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Veneza I, da Silva R, Ferreira C, Mendonça P, Sampaio I, Evangelista-Gomes G. Genetic connectivity and population expansion inferred from multilocus analysis in Lutjanus alexandrei (Lutjanidae-Perciformes), an endemic snapper from Northeastern Brazilian coast. PeerJ 2023; 11:e15973. [PMID: 37780387 PMCID: PMC10540771 DOI: 10.7717/peerj.15973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/06/2023] [Indexed: 10/03/2023] Open
Abstract
Previous studies about the genetic diversity, connectivity and demographic history in Lutjanidae fishes have reported a common pattern of genetic homogeneity and expansion in populations from Western South Atlantic. In the present work, we inferred the population structure, the levels of genetic diversity and the demographic history of the Brazilian snapper Lutjanus alexandrei, a recently described and endemic species from Northeastern coast of Brazil. Five different fragments, including mitochondrial DNA (Control Region, Cyt b and ND4) and nuclear DNA (Myostatin and S7) regions were analyzed in 120 specimens of L. alexandrei from four localities in Northeastern Brazil, representing the first study of population genetics in this species. High levels of genetic diversity were observed following a panmictic pattern, probably related to the larval dispersal by the current tides along the Brazilian coast. In addition, both demographic history and neutrality tests indicated that L. alexandrei has undergone population expansion during Pleistocene. In this sense, the sea level variation from this period could have increased the available resources and suitable habitats for the Brazilian snapper.
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Affiliation(s)
- Ivana Veneza
- Campus Universitário de Monte Alegre, Universidade Federal do Oeste do Pará, Monte Alegre, Pará, Brazil
| | - Raimundo da Silva
- Instituto de Estudos Costeiros/Laboratório de Genética Aplicada, Universidade Federal do Pará, Bragança, Pará, Brazil
| | - Charles Ferreira
- Instituto de Estudos Costeiros/Laboratório de Genética Aplicada, Universidade Federal do Pará, Bragança, Pará, Brazil
| | - Patrícia Mendonça
- Instituto de Estudos Costeiros/Grupo de Genética e Conservação, Universidade Federal do Pará, Bragança, Pará, Brazil
| | - Iracilda Sampaio
- Instituto de Estudos Costeiros/Laboratório de Genética e Biologia Molecular, Universidade Federal do Pará, Bragança, Pará, Brazil
| | - Grazielle Evangelista-Gomes
- Instituto de Estudos Costeiros/Laboratório de Genética Aplicada, Universidade Federal do Pará, Bragança, Pará, Brazil
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2
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Fainburg L, Sabadin D, Díaz de Astarloa JM, Fernández Iriarte P. Population structure of mud flounder Paralichthys orbignyanus from the south-western Atlantic Ocean. JOURNAL OF FISH BIOLOGY 2023; 102:455-464. [PMID: 36427018 DOI: 10.1111/jfb.15271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 11/13/2022] [Indexed: 06/16/2023]
Abstract
The mud flounder Paralichthys orbignyanus (Pleuronectiformes, Paralichthyidae) inhabits shallow waters of low salinities and mud bottoms in the temperate marine coastal regions of the Bonaerensean Ecoregion of the Argentinean Biogeographic Province in the south-western Atlantic Ocean. Specimens of P. orbignyanus were collected from Lagoa dos Patos (LDP) (southern Brazil), Mar Chiquita (MCH) and Marisol (MAR) both located in Buenos Aires (Argentina), and San Antonio Oeste (SAO) in the San Matías Gulf, Rio Negro (Argentina). A fragment of the mitochondrial DNA of the Control Region and seven microsatellite loci were characterized. In the Control Region, P. orbignyanus showed high variability, low nucleotide diversity, mild population expansion and a coalescence time of 35,000 years before the present. Flounders provided evidence of a genetic structure between the sampling sites LDP, MCH, MAR vs. SAO. On the other hand, P. orbignyanus displayed a lower to moderate contemporary genetic structure among all samples except between LDP and MCH. With no evidence of isolation by distance, this analysis supports a model of limited gene flow that is likely to be associated with a consistent larvae retention in all sampling sites. In addition, the present connectivity is ascribed to a lower migration process from SAO in the San Matías Gulf congruent with the prevailing littoral drift.
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Affiliation(s)
- Leandro Fainburg
- Departamento de Biología-Instituto de Investigaciones Marinas y Costeras, Laboratorio de Genética, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Mar del Plata, Argentina
| | - David Sabadin
- Instituto de Investigaciones Marinas y Costeras, Laboratorio Biología de Peces, Universidad Nacional de Mar del Plata, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Mar del Plata, Argentina
| | - Juan Martín Díaz de Astarloa
- Departamento de Biología-Instituto de Investigaciones Marinas y Costeras, Laboratorio de Biotaxonomía Morfológica y Molecular de Peces (BIMOPE), Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Mar del Plata, Argentina
| | - Pedro Fernández Iriarte
- Departamento de Biología-Instituto de Investigaciones Marinas y Costeras, Laboratorio de Genética, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Mar del Plata, Argentina
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3
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Grilly E, Reid K, Thanassekos S. Long-distance movements of Antarctic toothfish (Dissostichus mawsoni) as inferred from tag-recapture data. JOURNAL OF FISH BIOLOGY 2022; 100:1150-1157. [PMID: 34739139 DOI: 10.1111/jfb.14941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 05/26/2021] [Accepted: 11/02/2021] [Indexed: 06/13/2023]
Abstract
Examining the causes and consequences of animal movement is fundamental to understanding the ecology of any species. This analysis focuses on Antarctic toothfish movements in the Southern Ocean as inferred from tagging data collected from 2001 to 2019 with a focus on the characteristics of long-distance movements, defined as an individual recaptured greater than 200 km from their release location. The results of this analysis indicate that while adult Antarctic toothfish are generally quite sedentary a small proportion (~7%) move long distances, consistent with findings from previous studies examining movements of toothfish. There appears to be no relationship between time at liberty and long-distance movements, no strong influence of sex and results indicate a distinct bias in the direction of long-distance travel from release to recapture towards a counter-clockwise direction. Frequency and scale of long-distance movements are likely influenced by localized physical oceanographic processes and life-history traits. Knowledge of these movements patterns remains highly important for stock assessments and the design of spatial and temporal fisheries management regimes.
