1
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Schmidt TL, Endersby-Harshman NM, van Rooyen ARJ, Katusele M, Vinit R, Robinson LJ, Laman M, Karl S, Hoffmann AA. Global, asynchronous partial sweeps at multiple insecticide resistance genes in Aedes mosquitoes. Nat Commun 2024; 15:6251. [PMID: 39048545 DOI: 10.1038/s41467-024-49792-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 06/19/2024] [Indexed: 07/27/2024] Open
Abstract
Aedes aegypti (yellow fever mosquito) and Ae. albopictus (Asian tiger mosquito) are globally invasive pests that confer the world's dengue burden. Insecticide-based management has led to the evolution of insecticide resistance in both species, though the genetic architecture and geographical spread of resistance remains incompletely understood. This study investigates partial selective sweeps at resistance genes on two chromosomes and characterises their spread across populations. Sweeps at the voltage-sensitive sodium channel (VSSC) gene on chromosome 3 correspond to one resistance-associated nucleotide substitution in Ae. albopictus and three in Ae. aegypti, including two substitutions at the same nucleotide position (F1534C) that have evolved and spread independently. In Ae. aegypti, we also identify partial sweeps at a second locus on chromosome 2. This locus contains 15 glutathione S-transferase (GST) epsilon class genes with significant copy number variation among populations and where three distinct genetic backgrounds have spread across the Indo-Pacific region, the Americas, and Australia. Local geographical patterns and linkage networks indicate VSSC and GST backgrounds probably spread at different times and interact locally with different genes to produce resistance phenotypes. These findings highlight the rapid global spread of resistance and are evidence for the critical importance of GST genes in resistance evolution.
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Affiliation(s)
- Thomas L Schmidt
- Bio21 Institute, School of BioSciences, University of Melbourne, Parkville, Australia.
| | | | | | - Michelle Katusele
- PNG Institute of Medical Research, Madang, Madang Province, Papua New Guinea
| | - Rebecca Vinit
- PNG Institute of Medical Research, Madang, Madang Province, Papua New Guinea
| | - Leanne J Robinson
- PNG Institute of Medical Research, Madang, Madang Province, Papua New Guinea
- Australian Institute of Tropical Health and Medicine, James Cook University, Smithfield, Queensland, Australia
| | - Moses Laman
- PNG Institute of Medical Research, Madang, Madang Province, Papua New Guinea
| | - Stephan Karl
- Australian Institute of Tropical Health and Medicine, James Cook University, Smithfield, Queensland, Australia
- Burnet Institute of Medical Research, Melbourne, Victoria, Australia
| | - Ary A Hoffmann
- Bio21 Institute, School of BioSciences, University of Melbourne, Parkville, Australia
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2
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Jense C, Adams M, Raadik TA, Waters JM, Morgan DL, Barmuta LA, Hardie SA, Deagle BE, Burridge CP. Cryptic diversity within two widespread diadromous freshwater fishes (Teleostei: Galaxiidae). Ecol Evol 2024; 14:e11201. [PMID: 38799386 PMCID: PMC11116845 DOI: 10.1002/ece3.11201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 03/03/2024] [Accepted: 03/19/2024] [Indexed: 05/29/2024] Open
Abstract
Identification of taxonomically cryptic species is essential for the effective conservation of biodiversity. Freshwater-limited organisms tend to be genetically isolated by drainage boundaries, and thus may be expected to show substantial cryptic phylogenetic and taxonomic diversity. By comparison, populations of diadromous taxa, that migrate between freshwater and marine environments, are expected to show less genetic differentiation. Here we test for cryptic diversity in Australasian populations (both diadromous and non-diadromous) of two widespread Southern Hemisphere fish species, Galaxias brevipinnis and Galaxias maculatus. Both mtDNA and nuclear markers reveal putative cryptic species within these taxa. The substantial diversity detected within G. brevipinnis may be explained by its strong climbing ability which allows it to form isolated inland populations. In island populations, G. brevipinnis similarly show deeper genetic divergence than those of G. maculatus, which may be explained by the greater abundance of G. maculatus larvae in the sea allowing more ongoing dispersal. Our study highlights that even widespread, 'high-dispersal' species can harbour substantial cryptic diversity and therefore warrant increased taxonomic and conservation attention.
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Affiliation(s)
- Charlotte Jense
- Discipline of Biological Sciences, School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
| | - Mark Adams
- Evolutionary Biology UnitSouth Australian MuseumAdelaideSouth AustraliaAustralia
- School of Biological SciencesThe University of AdelaideAdelaideSouth AustraliaAustralia
| | - Tarmo A. Raadik
- Department of Energy, Environment and Climate ActionArthur Rylah Institute for Environmental ResearchHeidelbergVictoriaAustralia
| | | | - David L. Morgan
- Centre for Sustainable Aquatic Ecosystems, Harry Butler InstituteMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Leon A. Barmuta
- Discipline of Biological Sciences, School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
| | - Scott A. Hardie
- Discipline of Biological Sciences, School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
| | - Bruce E. Deagle
- Australian National Fish CollectionCSIRO National Research Collections AustraliaHobartTasmaniaAustralia
| | - Christopher P. Burridge
- Discipline of Biological Sciences, School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
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3
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Waters JM, King TM, Craw D. Gorges partition diversity within New Zealand flathead Galaxias populations. JOURNAL OF FISH BIOLOGY 2024; 104:950-956. [PMID: 38018507 DOI: 10.1111/jfb.15635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 11/23/2023] [Accepted: 11/27/2023] [Indexed: 11/30/2023]
Abstract
Understanding the landscape factors governing population connectivity in riverine ecosystems represents an ongoing challenge for freshwater biologists. We used DNA sequence analysis to test the hypothesis that major geomorphological features underpin freshwater-limited fish diversity in a tectonically dynamic region of New Zealand. Phylogeographic analysis of 101 Galaxias depressiceps cytochrome b sequences, incorporating 55 localities from southern New Zealand, revealed 26 haplotypes, with only one shared among rivers. We detect strong hierarchical genetic differentiation both among and within river systems. Genetic structuring is particularly pronounced across the Taieri River system (63 individuals from 35 sites, 18 haplotypes), with 92% of variation partitioned among locations. Distinctive within-river genetic clusters are invariably associated with major subcatchment units, typically isolated by substantial gorges. The anomalous distribution of a single lineage across a major drainage divide is consistent with local, tectonically driven headwater capture. We conclude that major landscape features such as gorges can strongly partition riverine fish diversity and constrain freshwater biodiversity.
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Affiliation(s)
| | - Tania M King
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Dave Craw
- Department of Geology, University of Otago, Dunedin, New Zealand
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4
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Fujimori C, Sugimoto K, Ishida M, Yang C, Kayo D, Tomihara S, Sano K, Akazome Y, Oka Y, Kanda S. Long-lasting redundant gnrh1/3 expression in GnRH neurons enabled apparent switching of paralog usage during evolution. iScience 2024; 27:109304. [PMID: 38464591 PMCID: PMC10924128 DOI: 10.1016/j.isci.2024.109304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 12/08/2023] [Accepted: 02/16/2024] [Indexed: 03/12/2024] Open
Abstract
Expressed subtype of paralogous genes in functionally homologous cells sometimes show differences across species, the reasons for which have not been explained. The present study examined hypophysiotropic gonadotropin-releasing hormone (GnRH) neurons in vertebrates to investigate this mechanism. These neurons express either gnrh1 or gnrh3 paralogs, depending on the species, and apparent switching of the expressed paralogs in them occurred at least four times in vertebrate evolution. First, we found redundant expression of gnrh1 and gnrh3 in a single neuron in piranha and hypothesized that it may represent an ancestral GnRH system. Moreover, the gnrh1/gnrh3 enhancer of piranha induced reporter RFP/GFP co-expression in a single hypophysiotropic GnRH neuron in both zebrafish and medaka, whose GnRH neurons only express either gnrh3 or gnrh1. Thus, we propose that redundant expression of gnrh1/3 of relatively recent common ancestors may be the key to apparent switching of the paralog usage among present-day species.
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Affiliation(s)
- Chika Fujimori
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
- Optics and Imaging Facility, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Kohei Sugimoto
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Mio Ishida
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Christopher Yang
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Department of Neuroscience, Johns Hopkins University, Baltimore, MD, USA
| | - Daichi Kayo
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Soma Tomihara
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
- Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, Japan
| | - Kaori Sano
- Department of Chemistry, Faculty of Science, Josai University, Sakado, Saitama, Japan
| | - Yasuhisa Akazome
- Department of Anatomy, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan
| | - Yoshitaka Oka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Shinji Kanda
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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5
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Karin BR, Lough-Stevens M, Lin TE, Reilly SB, Barley AJ, Das I, Iskandar DT, Arida E, Jackman TR, McGuire JA, Bauer AM. The natural and human-mediated expansion of a human-commensal lizard into the fringes of Southeast Asia. BMC Ecol Evol 2024; 24:25. [PMID: 38378475 PMCID: PMC10880348 DOI: 10.1186/s12862-024-02212-7] [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: 05/08/2023] [Accepted: 02/09/2024] [Indexed: 02/22/2024] Open
Abstract
BACKGROUND Human-commensal species often display deep ancestral genetic structure within their native range and founder-effects and/or evidence of multiple introductions and admixture in newly established areas. We investigated the phylogeography of Eutropis multifasciata, an abundant human-commensal scincid lizard that occurs across Southeast Asia, to determine the extent of its native range and to assess the sources and signatures of human introduction outside of the native range. We sequenced over 350 samples of E. multifasciata for the mitochondrial ND2 gene and reanalyzed a previous RADseq population genetic dataset in a phylogenetic framework. RESULTS Nuclear and mitochondrial trees are concordant and show that E. multifasciata has retained high levels of genetic structure across Southeast Asia despite being frequently moved by humans. Lineage boundaries in the native range roughly correspond to several major biogeographic barriers, including Wallace's Line and the Isthmus of Kra. Islands at the outer fringe of the range show evidence of founder-effects and multiple introductions. CONCLUSIONS Most of enormous range of E. multifasciata across Southeast Asia is native and it only displays signs of human-introduction or recent expansion along the eastern and northern fringe of its range. There were at least three events of human-introductions to Taiwan and offshore islands, and several oceanic islands in eastern Indonesia show a similar pattern. In Myanmar and Hainan, there is a founder-effect consistent with post-warming expansion after the last glacial maxima or human introduction.
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Affiliation(s)
- Benjamin R Karin
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA.
- Department of Biology, Villanova University, Villanova, PA, 19085, USA.
| | - Michael Lough-Stevens
- Department of Biology, Villanova University, Villanova, PA, 19085, USA
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Te-En Lin
- Endemic Species Research Institute, 1, Minsheng E Rd., Jiji Township, Nantou County, 55244, Taiwan
| | - Sean B Reilly
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, 95060, USA
| | - Anthony J Barley
- Department of Evolution and Ecology, University of California, 2320 Storer Hall, Davis, CA, 95616, USA
| | - Indraneil Das
- Institute of Biodiversity and Environmental Conservation, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Djoko T Iskandar
- School of Life Sciences and Technology, Bandung Institute of Technology, 10 Jalan Ganesa, Bandung, 40132, Indonesia
- Basic Sciences Commission, Indonesian Academy of Sciences, 11 Jalan Medan Merdeka Selatan, Jakarta, 10110, Indonesia
| | - Evy Arida
- Research Center for Ecology and Ethnobiology, Badan Riset dan Inovasi Nasional (BRIN), Cibinong Science Center, Jalan Raya Jakarta-Bogor km 46, Cibinong, 16911, Indonesia
| | - Todd R Jackman
- Department of Biology, Villanova University, Villanova, PA, 19085, USA
| | - Jimmy A McGuire
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - Aaron M Bauer
- Department of Biology, Villanova University, Villanova, PA, 19085, USA
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6
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Bastin S, Reyes-Betancort JA, Siverio de la Rosa F, Percy DM. Origins of the central Macaronesian psyllid lineages (Hemiptera; Psylloidea) with characterization of a new island radiation on endemic Convolvulus floridus (Convolvulaceae) in the Canary Islands. PLoS One 2024; 19:e0297062. [PMID: 38277393 PMCID: PMC10817144 DOI: 10.1371/journal.pone.0297062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 12/27/2023] [Indexed: 01/28/2024] Open
Abstract
A molecular survey of native and adventive psyllids in the central Macaronesian islands provides the first comprehensive phylogenetic assessment of the origins of the psyllid fauna of the Canary and Madeira archipelagos. We employ a maximum likelihood backbone constraint analysis to place the central Macaronesian taxa within the Psylloidea mitogenome phylogeny. The native psyllid fauna in these central Macaronesian islands results from an estimated 26 independent colonization events. Island host plants are predicted by host plants of continental relatives in nearly all cases and six plant genera have been colonized multiple times (Chamaecytisus, Convolvulus, Olea, Pistacia, Rhamnus, and Spartocytisus) from the continent. Post-colonization diversification varies from no further cladogenesis (18 events, represented by a single native taxon) to modest in situ diversification resulting in two to four native taxa and, surprisingly, given the diverse range of islands and habitats, only one substantial species radiation with more than four native species. Specificity to ancestral host plant genera or family is typically maintained during in situ diversification both within and among islands. Characterization of a recently discovered island radiation consisting of four species on Convolvulus floridus in the Canary Islands shows patterns and rates of diversification that reflect island topographic complexity and geological dynamism. Although modest in species diversity, this radiation is atypical in diversification on a single host plant species, but typical in the primary role of allopatry in the diversification process.
