Fat reserves appear extremely important to departure decisions and arrival in the YP. As habitat along the GOM is degraded, birds may be limited in their ability to acquire fat to cross the Gulf.
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Affiliation(s)
- Jill L Deppe
- Department of Biological Sciences, Eastern Illinois University, Charleston, IL 61920;
| | - Michael P Ward
- Department of Natural Resources and Environmental Sciences, University of Illinois, Urbana, IL 61801
| | - Rachel T Bolus
- Department of Natural Resources and Environmental Sciences, University of Illinois, Urbana, IL 61801; US Geological Survey, Northern Rocky Mountain Science Center, Bozeman, MT 59715
| | - Robert H Diehl
- US Geological Survey, Northern Rocky Mountain Science Center, Bozeman, MT 59715
| | - Antonio Celis-Murillo
- Department of Natural Resources and Environmental Sciences, University of Illinois, Urbana, IL 61801
| | - Theodore J Zenzal
- Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, MS 39406
| | - Frank R Moore
- Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, MS 39406
| | - Thomas J Benson
- Illinois Natural History Survey, University of Illinois, Champaign, IL 61820
| | - Jaclyn A Smolinsky
- Department of Entomology and Wildlife Ecology, University of Delaware, Newark, DE 19716
| | - Lynn N Schofield
- Department of Biological Sciences, Eastern Illinois University, Charleston, IL 61920
| | - David A Enstrom
- Illinois Natural History Survey, University of Illinois, Champaign, IL 61820
| | - Eben H Paxton
- US Geological Survey, Pacific Island Ecosystems Research Center, Hawaii National Park, HI 96718
| | - Gil Bohrer
- Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH 43210
| | - Tara A Beveroth
- Illinois Natural History Survey, University of Illinois, Champaign, IL 61820
| | - Arlo Raim
- Illinois Natural History Survey, University of Illinois, Champaign, IL 61820
| | - Renee L Obringer
- Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH 43210
| | - David Delaney
- Construction Engineering Research Laboratory, United States Army Corps of Engineers, Champaign, IL 61822
| | - William W Cochran
- Illinois Natural History Survey, University of Illinois, Champaign, IL 61820
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33
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Pap PL, Osváth G, Sándor K, Vincze O, Bărbos L, Marton A, Nudds RL, Vágási CI. Interspecific variation in the structural properties of flight feathers in birds indicates adaptation to flight requirements and habitat. Funct Ecol 2015. [DOI: 10.1111/1365-2435.12419] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Péter L. Pap
- MTA‐DE “Lendület” Behavioural Ecology Research Group Department of Evolutionary Zoology and Human Biology University of Debrecen Egyetem tér 1 Debrecen H–4032 Hungary
- Evolutionary Ecology Group Hungarian Department of Biology and Ecology Babeş‐Bolyai University Clinicilor Street 5–7 Cluj Napoca RO–400006 Romania
| | - Gergely Osváth
- Museum of Zoology Babeş‐Bolyai University Clinicilor Street 5–7 Cluj Napoca RO–400006 Romania
| | - Krisztina Sándor
- Evolutionary Ecology Group Hungarian Department of Biology and Ecology Babeş‐Bolyai University Clinicilor Street 5–7 Cluj Napoca RO–400006 Romania
| | - Orsolya Vincze
- MTA‐DE “Lendület” Behavioural Ecology Research Group Department of Evolutionary Zoology and Human Biology University of Debrecen Egyetem tér 1 Debrecen H–4032 Hungary
- Evolutionary Ecology Group Hungarian Department of Biology and Ecology Babeş‐Bolyai University Clinicilor Street 5–7 Cluj Napoca RO–400006 Romania
