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Chang SC, Ahyong ST, Tsang LM. Molecular phylogeny of deep-sea blind lobsters of the family Polychelidae (Decapoda: Polychelida), with implications for the origin and evolution of these "living fossils". Mol Phylogenet Evol 2024; 192:107998. [PMID: 38142793 DOI: 10.1016/j.ympev.2023.107998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 12/14/2023] [Accepted: 12/20/2023] [Indexed: 12/26/2023]
Abstract
A comprehensive molecular analysis of the deep-sea blind lobsters of the family Polychelidae, often referred to as "living fossils", is conducted based on all six modern genera and 27 of the 38 extant species. Using six genetic markers from both mitochondrial and nuclear genomes, the molecular phylogenetic results differ considerably from previous morphological analyses and reveal the genera Polycheles and Pentacheles to be para- or polyphyletic. As the splitting of Polycheles has strong support from both molecular and morphological data, two new genera, Dianecheles and Neopolycheles, are erected for those species excluded from the clade containing the type species of Polycheles. The pattern of polyphyly of Pentacheles, however, is not robustly resolved, so it is retained as a single genus. Fossil evidence suggests that fossil polychelids inhabited deep-sea environments as early as the Early to Middle Jurassic, demonstrating the enduring adaptation of extant polychelid species to the deep-sea. Time-calibrated phylogeny suggested that modern polychelids probably had an Atlantic origin during the Jurassic period. Since their emergence, this ancient lobster group has continued to diversify, particularly in the West Pacific, and has colonized the abyssal zone, with the deepest genus, Willemoesia, representing the more 'derived' members among extant polychelids. Differences in eye reduction among extant polychelid genera highlight the necessity for ongoing investigations to ascertain the relative degree of functionality of their eyes, if they indeed retain any function.
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Affiliation(s)
- Su-Ching Chang
- Department of Biological Resources, National Chiayi University, Chiayi 600355, Taiwan, ROC
| | - Shane T Ahyong
- Australian Museum, 1 William St, Sydney, NSW 2010, Australia; School of Biological, Earth & Environmental Sciences, University of New South Wales, Kensington, NSW 2052, Australia
| | - Ling-Ming Tsang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
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Guy-Haim T, Kolodny O, Frumkin A, Achituv Y, Velasquez X, Morov AR. Shedding light on the Ophel biome: the trans-Tethyan phylogeography of the sulfide shrimp Tethysbaena (Peracarida: Thermosbaenacea) in the Levant. PeerJ 2023; 11:e16690. [PMID: 38144178 PMCID: PMC10748474 DOI: 10.7717/peerj.16690] [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: 08/17/2023] [Accepted: 11/27/2023] [Indexed: 12/26/2023] Open
Abstract
Background Tethysbaena are small peracarid crustaceans inhabiting extreme environments such as subterranean lakes and thermal springs, represented by endemic species found around the ancient Tethys, including the Mediterranean, Arabian Sea, Mid-East Atlantic, and the Caribbean Sea. Two Tethysbaena species are known from the Levant: T. relicta, found along the Dead Sea-Jordan Rift Valley, and T. ophelicola, found in the Ayyalon cave complex in the Israeli coastal plain, both belonging to the same species-group based on morphological cladistics. Along the biospeleological research of the Levantine subterranean fauna, three biogeographic hypotheses determining their origins were proposed: (1) Pliocenic transgression, (2) Mid-late Miocenic transgression, and (3) The Ophel Paradigm, according to which these are inhabitants of a chemosynthetic biome as old as the Cambrian. Methods Tethysbaena specimens of the two Levantine species were collected from subterranean groundwaters. We used the mitochondrial cytochrome c oxidase subunit I (COI) gene and the nuclear ribosomal 28S (28S rRNA) gene to establish the phylogeny of the Levantine Tethysbaena species, and applied a molecular clock approach for inferring their divergence times. Results Contrary to the morphological cladistic-based classification, we found that T. relicta shares an ancestor with Tethysbaena species from Oman and the Dominican Republic, whereas the circum-Mediterranean species (including T. ophelicola) share another ancestor. The mean age of the node linking T. relicta from the Dead Sea-Jordan Rift Valley and Tethysbaena from Oman was 20.13 MYA. The mean estimate for the divergence of T. ophelicola from the Mediterranean Tethysbaena clade dated to 9.46 MYA. Conclusions Our results indicate a two-stage colonization of Tethysbaena in the Levant: a late Oligocene transgression, through a marine gulf extending from the Arabian Sea, leading to the colonization of T. relicta in the Dead Sea-Jordan Rift Valley, whereas T. ophelicola, originating from the Mesogean ancestor, inhabited anchialine caves in the coastal plain of Israel during the Mid-Miocene.
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Affiliation(s)
- Tamar Guy-Haim
- National Institute of Oceanography, Israel Oceanographic and Limnological Research, Haifa, Israel
| | - Oren Kolodny
- Department of Ecology, Evolution, and Behavior, Institute for Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Amos Frumkin
- Institute of Earth Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yair Achituv
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat-Gan, Israel
| | - Ximena Velasquez
- National Institute of Oceanography, Israel Oceanographic and Limnological Research, Haifa, Israel
| | - Arseniy R. Morov
- National Institute of Oceanography, Israel Oceanographic and Limnological Research, Haifa, Israel
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Łukowiak M, Meiro G, Peña B, Villanueva Guimerans P, Corbí H. Miocene sponge assemblages in the face of the Messinian Salinity Crisis-new data from the Atlanto-Mediterranean seaway. PeerJ 2023; 11:e16277. [PMID: 38025719 PMCID: PMC10657567 DOI: 10.7717/peerj.16277] [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: 07/12/2023] [Accepted: 09/20/2023] [Indexed: 12/01/2023] Open
Abstract
The Messinian Salinity Crisis is considered as one of the most influential Cenozoic events that impacted negatively on the benthic fauna of the Mediterranean area. Changing environmental conditions, including a sharp reduction of water exchange between the Mediterranean Sea and the Atlantic Ocean, altered the geographical ranges of many organisms, including sponges (Porifera). Here, we report a unique assemblage of isolated sponge spicules from the upper Miocene of southwestern Spain. The newly recognized sponge fauna was inhabiting the Guadalquivir Basin-the corridor between the Mediterranean and the Atlantic Ocean at that time. It represents a taxonomically rich sponge community that consisted of members of "soft" and "lithistid" demosponges and hexactinellids. Demosponges are represented by at least thirty-four taxa, while hexactinellids are significantly rarer; only six taxa have been identified. From among eighteen taxa recognized to the species level, at least eight seem to be inhabiting this area to these days; six are recorded from adjacent areas, such as the Western Mediterranean, South European Atlantic Shelf, and the Azores, and three are present in the Red Sea and/or the Northern Atlantic. Intriguingly, some taxa seem to have their closest relatives in distant areas, such as the Indo-Pacific and Japanese waters which suggests that the range of some once widely-distributed populations shrunk after the isolation of the Mediterranean and the Messinian Salinity Crisis, surviving to the present day only in refugia.
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Affiliation(s)
- Magdalena Łukowiak
- Department of Environmental Paleobiology, Institute of Paleobiology, Polish Academy of Sciences, Warszawa, Mazowieckie, Poland
| | | | | | | | - Hugo Corbí
- Department of Earth Sciences and the Environment, Universidad de Alicante, Alicante, Spain
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Liu T, Liu H, Wang Y, Yang Y. Climate Change Impacts on the Potential Distribution Pattern of Osphya (Coleoptera: Melandryidae), an Old but Small Beetle Group Distributed in the Northern Hemisphere. INSECTS 2023; 14:insects14050476. [PMID: 37233104 DOI: 10.3390/insects14050476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/15/2023] [Accepted: 05/17/2023] [Indexed: 05/27/2023]
Abstract
Exploring the development of species distribution patterns under climate change is the basis of biogeography and macroecology. However, under the background of global climate change, few studies focus on how the distribution pattern and the range of insects have or will change in response to long-term climate change. An old but small, Northern-Hemisphere-distributed beetle group Osphya is an ideal subject to conduct the study in this aspect. Here, based on a comprehensive geographic dataset, we analyzed the global distribution pattern of Osphya using ArcGIS techniques, which declared a discontinuous and uneven distribution pattern across the USA, Europe, and Asia. Furthermore, we predicted the suitable habitats of Osphya under different climate scenarios via the MaxEnt model. The results showed that the high suitability areas were always concentrated in the European Mediterranean and the western coast of USA, while a low suitability exhibited in Asia. Moreover, by integrating the analyses of biogeography and habitat suitability, we inferred that the Osphya species conservatively prefer a warm, stable, and rainy climate, and they tend to expand towards higher latitude in response to the climate warming from the past to future. These results are helpful in exploring the species diversity and protection of Osphya.
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Affiliation(s)
- Tong Liu
- The Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China
| | - Haoyu Liu
- The Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China
| | - Yongjie Wang
- Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510075, China
| | - Yuxia Yang
- The Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China
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Alqahtani AR, Yağmur EA, Badry A. Androctonus tihamicus sp. nov. from the Mecca Province, Saudi Arabia (Scorpiones, Buthidae). Zookeys 2023; 1152:9-34. [DOI: 10.3897/zookeys.1152.101100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 02/18/2023] [Indexed: 03/06/2023] Open
Abstract
We describe and illustrate a new scorpion species, Androctonus tihamicussp. nov., from the Mecca Province of southwestern Saudi Arabia. The new species is compared to the genus Androctonus Ehrenberg, 1828, which is distributed throughout the Middle East, and especially to A. australis (Linnaeus, 1758). We provide the molecular phylogeny for this species.