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Affiliation(s)
- Saskia Bastin
- Instituto Canario de Investigaciones Agrarias, Unidad de Protección Vegetal, La Laguna, Tenerife, Spain
| | - J. Alfredo Reyes-Betancort
- Instituto Canario de Investigaciones Agrarias, Jardín de Aclimatación de La Oratava, Puerto de la Cruz, Tenerife, Spain
| | - Felipe Siverio de la Rosa
- Instituto Canario de Investigaciones Agrarias, Unidad de Protección Vegetal, La Laguna, Tenerife, Spain
| | - Diana M. Percy
- Botany Department and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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7
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Ngoepe N, Muschick M, Kishe MA, Mwaiko S, Temoltzin-Loranca Y, King L, Courtney Mustaphi C, Heiri O, Wienhues G, Vogel H, Cuenca-Cambronero M, Tinner W, Grosjean M, Matthews B, Seehausen O. A continuous fish fossil record reveals key insights into adaptive radiation. Nature 2023; 622:315-320. [PMID: 37794187 PMCID: PMC10567567 DOI: 10.1038/s41586-023-06603-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 09/01/2023] [Indexed: 10/06/2023]
Abstract
Adaptive radiations have been instrumental in generating a considerable amount of life's diversity. Ecological opportunity is thought to be a prerequisite for adaptive radiation1, but little is known about the relative importance of species' ecological versatility versus effects of arrival order in determining which lineage radiates2. Palaeontological records that could help answer this are scarce. In Lake Victoria, a large adaptive radiation of cichlid fishes evolved in an exceptionally short and recent time interval3. We present a rich continuous fossil record extracted from a series of long sediment cores along an onshore-offshore gradient. We reconstruct the temporal sequence of events in the assembly of the fish community from thousands of tooth fossils. We reveal arrival order, relative abundance and habitat occupation of all major fish lineages in the system. We show that all major taxa arrived simultaneously as soon as the modern lake began to form. There is no evidence of the radiating haplochromine cichlid lineage arriving before others, nor of their numerical dominance upon colonization; therefore, there is no support for ecological priority effects. However, although many taxa colonized the lake early and several became abundant, only cichlids persisted in the new deep and open-water habitats once these emerged. Because these habitat gradients are also known to have played a major role in speciation, our findings are consistent with the hypothesis that ecological versatility was key to adaptive radiation, not priority by arrival order nor initial numerical dominance.
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Affiliation(s)
- Nare Ngoepe
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.
- Department of Fish Ecology and Evolution, EAWAG, Swiss Federal Institute for Aquatic Science and Technology, Kastanienbaum, Switzerland.
| | - Moritz Muschick
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, EAWAG, Swiss Federal Institute for Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Mary A Kishe
- Tanzania Fisheries Research Institute (TAFIRI), Dar es Salaam, Tanzania
| | - Salome Mwaiko
- Department of Fish Ecology and Evolution, EAWAG, Swiss Federal Institute for Aquatic Science and Technology, Kastanienbaum, Switzerland
| | | | - Leighton King
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, EAWAG, Swiss Federal Institute for Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Colin Courtney Mustaphi
- Geoecology, Department of Environmental Sciences, University of Basel, Basel, Switzerland
- Center for Water Infrastructure and Sustainable Energy (WISE) Futures, Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - Oliver Heiri
- Geoecology, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Giulia Wienhues
- Institute of Geography & Oeschger Centre for Climate Change Research, University of Bern, Bern, Switzerland
| | - Hendrik Vogel
- Institute of Geological Sciences & Oeschger Centre for Climate Change Research, University of Bern, Bern, Switzerland
| | - Maria Cuenca-Cambronero
- Department of Fish Ecology and Evolution, EAWAG, Swiss Federal Institute for Aquatic Science and Technology, Kastanienbaum, Switzerland
- Aquatic Ecology, University of Vic - Central University of Catalonia, Vic, Spain
| | - Willy Tinner
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Martin Grosjean
- Institute of Geography & Oeschger Centre for Climate Change Research, University of Bern, Bern, Switzerland
| | - Blake Matthews
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Ole Seehausen
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, EAWAG, Swiss Federal Institute for Aquatic Science and Technology, Kastanienbaum, Switzerland
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8
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Bisconti R, Carere C, Costantini D, Liparoto A, Chiocchio A, Canestrelli D. Evolution of personality and locomotory performance traits during a late Pleistocene island colonization in a tree frog. Curr Zool 2023; 69:631-641. [PMID: 37637312 PMCID: PMC10449429 DOI: 10.1093/cz/zoac062] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/02/2022] [Indexed: 08/29/2023] Open
Abstract
Recent empirical and theoretical studies suggest that personality and locomotory performance traits linked to dispersal abilities are crucial components of the dispersal syndromes, and that they can evolve during range expansions and colonization processes. Island colonization is one of the best characterized processes in dispersal biogeography, and its implication in the evolution of phenotypic traits has been investigated over a wide range of temporal scales. However, the effect of island colonization on personality and performance traits of natural populations, and how these traits could drive island colonization, has been little explored. Noteworthy, no studies have addressed these processes in the context of late Pleistocene range expansions. Here, we investigated the contribution of island colonization triggered by postglacial range expansions to intraspecific variation in personality and locomotory performance traits. We compared boldness, exploration, jumping performance, and stickiness abilities in populations from 3 equidistant areas of the Tyrrhenian tree frog Hyla sarda, 2 from the main island (Corsica Island), and 1 from the recently colonized island of Elba. Individuals from Elba were significantly bolder than individuals from Corsica, as they emerged sooner from a shelter (P = 0.028), while individuals from Corsica showed markedly higher jumping and stickiness performance (both P < 0.001), resulting as more performing than those of Elba. We discuss these results in the context of the major microevolutionary processes at play during range expansion, including selection, spatial sorting, founder effects, and their possible interaction with local adaptation processes.
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Affiliation(s)
- Roberta Bisconti
- Department of Ecological and Biological Science, Tuscia University, Largo dell’Università s.n.c., 01100 Viterbo, Italy
| | - Claudio Carere
- Department of Ecological and Biological Science, Tuscia University, Largo dell’Università s.n.c., 01100 Viterbo, Italy
| | - David Costantini
- Unité Physiologie Moléculaire et Adaptation (PhyMA), Muséum National d’Histoire Naturelle, CNRS, CP32, 57 rue Cuvier 75005 Paris, France
| | - Anita Liparoto
- Department of Ecological and Biological Science, Tuscia University, Largo dell’Università s.n.c., 01100 Viterbo, Italy
| | - Andrea Chiocchio
- Department of Ecological and Biological Science, Tuscia University, Largo dell’Università s.n.c., 01100 Viterbo, Italy
| | - Daniele Canestrelli
- Department of Ecological and Biological Science, Tuscia University, Largo dell’Università s.n.c., 01100 Viterbo, Italy
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9
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Gao W, Yang Y, Shi L. Seasonal dietary shifts alter the gut microbiota of a frugivorous lizard Teratoscincus roborowskii (Squamata, Sphaerodactylidae). Ecol Evol 2023; 13:e10363. [PMID: 37546566 PMCID: PMC10396791 DOI: 10.1002/ece3.10363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 07/03/2023] [Accepted: 07/14/2023] [Indexed: 08/08/2023] Open
Abstract
Seasonal dietary shifts in animals are important strategies for ecological adaptation. An increasing number of studies have shown that seasonal dietary shifts can influence or even determine the composition of gut microbiota. The Turpan wonder gecko, Teratoscincus roborowskii, lives in extreme desert environments and has a flexible dietary shift to fruit-eating in warm seasons. However, the effect of such shifts on the gut microbiota is poorly understood. In this study, 16S rRNA sequencing and LC-MS metabolomics were used to examine changes in the gut microbiota composition and metabolic patterns of T. roborowskii. The results demonstrated that the gut microbes of T. roborowskii underwent significant seasonal changes, and the abundance of phylum level in autumn was significantly higher than spring, but meanwhile, the diversity was lower. At the family level, the abundance and diversity of the gut microbiota were both higher in autumn. Firmicutes, Bacteroidetes, and Proteobacteria were the dominant gut microbes of T. roborowskii. Verrucomicrobia and Proteobacteria exhibited dynamic ebb and flow patterns between spring and autumn. Metabolomic profiling also revealed differences mainly related to the formation of secondary bile acids. The pantothenate and CoA biosynthesis, and lysine degradation pathways identified by KEGG enrichment symbolize the exuberant metabolic capacity of T. roborowskii. Furthermore, strong correlations were detected between metabolite types and bacteria, and this correlation may be an important adaptation of T. roborowskii to cope with dietary shifts and improve energy acquisition. Our study provides a theoretical basis for exploring the adaptive evolution of the special frugivorous behavior of T. roborowskii, which is an important progress in the study of gut microbes in desert lizards.
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Affiliation(s)
- Wei‐Zhen Gao
- College of Life SciencesXinjiang Agricultural UniversityUrumqiChina
| | - Yi Yang
- College of Life SciencesXinjiang Agricultural UniversityUrumqiChina
| | - Lei Shi
- College of Life SciencesXinjiang Agricultural UniversityUrumqiChina
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10
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Assis J, Alberto F, Macaya EC, Castilho Coelho N, Faugeron S, Pearson GA, Ladah L, Reed DC, Raimondi P, Mansilla A, Brickle P, Zuccarello GC, Serrão EA. Past climate-driven range shifts structuring intraspecific biodiversity levels of the giant kelp (Macrocystis pyrifera) at global scales. Sci Rep 2023; 13:12046. [PMID: 37491385 PMCID: PMC10368654 DOI: 10.1038/s41598-023-38944-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 07/17/2023] [Indexed: 07/27/2023] Open
Abstract
The paradigm of past climate-driven range shifts structuring the distribution of marine intraspecific biodiversity lacks replication in biological models exposed to comparable limiting conditions in independent regions. This may lead to confounding effects unlinked to climate drivers. We aim to fill in this gap by asking whether the global distribution of intraspecific biodiversity of giant kelp (Macrocystis pyrifera) is explained by past climate changes occurring across the two hemispheres. We compared the species' population genetic diversity and structure inferred with microsatellite markers, with range shifts and long-term refugial regions predicted with species distribution modelling (SDM) from the last glacial maximum (LGM) to the present. The broad antitropical distribution of Macrocystis pyrifera is composed by six significantly differentiated genetic groups, for which current genetic diversity levels match the expectations of past climate changes. Range shifts from the LGM to the present structured low latitude refugial regions where genetic relics with higher and unique diversity were found (particularly in the Channel Islands of California and in Peru), while post-glacial expansions following ~ 40% range contraction explained extensive regions with homogenous reduced diversity. The estimated effect of past climate-driven range shifts was comparable between hemispheres, largely demonstrating that the distribution of intraspecific marine biodiversity can be structured by comparable evolutionary forces across the global ocean. Additionally, the differentiation and endemicity of regional genetic groups, confers high conservation value to these localized intraspecific biodiversity hotspots of giant kelp forests.
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Affiliation(s)
- Jorge Assis
- CCMAR, CIMAR, Universidade do Algarve, Gambelas, Faro, Portugal.
