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Makova KD, Pickett BD, Harris RS, Hartley GA, Cechova M, Pal K, Nurk S, Yoo D, Li Q, Hebbar P, McGrath BC, Antonacci F, Aubel M, Biddanda A, Borchers M, Bomberg E, Bouffard GG, Brooks SY, Carbone L, Carrel L, Carroll A, Chang PC, Chin CS, Cook DE, Craig SJ, de Gennaro L, Diekhans M, Dutra A, Garcia GH, Grady PG, Green RE, Haddad D, Hallast P, Harvey WT, Hickey G, Hillis DA, Hoyt SJ, Jeong H, Kamali K, Kosakovsky Pond SL, LaPolice TM, Lee C, Lewis AP, Loh YHE, Masterson P, McCoy RC, Medvedev P, Miga KH, Munson KM, Pak E, Paten B, Pinto BJ, Potapova T, Rhie A, Rocha JL, Ryabov F, Ryder OA, Sacco S, Shafin K, Shepelev VA, Slon V, Solar SJ, Storer JM, Sudmant PH, Sweetalana, Sweeten A, Tassia MG, Thibaud-Nissen F, Ventura M, Wilson MA, Young AC, Zeng H, Zhang X, Szpiech ZA, Huber CD, Gerton JL, Yi SV, Schatz MC, Alexandrov IA, Koren S, O’Neill RJ, Eichler E, Phillippy AM. The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes. bioRxiv 2023:2023.11.30.569198. [PMID: 38077089 PMCID: PMC10705393 DOI: 10.1101/2023.11.30.569198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
Apes possess two sex chromosomes-the male-specific Y and the X shared by males and females. The Y chromosome is crucial for male reproduction, with deletions linked to infertility. The X chromosome carries genes vital for reproduction and cognition. Variation in mating patterns and brain function among great apes suggests corresponding differences in their sex chromosome structure and evolution. However, due to their highly repetitive nature and incomplete reference assemblies, ape sex chromosomes have been challenging to study. Here, using the state-of-the-art experimental and computational methods developed for the telomere-to-telomere (T2T) human genome, we produced gapless, complete assemblies of the X and Y chromosomes for five great apes (chimpanzee, bonobo, gorilla, Bornean and Sumatran orangutans) and a lesser ape, the siamang gibbon. These assemblies completely resolved ampliconic, palindromic, and satellite sequences, including the entire centromeres, allowing us to untangle the intricacies of ape sex chromosome evolution. We found that, compared to the X, ape Y chromosomes vary greatly in size and have low alignability and high levels of structural rearrangements. This divergence on the Y arises from the accumulation of lineage-specific ampliconic regions and palindromes (which are shared more broadly among species on the X) and from the abundance of transposable elements and satellites (which have a lower representation on the X). Our analysis of Y chromosome genes revealed lineage-specific expansions of multi-copy gene families and signatures of purifying selection. In summary, the Y exhibits dynamic evolution, while the X is more stable. Finally, mapping short-read sequencing data from >100 great ape individuals revealed the patterns of diversity and selection on their sex chromosomes, demonstrating the utility of these reference assemblies for studies of great ape evolution. These complete sex chromosome assemblies are expected to further inform conservation genetics of nonhuman apes, all of which are endangered species.
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Affiliation(s)
| | - Brandon D. Pickett
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Monika Cechova
- University of California Santa Cruz, Santa Cruz, CA, USA
| | - Karol Pal
- Penn State University, University Park, PA, USA
| | - Sergey Nurk
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - DongAhn Yoo
- University of Washington School of Medicine, Seattle, WA, USA
| | - Qiuhui Li
- Johns Hopkins University, Baltimore, MD, USA
| | - Prajna Hebbar
- University of California Santa Cruz, Santa Cruz, CA, USA
| | | | | | | | | | | | - Erich Bomberg
- University of Münster, Münster, Germany
- MPI for Developmental Biology, Tübingen, Germany
| | - Gerard G. Bouffard
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Shelise Y. Brooks
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lucia Carbone
- Oregon Health & Science University, Portland, OR, USA
- Oregon National Primate Research Center, Hillsboro, OR, USA
| | - Laura Carrel
- Penn State University School of Medicine, Hershey, PA, USA
| | | | | | - Chen-Shan Chin
- Foundation of Biological Data Sciences, Belmont, CA, USA
| | | | | | | | - Mark Diekhans
- University of California Santa Cruz, Santa Cruz, CA, USA
| | - Amalia Dutra
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gage H. Garcia
- University of Washington School of Medicine, Seattle, WA, USA
| | | | | | - Diana Haddad
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Pille Hallast
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Glenn Hickey
- University of California Santa Cruz, Santa Cruz, CA, USA
| | - David A. Hillis
- University of California Santa Barbara, Santa Barbara, CA, USA
| | | | - Hyeonsoo Jeong
- University of Washington School of Medicine, Seattle, WA, USA
| | | | | | | | - Charles Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | | | - Patrick Masterson
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Karen H. Miga
- University of California Santa Cruz, Santa Cruz, CA, USA
| | | | - Evgenia Pak
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Benedict Paten
- University of California Santa Cruz, Santa Cruz, CA, USA
| | | | | | - Arang Rhie
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Fedor Ryabov
- Masters Program in National Research University Higher School of Economics, Moscow, Russia
| | | | - Samuel Sacco
- University of California Santa Cruz, Santa Cruz, CA, USA
| | | | | | | | - Steven J. Solar
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Sweetalana
- Penn State University, University Park, PA, USA
