1
|
Kim D, Bauer BH, Near TJ. Introgression and Species Delimitation in the Longear Sunfish Lepomis megalotis (Teleostei: Percomorpha: Centrarchidae). Syst Biol 2021; 71:273-285. [PMID: 33944950 DOI: 10.1093/sysbio/syab029] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 04/20/2021] [Accepted: 04/27/2021] [Indexed: 11/14/2022] Open
Abstract
Introgression and hybridization are major impediments to genomic-based species delimitation because many implementations of the multispecies coalescent framework assume no gene flow among species. The sunfish genus Lepomis, one of the world's most popular groups of freshwater sport fish, has a complicated taxonomic history. The results of ddRAD phylogenomic analyses do not provide support for the current taxonomy that recognizes two species, L. megalotis and L. peltastes, in the L. megalotis complex. Instead, evidence from phylogenomics and phenotype warrants recognizing six relatively ancient evolutionary lineages in the complex. The introgressed and hybridizing populations in the L. megalotis complex are localized and appear to be the result of secondary contact or rare hybridization events between non-sister species. Segregating admixed populations from our multispecies coalescent analyses identifies six species with moderate to high genealogical divergence, whereas including admixed populations drives all but one lineage below the species threshold of genealogical divergence. Segregation of admixed individuals also helps reveal phenotypic distinctiveness among the six species in morphological traits used by ichthyologists to discover and delimit species over the last two centuries. Our protocols allow for the identification and accommodation of hybridization and introgression in species delimitation. Genomic-based species delimitation validated with multiple lines of evidence provides a path towards the discovery of new biodiversity and resolving long-standing taxonomic problems.
Collapse
Affiliation(s)
- Daemin Kim
- Department of Ecology and Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT 06520, USA
| | - Bruce H Bauer
- David A. Etnier Ichthyological Collection, 515 Hesler Biology Building, University of Tennessee, Knoxville, TN 37996, 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
| |
Collapse
|
2
|
Under the radar: genetic assessment of Rio Grande Shiner (Notropis jemezanus) and Speckled Chub (Macrhybopsis aestivalis), two Rio Grande basin endemic cyprinids that have experienced recent range contractions. CONSERV GENET 2021. [DOI: 10.1007/s10592-020-01328-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
|
3
|
Turner TF, Pilger TJ, Osborne MJ, Propst DL. Rio Grande Sucker Pantosteus plebeius is Native to the Gila River Basin. COPEIA 2019. [DOI: 10.1643/cg-19-202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Thomas F. Turner
- Department of Biology and Museum of Southwestern Biology, MSC 03-2020, University of New Mexico, Albuquerque, New Mexico 87131; (TFT) . Send reprint requests to TFT
| | - Tyler J. Pilger
- FISHBIO, 180 East 4th Street, Suite 160, Chico, California 95928
| | - Megan J. Osborne
- Department of Biology and Museum of Southwestern Biology, MSC 03-2020, University of New Mexico, Albuquerque, New Mexico 87131; (TFT) . Send reprint requests to TFT
| | - David L. Propst
- Department of Biology and Museum of Southwestern Biology, MSC 03-2020, University of New Mexico, Albuquerque, New Mexico 87131; (TFT) . Send reprint requests to TFT
| |
Collapse
|
4
|
Markle DF. DRAINAGE EVOLUTION AND FRESHWATER FISH ZOOGEOGRAPHY IN COASTAL OREGON AND WASHINGTON. ACTA ACUST UNITED AC 2019. [DOI: 10.1898/nwn-18-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Douglas F Markle
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR 97331 USA;
| |
Collapse
|
5
|
Ballesteros-Nova NE, Pérez-Rodríguez R, Beltrán-López RG, Domínguez-Domínguez O. Genetic differentiation in the southern population of the Fathead Minnow Pimephales promelas Rafinesque (Actinopterygii: Cyprinidae). PeerJ 2019; 7:e6224. [PMID: 31106042 PMCID: PMC6497047 DOI: 10.7717/peerj.6224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 12/05/2018] [Indexed: 12/27/2022] Open
Abstract