- Faculty of Bioscience and Aquaculture, Nord Universitet, Bodø, Norway.
| | - Filipe Alberto
- Department of Biological Sciences, University of Wisconsin, Milwaukee, USA
| | - Erasmo C Macaya
- Centro Fondap IDEAL and Departamento de Oceanografía, Universidad de Concepción, Concepción, Chile
| | - Nelson Castilho Coelho
- CCMAR, CIMAR, Universidade do Algarve, Gambelas, Faro, Portugal
- University of Pittsburgh School of Medicine, Pittsburgh, USA
| | - Sylvain Faugeron
- Núcleo Milenio MASH and IRL3614 Evolutionary Biology and Ecology of Algae, Facultad de Ciencias Biológicas, CNRS, Sorbonne Université, Universidad Austral de Chile, Pontificia Universidad Catolica de Chile, Santiago, Chile
| | | | - Lydia Ladah
- Departamento de Oceanografía Biológica, Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, Baja California, Mexico
| | - Daniel C Reed
- Marine Science Institute, University of California Santa Barbara, Santa Barbara, USA
| | | | - Andrés Mansilla
- Cape Horn International Center (CHIC), Universidad de Magallanes, Punta Arenas, Chile
| | - Paul Brickle
- South Atlantic Environmental Research Institute, Stanley, Falkland Islands
| | - Giuseppe C Zuccarello
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Ester A Serrão
- CCMAR, CIMAR, Universidade do Algarve, Gambelas, Faro, Portugal
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11
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Köhler A, Schmitt T. Northern Richness, Southern Dead End-Origin and Dispersal Events of Pseudolycoriella (Sciaridae, Diptera) between New Zealand's Main Islands. INSECTS 2023; 14:548. [PMID: 37367364 DOI: 10.3390/insects14060548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/02/2023] [Accepted: 06/07/2023] [Indexed: 06/28/2023]
Abstract
Sciaridae (Diptera) is a widespread insect family of which some species can reach high abundances in arboreal habitats. This trait, together with their (passive) mobility, enables them to quickly colonise suitable habitats. To reveal the biogeographic history of the New Zealand members of the sciarid genus Pseudolycoriella, we analysed three molecular markers of selected species and populations in a Bayesian approach. At the intra- and interspecific levels, we detected a pattern of northern richness vs. southern purity, which has probably developed as a result of Pleistocene glacial cycles. Since the late Miocene, we identified 13 dispersal events across the sea strait separating New Zealand's main islands. As nine of these dispersal events were south-directed, North Island can be considered the centre of radiation for this genus. An unequivocal re-colonisation of North Island was only observed once. Based on the inclusion of three undescribed species from Tasmania and on previously published data, three colonisations of New Zealand are likely, all of them assumed to be of Australian origin. One of these most probably took place during the late Miocene, and the other two during the late Pliocene or at the Pliocene-Pleistocene boundary.
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Affiliation(s)
- Arne Köhler
- Senckenberg German Entomological Institute, 15374 Müncheberg, Germany
- Developmental Biology, Institute of Biology, Martin Luther University of Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Thomas Schmitt
- Senckenberg German Entomological Institute, 15374 Müncheberg, Germany
- Entomology and Biogeography, Institute of Biochemistry and Biology, Faculty of Science, University of Potsdam, 14476 Potsdam, Germany
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12
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Vaux F, Fraser CI, Craw D, Read S, Waters JM. Integrating kelp genomic analyses and geological data to reveal ancient earthquake impacts. J R Soc Interface 2023; 20:20230105. [PMID: 37194268 PMCID: PMC10189309 DOI: 10.1098/rsif.2023.0105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 04/24/2023] [Indexed: 05/18/2023] Open
Abstract
Detached buoyant kelp can disperse thousands of kilometres at sea and can colonize newly available shores in the wake of disturbances that wipe out competitors. Localized earthquake uplift can cause extirpation of intertidal kelp populations followed by recolonization. Sources of recolonizing kelp can be detectable in genomic structure of contemporary populations. Our field observations combined with LiDAR mapping identified a previously unrecognized zone of uplifted rocky coastline in a region that is slowly subsiding. Intertidal kelp (Durvillaea antarctica) on the uplifted section of coast is genetically distinctive from nearby populations, with genomic signatures most similar to that of kelp 300 km to the south. Genetic divergence between these locations suggests reproductive isolation for thousands of years. Combined geological and genetic data suggest that this uplift event occurred during one of four major earthquakes between 6000 and 2000 years ago, with one of the younger events most likely. Extirpation of the pre-existing kelp required sudden uplift of approximately 2 metres, precluding several small incremental uplift events. Our results show the power of integrating biological (genomic) analyses with geological data to understand ancient geological processes and their ecological impacts.
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Affiliation(s)
- Felix Vaux
- Department of Zoology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Ceridwen I. Fraser
- Department of Marine Science, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Dave Craw
- Department of Geology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Stephen Read
- Department of Geology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Jonathan M. Waters
- Department of Zoology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
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13
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Platania L, Gómez-Zurita J. Analysis of intrinsic evolutionary factors leading to microendemic distributions in New Caledonian leaf beetles. Sci Rep 2023; 13:6909. [PMID: 37106022 PMCID: PMC10140066 DOI: 10.1038/s41598-023-34104-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 04/24/2023] [Indexed: 04/29/2023] Open
Abstract
Microendemicity, or the condition of some species having local ranges, is a relatively common pattern in nature. However, the factors that lead to this pattern are still largely unknown. Most studies addressing this issue tend to focus on extrinsic factors associated with microendemic distributions, such as environmental conditions, hypothesising a posteriori about underlying potential speciation mechanisms, linked or not to these conditions. Here, we use a multi-faceted approach mostly focusing on intrinsic factors instead, namely diversification dynamics and speciation modes in two endemic sibling genera of leaf beetles with microendemic distributions, Taophila and Tricholapita, in a microendemicity hotspot, New Caledonia. Results suggest that the diversification rate in this lineage slowed down through most of the Neogene and consistently with a protracted speciation model possibly combined with several ecological and environmental factors potentially adding rate-slowing effects through time. In turn, species accumulated following successive allopatric speciation cycles, possibly powered by marked geological and climatic changes in the region in the last 25 million years, with daughter species ranges uncorrelated with the time of speciation. In this case, microendemicity seems to reflect a mature state for the system, rather than a temporary condition for recent species, as suggested for many microendemic organisms.
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Affiliation(s)
- Leonardo Platania
- Botanical Institute of Barcelona (CSIC-Ajuntament Barcelona), Pg. del Migdia S/N, 08038, Barcelona, Spain
- Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - Jesús Gómez-Zurita
- Botanical Institute of Barcelona (CSIC-Ajuntament Barcelona), Pg. del Migdia S/N, 08038, Barcelona, Spain.
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14
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Maas DL, Prost S, de Leeuw CA, Bi K, Smith LL, Purwanto P, Aji LP, Tapilatu RF, Gillespie RG, Becking LE. Sponge diversification in marine lakes: Implications for phylogeography and population genomic studies on sponges. Ecol Evol 2023; 13:e9945. [PMID: 37066063 PMCID: PMC10099488 DOI: 10.1002/ece3.9945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 03/06/2023] [Accepted: 03/08/2023] [Indexed: 04/18/2023] Open
Abstract
The relative influence of geography, currents, and environment on gene flow within sessile marine species remains an open question. Detecting subtle genetic differentiation at small scales is challenging in benthic populations due to large effective population sizes, general lack of resolution in genetic markers, and because barriers to dispersal often remain elusive. Marine lakes can circumvent confounding factors by providing discrete and replicated ecosystems. Using high-resolution double digest restriction-site-associated DNA sequencing (4826 Single Nucleotide Polymorphisms, SNPs), we genotyped populations of the sponge Suberites diversicolor (n = 125) to test the relative importance of spatial scales (1-1400 km), local environmental conditions, and permeability of seascape barriers in shaping population genomic structure. With the SNP dataset, we show strong intralineage population structure, even at scales <10 km (average F ST = 0.63), which was not detected previously using single markers. Most variation was explained by differentiation between populations (AMOVA: 48.8%) with signatures of population size declines and bottlenecks per lake. Although the populations were strongly structured, we did not detect significant effects of geographic distance, local environments, or degree of connection to the sea on population structure, suggesting mechanisms such as founder events with subsequent priority effects may be at play. We show that the inclusion of morphologically cryptic lineages that can be detected with the COI marker can reduce the obtained SNP set by around 90%. Future work on sponge genomics should confirm that only one lineage is included. Our results call for a reassessment of poorly dispersing benthic organisms that were previously assumed to be highly connected based on low-resolution markers.
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Affiliation(s)
- Diede L. Maas
- Marine Animal EcologyWageningen University & ResearchWageningenThe Netherlands
| | - Stefan Prost
- LOEWE Centre for Translational Biodiversity GenomicsSenckenberg Natural History MuseumFrankfurt am MainGermany
- South African National Biodiversity InstituteNational Zoological Gardens of South AfricaPretoriaSouth Africa
| | | | - Ke Bi
- Museum of Vertebrate ZoologyUniversity of California BerkeleyBerkeleyCaliforniaUSA
- Computational Genomics Resource Laboratory, California Institute for Quantitative BiosciencesUniversity of California BerkeleyBerkeleyCaliforniaUSA
| | - Lydia L. Smith
- Museum of Vertebrate ZoologyUniversity of California BerkeleyBerkeleyCaliforniaUSA
| | | | - Ludi P. Aji
- Marine Animal EcologyWageningen University & ResearchWageningenThe Netherlands
- Research Centre for Oceanography, Indonesian Institute of SciencesLembaga Ilmu Pengetahuan IndonesiaJakartaIndonesia
| | - Ricardo F. Tapilatu
- Marine Science and Fisheries Departments and Research Center of Pacific Marine ResourcesState University of PapuaManokwariIndonesia
| | - Rosemary G. Gillespie
- Department of Environmental Science, Policy and ManagementUniversity of California BerkeleyBerkeleyCaliforniaUSA
| | - Leontine E. Becking
- Department of Environmental Science, Policy and ManagementUniversity of California BerkeleyBerkeleyCaliforniaUSA
- Aquaculture and Fisheries, Naturalis Biodiversity CenterWageningen University & ResearchWageningenThe Netherlands
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15
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An Invisible Boundary between Geographic Ranges of Cryptic Species of Narrow-Headed Voles (Stenocranius, Lasiopodomys, Cricetidae) in Transbaikalia. DIVERSITY 2023. [DOI: 10.3390/d15030439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
Abstract
The narrow-headed vole species complex is represented by Lasiopodomys gregalis and L. raddei, which probably diverged at the beginning of the Middle Pleistocene and came into secondary contact in the Transbaikal region. The current study analyzed mitochondrial gene cytochrome b, nuclear gene BRCA1, and microsatellite data and was aimed at clarifying geographic ranges of these species and searching for hybrid zones between them. It turned out that the geographic range of L. raddei is almost surrounded by that of L. gregalis; these species are strictly parapatric without a single detected sympatry zone. Although in none of the tested populations did the BRCA1 genotyping contradict the pattern revealed by mitochondrial cytb, microsatellite loci showed traces of hybridization in several populations. Results of species distribution modeling indicated that these species are characterized by quite similar (caused by the same environmental factors), but nevertheless significantly different, ecological preferences.
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16
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Kirschner P, Seifert B, Kröll J, Schlick‐Steiner BC, Steiner FM. Phylogenomic inference and demographic model selection suggest peripatric separation of the cryptic steppe ant species Plagiolepis pyrenaica stat. rev. Mol Ecol 2023; 32:1149-1168. [PMID: 36530155 PMCID: PMC10946478 DOI: 10.1111/mec.16828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/24/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022]
Abstract
The ant Plagiolepis taurica Santschi, 1920 (Hymenoptera, Formicidae) is a typical species of the Eurasian steppes, a large grassland dominated biome that stretches continuously from Central Asia to Eastern Europe and is represented by disjunct outposts also in Central and Western Europe. The extent of this biome has been influenced by the Pleistocene climate, and steppes expanded recurrently during cold stages and contracted in warm stages. Consequently, stenotopic steppe species such as P. taurica repeatedly went through periods of demographic expansion and severe isolation. Here, we explore the impact of these dynamics on the genetic diversification within P. taurica. Delimitation of P. taurica from other Plagiolepis species has been unclear since its initial description, which raised questions on both its classification and its spatiotemporal diversification early on. We re-evaluate species limits and explore underlying mechanisms driving speciation by using an integrative approach based on genomic and morphometric data. We found large intraspecific divergence within P. taurica and resolved geographically coherent western and eastern genetic groups, which likewise differed morphologically. A morphometric survey of type material showed that Plagiolepis from the western group were more similar to P. barbara pyrenaica Emery, 1921 than to P. taurica; we thus lift the former from synonymy and establish it as separate species, P. pyrenaica stat. rev. Explicit evolutionary model testing based on genomic data supported a peripatric speciation for the species pair, probably as a consequence of steppe contraction and isolation during the mid-Pleistocene. We speculate that this scenario could be exemplary for many stenotopic steppe species, given the emphasized dynamics of Eurasian steppes.