| | - Alex Sweeten
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Johns Hopkins University, Baltimore, MD, USA
| | | | - Françoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Alice C. Young
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Xinru Zhang
- Penn State University, University Park, PA, USA
| | | | | | | | - Soojin V. Yi
- University of California Santa Barbara, Santa Barbara, CA, USA
| | | | | | - Sergey Koren
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Evan Eichler
- University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Adam M. Phillippy
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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Taylor DJ, Chhetri SB, Tassia MG, Biddanda A, Battle A, McCoy RC. Sources of gene expression variation in a globally diverse human cohort. bioRxiv 2023:2023.11.04.565639. [PMID: 37965206 PMCID: PMC10635147 DOI: 10.1101/2023.11.04.565639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Genetic variation influencing gene expression and splicing is a key source of phenotypic diversity. Though invaluable, studies investigating these links in humans have been strongly biased toward participants of European ancestries, diminishing generalizability and hindering evolutionary research. To address these limitations, we developed MAGE, an open-access RNA-seq data set of lymphoblastoid cell lines from 731 individuals from the 1000 Genomes Project spread across 5 continental groups and 26 populations. Most variation in gene expression (92%) and splicing (95%) was distributed within versus between populations, mirroring variation in DNA sequence. We mapped associations between genetic variants and expression and splicing of nearby genes (cis-eQTLs and cis-sQTLs, respective), identifying >15,000 putatively causal eQTLs and >16,000 putatively causal sQTLs that are enriched for relevant epigenomic signatures. These include 1310 eQTLs and 1657 sQTLs that are largely private to previously underrepresented populations. Our data further indicate that the magnitude and direction of causal eQTL effects are highly consistent across populations and that apparent "population-specific" effects observed in previous studies were largely driven by low resolution or additional independent eQTLs of the same genes that were not detected. Together, our study expands understanding of gene expression diversity across human populations and provides an inclusive resource for studying the evolution and function of human genomes.
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Affiliation(s)
- Dylan J. Taylor
- Department of Biology, Johns Hopkins University, Baltimore MD, USA
| | - Surya B. Chhetri
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore MD, USA
| | | | - Arjun Biddanda
- Department of Biology, Johns Hopkins University, Baltimore MD, USA
| | - Alexis Battle
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore MD, USA
- Department of Computer Science, Johns Hopkins University, Baltimore MD, USA
- Department of Genetic Medicine, Johns Hopkins University, Baltimore MD, USA
- Malone Center for Engineering in Healthcare, Johns Hopkins University, Baltimore MD, USA
| | - Rajiv C. McCoy
- Department of Biology, Johns Hopkins University, Baltimore MD, USA
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DeBoy EA, Tassia MG, Schratz KE, Yan SM, Cosner ZL, McNally EJ, Gable DL, Xiang Z, Lombard DB, Antonarakis ES, Gocke CD, McCoy RC, Armanios M. Familial Clonal Hematopoiesis in a Long Telomere Syndrome. N Engl J Med 2023; 388:2422-2433. [PMID: 37140166 PMCID: PMC10501156 DOI: 10.1056/nejmoa2300503] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
BACKGROUND Telomere shortening is a well-characterized cellular aging mechanism, and short telomere syndromes cause age-related disease. However, whether long telomere length is advantageous is poorly understood. METHODS We examined the clinical and molecular features of aging and cancer in persons carrying heterozygous loss-of-function mutations in the telomere-related gene POT1 and noncarrier relatives. RESULTS A total of 17 POT1 mutation carriers and 21 noncarrier relatives were initially included in the study, and a validation cohort of 6 additional mutation carriers was subsequently recruited. A majority of the POT1 mutation carriers with telomere length evaluated (9 of 13) had long telomeres (>99th percentile). POT1 mutation carriers had a range of benign and malignant neoplasms involving epithelial, mesenchymal, and neuronal tissues in addition to B- and T-cell lymphoma and myeloid cancers. Five of 18 POT1 mutation carriers (28%) had T-cell clonality, and 8 of 12 (67%) had clonal hematopoiesis of indeterminate potential. A predisposition to clonal hematopoiesis had an autosomal dominant pattern of inheritance, as well as penetrance that increased with age; somatic DNMT3A and JAK2 hotspot mutations were common. These and other somatic driver mutations probably arose in the first decades of life, and their lineages secondarily accumulated a higher mutation burden characterized by a clocklike signature. Successive generations showed genetic anticipation (i.e., an increasingly early onset of disease). In contrast to noncarrier relatives, who had the typical telomere shortening with age, POT1 mutation carriers maintained telomere length over the course of 2 years. CONCLUSIONS POT1 mutations associated with long telomere length conferred a predisposition to a familial clonal hematopoiesis syndrome that was associated with a range of benign and malignant solid neoplasms. The risk of these phenotypes was mediated by extended cellular longevity and by the capacity to maintain telomeres over time. (Funded by the National Institutes of Health and others.).