The North American cyprinid Pimephales promelas is a species with a wide distribution range, occurring in distinct hydrographic basins in Mexico, Canada, and the United States. Previous morphological and meristic analyses of P. promelas concluded that at least three subspecies exist in the midwestern and northeast region of the United States. No studies have been carried out on the Mexican population of P. promelas, but the findings of cryptic diversity in United States populations of this species, as well as in other codistributed fish species in Mexico could be an indication that Mexican populations of P. promelas consist of cryptic species. Using the mitochondrial gene cyt b and the first intron of the S7 ribosomal protein-coding nuclear gene we carried out phylogenetic and phylogeographic analyses of populations of P. promelas across its distribution range in northwestern Mexico. Using this information were analyzed the structure and differentiation level between populations of P. promelas from distinct river basins in the region in identifying cryptic diversity. Twenty-four sequences were obtained for cyt b, and 30 for S7, which included the two heterozygous alleles. The results revealed the existence of four well-differentiated lineages: (1) Yaqui in the Pacific slope; (2) Santa Maria, and (3) Casas Grandes in the Guzman Basin; and (4) Nazas+Conchos in Chihuahua state. This challenges the current taxonomy of P. promelas. Differences in the relationships between markers and the small sample size for the Santa Maria population (n = 1), indicate that our results must be corroborated with more data and morphological analyses. Biogeographic analysis of these findings suggest that the evolutionary history of P. promelas is associated with the fragmentation of the ancestral Rio Grande river system since Miocene in northwestern Mexico consistent with findings for codistributed fish species.
Collapse
Affiliation(s)
- Nayarit E Ballesteros-Nova
- Programa Institucional de Doctorado en Ciencias Biológicas, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
| | - Rodolfo Pérez-Rodríguez
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México.,Laboratorio Nacional de Análisis y Síntesis Ecológica para la Conservación de Recursos Genéticos de México, Escuela Nacional de Estudios Superiores, Unidad Morelia, Universidad Nacional Autónoma de México, Morelia, Michoacán, México
| | - Rosa G Beltrán-López
- Programa Institucional de Doctorado en Ciencias Biológicas, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México.,Laboratorio de Ictiología, Centro de Investigaciones Biológicas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Omar Domínguez-Domínguez
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México.,Laboratorio Nacional de Análisis y Síntesis Ecológica para la Conservación de Recursos Genéticos de México, Escuela Nacional de Estudios Superiores, Unidad Morelia, Universidad Nacional Autónoma de México, Morelia, Michoacán, México
| |
Collapse
|
6
|
Schönhuth S, Gagne RB, Alda F, Neely DA, Mayden RL, Blum MJ. Phylogeography of the widespread creek chub Semotilus atromaculatus (Cypriniformes: Leuciscidae). JOURNAL OF FISH BIOLOGY 2018; 93:778-791. [PMID: 30101564 DOI: 10.1111/jfb.13778] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 08/06/2018] [Indexed: 06/08/2023]
Abstract
The extent and nature of genetic differentiation in Semotilus atromaculatus, one of the most abundant and widespread leuciscids in North America, were evaluated based on mitochondrial (mt) and nuclear DNA sequence variation. Phylogenetic relationships were first inferred based on a fragment of the cytochrome b (cytb) region and the nuclear intron s7 gene for S. atromaculatus and all other congeners as well as representative species from all other genera in the creek chub-plagopterin clade. The phylogeography of major haplogroups of S. atromaculatus was also assessed according to variation in a fragment of the mitochondrial cytb region from 567 individuals across its range. All analyses identified S. thoreauianus, S. lumbee and S. corporalis as reciprocally monophyletic groups. Analyses of nuclear sequence variation resolved S. atromaculatus as a single clade, where S. thoreauianus and S. lumbee were recovered as the sister group to S. atromaculatus, and S. corporalis was resolved as sister to all other species in the genus. Analyses of mtDNA sequence variation recovered S. atromaculatus as three well supported and differentiated monophyletic groups, with a widespread genetically homogeneous lineage extending across most of the current range of the species; a more geographically restricted and geographically structured lineage in the southern Appalachians, sister group to S. lumbee; and a geographically restricted lineage was identified from two Gulf Slope basins. Evidence of complex mito-nuclear discordance and phylogeographic differentiation within S. atromaculatus illustrates that further analysis of widespread species is warranted to understand North American freshwater fish diversity and distributions.
