1
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Brownstein CD, MacGuigan DJ, Kim D, Orr O, Yang L, David SR, Kreiser B, Near TJ. The genomic signatures of evolutionary stasis. Evolution 2024; 78:821-834. [PMID: 38437861 DOI: 10.1093/evolut/qpae028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 02/13/2024] [Accepted: 02/23/2024] [Indexed: 03/06/2024]
Abstract
Evolutionary stasis characterizes lineages that seldom speciate and show little phenotypic change over long stretches of geological time. Although lineages that appear to exhibit evolutionary stasis are often called living fossils, no single mechanism is thought to be responsible for their slow rates of morphological evolution and low species diversity. Some analyses of molecular evolutionary rates in a handful of living fossil lineages have indicated that these clades exhibit slow rates of genomic change. Here, we investigate mechanisms of evolutionary stasis using a dataset of 1,105 exons for 481 vertebrate species. We demonstrate that two ancient clades of ray-finned fishes classically called living fossils, gars and sturgeons, exhibit the lowest rates of molecular substitution in protein-coding genes among all jawed vertebrates. Comparably low rates of evolution are observed at fourfold degenerate sites in gars and sturgeons, implying a mechanism of stasis decoupled from selection that we speculate is linked to a highly effective DNA repair apparatus. We show that two gar species last sharing common ancestry over 100 million years ago produce morphologically intermediate and fertile hybrids in the wild. This makes gars the oldest naturally hybridizing divergence among eukaryotes and supports a theoretical prediction that slow rates of nucleotide substitution across the genome slow the accumulation of genetic incompatibilities, enabling hybridization across deeply divergent lineages and slowing the rate of speciation over geological timescales. Our results help establish molecular stasis as a barrier to speciation and phenotypic innovation and provide a mechanism to explain the low species diversity in living fossil lineages.
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Affiliation(s)
- Chase D Brownstein
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
- Stamford Museum and Nature Center, Stamford, CT, United States
| | - Daniel J MacGuigan
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, United States
| | - Daemin Kim
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
| | - Oliver Orr
- The Metropolitan Museum of Art, New York, NY, United States
| | - Liandong Yang
- Institute of Hydrobiology, Chinese Academy of Sciences, Beijing, China
| | - Solomon R David
- Department of Fisheries, Wildlife and Conservation Biology, University of Minnesota Twin Cities, Minneapolis, MN, United States
| | - Brian Kreiser
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS, United States
| | - Thomas J Near
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
- Peabody Museum, Yale University,, New Haven, CT, United States
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2
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MacGuigan DJ, Krabbenhoft TJ, Harrington RC, Wainwright DK, Backenstose NJC, Near TJ. Lacustrine speciation associated with chromosomal inversion in a lineage of riverine fishes. Evolution 2023:7140304. [PMID: 37094800 DOI: 10.1093/evolut/qpad067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Indexed: 04/26/2023]
Abstract
Geographic isolation is the primary driver of speciation in many vertebrate lineages. This trend is exemplified by North American darters, a clade of freshwater fishes where nearly all sister species pairs are allopatric and separated by millions of years of divergence. One of the only exceptions is the Lake Waccamaw endemic Etheostoma perlongum and its riverine sister species E. maculaticeps, which have no physical barriers to gene flow. Here we show that lacustrine speciation of E. perlongum is characterized by morphological and ecological divergence likely facilitated by a large chromosomal inversion. While Etheostoma perlongum is phylogenetically nested within the geographically widespread E. maculaticeps, there is a sharp genetic and morphological break coinciding with the lake-river boundary in the Waccamaw River system. Despite recent divergence, an active hybrid zone, and ongoing gene flow, analyses using a de novo reference genome reveal a 9 Mb chromosomal inversion with elevated divergence between E. perlongum and E. maculaticeps. This region exhibits striking synteny with known inversion supergenes in two distantly related fish lineages, suggesting deep evolutionary convergence of genomic architecture. Our results illustrate that rapid, ecological speciation with gene flow is possible even in lineages where geographic isolation is the dominant mechanism of speciation.