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Rogers AD, Appeltans W, Assis J, Ballance LT, Cury P, Duarte C, Favoretto F, Hynes LA, Kumagai JA, Lovelock CE, Miloslavich P, Niamir A, Obura D, O'Leary BC, Ramirez-Llodra E, Reygondeau G, Roberts C, Sadovy Y, Steeds O, Sutton T, Tittensor DP, Velarde E, Woodall L, Aburto-Oropeza O. Discovering marine biodiversity in the 21st century. ADVANCES IN MARINE BIOLOGY 2022; 93:23-115. [PMID: 36435592 DOI: 10.1016/bs.amb.2022.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
We review the current knowledge of the biodiversity of the ocean as well as the levels of decline and threat for species and habitats. The lack of understanding of the distribution of life in the ocean is identified as a significant barrier to restoring its biodiversity and health. We explore why the science of taxonomy has failed to deliver knowledge of what species are present in the ocean, how they are distributed and how they are responding to global and regional to local anthropogenic pressures. This failure prevents nations from meeting their international commitments to conserve marine biodiversity with the results that investment in taxonomy has declined in many countries. We explore a range of new technologies and approaches for discovery of marine species and their detection and monitoring. These include: imaging methods, molecular approaches, active and passive acoustics, the use of interconnected databases and citizen science. Whilst no one method is suitable for discovering or detecting all groups of organisms many are complementary and have been combined to give a more complete picture of biodiversity in marine ecosystems. We conclude that integrated approaches represent the best way forwards for accelerating species discovery, description and biodiversity assessment. Examples of integrated taxonomic approaches are identified from terrestrial ecosystems. Such integrated taxonomic approaches require the adoption of cybertaxonomy approaches and will be boosted by new autonomous sampling platforms and development of machine-speed exchange of digital information between databases.
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Affiliation(s)
- Alex D Rogers
- REV Ocean, Lysaker, Norway; Nekton Foundation, Begbroke Science Park, Oxford, United Kingdom.
| | - Ward Appeltans
- Intergovernmental Oceanographic Commission of UNESCO, Oostende, Belgium
| | - Jorge Assis
- Centre of Marine Sciences, University of Algarve, Faro, Portugal
| | - Lisa T Ballance
- Marine Mammal Institute, Oregon State University, Newport, OR, United States
| | | | - Carlos Duarte
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC) and Computational Bioscience Research Center (CBRC), Thuwal, Kingdom of Saudi Arabia
| | - Fabio Favoretto
- Autonomous University of Baja California Sur, La Paz, Baja California Sur, Mexico
| | - Lisa A Hynes
- Nekton Foundation, Begbroke Science Park, Oxford, United Kingdom
| | - Joy A Kumagai
- Senckenberg Biodiversity and Climate Research Institute, Frankfurt am Main, Germany
| | - Catherine E Lovelock
- School of Biological Sciences, The University of Queensland, St Lucia, QLD, Australia
| | - Patricia Miloslavich
- Scientific Committee on Oceanic Research (SCOR), College of Earth, Ocean and Environment, University of Delaware, Newark, DE, United States; Departamento de Estudios Ambientales, Universidad Simón Bolívar, Venezuela & Scientific Committee for Oceanic Research (SCOR), Newark, DE, United States
| | - Aidin Niamir
- Senckenberg Biodiversity and Climate Research Institute, Frankfurt am Main, Germany
| | | | - Bethan C O'Leary
- Centre for Ecology & Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn, United Kingdom; Department of Environment and Geography, University of York, York, United Kingdom
| | - Eva Ramirez-Llodra
- REV Ocean, Lysaker, Norway; Nekton Foundation, Begbroke Science Park, Oxford, United Kingdom
| | - Gabriel Reygondeau
- Yale Center for Biodiversity Movement and Global Change, Yale University, New Haven, CT, United States; Nippon Foundation-Nereus Program, Institute for the Oceans and Fisheries, University of British Columbia, Vancouver, BC, Canada
| | - Callum Roberts
- Centre for Ecology & Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn, United Kingdom
| | - Yvonne Sadovy
- School of Biological Sciences, Swire Institute of Marine Science, The University of Hong Kong, Hong Kong
| | - Oliver Steeds
- Nekton Foundation, Begbroke Science Park, Oxford, United Kingdom
| | - Tracey Sutton
- Nova Southeastern University, Halmos College of Natural Sciences and Oceanography, Dania Beach, FL, United States
| | | | - Enriqueta Velarde
- Instituto de Ciencias Marinas y Pesquerías, Universidad Veracruzana, Veracruz, Mexico
| | - Lucy Woodall
- Nekton Foundation, Begbroke Science Park, Oxford, United Kingdom; Department of Zoology, University of Oxford, Oxford, United Kingdom
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Machordom A, Ahyong ST, Andreakis N, Baba K, Buckley D, García-Jiménez R, McCallum AW, Rodríguez-Flores PC, Macpherson E. Deconstructing the crustacean squat lobster genus. INVERTEBR SYST 2022. [DOI: 10.1071/is22013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Unravelling the evolutionary history of taxa requires solid delimitation of the traits characterising these. This can be challenging especially in groups with a highly complex taxonomy. The squat lobster family Munididae contains more than 450 species distributed among 21 genera, Munida being the most speciose (~300 species). Previous phylogenetic studies, based on a small part of the diversity of the group, have suggested polyphyletic origins for Munida and the paraphyly of Munididae. Here, we use an integrative approach based on multi-locus phylogenies (two mitochondrial and three nuclear markers) paired with 120 morphological characters, to resolve taxonomic and evolutionary relationships within Munididae. Our study covers ~60% of the family’s known diversity (over 800 specimens of 291 species belonging to 19 of the 21 genera collected from the Atlantic, Indian and Pacific oceans). Using this information, we confirm the validity of most genera, proposing new ones in cases where the genetic analyses are compatible with morphological characters. Four well-defined munidid clades were recovered, suggesting that new genera should be erected in the currently recognised Munididae (three for the genus Agononida and eleven in Munida), and the genus Grimothea is resurrected. A key to all genera of the family is presented. Molecular clock estimates and ancestral biogeographic area reconstructions complement the taxonomic profiles and suggest some explosive diversification within Munididae during the Cretaceous and the Palaeogene. Further anagenetic events and narrow sympatry accounting for changes in distribution indicate a more limited dispersal capacity than previously considered. Our study unravels how diversification may occur in deep waters and further highlights the importance of the integrative approach in accurately delineating species in understanding the history of a family and the factors driving the evolution. ZooBank LSID: urn:lsid:zoobank.org:pub:16A61C4A-8D96-4372-820F-8EBDF179B43C
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Martins FMS, Godinho R, Palma L. Cores, edges and beyond: insights into the phylogeography of frigatebirds with a focus on ultraperipheral and endemic populations. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01466-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Jamaludin NA, Jamaluddin JAF, Rahim MA, Mohammed Akib NA, Ratmuangkhwang S, Mohd Arshaad W, Mohd Nor SA. Mitochondrial marker implies fishery separate management units for spotted sardinella, Amblygaster sirm (Walbaum, 1792) populations in the South China Sea and the Andaman Sea. PeerJ 2022; 10:e13706. [PMID: 35860045 PMCID: PMC9290996 DOI: 10.7717/peerj.13706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 06/19/2022] [Indexed: 01/17/2023] Open
Abstract
The spotted sardinella, Amblygaster sirm (Walbaum, 1792), is a commercial sardine commonly caught in Malaysia. Lack of management of these marine species in Malaysian waters could lead to overfishing and potentially declining fish stock populations. Therefore, sustainable management of this species is of paramount importance to ensure its longevity. As such, molecular information is vital in determining the A. sirm population structure and management strategy. In the present study, mitochondrial DNA Cytochrome b was sequenced from 10 A. sirm populations: the Andaman Sea (AS) (two), South China Sea (SCS) (six), Sulu Sea (SS) (one), and Celebes Sea (CS) (one). Accordingly, the intra-population haplotype diversity (Hd) was high (0.91-1.00), and nucleotide diversity (π) was low (0.002-0.009), which suggests a population bottleneck followed by rapid population growth. Based on the phylogenetic trees, minimum spanning network (MSN), population pairwise comparison, and F ST,and supported by analysis of molecular variance (AMOVA) and spatial analysis of molecular variance (SAMOVA) tests, distinct genetic structures were observed (7.2% to 7.6% genetic divergence) between populations in the SCS and its neighboring waters, versus those in the AS. Furthermore, the results defined A. sirm stock boundaries and evolutionary between the west and east coast (which shares the same waters as western Borneo) of Peninsular Malaysia. In addition, genetic homogeneity was revealed throughout the SCS, SS, and CS based on the non-significant F STpairwise comparisons. Based on the molecular evidence, separate management strategies may be required for A. sirm of the AS and the SCS, including its neighboring waters.