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Affiliation(s)
- Emily Grilly
- Commission for the Conservation of Antarctic Marine Living Resources, Hobart, Australia
| | - Keith Reid
- Commission for the Conservation of Antarctic Marine Living Resources, Hobart, Australia
| | - Stéphane Thanassekos
- Commission for the Conservation of Antarctic Marine Living Resources, Hobart, Australia
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Daane JM, William Detrich H. Adaptations and Diversity of Antarctic Fishes: A Genomic Perspective. Annu Rev Anim Biosci 2021; 10:39-62. [PMID: 34748709 DOI: 10.1146/annurev-animal-081221-064325] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Antarctic notothenioid fishes are the classic example of vertebrate adaptive radiation in a marine environment. Notothenioids diversified from a single common ancestor ∼25 Mya to more than 140 species today, and they represent ∼90% of fish biomass on the continental shelf of Antarctica. As they diversified in the cold Southern Ocean, notothenioids evolved numerous traits, including osteopenia, anemia, cardiomegaly, dyslipidemia, and aglomerular kidneys, that are beneficial or tolerated in their environment but are pathological in humans. Thus, notothenioids are models for understanding adaptive radiations, physiological and biochemical adaptations to extreme environments, and genetic mechanisms of human disease. Since 2014, 16 notothenioid genomes have been published, which enable a first-pass holistic analysis of the notothenioid radiation and the genetic underpinnings of novel notothenioid traits. Here, we review the notothenioid radiation from a genomic perspective and integrate our insights with recent observations from other fish radiations. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 10 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Jacob M Daane
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, Massachusetts, USA
| | - H William Detrich
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, Massachusetts, USA
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Schiavon L, Dulière V, La Mesa M, Marino IAM, Codogno G, Boscari E, Riginella E, Battistotti A, Lucassen M, Zane L, Papetti C. Species distribution, hybridization and connectivity in the genus
Chionodraco
: Unveiling unknown icefish diversity in antarctica. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13249] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Luca Schiavon
- Department of Biology University of Padova Padova Italy
| | - Valérie Dulière
- Royal Belgian Institute of Natural Sciences Brussels Belgium
| | | | - Ilaria Anna Maria Marino
- Department of Biology University of Padova Padova Italy
- Consorzio Nazionale Interuniversitario Per le Scienze del Mare (CoNISMa) Roma Italy
| | | | - Elisa Boscari
- Department of Biology University of Padova Padova Italy
- Consorzio Nazionale Interuniversitario Per le Scienze del Mare (CoNISMa) Roma Italy
| | | | | | - Magnus Lucassen
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research Bremerhaven Germany
| | - Lorenzo Zane
- Department of Biology University of Padova Padova Italy
- Consorzio Nazionale Interuniversitario Per le Scienze del Mare (CoNISMa) Roma Italy
| | - Chiara Papetti
- Department of Biology University of Padova Padova Italy
- Consorzio Nazionale Interuniversitario Per le Scienze del Mare (CoNISMa) Roma Italy
- Zoological Station Anton Dohrn Naples Italy
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Connectivity and population structure of albacore tuna across southeast Atlantic and southwest Indian Oceans inferred from multidisciplinary methodology. Sci Rep 2020; 10:15657. [PMID: 32973260 PMCID: PMC7519111 DOI: 10.1038/s41598-020-72369-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 07/09/2020] [Indexed: 11/17/2022] Open
Abstract
Albacore tuna (Thunnus alalunga) is an important target of tuna fisheries in the Atlantic and Indian Oceans. The commercial catch of albacore is the highest globally among all temperate tuna species, contributing around 6% in weight to global tuna catches over the last decade. The accurate assessment and management of this heavily exploited resource requires a robust understanding of the species’ biology and of the pattern of connectivity among oceanic regions, yet Indian Ocean albacore population dynamics remain poorly understood and its level of connectivity with the Atlantic Ocean population is uncertain. We analysed morphometrics and genetics of albacore (n = 1,874) in the southwest Indian (SWIO) and southeast Atlantic (SEAO) Oceans to investigate the connectivity and population structure. Furthermore, we examined the species’ dispersal potential by modelling particle drift through major oceanographic features. Males appear larger than females, except in South African waters, yet the length–weight relationship only showed significant male–female difference in one region (east of Madagascar and Reunion waters). The present study produced a genetic differentiation between the southeast Atlantic and southwest Indian Oceans, supporting their demographic independence. The particle drift models suggested dispersal potential of early life stages from SWIO to SEAO and adult or sub-adult migration from SEAO to SWIO.
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Sandoval-Huerta ER, Beltrán-López RG, Pedraza-Marrón CR, Paz-Velásquez MA, Angulo A, Robertson DR, Espinoza E, Domínguez-Domínguez O. The evolutionary history of the goby Elacatinus puncticulatus in the tropical eastern pacific: Effects of habitat discontinuities and local environmental variability. Mol Phylogenet Evol 2018; 130:269-285. [PMID: 30359746 DOI: 10.1016/j.ympev.2018.10.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 09/05/2018] [Accepted: 10/15/2018] [Indexed: 10/28/2022]
Abstract
Habitat discontinuities, temperature gradients, upwelling systems, and ocean currents, gyres and fronts, can affect distributions of species with narrow environmental tolerance or motility and influence the dispersal of pelagic larvae, with effects ranging from the isolation of adjacent populations to connections between them. The coast of the Tropical Eastern Pacific (TEP) is a highly dynamic environment, with various large gyres and upwelling systems, alternating currents and large rocky-habitat discontinuities, which may greatly influence the genetic connectivity of populations in different parts of the coast. Elacatinus puncticulatus is a cryptic, shallow-living goby that is distributed along the continental shore of virtually the entire TEP, which makes it a good model for testing the influence of these environmental characteristics in the molecular evolution of widespread species in this region. A multilocus phylogeny was used to evaluate the influence of habitat gaps, and oceanographic processes in the evolutionary history of E. puncticulatus throughout its geographical range in the TEP. Two well-supported allopatric clades (one with two allopatric subclades) were recovered, the geographic distribution of which does not correspond to any previously proposed major biogeographic provinces. These populations show strong genetic structure and substantial genetic distances between clades and sub-clades (cytb 0.8-7.3%), with divergence times between them ranging from 0.53 to 4.88 Mya, and recent population expansions dated at 170-130 Kya. The ancestral area of all populations appears to be the Gulf of Panama, while several isolation events have formed the phylogeographic patterns evident in this species. Local and regional oceanographic processes as well as habitat discontinuities have shaped the distribution patterns of the genetic lineages along the continental TEP. Large genetic distances, high genetic differentiation, and the results of species-tree and phylogenetic analyses indicate that E. puncticulatus comprises a complex of three allopatric species with an unusual geographic arrangement.
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Affiliation(s)
- E R Sandoval-Huerta
- Programa Institucional de Maestría en Ciencias Biológicas, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Edificio "R" planta baja, Ciudad Universitaria, Morelia, Michoacán 58030, Mexico; Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Edificio "R" planta baja, Ciudad Universitaria, Morelia, Michoacán 58030, Mexico
| | - R G Beltrán-López
- Programa Institucional de Doctorado en Ciencias Biológicas, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Edificio "R" planta baja, Ciudad Universitaria, Morelia, Michoacán 58030, Mexico; Laboratorio de Ictiología, Centro de Investigaciones Biológicas, Universidad Autónoma del Estado de Morelos, Av. Universidad no. 1001, Cuernavaca, Morelos 62209, Mexico.
| | - C R Pedraza-Marrón
- Programa Institucional de Maestría en Ciencias Biológicas, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Edificio "R" planta baja, Ciudad Universitaria, Morelia, Michoacán 58030, Mexico; Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Edificio "R" planta baja, Ciudad Universitaria, Morelia, Michoacán 58030, Mexico
| | - M A Paz-Velásquez
- Centro de Estudios del Mar y Acuicultura, Universidad de San Carlos de Guatemala, Guatemala City, Guatemala
| | - A Angulo
- Museo de Zoología y Centro de Investigación en Ciencias del Mar y Limnología, Universidad de Costa Rica. 11501-2060, San Pedro de Montes de Oca, San José, Costa Rica
| | - D R Robertson
- Naos Marine Laboratory, Smithsonian Tropical Research Institute, Balboa, Panama.
| | - E Espinoza
- Dirección del Parque Nacional Galápagos, Puerto Ayora, Islas Galápagos, Ecuador.
| | - O Domínguez-Domínguez
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Edificio "R" planta baja, Ciudad Universitaria, Morelia, Michoacán 58030, Mexico.