| | - Lőrinc Bărbos
- Evolutionary Ecology Group Hungarian Department of Biology and Ecology Babeş‐Bolyai University Clinicilor Street 5–7 Cluj Napoca RO–400006 Romania
- ‘Milvus Group’ Bird and Nature Protection Association Márton Áron street 9/BTîrgu Mureş RO–540058 Romania
| | - Attila Marton
- Evolutionary Ecology Group Hungarian Department of Biology and Ecology Babeş‐Bolyai University Clinicilor Street 5–7 Cluj Napoca RO–400006 Romania
- ‘Milvus Group’ Bird and Nature Protection Association Márton Áron street 9/BTîrgu Mureş RO–540058 Romania
| | - Robert L. Nudds
- Faculty of Life Sciences University of Manchester Manchester M13 9PT UK
| | - Csongor I. Vágási
- MTA‐DE “Lendület” Behavioural Ecology Research Group Department of Evolutionary Zoology and Human Biology University of Debrecen Egyetem tér 1 Debrecen H–4032 Hungary
- Evolutionary Ecology Group Hungarian Department of Biology and Ecology Babeş‐Bolyai University Clinicilor Street 5–7 Cluj Napoca RO–400006 Romania
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34
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Romanov MN, Farré M, Lithgow PE, Fowler KE, Skinner BM, O’Connor R, Fonseka G, Backström N, Matsuda Y, Nishida C, Houde P, Jarvis ED, Ellegren H, Burt DW, Larkin DM, Griffin DK. Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor. BMC Genomics 2014; 15:1060. [PMID: 25496766 PMCID: PMC4362836 DOI: 10.1186/1471-2164-15-1060] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 11/27/2014] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The availability of multiple avian genome sequence assemblies greatly improves our ability to define overall genome organization and reconstruct evolutionary changes. In birds, this has previously been impeded by a near intractable karyotype and relied almost exclusively on comparative molecular cytogenetics of only the largest chromosomes. Here, novel whole genome sequence information from 21 avian genome sequences (most newly assembled) made available on an interactive browser (Evolution Highway) was analyzed. RESULTS Focusing on the six best-assembled genomes allowed us to assemble a putative karyotype of the dinosaur ancestor for each chromosome. Reconstructing evolutionary events that led to each species' genome organization, we determined that the fastest rate of change occurred in the zebra finch and budgerigar, consistent with rapid speciation events in the Passeriformes and Psittaciformes. Intra- and interchromosomal changes were explained most parsimoniously by a series of inversions and translocations respectively, with breakpoint reuse being commonplace. Analyzing chicken and zebra finch, we found little evidence to support the hypothesis of an association of evolutionary breakpoint regions with recombination hotspots but some evidence to support the hypothesis that microchromosomes largely represent conserved blocks of synteny in the majority of the 21 species analyzed. All but one species showed the expected number of microchromosomal rearrangements predicted by the haploid chromosome count. Ostrich, however, appeared to retain an overall karyotype structure of 2n=80 despite undergoing a large number (26) of hitherto un-described interchromosomal changes. CONCLUSIONS Results suggest that mechanisms exist to preserve a static overall avian karyotype/genomic structure, including the microchromosomes, with widespread interchromosomal change occurring rarely (e.g., in ostrich and budgerigar lineages). Of the species analyzed, the chicken lineage appeared to have undergone the fewest changes compared to the dinosaur ancestor.