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Affiliation(s)
- Noorul Azliana Jamaludin
- Centre for Global Sustainability Studies (CGSS), Universiti Sains Malaysia, Penang, Malaysia,Marine Capture Fisheries Division, Fisheries Research Institute, Sitiawan, Perak, Malaysia
| | | | | | - Noor Adelyna Mohammed Akib
- Centre for Global Sustainability Studies (CGSS), Universiti Sains Malaysia, Penang, Malaysia,School of Biology, Universiti Sains Malaysia, Penang, Malaysia
| | - Sahat Ratmuangkhwang
- Andaman Coastal Research Station for Development, Kasetsart University, Ranong, Thailand
| | - Wahidah Mohd Arshaad
- Southeast Asia Fisheries Development Center (SEAFDEC), Marine Fisheries Resources Development and Management Department (MFRDMD), Kuala Terengganu, Terengganu, Malaysia
| | - Siti Azizah Mohd Nor
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Terengganu, Terengganu, Malaysia
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Boo GH, Leliaert F, Le Gall L, Coppejans E, De Clerck O, Van Nguyen T, Payri CE, Miller KA, Yoon HS. Ancient Tethyan Vicariance and Long-Distance Dispersal Drive Global Diversification and Cryptic Speciation in the Red Seaweed Pterocladiella. FRONTIERS IN PLANT SCIENCE 2022; 13:849476. [PMID: 35720545 PMCID: PMC9201827 DOI: 10.3389/fpls.2022.849476] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 05/13/2022] [Indexed: 05/27/2023]
Abstract
We investigated the globally distributed red algal genus Pterocladiella, comprising 24 described species, many of which are economically important sources of agar and agarose. We used DNA-based species delimitation approaches, phylogenetic, and historical biogeographical analyses to uncover cryptic diversity and infer the drivers of biogeographic patterns. We delimited 43 species in Pterocladiella, of which 19 are undescribed. Our multigene time-calibrated phylogeny and ancestral area reconstruction indicated that Pterocladiella most likely originated during the Early Cretaceous in the Tethys Sea. Ancient Tethyan vicariance and long-distance dispersal have shaped current distribution patterns. The ancestor of Eastern Pacific species likely arose before the formation of the formidable Eastern Pacific Barrier-a first confirmation using molecular data in red algae. Divergences of Northeast and Southeast Pacific species have been driven by the Central American Seaway barrier, which, paradoxically, served as a dispersal pathway for Atlantic species. Both long- and short-distance dispersal scenarios are supported by genetic relationships within cosmopolitan species based on haplotype analysis. Asymmetrical distributions and the predominance of peripatry and sympatry between sister species suggest the importance of budding speciation in Pterocladiella. Our study highlights the underestimation of global diversity in these crucial components of coastal ecosystems and provides evidence for the complex evolution of current species distributions.
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Affiliation(s)
- Ga Hun Boo
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Paris, France
- University Herbarium, University of California, Berkeley, CA, United States
| | - Frederik Leliaert
- Meise Botanic Garden, Meise, Belgium
- Phycology Research Group, Department of Biology, Ghent University, Ghent, Belgium
| | - Line Le Gall
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Paris, France
| | - Eric Coppejans
- Phycology Research Group, Department of Biology, Ghent University, Ghent, Belgium
| | - Olivier De Clerck
- Phycology Research Group, Department of Biology, Ghent University, Ghent, Belgium
| | - Tu Van Nguyen
- Department of Ecology, Institute of Tropical Biology, Vietnam Academy of Science and Technology, Ho Chi Minh City, Vietnam
| | - Claude E. Payri
- UMR Entropie (IRD, Ifremer, Univ Nouvelle-Calédonie, Univ La Réunion, CNRS), Nouméa, New Caledonia
| | - Kathy Ann Miller
- University Herbarium, University of California, Berkeley, CA, United States
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
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Stiller J, Short G, Hamilton H, Saarman N, Longo S, Wainwright P, Rouse GW, Simison WB. Phylogenomic analysis of Syngnathidae reveals novel relationships, origins of endemic diversity and variable diversification rates. BMC Biol 2022; 20:75. [PMID: 35346180 PMCID: PMC8962102 DOI: 10.1186/s12915-022-01271-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 03/04/2022] [Indexed: 12/03/2022] Open
Abstract
Background Seahorses, seadragons, pygmy pipehorses, and pipefishes (Syngnathidae, Syngnathiformes) are among the most recognizable groups of fishes because of their derived morphology, unusual life history, and worldwide distribution. Despite previous phylogenetic studies and recent new species descriptions of syngnathids, the evolutionary relationships among several major groups within this family remain unresolved. Results Here, we provide a reconstruction of syngnathid phylogeny based on genome-wide sampling of 1314 ultraconserved elements (UCEs) and expanded taxon sampling to assess the current taxonomy and as a basis for macroevolutionary insights. We sequenced a total of 244 new specimens across 117 species and combined with published UCE data for a total of 183 species of Syngnathidae, about 62% of the described species diversity, to compile the most data-rich phylogeny to date. We estimated divergence times using 14 syngnathiform fossils, including nine fossils with newly proposed phylogenetic affinities, to better characterize current and historical biogeographical patterns, and to reconstruct diversification through time. We present a phylogenetic hypothesis that is well-supported and provides several notable insights into syngnathid evolution. We found nine non-monophyletic genera, evidence for seven cryptic species, five potentially invalid synonyms, and identified a novel sister group to the seahorses, the Indo-Pacific pipefishes Halicampus macrorhynchus and H. punctatus. In addition, the morphologically distinct southwest Pacific seahorse Hippocampus jugumus was recovered as the sister to all other non-pygmy seahorses. As found in many other groups, a high proportion of syngnathid lineages appear to have originated in the Central Indo-Pacific and subsequently dispersed to adjoining regions. Conversely, we also found an unusually high subsequent return of lineages from southern Australasia to the Central Indo-Pacific. Diversification rates rose abruptly during the Middle Miocene Climate Transition and peaked after the closure of the Tethys Sea. Conclusions Our results reveal a previously underappreciated diversity of syngnathid lineages. The observed biogeographic patterns suggest a significant role of the southern Australasian region as a source and sink of lineages. Shifts in diversification rates imply possible links to declining global temperatures, the separation of the Atlantic and Pacific faunas, and the environmental changes associated with these events. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01271-w.
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Affiliation(s)
- Josefin Stiller
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, USA. .,Centre for Biodiversity Genomics, University of Copenhagen, 2100, Copenhagen, Denmark.
| | - Graham Short
- Ichthyology, Australian Museum, Sydney, Australia.,Ichthyology, California Academy of Sciences, San Francisco, USA.,Ichthyology, Burke Museum of Natural History and Culture, Seattle, USA
| | | | - Norah Saarman
- Department of Biology and Ecology Center, Utah State University, Logan, Utah, USA
| | - Sarah Longo
- Department of Biological Science, Towson University, Towson, MD, 21252, USA
| | - Peter Wainwright
- Department of Evolution & Ecology, University of California, Davis, USA
| | - Greg W Rouse
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, USA
| | - W Brian Simison
- Center for Comparative Genomics, California Academy of Sciences, San Francisco, USA
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Genis-Armero R, Błażewicz M, Clark PF, Palero F. Chelarctus and Crenarctus (Crustacea: Scyllaridae) from Coral Sea waters, with molecular identification of their larvae. THE EUROPEAN ZOOLOGICAL JOURNAL 2022. [DOI: 10.1080/24750263.2022.2036256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- R. Genis-Armero
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Paterna, Spain
- Department of Invertebrate Zoology and Hydrobiology, Faculty of Biology and Environmental Protection, University of Lodz, ul. Banacha 12/16, 90-237, Łódź, Poland
| | - M. Błażewicz
- Department of Invertebrate Zoology and Hydrobiology, Faculty of Biology and Environmental Protection, University of Lodz, ul. Banacha 12/16, 90-237, Łódź, Poland
| | - P. F. Clark
- Department of Life Sciences, The Natural History Museum, Cromwell Road, SW7 5BD, London, England
| | - F. Palero
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Paterna, Spain
- Department of Life Sciences, The Natural History Museum, Cromwell Road, SW7 5BD, London, England
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13
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Morhun H, Copilas-Ciocianu D, Rewicz T, Son MO, Khomenko A, Huseynov M, Utevsky S, Grabowski M. Molecular markers and SEM imaging reveal pseudocryptic diversity within the Ponto-Caspian low-profile amphipod invader Dikerogammarus bispinosus. THE EUROPEAN ZOOLOGICAL JOURNAL 2022. [DOI: 10.1080/24750263.2021.2018056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- H. Morhun
- Department of Zoology and Animal Ecology, V.N. Karazin Kharkiv National University, Kharkiv, Ukraine
- National Academy of Sciences of Ukraine, Institute of Marine Biology, Odesa, Ukraine
| | - D. Copilas-Ciocianu
- Laboratory of Evolutionary Ecology of Hydrobionts, Nature Research Centre, Vilnius, Lithuania
| | - T. Rewicz
- Department of Invertebrate Zoology and Hydrobiology, University of Lodz, Łódź, Poland
- Centre for Biodiversity Genomics, University of Guelph, Ontario, Canada
| | - M. O. Son
- National Academy of Sciences of Ukraine, Institute of Marine Biology, Odesa, Ukraine
| | - A. Khomenko
- Department of Zoology and Animal Ecology, V.N. Karazin Kharkiv National University, Kharkiv, Ukraine
| | - M. Huseynov
- National Academy of Sciences of Azerbaijan Republic, Zoology Institute, Baku, Azerbaijan
| | - S. Utevsky
- Department of Zoology and Animal Ecology, V.N. Karazin Kharkiv National University, Kharkiv, Ukraine
| | - M. Grabowski
- Department of Invertebrate Zoology and Hydrobiology, University of Lodz, Łódź, Poland
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14
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Delrieu-Trottin E, Hartmann-Salvo H, Saenz-Agudelo P, Landaeta MF, Pérez-Matus A. DNA reconciles morphology and colouration in the drunk blenny genus Scartichthys (Teleostei: Blenniidae) and provides insights into their evolutionary history. JOURNAL OF FISH BIOLOGY 2022; 100:507-518. [PMID: 34821381 DOI: 10.1111/jfb.14960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/17/2021] [Accepted: 11/22/2021] [Indexed: 06/13/2023]
Abstract
The blenniids of the genus Scartichthys are one of the most common fishes of Central and South American Pacific coastal reefs. This being said, Scartichthys spp. remain difficult to identify in the field, and identification is particularly challenging across the c. 6000 km where three of the four currently accepted species are known to occur in sympatry. A reason for this is that the main taxonomic characters from traditional taxonomy are indeed elusive. In addition, at the same time, species can display multiple colour patterns in the field, depending on their ontogenetic stage, habitat association and reproductive behaviour. Overall, molecular characterization is warranted to help address these issues. In this study, the authors have used a novel approach to revise the genus by combining colouration, morphological and molecular data of representative specimens of the four currently valid species and seven described colour patterns. From this, the authors show that only three of the four species should be considered as valid; Scartichthys gigas (Steindachner, 1876), Scartichthys variolatus (Valenciennes, 1836) and Scartichthys viridis (Valenciennes, 1836), whereas Scartichthys crapulatus (Williams, 1990) should be synonymized with S. viridis. In the same way, the analyses in this study show that one of the colour patterns attributed so far only to S. gigas is characteristic of the juvenile stages of S. viridis. The time-calibrated phylogeny of this study shows that this genus is relatively young and that the estimated time of divergence between S. gigas and S. viridis is c. 1.71 Ma. In comparison, the Desventuradas and Juan Fernandez Islands endemic S. variolatus diverged c. 1.95 Ma. The results of this study help to clarify the taxonomy of Scartichthys.