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Jenkins TL, Castilho R, Stevens JR. Meta-analysis of northeast Atlantic marine taxa shows contrasting phylogeographic patterns following post-LGM expansions. PeerJ 2018; 6:e5684. [PMID: 30280047 PMCID: PMC6166638 DOI: 10.7717/peerj.5684] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 08/30/2018] [Indexed: 01/09/2023] Open
Abstract
Background Comparative phylogeography enables the study of historical and evolutionary processes that have contributed to shaping patterns of contemporary genetic diversity across co-distributed species. In this study, we explored genetic structure and historical demography in a range of coastal marine species across the northeast Atlantic to assess whether there are commonalities in phylogeographic patterns across taxa and to evaluate whether the timings of population expansions were linked to the Last Glacial Maximum (LGM). Methods A literature search was conducted using Web of Science. Search terms were chosen to maximise the inclusion of articles reporting on population structure and phylogeography from the northeast Atlantic; titles and abstracts were screened to identify suitable articles within the scope of this study. Given the proven utility of mtDNA in comparative phylogeography and the availability of these data in the public domain, a meta-analysis was conducted using published mtDNA gene sequences. A standardised methodology was implemented to ensure that the genealogy and demographic history of all mtDNA datasets were reanalysed in a consistent and directly comparable manner. Results Mitochondrial DNA datasets were built for 21 species. The meta-analysis revealed significant population differentiation in 16 species and four main types of haplotype network were found, with haplotypes in some species unique to specific geographical locations. A signal of rapid expansion was detected in 16 species, whereas five species showed evidence of a stable population size. Corrected mutation rates indicated that the majority of expansions were estimated to have occurred after the earliest estimate for the LGM (∼26.5 Kyr), while few expansions were estimated to have pre-dated the LGM. Conclusion This study suggests that post-LGM expansion appeared to be common in a range of marine taxa, supporting the concept of rapid expansions after the LGM as the ice sheets started to retreat. However, despite the commonality of expansion patterns in many of these taxa, phylogeographic patterns appear to differ in the species included in this study. This suggests that species-specific evolutionary processes, as well as historical events, have likely influenced the distribution of genetic diversity of marine taxa in the northeast Atlantic.
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Affiliation(s)
- Tom L Jenkins
- Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Rita Castilho
- Center for Marine Sciences, Campus de Gambelas, University of Algarve, Faro, Portugal
| | - Jamie R Stevens
- Department of Biosciences, University of Exeter, Exeter, United Kingdom
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Díaz A, Gérard K, González-Wevar C, Maturana C, Féral JP, David B, Saucède T, Poulin E. Genetic structure and demographic inference of the regular sea urchin Sterechinus neumayeri (Meissner, 1900) in the Southern Ocean: The role of the last glaciation. PLoS One 2018; 13:e0197611. [PMID: 29874287 PMCID: PMC5991379 DOI: 10.1371/journal.pone.0197611] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 05/04/2018] [Indexed: 01/10/2023] Open
Abstract
One of the most relevant characteristics of the extant Southern Ocean fauna is its resiliency to survive glacial processes of the Quaternary. These climatic events produced catastrophic habitat reductions and forced some marine benthic species to move, adapt or go extinct. The marine benthic species inhabiting the Antarctic upper continental shelf faced the Quaternary glaciations with different strategies that drastically modified population sizes and thus affected the amount and distribution of intraspecific genetic variation. Here we present new genetic information for the most conspicuous regular sea urchin of the Antarctic continental shelf, Sterechinus neumayeri. We studied the patterns of genetic diversity and structure in this broadcast-spawner across three Antarctic regions: Antarctic Peninsula, the Weddell Sea and Adélie Land in East Antarctica. Genetic analyses based on mitochondrial and nuclear markers suggested that S. neumayeri is a single genetic unit around the Antarctic continent. The species is characterized by low levels of genetic diversity and exhibits a typical star-like haplotype genealogy that supports the hypothesis of a single in situ refugium. Based on two mutation rates standardized for this genus, the Bayesian Skyline plot analyses detected a rapid demographic expansion after the Last Glacial Maximum. We propose a scenario of rapid postglacial expansion and recolonization of Antarctic shallow areas from a less ice-impacted refugium where the species survived the LGM. Considering the patterns of genetic diversity and structure recorded in the species, this refugium was probably located in East Antarctica.
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Affiliation(s)
- Angie Díaz
- Departamento de Zoología, Universida d de Concepción, Barrio Universitario s/n, Concepción, Chile
| | - Karin Gérard
- Facultad de Ciencias, Universidad de Magallanes, Bulnes, Punta Arenas, Chile
- Laboratorio de Ecología Molecular Antártica y Subantártica, Universidad de Magallanes, Punta Arenas, Chile
| | - Claudio González-Wevar
- Laboratorio de Ecología Molecular Antártica y Subantártica, Universidad de Magallanes, Punta Arenas, Chile
- Instituto de Ciencias Marinas y Limnológicas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Instituto de Ecología y Biodiversidad (IEB), Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras, Ñuñoa, Santiago, Chile
| | - Claudia Maturana
- Instituto de Ecología y Biodiversidad (IEB), Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras, Ñuñoa, Santiago, Chile
| | - Jean-Pierre Féral
- UMR 7263—IMBE, Station Marine d’Endoume, Institut Méditerranéen de Biodiversité et d’Ecologie Marine et continentale, Chemin de la Batterie des Lions,Marseille, France
| | - Bruno David
- Biogéosciences, UMR CNRS 6282, Université de Bourgogne, boulevard Gabriel, Dijon, France
- Museum National d’Histoire Naturelle, Paris, France
| | - Thomas Saucède
- UMR 7263—IMBE, Station Marine d’Endoume, Institut Méditerranéen de Biodiversité et d’Ecologie Marine et continentale, Chemin de la Batterie des Lions,Marseille, France
| | - Elie Poulin
- Instituto de Ecología y Biodiversidad (IEB), Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras, Ñuñoa, Santiago, Chile
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Bennett KL, Kaddumukasa M, Shija F, Djouaka R, Misinzo G, Lutwama J, Linton YM, Walton C. Comparative phylogeography of Aedes mosquitoes and the role of past climatic change for evolution within Africa. Ecol Evol 2018; 8:3019-3036. [PMID: 29531714 PMCID: PMC5838080 DOI: 10.1002/ece3.3668] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 10/26/2017] [Accepted: 10/27/2017] [Indexed: 01/01/2023] Open
Abstract
The study of demographic processes involved in species diversification and evolution ultimately provides explanations for the complex distribution of biodiversity on earth, indicates regions important for the maintenance and generation of biodiversity, and identifies biological units important for conservation or medical consequence. African and forest biota have both received relatively little attention with regard to understanding their diversification, although one possible mechanism is that this has been driven by historical climate change. To investigate this, we implemented a standard population genetics approach along with Approximate Bayesian Computation, using sequence data from two exon-primed intron-crossing (EPIC) nuclear loci and mitochondrial cytochrome oxidase subunit I, to investigate the evolutionary history of five medically important and inherently forest dependent mosquito species of the genus Aedes. By testing different demographic hypotheses, we show that Aedes bromeliae and Aedes lilii fit the same model of lineage diversification, admixture, expansion, and recent population structure previously inferred for Aedes aegypti. In addition, analyses of population structure show that Aedes africanus has undergone lineage diversification and expansion while Aedes hansfordi has been impacted by population expansion within Uganda. This congruence in evolutionary history is likely to relate to historical climate-driven habitat change within Africa during the late Pleistocene and Holocene epoch. We find differences in the population structure of mosquitoes from Tanzania and Uganda compared to Benin and Uganda which could relate to differences in the historical connectivity of forests across the continent. Our findings emphasize the importance of recent climate change in the evolution of African forest biota.
