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Comita LS, Jones FA, Manzané-Pinzón EJ, Álvarez-Casino L, Cerón-Souza I, Contreras B, Jaén-Barrios N, Ferro N, Engelbrecht BMJ. Limited intraspecific variation in drought resistance along a pronounced tropical rainfall gradient. Proc Natl Acad Sci U S A 2024; 121:e2316971121. [PMID: 38809703 PMCID: PMC11161779 DOI: 10.1073/pnas.2316971121] [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: 09/29/2023] [Accepted: 04/08/2024] [Indexed: 05/31/2024] Open
Abstract
Assessing within-species variation in response to drought is crucial for predicting species' responses to climate change and informing restoration and conservation efforts, yet experimental data are lacking for the vast majority of tropical tree species. We assessed intraspecific variation in response to water availability across a strong rainfall gradient for 16 tropical tree species using reciprocal transplant and common garden field experiments, along with measurements of gene flow and key functional traits linked to drought resistance. Although drought resistance varies widely among species in these forests, we found little evidence for within-species variation in drought resistance. For the majority of functional traits measured, we detected no significant intraspecific variation. The few traits that did vary significantly between drier and wetter origins of the same species all showed relationships opposite to expectations based on drought stress. Furthermore, seedlings of the same species originating from drier and wetter sites performed equally well under drought conditions in the common garden experiment and at the driest transplant site. However, contrary to expectation, wetter-origin seedlings survived better than drier-origin seedlings under wetter conditions in both the reciprocal transplant and common garden experiment, potentially due to lower insect herbivory. Our study provides the most comprehensive picture to date of intraspecific variation in tropical tree species' responses to water availability. Our findings suggest that while drought plays an important role in shaping species composition across moist tropical forests, its influence on within-species variation is limited.
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Affiliation(s)
- Liza S. Comita
- The Forest School, Yale School of the Environment, Yale University, New Haven, CT06511
- Smithsonian Tropical Research InstituteApartadoPostal 0843-03092, Panama City, Panamá
| | - F. Andrew Jones
- Smithsonian Tropical Research InstituteApartadoPostal 0843-03092, Panama City, Panamá
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR
| | - Eric J. Manzané-Pinzón
- Smithsonian Tropical Research InstituteApartadoPostal 0843-03092, Panama City, Panamá
- Departamento de Ciencias Naturales, Facultad de Ciencias y Tecnología, Universidad Tecnológica de Panamá, Panama City, Panamá
| | - Leonor Álvarez-Casino
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, Seville, Spain
- Department of Plant Ecology, Center for Ecology and Environmental Research, University of Bayreuth, Bayreuth, Germany
| | - Ivania Cerón-Souza
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR
- Centro de Investigación Tibaitatá, Mosquera Corporación Colombiana de Investigación Agropecuaria (Agrosavia), Cundinamarca250047, Colombia
| | - Blexein Contreras
- Smithsonian Tropical Research InstituteApartadoPostal 0843-03092, Panama City, Panamá
| | - Nelson Jaén-Barrios
- Smithsonian Tropical Research InstituteApartadoPostal 0843-03092, Panama City, Panamá
- Department of Plant Biology, Institute of Biology, University of Campinas, CampinasCEP 13083-970, SP, Brazil
| | - Natalie Ferro
- Smithsonian Tropical Research InstituteApartadoPostal 0843-03092, Panama City, Panamá
| | - Bettina M. J. Engelbrecht
- Smithsonian Tropical Research InstituteApartadoPostal 0843-03092, Panama City, Panamá
- Department of Plant Ecology, Center for Ecology and Environmental Research, University of Bayreuth, Bayreuth, Germany
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Lowe WH, Addis BR, Cochrane MM. Outbreeding reduces survival during metamorphosis in a headwater stream salamander. Mol Ecol 2024; 33:e17375. [PMID: 38699973 DOI: 10.1111/mec.17375] [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: 03/06/2023] [Revised: 02/22/2024] [Accepted: 03/01/2024] [Indexed: 05/05/2024]
Abstract
Assessing direct fitness effects of individual genetic diversity is challenging due to the intensive and long-term data needed to quantify survival and reproduction in the wild. But resolving these effects is necessary to determine how inbreeding and outbreeding influence eco-evolutionary processes. We used 8 years of capture-recapture data and single nucleotide polymorphism genotypes for 1906 individuals to test for effects of individual heterozygosity on stage-specific survival probabilities in the salamander Gyrinophilus porphyriticus. The life cycle of G. porphyriticus includes an aquatic larval stage followed by metamorphosis into a semi-aquatic adult stage. In our study populations, the larval stage lasts 6-10 years, metamorphosis takes several months, and lifespan can reach 20 years. Previous studies showed that metamorphosis is a sensitive life stage, leading us to predict that fitness effects of individual heterozygosity would occur during metamorphosis. Consistent with this prediction, monthly probability of survival during metamorphosis declined with multi-locus heterozygosity (MLH), from 0.38 at the lowest MLH (0.10) to 0.06 at the highest MLH (0.38), a reduction of 84%. Body condition of larvae also declined significantly with increasing MLH. These relationships were consistent in the three study streams. With evidence of localised inbreeding within streams, these results suggest that outbreeding disrupts adaptations in pre-metamorphic and metamorphic individuals to environmental gradients along streams, adding to evidence that headwater streams are hotspots of microgeographic adaptation. Our results also underscore the importance of incorporating life history in analyses of the fitness effects of individual genetic diversity and suggest that metamorphosis and similar discrete life stage transitions may be critical periods of viability selection.