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Affiliation(s)
| | - Marta Farré
- />Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, NW1 0TU UK
| | - Pamela E Lithgow
- />School of Biosciences, University of Kent, Canterbury, CT2 7NJ UK
| | - Katie E Fowler
- />School of Biosciences, University of Kent, Canterbury, CT2 7NJ UK
- />School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, Kent CT1 1QU UK
| | - Benjamin M Skinner
- />Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP UK
| | - Rebecca O’Connor
- />School of Biosciences, University of Kent, Canterbury, CT2 7NJ UK
| | - Gothami Fonseka
- />School of Biosciences, University of Kent, Canterbury, CT2 7NJ UK
| | - Niclas Backström
- />Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Yoichi Matsuda
- />Laboratory of Animal Genetics, Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601 Japan
| | - Chizuko Nishida
- />Department of Natural History Sciences, Faculty of Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810 Japan
| | - Peter Houde
- />Department of Biology, New Mexico State University, Las Cruces, NM 88003 USA
| | - Erich D Jarvis
- />Department of Neurobiology, Duke University Medical Center, Box 3209, Durham, NC 27710 USA
| | - Hans Ellegren
- />Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - David W Burt
- />Department of Genomics and Genetics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, EH25 9PS UK
| | - Denis M Larkin
- />Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, NW1 0TU UK
| | - Darren K Griffin
- />School of Biosciences, University of Kent, Canterbury, CT2 7NJ UK
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35
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Jiang L, Li XN, Niu DK. Higher frequency of intron loss from the promoter proximally paused genes of Drosophila melanogaster. Fly (Austin) 2014; 8:120-5. [PMID: 25483256 DOI: 10.4161/fly.29489] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Although intron losses have been widely reported, it is not clear whether they are neutral and therefore random or driven by positive selection. Intron transcription and splicing are time-consuming and can delay the expression of its host gene. For genes that must be activated quickly to respond to physiological or stress signals, intron delay may be deleterious. Promoter proximally paused (PPP) genes are a group of rapidly expressed genes. To respond quickly to activation signals, they generally initiate transcription competently but stall after synthesizing a short RNA. In this study, performed in Drosophila melanogaster, the PPP genes were found to have a significantly higher rate of intron loss than control genes. However, further analysis did not find more significant shrinkage of intron size in PPP genes. Referring to previous studies on the rates of transcription and splicing and to the time saved by deletion of the introns from mouse gene Hes7, it is here suggested that transcription delay is comparable to splicing delay only when the intron is 28.5 kb or larger, which is greater in size than 95% of vertebrate introns, 99.5% of Drosophila introns, and all the annotated introns of Saccharomyces cerevisiae and Arabidopsis thaliana. Delays in intron splicing are probably a selective force, promoting intron loss from quickly expressed genes. In other genes, it may have been an exaptation during the emergency of developmental clocks.
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Affiliation(s)
- Li Jiang
- a MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development; College of Life Sciences; Beijing Normal University; Beijing, PR China
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36
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Yang L, Brunsfeld J, Scott L, Wichman H. Reviving the dead: history and reactivation of an extinct l1. PLoS Genet 2014; 10:e1004395. [PMID: 24968166 PMCID: PMC4072516 DOI: 10.1371/journal.pgen.1004395] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 04/07/2014] [Indexed: 11/18/2022] Open
Abstract
Although L1 sequences are present in the genomes of all placental mammals and marsupials examined to date, their activity was lost in the megabat family, Pteropodidae, ∼24 million years ago. To examine the characteristics of L1s prior to their extinction, we analyzed the evolutionary history of L1s in the genome of a megabat, Pteropus vampyrus, and found a pattern of periodic L1 expansion and quiescence. In contrast to the well-characterized L1s in human and mouse, megabat genomes have accommodated two or more simultaneously active L1 families throughout their evolutionary history, and major peaks of L1 deposition into the genome always involved multiple families. We compared the consensus sequences of the two major megabat L1 families at the time of their extinction to consensus L1s of a variety of mammalian species. Megabat L1s are comparable to the other mammalian L1s in terms of adenosine content and conserved amino acids in the open reading frames (ORFs). However, the intergenic region (IGR) of the reconstructed element from the more active family is dramatically longer than the IGR of well-characterized human and mouse L1s. We synthesized the reconstructed element from this L1 family and tested the ability of its components to support retrotransposition in a tissue culture assay. Both ORFs are capable of supporting retrotransposition, while the IGR is inhibitory to retrotransposition, especially when combined with either of the reconstructed ORFs. We dissected the inhibitory effect of the IGR by testing truncated and shuffled versions and found that length is a key factor, but not the only one affecting inhibition of retrotransposition. Although the IGR is inhibitory to retrotransposition, this inhibition does not account for the extinction of L1s in megabats. Overall, the evolution of the L1 sequence or the quiescence of L1 is unlikely the reason of L1 extinction.