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Affiliation(s)
- Kelly Louise Bennett
- Faculty of Life SciencesComputational Evolutionary Biology GroupUniversity of ManchesterManchesterUK
| | - Martha Kaddumukasa
- Department of Arbovirology, Emerging and Re‐emerging InfectionsUganda Virus Research InstituteEntebbeUganda
- WITS Institute for Malaria ResearchSchool of Pathology Faculty of Health SciencesUniversity of WitwatersrandParktownJohannesburg
| | - Fortunate Shija
- Faculty of Life SciencesComputational Evolutionary Biology GroupUniversity of ManchesterManchesterUK
- Department of Veterinary Microbiology and ParasitologySokoine University of AgricultureMorogoroTanzania
| | - Rousseau Djouaka
- Agro‐Eco‐Health Platform for West and Central AfricaInternational Institute for Tropical AgricultureCotonouRepublic of Benin
| | - Gerald Misinzo
- Agro‐Eco‐Health Platform for West and Central AfricaInternational Institute for Tropical AgricultureCotonouRepublic of Benin
| | - Julius Lutwama
- Department of Arbovirology, Emerging and Re‐emerging InfectionsUganda Virus Research InstituteEntebbeUganda
| | - Yvonne Marie Linton
- Department of EntomologyNational Museum of Natural HistorySmithsonian InstitutionWashingtonDCUSA
- Walter Reed Biosystematics UnitSmithsonian Institution Museum Support CenterSuitlandMDUSA
- Walter Reed Army Institute of ResearchSilver SpringMDUSA
- Uniformed Services University of Health SciencesBethesdaMDUSA
| | - Catherine Walton
- Faculty of Life SciencesComputational Evolutionary Biology GroupUniversity of ManchesterManchesterUK
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Abstract
Understanding how geography, oceanography, and climate have ultimately shaped marine biodiversity requires aligning the distributions of genetic diversity across multiple taxa. Here, we examine phylogeographic partitions in the sea against a backdrop of biogeographic provinces defined by taxonomy, endemism, and species composition. The taxonomic identities used to define biogeographic provinces are routinely accompanied by diagnostic genetic differences between sister species, indicating interspecific concordance between biogeography and phylogeography. In cases where individual species are distributed across two or more biogeographic provinces, shifts in genotype frequencies often align with biogeographic boundaries, providing intraspecific concordance between biogeography and phylogeography. Here, we provide examples of comparative phylogeography from (i) tropical seas that host the highest marine biodiversity, (ii) temperate seas with high productivity but volatile coastlines, (iii) migratory marine fauna, and (iv) plankton that are the most abundant eukaryotes on earth. Tropical and temperate zones both show impacts of glacial cycles, the former primarily through changing sea levels, and the latter through coastal habitat disruption. The general concordance between biogeography and phylogeography indicates that the population-level genetic divergences observed between provinces are a starting point for macroevolutionary divergences between species. However, isolation between provinces does not account for all marine biodiversity; the remainder arises through alternative pathways, such as ecological speciation and parapatric (semiisolated) divergences within provinces and biodiversity hotspots.
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13
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Delrieu-Trottin E, Mona S, Maynard J, Neglia V, Veuille M, Planes S. Population expansions dominate demographic histories of endemic and widespread Pacific reef fishes. Sci Rep 2017; 7:40519. [PMID: 28091580 PMCID: PMC5238389 DOI: 10.1038/srep40519] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 12/07/2016] [Indexed: 12/20/2022] Open
Abstract
Despite the unique nature of endemic species, their origin and population history remain poorly studied. We investigated the population history of 28 coral reef fish species, close related, from the Gambier and Marquesas Islands, from five families, with range size varying from widespread to small-range endemic. We analyzed both mitochondrial and nuclear sequence data using neutrality test and Bayesian analysis (EBSP and ABC). We found evidence for demographic expansions for most species (24 of 28), irrespective of range size, reproduction strategy or archipelago. The timing of the expansions varied greatly among species, from 8,000 to 2,000,000 years ago. The typical hypothesis for reef fish that links population expansions to the Last Glacial Maximum fit for 14 of the 24 demographic expansions. We propose two evolutionary processes that could lead to expansions older than the LGM: (a) we are retrieving the signature of an old colonization process for widespread, large-range endemic and paleoendemic species or (b) speciation; the expansion reflects the birth of the species for neoendemic species. We show for the first time that the demographic histories of endemic and widespread reef fish are not distinctly different and suggest that a number of processes drive endemism.
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Affiliation(s)
- Erwan Delrieu-Trottin
- Laboratoire d’Excellence «CORAIL», EPHE, PSL Research University, UPVD, CNRS, USR 3278 CRIOBE, F-66360 Perpignan, France
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Stefano Mona
- Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205 - CNRS, MNHN, UPMC, EPHE, Ecole Pratique des Hautes Etudes, Paris Sorbonne Universités, Paris, France
- EPHE, PSL Research University, Paris, France
| | - Jeffrey Maynard
- Laboratoire d’Excellence «CORAIL», EPHE, PSL Research University, UPVD, CNRS, USR 3278 CRIOBE, F-66360 Perpignan, France
- SymbioSeas and Marine Applied Research Center, Wilmington NC 28411, United States of America
| | - Valentina Neglia
- Laboratoire d’Excellence «CORAIL», EPHE, PSL Research University, UPVD, CNRS, USR 3278 CRIOBE, F-66360 Perpignan, France
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Michel Veuille
- Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205 - CNRS, MNHN, UPMC, EPHE, Ecole Pratique des Hautes Etudes, Paris Sorbonne Universités, Paris, France
- EPHE, PSL Research University, Paris, France
| | - Serge Planes
- Laboratoire d’Excellence «CORAIL», EPHE, PSL Research University, UPVD, CNRS, USR 3278 CRIOBE, F-66360 Perpignan, France
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14
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Dömel JS, Melzer RR, Harder AM, Mahon AR, Leese F. Nuclear and Mitochondrial Gene Data Support Recent Radiation within the Sea Spider Species Complex Pallenopsis patagonica. Front Ecol Evol 2017. [DOI: 10.3389/fevo.2016.00139] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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15
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Basher Z, Costello MJ. The past, present and future distribution of a deep-sea shrimp in the Southern Ocean. PeerJ 2016; 4:e1713. [PMID: 26925334 PMCID: PMC4768674 DOI: 10.7717/peerj.1713] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 01/29/2016] [Indexed: 01/22/2023] Open
Abstract
Shrimps have a widespread distribution across the shelf, slope and seamount regions of the Southern Ocean. Studies of Antarctic organisms have shown that individual species and higher taxa display different degrees of sensitivity and adaptability in response to environmental change. We use species distribution models to predict changes in the geographic range of the deep-sea Antarctic shrimp Nematocarcinus lanceopes under changing climatic conditions from the Last Glacial Maximum to the present and to the year 2100. The present distribution range indicates a pole-ward shift of the shrimp population since the last glaciation. This occurred by colonization of slopes from nearby refugia located around the northern part of Scotia Arc, southern tip of South America, South Georgia, Bouvet Island, southern tip of the Campbell plateau and Kerguelen plateau. By 2100, the shrimp are likely to expand their distribution in east Antarctica but have a continued pole-ward contraction in west Antarctica. The range extension and contraction process followed by the deep-sea shrimp provide a geographic context of how other deep-sea Antarctic species may have survived during the last glaciation and may endure with projected changing climatic conditions in the future.
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Affiliation(s)
- Zeenatul Basher
- Institute of Marine Science, Leigh Marine Laboratory, The University of Auckland, Auckland, New Zealand
| | - Mark J. Costello
- Institute of Marine Science, Leigh Marine Laboratory, The University of Auckland, Auckland, New Zealand
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16
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Kašparová E, Van de Putte AP, Marshall C, Janko K. Lifestyle and Ice: The Relationship between Ecological Specialization and Response to Pleistocene Climate Change. PLoS One 2015; 10:e0138766. [PMID: 26535569 PMCID: PMC4636791 DOI: 10.1371/journal.pone.0138766] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 09/03/2015] [Indexed: 11/19/2022] Open
Abstract
Major climatic changes in the Pleistocene had significant effects on marine organisms and the environments in which they lived. The presence of divergent patterns of demographic history even among phylogenetically closely-related species sharing climatic changes raises questions as to the respective influence of species-specific traits on population structure. In this work we tested whether the lifestyle of Antarctic notothenioid benthic and pelagic fish species from the Southern Ocean influenced the concerted population response to Pleistocene climatic fluctuations. This was done by a comparative analysis of sequence variation at the cyt b and S7 loci in nine newly sequenced and four re-analysed species. We found that all species underwent more or less intensive changes in population size but we also found consistent differences between demographic histories of pelagic and benthic species. Contemporary pelagic populations are significantly more genetically diverse and bear traces of older demographic expansions than less diverse benthic species that show evidence of more recent population expansions. Our findings suggest that the lifestyles of different species have strong influences on their responses to the same environmental events. Our data, in conjunction with previous studies showing a constant diversification tempo of these species during the Pleistocene, support the hypothesis that Pleistocene glaciations had a smaller effect on pelagic species than on benthic species whose survival may have relied upon ephemeral refugia in shallow shelf waters. These findings suggest that the interaction between lifestyle and environmental changes should be considered in genetic analyses.
