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Rogers RL, Grizzard SL, Garner JT. Strong, Recent Selective Sweeps Reshape Genetic Diversity in Freshwater Bivalve Megalonaias nervosa. Mol Biol Evol 2023; 40:7026026. [PMID: 36738170 PMCID: PMC9976758 DOI: 10.1093/molbev/msad024] [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: 05/27/2022] [Revised: 01/16/2023] [Accepted: 01/24/2023] [Indexed: 02/05/2023] Open
Abstract
Freshwater Unionid bivalves have recently faced ecological upheaval through pollution, barriers to dispersal, harvesting, and changes in fish-host prevalence. Currently, over 70% of species in North America are threatened, endangered or extinct. To characterize the genetic response to recent selective pressures, we collected population genetic data for one successful bivalve species, Megalonaias nervosa. We identify megabase-sized regions that are nearly monomorphic across the population, signals of strong, recent selection reshaping diversity across 73 Mb total. These signatures of selection are greater than is commonly seen in population genetic models. We observe 102 duplicate genes with high dN/dS on terminal branches among regions with sweeps, suggesting that gene duplication is a causative mechanism of recent adaptation in M. nervosa. Genes in sweeps reflect functional classes important for Unionid survival, including anticoagulation genes important for fish host parasitization, detox genes, mitochondria management, and shell formation. We identify sweeps in regions with no known functional impacts, suggesting mechanisms of adaptation that deserve greater attention in future work on species survival. In contrast, polymorphic transposable elements (TEs) appear to be detrimental and underrepresented among regions with sweeps. TE site frequency spectra are skewed toward singleton variants, and TEs among regions with sweeps are present at low frequency. Our work suggests that duplicate genes are an essential source of genetic novelty that has helped this species succeed in environments where others have struggled. These results suggest that gene duplications deserve greater attention in non-model population genomics, especially in species that have recently faced sudden environmental challenges.
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Affiliation(s)
- Rebekah L Rogers
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, NC 28223, USA
| | | | - Jeffrey T Garner
- Division of Wildlife and Freshwater Fisheries, Alabama Department of Conservation and Natural Resources, Florence, AL, USA
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Tessler M, Galen SC, DeSalle R, Schierwater B. Let’s end taxonomic blank slates with molecular morphology. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1016412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Many known evolutionary lineages have yet to be described formally due to a lack of traditional morphological characters. This is true for genetically distinctive groups within the amoeboid Placozoa animals, the protists in ponds, and the bacteria that cover nearly everything. These taxonomic tabula rasae, or blank slates, are problematic; without names, communication is hampered and other scientific progress is slowed. We suggest that the morphology of molecules be used to help alleviate this issue. Molecules, such as proteins, have structure. Proteins are even visualizable with X-ray crystallography, albeit more easily detected by and easier to work with using genomic sequencing. Given their structured nature, we believe they should not be considered as anything less than traditional morphology. Protein-coding gene content (presence/absence) can also be used easily with genomic sequences, and is a convenient binary character set. With molecular morphology, we believe that each taxonomic tabula rasa can be solved.
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Ansari B, Altafa J, Ramzan A, Ahmed Z, Khalil S, Qamar SUR, Awan SA, Jehangir K, Khalid R, Aziz S, Sultana T, Sultana S, Alsamadany H, Alshamrani R, Awan FS. Molecular Phylogenetics of Physa acuta (Pulmonata: Basommatophora): an Invasive species in Central Punjab Pakistan. BRAZ J BIOL 2021; 83:e246984. [PMID: 34431913 DOI: 10.1590/1519-6984.246984] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 02/11/2021] [Indexed: 11/21/2022] Open
Abstract
Physids belong to Class Gastropoda; belong to Phylum Mollusca and being bioindicators, intermediate hosts of parasites and pests hold a key position in the ecosystem. There are three species of Genus Physa i.e. P. fontinalis, Physa acuta and P. gyrina water bodies of Central Punjab and were characterized on the basis of molecular markers High level of genetic diversity was revealed by polymorphic RAPD, however SSR markers were not amplified. The multivariate analysis revealed polymorphism ranging from 9.09 percent to 50 percent among the three Physid species. Total number of 79 loci were observed for the three species under study and 24 loci were observed to be polymorphic. These RAPD fragment(s) can be developed into co dominant markers (SCAR) by cloning and can be further sequenced for the development of the Physa species specific markers to identify the introduced and native species in Pakistan.