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Affiliation(s)
- Winsor H Lowe
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Brett R Addis
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Madaline M Cochrane
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
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Sgambelluri LR, Jarvis JC, Kamel SJ. Multiple paternity, fertilization success, and male quality: Mating system variation in the eelgrass, Zostera marina. Ecol Evol 2024; 14:e11608. [PMID: 38919644 PMCID: PMC11197038 DOI: 10.1002/ece3.11608] [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: 02/14/2024] [Revised: 05/31/2024] [Accepted: 06/05/2024] [Indexed: 06/27/2024] Open
Abstract
Genetic diversity can modulate a population's response to a changing environment and plays a critical role in its ecological function. While multiple processes act to maintain genetic diversity, sexual reproduction remains the primary driving force. Eelgrass (Zostera marina) is an important habitat-forming species found in temperate coastal ecosystems across the globe. Recent increases in sea surface temperatures have resulted in shifts to a mixed-annual life-history strategy (i.e., displaying characteristics of both annual and perennial meadows) at its southern edge-of-range. Given that mating systems are intimately linked to standing levels of genetic variation, understanding the scope of sexual reproduction can illuminate the processes that shape genetic diversity. To characterize edge-of-range eelgrass mating systems, developing seeds on flowering Z. marina shoots were genotyped from three meadows in Topsail, North Carolina. In all meadows, levels of multiple mating were high, with shoots pollinated by an average of eight sires (range: 3-16). The number of fertilized seeds (i.e., reproductive success) varied significantly across sires (range: 1-25) and was positively correlated with both individual heterozygosity and self-fertilization. Outcrossing rates were high (approx. 70%) and varied across spathes. No clones were detected, and kinship among sampled flowering shoots was low, supporting observed patterns of reproductive output. Given the role that genetic diversity plays in enhancing resistance to and resilience from ecological disturbance, disentangling the links between life history, sexual reproduction, and genetic variation will aid in informing the management and conservation of this key foundation species.
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Affiliation(s)
- Lauren R. Sgambelluri
- Department of Biology and Marine Biology, Center for Marine ScienceUniversity of North Carolina WilmingtonWilmingtonNorth CarolinaUSA
| | - Jessie C. Jarvis
- Department of Biology and Marine Biology, Center for Marine ScienceUniversity of North Carolina WilmingtonWilmingtonNorth CarolinaUSA
| | - Stephanie J. Kamel
- Department of Biology and Marine Biology, Center for Marine ScienceUniversity of North Carolina WilmingtonWilmingtonNorth CarolinaUSA
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Sochor M, Duchoslav M, Forejtová V, Hroneš M, Konečná M, Trávníček B. Distinct geographic parthenogenesis in spite of niche conservatism and a single ploidy level: A case of Rubus ser. Glandulosi (Rosaceae). THE NEW PHYTOLOGIST 2024; 242:1348-1362. [PMID: 38407427 DOI: 10.1111/nph.19618] [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: 01/18/2024] [Accepted: 02/06/2024] [Indexed: 02/27/2024]
Abstract
Asexual organisms often differ in their geographic distributions from their sexual relatives. This phenomenon, termed geographic parthenogenesis, has long been known, but the underlying factors behind its diverse patterns have been under dispute. Particularly problematic is an association between asexuality and polyploidy in most taxa. Here, we present a new system of geographic parthenogenesis on the tetraploid level, promising new insights into this complex topic. We used flow cytometric seed screen and microsatellite genotyping to characterise the patterns of distribution of sexuals and apomicts and genotypic distributions in Rubus ser. Glandulosi across its range. Ecological modelling and local-scale vegetation and soil analyses were used to test for niche differentiation between the reproductive groups. Apomicts were detected only in North-western Europe, sexuals in the rest of the range in Europe and West Asia, with a sharp borderline stretched across Central Europe. Despite that, we found no significant differences in ecological niches. Genotypic richness distributions suggested independence of the reproductive groups and a secondary contact. We argue that unless a niche differentiation (resulting from polyploidy and/or hybridity) evolves, the main factors behind the patterns of geographic parthenogenesis in plants are phylogeographic history and neutral microevolutionary processes, such as clonal turnover.
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Affiliation(s)
- Michal Sochor
- Centre of the Region Haná for Biotechnological and Agricultural Research, Crop Research Institute, Šlechtitelů 29, Olomouc, 78371, Czech Republic
| | - Martin Duchoslav
- Plant Biosystematics and Ecology Research Group, Department of Botany, Faculty of Science, Palacký University, Šlechtitelů 27, Olomouc, 78371, Czech Republic
| | - Věra Forejtová
- Plant Biosystematics and Ecology Research Group, Department of Botany, Faculty of Science, Palacký University, Šlechtitelů 27, Olomouc, 78371, Czech Republic
- Station of Apple Breeding for Disease Resistance, Institute of Experimental Botany, Czech Academy of Sciences, Rozvojová 313, Prague 6-Lysolaje, 16502, Czech Republic
| | - Michal Hroneš
- Plant Biosystematics and Ecology Research Group, Department of Botany, Faculty of Science, Palacký University, Šlechtitelů 27, Olomouc, 78371, Czech Republic
| | - Michaela Konečná
- Plant Biosystematics and Ecology Research Group, Department of Botany, Faculty of Science, Palacký University, Šlechtitelů 27, Olomouc, 78371, Czech Republic
| | - Bohumil Trávníček
- Plant Biosystematics and Ecology Research Group, Department of Botany, Faculty of Science, Palacký University, Šlechtitelů 27, Olomouc, 78371, Czech Republic
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Schmidt DA, Galbreath KE, Russello MA. Phylogenomics of American pika (Ochotona princeps) lineage diversification. Mol Phylogenet Evol 2024; 193:108030. [PMID: 38341008 DOI: 10.1016/j.ympev.2024.108030] [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: 10/04/2023] [Revised: 01/31/2024] [Accepted: 02/05/2024] [Indexed: 02/12/2024]
Abstract
Quaternary climate oscillations have profoundly influenced current species distributions. For many montane species, these fluctuations were a prominent driver in species range shifts, often resulting in intraspecific diversification, as has been the case for American pikas (Ochotona princeps). Range shifts and population declines in this thermally-sensitive lagomorph have been linked to historical and contemporary environmental changes across its western North American range, with previous research reconstructing five mitochondrial DNA lineages. Here, we paired genome-wide data (25,244 SNPs) with range-wide sampling to re-examine the number and distribution of intra-specific lineages, and investigate patterns of within- and among-lineage divergence and diversity. Our results provide genomic evidence of O. princeps monophyly, reconstructing six distinct lineages that underwent multiple rounds of divergence (0.809-2.81 mya), including a new Central Rocky Mountain lineage. We further found evidence for population differentiation across multiple spatial scales, and reconstructed levels of standing variation comparable to those found in other small mammals. Overall, our findings demonstrate the influence of past glacial cycles on O. princeps lineage diversification, suggest that current subspecific taxonomy may need to be revisited, and provide an important framework for investigations of American pika adaptive potential in the face of anthropogenic climate change.