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Affiliation(s)
- Eva Kašparová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Rumburska 89, 27721 Libechov, Czech Republic
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Kvetna 8, 603 65, Brno, Czech Republic
- * E-mail: (EK); (KJ)
| | - Anton P. Van de Putte
- Laboratory of Biodiversity and Evolutionary Genomics, Katholieke Universiteit Leuven, Ch. Deberiotstraat 32, B-3000 Leuven, Belgium
| | - Craig Marshall
- Department of Biochemistry, and Genetics Otago, University of Otago, P.O. Box 56, Dunedin, New Zealand
| | - Karel Janko
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Rumburska 89, 27721 Libechov, Czech Republic
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Kvetna 8, 603 65, Brno, Czech Republic
- Centre for Polar Ecology, University of South Bohemia in Ceské Budejovice, Na Zlate stoce 3, 370 05, Ceske Budejovice, Czech Republic
- Life Science Research Centre, Department of Biology and Ecology, Faculty of Natural Sciences, University of Ostrava, Chittussiho 10, 710 00 Silesian Ostrava, Czech Republic
- * E-mail: (EK); (KJ)
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17
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Young EF, Belchier M, Hauser L, Horsburgh GJ, Meredith MP, Murphy EJ, Pascoal S, Rock J, Tysklind N, Carvalho GR. Oceanography and life history predict contrasting genetic population structure in two Antarctic fish species. Evol Appl 2015; 8:486-509. [PMID: 26029262 PMCID: PMC4430772 DOI: 10.1111/eva.12259] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 02/27/2015] [Indexed: 01/27/2023] Open
Abstract
Understanding the key drivers of population connectivity in the marine environment is essential for the effective management of natural resources. Although several different approaches to evaluating connectivity have been used, they are rarely integrated quantitatively. Here, we use a 'seascape genetics' approach, by combining oceanographic modelling and microsatellite analyses, to understand the dominant influences on the population genetic structure of two Antarctic fishes with contrasting life histories, Champsocephalus gunnari and Notothenia rossii. The close accord between the model projections and empirical genetic structure demonstrated that passive dispersal during the planktonic early life stages is the dominant influence on patterns and extent of genetic structuring in both species. The shorter planktonic phase of C. gunnari restricts direct transport of larvae between distant populations, leading to stronger regional differentiation. By contrast, geographic distance did not affect differentiation in N. rossii, whose longer larval period promotes long-distance dispersal. Interannual variability in oceanographic flows strongly influenced the projected genetic structure, suggesting that shifts in circulation patterns due to climate change are likely to impact future genetic connectivity and opportunities for local adaptation, resilience and recovery from perturbations. Further development of realistic climate models is required to fully assess such potential impacts.
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Affiliation(s)
| | | | - Lorenz Hauser
- School of Aquatic and Fishery Sciences, University of Washington Seattle, WA, USA
| | - Gavin J Horsburgh
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield Sheffield, UK
| | | | | | - Sonia Pascoal
- School of Biological Sciences, Bangor University Bangor, Gwynedd, UK
| | - Jennifer Rock
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield Sheffield, UK ; School of Biological Sciences, Bangor University Bangor, Gwynedd, UK ; Present address: Department of Zoology, University of Otago Dunedin, 9054, New Zealand
| | - Niklas Tysklind
- School of Biological Sciences, Bangor University Bangor, Gwynedd, UK ; Present address: Campus Agronomique BP 709-97387, Kourou Cedex, France
| | - Gary R Carvalho
- School of Biological Sciences, Bangor University Bangor, Gwynedd, UK
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18
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Trucchi E, Gratton P, Whittington JD, Cristofari R, Le Maho Y, Stenseth NC, Le Bohec C. King penguin demography since the last glaciation inferred from genome-wide data. Proc Biol Sci 2014; 281:rspb.2014.0528. [PMID: 24920481 DOI: 10.1098/rspb.2014.0528] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
How natural climate cycles, such as past glacial/interglacial patterns, have shaped species distributions at the high-latitude regions of the Southern Hemisphere is still largely unclear. Here, we show how the post-glacial warming following the Last Glacial Maximum (ca 18 000 years ago), allowed the (re)colonization of the fragmented sub-Antarctic habitat by an upper-level marine predator, the king penguin Aptenodytes patagonicus. Using restriction site-associated DNA sequencing and standard mitochondrial data, we tested the behaviour of subsets of anonymous nuclear loci in inferring past demography through coalescent-based and allele frequency spectrum analyses. Our results show that the king penguin population breeding on Crozet archipelago steeply increased in size, closely following the Holocene warming recorded in the Epica Dome C ice core. The following population growth can be explained by a threshold model in which the ecological requirements of this species (year-round ice-free habitat for breeding and access to a major source of food such as the Antarctic Polar Front) were met on Crozet soon after the Pleistocene/Holocene climatic transition.