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Affiliation(s)
- Emily A DeBoy
- From the Departments of Oncology (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., E.S.A., C.D.G., M.A.), Pathology (C.D.G., M.A.), and Genetic Medicine (M.A.), the Medical Scientist Training Program (E.A.D.), the Telomere Center (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., M.A.), and Sidney Kimmel Comprehensive Cancer Center (K.E.S., E.S.A., C.D.G., M.A.), Johns Hopkins University School of Medicine, and the Department of Biology, Krieger School of Arts and Sciences, Johns Hopkins University (M.G.T., S.M.Y., R.C.M.) - both in Baltimore; the Child Neurology Residency Program, Boston Children's Hospital, Boston (D.L.G.); the Department of Pathology and Laboratory Medicine, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami (D.B.L.); and the Division of Hematology, Oncology, and Transplantation, University of Minnesota Masonic Cancer Center, Minneapolis (E.S.A.)
| | - Michael G Tassia
- From the Departments of Oncology (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., E.S.A., C.D.G., M.A.), Pathology (C.D.G., M.A.), and Genetic Medicine (M.A.), the Medical Scientist Training Program (E.A.D.), the Telomere Center (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., M.A.), and Sidney Kimmel Comprehensive Cancer Center (K.E.S., E.S.A., C.D.G., M.A.), Johns Hopkins University School of Medicine, and the Department of Biology, Krieger School of Arts and Sciences, Johns Hopkins University (M.G.T., S.M.Y., R.C.M.) - both in Baltimore; the Child Neurology Residency Program, Boston Children's Hospital, Boston (D.L.G.); the Department of Pathology and Laboratory Medicine, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami (D.B.L.); and the Division of Hematology, Oncology, and Transplantation, University of Minnesota Masonic Cancer Center, Minneapolis (E.S.A.)
| | - Kristen E Schratz
- From the Departments of Oncology (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., E.S.A., C.D.G., M.A.), Pathology (C.D.G., M.A.), and Genetic Medicine (M.A.), the Medical Scientist Training Program (E.A.D.), the Telomere Center (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., M.A.), and Sidney Kimmel Comprehensive Cancer Center (K.E.S., E.S.A., C.D.G., M.A.), Johns Hopkins University School of Medicine, and the Department of Biology, Krieger School of Arts and Sciences, Johns Hopkins University (M.G.T., S.M.Y., R.C.M.) - both in Baltimore; the Child Neurology Residency Program, Boston Children's Hospital, Boston (D.L.G.); the Department of Pathology and Laboratory Medicine, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami (D.B.L.); and the Division of Hematology, Oncology, and Transplantation, University of Minnesota Masonic Cancer Center, Minneapolis (E.S.A.)
| | - Stephanie M Yan
- From the Departments of Oncology (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., E.S.A., C.D.G., M.A.), Pathology (C.D.G., M.A.), and Genetic Medicine (M.A.), the Medical Scientist Training Program (E.A.D.), the Telomere Center (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., M.A.), and Sidney Kimmel Comprehensive Cancer Center (K.E.S., E.S.A., C.D.G., M.A.), Johns Hopkins University School of Medicine, and the Department of Biology, Krieger School of Arts and Sciences, Johns Hopkins University (M.G.T., S.M.Y., R.C.M.) - both in Baltimore; the Child Neurology Residency Program, Boston Children's Hospital, Boston (D.L.G.); the Department of Pathology and Laboratory Medicine, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami (D.B.L.); and the Division of Hematology, Oncology, and Transplantation, University of Minnesota Masonic Cancer Center, Minneapolis (E.S.A.)
| | - Zoe L Cosner
- From the Departments of Oncology (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., E.S.A., C.D.G., M.A.), Pathology (C.D.G., M.A.), and Genetic Medicine (M.A.), the Medical Scientist Training Program (E.A.D.), the Telomere Center (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., M.A.), and Sidney Kimmel Comprehensive Cancer Center (K.E.S., E.S.A., C.D.G., M.A.), Johns Hopkins University School of Medicine, and the Department of Biology, Krieger School of Arts and Sciences, Johns Hopkins University (M.G.T., S.M.Y., R.C.M.) - both in Baltimore; the Child Neurology Residency Program, Boston Children's Hospital, Boston (D.L.G.); the Department of Pathology and Laboratory Medicine, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami (D.B.L.); and the Division of Hematology, Oncology, and Transplantation, University of Minnesota Masonic Cancer Center, Minneapolis (E.S.A.)