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Affiliation(s)
- B Ansari
- Government College University Faisalabad, Department of Zoology, Punjab, Pakistan
| | | | - A Ramzan
- Government College University Faisalabad, Department of Zoology, Punjab, Pakistan
| | - Z Ahmed
- University of Agriculture, Center for Advanced Studies in Agriculture and Food Security - CAS-AFS, Department of Plant Breeding and Genetics, Faisalabad, Pakistan
| | - S Khalil
- The Islamia University of Bahawalpur, Faculty of Agriculture & Environmental Science, Department Forestry Range & Wildlife Management, Bagdad Ul Jadeed Campus, Bahawalpur, Pakistan
| | - S U R Qamar
- Government College University Faisalabad, Department of Zoology, Punjab, Pakistan.,Chulabhorn Graduate Institute, Department of Applied Biological Sciences, Lak Si, Bangkok, Thailand
| | - S A Awan
- University of Agriculture, Department of Computer Science, Faisalabad, Pakistan
| | - K Jehangir
- Government College University Faisalabad, Department of Zoology, Punjab, Pakistan
| | - R Khalid
- Government College University Faisalabad, Department of Zoology, Punjab, Pakistan
| | - S Aziz
- Government College University Faisalabad, Department of Zoology, Punjab, Pakistan
| | - T Sultana
- Government College University Faisalabad, Department of Zoology, Punjab, Pakistan
| | - S Sultana
- Government College University Faisalabad, Department of Zoology, Punjab, Pakistan
| | - H Alsamadany
- King Abdulaziz University, Faculty of Science, Department of Biological Sciences, Jeddah, Saudi Arabia
| | - R Alshamrani
- King Abdulaziz University, Faculty of Science, Department of Biological Sciences, Jeddah, Saudi Arabia
| | - F S Awan
- University of Agriculture, Center of Agricultural Biochemistry and Biotechnology, Faisalabad, Pakistan
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Pfeiffer JM, Graf DL, Cummings KS, Page LM. Taxonomic revision of a radiation of South-east Asian freshwater mussels (Unionidae : Gonideinae : Contradentini+Rectidentini). INVERTEBR SYST 2021. [DOI: 10.1071/is20044] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The tribes Contradentini and Rectidentini (Unionidae) comprise a diverse clade of freshwater mussels endemic to South-east Asia. Our understanding of the diversity and phylogeny of this radiation has improved dramatically in recent years, but this systematic transformation has not yet benefited from comprehensive museum sampling or phylogenomic methods. A synthetic taxonomic revision of the Contradentini+Rectidentini that leverages these useful and accessible methods is needed. We set out to (1) generate a phylogenomic reconstruction of the supraspecific relationships of the Contradentini+Rectidentini using anchored hybrid enrichment, (2) revise the taxonomy and geographic boundaries of the generic and species-level diversity of the radiation, and (3) identify patterns of freshwater mussel diversity and distribution in this clade and discuss the processes that may have precipitated them. Our phylogenomic reconstruction using over 1600 loci, with a total alignment length of over a half a million nucleotides, recovers a well supported phylogeny of the clade that resolves four independent multispecies radiations endemic to the Mekong drainage. We examined, digitised, and imaged 1837 records from 15 natural history museums that provided the necessary data to document the morphological variation and geographic distributions of the focal taxa. We also analysed 860 COI sequences, 519 of which were generated in this study, to better understand the species boundaries and geographic distributions of the recovered clades. We recognise 54 valid species in the tribes Contradentini and Rectidentini, including 9 described herein as new to science. Out of this revision emerged several interesting biogeographic patterns that appear to have resulted from recent stream capture, historical confluence, and intradrainage barriers to dispersal. We hypothesise that these phenomena shaped the diversity and distribution of the Contradentini+Rectidentini, contributing to the formation of several characteristic freshwater mussel provinces in South-east Asia.
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Bolotov IN, Konopleva ES, Vikhrev IV, Gofarov MY, Lopes-Lima M, Bogan AE, Lunn Z, Chan N, Win T, Aksenova OV, Tomilova AA, Tanmuangpak K, Tumpeesuwan S, Kondakov AV. New freshwater mussel taxa discoveries clarify biogeographic division of Southeast Asia. Sci Rep 2020; 10:6616. [PMID: 32313058 PMCID: PMC7171101 DOI: 10.1038/s41598-020-63612-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 03/31/2020] [Indexed: 01/22/2023] Open
Abstract
While a growing body of modern phylogenetic research reveals that the Western Indochina represents a separate biogeographic subregion having a largely endemic freshwater fauna, the boundaries of this subregion are still unclear. We use freshwater mussels (Unionidae) as a model to reconstruct spatial patterns of freshwater biogeographic divides throughout Asia. Here, we present an updated freshwater biogeographic division of mainland Southeast Asia and describe 12 species and 4 genera of freshwater mussels new to science. We show that the Isthmus of Kra represents a significant southern biogeographic barrier between freshwater mussel faunas of the Western Indochina and Sundaland subregions, while the Indian and Western Indochina subregions are separated by the Naga Hills, Chin Hills, and Rakhine Yoma mountain ranges. Our findings highlight that the freshwater bivalve fauna of Southeast Asia primarily originated within three evolutionary hotspots (Western Indochina, Sundaland, and East Asian) supplemented by ancient immigrants from the Indian Subcontinent.