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Affiliation(s)
- Philipp Kirschner
- Department of EcologyUniversity of InnsbruckInnsbruckAustria
- Department of BotanyUniversity of InnsbruckInnsbruckAustria
| | | | - Joelle Kröll
- Department of EcologyUniversity of InnsbruckInnsbruckAustria
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17
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Wenzell KE, Skogen KA, Fant JB. Range‐wide floral trait variation reflects shifts in pollinator assemblages, consistent with pollinator‐mediated divergence despite generalized visitation. OIKOS 2023. [DOI: 10.1111/oik.09708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Katherine E. Wenzell
- John Innes Centre Colney Lane Norwich UK
- Northwestern Univ., Program in Plant Biology and Conservation Evanston IL USA
- Negaunee Inst. for Plant Conservation Science and Action, Chicago Botanic Garden Glencoe IL USA
| | - Krissa A. Skogen
- Northwestern Univ., Program in Plant Biology and Conservation Evanston IL USA
- Negaunee Inst. for Plant Conservation Science and Action, Chicago Botanic Garden Glencoe IL USA
- Clemson Univ., Dept of Biological Sciences Clemson SC USA
| | - Jeremie B. Fant
- Northwestern Univ., Program in Plant Biology and Conservation Evanston IL USA
- Negaunee Inst. for Plant Conservation Science and Action, Chicago Botanic Garden Glencoe IL USA
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18
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Nimbs MJ, Wernberg T, Davis TR, Champion C, Coleman MA. Climate change threatens unique evolutionary diversity in Australian kelp refugia. Sci Rep 2023; 13:1248. [PMID: 36690643 PMCID: PMC9870953 DOI: 10.1038/s41598-023-28301-z] [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: 03/28/2022] [Accepted: 01/17/2023] [Indexed: 01/24/2023] Open
Abstract
Climate change has driven contemporary decline and loss of kelp forests globally with an accompanying loss of their ecological and economic values. Kelp populations at equatorward-range edges are particularly vulnerable to climate change as these locations are undergoing warming at or beyond thermal tolerance thresholds. Concerningly, these range-edge populations may contain unique adaptive or evolutionary genetic diversity that is vulnerable to warming. We explore haplotype diversity by generating a Templeton-Crandall-Sing (TCS) network analysis of 119 Cytochrome C Oxidase (COI) sequences among four major population groupings for extant and putatively extinct populations only known from herbarium specimens of the dominant Laminarian kelp Ecklonia radiata in the south-western Pacific, a region warming at 2-4 times the global average. Six haplotypes occurred across the region with one being widespread across most populations. Three unique haplotypes were found in a deep-water range-edge population off Moreton Island, Queensland, which likely represents both a contemporary and historic refuge during periods of climatic change. Hindcasting E. radiata cover estimates using extant data, we reveal that this region likely supported the highest kelp cover in eastern Australia during the last glacial maximum. The equatorward range edge, deep-water kelp populations off Moreton Island represent a genetically diverse evolutionary refuge that is currently threatened by warming and requires prompt ex-situ conservation measures.
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Affiliation(s)
- Matt J Nimbs
- New South Wales Department of Primary Industries, National Marine Science Centre, Coffs Harbour, NSW, Australia.
- National Marine Science Centre, Southern Cross University, Coffs Harbour, NSW, Australia.
| | - Thomas Wernberg
- Oceans Institute and School of Biological Sciences, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Tom R Davis
- New South Wales Department of Primary Industries, National Marine Science Centre, Coffs Harbour, NSW, Australia
- National Marine Science Centre, Southern Cross University, Coffs Harbour, NSW, Australia
| | - Curtis Champion
- New South Wales Department of Primary Industries, National Marine Science Centre, Coffs Harbour, NSW, Australia
- National Marine Science Centre, Southern Cross University, Coffs Harbour, NSW, Australia
| | - Melinda A Coleman
- New South Wales Department of Primary Industries, National Marine Science Centre, Coffs Harbour, NSW, Australia
- National Marine Science Centre, Southern Cross University, Coffs Harbour, NSW, Australia
- Oceans Institute and School of Biological Sciences, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
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19
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Bernos TA, Avlijaš S, Hill J, Morissette O, Ricciardi A, Mandrak NE, Jeffries KM. Genetic diversity and structure of a recent fish invasion: Tench ( Tinca tinca) in eastern North America. Evol Appl 2023; 16:173-188. [PMID: 36699124 PMCID: PMC9850014 DOI: 10.1111/eva.13520] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 10/22/2022] [Accepted: 12/02/2022] [Indexed: 01/20/2023] Open
Abstract
Introduced and geographically expanding populations experience similar eco-evolutionary challenges, including founder events, genetic bottlenecks, and novel environments. Theory predicts that reduced genetic diversity resulting from such phenomena limits the success of introduced populations. Using 1900 SNPs obtained from restriction-site-associated DNA sequencing, we evaluated hypotheses related to the invasion history and connectivity of an invasive population of Tench (Tinca tinca), a Eurasian freshwater fish that has been expanding geographically in eastern North America for three decades. Consistent with the reported history of a single introduction event, our findings suggest that multiple introductions from distinct genetic sources are unlikely as Tench had a small effective population size (~114 [95% CI = 106-123] individuals), no strong population subdivision across time and space, and evidence of a recent genetic bottleneck. The large genetic neighbourhood size (220 km) and weak within-population genetic substructure suggested high connectivity across the invaded range, despite the relatively large area occupied. There was some evidence for a small decay in genetic diversity as the species expanded northward, but not southward, into new habitats. As eradicating the species within a ~112 km radius would be necessary to prevent recolonization, eradicating Tench is likely not feasible at watershed-and possibly local-scales. Management should instead focus on reducing abundance in priority conservation areas to mitigate adverse impacts. Our study indicates that introduced populations can thrive and exhibit relatively high levels of genetic diversity despite severe bottlenecks (<1.5% of the ancestral effective population size) and suggests that landscape heterogeneity and population demographics can generate variability in spatial patterns of genetic diversity within a single range expansion.
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Affiliation(s)
- Thaïs A. Bernos
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoOntarioCanada
- Department of Biological SciencesUniversity of Toronto ScarboroughScarboroughOntarioCanada
| | - Sunčica Avlijaš
- Redpath MuseumMcGill UniversityMontrealQuébecCanada
- Department of BiologyMcGill UniversityMontrealQuébecCanada
| | - Jaclyn Hill
- Maurice Lamontagne InstituteFisheries and Oceans CanadaMont‐JoliQuébecCanada
| | - Olivier Morissette
- Département des Sciences FondamentalesUniversité du Québec à ChicoutimiChicoutimiQuébecCanada
| | | | - Nicholas E. Mandrak
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoOntarioCanada
| | - Kenneth M. Jeffries
- Department of Biological SciencesUniversity of ManitobaWinnipegManitobaCanada
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20
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Maxombe EL, Vieira LD, Sierens T, Triest L, Collevatti RG. Holocene climate changes explain the spatial pattern in genetic diversity in populations of Cyperus papyrus from Southeast Africa wetlands. Heredity (Edinb) 2022; 129:295-304. [PMID: 36163272 PMCID: PMC9613894 DOI: 10.1038/s41437-022-00563-9] [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: 12/21/2021] [Revised: 09/12/2022] [Accepted: 09/13/2022] [Indexed: 11/08/2022] Open
Abstract
Wetlands are one of the most threatened ecosystems in the world because more than 70% of the area worldwide has been lost since 1900. Wetland plant species rely greatly on water for seeds and propagules, which may lead to a downstream unidirectional dispersal and accumulation of genetic diversity downstream. However, several species show no support for unidirectional genetic diversity, revealing the complexity of population dynamics and gene flow in wetlands. Here, we used microsatellite loci to address how the past demographic dynamics shaped the contemporary spatial pattern in genetic diversity and population structure of Cyperus papyrus in wetlands of Southeast Africa. Using spatially explicit analysis and coalescent modelling, we found no support for unidirectional dispersal. Instead, we found higher genetic diversity in populations upstream than downstream in the river basin. We also found high admixture among populations, most likely due to connections between adjacent river basins during sporadic floods, and ongoing gene flow due to bird-mediated seed dispersal. Our results suggest stepping-stone migration due to strong isolation-by-distance, but not necessarily unidirectional. Moreover, the past demographic dynamics in the Holocene shaped the current pattern of genetic diversity and structure, leading to higher genetic diversity in populations upstream the Zambezi river basin. Our results also point to the very low genetic diversity of C. papyrus populations in Southeast Africa and the need for management and conservation strategies to guarantee the long-term persistence of the species in the region.
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Affiliation(s)
- Elias Luís Maxombe
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, 74001-970, Brazil
- Faculdade de Geociências, Universidade Rovuma, Avenida Josina Machel, Caixa Postal 544, Nampula, Mozambique
| | - Lucas Donizetti Vieira
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, 74001-970, Brazil
| | - Tim Sierens
- Plant Biology and Nature Management, Biology Department, Vrije Universiteit Brussel Pleinlaan 2, B-1050, Brussel, Belgium
| | - Ludwig Triest
- Plant Biology and Nature Management, Biology Department, Vrije Universiteit Brussel Pleinlaan 2, B-1050, Brussel, Belgium
| | - Rosane Garcia Collevatti
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, 74001-970, Brazil.
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21
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Ye J, Li D. Diversification of East Asian subtropical evergreen broadleaved forests over the last 8 million years. Ecol Evol 2022; 12:e9451. [PMID: 36329812 PMCID: PMC9618824 DOI: 10.1002/ece3.9451] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 09/26/2022] [Accepted: 10/10/2022] [Indexed: 11/25/2022] Open
Abstract
The evolution of subtropical evergreen broadleaved forests (EBLFs) in East Asia is interesting while complicated. Genus‐level phylogenies indicate that the origins of EBLFs could trace back to the Oligocene–Miocene boundary or even the Eocene, while population‐level phylogeographic evidence suggests that they diversified after the Miocene, particularly in the Pleistocene. Here, we review the origins of dominant plant species to better understand the evolution of EBLFs. We compiled published estimates of the timing of origin of dominant species and diversification of evergreen relict genera from East Asian EBLFs. We also traced and visualized the evolution of EBLFs in the region using dated phylogenies and geographic distributions of the reviewed taxa. Most (76.1%) of the dominant species originated after the late Miocene, ca. 8 million years ago. Of the 10 evergreen relict genera, eight diverged near the late Miocene–Pliocene boundary or during the late Pliocene, and the remaining two diverged during the Pleistocene. Over the past 8 million years, geo‐climatic changes have triggered origins of most of the dominant EBLF species and provided refugia for evergreen relict genera. Three pulsed phases of evolution are suggested by genetic studies at the genus, species, and population levels. Fossil evidence and spatiotemporal investigations should be integrated to fully understand the evolution of EBLFs in East Asia.
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Affiliation(s)
- Jun‐Wei Ye
- Germplasm Bank of Wild Species in Southwest China, Kunming Institute of BotanyChinese Academy of SciencesKunmingChina,Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of EducationSouthwest Forestry UniversityKunmingChina
| | - De‐Zhu Li
- Germplasm Bank of Wild Species in Southwest China, Kunming Institute of BotanyChinese Academy of SciencesKunmingChina
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22
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Changing patterns of genetic differentiation in the slender wild oat, Avena barbata. Proc Natl Acad Sci U S A 2022; 119:e2121248119. [PMID: 36161958 DOI: 10.1073/pnas.2121248119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The slender wild oat (Avena barbata) was widely studied in California using allozymes in the 1970s and interpreted as a case of ecotypic adaptation to contrasting moisture environments. However, common garden studies suggested that the moist-associated ("mesic") ecotype had high fitness in both moist and dry habitats, thus predicting an adaptive spread into areas occupied by the dry associated ("xeric") ecotype. To test this prediction, we revisited 100 populations of A. barbata that were screened genetically 40 y ago. As expected, mesic allozyme and morphological markers are much more common than in the 1970s. The less-fit xeric ecotype, while still widespread, has declined markedly in range and frequency. Genotyping by sequencing of modern populations reveals striking genetic uniformity within each of the two ecotypes. In recombinants between the two ecotypes, the mesic allele at a major fitness quantitative trait locus (QTL) shows a high frequency but so do many other genomic regions not identified as fitness QTL. Additional introduced genotypes are diverse and more widespread than in the past, and our results show that these have spread into the former range of the xeric ecotype to an even greater extent than the mesic ecotype has. While these results confirm the prediction of contemporary evolution from common gardens, they also suggest that much of the change has been driven by additional waves of introduced genotypes.