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Affiliation(s)
- Daniel J MacGuigan
- Department of Biological Sciences, University at Buffalo, 109 Cooke Hall, Buffalo, NY 14226 USA
| | - Trevor J Krabbenhoft
- Department of Biological Sciences, University at Buffalo, 109 Cooke Hall, Buffalo, NY 14226 USA
- RENEW Institute, University at Buffalo, 112 Cooke Hall, Buffalo, NY 14226 USA
| | - Richard C Harrington
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06520, USA
| | - Dylan K Wainwright
- Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN 47907, USA
| | - Nathan J C Backenstose
- Department of Biological Sciences, University at Buffalo, 109 Cooke Hall, Buffalo, NY 14226 USA
| | - Thomas J Near
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06520, USA
- Yale Peabody Museum of Natural History, 170 Whitney Ave, New Haven, CT 06520, USA
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3
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MacGuigan DJ, Orr OD, Near TJ. Phylogeography, hybridization, and species discovery in the Etheostoma nigrum complex (Percidae: Etheostoma: Boleosoma). Mol Phylogenet Evol 2023; 178:107645. [PMID: 36252933 DOI: 10.1016/j.ympev.2022.107645] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 07/29/2022] [Accepted: 10/11/2022] [Indexed: 11/05/2022]
Abstract
The history of riverine fish diversification is largely a product of geographic isolation. Physical barriers that reduce or eliminate gene flow between populations facilitate divergence via genetic drift and natural selection, eventually leading to speciation. For freshwater organisms, diversification is often the product of drainage basin rearrangements. In young clades where the history of isolation is the most recent, evolutionary relationships can resemble a tangled web. One especially recalcitrant group of freshwater fishes is the Johnny Darter (Etheostoma nigrum) species complex, where traditional taxonomy and molecular phylogenetics indicate a history of gene flow and conflicting inferences of species diversity. Here we assemble a genomic dataset using double digest restriction site associated DNA (ddRAD) sequencing and use phylogenomic and population genetic approaches to investigate the evolutionary history of the complex of species that includes E. nigrum, E. olmstedi, E. perlongum, and E. susanae. We reveal and validate several evolutionary lineages that we delimit as species, highlighting the need for additional work to formally describe the diversity of the Etheostoma nigrum complex. Our analyses also identify gene flow among recently diverged lineages, including one instance involving E. susanae, a localized and endangered species. Phylogeographic structure within the Etheostoma nigrum species complex coincides with major geologic events, such as parallel divergence in river basins during Pliocene inundation of the Atlantic coastal plain and multiple northward post-glacial colonization routes tracking river basin rearrangements. Our study serves as a nuanced example of how low dispersal rates coupled with geographic isolation among disconnected river systems in eastern North America has produced one of the world's freshwater biodiversity hotspots.
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Affiliation(s)
- Daniel J MacGuigan
- Department of Biological Sciences, 109 Cooke Hall, University at Buffalo, Buffalo, NY 14260, USA.
| | - Oliver D Orr
- Department of Ecology and Evolutionary Biology, 165 Prospect Street, Yale University, New Haven, CT 06520, USA; Yale Peabody Museum of Natural History, 170 Whitney Ave, New Haven, CT 06520, USA
| | - Thomas J Near
- Department of Ecology and Evolutionary Biology, 165 Prospect Street, Yale University, New Haven, CT 06520, USA; Yale Peabody Museum of Natural History, 170 Whitney Ave, New Haven, CT 06520, USA
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4
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MacGuigan DJ, Mount GG, Watkins-Colwell GJ, Near TJ, Lambert MR. Genomic Data Clarify Aquarana Systematics and Reveal Isolation-by-Distance Dominates Phylogeography of the Wide-Ranging Frog Rana clamitans. Ichthyology & Herpetology 2022. [DOI: 10.1643/h2021129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Daniel J. MacGuigan
- Department of Biological Sciences, University at Buffalo, Buffalo, New York 14260;
| | | | - Gregory J. Watkins-Colwell
- Division of Vertebrate Zoology, Peabody Museum of Natural History, Yale University, New Haven, Connecticut 06511; (GJWC) gregory.
| | - Thomas J. Near
- Division of Vertebrate Zoology, Peabody Museum of Natural History, Yale University, New Haven, Connecticut 06511; (GJWC) gregory.