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Affiliation(s)
- Lei Yang
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America
| | - John Brunsfeld
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - LuAnn Scott
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Holly Wichman
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America
- * E-mail:
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37
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Poelstra JW, Vijay N, Bossu CM, Lantz H, Ryll B, Muller I, Baglione V, Unneberg P, Wikelski M, Grabherr MG, Wolf JBW. The genomic landscape underlying phenotypic integrity in the face of gene flow in crows. Science 2014; 344:1410-4. [DOI: 10.1126/science.1253226] [Citation(s) in RCA: 411] [Impact Index Per Article: 41.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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38
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van Oers K, Santure AW, De Cauwer I, van Bers NEM, Crooijmans RPMA, Sheldon BC, Visser ME, Slate J, Groenen MAM. Replicated high-density genetic maps of two great tit populations reveal fine-scale genomic departures from sex-equal recombination rates. Heredity (Edinb) 2014; 112:307-16. [PMID: 24149651 PMCID: PMC3931172 DOI: 10.1038/hdy.2013.107] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 09/16/2013] [Indexed: 01/03/2023] Open
Abstract
Linking variation in quantitative traits to variation in the genome is an important, but challenging task in the study of life-history evolution. Linkage maps provide a valuable tool for the unravelling of such trait-gene associations. Moreover, they give insight into recombination landscapes and between-species karyotype evolution. Here we used genotype data, generated from a 10k single-nucleotide polymorphism (SNP) chip, of over 2000 individuals to produce high-density linkage maps of the great tit (Parus major), a passerine bird that serves as a model species for ecological and evolutionary questions. We created independent maps from two distinct populations: a captive F2-cross from The Netherlands (NL) and a wild population from the United Kingdom (UK). The two maps contained 6554 SNPs in 32 linkage groups, spanning 2010 cM and 1917 cM for the NL and UK populations, respectively, and were similar in size and marker order. Subtle levels of heterochiasmy within and between chromosomes were remarkably consistent between the populations, suggesting that the local departures from sex-equal recombination rates have evolved. This key and surprising result would have been impossible to detect if only one population was mapped. A comparison with zebra finch Taeniopygia guttata, chicken Gallus gallus and the green anole lizard Anolis carolinensis genomes provided further insight into the evolution of avian karyotypes.
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Affiliation(s)
- K van Oers
- Department of Animal Ecology, Netherlands
Institute of Ecology (NIOO-KNAW), Wageningen, The
Netherlands
| | - A W Santure
- Department of Animal and Plant Sciences,
University of Sheffield, Sheffield, UK
| | - I De Cauwer
- Department of Animal and Plant Sciences,
University of Sheffield, Sheffield, UK
- Laboratoire de Génétique et
Evolution des Populations Végétales, UMR CNRS 8198, Bâtiment SN2,
Université des Sciences et Technologies de Lille - Lille 1,
Villeneuve d'Ascq Cedex, France
| | - N EM van Bers
- Department of Animal Ecology, Netherlands
Institute of Ecology (NIOO-KNAW), Wageningen, The
Netherlands
- Animal Breeding and Genomics Centre,
Wageningen University, De Elst 1, Wageningen, The
Netherlands
| | - R PMA Crooijmans
- Animal Breeding and Genomics Centre,
Wageningen University, De Elst 1, Wageningen, The
Netherlands
| | - B C Sheldon
- Edward Grey Institute, Department of Zoology,
University of Oxford, Oxford, UK
| | - M E Visser
- Department of Animal Ecology, Netherlands
Institute of Ecology (NIOO-KNAW), Wageningen, The
Netherlands
| | - J Slate
- Department of Animal and Plant Sciences,
University of Sheffield, Sheffield, UK
| | - M AM Groenen
- Animal Breeding and Genomics Centre,
Wageningen University, De Elst 1, Wageningen, The
Netherlands
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39