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23
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Scarsbrook L, Mitchell KJ, Mcgee MD, Closs GP, Rawlence NJ. Ancient DNA from the extinct New Zealand grayling ( Prototroctes oxyrhynchus) reveals evidence for Miocene marine dispersal. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
The evolutionary history of Southern Hemisphere graylings (Retropinnidae) in New Zealand (NZ), including their relationship to the Australian grayling, is poorly understood. The NZ grayling (Prototroctes oxyrhynchus) is the only known fish in NZ to have gone extinct since human arrival there. Despite its historical abundance, only 23 wet and dried, formalin-fixed specimens exist in museums. We used high-throughput DNA sequencing to generate mitogenomes from formalin-fixed P. oxyrhynchus specimens, and analysed these in a temporal phylogenetic framework of retropinnids and osmerids. We recovered a strong sister-relationship between NZ and Australian grayling (P. mareana), with a common ancestor ~13.8 Mya [95% highest posterior density (HPD): 6.1–23.2 Mya], after the height of Oligocene marine inundation in NZ. Our temporal phylogenetic analysis suggests a single marine dispersal between NZ and Australia, although the direction of dispersal is equivocal, followed by divergence into genetically and morphologically distinguishable species through isolation by distance. This study provides further insights into the possible extinction drivers of the NZ grayling, informs discussion regarding reintroduction of Prototroctes to NZ and highlights how advances in palaeogenetics can be used to test evolutionary hypotheses in fish, which, until relatively recently, have been comparatively neglected in ancient-DNA research.
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Affiliation(s)
- Lachie Scarsbrook
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago , Dunedin , New Zealand
- Palaeogenomics and Bio-Archaeology Research Network, School of Archaeology, University of Oxford , Oxford , UK
| | - Kieren J Mitchell
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago , Dunedin , New Zealand
| | - Matthew D Mcgee
- Behavioural Studies Group, School of Biological Sciences, Monash University , Melbourne, Victoria , Australia
| | - Gerard P Closs
- Department of Zoology, University of Otago , Dunedin , New Zealand
| | - Nicolas J Rawlence
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago , Dunedin , New Zealand
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Lamarca AP, de Almeida LGP, Francisco RDS, Cavalcante L, Brustolini O, Gerber AL, Guimarães APDC, de Oliveira TH, dos Santos Nascimento ÉR, Policarpo C, de Souza IV, de Carvalho EM, Ribeiro MS, Carvalho S, Dias da Silva F, de Oliveira Garcia MH, de Souza LM, Da Silva CG, Ribeiro CLP, Cavalcanti AC, de Mello CMB, Tanuri A, Vasconcelos ATRD. Phylodynamic analysis of SARS-CoV-2 spread in Rio de Janeiro, Brazil, highlights how metropolitan areas act as dispersal hubs for new variants. Microb Genom 2022; 8. [DOI: 10.1099/mgen.0.000859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During the first semester of 2021, all of Brazil has suffered an intense wave of COVID-19 associated with the Gamma variant. In July, the first cases of Delta variant were detected in the state of Rio de Janeiro. In this work, we have employed phylodynamic methods to analyse more than 1 600 genomic sequences of Delta variant collected until September in Rio de Janeiro to reconstruct how this variant has surpassed Gamma and dispersed throughout the state. After the introduction of Delta, it has initially spread mostly in the homonymous city of Rio de Janeiro, the most populous of the state. In a second stage, dispersal occurred to mid- and long-range cities, which acted as new close-range hubs for spread. We observed that the substitution of Gamma by Delta was possibly caused by its higher viral load, a proxy for transmissibility. This variant turnover prompted a new surge in cases, but with lower lethality than was observed during the peak caused by Gamma. We reason that high vaccination rates in the state of Rio de Janeiro were possibly what prevented a higher number of deaths.
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Affiliation(s)
- Alessandra Pavan Lamarca
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Luiz G. P. de Almeida
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | | | - Liliane Cavalcante
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Otávio Brustolini
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Alexandra L. Gerber
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | | | - Thiago Henrique de Oliveira
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Cintia Policarpo
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | | | - Silvia Carvalho
- Secretaria Estadual de Saúde do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | | | | | | | - Andréa Cony Cavalcanti
- Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Laboratório Central de Saúde Pública Noel Nutels, Rio de Janeiro, Brazil
| | | | - Amilcar Tanuri
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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Johnston-Monje D, Gutiérrez JP, Becerra Lopez-Lavalle LA. Stochastic Inoculum, Biotic Filtering and Species-Specific Seed Transmission Shape the Rare Microbiome of Plants. Life (Basel) 2022; 12:life12091372. [PMID: 36143410 PMCID: PMC9506401 DOI: 10.3390/life12091372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/22/2022] [Accepted: 08/31/2022] [Indexed: 11/17/2022] Open
Abstract
A plant’s health and productivity is influenced by its associated microbes. Although the common/core microbiome is often thought to be the most influential, significant numbers of rare or uncommon microbes (e.g., specialized endosymbionts) may also play an important role in the health and productivity of certain plants in certain environments. To help identify rare/specialized bacteria and fungi in the most important angiosperm plants, we contrasted microbiomes of the seeds, spermospheres, shoots, roots and rhizospheres of Arabidopsis, Brachypodium, maize, wheat, sugarcane, rice, tomato, coffee, common bean, cassava, soybean, switchgrass, sunflower, Brachiaria, barley, sorghum and pea. Plants were grown inside sealed jars on sterile sand or farm soil. Seeds and spermospheres contained some uncommon bacteria and many fungi, suggesting at least some of the rare microbiome is vertically transmitted. About 95% and 86% of fungal and bacterial diversity inside plants was uncommon; however, judging by read abundance, uncommon fungal cells are about half of the mycobiome, while uncommon bacterial cells make up less than 11% of the microbiome. Uncommon-seed-transmitted microbiomes consisted mostly of Proteobacteria, Firmicutes, Bacteriodetes, Ascomycetes and Basidiomycetes, which most heavily colonized shoots, to a lesser extent roots, and least of all, rhizospheres. Soil served as a more diverse source of rare microbes than seeds, replacing or excluding the majority of the uncommon-seed-transmitted microbiome. With the rarest microbes, their colonization pattern could either be the result of stringent biotic filtering by most plants, or uneven/stochastic inoculum distribution in seeds or soil. Several strong plant–microbe associations were observed, such as seed transmission to shoots, roots and/or rhizospheres of Sarocladium zeae (maize), Penicillium (pea and Phaseolus), and Curvularia (sugarcane), while robust bacterial colonization from cassava field soil occurred with the cyanobacteria Leptolyngbya into Arabidopsis and Panicum roots, and Streptomyces into cassava roots. Some abundant microbes such as Sakaguchia in rice shoots or Vermispora in Arabidopsis roots appeared in no other samples, suggesting that they were infrequent, stochastically deposited propagules from either soil or seed (impossible to know based on the available data). Future experiments with culturing and cross-inoculation of these microbes between plants may help us better understand host preferences and their role in plant productivity, perhaps leading to their use in crop microbiome engineering and enhancement of agricultural production.
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Affiliation(s)
- David Johnston-Monje
- Max Planck Tandem Group in Plant Microbial Ecology, Universidad del Valle, Cali 76001, Colombia
- International Center for Tropical Agriculture (CIAT), Cali 763537, Colombia
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
- Correspondence: ; Tel.: +57-315-545-6227
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Vaux F, Parvizi E, Craw D, Fraser CI, Waters J. Parallel recolonizations generate distinct genomic sectors in kelp following high-magnitude earthquake disturbance. Mol Ecol 2022; 31:4818-4831. [PMID: 35582778 PMCID: PMC9540901 DOI: 10.1111/mec.16535] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 04/25/2022] [Accepted: 05/12/2022] [Indexed: 11/30/2022]
Abstract
Large-scale disturbance events have the potential to drastically reshape biodiversity patterns. Notably, newly vacant habitat space cleared by disturbance can be colonized by multiple lineages, which can lead to the evolution of distinct spatial "sectors" of genetic diversity within a species. We test for disturbance-driven sectoring of genetic diversity in intertidal southern bull kelp, Durvillaea antarctica (Chamisso) Hariot, following the high-magnitude 1855 Wairarapa earthquake in New Zealand. Specifically, we use genotyping-by-sequencing (GBS) to analyse fine-scale population structure across the uplift zone and apply machine learning to assess the fit of alternative recolonizaton models. Our analysis reveals that specimens from the uplift zone carry distinctive genomic signatures potentially linked to post-earthquake recolonization processes. Specifically, our analysis identifies two parapatric spatial-genomic sectors of D. antarctica at Turakirae Head, which experienced the most dramatic uplift. Based on phylogeographical modelling, we infer that bull kelp in the Wellington region was probably a source for recolonization of the heavily uplifted Turakirae Head coastline, via two parallel, eastward recolonization events. By identifying multiple parapatric genotypic sectors within a recently recolonized coastal region, the current study provides support for the hypothesis that competing lineage expansions can generate striking spatial structuring of genetic diversity, even in highly dispersive taxa.
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Affiliation(s)
- Felix Vaux
- Department of ZoologyUniversity of OtagoDunedinNew Zealand
| | - Elahe Parvizi
- Department of ZoologyUniversity of OtagoDunedinNew Zealand
| | - Dave Craw
- Department of GeologyUniversity of OtagoDunedinNew Zealand
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Campbell BC, Greenfield P, Gong S, Barnhart EP, Midgley DJ, Paulsen IT, George SC. Methanogenic archaea in subsurface coal seams are biogeographically distinct: an analysis of metagenomically-derived mcrA sequences. Environ Microbiol 2022; 24:4065-4078. [PMID: 35437913 PMCID: PMC9790511 DOI: 10.1111/1462-2920.16014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 04/08/2022] [Accepted: 04/10/2022] [Indexed: 12/30/2022]
Abstract
The production of methane as an end-product of organic matter degradation in the absence of other terminal electron acceptors is common, and has often been studied in environments such as animal guts, soils and wetlands due to its potency as a greenhouse gas. To date, however, the study of the biogeographic distribution of methanogens across coal seam environments has been minimal. Here, we show that coal seams are host to a diverse range of methanogens, which are distinctive to each geological basin. Based on comparisons to close relatives from other methanogenic environments, the dominant methanogenic pathway in these basins is hydrogenotrophic, with acetoclastic being a second major pathway in the Surat Basin. Finally, mcrA and 16S rRNA gene primer biases were predominantly seen to affect the detection of Methanocellales, Methanomicrobiales and Methanosarcinales taxa in this study. Subsurface coal methanogenic community distributions and pathways presented here provide insights into important metabolites and bacterial partners for in situ coal biodegradation.