| | - Max R. Lambert
- Science Division, Habitat Program, Washington Department of Fish & Wildlife, Olympia, Washington 98501;
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5
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Krabbenhoft TJ, MacGuigan DJ, Backenstose NJC, Waterman H, Lan T, Pelosi JA, Tan M, Sandve SR. Chromosome-Level Genome Assembly of Chinese Sucker (Myxocyprinus asiaticus) Reveals Strongly Conserved Synteny Following a Catostomid-Specific Whole-Genome Duplication. Genome Biol Evol 2021; 13:6349175. [PMID: 34383883 PMCID: PMC8412299 DOI: 10.1093/gbe/evab190] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2021] [Indexed: 12/27/2022] Open
Abstract
Fishes of the family Catostomidae (“suckers”; Teleostei: Cypriniformes) are hypothesized to have undergone an allopolyploidy event approximately 60 Ma. However, genomic evidence has previously been unavailable to assess this hypothesis. We sequenced and assembled the first chromosome-level catostomid genome, Chinese sucker (Myxocyprinus asiaticus), and present clear evidence of a catostomid-specific whole-genome duplication (WGD) event (“Cat-4R”). Our results reveal remarkably strong, conserved synteny since this duplication event, as well as between Myxocyprinus and an unduplicated outgroup, zebrafish (Danio rerio). Gene content and repetitive elements are also approximately evenly distributed across homeologous chromosomes, suggesting that both subgenomes retain some function, with no obvious bias in gene fractionation or subgenome dominance. The Cat-4R duplication provides another independent example of genome evolution following WGD in animals, in this case at the extreme end of conserved genome architecture over at least 25.2 Myr since the duplication. The M. asiaticus genome is a useful resource for researchers interested in understanding genome evolution following WGD in animals.
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Affiliation(s)
- Trevor J Krabbenhoft
- Department of Biological Sciences and the RENEW Institute, University at Buffalo, USA
- Corresponding author: E-mail:
| | | | | | - Hannah Waterman
- Department of Biological Sciences, University at Buffalo, USA
| | - Tianying Lan
- Department of Biological Sciences, University at Buffalo, USA
- Present address: Arbor Biosciences, Ann Arbor, MI, USA
| | | | - Milton Tan
- Illinois Natural History Survey, University of Illinois at Urbana-Champaign, USA
| | - Simen R Sandve
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
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6
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MacGuigan DJ, Hoagstrom CW, Domisch S, Hulsey CD, Near TJ. Integrative ichthyological species delimitation in the Greenthroat Darter complex (Percidae: Etheostomatinae). ZOOL SCR 2021. [DOI: 10.1111/zsc.12504] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | - Sami Domisch
- Department of Ecosystem Research Leibniz‐Institute of Freshwater Ecology and Inland Fisheries Berlin Germany
| | - C. Darrin Hulsey
- Laboratory for Zoology and Evolutionary Biology Department of Biology University of Konstanz Konstanz Germany
| | - Thomas J. Near
- Department of Ecology and Evolutionary Biology Yale University New Haven CT USA
- Peabody Museum of Natural History Yale University New Haven CT USA
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7
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Melo BF, Sidlauskas BL, Near TJ, Roxo FF, Ghezelayagh A, Ochoa LE, Stiassny MLJ, Arroyave J, Chang J, Faircloth BC, MacGuigan DJ, Harrington RC, Benine RC, Burns MD, Hoekzema K, Sanches NC, Maldonado-Ocampo JA, Castro RMC, Foresti F, Alfaro ME, Oliveira C. Accelerated Diversification Explains the Exceptional Species Richness of Tropical Characoid Fishes. Syst Biol 2021; 71:78-92. [PMID: 34097063 DOI: 10.1093/sysbio/syab040] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 06/01/2021] [Accepted: 06/04/2021] [Indexed: 11/12/2022] Open
Abstract
The Neotropics harbor the most species-rich freshwater fish fauna on the planet, but the timing of that exceptional diversification remains unclear. Did the Neotropics accumulate species steadily throughout their long history, or attain their remarkable diversity recently? Biologists have long debated the relative support for these museum and cradle hypotheses, but few phylogenies of megadiverse tropical clades have included sufficient taxa to distinguish between them. We used 1,288 ultraconserved element loci (UCE) spanning 293 species, 211 genera and 21 families of characoid fishes to reconstruct a new, fossil-calibrated phylogeny and infer the most likely diversification scenario for a clade that includes a third of Neotropical fish diversity. This phylogeny implies paraphyly of the traditional delimitation of Characiformes because it resolves the largely Neotropical Characoidei as the sister lineage of Siluriformes (catfishes), rather than the African Citharinodei. Time-calibrated phylogenies indicate an ancient origin of major characoid lineages and reveal a much more recent emergence of most characoid species. Diversification rate analyses infer increased speciation and decreased extinction rates during the Oligocene at around 30 million years ago (Ma) during a period of mega-wetland formation in the proto-Orinoco-Amazonas. Three species-rich and ecomorphologically diverse lineages (Anostomidae, Serrasalmidae, and Characidae) that originated more than 60 Ma in the Paleocene experienced particularly notable bursts of Oligocene diversification and now account collectively for 68% of the approximately 2,150 species of Characoidei. In addition to paleogeographic changes, we discuss potential accelerants of diversification in these three lineages. While the Neotropics accumulated a museum of ecomorphologically diverse characoid lineages long ago, this geologically dynamic region also cradled a much more recent birth of remarkable species-level diversity.