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Affiliation(s)
- Emiliano Trucchi
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, Oslo 0316, Norway
| | - Paolo Gratton
- Department of Biology, University of Rome 'Tor Vergata', Via della Ricerca Scientifica, Rome 00133, Italy
| | - Jason D Whittington
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, Oslo 0316, Norway Institut Pluridisciplinaire Hubert Curien, Physiologie et Ethologie, Université de Strasbourg, 23 Rue Becquerel, Strasbourg Cedex 02 67087, France Centre National de la Recherche Scientifique (UMR 7178 and LIA-647 BioSensib), 23 Rue Becquerel, Strasbourg Cedex 02 67087, France Centre Scientifique de Monaco (LIA-647 BioSensib), 8 Quai Antoine 1er, Monaco 98000, Principality of Monaco
| | - Robin Cristofari
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, Oslo 0316, Norway Institut Pluridisciplinaire Hubert Curien, Physiologie et Ethologie, Université de Strasbourg, 23 Rue Becquerel, Strasbourg Cedex 02 67087, France Centre National de la Recherche Scientifique (UMR 7178 and LIA-647 BioSensib), 23 Rue Becquerel, Strasbourg Cedex 02 67087, France Centre Scientifique de Monaco (LIA-647 BioSensib), 8 Quai Antoine 1er, Monaco 98000, Principality of Monaco
| | - Yvon Le Maho
- Institut Pluridisciplinaire Hubert Curien, Physiologie et Ethologie, Université de Strasbourg, 23 Rue Becquerel, Strasbourg Cedex 02 67087, France Centre National de la Recherche Scientifique (UMR 7178 and LIA-647 BioSensib), 23 Rue Becquerel, Strasbourg Cedex 02 67087, France
| | - Nils Chr Stenseth
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, Oslo 0316, Norway
| | - Céline Le Bohec
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, Oslo 0316, Norway Institut Pluridisciplinaire Hubert Curien, Physiologie et Ethologie, Université de Strasbourg, 23 Rue Becquerel, Strasbourg Cedex 02 67087, France Centre National de la Recherche Scientifique (UMR 7178 and LIA-647 BioSensib), 23 Rue Becquerel, Strasbourg Cedex 02 67087, France Centre Scientifique de Monaco (LIA-647 BioSensib), 8 Quai Antoine 1er, Monaco 98000, Principality of Monaco
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19
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Henriques R, Potts WM, Santos CV, Sauer WHH, Shaw PW. Population connectivity and phylogeography of a coastal fish, Atractoscion aequidens (Sciaenidae), across the Benguela Current region: evidence of an ancient vicariant event. PLoS One 2014; 9:e87907. [PMID: 24586296 PMCID: PMC3930521 DOI: 10.1371/journal.pone.0087907] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 12/30/2013] [Indexed: 11/18/2022] Open
Abstract
Contemporary patterns of genetic diversity and population connectivity within species can be influenced by both historical and contemporary barriers to gene flow. In the marine environment, present day oceanographic features such as currents, fronts and upwelling systems can influence dispersal of eggs/larvae and/juveniles/adults, shaping population substructuring. The Benguela Current system in the southeastern Atlantic is one of the oldest upwelling systems in the world, and provides a unique opportunity to investigate the relative influence of contemporary and historical mechanisms shaping the evolutionary history of warm-temperate fish species. Using the genetic variation in the mitochondrial DNA Control Region and eight nuclear microsatellite DNA loci, we identified the presence of two highly divergent populations in a vagile and warm-temperate fish species, Atractoscion aequidens, across the Benguela region. The geographical distributions of the two populations, on either side of the perennial upwelling cell, suggest a strong correlation between the oceanographic features of the system and the breakdown of gene flow within this species. Genetic divergence (mtDNA φ ST = 0.902, microsatellite F ST = 0.055: probability of genetic homogeneity for either marker = p<0.001), absence of migrants (less than 1% per generation) between populations and coalescent estimates of time since most recent common ancestor suggest that the establishment of the main oceanographic features of the system (2 million years ago), particularly the strengthening and position of the perennial upwelling cell, is the most likely mechanism behind the observed isolation. Concordance between mitochondrial and nuclear genetic markers indicates that isolation and divergence of the northern and southern Benguela populations of A. aequidens occurred deep in the past and has continued to the present day. These findings suggest that the Benguela Current system may constitute an ancient and impermeable barrier to gene flow for warm-temperate fish species.
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Affiliation(s)
- Romina Henriques
- Centre for Ecology, Evolution and Behavior, School of Biological Sciences, Royal Holloway University of London, Egham, United Kingdom
- Department of Ichthyology and Fisheries Science, Rhodes University, Grahamstown, South Africa
| | - Warren M. Potts
- Department of Ichthyology and Fisheries Science, Rhodes University, Grahamstown, South Africa
| | - Carmen V. Santos
- Faculdade de Ciências, Universidade Agostinho Neto, Luanda, Angola
| | - Warwick H. H. Sauer
- Department of Ichthyology and Fisheries Science, Rhodes University, Grahamstown, South Africa
| | - Paul W. Shaw
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
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20
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Damerau M, Matschiner M, Salzburger W, Hanel R. Population divergences despite long pelagic larval stages: lessons from crocodile icefishes (Channichthyidae). Mol Ecol 2013; 23:284-99. [DOI: 10.1111/mec.12612] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Revised: 11/25/2013] [Accepted: 11/27/2013] [Indexed: 11/28/2022]
Affiliation(s)
- M. Damerau
- Thünen-Institute of Fisheries Ecology; Palmaille 9 22767 Hamburg Germany
| | - M. Matschiner
- Department of Mathematics and Statistics; Allan Wilson Centre of Molecular Ecology and Evolution; University of Canterbury; Private Bag 4800 Christchurch New Zealand
- Zoological Institute; University of Basel; Vesalgasse 1 4051 Basel Switzerland
| | - W. Salzburger
- Zoological Institute; University of Basel; Vesalgasse 1 4051 Basel Switzerland
| | - R. Hanel
- Thünen-Institute of Fisheries Ecology; Palmaille 9 22767 Hamburg Germany
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21
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Konopiński MK, Amirowicz A, Kotlík P, Kukuła K, Bylak A, Pekarik L, Šediva A. Back from the brink: the Holocene history of the Carpathian barbel Barbus carpathicus. PLoS One 2013; 8:e82464. [PMID: 24349291 PMCID: PMC3861402 DOI: 10.1371/journal.pone.0082464] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2013] [Accepted: 11/04/2013] [Indexed: 11/18/2022] Open
Abstract
As a result of specific adaptations and habitat preferences strongly rheophilic fish species may show high levels of endemism. Many temperate rheophilic fish species were subjected to a series of range contractions during the Pleistocene, and then successfully expanded during the Holocene, colonising previously abandoned areas. The Carpathian barbel (Barbus carpathicus Kotlík, Tsigenopoulos, Ráb et Berrebi 2002) occurs in the montane streams in three basins of the main Central European rivers in the northern part of the Carpathian range. We used genetic variation within 3 mitochondrial and 9 microsatellite loci to determine a pattern of postglacial expansion in B. carpathicus. We found that overall genetic variation within the species is relatively low. Estimate of time to the most recent common ancestor (tMRCA) of mitochondrial sequences falls within the Holocene. The highest levels of genetic variation found in upper reaches of the Tisa river in the Danube basin suggest that glacial refugia were located in the south-eastern part of the species range. Our data suggest that the species crossed different watersheds at least six times as three genetically distinct groups (probably established in different expansion episodes) were found in northern part of the species range. Clines of genetic variation were observed in both the Danube and Vistula basins, which probably resulted from subsequent bottlenecks while colonizing successive habitats (south eastern populations) or due to the admixture of genetically diverse individuals to a previously uniform population (Vistula basin). Therefore, B. carpathicus underwent both demographic breakdowns and expansions during the Holocene, showing its distribution and demography are sensitive to environmental change. Our findings are important in the light of the current human-induced habitats alterations.
