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Espinasa L, Smith DM, Lindquist JM. The Pennsylvania grotto sculpin: population genetics. SUBTERRANEAN BIOLOGY 2021. [DOI: 10.3897/subtbiol.38.60865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Pennsylvania grotto sculpin is known from just two caves of the Nippenose Valley in central Pennsylvania, USA. They exhibit emergent troglobitic morphological traits and are the second northern-most cave adapted fish in the world. Two mitochondrial (16S rRNA and D-loop gene) and one nuclear (S7 ribosomal protein gene intron) gene in both cave and epigean populations were sequenced. For the three markers, a large proportion of cave specimens possess unique haplotypes not found in their local surface counterparts, suggesting a vicariance in their evolutionary history. The cave population also has haplotypes from two separate lineages of surface sculpins of the Cottus cognatus/bairdii species complex. Since morphology, nuclear, and mitochondrial markers are not correlated among cave individuals, hybridization with introgression is suggested.
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Campbell DC, Piller KR. Let's jump in: A phylogenetic study of the great basin springfishes and poolfishes, Crenichthys and Empetrichthys (Cyprinodontiformes: Goodeidae). PLoS One 2017; 12:e0185425. [PMID: 29077708 PMCID: PMC5659628 DOI: 10.1371/journal.pone.0185425] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 09/12/2017] [Indexed: 12/04/2022] Open
Abstract
North America's Great Basin has long been of interest to biologists due to its high level of organismal endemicity throughout its endorheic watersheds. One example of such a group is the subfamily Empetricthyinae. In this paper, we analyzed the relationships of the Empetrichtyinae and assessed the validity of the subspecies designations given by Williams and Wilde within the group using concatenated phylogenetic tree estimation and species tree estimation. Samples from 19 populations were included covering the entire distribution of the three extant species of Empetricthyinae-Crenichthys nevadae, Crenichthys baileyi and Empetricthys latos. Three nuclear introns (S8 intron 4, S7 intron 1, and P0 intron 1) and one mitochondrial gene (Cytb) were sequenced for phylogenetic analysis. Using these sequences, we generated two separate hypotheses of the evolutionary relationships of Empetrichtyinae- one based on the mitochondrial data and one based on the nuclear data using Bayesian phylogenetics. Haplotype networks were also generated to look at the relationships of the populations within Empetrichthyinae. After comparing the two phylogenetic hypotheses, species trees were generated using *BEAST with the nuclear data to further test the validity of the subspecies within Empetrichthyinae. The mitochondrial analyses supported four lineages within C. baileyi and 2 within C. nevadae. The concatenated nuclear tree was more conserved, supporting one clade and an unresolved polytomy in both species. The species tree analysis supported the presence of two species within both C. baileyi and C. nevadae. Based on the results of these analyses, the subspecies designations of Williams and Wilde are not valid, rather a conservative approach suggests there are two species within C. nevadae and two species within C. baileyi. No structure was found for E. latos or the populations of Empetricthyinae. This study represents one of many demonstrating the invalidity of subspecies and their detriment to species identification, conservation, and understanding.
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Affiliation(s)
- D. Cooper Campbell
- Southeastern Louisiana University, Dept. of Biological Sciences, Hammond,United States of America
| | - Kyle R. Piller
- Southeastern Louisiana University, Dept. of Biological Sciences, Hammond,United States of America
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Silva RDA, Silva D, Veneza I, Sampaio I, Schneider H, Gomes G. Development of EPIC-PCR Markers for Lutjanus purpureus (Lutjanidae-Perciformes) and their Potential Applicability in Population Analyses. AN ACAD BRAS CIENC 2017; 89:2095-2100. [PMID: 28678957 DOI: 10.1590/0001-3765201720150476] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 05/25/2016] [Indexed: 11/21/2022] Open
Abstract
In the present study, a novel set of eight EPIC primers were developed for Lutjanus purpureus and assayed in five other marine teleosts including three lutjanids, one scianid and one anablepid. Most of the genomic regions used in this study presented genetic diversity indexes equal or greater than the intragenic regions commonly used in population genetics studies. Moreover, six out of eight markers showed cross-amplification with other taxa. Thus, the primers described here may be used to elucidate questions at the intraspecific level for a large number of taxa.