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Affiliation(s)
- Bruno F Melo
- Dept of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu, SP, 16818-689, Brazil
| | - Brian L Sidlauskas
- Dept of Fisheries and Wildlife, Oregon State University, Corvallis, OR, 97331, USA
| | - Thomas J Near
- Dept of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Fabio F Roxo
- Sector of Zoology, Institute of Biosciences, São Paulo State University, Botucatu, SP, 18618-689, Brazil
| | - Ava Ghezelayagh
- Dept of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Luz E Ochoa
- Dept of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu, SP, 16818-689, Brazil.,Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Palmira, Valle del Cauca, 763547, Colombia
| | - Melanie L J Stiassny
- Dept of Ichthyology, American Museum of Natural History, New York, NY, 10024, USA
| | - Jairo Arroyave
- Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, 04510, México
| | - Jonathan Chang
- School of Biological Sciences, Monash University, Melbourne, VIC, 3800, Australia
| | - Brant C Faircloth
- Dept of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Daniel J MacGuigan
- Dept of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Richard C Harrington
- Dept of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Ricardo C Benine
- Sector of Zoology, Institute of Biosciences, São Paulo State University, Botucatu, SP, 18618-689, Brazil
| | - Michael D Burns
- Cornell Lab of Ornithology, Cornell University Museum of Vertebrates, Ithaca, NY, 14850, USA
| | - Kendra Hoekzema
- Dept of Fisheries and Wildlife, Oregon State University, Corvallis, OR, 97331, USA
| | - Natalia C Sanches
- Dept of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu, SP, 16818-689, Brazil
| | - Javier A Maldonado-Ocampo
- Dept de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, DC, Colombia (in memoriam)
| | - Ricardo M C Castro
- Faculdade de Filosofia, Ciências e Letras, Universidade de São Paulo, Ribeirão Preto, SP, 14040-901, Brazil
| | - Fausto Foresti
- Dept of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu, SP, 16818-689, Brazil
| | - Michael E Alfaro
- Dept of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA
| | - Claudio Oliveira
- Dept of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu, SP, 16818-689, Brazil
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8
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Near TJ, MacGuigan DJ, Boring EL, Simmons JW, Albanese B, Keck BP, Harrington RC, Dinkins GR. A New Species of Bridled Darter Endemic to the Etowah River System in Georgia (Percidae: Etheostomatinae: Percina). Bulletin of the Peabody Museum of Natural History 2021. [DOI: 10.3374/014.062.0102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Thomas J. Near
- Department of Ecology and Evolutionary Biology, Osborn Memorial Labs, Yale University, New Haven CT 06520-8106 USA; and Peabody Museum of Natural History, Yale University, New Haven, CT 06520-8118 USA —
| | - Daniel J. MacGuigan
- Department of Ecology and Evolutionary Biology, Osborn Memorial Labs, Yale University, New Haven CT 06520-8106 USA; and Peabody Museum of Natural History, Yale University, New Haven, CT 06520-8118 USA
| | - Emily L. Boring
- Pierson College and Department of Ecology and Evolutionary Biology, Osborn Memorial Labs, Yale University, New Haven CT 06520-8106 USA
| | - Jeffrey W. Simmons
- River and Reservoir Compliance Monitoring, Tennessee Valley Authority, Chattanooga, TN 37402-2881 USA
| | - Brett Albanese
- Wildlife Conservation Section, Georgia Department of Natural Resources, Social Circle, GA 30025 USA
| | - Benjamin P. Keck
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996-1610 USA
| | - Richard C. Harrington
- Department of Ecology and Evolutionary Biology, Osborn Memorial Labs, Yale University, New Haven CT 06520-8106 USA; and Peabody Museum of Natural History, Yale University, New Haven, CT 06520-8118 USA
| | - Gerald R. Dinkins
- McClung Museum of Natural History and Culture, University of Tennessee, Knoxville, TN 37996-3200 USA
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9
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Daane JM, Dornburg A, Smits P, MacGuigan DJ, Hawkins MB, Near TJ, Detrich HW, Harris MP. Author Correction: Historical contingency shapes adaptive radiation in Antarctic fishes. Nat Ecol Evol 2020; 4:659. [PMID: 32157252 DOI: 10.1038/s41559-020-1169-7] [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] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Jacob M Daane
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, MA, USA.