| | - Emily J McNally
- From the Departments of Oncology (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., E.S.A., C.D.G., M.A.), Pathology (C.D.G., M.A.), and Genetic Medicine (M.A.), the Medical Scientist Training Program (E.A.D.), the Telomere Center (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., M.A.), and Sidney Kimmel Comprehensive Cancer Center (K.E.S., E.S.A., C.D.G., M.A.), Johns Hopkins University School of Medicine, and the Department of Biology, Krieger School of Arts and Sciences, Johns Hopkins University (M.G.T., S.M.Y., R.C.M.) - both in Baltimore; the Child Neurology Residency Program, Boston Children's Hospital, Boston (D.L.G.); the Department of Pathology and Laboratory Medicine, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami (D.B.L.); and the Division of Hematology, Oncology, and Transplantation, University of Minnesota Masonic Cancer Center, Minneapolis (E.S.A.)
| | - Dustin L Gable
- From the Departments of Oncology (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., E.S.A., C.D.G., M.A.), Pathology (C.D.G., M.A.), and Genetic Medicine (M.A.), the Medical Scientist Training Program (E.A.D.), the Telomere Center (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., M.A.), and Sidney Kimmel Comprehensive Cancer Center (K.E.S., E.S.A., C.D.G., M.A.), Johns Hopkins University School of Medicine, and the Department of Biology, Krieger School of Arts and Sciences, Johns Hopkins University (M.G.T., S.M.Y., R.C.M.) - both in Baltimore; the Child Neurology Residency Program, Boston Children's Hospital, Boston (D.L.G.); the Department of Pathology and Laboratory Medicine, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami (D.B.L.); and the Division of Hematology, Oncology, and Transplantation, University of Minnesota Masonic Cancer Center, Minneapolis (E.S.A.)
| | - Zhimin Xiang
- From the Departments of Oncology (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., E.S.A., C.D.G., M.A.), Pathology (C.D.G., M.A.), and Genetic Medicine (M.A.), the Medical Scientist Training Program (E.A.D.), the Telomere Center (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., M.A.), and Sidney Kimmel Comprehensive Cancer Center (K.E.S., E.S.A., C.D.G., M.A.), Johns Hopkins University School of Medicine, and the Department of Biology, Krieger School of Arts and Sciences, Johns Hopkins University (M.G.T., S.M.Y., R.C.M.) - both in Baltimore; the Child Neurology Residency Program, Boston Children's Hospital, Boston (D.L.G.); the Department of Pathology and Laboratory Medicine, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami (D.B.L.); and the Division of Hematology, Oncology, and Transplantation, University of Minnesota Masonic Cancer Center, Minneapolis (E.S.A.)
| | - David B Lombard
- From the Departments of Oncology (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., E.S.A., C.D.G., M.A.), Pathology (C.D.G., M.A.), and Genetic Medicine (M.A.), the Medical Scientist Training Program (E.A.D.), the Telomere Center (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., M.A.), and Sidney Kimmel Comprehensive Cancer Center (K.E.S., E.S.A., C.D.G., M.A.), Johns Hopkins University School of Medicine, and the Department of Biology, Krieger School of Arts and Sciences, Johns Hopkins University (M.G.T., S.M.Y., R.C.M.) - both in Baltimore; the Child Neurology Residency Program, Boston Children's Hospital, Boston (D.L.G.); the Department of Pathology and Laboratory Medicine, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami (D.B.L.); and the Division of Hematology, Oncology, and Transplantation, University of Minnesota Masonic Cancer Center, Minneapolis (E.S.A.)
| | - Emmanuel S Antonarakis
- From the Departments of Oncology (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., E.S.A., C.D.G., M.A.), Pathology (C.D.G., M.A.), and Genetic Medicine (M.A.), the Medical Scientist Training Program (E.A.D.), the Telomere Center (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., M.A.), and Sidney Kimmel Comprehensive Cancer Center (K.E.S., E.S.A., C.D.G., M.A.), Johns Hopkins University School of Medicine, and the Department of Biology, Krieger School of Arts and Sciences, Johns Hopkins University (M.G.T., S.M.Y., R.C.M.) - both in Baltimore; the Child Neurology Residency Program, Boston Children's Hospital, Boston (D.L.G.); the Department of Pathology and Laboratory Medicine, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami (D.B.L.); and the Division of Hematology, Oncology, and Transplantation, University of Minnesota Masonic Cancer Center, Minneapolis (E.S.A.)