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Affiliation(s)
- Erwan Delrieu-Trottin
- ISEM, CNRS, EPHE, IRD, Université de Montpellier, Montpellier cedex 5, France
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
- CEFE, Univ Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
| | - Hans Hartmann-Salvo
- Subtidal Ecology Laboratory, Estación Costera de Investigaciones Marinas, Departamento de Ecología, Facultad de Ciencias Biológicas Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Pablo Saenz-Agudelo
- Instituto de Ciencias Ambientales y Evolutivas (ICAEV), Universidad Austral de Chile, Valdivia, Chile
- Millennium Nucleus for Ecology and Conservation of Temperate Mesophotic Reef Ecosystem (NUTME)
| | - Mauricio F Landaeta
- Millennium Nucleus for Ecology and Conservation of Temperate Mesophotic Reef Ecosystem (NUTME)
- Laboratorio de Ictioplancton (LABITI), Instituto de Biología, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
- Centro de Observación Marino para Estudios del Ambiente Costero (COSTA-R), Universidad de Valparaíso, Valparaíso, Chile
| | - Alejandro Pérez-Matus
- Subtidal Ecology Laboratory, Estación Costera de Investigaciones Marinas, Departamento de Ecología, Facultad de Ciencias Biológicas Pontificia Universidad Católica de Chile, Santiago, Chile
- Millennium Nucleus for Ecology and Conservation of Temperate Mesophotic Reef Ecosystem (NUTME)
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15
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Hutchins BT, Schwartz BF, Coleman WT. Three new microcerberids (Isopoda: Microcerberidae) from subterranean freshwater habitats in Texas, USA. J NAT HIST 2022. [DOI: 10.1080/00222933.2021.2009054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Benjamin T. Hutchins
- Edwards Aquifer Research and Data Center, Texas State University, San Marcos, TX, USA
| | - Benjamin F. Schwartz
- Edwards Aquifer Research and Data Center, Texas State University, San Marcos, TX, USA
- Department of Biology, Texas State University, San Marcos, TX, USA
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16
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Influence of historical changes in tropical reef habitat on the diversification of coral reef fishes. Sci Rep 2021; 11:20731. [PMID: 34671048 PMCID: PMC8528860 DOI: 10.1038/s41598-021-00049-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 09/28/2021] [Indexed: 11/11/2022] Open
Abstract
Past environmental changes are expected to have profoundly impacted diversity dynamics through time. While some previous studies showed an association between past climate changes or tectonic events and important shifts in lineage diversification, it is only recently that past environmental changes have been explicitly integrated in diversification models to test their influence on diversification rates. Here, we used a global reconstruction of tropical reef habitat dynamics during the Cenozoic and phylogenetic diversification models to test the influence of (i) major geological events, (ii) reef habitat fragmentation and (iii) reef area on the diversification of 9 major clades of tropical reef fish (Acanthuridae, Balistoidea, Carangoidea, Chaetodontidae, Haemulinae, Holocentridae, Labridae, Pomacentridae and Sparidae). The diversification models revealed a weak association between paleo-habitat changes and diversification dynamics. Specifically, the fragmentation of tropical reef habitats over the Cenozoic was found to be a driver of tropical reef fish diversification for 2 clades. However, overall, our approach did not allow the identification of striking associations between diversification dynamics and paleo-habitat fragmentation in contrast with theoretical model's predictions.
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17
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Cain S, Loria SF, Ben-Shlomo R, Prendini L, Gefen E. Dated phylogeny and ancestral range estimation of sand scorpions (Buthidae: Buthacus) reveal Early Miocene divergence across land bridges connecting Africa and Asia. Mol Phylogenet Evol 2021; 164:107212. [PMID: 34029718 DOI: 10.1016/j.ympev.2021.107212] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 05/10/2021] [Accepted: 05/19/2021] [Indexed: 11/15/2022]
Abstract
Sand scorpions of the genus Buthacus Birula, 1908 (Buthidae C.L. Koch, 1837) are widespread in the sandy deserts of the Palearctic region, occurring from the Atlantic coast of West Africa across the Sahara, and throughout the Middle East to Central Asia. The limits of Buthacus, its two species groups, and many of its species remain unclear, and in need of revision using modern systematic methods. The study presented here set out to investigate the phylogeny and biogeography of the Buthacus species occurring in the Levant, last studied in 1980. A phylogenetic analysis was performed on 104 terminals, including six species collected from more than thirty localities in Israel and other countries in the region. Three mitochondrial and two nuclear gene loci were sequenced for a total of 2,218 aligned base-pairs. Morphological datasets comprising 22 qualitative and 48 quantitative morphological characters were compiled. Molecular and morphological datasets were analyzed separately and simultaneously with Bayesian Inference, Maximum Likelihood, and parsimony. Divergence time and ancestral range estimation analyses were performed, to understand dispersal and diversification. The results support a revised classification of Levantine Buthacus, and invalidate the traditional species groups of Buthacus, instead recovering two geographically-delimited clades, an African clade and an Asian clade, approximately separated by the Jordan Valley (the Jordan Rift Valley or Syro-African Depression), the northernmost part of the Great Rift Valley. The divergence between these clades occurred in the Early Miocene (ca. 19 Ma) in the Levant, coinciding temporally with the existence of two land bridges, which allowed faunal exchange between Africa and Asia.
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Affiliation(s)
- Shlomo Cain
- Department of Evolutionary and Environmental Biology, Faculty of Natural Sciences, University of Haifa, Israel
| | - Stephanie F Loria
- Scorpion Systematics Research Group, Arachnology Lab, Division of Invertebrate Zoology, American Museum of Natural History, New York, USA
| | - Rachel Ben-Shlomo
- Department of Biology and Environment, Faculty of Natural Sciences, University of Haifa - Oranim, Israel
| | - Lorenzo Prendini
- Scorpion Systematics Research Group, Arachnology Lab, Division of Invertebrate Zoology, American Museum of Natural History, New York, USA
| | - Eran Gefen
- Department of Biology and Environment, Faculty of Natural Sciences, University of Haifa - Oranim, Israel.