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Affiliation(s)
- Maciej K. Konopiński
- Institute of Nature Conservation, Polish Academy of Sciences, Kraków, Poland
- * E-mail:
| | - Antoni Amirowicz
- Institute of Nature Conservation, Polish Academy of Sciences, Kraków, Poland
| | - Petr Kotlík
- Institute of Animal Physiology and Genetics AS CR, Liběchov, Czech Republic
| | - Krzysztof Kukuła
- University of Rzeszów, Department of Environmental Biology, Rzeszów, Poland
| | - Aneta Bylak
- University of Rzeszów, Department of Environmental Biology, Rzeszów, Poland
| | - Ladislav Pekarik
- Institut of Zoology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Alena Šediva
- Institut of Zoology, Slovak Academy of Sciences, Bratislava, Slovakia
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22
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Marino IAM, Benazzo A, Agostini C, Mezzavilla M, Hoban SM, Patarnello T, Zane L, Bertorelle G. Evidence for past and present hybridization in three Antarctic icefish species provides new perspectives on an evolutionary radiation. Mol Ecol 2013; 22:5148-61. [DOI: 10.1111/mec.12458] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Revised: 07/17/2013] [Accepted: 07/18/2013] [Indexed: 11/27/2022]
Affiliation(s)
- I. A. M. Marino
- Department of Biology; University of Padova; via U. Bassi 58/b 35121 Padova Italy
| | - A. Benazzo
- Department of Life Sciences and Biotechnology; University of Ferrara; via L. Borsari 46 44100 Ferrara Italy
| | - C. Agostini
- Department of Biology; University of Padova; via U. Bassi 58/b 35121 Padova Italy
| | - M. Mezzavilla
- Institute for Maternal and Child Health - IRCCS Burlo Garofolo and University of Trieste; Via dell'Istria, 65/1 34137 Trieste Italy
| | - S. M. Hoban
- Department of Life Sciences and Biotechnology; University of Ferrara; via L. Borsari 46 44100 Ferrara Italy
| | - T. Patarnello
- Department of Comparative Biomedicine and Food Science; University of Padova; viale dell'Università 16 35020 Agripolis Legnaro Padova Italy
| | - L. Zane
- Department of Biology; University of Padova; via U. Bassi 58/b 35121 Padova Italy
| | - G. Bertorelle
- Department of Life Sciences and Biotechnology; University of Ferrara; via L. Borsari 46 44100 Ferrara Italy
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23
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Effects of species biology on the historical demography of sharks and their implications for likely consequences of contemporary climate change. CONSERV GENET 2012. [DOI: 10.1007/s10592-012-0437-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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24
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Van de Putte AP, Janko K, Kasparova E, Maes GE, Rock J, Koubbi P, Volckaert FA, Choleva L, Fraser KP, Smykla J, Van Houdt JK, Marshall C. Comparative phylogeography of three trematomid fishes reveals contrasting genetic structure patterns in benthic and pelagic species. Mar Genomics 2012. [DOI: 10.1016/j.margen.2012.05.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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25
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Dambach J, Thatje S, Rödder D, Basher Z, Raupach MJ. Effects of late-cenozoic glaciation on habitat availability in Antarctic benthic shrimps (Crustacea: Decapoda: Caridea). PLoS One 2012; 7:e46283. [PMID: 23029463 PMCID: PMC3459913 DOI: 10.1371/journal.pone.0046283] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 08/29/2012] [Indexed: 02/05/2023] Open
Abstract
Marine invertebrates inhabiting the high Antarctic continental shelves are challenged by disturbance of the seafloor by grounded ice, low but stable water temperatures and variable food availability in response to seasonal sea-ice cover. Though a high diversity of life has successfully adapted to such conditions, it is generally agreed that during the Last Glacial Maximum (LGM) the large-scale cover of the Southern Ocean by multi-annual sea ice and the advance of the continental ice sheets across the shelf faced life with conditions, exceeding those seen today by an order of magnitude. Conditions prevailing at the LGM may have therefore acted as a bottleneck event to both the ecology as well as genetic diversity of today's fauna. Here, we use for the first time specific Species Distribution Models (SDMs) for marine arthropods of the Southern Ocean to assess effects of habitat contraction during the LGM on the three most common benthic caridean shrimp species that exhibit a strong depth zonation on the Antarctic continental shelf. While the shallow-water species Chorismus antarcticus and Notocrangon antarcticus were limited to a drastically reduced habitat during the LGM, the deep-water shrimp Nematocarcinus lanceopes found refuge in the Southern Ocean deep sea. The modeling results are in accordance with genetic diversity patterns available for C. antarcticus and N. lanceopes and support the hypothesis that habitat contraction at the LGM resulted in a loss of genetic diversity in shallow water benthos.
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26
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Allcock AL, Strugnell JM. Southern Ocean diversity: new paradigms from molecular ecology. Trends Ecol Evol 2012; 27:520-8. [DOI: 10.1016/j.tree.2012.05.009] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Revised: 05/22/2012] [Accepted: 05/24/2012] [Indexed: 01/29/2023]
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27
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Ludt WB, Bernal MA, Bowen BW, Rocha LA. Living in the past: phylogeography and population histories of Indo-Pacific wrasses (genus Halichoeres) in shallow lagoons versus outer reef slopes. PLoS One 2012; 7:e38042. [PMID: 22701597 PMCID: PMC3368945 DOI: 10.1371/journal.pone.0038042] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2011] [Accepted: 05/01/2012] [Indexed: 11/19/2022] Open
Abstract
Sea level fluctuations during glacial cycles affect the distribution of shallow marine biota, exposing the continental shelf on a global scale, and displacing coral reef habitat to steep slopes on oceanic islands. In these circumstances we expect that species inhabiting lagoons should show shallow genetic architecture relative to species inhabiting more stable outer reefs. Here we test this expectation on an ocean-basin scale with four wrasses (genus Halichoeres): H. claudia (N = 194, with ocean-wide distribution) and H. ornatissimus (N = 346, a Hawaiian endemic) inhabit seaward reef slopes, whereas H. trimaculatus (N = 239) and H. margaritaceus (N = 118) inhabit lagoons and shallow habitats throughout the Pacific. Two mitochondrial markers (cytochrome oxidase I and control region) were sequenced to resolve population structure and history of each species. Haplotype and nucleotide diversity were similar among all four species. The outer reef species showed significantly less population structure, consistent with longer pelagic larval durations. Mismatch distributions and significant negative Fu's F values indicate Pleistocene population expansion for all species, and (contrary to expectations) shallower histories in the outer slope species. We conclude that lagoonal wrasses may persist through glacial habitat disruptions, but are restricted to refugia during lower sea level stands. In contrast, outer reef slope species have homogeneous and well-connected populations through their entire ranges regardless of sea level fluctuations. These findings contradict the hypothesis that shallow species are less genetically diverse as a consequence of glacial cycles.
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Affiliation(s)
- William B Ludt
- Department of Marine Science, University of Texas, Austin, Texas, United States of America.
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Smith PJ, Steinke D, Dettai A, McMillan P, Welsford D, Stewart A, Ward RD. DNA barcodes and species identifications in Ross Sea and Southern Ocean fishes. Polar Biol 2012. [DOI: 10.1007/s00300-012-1173-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Comparative evolution of S7 Intron 1 and ribosomal internal transcribed spacer in Coilia nasus (Clupeiformes: Engraulidae). Int J Mol Sci 2012; 13:3085-3100. [PMID: 22489143 PMCID: PMC3317704 DOI: 10.3390/ijms13033085] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Revised: 01/17/2012] [Accepted: 02/28/2012] [Indexed: 11/17/2022] Open
Abstract
Coilia nasus is widely distributed in the Yangtze River, the coastal waters of China, Korea and the Ariake Sound of Japan. Several ecotypes exist and this provides a useful model for the study of comparative diversity between molecular markers. Here we analyze and compare the nucleotide sequences between single-copy ribosomal protein S7 gene intron 1 (rpS7) and multiple-copy ribosomal internal transcribed spacer 1 (ITS1) in this species to compare the phylogenetic signal of the two nuclear genes. Nucleotide substitutions among the two gene sequences and partial sequence of mitochondrial cytochrome c oxidase subunit I (COI) gene were also analyzed. A total of 115 clones for rpS7 and 122 clones for ITS1 were obtained from 37 specimens. The nucleotide sequence length is 741 to 743 bp for rpS7 and 334 to 348 bp for ITS1. Intra- and inter-specimen variation in rpS7 results from nucleotide substitution, while such variation in ITS1 is mainly due to different numbers of short base repeats. The content of G + C is lower in rpS7 (43.5%) than in ITS1 (68.2%). Our results indicate that the proportion of the sequence variable sites is higher in rpS7 (61) than in ITS1 (23); the informative parsimony of rpS7 is evidently higher than that of ITS1 (26 vs. 2); the overall ratio between transitions and transversions in ITS1 is slightly lower than in rpS7, but remarkably lower than in COI. These results suggest that rpS7 is more suitable than ITS1 as a marker for genetic divergence of this group. Furthermore, gene flow is observed between the different geographic populations of C. nasus from the phylogeny of this species based on rpS7, showing that rpS7 has more evolutionary characteristics for understanding the processes of genomic evolution at the intraspecific level.