Collapse
Affiliation(s)
- Susana Schönhuth
- Department of Biology, Saint Louis University, St Louis, Missouri
| | - Roderick B Gagne
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, Louisiana
| | - Fernando Alda
- Louisiana State University, Museum of Natural Science, Baton Rouge, Louisiana
| | - David A Neely
- Tennessee Aquarium Conservation Institute, Chattanooga, Tennessee
| | - Richard L Mayden
- Department of Biology, Saint Louis University, St Louis, Missouri
| | - Michael J Blum
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, Louisiana
| |
Collapse
|
7
|
Spatial genetic variation and habitat association of Rhinichthys cataractae, the longnose dace, in the Driftless Area of the upper Mississippi River basin. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1106-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
8
|
Eaton KR, Loxterman JL, Keeley ER. Connections and containers: Using genetic data to understand how watershed evolution and human activities influence cutthroat trout biogeography. PLoS One 2018; 13:e0202043. [PMID: 30096159 PMCID: PMC6086439 DOI: 10.1371/journal.pone.0202043] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 07/26/2018] [Indexed: 11/19/2022] Open
Abstract
Species with large geographic distributions often exhibit complex patterns of diversity that can be further complicated by human activities. Cutthroat trout (Oncorhynchus clarkii) are one of the most widely distributed freshwater fish species in western North America exhibiting substantial phenotypic and genetic variability; however, fish stocking practices have translocated populations outside of their native range and may have obscured intraspecific boundaries. This study focuses on cutthroat trout populations representing three distinct evolutionary clades that are found intermixed within a contact zone between the Bonneville and upper Snake River watersheds in the western United States. We used mitochondrial and microsatellite genetic data, as well as historical stocking records, to evaluate whether populations of cutthroat trout in the contact zone are native or are introduced. We found significant genetic differentiation and fine-scale genetic population structure that was organized primarily by watershed boundaries. While we detected increased genetic diversity in some areas in close proximity to the greatest number of stocking events, the highly organized population structure both within and between areas of the contact zone indicates that the populations are native to the watersheds. Intermixing of distinct evolutionary lineages of cutthroat trout appears to be the result of historical connections between paleodrainages. Our analyses provide a context for understanding how genetic data can be used to assess the status of populations as native or introduced.
Collapse
Affiliation(s)
- Kendra R. Eaton
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, United States of America
| | - Janet L. Loxterman
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, United States of America
| | - Ernest R. Keeley
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, United States of America
| |
Collapse
|
9
|
Adams NE, Inoue K, Seidel RA, Lang BK, Berg DJ. Isolation drives increased diversification rates in freshwater amphipods. Mol Phylogenet Evol 2018; 127:746-757. [PMID: 29908996 DOI: 10.1016/j.ympev.2018.06.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 02/21/2018] [Accepted: 06/11/2018] [Indexed: 01/06/2023]
Abstract
Vicariance and dispersal events affect current biodiversity patterns in desert springs. Whether major diversification events are due to environmental changes leading to radiation or due to isolation resulting in relict species is largely unknown. We seek to understand whether the Gammarus pecos species complex underwent major diversification events due to environmental changes in the area leading either to radiation into novel habitats, or formation of relicts due to isolation. Specifically, we tested the hypothesis that Gammarus in the northern Chihuahuan Desert of New Mexico and Texas, USA are descendants of an ancient marine lineage now containing multiple undescribed species. We sequenced a nuclear (28S) and two mitochondrial (16S, COI) genes from gammarid amphipods representing 16 desert springs in the northern Chihuahuan Desert. We estimated phylogenetic relationships, divergence times, and diversification rates of the Gammarus pecos complex. Our results revealed that the region contained two evolutionarily independent lineages: a younger Freshwater Lineage that shared a most-recent-common-ancestor with an older Saline Lineage ∼66.3 MYA (95.6-42.4 MYA). Each spring system generally formed a monophyletic clade based on the concatenated dataset. Freshwater Lineage diversification rates were 2.0-9.8 times higher than rates of the Saline Lineage. A series of post-Cretaceous colonizations by ancestral Gammarus taxa was likely followed by isolation. Paleo-geological, hydrological, and climatic events in the Neogene-to-Quaternary periods (23.03 MYA - present) in western North America promoted allopatric speciation of both lineages. We suggest that Saline Lineage populations include two undescribed Gammarus species, while the Freshwater Lineage shows repetition of fine-scale genetic structure in all major clades suggesting incipient speciation. Such ongoing speciation suggests that this region will continue to be a biodiversity hotspot for amphipods and other freshwater taxa.