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Affiliation(s)
- Bronwyn C. Campbell
- Energy Business UnitCommonwealth Scientific and Industrial Research Organisation (CSIRO)LindfieldNSW2070Australia,School of Natural SciencesMacquarie UniversityNorth RydeNSW2109Australia
| | - Paul Greenfield
- Energy Business UnitCommonwealth Scientific and Industrial Research Organisation (CSIRO)LindfieldNSW2070Australia,School of Natural SciencesMacquarie UniversityNorth RydeNSW2109Australia
| | - Se Gong
- Energy Business UnitCommonwealth Scientific and Industrial Research Organisation (CSIRO)LindfieldNSW2070Australia
| | | | - David J. Midgley
- Energy Business UnitCommonwealth Scientific and Industrial Research Organisation (CSIRO)LindfieldNSW2070Australia
| | - Ian T. Paulsen
- School of Natural SciencesMacquarie UniversityNorth RydeNSW2109Australia
| | - Simon C. George
- School of Natural SciencesMacquarie UniversityNorth RydeNSW2109Australia
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Hinneberg H, Bamann T, Geue JC, Foerster K, Thomassen HA, Kupfer A. Truly invasive or simply non‐native? Insights from an artificial crested newt hybrid zone. CONSERVATION SCIENCE AND PRACTICE 2022. [DOI: 10.1111/csp2.12752] [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] Open
Affiliation(s)
- Heiko Hinneberg
- University of Applied Forest Sciences Rottenburg Germany
- University of Tübingen, Institute of Evolution and Ecology Tübingen Germany
| | | | - Julia C. Geue
- Umeå University, Department of Ecology and Environmental Sciences Umeå Sweden
| | - Katharina Foerster
- University of Tübingen, Institute of Evolution and Ecology Tübingen Germany
| | - Henri A. Thomassen
- University of Tübingen, Institute of Evolution and Ecology Tübingen Germany
| | - Alexander Kupfer
- Department of Zoology, State Museum of Natural History Stuttgart Stuttgart Germany
- Institute of Biology, University of Hohenheim Stuttgart Germany
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Trewick SA, Henderson IM, Pohe SR, Morgan-Richards M. Spatial Variation of Acanthophlebia cruentata (Ephemeroptera), a Mayfly Endemic to Te Ika-a-Māui—North Island of Aotearoa, New Zealand. INSECTS 2022; 13:insects13070567. [PMID: 35886743 PMCID: PMC9316242 DOI: 10.3390/insects13070567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/09/2022] [Accepted: 06/21/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary Patterns of variation within a widespread species can provide evidence of population history. Adjacent stable populations with gene flow show clinal genetic divergence forming a pattern of isolation by distance. Populations that have grown due to an increase in potential habitat such as forest cover since the last glacial maximum will have low genetic variation showing patterns of range expansion. The mayfly Acanthophlebia cruentata of Aotearoa, New Zealand, is widespread in streams of North Island but absent from the cooler South Island. Mayfly nymphs are restricted to streams but adults fly, facilitating gene flow among catchments. We detected higher genetic diversity at lower latitudes of this mayfly’s range compared to most of its distribution, concordant with predictions of limited forest cover in New Zealand during Pleistocene glacial periods. A signature of recent range expansion was observed in the higher latitudes. Despite initial observation suggesting mayfly size correlated with latitude, we found sex, elevation and sampling date were significant predictors of size, and some size variation is also explained by three regional groups based on haplotype distribution. Abstract The mayfly Acanthophlebia cruentata of Aotearoa, New Zealand, is widespread in Te Ika-a-Māui North Island streams, but has never been collected from South Island despite land connection during the last glacial maximum. Population structure of this mayfly might reflect re-colonisation after volcanic eruptions in North Island c1800 years ago, climate cycling or conceal older, cryptic diversity. We collected population samples from 33 locations to estimate levels of population genetic diversity and to document phenotypic variation. Relatively low intraspecific haplotype divergence was recorded among mitochondrial cytb sequences from 492 individuals, but these resolved three geographic-haplotype regions (north, west, east). We detected a signature of isolation by distance at low latitudes (north) but evidence of recent population growth in the west and east. We did not detect an effect of volcanic eruptions but infer range expansion into higher latitudes from a common ancestor during the last glacial period. As judged from wing length, both sexes of adult mayflies were larger at higher elevation and we found that haplotype region was also a significant predictor of Acanthophlebia cruentata size. This suggests that our mitochondrial marker is concordant with nuclear genetic differences that might be explained by founder effect during range expansion.
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Affiliation(s)
- Steven A. Trewick
- Wildlife & Ecology Group, School of Natural Science, Massey University, Private Bag 11-222, Palmerston North 4442, New Zealand; (I.M.H.); (M.M.-R.)
- Correspondence:
| | - Ian M. Henderson
- Wildlife & Ecology Group, School of Natural Science, Massey University, Private Bag 11-222, Palmerston North 4442, New Zealand; (I.M.H.); (M.M.-R.)
| | | | - Mary Morgan-Richards
- Wildlife & Ecology Group, School of Natural Science, Massey University, Private Bag 11-222, Palmerston North 4442, New Zealand; (I.M.H.); (M.M.-R.)
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30
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McGlone MS, Heenan PB, Perry GLW. Eco-evolutionary priority and the assembly of the New Zealand flora. J R Soc N Z 2022. [DOI: 10.1080/03036758.2022.2076703] [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]
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31
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Marske KA, Boyer SL. Phylogeography reveals the complex impact of the Last Glacial Maximum on New Zealand’s terrestrial biota. J R Soc N Z 2022. [DOI: 10.1080/03036758.2022.2079682] [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]
Affiliation(s)
| | - Sarah L. Boyer
- Biology Department, Macalester College, St. Paul, MN, USA
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Hariharan J, Buckley DH. Elevational Gradients Impose Dispersal Limitation on Streptomyces. Front Microbiol 2022; 13:856263. [PMID: 35592003 PMCID: PMC9113539 DOI: 10.3389/fmicb.2022.856263] [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: 01/17/2022] [Accepted: 03/25/2022] [Indexed: 11/16/2022] Open
Abstract
Dispersal governs microbial biogeography, but the rates and mechanisms of dispersal remain poorly characterized for most microbial taxa. Dispersal limitation is driven by limits on dissemination and establishment, respectively. Elevation gradients create striking patterns of biogeography because they produce steep environmental gradients at small spatial scales, and these gradients offer a powerful tool to examine mechanisms of dispersal limitation. We focus on Streptomyces, a bacterial genus common to soil, by using a taxon-specific phylogenetic marker, the RNA polymerase-encoding rpoB gene. By targeting Streptomyces, we assess dispersal limitation at finer phylogenetic resolution than is possible using whole community analyses. We characterized Streptomyces diversity at local spatial scales (100 to 3,000 m) in two temperate forest sites located in the Adirondacks region of New York State: Woods Lake (<100 m elevation change), and Whiteface Mountain (>1,000 m elevation change). Beta diversity varied considerably at both locations, indicative of dispersal limitation acting at local spatial scales, but beta diversity was significantly higher at Whiteface Mountain. Beta diversity varied across elevation at Whiteface Mountain, being lowest at the mountain’s base. We show that Streptomyces taxa exhibit elevational preferences, and these preferences are phylogenetically conserved. These results indicate that habitat preferences influence Streptomyces biogeography and suggest that barriers to establishment structure Streptomyces communities at higher elevations. These data illustrate that Streptomyces biogeography is governed by dispersal limitation resulting from a complex mixture of stochastic and deterministic processes.
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Affiliation(s)
- Janani Hariharan
- School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Daniel H Buckley
- School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
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Chang JT, Chao CT, Nakamura K, Liu HL, Luo MX, Liao PC. Divergence With Gene Flow and Contrasting Population Size Blur the Species Boundary in Cycas Sect. Asiorientales, as Inferred From Morphology and RAD-Seq Data. FRONTIERS IN PLANT SCIENCE 2022; 13:824158. [PMID: 35615129 PMCID: PMC9125193 DOI: 10.3389/fpls.2022.824158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 03/15/2022] [Indexed: 06/15/2023]
Abstract
The divergence process of incipient species is fascinating but elusive by incomplete lineage sorting or gene flow. Species delimitation is also challenging among those morphologically similar allopatric species, especially when lacking comprehensive data. Cycas sect. Asiorientales, comprised of C. taitungensis and C. revoluta in the Ryukyu Archipelago and Taiwan, diverged recently with continuous gene flow, resulting in a reciprocal paraphyletic relationship. Their previous evolutionary inferences are questioned from few genetic markers, incomplete sampling, and incomprehensive morphological comparison by a long-term taxonomic misconception. By whole range sampling, this study tests the geographic mode of speciation in the two species of Asiorientales by approximate Bayesian computation (ABC) using genome-wide single nucleotide polymorphisms (SNPs). The individual tree was reconstructed to delimit the species and track the gene-flow trajectory. With the comparison of diagnostic morphological traits and genetic data, the allopatric speciation was rejected. Alternatively, continuous but spatially heterogeneous gene flow driven by transoceanic vegetative dispersal and pollen flow with contrasting population sizes blurred their species boundary. On the basis of morphological, genetic, and evolutionary evidence, we synonymized these two Cycas species. This study highlights not only the importance of the Kuroshio Current to species evolution but also the disadvantage of using species with geographically structured genealogies as conservation units.
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Affiliation(s)
- Jui-Tse Chang
- School of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Chien-Ti Chao
- School of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Koh Nakamura
- Botanic Garden, Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Japan
| | - Hsiao-Lei Liu
- Department of Anthropology, Smithsonian Institution, National Museum of Natural History, Washington, DC, United States
| | - Min-Xin Luo
- School of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Pei-Chun Liao
- School of Life Science, National Taiwan Normal University, Taipei, Taiwan
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Comparative population genomics in Tabebuia alliance shows evidence of adaptation in Neotropical tree species. Heredity (Edinb) 2022; 128:141-153. [PMID: 35132209 PMCID: PMC8897506 DOI: 10.1038/s41437-021-00491-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 12/07/2021] [Accepted: 12/07/2021] [Indexed: 11/08/2022] Open
Abstract
The role of natural selection in shaping spatial patterns of genetic diversity in the Neotropics is still poorly understood. Here, we perform a genome scan with 24,751 probes targeting 11,026 loci in two Neotropical Bignoniaceae tree species: Handroanthus serratifolius from the seasonally dry tropical forest (SDTF) and Tabebuia aurea from savannas, and compared with the population genomics of H. impetiginosus from SDTF. OutFLANK detected 29 loci in 20 genes with selection signal in H. serratifolius and no loci in T. aurea. Using BayPass, we found evidence of selection in 335 loci in 312 genes in H. serratifolius, 101 loci in 92 genes in T. aurea, and 448 loci in 416 genes in H. impetiginosus. All approaches evidenced several genes affecting plant response to environmental stress and primary metabolic processes. The three species shared no SNPs with selection signal, but we found SNPs affecting the same gene in pair of species. Handroanthus serratifolius showed differences in allele frequencies at SNPs with selection signal among ecosystems, mainly between Caatinga/Cerrado and Atlantic Forest, while H. impetiginosus had one allele fixed across all populations, and T. aurea had similar allele frequency distribution among ecosystems and polymorphism across populations. Taken together, our results indicate that natural selection related to environmental stress shaped the spatial pattern of genetic diversity in the three species. However, the three species have different geographical distribution and niches, which may affect tolerances and adaption, and natural selection may lead to different signatures due to the differences in adaptive landscapes in different niches.
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Marić S, Stanković D, Sušnik Bajec S, Vukić J, Šanda R, Stefanov T, Nikolić D, Snoj A. Perils of brown trout (Salmo spp.) mitigation-driven translocations: a case study from the Vlasina Plateau, Southeast Serbia. Biol Invasions 2022. [DOI: 10.1007/s10530-021-02688-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Slow expanders invade by forming dented fronts in microbial colonies. Proc Natl Acad Sci U S A 2022; 119:2108653119. [PMID: 34983839 PMCID: PMC8740590 DOI: 10.1073/pnas.2108653119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/08/2021] [Indexed: 12/19/2022] Open
Abstract
Living organisms never cease to evolve, so there is a significant interest in predicting and controlling evolution in all branches of life sciences. The most basic question is whether a trait should increase or decrease in a given environment. The answer seems to be trivial for traits such as the growth rate in a bioreactor or the expansion rate of a tumor. Yet, it has been suggested that such traits can decrease, rather than increase, during evolution. Here, we report a mutant that outcompeted the ancestor despite having a slower expansion velocity when in isolation. To explain this observation, we developed and validated a theory that describes spatial competition between organisms with different expansion rates and arbitrary competitive interactions. Most organisms grow in space, whether they are viruses spreading within a host tissue or invasive species colonizing a new continent. Evolution typically selects for higher expansion rates during spatial growth, but it has been suggested that slower expanders can take over under certain conditions. Here, we report an experimental observation of such population dynamics. We demonstrate that mutants that grow slower in isolation nevertheless win in competition, not only when the two types are intermixed, but also when they are spatially segregated into sectors. The latter was thought to be impossible because previous studies focused exclusively on the global competitions mediated by expansion velocities, but overlooked the local competitions at sector boundaries. Local competition, however, can enhance the velocity of either type at the sector boundary and thus alter expansion dynamics. We developed a theory that accounts for both local and global competitions and describes all possible sector shapes. In particular, the theory predicted that a slower on its own, but more competitive, mutant forms a dented V-shaped sector as it takes over the expansion front. Such sectors were indeed observed experimentally, and their shapes matched quantitatively with the theory. In simulations, we further explored several mechanisms that could provide slow expanders with a local competitive advantage and showed that they are all well-described by our theory. Taken together, our results shed light on previously unexplored outcomes of spatial competition and establish a universal framework to understand evolutionary and ecological dynamics in expanding populations.