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Affiliation(s)
- Danielle A Schmidt
- Department of Biology, The University of British Columbia, Kelowna, BC, Canada
| | - Kurt E Galbreath
- Department of Biology, Northern Michigan University, Marquette, MI, USA
| | - Michael A Russello
- Department of Biology, The University of British Columbia, Kelowna, BC, Canada.
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Pejhanmehr M, Kantar MB, Yorkston M, Morden CW. Population genetics of Sida fallax Walp. (Malvaceae) in the Hawaiian Islands. FRONTIERS IN PLANT SCIENCE 2024; 15:1304078. [PMID: 38495376 PMCID: PMC10941843 DOI: 10.3389/fpls.2024.1304078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 02/12/2024] [Indexed: 03/19/2024]
Abstract
Introduction Sida fallax (Malvaceae) is the most widespread and variable taxon of Malvaceae in the Hawaiian Islands, growing with a diversity of morphological forms in different habitats including Midway Atoll, Nihoa, and all the main islands. Morphological variation exists within and among populations. The study aimed to investigate the genetic variation within and among populations from various habitats and geographic locations throughout the Hawaiian range of S. fallax. Methods A total of 124 samples, with up to five samples per population where possible, were collected from 26 populations across six of the main Hawaiian Islands (Kaua'i, O'ahu, Maui, Moloka'i, Lāna'i, and Hawai'i) and Nihoa in the Northwestern Hawaiian Islands. The sampling strategy encompassed collecting populations from different habitats and geographic locations, including coastal and mountain ecotypes, with many intermediate morphological forms. Multiplexed ISSR genotyping by sequencing (MIG-seq) was used to detect single nucleotide polymorphisms (SNP) and genetic differences among individuals and populations were evaluated using PCO analyses. Results The relationship of FST with the geographical distance between the populations was assessed using the Mantel test. The results showed that populations on a single island were more closely related to each other and to populations on islands within their respective groups than they were to populations on other islands. Discussion The overall genetic relationships among islands were, to a large extent, predictive based on island position within the chain and, to a lesser extent, within island topography.
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Affiliation(s)
| | - Michael Benjamin Kantar
- Department of Tropical Plant and Soil Sciences, University of Hawaiʻi, Honolulu, HI, United States
| | - Mitsuko Yorkston
- School of Life Sciences, University of Hawaiʻi, Honolulu, HI, United States
| | - Clifford W. Morden
- School of Life Sciences, University of Hawaiʻi, Honolulu, HI, United States
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Reutemann AV, Honfi AI, Karunarathne P, Eckers F, Hojsgaard DH, Martínez EJ. Comparative analysis of molecular and morphological diversity in two diploid Paspalum species (Poaceae) with contrasting mating systems. PLANT REPRODUCTION 2024; 37:15-32. [PMID: 37566236 DOI: 10.1007/s00497-023-00478-3] [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: 03/15/2023] [Accepted: 07/22/2023] [Indexed: 08/12/2023]
Abstract
KEY MESSAGE Interspecific comparison of two Paspalum species has demonstrated that mating systems (selfing and outcrossing) contribute to variation (genetically and morphologically) within species through similar but mutually exclusive processes. Mating systems play a key role in the genetic dynamics of populations. Studies show that populations of selfing plants have less genetic diversity than outcrossing plants. Yet, many such studies have ignored morphological diversity. Here, we compared the morphological and molecular diversity patterns in populations of two phylogenetically-related sexual diploids that differ in their mating system: self-sterile Paspalum indecorum and self-fertile P. pumilum. We assessed the morphological variation using 16 morpho-phenological characters and the molecular diversity using three combinations of AFLPs. We compared the morphological and molecular diversity within and among populations in each mating system. Contrary to expectations, selfers showed higher morphological variation within populations, mainly in vegetative and phenological traits, compared to outcrossers. The high morphological variation within populations of selfers led to a low differentiation among populations. At molecular level, selfing populations showed lower levels of genotypic and genetic diversity than outcrossing populations. As expected, selfers showed higher population structure than outcrossers (PhiST = 0.301 and PhiST = 0.108, respectively). Increased homozygous combinations for the same trait/locus enhance morphological variation and reduce molecular variation within populations in selfing P. pumilum. Thus, selfing outcomes are opposite when comparing morphological and molecular variation in P. pumilum. Meanwhile, pollen flow in obligate outcrossing populations of P. indecorum increases within-population molecular variation, but tends to homogenize phenotypes within-population. Pollen flow in obligate outcrossers tends to merge geographically closer populations; but isolation by distance can lead to a weak differentiation among distant populations of P. indecorum.
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Affiliation(s)
- A Verena Reutemann
- Instituto de Botánica del Nordeste (IBONE-CONICET-UNNE), Facultad de Ciencias Agrarias, Universidad Nacional del Nordeste (FCA-UNNE), 3400, Corrientes, Argentina
| | - Ana I Honfi
- Programa de Estudios Florísticos y Genética Vegetal, Instituto de Biología Subtropical (PEFyGV, IBS-UNaM-CONICET), 3300, Posadas, Argentina
| | - Piyal Karunarathne
- Department of Systematics, Biodiversity and Evolution of Plants, Albrecht-Von-Haller Institute for Plant Sciences, University of Goettingen, 37073, Goettingen, Germany
- Institute for Population Genetics, Heinrich Heine University, 40225, Düsseldorf, Germany
| | - Fabiana Eckers
- Programa de Estudios Florísticos y Genética Vegetal, Instituto de Biología Subtropical (PEFyGV, IBS-UNaM-CONICET), 3300, Posadas, Argentina
| | - Diego H Hojsgaard
- Taxonomy and Evolutionary Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany
| | - Eric J Martínez
- Instituto de Botánica del Nordeste (IBONE-CONICET-UNNE), Facultad de Ciencias Agrarias, Universidad Nacional del Nordeste (FCA-UNNE), 3400, Corrientes, Argentina.