Collapse
Affiliation(s)
- Nicole E Adams
- Department of Biology, Miami University, Oxford, OH 45056, United States.
| | - Kentaro Inoue
- Department of Biology, Miami University, Oxford, OH 45056, United States
| | - Richard A Seidel
- Department of Biology, Miami University, Oxford, OH 45056, United States
| | - Brian K Lang
- New Mexico Department of Game and Fish, Santa Fe, NM 87507, United States
| | - David J Berg
- Department of Biology, Miami University, Hamilton, OH 45011, United States
| |
Collapse
|
10
|
Ruskey JA, Taylor EB. Morphological and genetic analysis of sympatric dace within the Rhinichthys cataractaespecies complex: a case of isolation lost. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12657] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jennifer A. Ruskey
- Department of Zoology; Biodiversity Research Centre and Beaty Biodiversity Museum; University of British Columbia; #4200-6270 University Blvd Vancouver BC V6T 1Z4 Canada
| | - Eric B. Taylor
- Department of Zoology; Biodiversity Research Centre and Beaty Biodiversity Museum; University of British Columbia; #4200-6270 University Blvd Vancouver BC V6T 1Z4 Canada
| |
Collapse
|
11
|
Taylor EB, McPhail J, Ruskey J. Phylogeography of the longnose dace (Rhinichthys cataractae) species group in northwestern North America — the Nooksack dace problem. CAN J ZOOL 2015. [DOI: 10.1139/cjz-2015-0014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The longnose dace (Rhinichthys cataractae (Valenciennes, 1842); Cyprinidae) is one of the most widespread freshwater fishes in North America, and across its range there have been several divergent forms described that are of uncertain taxonomic status. One of these forms, the Nooksack dace, is found in southwestern British Columbia and adjacent portions of western Washington, and is distinguished from longnose dace by a lower number of lateral-line scales. We sequenced a total of approximately 1400 base pairs (bp) of mitochondrial DNA (mtDNA) and noted that the longnose dace found west of the Continental Divide and Nooksack dace constituted reciprocally monophyletic clades that differed from each other by between 2% and 3% sequence divergence. Sequence analysis at two nuclear loci (the S7 ribosomal protein intron 1 (S7) and recombination activation gene 1 (RAG1)), however, showed no consistent difference between longnose dace and Nooksack dace and several alleles were shared between them. By contrast, consistent differences at both mtDNA and nuclear DNA loci were resolved between R. cataractae samples from east and west of the Continental Divide. The Nooksack dace does not appear to warrant separate taxonomic status from the longnose dace, but the mtDNA differences support its recognition as an important component of the evolutionary and biogeographic legacy of R. cataractae.
Collapse
Affiliation(s)
- Eric B. Taylor
- Department of Zoology, Biodiversity Research Centre and Beaty Biodiversity Museum, The University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
- Department of Zoology, Biodiversity Research Centre and Beaty Biodiversity Museum, The University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
| | - J.D. McPhail
- Department of Zoology, Biodiversity Research Centre and Beaty Biodiversity Museum, The University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
- Department of Zoology, Biodiversity Research Centre and Beaty Biodiversity Museum, The University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
| | - J.A. Ruskey
- Department of Zoology, Biodiversity Research Centre and Beaty Biodiversity Museum, The University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
- Department of Zoology, Biodiversity Research Centre and Beaty Biodiversity Museum, The University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
| |
Collapse
|
12
|
Inoue K, Lang BK, Berg DJ. Past climate change drives current genetic structure of an endangered freshwater mussel species. Mol Ecol 2015; 24:1910-26. [DOI: 10.1111/mec.13156] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 03/01/2015] [Accepted: 03/04/2015] [Indexed: 12/01/2022]
Affiliation(s)
- Kentaro Inoue
- Department of Biology; Miami University; 700 E. High Street Oxford OH 45056 USA
| | - Brian K. Lang
- New Mexico Department of Game and Fish; One Wildlife Way Santa Fe NM 87507 USA
| | - David J. Berg
- Department of Biology; Miami University; 1601 University Boulevard Hamilton OH 45011 USA
| |
Collapse
|