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Wright NA, Gregory TR, Witt CC. Metabolic 'engines' of flight drive genome size reduction in birds. Proc Biol Sci 2014; 281:20132780. [PMID: 24478299 DOI: 10.1098/rspb.2013.2780] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The tendency for flying organisms to possess small genomes has been interpreted as evidence of natural selection acting on the physical size of the genome. Nonetheless, the flight-genome link and its mechanistic basis have yet to be well established by comparative studies within a volant clade. Is there a particular functional aspect of flight such as brisk metabolism, lift production or maneuverability that impinges on the physical genome? We measured genome sizes, wing dimensions and heart, flight muscle and body masses from a phylogenetically diverse set of bird species. In phylogenetically controlled analyses, we found that genome size was negatively correlated with relative flight muscle size and heart index (i.e. ratio of heart to body mass), but positively correlated with body mass and wing loading. The proportional masses of the flight muscles and heart were the most important parameters explaining variation in genome size in multivariate models. Hence, the metabolic intensity of powered flight appears to have driven genome size reduction in birds.
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Affiliation(s)
- Natalie A Wright
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, , Albuquerque, NM 87131, USA, Department of Integrative Biology, University of Guelph, , Guelph, Ontario, Canada , N1G 2W1
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40
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Smith JDL, Bickham JW, Gregory TR. Patterns of genome size diversity in bats (order Chiroptera). Genome 2013; 56:457-72. [PMID: 24168629 DOI: 10.1139/gen-2013-0046] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Despite being a group of particular interest in considering relationships between genome size and metabolic parameters, bats have not been well studied from this perspective. This study presents new estimates for 121 "microbat" species from 12 families and complements a previous study on members of the family Pteropodidae ("megabats"). The results confirm that diversity in genome size in bats is very limited even compared with other mammals, varying approximately 2-fold from 1.63 pg in Lophostoma carrikeri to 3.17 pg in Rhinopoma hardwickii and averaging only 2.35 pg ± 0.02 SE (versus 3.5 pg overall for mammals). However, contrary to some other vertebrate groups, and perhaps owing to the narrow range observed, genome size correlations were not apparent with any chromosomal, physiological, flight-related, developmental, or ecological characteristics within the order Chiroptera. Genome size is positively correlated with measures of body size in bats, though the strength of the relationships differs between pteropodids ("megabats") and nonpteropodids ("microbats").
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Affiliation(s)
- Jillian D L Smith
- a Department of Integrative Biology, University of Guelph, 50 Stone Road E., Guelph, ON N1G 2W1, Canada
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41
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Walton S, Hofmeyr MD, van der Horst G. Accurate automated quantitative imaging of tortoise erythrocytes using the NIS image analysis system. Biotech Histochem 2013; 88:242-9. [PMID: 23387424 DOI: 10.3109/10520295.2013.765594] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The standard method for assessing blood cell characteristics using an ocular micrometer is time-consuming and limited. We used the Nikon NIS Elements imaging software and May- Grünwald-Giemsa staining to determine whether automated image analysis is suitable for rapid and accurate quantitative morphometry of erythrocytes. Blood was collected during four seasons from 126 geometric tortoises and the blood smears were evaluated for cell (C) and nuclear (N) characteristics of the erythrocytes. We measured area, length (L), width (W), perimeter, elongation and pixelation intensity, and calculated L/W and N/C areas. Erythrocyte size differed among cohorts; females, the larger sex, had smaller erythrocytes than either males or juveniles. Males had more elongated erythrocytes than females and erythrocytes of adults were more elongated than those of juveniles. Erythrocyte size and shape influence the efficiency of gas exchange owing to surface area to volume ratios, which are greater for small, elongated cells than for large, round cells. The high N/C ratio and low pixelation intensities of males and juveniles indicate that they may have had more immature erythrocytes in their circulation than females. The use of pixelation intensity to indicate the presence of immature erythrocytes was validated by seasonal differences that corresponded to the biology of the tortoises. Pixelation intensity was lowest in winter. We found that automated image analysis is a rapid and reliable method for determining cell size and shape, and it offers the potential for distinguishing among developmental stages that differ in staining intensity. The method should be useful for rapid health assessments, particularly of threatened species, and for comparative studies among different vertebrates.