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18
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Santaquiteria A, Siqueira AC, Duarte-Ribeiro E, Carnevale G, White W, Pogonoski J, Baldwin CC, Ortí G, Arcila D, Betancur RR. Phylogenomics and Historical Biogeography of Seahorses, Dragonets, Goatfishes, and Allies (Teleostei: Syngnatharia): Assessing Factors Driving Uncertainty in Biogeographic Inferences. Syst Biol 2021; 70:1145-1162. [PMID: 33892493 DOI: 10.1093/sysbio/syab028] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 04/19/2021] [Indexed: 11/14/2022] Open
Abstract
The charismatic trumpetfishes, goatfishes, dragonets, flying gurnards, seahorses, and pipefishes encompass a recently defined yet extraordinarily diverse clade of percomorph fishes-the series Syngnatharia. This group is widely distributed in tropical and warm-temperate regions, with a great proportion of its extant diversity occurring in the Indo-Pacific. Because most syngnatharians feature long-range dispersal capabilities, tracing their biogeographic origins is challenging. Here, we applied an integrative phylogenomic approach to elucidate the evolutionary biogeography of syngnatharians. We built upon a recently published phylogenomic study that examined ultraconserved elements by adding 62 species (total 169 species) and one family (Draconettidae), to cover ca. 25% of the species diversity and all 10 families in the group. We inferred a set of time-calibrated trees and conducted ancestral range estimations. We also examined the sensitivity of these analyses to phylogenetic uncertainty (estimated from multiple genomic subsets), area delimitation, and biogeographic models that include or exclude the jump-dispersal parameter (j). Of the three factors examined, we found that the j parameter has the strongest effect in ancestral range estimates, followed by number of areas defined, and tree topology and divergence times. After accounting for these uncertainties, our results reveal that syngnatharians originated in the ancient Tethys Sea ca. 87 Ma (84-94 Ma; Late Cretaceous) and subsequently occupied the Indo-Pacific. Throughout syngnatharian history, multiple independent lineages colonized the eastern Pacific (6-8 times) and the Atlantic (6-14 times) from their center of origin, with most events taking place following an east-to-west route prior to the closure of the Tethys Seaway ca. 12-18 Ma. Ultimately, our study highlights the importance of accounting for different factors generating uncertainty in macroevolutionary and biogeographic inferences.
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Affiliation(s)
- Aintzane Santaquiteria
- Department of Biology, The University of Oklahoma, 730 Van Vleet Oval, Norman, OK 73019, USA
| | - Alexandre C Siqueira
- Research Hub for Coral Reef Ecosystem Functions, College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia
| | - Emanuell Duarte-Ribeiro
- Department of Biology, The University of Oklahoma, 730 Van Vleet Oval, Norman, OK 73019, USA
| | - Giorgio Carnevale
- Dipartimento di Scienze della Terra, Università degli Studi di Torino, via Valperga Caluso 35, 10125, Torino, Italy
| | - William White
- CSIRO Australian National Fish Collection, National Research Collections of Australia, Hobart, TAS, Australia
| | - John Pogonoski
- CSIRO Australian National Fish Collection, National Research Collections of Australia, Hobart, TAS, Australia
| | - Carole C Baldwin
- Department of Vertebrate Zoology, Smithsonian National Museum of Natural History, 10th St. & Constitution Ave. NW, Washington, DC 20560, USA
| | - Guillermo Ortí
- Department of Vertebrate Zoology, Smithsonian National Museum of Natural History, 10th St. & Constitution Ave. NW, Washington, DC 20560, USA.,Department of Biological Sciences, George Washington University, 2029 G St. NW, Washington, DC 20052, USA
| | - Dahiana Arcila
- Department of Biology, The University of Oklahoma, 730 Van Vleet Oval, Norman, OK 73019, USA.,Sam Noble Oklahoma Museum of Natural History, 2401 Chautauqua Ave, Norman, OK 73072, USA
| | - Ricardo R Betancur
- Department of Biology, The University of Oklahoma, 730 Van Vleet Oval, Norman, OK 73019, USA
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19
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Takayama K, Tateishi Y, Kajita T. Global phylogeography of a pantropical mangrove genus Rhizophora. Sci Rep 2021; 11:7228. [PMID: 33785819 PMCID: PMC8009884 DOI: 10.1038/s41598-021-85844-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 03/05/2021] [Indexed: 02/01/2023] Open
Abstract
Rhizophora is a key genus for revealing the formation process of the pantropical distribution of mangroves. In this study, in order to fully understand the historical scenario of Rhizophora that achieved pantropical distribution, we conducted phylogeographic analyses based on nucleotide sequences of chloroplast and nuclear DNA as well as microsatellites for samples collected worldwide. Phylogenetic trees suggested the monophyly of each AEP and IWP lineages respectively except for R. samoensis and R. × selala. The divergence time between the two lineages was 10.6 million years ago on a dated phylogeny, and biogeographic stochastic mapping analyses supported these lineages separated following a vicariant event. These data suggested that the closure of the Tethys Seaway and the reduction in mangrove distribution followed by Mid-Miocene cooling were key factors that caused the linage diversification. Phylogeographic analyses also suggested the formation of the distinctive genetic structure at the AEP region across the American continents around Pliocene. Furthermore, long-distance trans-pacific dispersal occurred from the Pacific coast of American continents to the South Pacific and formed F1 hybrid, resulting in gene exchange between the IWP and AEP lineages after 11 million years of isolation. Considering the phylogeny and phylogeography with divergence time, a comprehensive picture of the historical scenario behind the pantropical distribution of Rhizophora is updated.
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Affiliation(s)
- Koji Takayama
- grid.258799.80000 0004 0372 2033Department of Botany, Graduate School of Science, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Yoichi Tateishi
- grid.267625.20000 0001 0685 5104Faculty of Education, University of the Ryukyus, Senbaru 1, Nakagami-gun, Okinawa, 903-0129 Japan
| | - Tadashi Kajita
- grid.267625.20000 0001 0685 5104Iriomote Station, Tropical Biosphere Research Center, University of the Ryukyus, 870 Uehara, Taketomi-cho, Yaeyama-gun, Okinawa, 907-1541 Japan ,grid.258333.c0000 0001 1167 1801United Graduate School of Agricultural Science, Kagoshima University, Kagoshima, Japan
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20
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Yang Y, Abalde S, Afonso CL, Tenorio MJ, Puillandre N, Templado J, Zardoya R. Mitogenomic phylogeny of mud snails of the mostly Atlantic/Mediterranean genus
Tritia
(Gastropoda: Nassariidae). ZOOL SCR 2021. [DOI: 10.1111/zsc.12489] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Yi Yang
- Museo Nacional de Ciencias Naturales (MNCN‐CSIC) Madrid Spain
| | - Samuel Abalde
- Museo Nacional de Ciencias Naturales (MNCN‐CSIC) Madrid Spain
| | | | - Manuel J. Tenorio
- Departamento CMIM y Q. Inorgánica‐INBIO Facultad de Ciencias Universidad de Cadiz Puerto Real Spain
| | - Nicolas Puillandre
- Institut de Systématique, Évolution, Biodiversité (ISYEB) Muséum National d’Histoire NaturelleCNRSSorbonne UniversitéEPHEUniversité des Antilles Paris France
| | - José Templado
- Museo Nacional de Ciencias Naturales (MNCN‐CSIC) Madrid Spain
| | - Rafael Zardoya
- Museo Nacional de Ciencias Naturales (MNCN‐CSIC) Madrid Spain
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21
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Li C, Olave M, Hou Y, Qin G, Schneider RF, Gao Z, Tu X, Wang X, Qi F, Nater A, Kautt AF, Wan S, Zhang Y, Liu Y, Zhang H, Zhang B, Zhang H, Qu M, Liu S, Chen Z, Zhong J, Zhang H, Meng L, Wang K, Yin J, Huang L, Venkatesh B, Meyer A, Lu X, Lin Q. Genome sequences reveal global dispersal routes and suggest convergent genetic adaptations in seahorse evolution. Nat Commun 2021; 12:1094. [PMID: 33597547 PMCID: PMC7889852 DOI: 10.1038/s41467-021-21379-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 01/25/2021] [Indexed: 01/31/2023] Open
Abstract
Seahorses have a circum-global distribution in tropical to temperate coastal waters. Yet, seahorses show many adaptations for a sedentary, cryptic lifestyle: they require specific habitats, such as seagrass, kelp or coral reefs, lack pelvic and caudal fins, and give birth to directly developed offspring without pronounced pelagic larval stage, rendering long-range dispersal by conventional means inefficient. Here we investigate seahorses' worldwide dispersal and biogeographic patterns based on a de novo genome assembly of Hippocampus erectus as well as 358 re-sequenced genomes from 21 species. Seahorses evolved in the late Oligocene and subsequent circum-global colonization routes are identified and linked to changing dynamics in ocean currents and paleo-temporal seaway openings. Furthermore, the genetic basis of the recurring "bony spines" adaptive phenotype is linked to independent substitutions in a key developmental gene. Analyses thus suggest that rafting via ocean currents compensates for poor dispersal and rapid adaptation facilitates colonizing new habitats.