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Affiliation(s)
- Raimundo DA Silva
- Laboratório de Genética Aplicada, Instituto de Estudos Costeiros, Universidade Federal do Pará, Campus Bragança, Alameda Leandro Ribeiro, s/n, Aldeia, 68600-000 Bragança, PA, Brazil
| | - Danillo Silva
- Laboratório de Genética Aplicada, Instituto de Estudos Costeiros, Universidade Federal do Pará, Campus Bragança, Alameda Leandro Ribeiro, s/n, Aldeia, 68600-000 Bragança, PA, Brazil
| | - Ivana Veneza
- Laboratório de Genética Aplicada, Instituto de Estudos Costeiros, Universidade Federal do Pará, Campus Bragança, Alameda Leandro Ribeiro, s/n, Aldeia, 68600-000 Bragança, PA, Brazil
| | - Iracilda Sampaio
- Laboratório de Genética e Biologia Molecular, Instituto de Estudos Costeiros, Universidade Federal do Pará, Campus Bragança, Alameda Leandro Ribeiro, s/n, Aldeia, 68600-000 Bragança, PA, Brazil
| | - Horacio Schneider
- Laboratório de Genética e Biologia Molecular, Instituto de Estudos Costeiros, Universidade Federal do Pará, Campus Bragança, Alameda Leandro Ribeiro, s/n, Aldeia, 68600-000 Bragança, PA, Brazil
| | - Grazielle Gomes
- Laboratório de Genética Aplicada, Instituto de Estudos Costeiros, Universidade Federal do Pará, Campus Bragança, Alameda Leandro Ribeiro, s/n, Aldeia, 68600-000 Bragança, PA, Brazil
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Almada F, Francisco SM, Lima CS, FitzGerald R, Mirimin L, Villegas-Ríos D, Saborido-Rey F, Afonso P, Morato T, Bexiga S, Robalo JI. Historical gene flow constraints in a northeastern Atlantic fish: phylogeography of the ballan wrasse Labrus bergylta across its distribution range. ROYAL SOCIETY OPEN SCIENCE 2017; 4:160773. [PMID: 28386433 PMCID: PMC5367310 DOI: 10.1098/rsos.160773] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 01/16/2017] [Indexed: 05/17/2023]
Abstract
The distribution and demographic patterns of marine organisms in the north Atlantic were largely shaped by climatic changes during the Pleistocene, when recurrent glacial maxima forced them to move south or to survive in northern peri-glacial refugia. These patterns were also influenced by biological and ecological factors intrinsic to each species, namely their dispersion ability. The ballan wrasse (Labrus bergylta), the largest labrid fish along Europe's continental margins, is a target for fisheries and aquaculture industry. The phylogeographic pattern, population structure, potential glacial refugia and recolonization routes for this species were assessed across its full distribution range, using mitochondrial and nuclear markers. The existence of a marked population structure can reflect both recolonization from three distinct glacial refugia and current and past oceanographic circulation patterns. Although isolated in present times, shared haplotypes between continental and Azores populations and historical exchange of migrants in both directions point to a common origin of L. bergylta. This situation is likely to be maintained and/or accentuated by current circulation patterns in the north Atlantic, and may lead to incipient speciation in the already distinct Azorean population. Future monitoring of this species is crucial to evaluate how this species is coping with current environmental changes.
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Affiliation(s)
- Frederico Almada
- MARE—Marine and Environmental Sciences Centre, ISPA Instituto Universitário, Rua Jardim do Tabaco 34, 1149-041 Lisboa, Portugal
| | - Sara M. Francisco
- MARE—Marine and Environmental Sciences Centre, ISPA Instituto Universitário, Rua Jardim do Tabaco 34, 1149-041 Lisboa, Portugal
| | - Cristina S. Lima
- MARE—Marine and Environmental Sciences Centre, ISPA Instituto Universitário, Rua Jardim do Tabaco 34, 1149-041 Lisboa, Portugal
| | - Richard FitzGerald
- Carna Research Station, Ryan Institute, National University of Ireland, Galway, Republic of Ireland
| | - Luca Mirimin
- Marine and Freshwater Research Centre, Galway-Mayo Institute of Technology, Dublin Road, Galway, Republic of Ireland
| | - David Villegas-Ríos
- Institute of Marine Research (IMR), Flødevigen Marine Research Station, 4817 His, Norway
| | | | - Pedro Afonso
- MARE—Marine and Environmental Sciences Centre, Universidade dos Açores, 9901-862 Horta, Portugal
- Departamento de Oceanografia e Pescas da Universidade dos Açores, IMAR—Institute of Marine Research, 9901-862 Horta, Portugal
| | - Telmo Morato
- MARE—Marine and Environmental Sciences Centre, Universidade dos Açores, 9901-862 Horta, Portugal
| | - Sérgio Bexiga
- MARE—Marine and Environmental Sciences Centre, ISPA Instituto Universitário, Rua Jardim do Tabaco 34, 1149-041 Lisboa, Portugal
| | - Joana I. Robalo
- MARE—Marine and Environmental Sciences Centre, ISPA Instituto Universitário, Rua Jardim do Tabaco 34, 1149-041 Lisboa, Portugal
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