| | - Christopher D Gocke
- From the Departments of Oncology (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., E.S.A., C.D.G., M.A.), Pathology (C.D.G., M.A.), and Genetic Medicine (M.A.), the Medical Scientist Training Program (E.A.D.), the Telomere Center (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., M.A.), and Sidney Kimmel Comprehensive Cancer Center (K.E.S., E.S.A., C.D.G., M.A.), Johns Hopkins University School of Medicine, and the Department of Biology, Krieger School of Arts and Sciences, Johns Hopkins University (M.G.T., S.M.Y., R.C.M.) - both in Baltimore; the Child Neurology Residency Program, Boston Children's Hospital, Boston (D.L.G.); the Department of Pathology and Laboratory Medicine, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami (D.B.L.); and the Division of Hematology, Oncology, and Transplantation, University of Minnesota Masonic Cancer Center, Minneapolis (E.S.A.)
| | - Rajiv C McCoy
- From the Departments of Oncology (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., E.S.A., C.D.G., M.A.), Pathology (C.D.G., M.A.), and Genetic Medicine (M.A.), the Medical Scientist Training Program (E.A.D.), the Telomere Center (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., M.A.), and Sidney Kimmel Comprehensive Cancer Center (K.E.S., E.S.A., C.D.G., M.A.), Johns Hopkins University School of Medicine, and the Department of Biology, Krieger School of Arts and Sciences, Johns Hopkins University (M.G.T., S.M.Y., R.C.M.) - both in Baltimore; the Child Neurology Residency Program, Boston Children's Hospital, Boston (D.L.G.); the Department of Pathology and Laboratory Medicine, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami (D.B.L.); and the Division of Hematology, Oncology, and Transplantation, University of Minnesota Masonic Cancer Center, Minneapolis (E.S.A.)
| | - Mary Armanios
- From the Departments of Oncology (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., E.S.A., C.D.G., M.A.), Pathology (C.D.G., M.A.), and Genetic Medicine (M.A.), the Medical Scientist Training Program (E.A.D.), the Telomere Center (E.A.D., K.E.S., Z.L.C., E.J.M., Z.X., M.A.), and Sidney Kimmel Comprehensive Cancer Center (K.E.S., E.S.A., C.D.G., M.A.), Johns Hopkins University School of Medicine, and the Department of Biology, Krieger School of Arts and Sciences, Johns Hopkins University (M.G.T., S.M.Y., R.C.M.) - both in Baltimore; the Child Neurology Residency Program, Boston Children's Hospital, Boston (D.L.G.); the Department of Pathology and Laboratory Medicine, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami (D.B.L.); and the Division of Hematology, Oncology, and Transplantation, University of Minnesota Masonic Cancer Center, Minneapolis (E.S.A.)
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Vandepas LE, Tassia MG, Halanych KM, Amemiya CT. Unexpected Distribution of Chitin and Chitin Synthase across Soft-Bodied Cnidarians. Biomolecules 2023; 13:biom13050777. [PMID: 37238647 DOI: 10.3390/biom13050777] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/19/2023] [Accepted: 04/19/2023] [Indexed: 05/28/2023] Open
Abstract
Cnidarians are commonly recognized as sea jellies, corals, or complex colonies such as the Portuguese man-of-war. While some cnidarians possess rigid internal calcareous skeletons (e.g., corals), many are soft-bodied. Intriguingly, genes coding for the chitin-biosynthetic enzyme, chitin synthase (CHS), were recently identified in the model anemone Nematostella vectensis, a species lacking hard structures. Here we report the prevalence and diversity of CHS across Cnidaria and show that cnidarian chitin synthase genes display diverse protein domain organizations. We found that CHS is expressed in cnidarian species and/or developmental stages with no reported chitinous or rigid morphological structures. Chitin affinity histochemistry indicates that chitin is present in soft tissues of some scyphozoan and hydrozoan medusae. To further elucidate the biology of chitin in cnidarian soft tissues, we focused on CHS expression in N. vectensis. Spatial expression data show that three CHS orthologs are differentially expressed in Nematostella embryos and larvae during development, suggesting that chitin has an integral role in the biology of this species. Understanding how a non-bilaterian lineage such as Cnidaria employs chitin may provide new insight into hitherto unknown functions of polysaccharides in animals, as well as their role in the evolution of biological novelty.