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Affiliation(s)
- Chunyan Li
- grid.458498.c0000 0004 1798 9724CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China ,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China ,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Melisa Olave
- grid.9811.10000 0001 0658 7699Department of Biology, University of Konstanz, Konstanz, Germany ,grid.423606.50000 0001 1945 2152Present Address: Argentine Dryland Research Institute, National Council for Scientific and Technical Research (IADIZA-CONICET), Mendoza, Argentina
| | - Yali Hou
- grid.464209.d0000 0004 0644 6935Beijing Institute of Genomics, Chinese Academy of Sciences; China National Center for Bioinformation, Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Geng Qin
- grid.458498.c0000 0004 1798 9724CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China ,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Ralf F. Schneider
- grid.9811.10000 0001 0658 7699Department of Biology, University of Konstanz, Konstanz, Germany ,Marine Ecology, Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Zexia Gao
- grid.35155.370000 0004 1790 4137College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | | | - Xin Wang
- grid.458498.c0000 0004 1798 9724CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Furong Qi
- grid.464209.d0000 0004 0644 6935Beijing Institute of Genomics, Chinese Academy of Sciences; China National Center for Bioinformation, Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Alexander Nater
- grid.9811.10000 0001 0658 7699Department of Biology, University of Konstanz, Konstanz, Germany
| | - Andreas F. Kautt
- grid.9811.10000 0001 0658 7699Department of Biology, University of Konstanz, Konstanz, Germany ,grid.38142.3c000000041936754XPresent Address: Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA USA
| | - Shiming Wan
- grid.458498.c0000 0004 1798 9724CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Yanhong Zhang
- grid.458498.c0000 0004 1798 9724CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Yali Liu
- grid.458498.c0000 0004 1798 9724CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Huixian Zhang
- grid.458498.c0000 0004 1798 9724CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Bo Zhang
- grid.458498.c0000 0004 1798 9724CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Hao Zhang
- grid.458498.c0000 0004 1798 9724CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Meng Qu
- grid.458498.c0000 0004 1798 9724CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Shuaishuai Liu
- grid.458498.c0000 0004 1798 9724CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Zeyu Chen
- grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China ,grid.419010.d0000 0004 1792 7072State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Jia Zhong
- grid.458498.c0000 0004 1798 9724CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - He Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | | | - Kai Wang
- grid.443651.1School of Agriculture, Ludong University, Yantai, China
| | - Jianping Yin
- grid.458498.c0000 0004 1798 9724CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Liangmin Huang
- grid.458498.c0000 0004 1798 9724CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Byrappa Venkatesh
- grid.418812.60000 0004 0620 9243Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore, Singapore
| | - Axel Meyer
- grid.9811.10000 0001 0658 7699Department of Biology, University of Konstanz, Konstanz, Germany
| | - Xuemei Lu
- grid.419010.d0000 0004 1792 7072State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Qiang Lin
- grid.458498.c0000 0004 1798 9724CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China ,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China ,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
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22
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Mendoza-Portillo V, Galván-Tirado C, Portnoy DS, Valenzuela-Quiñonez F, Domínguez-Domínguez O, Durand JD, Pérez-Urbiola JC, García-De León FJ. Genetic diversity and structure of circumtropical almaco jack, Seriola rivoliana: tool for conservation and management. JOURNAL OF FISH BIOLOGY 2020; 97:882-894. [PMID: 32598029 DOI: 10.1111/jfb.14450] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/13/2020] [Accepted: 06/26/2020] [Indexed: 06/11/2023]
Abstract
The almaco jack, Seriola rivoliana, is a circumtropical pelagic fish of importance both in commercial fisheries and in aquaculture. To understand levels of genetic diversity within and among populations in the wild, population genetic structure and the relative magnitude of migration were assessed using mtDNA sequence data and single nucleotide polymorphisms (SNPs) from individuals sampled from locations in the Pacific and Atlantic Oceans. A total of 25 variable sites of cytochrome c oxidase subunit 1 and 3678 neutral SNPs were recovered. Three genetic groups were identified, with both marker types distributed in different oceanic regions: Pacific-1 in central Pacific, Pacific-2 in eastern Pacific and Atlantic in western Atlantic. Nonetheless, the analysis of SNP identified a fourth population in the Pacific coast of Baja California Sur, Mexico (Pacific-3), whereas that of mtDNA did not. This mito-nuclear discordance is likely explained by a recently diverged Pacific-3 population. In addition, two mtDNA haplogroups were found within the western Atlantic, likely indicating that the species came into the Atlantic from the Indian Ocean with historical gene flow from the eastern Pacific. Relative gene flow among ocean basins was low with r m < 0.2, whereas in the eastern Pacific it was asymmetric and higher from south to north (r m > 0.79). The results reflect the importance of assessing genetic structure and gene flow of natural populations for the purposes of sustainable management.
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Affiliation(s)
- Verónica Mendoza-Portillo
- Laboratorio de Genética para la Conservación, Centro de Investigaciones Biológicas del Noroeste, La Paz, Mexico
| | | | - David S Portnoy
- Marine Genomics Laboratory, Department of Life Sciences, Texas A&M University-Corpus Christi, USA
| | | | - Omar Domínguez-Domínguez
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
- Instituto Nacional de Biodiversidad, Quito, Ecuador
| | | | | | - Francisco J García-De León
- Laboratorio de Genética para la Conservación, Centro de Investigaciones Biológicas del Noroeste, La Paz, Mexico
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23
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Rodríguez‐Flores PC, Buckley D, Macpherson E, Corbari L, Machordom A. Deep‐sea squat lobster biogeography (Munidopsidae:
Leiogalathea
) unveils Tethyan vicariance and evolutionary patterns shared by shallow‐water relatives. ZOOL SCR 2020. [DOI: 10.1111/zsc.12414] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Paula C. Rodríguez‐Flores
- Museo Nacional de Ciencias Naturales (MNCN‐CSIC) Madrid Spain
- Centre d'Estudis Avançats de Blanes (CEAB‐CSIC) Blanes Spain
| | - David Buckley
- Departamento de Biología (Genética) Facultad de Biología Universidad Autónoma de Madrid Madrid Spain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC‐UAM) Facultad de Biología Universidad Autónoma de Madrid Madrid Spain
| | | | - Laure Corbari
- Institut de Systématique Évolution Biodiversité (ISYEB, UMR 7205) Muséum national d'Histoire naturelle CNRS Sorbonne UniversitéEPHE Paris France
| | - Annie Machordom
- Museo Nacional de Ciencias Naturales (MNCN‐CSIC) Madrid Spain
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24
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Li Y, Li S, Liu H, Kurenshchikov DK, Hou Z. Eocene–Oligocene sea‐level fall drove amphipod habitat shift from marine to freshwater in the Far East. ZOOL SCR 2020. [DOI: 10.1111/zsc.12409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Yulong Li
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Shuqiang Li
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Hongguang Liu
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Dmitry K. Kurenshchikov
- Laboratory of the Animal Ecology Institute of Water and Ecology Problems Far East Branch of the Russian Academy of Sciences Khabarovsk Russia
| | - Zhonge Hou
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
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25
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Froufe E, Bolotov I, Aldridge DC, Bogan AE, Breton S, Gan HM, Kovitvadhi U, Kovitvadhi S, Riccardi N, Secci-Petretto G, Sousa R, Teixeira A, Varandas S, Zanatta D, Zieritz A, Fonseca MM, Lopes-Lima M. Mesozoic mitogenome rearrangements and freshwater mussel (Bivalvia: Unionoidea) macroevolution. Heredity (Edinb) 2020; 124:182-196. [PMID: 31201385 PMCID: PMC6906506 DOI: 10.1038/s41437-019-0242-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 05/28/2019] [Accepted: 05/30/2019] [Indexed: 11/08/2022] Open
Abstract
Using a new fossil-calibrated mitogenome-based approach, we identified macroevolutionary shifts in mitochondrial gene order among the freshwater mussels (Unionoidea). We show that the early Mesozoic divergence of the two Unionoidea clades, Margaritiferidae and Unionidae, was accompanied by a synchronous split in the gene arrangement in the female mitogenome (i.e., gene orders MF1 and UF1). Our results suggest that this macroevolutionary jump was completed within a relatively short time interval (95% HPD 201-226 Ma) that coincided with the Triassic-Jurassic mass extinction. Both gene orders have persisted within these clades for ~200 Ma. The monophyly of the so-called "problematic" Gonideinae taxa was supported by all the inferred phylogenies in this study using, for the first time, the M- and F-type mitogenomes either singly or combined. Within Gonideinae, two additional splits in the gene order (UF1 to UF2, UF2 to UF3) occurred in the Mesozoic and have persisted for ~150 and ~100 Ma, respectively. Finally, the mitogenomic results suggest ancient connections between freshwater basins of East Asia and Europe near the Cretaceous-Paleogene boundary, probably via a continuous paleo-river system or along the Tethys coastal line, which are well supported by at least three independent but almost synchronous divergence events.