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Affiliation(s)
- S Walton
- Departments of Biodiversity and Conservation Biology, Pretoria, South Africa
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42
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Nam K, Ellegren H. Recombination drives vertebrate genome contraction. PLoS Genet 2012; 8:e1002680. [PMID: 22570634 PMCID: PMC3342960 DOI: 10.1371/journal.pgen.1002680] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Accepted: 03/15/2012] [Indexed: 11/19/2022] Open
Abstract
Selective and/or neutral processes may govern variation in DNA content and, ultimately, genome size. The observation in several organisms of a negative correlation between recombination rate and intron size could be compatible with a neutral model in which recombination is mutagenic for length changes. We used whole-genome data on small insertions and deletions within transposable elements from chicken and zebra finch to demonstrate clear links between recombination rate and a number of attributes of reduced DNA content. Recombination rate was negatively correlated with the length of introns, transposable elements, and intergenic spacer and with the rate of short insertions. Importantly, it was positively correlated with gene density, the rate of short deletions, the deletion bias, and the net change in sequence length. All these observations point at a pattern of more condensed genome structure in regions of high recombination. Based on the observed rates of small insertions and deletions and assuming that these rates are representative for the whole genome, we estimate that the genome of the most recent common ancestor of birds and lizards has lost nearly 20% of its DNA content up until the present. Expansion of transposable elements can counteract the effect of deletions in an equilibrium mutation model; however, since the activity of transposable elements has been low in the avian lineage, the deletion bias is likely to have had a significant effect on genome size evolution in dinosaurs and birds, contributing to the maintenance of a small genome. We also demonstrate that most of the observed correlations between recombination rate and genome contraction parameters are seen in the human genome, including for segregating indel polymorphisms. Our data are compatible with a neutral model in which recombination drives vertebrate genome size evolution and gives no direct support for a role of natural selection in this process. One major implication from genetic work done several decades ago is that the genome contains a lot of sequences that do not constitute genes or other functional elements. The total amount of DNA—the genome size—is thus not necessarily an indicator of DNA complexity or organismal complexity, an observation often referred to as the C-value paradox (C-value being a measure of DNA content). What then is it that determines genome size? One model posits that the evolution of genome size is not a consequence of natural selection but is instead governed by the incidence and character of naturally occurring mutations that affect the length of DNA, a process that is not affected by selection. Here we present the results of an analysis of how recombination affects the size of avian and human genomes. We find strong evidence that the rate of recombination is a driving force of genome size evolution. In regions of the genome where recombination occurs frequently, the loss of DNA caused by small deletions is particularly pronounced. Our simulations show that the effect of such recombination-driven genome contraction can be profound over evolutionary time scales. These observations lead to a model in which recombination is mutagenic for length changes and that the incidence of deletions increases with increasing recombination rate. Although we cannot formally exclude that natural selection contributes to the observed relationship between recombination and genome contraction, we find no evidence to support such a scenario.