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Rengefors K, Annenkova N, Wallenius J, Svensson M, Kremp A, Ahrén D. Population genomic analyses reveal that salinity and geographic isolation drive diversification in a free-living protist. Sci Rep 2024; 14:4986. [PMID: 38424140 PMCID: PMC10904836 DOI: 10.1038/s41598-024-55362-5] [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: 11/13/2023] [Accepted: 02/22/2024] [Indexed: 03/02/2024] Open
Abstract
Protists make up the vast diversity of eukaryotic life and play a critical role in biogeochemical cycling and in food webs. Because of their small size, cryptic life cycles, and large population sizes, our understanding of speciation in these organisms is very limited. We performed population genomic analyses on 153 strains isolated from eight populations of the recently radiated dinoflagellate genus Apocalathium, to explore the drivers and mechanisms of speciation processes. Species of this genus inhabit both freshwater and saline habitats, lakes and seas, and are found in cold temperate environments across the world. RAD sequencing analyses revealed that the populations were overall highly differentiated, but morphological similarity was not congruent with genetic similarity. While geographic isolation was to some extent coupled to genetic distance, this pattern was not consistent. Instead, we found evidence that the environment, specifically salinity, is a major factor in driving ecological speciation in Apocalathium. While saline populations were unique in loci coupled to genes involved in osmoregulation, freshwater populations appear to lack these. Our study highlights that adaptation to freshwater through loss of osmoregulatory genes may be an important speciation mechanism in free-living aquatic protists.
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Affiliation(s)
- Karin Rengefors
- Department of Biology, Lund University, 223 62, Lund, Sweden.
| | - Nataliia Annenkova
- Department of Biology, Lund University, 223 62, Lund, Sweden
- Institute of Cytology of the Russian Academy of Science, Tikhoretsky Avenue 4, St. Petersburg, 194064, Russia
| | - Joel Wallenius
- Department of Biology, Lund University, 223 62, Lund, Sweden
- Department of Clinical Sciences, Faculty of Medicine, Lund University, 223 62, Lund, Sweden
| | - Marie Svensson
- Department of Biology, Lund University, 223 62, Lund, Sweden
| | - Anke Kremp
- Biology Department, Leibniz Institute for Baltic Sea Research Warnemuende, Seestr. 15, 18119, Rostock, Germany
| | - Dag Ahrén
- Department of Biology, Lund University, 223 62, Lund, Sweden
- National Bioinformatics Infrastructure Sweden (NBIS), SciLifeLab, Department of Biology, Lund University, Lund, Sweden
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Mahdieh M, Talebi SM, Dehghan T, Tabaripour R, Matsyura A. Molecular genetics, seed morphology and fatty acids diversity in castor (Ricinus communis L., Euphorbiaceae) Iranian populations. Mol Biol Rep 2023; 50:9859-9873. [PMID: 37848759 DOI: 10.1007/s11033-023-08904-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 10/06/2023] [Indexed: 10/19/2023]
Abstract
BACKGROUND Castor (Ricinus communis L.) seeds contain a large amount of oil that has several biological activities. In the current research, phytogeographic distribution, seed morphological characteristics, molecular genetic diversity and structure, and fatty acid composition were investigated in nine Iranian castor populations. METHODS AND RESULTS The cetyltrimethylammonium bromide (CTAB) protocol was used to extract the nuclear genomes. These were later amplified using 13 SCoT molecular primers. The phytogeographic distribution was determined based on the Zohary mapping, GC apparatus determined the fatty acid composition of the seeds. GenAlex, STRUCTURE, GenoDive, PopGene, and PopART software were used for the statistical analyzes. On phytogeographic mapping, the harvested populations belonged to different districts of the Euro-Siberian and Irano-Turanian regions (Holarctic kingdom). Most of the quantitative morphological traits of the seeds differed significantly (P ≤ 0.05) between the populations. The AMOVA test demonstrated a large proportion of significant genetic diversity assigned among populations, which were approved by some estimated parameters of genetic diversity such as Nm, Ht, Hs, and Gst. Nei's genetic distance and structure analysis confirmed the existence of two main genotype groups and some intermediates. However, there was no isolation by distance between the genotypes. Unsaturated fatty acids were detected as the main component of seed oil with linoleic and ricinoleic acids. Significant correlations were detected between the main fatty acids of seed oil with seed morphological traits, geographic distance and the geographic parameters of habitats. According to the composition of the seed fatty acids, four chemotypes groups were detected. CONCLUSIONS The classification patterns of the populations based on molecular genetic data, fatty acid composition, and phytogeographic mapping were not identical. These findings indicated that Iranian castor populations had unusual seed fatty acid composition which strongly depended on habitat geographic factors and seed morphological traits. However, the identified chemotypes and genotypes can be used in future breeding programs.
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Affiliation(s)
- Majid Mahdieh
- Department of Biology, Faculty of Sciences, Arak University, Arak, 38156-8-8349, Iran
| | - Seyed Mehdi Talebi
- Department of Biology, Faculty of Sciences, Arak University, Arak, 38156-8-8349, Iran.
| | - Tahereh Dehghan
- Department of Biology, Faculty of Sciences, Arak University, Arak, 38156-8-8349, Iran
| | - Raheleh Tabaripour
- Department of Plant Sciences, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
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Graham BA, Szabo I, Cicero C, Strickland D, Woods J, Coneybeare H, Dohms KM, Burg TM. Habitat and climate influence hybridization among three genetically distinct Canada jay (Perisoreus canadensis) morphotypes in an avian hybrid zone complex. Heredity (Edinb) 2023; 131:361-373. [PMID: 37813941 PMCID: PMC10674025 DOI: 10.1038/s41437-023-00652-3] [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: 04/21/2023] [Revised: 09/22/2023] [Accepted: 09/27/2023] [Indexed: 10/11/2023] Open
Abstract
Examining the frequency and distribution of hybrids across contact zones provide insights into the factors mediating hybridization. In this study, we examined the effect of habitat and climate on hybridization patterns for three phenotypically, genetically, and ecologically distinct groups of the Canada jay (Perisoreus canadensis) in a secondary contact zone in western North America. Additionally, we tested whether the frequency of hybridization involving the three groups (referred to as Boreal, Pacific and Rocky Mountain morphotypes) is similar across the hybrid zones or whether some pairs have hybridized more frequently than others. We reanalyzed microsatellite, mtDNA and plumage data, and new microsatellite and plumage data for 526 individuals to identify putative genetic and phenotypic hybrids. The genetically and phenotypically distinct groups are associated with different habitats and occupy distinct climate niches across the contact zone. Most putative genetic hybrids (86%) had Rocky Mountain ancestry. Hybrids were observed most commonly in intermediate climate niches and in habitats where Engelmann spruce (Picea engelmannii) overlaps broadly with boreal and subalpine tree species. Our finding that hybrids occupy intermediate climate niches relative to parental morphotypes matches patterns for other plant and animal species found in this region. This study demonstrates how habitat and climate influence hybridization patterns in areas of secondary contact and adds to the growing body of research on tri-species hybrid zones.