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Affiliation(s)
- Elsa Froufe
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, Matosinhos, 4450-208, Portugal.
| | - Ivan Bolotov
- IBIGER - Institute of Biogeography and Genetic Resources, Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Severnaya Dvina Emb. 23, Arkhangelsk, 163000, Russian Federation
- Northern Arctic Federal University, Severnaya Dvina Emb. 17, Arkhangelsk, 163000, Russian Federation
| | - David C Aldridge
- Department of Zoology, University of Cambridge, The David Attenborough Building, Pembroke Street, Cambridge, CB2 3QZ, UK
| | - Arthur E Bogan
- North Carolina State Museum of Natural Sciences, 11 West Jones St., Raleigh, NC, 27601, USA
| | - Sophie Breton
- Département de Sciences Biologiques, Université de Montréal, Montréal, QC, H2V 2S9, Canada
| | - Han Ming Gan
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, 3220, VIC, Australia
| | - Uthaiwan Kovitvadhi
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Satit Kovitvadhi
- Department of Agriculture, Faculty of Science and Technology, Bansomdejchaopraya Rajabhat University, Bangkok, 10600, Thailand
| | | | - Giulia Secci-Petretto
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, Matosinhos, 4450-208, Portugal
| | - Ronaldo Sousa
- CBMA - Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus Gualtar, Braga, 4710-057, Portugal
| | - Amilcar Teixeira
- CIMO/ESA/IPB - Mountain Research Centre, School of Agriculture, Polytechnic Institute of Bragança, Campus de Santa Apolónia, Apartado 1172, Bragança, 5301-854, Portugal
| | - Simone Varandas
- CITAB/UTAD - Centre for Research and Technology of Agro-Environment and Biological Sciences, University of Trás-os-Montes and Alto Douro, Forestry Department, Vila Real, 5000-801, Portugal
| | - David Zanatta
- Biology Department, Institute for Great Lakes Research, Central Michigan University, Biosciences Bldg. 2408, Mount Pleasant, MI, 48859, USA
| | - Alexandra Zieritz
- School of Environmental and Geographical Sciences, University of Nottingham Malaysia Campus, Jalan Broga, Semenyih, 43500, Malaysia
| | - Miguel M Fonseca
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, Matosinhos, 4450-208, Portugal
| | - Manuel Lopes-Lima
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, Matosinhos, 4450-208, Portugal
- CIBIO/InBIO - Research Center in Biodiversity and Genetic Resources, University of Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas 7, Vairão, Porto, 4485-661, Portugal
- SSC/IUCN - Mollusc Specialist Group, Species Survival Commission, International Union for Conservation of Nature, c/o The David Attenborough Building, Pembroke Street, Cambridge, CB2 3QZ, UK
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26
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Nikolic N, Liu S, Jacobsen MW, Jónsson B, Bernatchez L, Gagnaire PA, Hansen MM. Speciation history of European (Anguilla anguilla) and American eel (A. rostrata), analysed using genomic data. Mol Ecol 2019; 29:565-577. [PMID: 31863605 DOI: 10.1111/mec.15342] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 12/11/2019] [Accepted: 12/16/2019] [Indexed: 02/01/2023]
Abstract
Speciation in the ocean could differ from terrestrial environments due to fewer barriers to gene flow. Hence, sympatric speciation might be common, with American and European eel being candidates for exemplifying this. They show disjunct continental distributions on both sides of the Atlantic, but spawn in overlapping regions of the Sargasso Sea from where juveniles are advected to North American, European and North African coasts. Hybridization and introgression are known to occur, with hybrids almost exclusively observed in Iceland. Different speciation scenarios have been suggested, involving either vicariance or sympatric ecological speciation. Using RAD sequencing and whole-genome sequencing data from parental species and F1 hybrids, we analysed speciation history based on the joint allele frequency spectrum (JAFS) and pairwise sequentially Markovian coalescent (PSMC) plots. JAFS supported a model involving a split without gene flow 150,000-160,000 generations ago, followed by secondary contact 87,000-92,000 generations ago, with 64% of the genome experiencing restricted gene flow. This supports vicariance rather than sympatric speciation, likely associated with Pleistocene glaciation cycles and ocean current changes. Whole-genome PSMC analysis of F1 hybrids from Iceland suggested divergence 200,000 generations ago and indicated subsequent gene flow rather than strict isolation. Finally, simulations showed that results from both approaches (JAFS and PSMC) were congruent. Hence, there is strong evidence against sympatric speciation in North Atlantic eels. These results reiterate the need for careful consideration of cases of possible sympatric speciation, as even in seemingly barrier-free oceanic environments palaeoceanographic factors may have promoted vicariance and allopatric speciation.
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Affiliation(s)
- Natacha Nikolic
- Agence de Recherche pour la Biodiversité à la Réunion, ARBRE, Saint-Leu, Réunion
| | - Shenglin Liu
- Department of Bioscience, Aarhus University, Aarhus C, Denmark
| | | | | | - Louis Bernatchez
- IBIS (Institut de Biologie Intégrative et des Systèmes), Université Laval, Québec, QC, Canada
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27
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Bribiesca-Contreras G, Pineda-Enríquez T, Márquez-Borrás F, Solís-Marín FA, Verbruggen H, Hugall AF, O'Hara TD. Dark offshoot: Phylogenomic data sheds light on the evolutionary history of a new species of cave brittle star. Mol Phylogenet Evol 2019; 136:151-163. [PMID: 30981811 DOI: 10.1016/j.ympev.2019.04.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 02/28/2019] [Accepted: 04/10/2019] [Indexed: 11/28/2022]
Abstract
Caves are a useful system for testing evolutionary and biogeographic hypotheses, as they are isolated, and their environmental conditions have resulted in adaptive selection across different taxa. Although in recent years many more cave species have been discovered, cave-dwelling members of the class Ophiuroidea (brittle stars) remain scarce. Out of the more than two thousand species of brittle stars described to date, only three are regarded as true cave-dwellers. These occurrences represent rare colonising events, compared to other groups that are known to have successfully diversified in these systems. A third species from an anchihaline cave system in the Yucatan Peninsula, Mexico, has been previously identified from cytochrome oxidase I (COI) barcodes. In this study, we reassess the species boundaries of this putative cave species using a phylogenomic dataset (20 specimens in 13 species, 100 exons, 18.7 kbp). We perform species delimitation analyses using robust full-coalescent methods for discovery and validation of hypotheses on species boundaries, as well as infer its phylogenetic relationships with species distributed in adjacent marine regions, in order to investigate the origin of this cave-adapted species. We assess which hypotheses on the origin of subterranean taxa can be applied to this species by taking into account its placement within the genus Ophionereis and its demographic history. We provide a detailed description of Ophionereis commutabilis n. sp., and evaluate its morphological characters in the light of its successful adaptation to life in caves.
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Affiliation(s)
- Guadalupe Bribiesca-Contreras
- Museum Victoria, GPO Box 666, Melbourne 3001, Australia; School of Biosciences, University of Melbourne, Victoria 3010, Australia.
| | - Tania Pineda-Enríquez
- Department of Biology, Division of Invertebrate Zoology, Florida Museum of Natural History, University of Florida, Gainesville, FL, USA; Natural History Museum of Los Angeles County, 900 Exposition Blvd, Los Angeles, CA 90007, USA
| | - Francisco Márquez-Borrás
- Laboratorio de Sistemática y Ecología de Equinodermos, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Circuito Universitario s/n, Ciudad de México CP 04510, Mexico; Posgrado en Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Circuito Universitario s/n, Ciudad de México CP 04510, Mexico
| | - Francisco A Solís-Marín
- Laboratorio de Sistemática y Ecología de Equinodermos, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Circuito Universitario s/n, Ciudad de México CP 04510, Mexico
| | - Heroen Verbruggen
- School of Biosciences, University of Melbourne, Victoria 3010, Australia
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28
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Wu F, He D, Fang G, Deng T. Into Africa via docked India: a fossil climbing perch from the Oligocene of Tibet helps solve the anabantid biogeographical puzzle. Sci Bull (Beijing) 2019; 64:455-463. [PMID: 36659795 DOI: 10.1016/j.scib.2019.03.029] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 03/22/2019] [Accepted: 03/22/2019] [Indexed: 01/21/2023]
Abstract
The northward drift of the Indian Plate and its collision with Eurasia have profoundly impacted the evolutionary history of the terrestrial organisms, especially the ones along the Indian Ocean rim. Climbing perches (Anabantidae) are primary freshwater fishes showing a disjunct south Asian-African distribution, but with an elusive paleobiogeographic history due to the lack of fossil evidence. Here, based on an updated time-calibrated anabantiform phylogeny integrating a number of relevant fossils, the divergence between Asian and African climbing perches is estimated to have occurred in the middle Eocene (ca. 40 Ma, Ma: million years ago), a time when India had already joined with Eurasia. The key fossil lineage is †Eoanabas, the oldest anabantid known so far, from the upper Oligocene of the Tibetan Plateau. Ancestral range reconstructions suggest a Southeast Asian origin in the early Eocene (ca. 48 Ma) and subsequent dispersals to Tibet and then India for this group. Thereby we propose their westbound dispersal to Africa via the biotic bridge between India and Africa. If so, climbing perch precursors had probably followed the paleobiogeographical route of snakehead fishes, which have a slightly older divergence between African and Asian taxa. As such, our study echoes some recent molecular analyses in rejecting the previously held "Gondwana continental drift vicariance" or late Mesozoic dispersal scenarios for the climbing perches, but provides a unique biogeographical model to highlight the role of the pre-uplift Tibet and the docked India in shaping the disjunct distribution of some air-breathing freshwater fishes around the Indian Ocean.