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Affiliation(s)
- Lauren E Vandepas
- Benaroya Research Institute at Virginia Mason, Seattle, WA 98101, USA
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Michael G Tassia
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Kenneth M Halanych
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
- Departments of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC 28403, USA
| | - Chris T Amemiya
- Department of Molecular and Cell Biology, University of California at Merced, Merced, CA 95343, USA
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Tassia MG, Hallowell HA, Waits DS, Range RC, Lowe CJ, Graze RM, Schwartz EH, Halanych KM. Induced immune reaction in the acorn worm, Saccoglossus kowalevskii, informs the evolution of antiviral immunity. Mol Biol Evol 2023; 40:7146702. [PMID: 37116212 DOI: 10.1093/molbev/msad097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 03/27/2023] [Accepted: 04/24/2023] [Indexed: 04/30/2023] Open
Abstract
Evolutionary perspectives on the deployment of immune factors following infection have been shaped by studies on a limited number of biomedical model systems with a heavy emphasis on vertebrate species. Though their contributions to contemporary immunology cannot be understated, a broader phylogenetic perspective is needed to understand the evolution of immune systems across Metazoa. In our study, we leverage differential gene expression analyses to identify genes implicated in the antiviral immune response of the acorn worm hemichordate, Saccoglossus kowalevskii, and place them in the context of immunity evolution within deuterostomes - the animal clade composed of chordates, hemichordates, and echinoderms. Following acute exposure to the synthetic viral dsRNA analog, poly(I:C), we show that S. kowalevskii responds by regulating the transcription of genes associated with canonical innate immunity signaling pathways (e.g., NF-κB and IRF signaling) and metabolic processes (e.g., lipid metabolism), as well as many genes without clear evidence of orthology with those of model species. Aggregated across all experimental time point contrasts, we identify 423 genes that are differentially expressed in response to poly(I:C). We also identify 147 genes with altered temporal patterns of expression in response to immune challenge. By characterizing the molecular toolkit involved in hemichordate antiviral immunity, our findings provide vital evolutionary context for understanding the origins of immune systems within Deuterostomia.
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Affiliation(s)
- Michael G Tassia
- Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Haley A Hallowell
- Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Damien S Waits
- Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA
- Center for Marine Science, University of North Carolina Wilmington, NC, 28409, USA
| | - Ryan C Range
- Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Christopher J Lowe
- Hopkins Marine Station, Stanford University, Pacific Grove, CA 93950, USA
| | - Rita M Graze
- Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA
| | | | - Kenneth M Halanych
- Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA
- Center for Marine Science, University of North Carolina Wilmington, NC, 28409, USA
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Tassia MG, David KT, Townsend JP, Halanych KM. TIAMMAt: Leveraging biodiversity to revise protein domain models, evidence from innate immunity. Mol Biol Evol 2021; 38:5806-5818. [PMID: 34459919 PMCID: PMC8662601 DOI: 10.1093/molbev/msab258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Sequence annotation is fundamental for studying the evolution of protein families, particularly when working with nonmodel species. Given the rapid, ever-increasing number of species receiving high-quality genome sequencing, accurate domain modeling that is representative of species diversity is crucial for understanding protein family sequence evolution and their inferred function(s). Here, we describe a bioinformatic tool called Taxon-Informed Adjustment of Markov Model Attributes (TIAMMAt) which revises domain profile hidden Markov models (HMMs) by incorporating homologous domain sequences from underrepresented and nonmodel species. Using innate immunity pathways as a case study, we show that revising profile HMM parameters to directly account for variation in homologs among underrepresented species provides valuable insight into the evolution of protein families. Following adjustment by TIAMMAt, domain profile HMMs exhibit changes in their per-site amino acid state emission probabilities and insertion/deletion probabilities while maintaining the overall structure of the consensus sequence. Our results show that domain revision can heavily impact evolutionary interpretations for some families (i.e., NLR’s NACHT domain), whereas impact on other domains (e.g., rel homology domain and interferon regulatory factor domains) is minimal due to high levels of sequence conservation across the sampled phylogenetic depth (i.e., Metazoa). Importantly, TIAMMAt revises target domain models to reflect homologous sequence variation using the taxonomic distribution under consideration by the user. TIAMMAt’s flexibility to revise any subset of the Pfam database using a user-defined taxonomic pool will make it a valuable tool for future protein evolution studies, particularly when incorporating (or focusing) on nonmodel species.