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Affiliation(s)
- B A Graham
- Department of Biological Sciences, University of Lethbridge, 4401 University Drive W, Lethbridge, AB, T1K 3M4, Canada.
| | - I Szabo
- Beaty Biodiversity Museum, University of British Columbia, 2212 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - C Cicero
- Museum of Vertebrate Zoology, University of California, 3101 Valley Life Sciences Building, Berkeley, CA, 94720-3160, USA
| | - D Strickland
- 1063 Oxtongue Lake Road, Dwight, ON, P0A 1H0, Canada
| | - J Woods
- 1221 23rd Avenue SW, Salmon Arm, BC, V1E 0A9, Canada
| | - H Coneybeare
- 5210 Frederick Road, Armstrong, BC, V0E 1B4, Canada
| | - K M Dohms
- Canadian Wildlife Services, Environment and Climate Change Canada, 5421 Robertson Road, Delta, BC, V4K 3N2, Canada
| | - T M Burg
- Department of Biological Sciences, University of Lethbridge, 4401 University Drive W, Lethbridge, AB, T1K 3M4, Canada
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Coleman JL, Wyffels JT, Penfold LM, Richardson D, Maddox JD. Development of genetic markers for reproductive management of toucans. Zoo Biol 2023; 42:825-833. [PMID: 37338091 DOI: 10.1002/zoo.21792] [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: 05/07/2022] [Revised: 04/26/2023] [Accepted: 06/08/2023] [Indexed: 06/21/2023]
Abstract
Retention of genetic diversity in successive generations is key to successful ex situ programs and will become increasingly important to restore wild populations of threatened animals. When animal genealogy is partly unknown or gaps exist in studbook records, the application of molecular resources facilitates informed breeding. Here, we apply molecular resources to an ex situ breeding population of toucans (Ramphastidae), a bird family zoos commonly maintain. Toucans face population declines from illegal poaching and habitat degradation. We developed novel microsatellite markers using blood samples from 15 Keel-billed Toucans (Ramphastos sulfuratus Lesson 1830). Parentage of two individuals was known a priori, but possible sibship among 13 putative founders-including the parents-was unknown. We compared available avian heterologous and novel microsatellite markers to recover known relationships and reconstruct sibship. Eight of 61 heterologous markers amplified consistently and were polymorphic, but less so than the 18 novel markers. Known sibship (and three sibling pairs whose relatedness was unknown a priori) and paternity-though not maternity except in one case-were well-recovered using both likelihood and pairwise relatedness methods, when incorporating novel but not heterologous markers. Zoo researchers seeking microsatellite primer sets for their breeding toucan populations will likely benefit from our heterologous markers, which can be leveraged both to assess relatedness and select breeding pairs. We recommend that zoo biologists rely on species-specific primers and not optimize heterologous primers for toucan species without molecular resources. We conclude with a brief discussion of modern genotyping methods of interest to zoo researchers.
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Affiliation(s)
- Jeffrey L Coleman
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois, USA
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA
| | - Jennifer T Wyffels
- Center for Bioinformatics & Computational Biology, University of Delaware, Newark, Delaware, USA
- Ripley's Aquariums, Orlando, Florida, USA
| | - Linda M Penfold
- South-East Zoo Alliance for Reproduction & Conservation, Yulee, Florida, USA
| | | | - J Dylan Maddox
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois, USA
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12
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Wang C, Yap ZY, Wan P, Chen K, Folk RA, Damrel DZ, Barger W, Diamond A, Horn C, Landry GP, Samarakoon T, Harvey S, Morgan DR, Qiu Y, Li P. Molecular phylogeography and historical demography of a widespread herbaceous species from eastern North America, Podophyllum peltatum. AMERICAN JOURNAL OF BOTANY 2023; 110:e16254. [PMID: 37938809 DOI: 10.1002/ajb2.16254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 11/10/2023]
Abstract
PREMISE Glacial/interglacial cycles and topographic complexity are both considered to have shaped today's diverse phylogeographic patterns of taxa from unglaciated eastern North America (ENA). However, few studies have focused on the phylogeography and population dynamics of wide-ranging ENA herbaceous species occurring in forest understory habitat. We examined the phylogeographic pattern and evolutionary history of Podophyllum peltatum L., a widely distributed herb inhabiting deciduous forests of ENA. METHODS Using chloroplast DNA (cpDNA) sequences and nuclear microsatellite loci, we investigated the population structure and genetic diversity of the species. Molecular dating, demographic history analyses, and ecological niche modeling were also performed to illustrate the phylogeographic patterns. RESULTS Our cpDNA results identified three main groups that are largely congruent with boundaries along the Appalachian Mountains and the Mississippi River, two major geographic barriers in ENA. Populations located to the east of the Appalachians and along the central Appalachians exhibited relatively higher levels of genetic diversity. Extant lineages may have diverged during the late Miocene, and range expansions of different groups may have happened during the Pleistocene glacial/interglacial cycles. CONCLUSIONS Our findings indicate that geographic barriers may have started to facilitate the population divergence in P. peltatum before the Pleistocene. Persistence in multiple refugia, including areas around the central Appalachians during the Quaternary glacial period, and subsequent expansions under hospitable climatic condition, especially westward expansion, are likely responsible for the species' contemporary genetic structure and phylogeographic pattern.