| | - Alex Dornburg
- North Carolina Museum of Natural Sciences, Raleigh, NC, USA
| | - Patrick Smits
- Orthopaedic Research Laboratories, Department of Orthopaedic Surgery, Boston Children's Hospital, Boston, MA, USA
| | - Daniel J MacGuigan
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - M Brent Hawkins
- Orthopaedic Research Laboratories, Department of Orthopaedic Surgery, Boston Children's Hospital, Boston, MA, USA.,Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Thomas J Near
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.,Peabody Museum of Natural History, Yale University, New Haven, CT, USA
| | - H William Detrich
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, MA, USA.
| | - Matthew P Harris
- Orthopaedic Research Laboratories, Department of Orthopaedic Surgery, Boston Children's Hospital, Boston, MA, USA. .,Department of Genetics, Harvard Medical School, Boston, MA, USA.
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10
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Bowman LL, MacGuigan DJ, Gorchels ME, Cahillane MM, Moore MV. Revealing paraphyly and placement of extinct species within Epischura (Copepoda: Calanoida) using molecular data and quantitative morphometrics. Mol Phylogenet Evol 2019; 140:106578. [PMID: 31401068 DOI: 10.1016/j.ympev.2019.106578] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 08/02/2019] [Accepted: 08/07/2019] [Indexed: 10/26/2022]
Abstract
Epischura (Calanoida: Temoridae) is a Holarctic group of copepods serving important ecological roles, but it is difficult to study because of small range sizes of individual species and widespread distribution of the genus. This genus includes Tertiary relicts, some endemic to single, isolated lakes and can play major roles in unique ecosystems like Lakes Baikal and Tahoe. We present the first molecular and morphological analysis of Epischura that reveals their spatio-temporal evolutionary history. Morphological measurements of mandibles and genetics estimated phylogenetic relationships among all species represented in Epischura, including E. massachusettsensis, whose extinction status is of concern. Analyses used three gene regions for six previously unsequenced species to infer highly-resolved and well-supported phylogenies confirming a split between Siberian and North American species. Previously published age estimates and sequence data from broad taxonomic sampling of calanoid copepods estimated divergence times between the two Epischura groups. Divergence time estimates for Epischura were consistent with earlier molecular clock estimates and late-Miocene cooling events. Additionally, we provide the first taxonomically broad estimates of divergence times within Calanoida. The paraphyletic nature of the genus Epischura (and the family Temoridae) is apparent and requires the resurrection of the genus Epischurella (Smirnov, 1936) to describe the Siberian species.