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Affiliation(s)
- Michael G Tassia
- Department of Biological Sciences, Auburn University, Auburn, Alabama
| | - Kyle T David
- Department of Biological Sciences, Auburn University, Auburn, Alabama
| | - James P Townsend
- Whitman Center, Marine Biological Laboratory, Woods Hole, Massachusetts.,Department of Biology, Providence College, Providence, Rhode Island
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Li Y, Tassia MG, Waits DS, Bogantes VE, David KT, Halanych KM. Genomic adaptations to chemosymbiosis in the deep-sea seep-dwelling tubeworm Lamellibrachia luymesi. BMC Biol 2019; 17:91. [PMID: 31739792 PMCID: PMC6862839 DOI: 10.1186/s12915-019-0713-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 10/24/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Symbiotic relationships between microbes and their hosts are widespread and diverse, often providing protection or nutrients, and may be either obligate or facultative. However, the genetic mechanisms allowing organisms to maintain host-symbiont associations at the molecular level are still mostly unknown, and in the case of bacterial-animal associations, most genetic studies have focused on adaptations and mechanisms of the bacterial partner. The gutless tubeworms (Siboglinidae, Annelida) are obligate hosts of chemoautotrophic endosymbionts (except for Osedax which houses heterotrophic Oceanospirillales), which rely on the sulfide-oxidizing symbionts for nutrition and growth. Whereas several siboglinid endosymbiont genomes have been characterized, genomes of hosts and their adaptations to this symbiosis remain unexplored. RESULTS Here, we present and characterize adaptations of the cold seep-dwelling tubeworm Lamellibrachia luymesi, one of the longest-lived solitary invertebrates. We sequenced the worm's ~ 688-Mb haploid genome with an overall completeness of ~ 95% and discovered that L. luymesi lacks many genes essential in amino acid biosynthesis, obligating them to products provided by symbionts. Interestingly, the host is known to carry hydrogen sulfide to thiotrophic endosymbionts using hemoglobin. We also found an expansion of hemoglobin B1 genes, many of which possess a free cysteine residue which is hypothesized to function in sulfide binding. Contrary to previous analyses, the sulfide binding mediated by zinc ions is not conserved across tubeworms. Thus, the sulfide-binding mechanisms in sibgolinids need to be further explored, and B1 globins might play a more important role than previously thought. Our comparative analyses also suggest the Toll-like receptor pathway may be essential for tolerance/sensitivity to symbionts and pathogens. Several genes related to the worm's unique life history which are known to play important roles in apoptosis, cell proliferation, and aging were also identified. Last, molecular clock analyses based on phylogenomic data suggest modern siboglinid diversity originated in 267 mya (± 70 my) support previous hypotheses indicating a Late Mesozoic or Cenozoic origins of approximately 50-126 mya for vestimentiferans. CONCLUSIONS Here, we elucidate several specific adaptations along various molecular pathways that link phenome to genome to improve understanding of holobiont evolution. Our findings of adaptation in genomic mechanisms to reducing environments likely extend to other chemosynthetic symbiotic systems.
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Affiliation(s)
- Yuanning Li
- Department of Biological Sciences & Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, Auburn, AL, 36849, USA.
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect St, New Haven, CT, 06511, USA.
| | - Michael G Tassia
- Department of Biological Sciences & Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, Auburn, AL, 36849, USA
| | - Damien S Waits
- Department of Biological Sciences & Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, Auburn, AL, 36849, USA
| | - Viktoria E Bogantes
- Department of Biological Sciences & Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, Auburn, AL, 36849, USA
| | - Kyle T David
- Department of Biological Sciences & Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, Auburn, AL, 36849, USA
| | - Kenneth M Halanych
- Department of Biological Sciences & Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, Auburn, AL, 36849, USA.
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Abernath K, Banach M, Barela Hudgell MA, Blackmon LE, Breaux B, Brusch GA, Criscitiello MF, Deiss TC, Ding Y, Flowers E, Kenney E, Matz H, Modak T, Ott J, Rhoo KH, Rusnak ED, Shibasaki Y, Tassia MG, Wcisel D, Yaparla A. Conference report: The 14th congress of the International Society of Developmental and Comparative Immunology. Dev Comp Immunol 2019; 96:83-92. [PMID: 30851292 DOI: 10.1016/j.dci.2019.02.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 02/05/2019] [Accepted: 02/24/2019] [Indexed: 06/09/2023]
Affiliation(s)
- Kelsey Abernath
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA; Institute of Marine and Environmental Technology (IMET), Baltimore, MD, 21231, USA
| | - Maureen Banach
- Department of Immunology & Microbiology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Megan A Barela Hudgell
- Department of Biological Sciences, The George Washington University, Washington, DC, 20052, USA
| | - Laura E Blackmon
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, 39216, USA
| | - Breanna Breaux
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, 94305, USA
| | - George A Brusch
- School of Life Sciences, Arizona State University, Tempe, AZ, 85281, USA
| | - Michael F Criscitiello
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA.