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Affiliation(s)
- Chenxi Wang
- Systematic & Evolutionary Botany and Biodiversity group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Zhao-Yan Yap
- Systematic & Evolutionary Botany and Biodiversity group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Penglei Wan
- Systematic & Evolutionary Botany and Biodiversity group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Kuangqi Chen
- Systematic & Evolutionary Botany and Biodiversity group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Ryan A Folk
- Department of Biological Sciences, Mississippi State University, Starkville, Mississippi, 39762, USA
| | - Dixie Z Damrel
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, 29634-0314, USA
| | - Wayne Barger
- Department of Conservation and Natural Resources, State Lands Division, Natural Heritage Section, Montgomery, Alabama, 36130, USA
| | - Alvin Diamond
- Department of Biological and Environmental Sciences, Troy University, Troy, Alabama, 36082, USA
| | - Charles Horn
- Department of Sciences and Mathematics, Newberry College, Newberry, South Carolina, 29108, USA
| | | | | | - Stephanie Harvey
- Department of Biology, Georgia Southwestern State University, Americus, Georgia, 31709-4376, USA
| | - David R Morgan
- Department of Natural Sciences, University of West Georgia, Carrollton, Georgia, 30118-2220, USA
| | - Yingxiong Qiu
- Systematic & Evolutionary Botany and Biodiversity group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- Plant Biodiversity Research Centre, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Pan Li
- Systematic & Evolutionary Botany and Biodiversity group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
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13
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Weaver MA, Bowen C, Park LC, Bastidas A, Drewry SG, Mandel JR. Genetic Diversity of Aspergillus flavus on Maize in Guatemala. Foods 2023; 12:3864. [PMID: 37893757 PMCID: PMC10606850 DOI: 10.3390/foods12203864] [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: 09/12/2023] [Revised: 10/06/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
Aflatoxin contamination of maize is a leading threat to health in Guatemala. This contamination is the result of infection from Aspergillus flavus and has been effectively reduced in other countries through application of nonaflatoxigenic, indigenous strains of A. flavus. We collected 82 maize samples from throughout Guatemala in two years and isolated 272 A. flavus from these samples, including 126 unique genotypes. We provide here a phenotypic and simple sequence repeat (SSR)-based genotypic description of these isolates, as well as an analysis of the diversity of this population. High levels of genetic diversity were observed with the nonaflatoxigenic isolates in this study, but this information contributes to the development of indigenous aflatoxin biocontrol products.
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Affiliation(s)
- Mark A. Weaver
- USDA ARS National Biological Control Laboratory, 59 Lee Road, Stoneville, MS 38776, USA;
| | - Curt Bowen
- Semilla Nueva, 7 Avenida 14-44 Zona 9 Edificio La Galería, Oficina 35 Guatemala, Guatemala City 01009, Guatemala; (C.B.)
| | - Lilly C. Park
- USDA ARS National Biological Control Laboratory, 59 Lee Road, Stoneville, MS 38776, USA;
| | - Angela Bastidas
- Semilla Nueva, 7 Avenida 14-44 Zona 9 Edificio La Galería, Oficina 35 Guatemala, Guatemala City 01009, Guatemala; (C.B.)
| | - Samantha G. Drewry
- Department of Biological Sciences, University of Memphis, 3774 Walker Avenue, Memphis, TN 38152, USA; (S.G.D.); (J.R.M.)
| | - Jennifer R. Mandel
- Department of Biological Sciences, University of Memphis, 3774 Walker Avenue, Memphis, TN 38152, USA; (S.G.D.); (J.R.M.)
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14
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Kikkawa HS, Sato MP, Matsuo A, Sasaki T, Suyama Y, Tsuge K. Discrimination of Camellia cultivars using iD-NA analysis. Sci Rep 2023; 13:17674. [PMID: 37848466 PMCID: PMC10582245 DOI: 10.1038/s41598-023-44404-z] [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: 05/02/2023] [Accepted: 10/07/2023] [Indexed: 10/19/2023] Open
Abstract
Recently, many new cultivars have been taken abroad illegally, which is now considered an international issue. Botanical evidence found at a crime scene provides valuable information about the origin of the sample. However, botanical resources for forensic evidence remain underutilized because molecular markers, such as microsatellites, are not available without a limited set of species. Multiplexed intersimple sequence repeat (ISSR) genotyping by sequencing (MIG-seq) and its analysis method, identification of not applicable (iD-NA), have been used to determine several genome-wide genetic markers, making them applicable to all plant species, including those with limited available genetic information. Camellia cultivars are popular worldwide and are often planted in many gardens and bred to make new cultivars. In this study, we aimed to analyze Camellia cultivars/species through MIG-seq. MIG-seq could discriminate similar samples, such as bud mutants and closely related samples that could not be distinguished based on morphological features. This discrimination was consistent with that of a previous study that classified cultivars based on short tandem repeat (STR) markers, indicating that MIG-seq has the same or higher discrimination ability as STR markers. Furthermore, we observed unknown phylogenetic relationships. Because MIG-seq can be applied to unlimited species and low-quality DNA, it may be useful in various scientific fields.
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Affiliation(s)
- Hitomi S Kikkawa
- National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba, 277-0882, Japan.
| | - Mitsuhiko P Sato
- Kazusa DNA Research Institute, 2-6-7 Kazusakamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Ayumi Matsuo
- Kawatabi Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-Onsen, Osaki, Miyagi, 989-6711, Japan
| | - Takanori Sasaki
- Kawatabi Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-Onsen, Osaki, Miyagi, 989-6711, Japan
| | - Yoshihisa Suyama
- Kawatabi Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-Onsen, Osaki, Miyagi, 989-6711, Japan
| | - Kouichiro Tsuge
- National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba, 277-0882, Japan
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15
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Maekawa M, Yoshii E, Akase Y, Huang H, Yoshikawa S, Matsuda M, Kuruma Y, Sawayama E. Sex-Associated SNP Confirmation of Sex-Reversed Male Farmed Japanese Flounder Paralichthys olivaceus. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023; 25:718-728. [PMID: 37541964 DOI: 10.1007/s10126-023-10235-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 07/21/2023] [Indexed: 08/06/2023]
Abstract
Female Japanese flounder Paralichthys olivaceus grow more rapidly than the male. The goal of all-female commercial production requires an efficient method of genetic sex identification. We conducted genome-wide association analysis of female and male farmed Japanese flounder (n = 24 per phenotypic sex) and found all regions of chromosome 24 to be significantly associated with phenotypic sex, suggesting it as the sex chromosome. Genetic sex was identified based on single nucleotide polymorphisms (SNP) on chromosome 24 (n = 3568) using multidimensional scaling analysis, and individuals were clearly separated according to sex by the first dimension. The 61 SNPs most highly associated with sex were selected, and an amplicon-based SNP panel was developed. This was used to determine genetic sex of 39 females and 40 males. Eleven phenotypic males were assigned as female with XX genotype, suggesting sex reversal. Genetic sex was also assessed based on the indel of the amh gene promoter, which is the major candidate sex gene of Japanese flounder. We found four SNPs perfectly associated with genotypic sex in the sex-associated SNP panel, one of which was located in exon 2 of the amh gene. Along with the indel of the amh gene promoter, the sex-associated SNP panel will be of value in identifying genetic sex of farmed Japanese flounder. Molecular sexing will facilitate all-female production by breeding sex-reversed males.