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Affiliation(s)
- Larry L Bowman
- Department of Ecology and Evolutionary Biology, Yale University, Osborn Memorial Laboratories, 165 Prospect St., New Haven, CT 06511, USA.
| | - Daniel J MacGuigan
- Department of Ecology and Evolutionary Biology, Yale University, Osborn Memorial Laboratories, 165 Prospect St., New Haven, CT 06511, USA
| | - Madeline E Gorchels
- Department of Biological Sciences, Wellesley College, 106 Central St., Wellesley, MA 02481-0832, USA
| | - Madeline M Cahillane
- Department of Biological Sciences, Wellesley College, 106 Central St., Wellesley, MA 02481-0832, USA
| | - Marianne V Moore
- Department of Biological Sciences, Wellesley College, 106 Central St., Wellesley, MA 02481-0832, USA
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11
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Daane JM, Dornburg A, Smits P, MacGuigan DJ, Brent Hawkins M, Near TJ, William Detrich Iii H, Harris MP. Historical contingency shapes adaptive radiation in Antarctic fishes. Nat Ecol Evol 2019; 3:1102-1109. [PMID: 31182814 PMCID: PMC7147983 DOI: 10.1038/s41559-019-0914-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 05/02/2019] [Indexed: 12/02/2022]
Abstract
Adaptive radiation illustrates links between ecological opportunity, natural selection and the generation of biodiversity. Central to adaptive radiation is the association between a diversifying lineage and the evolution of phenotypic variation that facilitates the use of new environments or resources. However, is not clear whether adaptive evolution or historical contingency is more important for the origin of key phenotypic traits in adaptive radiation. Here we use targeted sequencing of >250,000 loci across 46 species to examine hypotheses concerning the origin and diversification of key traits in the adaptive radiation of Antarctic notothenioid fishes. Contrary to expectations of adaptive evolution, we show that notothenioids experienced a punctuated burst of genomic diversification and evolved key skeletal modifications before the onset of polar conditions in the Southern Ocean. We show that diversifying selection in pathways associated with human skeletal dysplasias facilitates ecologically important variation in buoyancy among Antarctic notothenioid species, and demonstrate the sufficiency of altered trip11, col1a2 and col1a1a function in zebrafish (Danio rerio) to phenocopy skeletal reduction in Antarctic notothenioids. Rather than adaptation being driven by the cooling of the Antarctic, our results highlight the role of historical contingency in shaping the adaptive radiation of notothenioids. Understanding the historical and environmental context for the origin of key traits in adaptive radiations extends beyond reconstructing events that result in evolutionary innovation, as it also provides a context in forecasting the effects of climate change on the stability and evolvability of natural populations.
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Affiliation(s)
- Jacob M Daane
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, MA, USA.
| | - Alex Dornburg
- North Carolina Museum of Natural Sciences, Raleigh, NC, USA
| | - Patrick Smits
- Orthopaedic Research Laboratories, Department of Orthopaedic Surgery, Boston Children's Hospital, Boston, MA, USA
| | - Daniel J MacGuigan
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - M Brent Hawkins
- Orthopaedic Research Laboratories, Department of Orthopaedic Surgery, Boston Children's Hospital, Boston, MA, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Thomas J Near
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
- Peabody Museum of Natural History, Yale University, New Haven, CT, USA
| | - H William Detrich Iii
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, MA, USA.
| | - Matthew P Harris
- Orthopaedic Research Laboratories, Department of Orthopaedic Surgery, Boston Children's Hospital, Boston, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
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12
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MacGuigan DJ, Near TJ. Phylogenomic Signatures of Ancient Introgression in a Rogue Lineage of Darters (Teleostei: Percidae). Syst Biol 2019; 68:329-346. [PMID: 30395332 DOI: 10.1093/sysbio/syy074] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 10/29/2018] [Indexed: 12/17/2022] Open
Abstract
Evolutionary history is typically portrayed as a branching phylogenetic tree, yet not all evolution proceeds in a purely bifurcating manner. Introgressive hybridization is one process that results in reticulate evolution. Most known examples of genome-wide introgression occur among closely related species with relatively recent common ancestry; however, we present evidence for ancient hybridization and genome-wide introgression between major stem lineages of darters, a species-rich clade of North American freshwater fishes. Previous attempts to resolve the relationships of darters have been confounded by the uncertain phylogenetic resolution of the lineage Allohistium. In this study, we investigate the phylogenomics of darters, specifically the relationships of Allohistium, through analyses of approximately 30,000 RADseq loci sampled from 112 species. Our phylogenetic inferences are based on traditional approaches in combination with strategies that accommodate reticulate evolution. These analyses result in a novel phylogenetic hypothesis for darters that includes ancient introgression between Allohistium and other two major darter lineages, minimally occurring 20 million years ago. Darters offer a compelling case for the necessity of incorporating phylogenetic networks in reconstructing the evolutionary history of diversification in species-rich lineages. We anticipate that the growing wealth of genomic data for clades of non-model organisms will reveal more examples of ancient hybridization, eventually requiring a re-evaluation of how evolutionary history is visualized and utilized in macroevolutonary investigations.