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OUP accepted manuscript. Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blac043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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38
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Tahami MS, Dincă V, Lee KM, Vila R, Joshi M, Heikkilä M, Dapporto L, Schmid S, Huemer P, Mutanen M. Genomics Reveal Admixture and Unexpected Patterns of Diversity in a Parapatric Pair of Butterflies. Genes (Basel) 2021; 12:genes12122009. [PMID: 34946956 PMCID: PMC8700966 DOI: 10.3390/genes12122009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 11/16/2022] Open
Abstract
We studied the evolutionary relationship of two widely distributed parapatric butterfly species, Melitaea athalia and Melitaea celadussa, using the ddRAD sequencing approach, as well as genital morphology and mtDNA data. M. athalia was retrieved as paraphyletic with respect to M. celadussa. Several cases of mito-nuclear discordance and morpho-genetic mismatch were found in the contact zone. A strongly diverged and marginally sympatric clade of M. athalia from the Balkans was revealed. An in-depth analysis of genomic structure detected high levels of admixture between M. athalia and M. celadussa at the contact zone, though not reaching the Balkan clade. The demographic modelling of populations supported the intermediate genetic make-up of European M. athalia populations with regards to M. celadussa and the Balkan clade. However, the dissimilarity matrix of genotype data (PCoA) suggested the Balkan lineage having a genetic component that is unrelated to the athalia-celadussa group. Although narrowly sympatric, almost no signs of gene flow were found between the main M. athalia group and the Balkan clade. We propose two possible scenarios on the historical evolution of our model taxa and the role of the last glacial maximum in shaping their current distribution. Finally, we discuss the complexities regarding the taxonomic delimitation of parapatric taxa.
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Affiliation(s)
- Mohadeseh Sadat Tahami
- Ecology and Genetics Research Unit, University of Oulu, P.O. Box 3000, 90014 Oulu, Finland; (V.D.); (K.M.L.); (M.J.); (M.M.)
- Correspondence:
| | - Vlad Dincă
- Ecology and Genetics Research Unit, University of Oulu, P.O. Box 3000, 90014 Oulu, Finland; (V.D.); (K.M.L.); (M.J.); (M.M.)
| | - Kyung Min Lee
- Ecology and Genetics Research Unit, University of Oulu, P.O. Box 3000, 90014 Oulu, Finland; (V.D.); (K.M.L.); (M.J.); (M.M.)
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC—Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta, 37, 08003 Barcelona, Spain;
| | - Mukta Joshi
- Ecology and Genetics Research Unit, University of Oulu, P.O. Box 3000, 90014 Oulu, Finland; (V.D.); (K.M.L.); (M.J.); (M.M.)
| | - Maria Heikkilä
- Zoology Unit, Finnish Museum of Natural History, University of Helsinki, P.O. Box 17, 00014 Helsinki, Finland;
| | - Leonardo Dapporto
- Numerical and Experimental Zoology Laboratory (ZEN Lab), Dipartimento di Biologia, Dell’ Università di Firenze, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy;
| | - Sarah Schmid
- Departement de Biologie Computationnelle, Faculte de Biologie et Medecine, Universite de Lausanne, 1015 Lausanne, Switzerland;
| | - Peter Huemer
- Tiroler Landesmuseen Betriebsges.m.b.H., Naturwissenschaftliche Sammlungen, Krajnc-Str. 1, A-6060 Hall, Austria;
| | - Marko Mutanen
- Ecology and Genetics Research Unit, University of Oulu, P.O. Box 3000, 90014 Oulu, Finland; (V.D.); (K.M.L.); (M.J.); (M.M.)
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Hodges JA, Price JN, Nicotra AB, Neeman T, Guja LK. Smoke and heat accelerate and increase germination in fire‐prone temperate grassy ecosystems. Ecosphere 2021. [DOI: 10.1002/ecs2.3851] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Joshua A. Hodges
- Institute for Land, Water and Society Charles Sturt University Thurgoona New South Wales Australia
- Research School of Biology Australian National University Canberra Australian Capital Territory Australia
- National Seed Bank Australian National Botanic Gardens Canberra Australian Capital Territory Australia
| | - Jodi N. Price
- Institute for Land, Water and Society Charles Sturt University Thurgoona New South Wales Australia
| | - Adrienne B. Nicotra
- Research School of Biology Australian National University Canberra Australian Capital Territory Australia
| | - Teresa Neeman
- Statistical Consulting Unit Australian National University Canberra Australian Capital Territory Australia
| | - Lydia K. Guja
- National Seed Bank Australian National Botanic Gardens Canberra Australian Capital Territory Australia
- Centre for Australian National Biodiversity Research Canberra Australian Capital Territory Australia
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40
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Hedenäs L, Hylander K, Lönnell N, Bisang I. Genetic variation and reproductive patterns in wetland mosses suggest efficient initial colonization of disturbed sites. Ecol Evol 2021; 11:15846-15859. [PMID: 34824794 PMCID: PMC8601880 DOI: 10.1002/ece3.8255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 06/16/2021] [Accepted: 06/21/2021] [Indexed: 11/08/2022] Open
Abstract
To understand colonization processes, it is critical to fully assess the role of dispersal in shaping biogeographical patterns at the gene, individual, population, and community levels. We test two alternative hypotheses (H I and H II) for the colonization of disturbed sites by clonal plants, by analyzing intraspecific genetic variation in one and reproductive traits in two typical fen mosses with separate sexes and intermittent spore dispersal, comparing disturbed, early-succession (limed) fens and late-successional rich fens. H I suggests initial colonization of disturbed sites by diverse genotypes of which fewer remain in late-successional fens and an initially balanced sex ratio that develops into a possibly skewed population sex ratio. H II suggests initial colonization by few genotypes and gradual accumulation of additional genotypes and an initially skewed sex ratio that alters into the species-specific sex ratio, during succession. Under both scenarios, we expect enhanced sexual reproduction in late-successional fens due to resource gains and decreased intermate distances when clones expand. We show that the intraspecific genetic diversity, assessed by two molecular markers, in Scorpidium cossonii was higher and the genetic variation among sites was smaller in disturbed than late-successional rich fens. Sex ratio was balanced in S. cossonii and Campylium stellatum in disturbed fens and skewed in C. stellatum in late-successional fens, thus supporting H I. In line with our prediction, sex expression incidence was higher in, and sporophytes were confined to, late-succession compared to disturbed rich fens. Late-successional S. cossonii sites had more within-site patches with two or more genotypes, and both species displayed higher sex expression levels in late-successional than in disturbed sites. We conclude that diverse genotypes and both sexes disperse efficiently to, and successfully colonize new sites, while patterns of genetic variation and sexual reproduction in late-successional rich fens are gradually shaped by local conditions and interactions over extended time periods.
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Affiliation(s)
- Lars Hedenäs
- Department of BotanySwedish Museum of Natural HistoryStockholmSweden
| | - Kristoffer Hylander
- Department of EcologyEnvironment and Plant SciencesStockholm UniversityStockholmSweden
| | - Niklas Lönnell
- SLU Swedish Species Information CentreSwedish University of Agricultural SciencesUppsalaSweden
| | - Irene Bisang
- Department of BotanySwedish Museum of Natural HistoryStockholmSweden
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41
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Parvizi E, Dutoit L, Fraser CI, Craw D, Waters JM. Concordant phylogeographic responses to large-scale coastal disturbance in intertidal macroalgae and their epibiota. Mol Ecol 2021; 31:646-657. [PMID: 34695264 DOI: 10.1111/mec.16245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 10/13/2021] [Accepted: 10/20/2021] [Indexed: 01/05/2023]
Abstract
Major ecological disturbance events can provide opportunities to assess multispecies responses to upheaval. In particular, catastrophic disturbances that regionally extirpate habitat-forming species can potentially influence the genetic diversity of large numbers of codistributed taxa. However, due to the rarity of such disturbance events over ecological timeframes, the genetic dynamics of multispecies recolonization processes have remained little understood. Here, we use single nucleotide polymorphism (SNP) data from multiple coastal species to track the dynamics of cocolonization events in response to ancient earthquake disturbance in southern New Zealand. Specifically, we use a comparative phylogeographic approach to understand the extent to which epifauna (with varying ecological associations with their macroalgal hosts) share comparable spatial and temporal recolonization patterns. Our study reveals concordant disturbance-related phylogeographic breaks in two intertidal macroalgal species along with two associated epibiotic species (a chiton and an isopod). By contrast, two codistributed species, one of which is an epibiotic amphipod and the other a subtidal macroalga, show few, if any, genetic effects of palaeoseismic coastal uplift. Phylogeographic model selection reveals similar post-uplift recolonization routes for the epibiotic chiton and isopod and their macroalgal hosts. Additionally, codemographic analyses support synchronous population expansions of these four phylogeographically similar taxa. Our findings indicate that coastal paleoseismic activity has driven concordant impacts on multiple codistributed species, with concerted recolonization events probably facilitated by macroalgal rafting. These results highlight that high-resolution comparative genomic data can help reconstruct concerted multispecies responses to recent ecological disturbance.
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Affiliation(s)
- Elahe Parvizi
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Ludovic Dutoit
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Ceridwen I Fraser
- Department of Marine Science, University of Otago, Dunedin, New Zealand
| | - Dave Craw
- Department of Geology, University of Otago, Dunedin, New Zealand
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42
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Stillman AN, Lorenz TJ, Siegel RB, Wilkerson RL, Johnson M, Tingley MW. Conditional natal dispersal provides a mechanism for populations tracking resource pulses after fire. Behav Ecol 2021. [DOI: 10.1093/beheco/arab106] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Abstract
Animals that persist in spatially structured populations face the challenge of tracking the rise and fall of resources across space and time. To combat these challenges, theory predicts that species should use conditional dispersal strategies that allow them to emigrate from patches with declining resources and colonize new resource patches as they appear. We studied natal dispersal movements in the black-backed woodpecker (Picoides arcticus), a species known for its strong association with recent post-fire forests in western North America. We radio-tracked juveniles originating from seven burned areas and tested hypotheses that environmental and individual factors influence dispersal distance and emigration rates—investigating emigration while additionally accounting for imperfect detection with a novel Bayesian model. We found that juveniles were more likely to leave natal areas and disperse longer distances if they were heavier or hatched in older burned areas where resources are increasingly scarce. Juveniles were also more likely to leave their natal burn if they hatched in a nest closer to the fire perimeter. While dispersing across the landscape, black-backed woodpeckers selected for burned forest relative to unburned available habitat. Together, these results strongly support the hypothesis that black-backed woodpecker populations track resource pulses across fire-prone landscapes, with conditional natal dispersal acting as a mechanism for locating and colonizing newly burned areas. Lending empirical support to theoretical predictions, our findings suggest that changes in resource distribution may shape dispersal patterns and, consequently, the distribution and persistence of spatially structured populations.
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Affiliation(s)
- Andrew N Stillman
- Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, Unit 3043, Storrs, CT 06269, USA
| | - Teresa J Lorenz
- USDA Forest Service, Pacific Northwest Research Station, 3625 93rd Ave. SW, Olympia, WA 98512, USA
| | - Rodney B Siegel
- The Institute for Bird Populations, P.O. Box 518, Petaluma, CA 94953, USA
| | - Robert L Wilkerson
- The Institute for Bird Populations, P.O. Box 518, Petaluma, CA 94953, USA
| | - Matthew Johnson
- U.S. National Park Service, Southern Colorado Plateau Network - Inventory & Monitoring Division, 2255 N Gemini Dr, Flagstaff, AZ 86001, USA
| | - Morgan W Tingley
- Ecology and Evolutionary Biology, University of California – Los Angeles, 621 Charles E Young Dr S #951606, Los Angeles, CA 90095, USA
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43
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Genetic structure of endangered species Adenophora liliifolia and footprints of postglacial recolonisation in Central Europe. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01396-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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44
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Pérez-Portela R, Garcia-Cisneros A, Campos-Canet M, Palacín C. Genetic homogeneity, lack of larvae recruitment, and clonality in absence of females across western Mediterranean populations of the starfish Coscinasterias tenuispina. Sci Rep 2021; 11:16819. [PMID: 34413402 PMCID: PMC8376918 DOI: 10.1038/s41598-021-96331-6] [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: 04/27/2021] [Accepted: 08/05/2021] [Indexed: 02/07/2023] Open
Abstract
We here analysed the populations' genetic structure of Coscinasterias tenuispina, an Atlantic-Mediterranean fissiparous starfish, focusing on the western Mediterranean, to investigate: the distribution and prevalence of genetic variants, the relative importance of asexual reproduction, connectivity across the Atlantic-Mediterranean transition, and the potential recent colonisation of the Mediterranean Sea. Individuals from 11 Atlantic-Mediterranean populations of a previous study added to 172 new samples from five new W Mediterranean sites. Individuals were genotyped at 12 microsatellite loci and their gonads histologically analysed for sex determination. Additionally, four populations were genotyped at two-time points. Results demonstrated genetic homogeneity and low clonal richness within the W Mediterranean, due to the dominance of a superclone, but large genetic divergence with adjacent areas. The lack of new genotypes recruitment over time, and the absence of females, confirmed that W Mediterranean populations were exclusively maintained by fission and reinforced the idea of its recent colonization. The existence of different environmental conditions among basins and/or density-depend processes could explain this lack of recruitment from distant areas. The positive correlation between clonal richness and heterozygote excess suggests that most genetic diversity is retained within individuals in the form of heterozygosity in clonal populations, which might increase their resilience.