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Affiliation(s)
- Feixiang Wu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100101, China.
| | - Dekui He
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
| | - Gengyu Fang
- College of Earth Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tao Deng
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100101, China; College of Earth Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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29
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Recent diversification in an ancient lineage of Notothenioid fishes (Bovichtus: Notothenioidei). Polar Biol 2019. [DOI: 10.1007/s00300-019-02489-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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30
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Randsø PV, Yamasaki H, Bownes SJ, Herranz M, Di Domenico M, Qii GB, Sørensen MV. Phylogeny of the Echinoderes coulli-group (Kinorhyncha : Cyclorhagida : Echinoderidae) – a cosmopolitan species group trapped in the intertidal. INVERTEBR SYST 2019. [DOI: 10.1071/is18069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Kinorhyncha is a phylum of microscopic, benthic marine invertebrates found throughout the world, from the Arctic to Antarctica and from the intertidal zone to the deep sea. Within the most species-rich genus, Echinoderes, we find a putatively monophyletic species group, the so-called Echinoderes coulli-group. The remarkable morphological similarities of the E. coulli-group species and the fact that the group has a global distribution even though most of the species are restricted to intertidal habitats, has led to the hypothesis that dispersal and speciation within the group has been driven by the process of continental drift. However, this has never been confirmed empirically. With morphology and two molecular loci, COI and 18S, we calculated phylogenetic trees by analysing datasets separately and in combination using Maximum Parsimony, Maximum Likelihood and Bayesian Inference. Using different models of evolution in combination with different statistical approaches, we show that two major clade divergences were consistent with historic drifting of continents, suggesting that vicariance has played an important role for the speciation within the E. coulli-group. Furthermore, we found that reconstructions of past tectonic drifting since the Devonian (416–359 million years ago) were able to explain present species distributions, and suggest that the group originated in a supposedly vast shallow marine environment in north-eastern Gondwana by the mid-late Silurian, 426–416 million years ago.
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31
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Zhang QL, Zhang GL, Yuan ML, Dong ZX, Li HW, Guo J, Wang F, Deng XY, Chen JY, Lin LB. A Phylogenomic Framework and Divergence History of Cephalochordata Amphioxus. Front Physiol 2018; 9:1833. [PMID: 30618839 PMCID: PMC6305399 DOI: 10.3389/fphys.2018.01833] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 12/06/2018] [Indexed: 11/21/2022] Open
Abstract
Amphioxus, or cephalochordates, are often used as the living invertebrate proxy of vertebrate ancestors and are widely used as evolutionary biology models of chordates. However, their phylogeny, divergence history, and speciation characteristics remain poorly understood, and phylogenomic studies to explore these problems lacking entirely from the literature. Here, we determined a new transcriptome of Branchiostoma japonicum. Combined with mass sequences of all other 18 species, a 19-way phylogeny was constructed via multiple methods (ML, BI, PhyloBayes, and ASTRAL), consistently supporting a phylogeny of [(B. belcheri + B. japonicum) + (B. lanceolatum + B. floridae) + Asymmetron lucayanum] in amphioxus. Congruent phylogenetic signals were found across mitochondrial genes, 12S RNA, and complete mitochondrial genomes according to previous reports, indicating that 12S RNA may have potential as a molecular marker for phylogenetic analysis in amphioxus. Molecular dating analysis indicated a radiation of the cephalochordates during the Cretaceous (∼104-61 million years ago), supporting an association between the diversification and speciation of cephalochordates with continental drift and associated changes in their respective habitats during this time. The identified functional enrichment analysis for species-specific domains indicated that their function mainly involves immune response, apoptosis, and lipid metabolism and utilization, signaling that pathogens and changes of energy requirements are an important driving force for amphioxus speciation. This study represents the first large-scale phylogenomic analysis of most major amphioxus genera based on phylogenomic data, providing a new perspective on both phylogeny and divergence speciation of cephalochordates.
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Affiliation(s)
- Qi-Lin Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China.,Evo-Devo Institute, School of Life Sciences, Nanjing University, Nanjing, China
| | - Guan-Ling Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Ming-Long Yuan
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, China
| | - Zhi-Xiang Dong
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Hong-Wei Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Jun Guo
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Feng Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Xian-Yu Deng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Jun-Yuan Chen
- Evo-Devo Institute, School of Life Sciences, Nanjing University, Nanjing, China.,State Key Laboratory of Palaeobiology and Stratigraphy (LPS), Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, China
| | - Lian-Bing Lin
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
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32
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Bolotov IN, Aksenova OV, Bakken T, Glasby CJ, Gofarov MY, Kondakov AV, Konopleva ES, Lopes-Lima M, Lyubas AA, Wang Y, Bychkov AY, Sokolova AM, Tanmuangpak K, Tumpeesuwan S, Vikhrev IV, Shyu JBH, Win T, Pokrovsky OS. Discovery of a silicate rock-boring organism and macrobioerosion in fresh water. Nat Commun 2018; 9:2882. [PMID: 30038289 PMCID: PMC6056532 DOI: 10.1038/s41467-018-05133-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 06/15/2018] [Indexed: 11/16/2022] Open
Abstract
Macrobioerosion is a common process in marine ecosystems. Many types of rock-boring organisms break down hard substrates, particularly carbonate rocks and calcareous structures such as dead corals and shells. In paleontology, the presence of rocks with boreholes and fossil macroboring assemblage members is one of the primary diagnostic features of shallow marine paleo-environments. Here we describe a silicate rock-boring organism and an associated community in submerged siltstone rock outcrops in Kaladan River, Myanmar. The rock-boring mussel Lignopholas fluminalis is a close relative of the marine piddocks, and its borings belong to the ichnospecies Gastrochaenolites anauchen. The neotectonic uplift of the area leading to gradual decrease of the sea level with subsequent shift from estuarine to freshwater environment was the most likely driver for the origin of this community. Our findings highlight that rocks with macroborings are not an exclusive indicator of marine paleo-ecosystems, but may also reflect freshwater habitats. Macrobioerosion, the boring of rock and other hard substrates by living organisms, is used as a marker of marine paleo-environments. Here, Bolotov et al. describe a rock-boring mussel and its associated community from freshwater in Myanmar, demonstrating that macrobioerosion is a wider phenomenon.
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Affiliation(s)
- Ivan N Bolotov
- Northern Arctic Federal University, Arkhangelsk, Russia, 163002. .,Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Arkhangelsk, Russia, 163000.
| | - Olga V Aksenova
- Northern Arctic Federal University, Arkhangelsk, Russia, 163002.,Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Arkhangelsk, Russia, 163000
| | - Torkild Bakken
- Norwegian University of Science and Technology, NTNU University Museum, 7491, Trondheim, Norway
| | | | - Mikhail Yu Gofarov
- Northern Arctic Federal University, Arkhangelsk, Russia, 163002.,Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Arkhangelsk, Russia, 163000
| | - Alexander V Kondakov
- Northern Arctic Federal University, Arkhangelsk, Russia, 163002.,Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Arkhangelsk, Russia, 163000
| | - Ekaterina S Konopleva
- Northern Arctic Federal University, Arkhangelsk, Russia, 163002.,Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Arkhangelsk, Russia, 163000
| | - Manuel Lopes-Lima
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4450-208, Matosinhos, Portugal.,CIBIO/InBIO-Research Center in Biodiversity and Genetic Resources, University of Porto, 4485-661, Vairão, Portugal
| | - Artyom A Lyubas
- Northern Arctic Federal University, Arkhangelsk, Russia, 163002.,Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Arkhangelsk, Russia, 163000
| | - Yu Wang
- Earth Observatory of Singapore, Nanyang Technological University, Singapore, 639798, Singapore.,Department of Geosciences, National Taiwan University, Taipei, 10617, Taiwan
| | - Andrey Yu Bychkov
- Faculty of Geology, Lomonosov Moscow State University, Moscow, Russia, 119991.,V. I. Vernadsky Institute of Geochemistry and Analytical Chemistry, Russian Academy of Sciences, Moscow, Russia, 119991
| | - Agniya M Sokolova
- A. N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia, 119071.,N. K. Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia, 119991
| | - Kitti Tanmuangpak
- Department of Science, Faculty of Science and Technology, Loei Rajabhat University, Loei, 42000, Thailand
| | - Sakboworn Tumpeesuwan
- Department of Biology, Faculty of Science, Mahasarakham University, Maha Sarakham, 44150, Thailand
| | - Ilya V Vikhrev
- Northern Arctic Federal University, Arkhangelsk, Russia, 163002.,Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Arkhangelsk, Russia, 163000
| | - J Bruce H Shyu
- Department of Geosciences, National Taiwan University, Taipei, 10617, Taiwan
| | - Than Win
- Department of Zoology, Hpa-An University, Hpa-An, Kayin State, 13017, Myanmar
| | - Oleg S Pokrovsky
- Geosciences and Environment Toulouse, UMR 5563 CNRS, 31400, Toulouse, France.,BIO-GEO-CLIM Laboratory, Tomsk State University, Tomsk, Russia, 634050
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Hou Z, Li S. Four new Gammarus species from Tibetan Plateau with a key to Tibetan freshwater gammarids (Crustacea, Amphipoda, Gammaridae). Zookeys 2018:1-40. [PMID: 29674901 PMCID: PMC5904427 DOI: 10.3897/zookeys.747.21999] [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: 11/01/2017] [Accepted: 03/07/2018] [Indexed: 11/12/2022] Open
Abstract
Four new species of the genus Gammarus are described and illustrated from Tibetan Plateau. Gammarusaltussp. n. and G.limosussp. n. are characterized by pereopods III–IV with a few short setae and uropod III with marginal spines accompanied by short setae. Gammaruskangdingensissp. n. and G.gonggaensissp. n. are characterized by pereopods III–IV with long straight setae on posterior margins and inner ramus of uropod III 0.4 times as long as outer ramus. Detailed morphological comparisons with related species are discussed. A key to 15 Gammarus species from the Tibetan Plateau and a map of their distributions are provided.
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Affiliation(s)
- Zhonge Hou
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shuqiang Li
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw 05282, Myanmar
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