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Affiliation(s)
- Daniel J MacGuigan
- Department of Ecology and Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT 06520, USA
| | - Thomas J Near
- Department of Ecology and Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT 06520, USA.,Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA
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Near TJ, MacGuigan DJ, Parker E, Struthers CD, Jones CD, Dornburg A. Phylogenetic analysis of Antarctic notothenioids illuminates the utility of RADseq for resolving Cenozoic adaptive radiations. Mol Phylogenet Evol 2018; 129:268-279. [PMID: 30195039 DOI: 10.1016/j.ympev.2018.09.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 08/31/2018] [Accepted: 09/01/2018] [Indexed: 10/28/2022]
Abstract
Notothenioids are a clade of ∼120 species of marine fishes distributed in extreme southern hemisphere temperate near-shore habitats and in the Southern Ocean surrounding Antarctica. Over the past 25 years, molecular and morphological approaches have redefined hypotheses of relationships among notothenioid lineages as well as their relationships among major lineages of percomorph teleosts. These phylogenies provide a basis for investigation of mechanisms of evolutionary diversification within the clade and have enhanced our understanding of the notothenioid adaptive radiation. Despite extensive efforts, there remain several questions concerning the phylogeny of notothenioids. In this study, we deploy DNA sequences of ∼100,000 loci obtained using RADseq to investigate the phylogenetic relationships of notothenioids and to assess the utility of RADseq loci for lineages that exhibit divergence times ranging from the Paleogene to the Quaternary. The notothenioid phylogenies inferred from the RADseq loci provide unparalleled resolution and node support for several long-standing problems including, (1) relationships among species of Trematomus, (2) resolution of Indonotothenia cyanobrancha as the sister lineage of Trematomus, (3) the deep paraphyly of Nototheniidae, (4) the paraphyly of Lepidonotothen s.l., (5) paraphyly of Artedidraco, and 6) the monophyly of the Bathydraconidae. Assessment of site rates demonstrates that RADseq loci are similar to mtDNA protein coding genes and exhibit peak phylogenetic informativeness at the time interval during which the major Antarctic notothenioid lineages originated and diversified. In addition to providing a well-resolved phylogenetic hypothesis for notothenioids, our analyses quantify the predicted utility of RADseq loci for Cenozoic phylogenetic inferences.
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Affiliation(s)
- Thomas J Near
- Department of Ecology & Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT 06520, USA; Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA.
| | - Daniel J MacGuigan
- Department of Ecology & Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT 06520, USA
| | - Elyse Parker
- Department of Ecology & Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT 06520, USA
| | - Carl D Struthers
- Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand
| | - Christopher D Jones
- Antarctic Ecosystem Research Division, NOAA Southwest Fisheries Science Center, La Jolla, CA 92037, USA
| | - Alex Dornburg
- North Carolina Museum of Natural Sciences, Raleigh, NC 27601, USA
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Kozal LC, Simmons JW, Mollish JM, MacGuigan DJ, Benavides E, Keck BP, Near TJ. Phylogenetic and Morphological Diversity of theEtheostoma zonistiumSpecies Complex with the Description of a New Species Endemic to the Cumberland Plateau of Alabama. Bulletin of the Peabody Museum of Natural History 2017. [DOI: 10.3374/014.058.0202] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Logan C. Kozal
- Department of Ecology and Evolutionary Biology, Osborn Memorial Labs, Yale University, New Haven CT 06520-8106 USA
- Berkeley College, Yale University, New Haven CT 06520-8106 USA
| | - Jeffrey W. Simmons
- Resources and River Management, Tennessee Valley Authority, Chattanooga, TN 37402-2881 USA
| | - Jon Michael Mollish
- Resources and River Management, Tennessee Valley Authority, Chattanooga, TN 37402-2881 USA
| | - Daniel J. MacGuigan
- Department of Ecology and Evolutionary Biology, Osborn Memorial Labs, Yale University, New Haven CT 06520-8106 USA
| | - Edgar Benavides
- Department of Ecology and Evolutionary Biology, Osborn Memorial Labs, Yale University, New Haven CT 06520-8106 USA
| | - Benjamin P. Keck
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996 USA
| | - Thomas J. Near