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Affiliation(s)
- Ivan N Bolotov
- Northern Arctic Federal University, Northern Dvina Emb. 17, 163002, Arkhangelsk, Russian Federation.
- Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Northern Dvina Emb. 23, 163000, Arkhangelsk, Russian Federation.
| | - Ekaterina S Konopleva
- Northern Arctic Federal University, Northern Dvina Emb. 17, 163002, Arkhangelsk, Russian Federation
- Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Northern Dvina Emb. 23, 163000, Arkhangelsk, Russian Federation
| | - Ilya V Vikhrev
- Northern Arctic Federal University, Northern Dvina Emb. 17, 163002, Arkhangelsk, Russian Federation
- Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Northern Dvina Emb. 23, 163000, Arkhangelsk, Russian Federation
| | - Mikhail Yu Gofarov
- Northern Arctic Federal University, Northern Dvina Emb. 17, 163002, Arkhangelsk, Russian Federation
- Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Northern Dvina Emb. 23, 163000, Arkhangelsk, Russian Federation
| | - Manuel Lopes-Lima
- CIBIO/InBIO - Research Center in Biodiversity and Genetic Resources, University of Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas 7, 4485-661, Vairão, Portugal
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal
- SSC/IUCN - Mollusc Specialist Group, Species Survival Commission, International Union for Conservation of Nature, c/o The David Attenborough Building, Pembroke Street, CB2 3QZ, Cambridge, United Kingdom
| | - Arthur E Bogan
- North Carolina Museum of Natural Sciences, 11 West Jones St., Raleigh, NC, 27601, USA
| | - Zau Lunn
- Fauna & Flora International - Myanmar Programme, Yangon, Myanmar
| | - Nyein Chan
- Fauna & Flora International - Myanmar Programme, Yangon, Myanmar
| | - Than Win
- Department of Zoology, Dawei University, Dawei, Tanintharyi Region, Myanmar
| | - Olga V Aksenova
- Northern Arctic Federal University, Northern Dvina Emb. 17, 163002, Arkhangelsk, Russian Federation
- Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Northern Dvina Emb. 23, 163000, Arkhangelsk, Russian Federation
| | - Alena A Tomilova
- Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Northern Dvina Emb. 23, 163000, Arkhangelsk, Russian Federation
| | - Kitti Tanmuangpak
- Department of Science, Faculty of Science and Technology, Loei Rajabhat University, Loei, Thailand
| | - Sakboworn Tumpeesuwan
- Department of Biology, Faculty of Science, Mahasarakham University, Maha Sarakham, Thailand
| | - Alexander V Kondakov
- Northern Arctic Federal University, Northern Dvina Emb. 17, 163002, Arkhangelsk, Russian Federation
- Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Northern Dvina Emb. 23, 163000, Arkhangelsk, Russian Federation
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Konopleva ES, Bolotov IN, Vikhrev IV, Gofarov MY, Kondakov AV. An integrative approach underscores the taxonomic status of Lamellidens exolescens, a freshwater mussel from the Oriental tropics (Bivalvia: Unionidae). SYST BIODIVERS 2016. [DOI: 10.1080/14772000.2016.1249530] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Ekaterina S. Konopleva
- IBIGER – Institute of Biogeography and Genetic Resources, Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Severnaya Dvina Emb. 23, 163000 Arkhangelsk, Russian Federation
| | - Ivan N. Bolotov
- IBIGER – Institute of Biogeography and Genetic Resources, Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Severnaya Dvina Emb. 23, 163000 Arkhangelsk, Russian Federation
| | - Ilya V. Vikhrev
- IBIGER – Institute of Biogeography and Genetic Resources, Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Severnaya Dvina Emb. 23, 163000 Arkhangelsk, Russian Federation
| | - Mikhail Y. Gofarov
- IBIGER – Institute of Biogeography and Genetic Resources, Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Severnaya Dvina Emb. 23, 163000 Arkhangelsk, Russian Federation
| | - Alexander V. Kondakov
- IBIGER – Institute of Biogeography and Genetic Resources, Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Severnaya Dvina Emb. 23, 163000 Arkhangelsk, Russian Federation
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