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Affiliation(s)
- Rocío Pérez-Portela
- grid.5841.80000 0004 1937 0247Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, 643 Diagonal Avenue, 08028 Barcelona, Spain ,grid.5841.80000 0004 1937 0247Research Institute of Biodiversity (IRBIO), University of Barcelona, Barcelona, Spain
| | - Alex Garcia-Cisneros
- grid.5841.80000 0004 1937 0247Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, 643 Diagonal Avenue, 08028 Barcelona, Spain
| | - Marta Campos-Canet
- grid.5841.80000 0004 1937 0247Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, 643 Diagonal Avenue, 08028 Barcelona, Spain
| | - Creu Palacín
- grid.5841.80000 0004 1937 0247Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, 643 Diagonal Avenue, 08028 Barcelona, Spain ,grid.5841.80000 0004 1937 0247Research Institute of Biodiversity (IRBIO), University of Barcelona, Barcelona, Spain
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45
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Ali JR, Fritz U. Origins of Galápagos’ land-locked vertebrates: what, whence, when, how? Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Based on a synthesis of new molecular phylogenetic data, a detailed review is presented for the origins of the Galápagos’ native land-locked vertebrates [42 species; 11 clades: geckos (3), lava lizards (2), giant tortoises (1), iguanas (1), racer snakes (1) and oryzomyine rodents (3)]. Nine groups have roots in coastal Ecuador and Peru and would have been transported to the archipelago on rafts, many on the Humboldt Current. Inferring the sources of the giant tortoises, which probably floated over unaided, and the iguanas is more challenging because their closest living relatives occupy ground remote from the Pacific. Acknowledging uncertainties with the age-dating of both the phylogenetic tree nodes and the landmass emergences, seven, probably eight, of the colonizations likely involved beachings on the modern-day islands within the last 4 Myr. Three, possibly four, of the earlier arrivals may have been on now-submerged landmasses that were created by the Galápagos volcanic hotspot. Alternatively, the true sister taxa of the Galápagos species could be extinct and these colonizations, too, are more recent. This is likely for the giant tortoises. The assembled data set hints at the oldest/youngest clades showing the highest/lowest levels of diversification, although other factors also exert an influence.
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Affiliation(s)
- Jason R Ali
- Department of Earth Sciences, University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Uwe Fritz
- Museum of Zoology, Senckenberg Dresden, Dresden, Germany
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46
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Vranken S, Wernberg T, Scheben A, Severn-Ellis AA, Batley J, Bayer PE, Edwards D, Wheeler D, Coleman MA. Genotype-Environment mismatch of kelp forests under climate change. Mol Ecol 2021; 30:3730-3746. [PMID: 34018645 DOI: 10.1111/mec.15993] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 01/23/2023]
Abstract
Climate change is increasingly impacting ecosystems globally. Understanding adaptive genetic diversity and whether it will keep pace with projected climatic change is necessary to assess species' vulnerability and design efficient mitigation strategies such as assisted adaptation. Kelp forests are the foundations of temperate reefs globally but are declining in many regions due to climate stress. A lack of knowledge of kelp's adaptive genetic diversity hinders assessment of vulnerability under extant and future climates. Using 4245 single nucleotide polymorphisms (SNPs), we characterized patterns of neutral and putative adaptive genetic diversity for the dominant kelp in the southern hemisphere (Ecklonia radiata) from ~1000 km of coastline off Western Australia. Strong population structure and isolation-by-distance was underpinned by significant signatures of selection related to temperature and light. Gradient forest analysis of temperature-linked SNPs under selection revealed a strong association with mean annual temperature range, suggesting adaptation to local thermal environments. Critically, modelling revealed that predicted climate-mediated temperature changes will probably result in high genomic vulnerability via a mismatch between current and future predicted genotype-environment relationships such that kelp forests off Western Australia will need to significantly adapt to keep pace with projected climate change. Proactive management techniques such as assisted adaptation to boost resilience may be required to secure the future of these kelp forests and the immense ecological and economic values they support.
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Affiliation(s)
- Sofie Vranken
- UWA Oceans Institute, Crawley, WA, Australia
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia
| | - Thomas Wernberg
- UWA Oceans Institute, Crawley, WA, Australia
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia
- Institute of Marine Research, His, Norway
| | - Armin Scheben
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | | | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia
| | - Philipp Emanuel Bayer
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia
| | - David Edwards
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia
| | - David Wheeler
- New South Wales Department of Primary Industries, Orange Agricultural Institute, Orange, NSW, Australia
| | - Melinda Ann Coleman
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia
- New South Wales Fisheries, National Marine Science Centre, Coffs Harbour, NSW, Australia
- National Marine Science Centre, Southern Cross University, Coffs Harbour, NSW, Australia
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47
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Fenker J, Tedeschi LG, Melville J, Moritz C. Predictors of phylogeographic structure among codistributed taxa across the complex Australian monsoonal tropics. Mol Ecol 2021; 30:4276-4291. [PMID: 34216506 DOI: 10.1111/mec.16057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 06/16/2021] [Accepted: 06/28/2021] [Indexed: 11/28/2022]
Abstract
Differences in the geographic scale and depth of phylogeographic structure across codistributed taxa can reveal how microevolutionary processes such as population isolation and persistence drive diversification. In turn, environmental heterogeneity, species' traits, and historical biogeographic barriers may influence the potential for isolation and persistence. Using extensive SNP data and a combination of population genetic summary statistics and landscape genomic analyses, we explored predictors of the scale and depth of phylogeographic structure in codistributed lizard taxa from the topographically and climatically complex monsoonal tropics (AMT) of Australia. We first resolved intraspecific lineages and then tested whether genetic divergence across space within lineages is related to isolation by distance, resistance and/or environment and whether these factors differ across genera or between rock-related versus habitat generalist taxa. We then tested whether microevolutionary processes within lineages explain differences in the geographic scale and depth of intraspecific phylogeographic lineages. The results indicated that landscape predictors of phylogeographic structure differ between taxa. Within lineages, there was prevalent isolation by distance, but the strength of isolation by distance is independent of the taxonomic family, habitat specialization, and climate. Isolation by environment is the strongest predictor of landscape-scale genetic divergence for all taxa, with both temperature and precipitation acting as limiting factors. The strength of isolation by distance does not predict the geographic scale of the phylogeographic structure. However, more localized lineages had higher mean individual heterozygosity and less negative Tajima's D. This result implies that finer-scale phylogeographic structuring within species is associated with larger and more stable populations and, hence, persistence.
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Affiliation(s)
- Jessica Fenker
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Leonardo G Tedeschi
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Jane Melville
- Department of Sciences, Museums Victoria, Melbourne, VIC, Australia.,School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Craig Moritz
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, ACT, Australia
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48
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Christie K, Doan JP, Mcbride WC, Strauss SY. Asymmetrical reproductive barriers in sympatric jewelflowers: are floral isolation, genetic incompatibilities and floral trait displacement connected? Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Floral visitors influence reproductive interactions among sympatric plant species, either by facilitating assortative mating and contributing to reproductive isolation, or by promoting heterospecific pollen transfer, potentially leading to reproductive interference or hybridization. We assessed preference and constancy of floral visitors on two co-occurring jewelflowers [Streptanthus breweri and Streptanthus hesperidis (Brassicaceae)] using field arrays, and quantified two floral rewards potentially important to foraging choice – pollen production and nectar sugar concentration – in a greenhouse common garden. Floral visitors made an abundance of conspecific transitions between S. breweri individuals, which thus experienced minimal opportunities for heterospecific pollen transfer from S. hesperidis. In contrast, behavioural isolation for S. hesperidis was essentially absent due to pollinator inconstancy. This pattern emerged across multiple biotic environments and was unrelated to local density dependence. S. breweri populations that were sympatric with S. hesperidis had higher nectar sugar concentrations than their sympatric congeners, as well as allopatric conspecifics. Previous work shows that S. breweri suffers a greater cost to hybridization than S. hesperidis, and here we find that it also shows asymmetrical floral isolation and floral trait displacement in sympatry. These findings suggest that trait divergence may reduce negative reproductive interactions between sympatric but genetically incompatible relatives.
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Affiliation(s)
- Kyle Christie
- Department of Evolution and Ecology, University of California Davis, One Shields Avenue, Davis, CA, USA
- Center for Population Biology, University of California Davis, One Shields Avenue, Davis, CA, USA
| | - Jonathan P Doan
- Department of Evolution and Ecology, University of California Davis, One Shields Avenue, Davis, CA, USA
| | - Wendy C Mcbride
- Deaver Herbarium, Northern Arizona University, Flagstaff, AZ, USA
| | - Sharon Y Strauss
- Department of Evolution and Ecology, University of California Davis, One Shields Avenue, Davis, CA, USA
- Center for Population Biology, University of California Davis, One Shields Avenue, Davis, CA, USA
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49
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Wang X, Yi T, Li W, Xu C, Wang S, Wang Y, Li Y, Liu X. Anthropogenic habitat loss accelerates the range expansion of a global invader. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13359] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Xuyu Wang
- Key Laboratory of Animal Ecology and Conservation Biology Institute of Zoology Chinese Academy of Sciences Beijing China
- Institute of Physical Science and Information Technology Anhui University Hefei China
| | - Tao Yi
- College of Biological Sciences and Biotechnology Beijing Forestry University Beijing China
| | - Wenhao Li
- Key Laboratory of Animal Ecology and Conservation Biology Institute of Zoology Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Chunxia Xu
- Key Laboratory of Animal Ecology and Conservation Biology Institute of Zoology Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Supen Wang
- Key Laboratory of Animal Ecology and Conservation Biology Institute of Zoology Chinese Academy of Sciences Beijing China
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources College of Life Sciences Anhui Normal University Wuhu China
| | - Yanping Wang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology College of Life Sciences Nanjing Normal University Nanjing China
| | - Yiming Li
- Key Laboratory of Animal Ecology and Conservation Biology Institute of Zoology Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Xuan Liu
- Key Laboratory of Animal Ecology and Conservation Biology Institute of Zoology Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
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50
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Magota K, Sakaguchi S, Lee JS, Yamamoto M, Takahashi D, Nagano AJ, Setoguchi H. Phylogeographic analysis of Saxifraga fortunei complex (Saxifragaceae) reveals multiple origins of morphological and ecological variations in the Japanese Archipelago. Mol Phylogenet Evol 2021; 163:107230. [PMID: 34133947 DOI: 10.1016/j.ympev.2021.107230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 06/04/2021] [Accepted: 06/11/2021] [Indexed: 11/28/2022]
Abstract
Phenotypic polymorphism within a species is a notable phenomenon in evolutionary biology to understand the process of adaptive speciation and other historical events. The Saxifraga fortunei complex is a widespread herb found in East Asia. It includes several ecotypic taxa corresponding to their habitat environments. The distribution of the various ecotypes in a limited area of the Japanese Archipelago makes the species a suitable model to investigate the impact of population demographic history and natural selection on lineage diversification. Here, Sanger-based sequencing was used to estimate the divergence timeframe between populations of the Eurasian continent and Japan. Genome-wide SNPs obtained by ddRAD sequencing were used to investigate the phylogeographic origins of ecotypic taxa. The phylogenetic analyses revealed the divergence of the Japanese population from the continental population in the late Miocene. Two distinct regional clades of North and South Japan were identified; phenotypic diversification was evident only in the southern clade. The South Japan clades displayed a historical distribution expansion from north to south. The phenotypic variations appeared to have generated during the expansion. The ecotypic boundaries were incongruent with the genetic grouping. We propose that morphological and ecological specialization in Japanese populations was repeatedly generated by local natural selection.
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Affiliation(s)
- Kana Magota
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida Nihonmatsu-cho, Sakyo-ku, Kyoto, Kyoto 606-8501, Japan.
| | - Shota Sakaguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida Nihonmatsu-cho, Sakyo-ku, Kyoto, Kyoto 606-8501, Japan
| | - Jung-Sim Lee
- Korean National Arboretum, 415 Gwangneung Sumokwon-ro, Soheul-eup, Pocheon-si, Gyeonggi-Province 11186, Republic of Korea
| | - Masaya Yamamoto
- Hyogo University of Teacher Education, 942-1 Shimokume, Kato, Hyogo 673-1494, Japan
| | - Daiki Takahashi
- Kawatabi Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu, Shiga 520-2194, Japan
| | - Hiroaki Setoguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida Nihonmatsu-cho, Sakyo-ku, Kyoto, Kyoto 606-8501, Japan
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