- Department of Ecology and Evolutionary Biology, Osborn Memorial Labs, Yale University, New Haven CT 06520-8106 USA; Peabody Museum of Natural History, Yale University, New Haven, CT 06520-8106 USA
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MacGuigan DJ, Geneva AJ, Glor RE. A genomic assessment of species boundaries and hybridization in a group of highly polymorphic anoles ( distichus species complex). Ecol Evol 2017; 7:3657-3671. [PMID: 28616163 PMCID: PMC5468153 DOI: 10.1002/ece3.2751] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 08/12/2016] [Accepted: 12/22/2016] [Indexed: 02/05/2023] Open
Abstract
Delimiting young species is one of the great challenges of systematic biology, particularly when the species in question exhibit little morphological divergence. Anolis distichus, a trunk anole with more than a dozen subspecies that are defined primarily by dewlap color, may actually represent several independent evolutionary lineages. To test this, we utilized amplified fragment length polymorphisms (AFLP) genome scans and genetic clustering analyses in conjunction with a coalescent‐based species delimitation method. We examined a geographically widespread set of samples and two heavily sampled hybrid zones. We find that genetic divergence is associated with a major biogeographic barrier, the Hispaniolan paleo‐island boundary, but not with dewlap color. Additionally, we find support for hypotheses regarding colonization of two Hispaniolan satellite islands and the Bahamas from mainland Hispaniola. Our results show that A. distichus is composed of seven distinct evolutionary lineages still experiencing a limited degree of gene flow. We suggest that A. distichus merits taxonomic revision, but that dewlap color cannot be relied upon as the primary diagnostic character.
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Affiliation(s)
- Daniel J MacGuigan
- Department of Ecology and Evolutionary Biology Yale University New Haven CT USA
| | - Anthony J Geneva
- Department of Organismic and Evolutionary Biology Harvard University Cambridge MA USA
| | - Richard E Glor
- Herpetology Division Biodiversity Institute University of Kansas Lawrence KS USA.,Department of Ecology and Evolutionary Biology University of Kansas Lawrence KS USA
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Ng J, Kelly AL, MacGuigan DJ, Glor RE. The role of heritable and dietary factors in the sexual signal of a Hispaniolan Anolis lizard, Anolis distichus. ACTA ACUST UNITED AC 2013; 104:862-73. [PMID: 24078680 DOI: 10.1093/jhered/est060] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The diversity of sexual signals is astounding, and divergence in these traits is believed to be associated with the early stages of speciation. An increasing number of studies also suggest a role for natural selection in driving signal divergence for effective transmission in heterogeneous environments. Both speciation and adaptive divergence, however, are contingent on the sexual signal being heritable, yet this often remains assumed and untested. It is particularly critical that the heritability of carotenoid-based sexual signals is investigated because such traits may instead be phenotypically plastic indicators of an individual's quality that exhibit no or little heritable variation. We present the first study to investigate the relative contribution of genetic and environmental factors to the striking diversity of dewlap color and pattern in Anolis lizards. Using a breeding experiment with Anolis distichus populations exhibiting different dewlap phenotypes, we raise F1 offspring in a common garden experiment to assess whether dewlap color is inherited. We follow this with carotenoid supplementation to investigate the influence of dietary pigments to dewlap color variation. We find significant differences in several aspects of dewlap color and pattern to persist to the F1 generation (fathers: N = 19; F1 males: N = 50; P < 0.01) with no change in dewlap phenotype with carotenoid supplementation (N = 52; P > 0.05). These results strongly support that genetic differences underlie dewlap color variation, thereby satisfying a key requirement of natural selection. Our findings provide an important stepping-stone to understanding the evolution of an incredibly diverse signal important for sexual selection and species recognition.
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Affiliation(s)
- Julienne Ng
- the Department of Biology, University of Rochester, RC Box 270211, Rochester, NY 14627. Richard Glor is now at the Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS
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