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Affiliation(s)
- Mari Maekawa
- Department of Marine Science, College of Bioresource Sciences, Nihon University, Kanagawa, Japan
| | - Emiri Yoshii
- Department of Marine Science, College of Bioresource Sciences, Nihon University, Kanagawa, Japan
| | - Yuri Akase
- R&D Division, Marua Suisan Co., Ltd., Ehime, Japan
| | - He Huang
- Bioengineering Lab. Co., Ltd., Kanagawa, Japan
| | - Sota Yoshikawa
- Nagasaki Prefectural Institute of Fisheries, Nagasaki, Japan
| | | | - Yosuke Kuruma
- Nagasaki Prefectural Institute of Fisheries, Nagasaki, Japan
| | - Eitaro Sawayama
- Department of Marine Science, College of Bioresource Sciences, Nihon University, Kanagawa, Japan.
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16
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Gerard D. Double reduction estimation and equilibrium tests in natural autopolyploid populations. Biometrics 2023; 79:2143-2156. [PMID: 35848417 DOI: 10.1111/biom.13722] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 07/11/2022] [Indexed: 11/27/2022]
Abstract
Many bioinformatics pipelines include tests for equilibrium. Tests for diploids are well studied and widely available, but extending these approaches to autopolyploids is hampered by the presence of double reduction, the comigration of sister chromatid segments into the same gamete during meiosis. Though a hindrance for equilibrium tests, double reduction rates are quantities of interest in their own right, as they provide insights about the meiotic behavior of autopolyploid organisms. Here, we develop procedures to (i) test for equilibrium while accounting for double reduction, and (ii) estimate the double reduction rate given equilibrium. To do so, we take two approaches: a likelihood approach, and a novel U-statistic minimization approach that we show generalizes the classical equilibrium χ2 test in diploids. For small sample sizes and uncertain genotypes, we further develop a bootstrap procedure based on our U-statistic to test for equilibrium. We validate our methods on both simulated and real data.
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Affiliation(s)
- David Gerard
- Department of Mathematics and Statistics, American University, Washington, District of Columbia, USA
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17
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Pereyra RT, Rafajlović M, De Wit P, Pinder M, Kinnby A, Töpel M, Johannesson K. Clones on the run: The genomics of a recently expanded partially clonal species. Mol Ecol 2023; 32:4209-4223. [PMID: 37199478 DOI: 10.1111/mec.16996] [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: 02/25/2023] [Revised: 05/03/2023] [Accepted: 05/05/2023] [Indexed: 05/19/2023]
Abstract
Why species that in their core areas mainly reproduce sexually become enriched with clones in marginal populations ("geographic parthenogenesis") remains unclear. Earlier hypotheses have emphasized that selection might promote clonality because it protects locally adapted genotypes. On the other hand, it also hampers recombination and adaptation to changing conditions. The aim of the present study was to investigate the early stages of range expansion in a partially clonal species and what drives an increase in cloning during such expansion. We used genome-wide sequencing to investigate the origin and evolution of large clones formed in a macroalgal species (Fucus vesiculosus) during a recent expansion into the postglacial Baltic Sea. We found low but persistent clonality in core populations, while at range margins, large dominant clonal lineages had evolved repeatedly from different sexual populations. A range expansion model showed that even when asexual recruitment is less favourable than sexual recruitment in core populations, repeated bottlenecks at the expansion front can establish a genetically eroded clonal wave that spreads ahead of a sexual wave into the new area. Genetic variation decreases by drift following repeated bottlenecks at the expansion front. This results in the emerging clones having low expected heterozygosity, which corroborated our empirical observations. We conclude that Baker's Law (clones being favoured by uniparental reproductive assurance in new areas) can play an important role during range expansion in partially clonal species, resulting in a complex spatiotemporal mosaic of clonal and sexual lineages that might persist during thousands of generations.
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Affiliation(s)
- Ricardo T Pereyra
- Department of Marine Sciences, University of Gothenburg, Strömstad, Sweden
- Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden
| | - Marina Rafajlović
- Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Pierre De Wit
- Department of Marine Sciences, University of Gothenburg, Strömstad, Sweden
- Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden
| | - Matthew Pinder
- Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Alexandra Kinnby
- Department of Marine Sciences, University of Gothenburg, Strömstad, Sweden
- Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden
| | - Mats Töpel
- Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Kerstin Johannesson
- Department of Marine Sciences, University of Gothenburg, Strömstad, Sweden
- Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden
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18
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Najafikhah A, Zeinalabedini M, Arefnezhad B, Mardi M, Nafari M, Nasrolahpourmoghadam M, Jafari O. Genome-wide data suggest a revision in management of the Caspian Sea trout Salmo caspius. PLoS One 2023; 18:e0287777. [PMID: 37471390 PMCID: PMC10358921 DOI: 10.1371/journal.pone.0287777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 06/13/2023] [Indexed: 07/22/2023] Open
Abstract
Salmo caspius Kessler, 1877 is one of the most commercially important species of Salmonidae in the southern basin of the Caspian Sea. The occurrence of its wild populations has undergone sever reduction during the last years. In spite of the yearly restocking activity, still no progress on the recovery of its wild population has been observed. Hence, the present study was done in order to assess the efficiency of the current restocking activity in the southern Caspian basin in term of genetic diversity. DNA extracts of 32 S. caspius from four different groups were screened using 62621 genome-wide single nucleotide polymorphisms (SNP). The overal genetic diversity and Fst values were 0.18 and 0.08, respectively. Considering the observed admixture pattern and the positive values for inbreeding coeficient it seems that S. caspius suffers from its small effective population size. In order to obtain the maximum performance, alonside with expanding the size of brood stocks, rehabilitation of the habitats and spawning rivers of this nationally endangered species is of great importance.