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Affiliation(s)
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
- * E-mail:
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43
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Organ CL, Brusatte SL, Stein K. Sauropod dinosaurs evolved moderately sized genomes unrelated to body size. Proc Biol Sci 2009; 276:4303-8. [PMID: 19793755 DOI: 10.1098/rspb.2009.1343] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Sauropodomorph dinosaurs include the largest land animals to have ever lived, some reaching up to 10 times the mass of an African elephant. Despite their status defining the upper range for body size in land animals, it remains unknown whether sauropodomorphs evolved larger-sized genomes than non-avian theropods, their sister taxon, or whether a relationship exists between genome size and body size in dinosaurs, two questions critical for understanding broad patterns of genome evolution in dinosaurs. Here we report inferences of genome size for 10 sauropodomorph taxa. The estimates are derived from a Bayesian phylogenetic generalized least squares approach that generates posterior distributions of regression models relating genome size to osteocyte lacunae volume in extant tetrapods. We estimate that the average genome size of sauropodomorphs was 2.02 pg (range of species means: 1.77-2.21 pg), a value in the upper range of extant birds (mean = 1.42 pg, range: 0.97-2.16 pg) and near the average for extant non-avian reptiles (mean = 2.24 pg, range: 1.05-5.44 pg). The results suggest that the variation in size and architecture of genomes in extinct dinosaurs was lower than the variation found in mammals. A substantial difference in genome size separates the two major clades within dinosaurs, Ornithischia (large genomes) and Saurischia (moderate to small genomes). We find no relationship between body size and estimated genome size in extinct dinosaurs, which suggests that neutral forces did not dominate the evolution of genome size in this group.
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Affiliation(s)
- Chris L Organ
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA.
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44
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Gregory TR, Andrews CB, McGuire JA, Witt CC. The smallest avian genomes are found in hummingbirds. Proc Biol Sci 2009; 276:3753-7. [PMID: 19656792 DOI: 10.1098/rspb.2009.1004] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
It has often been suggested that the genome sizes of birds are constrained relative to other tetrapods owing to the high metabolic demands of powered flight and the link between nuclear DNA content and red blood cell size. This hypothesis predicts that hummingbirds, which engage in energy-intensive hovering flight, will display especially constrained genomes even relative to other birds. We report genome size measurements for 37 species of hummingbirds that confirm this prediction. Our results suggest that genome size was reduced before the divergence of extant hummingbird lineages, and that only minimal additional reduction occurred during hummingbird diversification. Unlike in some other avian taxa, the small amount of variation observed within hummingbirds is not explained by variation in respiratory and flight-related parameters. Unexpectedly, genome size appears to have increased in four unrelated hummingbird species whose distributions are centred on humid forests of the upper-tropical elevational zone on the eastern slope of the Andes. This suggests that the secondary expansion of the genome may have been mediated by biogeographical and demographic effects.
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Affiliation(s)
- T Ryan Gregory
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada.
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45
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Revell LJ. Size-correction and principal components for interspecific comparative studies. Evolution 2009; 63:3258-68. [PMID: 19663993 DOI: 10.1111/j.1558-5646.2009.00804.x] [Citation(s) in RCA: 532] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phylogenetic methods for the analysis of species data are widely used in evolutionary studies. However, preliminary data transformations and data reduction procedures (such as a size-correction and principal components analysis, PCA) are often performed without first correcting for nonindependence among the observations for species. In the present short comment and attached R and MATLAB code, I provide an overview of statistically correct procedures for phylogenetic size-correction and PCA. I also show that ignoring phylogeny in preliminary transformations can result in significantly elevated variance and type I error in our statistical estimators, even if subsequent analysis of the transformed data is performed using phylogenetic methods. This means that ignoring phylogeny during preliminary data transformations can possibly lead to spurious results in phylogenetic statistical analyses of species data.