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Janko K, Marshall C, Musilová Z, Houdt JV, Couloux A, Cruaud C, Lecointre G. Multilocus analyses of an Antarctic fish species flock (Teleostei, Notothenioidei, Trematominae): Phylogenetic approach and test of the early-radiation event. Mol Phylogenet Evol 2011; 60:305-16. [DOI: 10.1016/j.ympev.2011.03.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Revised: 01/22/2011] [Accepted: 03/07/2011] [Indexed: 11/16/2022]
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Bortolotto E, Bucklin A, Mezzavilla M, Zane L, Patarnello T. Gone with the currents: lack of genetic differentiation at the circum-continental scale in the Antarctic krill Euphausia superba. BMC Genet 2011; 12:32. [PMID: 21486439 PMCID: PMC3095564 DOI: 10.1186/1471-2156-12-32] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Accepted: 04/12/2011] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Southern Ocean fauna represent a significant amount of global biodiversity, whose origin may be linked to glacial cycles determining local extinction/eradication with ice advance, survival of refugee populations and post-glacial re-colonization. This pattern implies high potential for differentiation in benthic shelf species with limited dispersal, yet consequences for pelagic organisms are less clear. The present study investigates levels of genetic variation and population structure of the Antarctic krill Euphausia superba using mitochondrial DNA and EST-linked microsatellite markers for an unprecedentedly comprehensive sampling of its populations over a circum-Antarctic range. RESULTS MtDNA (ND1) sequences and EST-linked microsatellite markers indicated no clear sign of genetic structure among populations over large geographic scales, despite considerable power to detect differences inferred from forward-time simulations. Based on ND1, few instances of genetic heterogeneity, not significant after correction for multiple tests, were detected between geographic or temporal samples. Neutrality tests and mismatch distribution based on mtDNA sequences revealed strong evidence of past population expansion. Significant positive values of the parameter g (a measure of population growth) were obtained from microsatellite markers using a coalescent-based genealogical method and suggested a recent start (60,000 - 40,000 years ago) for the expansion. CONCLUSIONS The results provide evidence of lack of genetic heterogeneity of Antarctic krill at large geographic scales and unequivocal support for recent population expansion. Lack of genetic structuring likely reflects the tight link between krill and circum-Antarctic ocean currents and is consistent with the hypothesis that differentiation processes in Antarctic species are largely influenced by dispersal potential, whereas small-scale spatial and temporal differentiation might be due to local conditions leading to genetic patchiness. The signal of recent population growth suggests differential impact of glacial cycles on pelagic Antarctic species, which experienced population expansion during glaciations with increased available habitat, versus sedentary benthic shelf species. EST-linked microsatellites provide new perspectives to complement the results based on mtDNA and suggest that data-mining of EST libraries will be a useful approach to facilitate use of microsatellites for additional species.
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Affiliation(s)
- Erica Bortolotto
- Department of Biology, University of Padova, via U. Bassi 58B -35121 Padova, Italy
| | - Ann Bucklin
- Department of Marine Sciences, University of Connecticut, Groton CT 06340 USA
| | - Massimo Mezzavilla
- Department of Biology, University of Padova, via U. Bassi 58B -35121 Padova, Italy
| | - Lorenzo Zane
- Department of Biology, University of Padova, via U. Bassi 58B -35121 Padova, Italy
| | - Tomaso Patarnello
- Department of Public Health, Comparative Pathology and Veterinary Hygiene, University of Padova, Viale dell'Università 16, 35020 Legnaro (PD), Italy
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Extreme Glacial Legacies: A Synthesis of the Antarctic Springtail Phylogeographic Record. INSECTS 2011; 2:62-82. [PMID: 26467614 PMCID: PMC4553450 DOI: 10.3390/insects2020062] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2010] [Revised: 02/15/2011] [Accepted: 04/02/2011] [Indexed: 11/16/2022]
Abstract
We review current phylogeographic knowledge from across the Antarctic terrestrial landscape with a focus on springtail taxa. We describe consistent patterns of high genetic diversity and structure among populations which have persisted in glacial refugia across Antarctica over both short (10 Mya) timescales. Despite a general concordance of results among species, we explain why location is important in determining population genetic patterns within bioregions. We complete our review by drawing attention to the main limitations in the field of Antarctic phylogeography, namely that the scope of geographic focus is often lacking within studies, and that large gaps remain in our phylogeographic knowledge for most terrestrial groups.
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Patarnello T, Verde C, di Prisco G, Bargelloni L, Zane L. How will fish that evolved at constant sub-zero temperatures cope with global warming? Notothenioids as a case study. Bioessays 2011; 33:260-8. [PMID: 21290397 DOI: 10.1002/bies.201000124] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Current climate change has raised concerns over the fate of the stenothermal Antarctic marine fauna (animals that evolved to live in narrow ranges of cold temperatures). The present paper focuses on Notothenioidei, a taxonomic group that dominates Antarctic fish. Notothenioids evolved in the Southern Ocean over the last 20 million years, providing an example of a marine species flock with unique adaptations to the cold at morphological, physiological and biochemical levels. Their phenotypic modifications are often accompanied by 'irreversible' genomic losses or gene amplifications. On a micro-evolutionary scale, relatively 'shallow' genetic variation is observed, on account of past fluctuations in population size, and a significant genetic structure is evident, suggesting low population connectivity. These features suggest that Antarctic fish might have relatively little potential to adapt to global warming, at least at a genetic level. The extent of their phenotypic plasticity, which is evident to some degree, awaits further research.
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Affiliation(s)
- Tomaso Patarnello
- Department of Public Health, Comparative Pathology and Veterinary Hygiene AGRIPOLIS, Legnaro (PD), Italy.
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Evidence for a role of bathymetry and emergence in speciation in the genus Glycera (Glyceridae, Polychaeta) from the deep Eastern Weddell Sea. Polar Biol 2010. [DOI: 10.1007/s00300-010-0913-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Fazalova V, Nevado B, Peretolchina T, Petunina J, Sherbakov D. When environmental changes do not cause geographic separation of fauna: differential responses of Baikalian invertebrates. BMC Evol Biol 2010; 10:320. [PMID: 20969796 PMCID: PMC2993716 DOI: 10.1186/1471-2148-10-320] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2010] [Accepted: 10/23/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND While the impact of climate fluctuations on the demographic histories of species caused by changes in habitat availability is well studied, populations of species from systems without geographic isolation have received comparatively little attention. Using CO1 mitochondrial sequences, we analysed phylogeographic patterns and demographic histories of populations of five species (four gastropod and one amphipod species) co-occurring in the southwestern shore of Lake Baikal, an area where environmental oscillations have not resulted in geographical isolation of habitats. RESULTS Species with stronger habitat preferences (gastropods B. turriformis, B. carinata and B. carinatocostata) exhibit rather stable population sizes through their evolutionary history, and their phylogeographic pattern indicates moderate habitat fragmentation. Conversely, species without strong habitat preference (gastropod M. herderiana and amphipod G. fasciatus) exhibit haplotype networks with a very abundant and widespread central haplotype and a big number of singleton haplotypes, while their reconstructed demographic histories show a population expansion starting about 25-50 thousand years ago, a period marked by climate warming and increase in diatom abundance as inferred from bottom-lake sedimentary cores. CONCLUSIONS In agreement with previous studies, we found that species reacted differently to the same environmental changes. Our results highlight the important role of dispersal ability and degree of ecological specialization in defining a species' response to environmental changes.
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Affiliation(s)
- Varvara Fazalova
- Laboratory of Molecular Systematics, Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia.
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Kuhn KL, Near TJ, Jones CD, Eastman JT. Aspects of the Biology and Population Genetics of the Antarctic Nototheniid Fish Trematomus nicolai. COPEIA 2009. [DOI: 10.1643/cg-08-087] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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MATSCHINER MICHAEL, HANEL REINHOLD, SALZBURGER WALTER. Gene flow by larval dispersal in the Antarctic notothenioid fishGobionotothen gibberifrons. Mol Ecol 2009; 18:2574-87. [DOI: 10.1111/j.1365-294x.2009.04220.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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