| | - Thaddeus C Deiss
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Yang Ding
- Department of Pathobiology, University of Pennsylvania, School of Veterinary Medicine, Philadelphia, PA, 19104, USA
| | - Emily Flowers
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Eric Kenney
- Department of Biological Sciences, The George Washington University, Washington, DC, 20052, USA
| | - Hanover Matz
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA; Institute of Marine and Environmental Technology (IMET), Baltimore, MD, 21231, USA
| | - Tejashree Modak
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI, 02881, USA
| | - Jeannine Ott
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77845, USA
| | - Kun Hyoe Rhoo
- Department of Microbiology & Immunology, University of Rochester Medical Center, Rochester, NY, 14607, USA
| | - Elana D Rusnak
- Rosensteil School of Marine and Atmospheric Science, University of Miami, USA
| | - Yasuhiro Shibasaki
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Michael G Tassia
- Department of Biological Sciences, Auburn University, Auburn, AL, 36830, USA
| | - Dustin Wcisel
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC, 27607, USA
| | - Amulya Yaparla
- Department of Biological Sciences, The George Washington University, Washington, DC, 20052, USA
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Li Y, Kocot KM, Tassia MG, Cannon JT, Bernt M, Halanych KM. Mitogenomics Reveals a Novel Genetic Code in Hemichordata. Genome Biol Evol 2019; 11:29-40. [PMID: 30476024 PMCID: PMC6319601 DOI: 10.1093/gbe/evy254] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2018] [Indexed: 01/26/2023] Open
Abstract
The diverse array of codon reassignments demonstrate that the genetic code is not universal in nature. Exploring mechanisms underlying codon reassignment is critical for understanding the evolution of the genetic code during translation. Hemichordata, comprising worm-like Enteropneusta and colonial filter-feeding Pterobranchia, is the sister taxon of echinoderms and is more distantly related to chordates. However, only a few hemichordate mitochondrial genomes have been sequenced, hindering our understanding of mitochondrial genome evolution within Deuterostomia. In this study, we sequenced four mitochondrial genomes and two transcriptomes, including representatives of both major hemichordate lineages and analyzed together with public available data. Contrary to the current understanding of the mitochondrial genetic code in hemichordates, our comparative analyses suggest that UAA encodes Tyr instead of a "Stop" codon in the pterobranch lineage Cephalodiscidae. We also predict that AAA encodes Lys in pterobranch and enteropneust mitochondrial genomes, contradicting the previous assumption that hemichordates share the same genetic code with echinoderms for which AAA encodes Asn. Thus, we propose a new mitochondrial genetic code for Cephalodiscus and a revised code for enteropneusts. Moreover, our phylogenetic analyses are largely consistent with previous phylogenomic studies. The only exception is the phylogenetic position of the enteropneust Stereobalanus, whose placement as sister to all other described enteropneusts. With broader taxonomic sampling, we provide evidence that evolution of mitochondrial gene order and genetic codes in Hemichordata are more dynamic than previously thought and these findings provide insights into mitochondrial genome evolution within this clade.
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Affiliation(s)
- Yuanning Li
- Department of Biological Sciences & Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University
| | - Kevin M Kocot
- Department of Biological Sciences & Alabama Museum of Natural History, The University of Alabama
| | - Michael G Tassia
- Department of Biological Sciences & Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University
| | - Johanna T Cannon
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara
| | - Matthias Bernt
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Kenneth M Halanych
- Department of Biological Sciences & Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University
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Abstract
Phylum Hemichordata, composed of worm-like Enteropneusta and colonial Pterobranchia, has been reported to only contain about 100 species. However, recent studies of hemichordate phylogeny and taxonomy suggest the species number has been largely underestimated. One issue is that species must be described by experts, and historically few taxonomists have studied this group of marine invertebrates. Despite this previous lack of coverage, interest in hemichordates has piqued in the past couple of decades, as they are critical to understanding the evolution of chordates–as acorn worms likely resemble the deuterostome ancestor more closely than any other extant animal. This review provides an overview of our current knowledge of hemichordates, focusing specifically on their global biodiversity, geographic distribution, and taxonomy. Using information available in the World Register of Marine Species and published literature, we assembled a list of 130 described, extant species. The majority (83%) of these species are enteropneusts, and more taxonomic descriptions are forthcoming. Ptychoderidae contained the greatest number of species (41 species), closely followed by Harrimaniidae (40 species), of the recognized hemichordate families. Hemichordates are found throughout the world’s oceans, with the highest reported numbers by regions with marine labs and diligent taxonomic efforts (e.g. North Pacific and North Atlantic). Pterobranchs are abundant in Antarctica, but have also been found at lower latitudes. We consider this a baseline report and expect new species of Hemichordata will continue to be discovered and described as new marine habitats are characterized and explored.
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Affiliation(s)
- Michael G. Tassia
- Department of Biology, University of Washington, Seattle, WA, United States of America
- Friday Harbor Laboratories, University of Washington, Friday Harbor, WA, United States of America
- Department of Biological Sciences, Auburn University, Auburn, AL, 36849, United States of America
| | - Johanna T. Cannon
- Friday Harbor Laboratories, University of Washington, Friday Harbor, WA, United States of America
- Department of Biological Sciences, Auburn University, Auburn, AL, 36849, United States of America
- Department of Zoology, Naturhistoriska riksmuseet, Stockholm, SE-104 05, Sweden
| | - Charlotte E. Konikoff
- Department of Biology, University of Washington, Seattle, WA, United States of America
| | - Noa Shenkar
- Department of Biology, University of Washington, Seattle, WA, United States of America
- Friday Harbor Laboratories, University of Washington, Friday Harbor, WA, United States of America
- Department of Zoology, George S. Wise Faculty of Life Science, Tel-Aviv University, Tel-Aviv, Israel
| | - Kenneth M. Halanych
- Friday Harbor Laboratories, University of Washington, Friday Harbor, WA, United States of America
- Department of Biological Sciences, Auburn University, Auburn, AL, 36849, United States of America
| | - Billie J. Swalla
- Department of Biology, University of Washington, Seattle, WA, United States of America
- Friday Harbor Laboratories, University of Washington, Friday Harbor, WA, United States of America
- * E-mail:
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