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Affiliation(s)
- Liam J Revell
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
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46
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Smith JD, Gregory TR. The genome sizes of megabats (Chiroptera: Pteropodidae) are remarkably constrained. Biol Lett 2009; 5:347-51. [PMID: 19324635 PMCID: PMC2679926 DOI: 10.1098/rsbl.2009.0016] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2009] [Revised: 02/05/2009] [Accepted: 02/05/2009] [Indexed: 11/12/2022] Open
Abstract
It has long been recognized that bats and birds contain less DNA in their genomes than their non-flying relatives. It has been suggested that this relates to the high metabolic demands of powered flight, a notion that is supported by the fact that pterosaurs also appear to have exhibited small genomes. Given the long-standing interest in this question, it is surprising that almost no data have been presented regarding genome size diversity among megabats (family Pteropodidae). The present study provides genome size estimates for 43 species of megabats in an effort to fill this gap and to test the hypothesis that all bats, and not just microbats, possess small genomes. Intriguingly, megabats appear to be even more constrained in terms of genome size than the members of other bat families.
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Affiliation(s)
| | - T. Ryan Gregory
- Department of Integrative Biology, University of GuelphGuelph, Ontario, Canada N1G 2W1
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47
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Ardila‐Garcia AM, Gregory TR. An exploration of genome size diversity in dragonflies and damselflies (Insecta: Odonata). J Zool (1987) 2009. [DOI: 10.1111/j.1469-7998.2009.00557.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - T. R. Gregory
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
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48
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Organ CL, Shedlock AM. Palaeogenomics of pterosaurs and the evolution of small genome size in flying vertebrates. Biol Lett 2009; 5:47-50. [PMID: 18940771 DOI: 10.1098/rsbl.2008.0491] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The two living groups of flying vertebrates, birds and bats, both have constricted genome sizes compared with their close relatives. But nothing is known about the genomic characteristics of pterosaurs, which took to the air over 70 Myr before birds and were the first group of vertebrates to evolve powered flight. Here, we estimate genome size for four species of pterosaurs and seven species of basal archosauromorphs using a Bayesian comparative approach. Our results suggest that small genomes commonly associated with flight in bats and birds also evolved in pterosaurs, and that the rate of genome-size evolution is proportional to genome size within amniotes, with the fastest rates occurring in lineages with the largest genomes. We examine the role that drift may have played in the evolution of genome size within tetrapods by testing for correlated evolution between genome size and body size, but find no support for this hypothesis. By contrast, we find evidence suggesting that a combination of adaptation and phylogenetic inertia best explains the correlated evolution of flight and genome-size contraction. These results suggest that small genome/cell size evolved prior to or concurrently with flight in pterosaurs. We predict that, similar to the pattern seen in theropod dinosaurs, genome-size contraction preceded flight in pterosaurs and bats.
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Affiliation(s)
- Chris L Organ
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA.
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49
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Gillis GB. SMALL GENOMES TAKE FLIGHT. J Exp Biol 2009. [DOI: 10.1242/jeb.021659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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50
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Andrews CB, Gregory TR. Genome size is inversely correlated with relative brain size in parrots and cockatoos. Genome 2009; 52:261-7. [DOI: 10.1139/g09-003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Genome size (haploid nuclear DNA content) has been found to correlate positively with cell size and negatively with cell division rate in a variety of taxa. These cytological relationships manifest in various ways at the organism level, for example, in terms of body size, metabolic rate, or developmental rate, depending on the biology of the organisms. In birds, it has been suggested that high metabolic rate and strong flight ability are linked to small genome size. However, it was also hypothesized that the exceptional cognitive abilities of birds may impose additional constraints on genome size through effects on neuron size and differentiation, as has been observed in amphibians. To test this hypothesis, a comparative analysis was made between genome size, cell (erythrocyte) size, and brain size in 54 species of parrots and cockatoos (order Psittaciformes, family Psittacidae). Relative brain volume, which is taken as an indicator of investment in brain tissue and is widely correlated with behavioural and ecological traits, was found to correlate inversely with genome size. Several possible and mutually compatible explanations for this relationship are described.
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Affiliation(s)
- Chandler B. Andrews
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - T. Ryan Gregory
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
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