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Affiliation(s)
- Arezo Najafikhah
- Department of Biotechnology, Payame Noor University, Tehran, Iran
| | - Mehrshad Zeinalabedini
- Department of Genomics, Agricultural Biotechnology Research Institute of Iran (ABRII), Karaj, Iran
| | | | - Mohsen Mardi
- Seed and Plant Certification and Registration Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | | | | | - Omid Jafari
- International Sturgeon Research Institute, Iranian Fisheries Science Research Institute, Agricultural Research, Education and Extension Organization, Rasht, Iran
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19
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Whitney JL, Coleman RR, Deakos MH. Genomic evidence indicates small island-resident populations and sex-biased behaviors of Hawaiian reef Manta Rays. BMC Ecol Evol 2023; 23:31. [PMID: 37422622 PMCID: PMC10329317 DOI: 10.1186/s12862-023-02130-0] [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: 11/19/2022] [Accepted: 06/07/2023] [Indexed: 07/10/2023] Open
Abstract
BACKGROUND Reef manta rays (Mobula alfredi) are globally distributed in tropical and subtropical seas. Their life history traits (slow growth, late maturity, low reproductive output) make them vulnerable to perturbations and therefore require informed management strategies. Previous studies have reported wide-spread genetic connectivity along continental shelves suggesting high gene flow along continuous habitats spanning hundreds of kilometers. However, in the Hawaiian Islands, tagging and photo-identification evidence suggest island populations are isolated despite proximity, a hypothesis that has not yet been evaluated with genetic data. RESULTS This island-resident hypothesis was tested by analyzing whole mitogenome haplotypes and 2048 nuclear single nucleotide polymorphisms (SNPs) between M. alfredi (n = 38) on Hawai'i Island and Maui Nui (the 4-island complex of Maui, Moloka'i, Lāna'i and Kaho'olawe). Strong divergence in the mitogenome (ΦST = 0.488) relative to nuclear genome-wide SNPs (neutral FST = 0.003; outlier FST = 0.186), and clustering of mitochondrial haplotypes among islands provides robust evidence that female reef manta rays are strongly philopatric and do not migrate between these two island groups. Combined with restricted male-mediated migration, equivalent to a single male moving between islands every 2.2 generations (~ 64 years), we provide evidence these populations are significantly demographically isolated. Estimates of contemporary effective population size (Ne) are 104 (95% CI: 99-110) in Hawai'i Island and 129 (95% CI: 122-136) in Maui Nui. CONCLUSIONS Concordant with evidence from photo identification and tagging studies, these genetic results indicate reef manta rays in Hawai'i have small, genetically-isolated resident island populations. We hypothesize that due to the Island Mass Effect, large islands provide sufficient resources to support resident populations, thereby making crossing deep channels separating island groups unnecessary. Small effective population size, low genetic diversity, and k-selected life history traits make these isolated populations vulnerable to region-specific anthropogenic threats, which include entanglement, boat strikes, and habitat degradation. The long-term persistence of reef manta rays in the Hawaiian Islands will require island-specific management strategies.
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Affiliation(s)
- Jonathan L Whitney
- National Oceanic and Atmospheric Administration, Pacific Islands Fisheries Science Center, Honolulu, Hawai'i, USA.
| | - Richard R Coleman
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Sciences, University of Miami, Miami, FL, USA
| | - Mark H Deakos
- Hawai'i Association for Marine Education and Research, Lahaina, Maui, Hawai'i, USA
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20
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Cao Y, Fan XR, Njeri HK, Pu YH, Li W, Chen YY. The Correlation between Genotype Richness of Submerged Macrophytes and Periphyton Biomass: A Mesocosm Study Based on Five Dominant Submerged Macrophytes from Yangtze River. PLANTS (BASEL, SWITZERLAND) 2023; 12:2492. [PMID: 37447052 DOI: 10.3390/plants12132492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023]
Abstract
Submerged macrophyte and periphyton are main primary producers which strongly interact with each other in clear water shallow lakes. In this study, the effects of genetic variation of the macrophyte species on periphyton biomass were studied in five submerged species. A two-year mesocosm study was conducted with four levels of genetic diversity (1, 4, 8 and 16 genotypes) for each submerged macrophyte, including 1600 individuals and 320 boxes in 20 mesocosms. Of the five submerged species, only Vallisneria spinulosa showed a positive correlation between its levels of genotype richness and the periphyton biomass. The correlation between genetic distance of genotypes and periphyton biomass was tested, which varied with the difference of seasons and species. In summary, we found that in freshwater mesocosms, the genetic diversity of submerged macrophytes may play a role in regulating the periphyton biomass, but the interaction between genetic diversity of macrophytes and periphyton biomass was not straightforward. This study will provide new insights into the interaction dynamics between the two primary producers in shallow lakes.
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Affiliation(s)
- Yu Cao
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Xiang-Rong Fan
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Henry Kariuki Njeri
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Yun-Hai Pu
- Wildlife Conservation Station of Hubei Province, Wuhan 430079, China
| | - Wei Li
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Research Center for Ecology, College of Science, Tibet University, Lhasa 850000, China
| | - Yuan-Yuan Chen
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
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21
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Beshera KA, Harris PM, Michael SK. Relative Genetic Homogeneity within a Phenotypically Diverse group: The Case of Lake Tana Labeobarbus (Cyprinidae) Species Flock, Ethiopia. Zootaxa 2023; 5301:182-198. [PMID: 37518566 DOI: 10.11646/zootaxa.5301.2.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Indexed: 08/01/2023]
Abstract
The Lake Tana Labeobarbus species flock represents one of the world's most famous examples of lacustrine species radiations. Previous studies of this group have resulted in the description of at least 15 species based on their differences in functional morphology and definition of two clades (lacustrine and riverine spawning clades) based on life history traits. A total of 166 fish representing 14 Labeobarbus species were genotyped using 10 lineage-specific hexaploid microsatellite loci. Six of these loci were developed for this study based on DNA sequence contigs derived from a microsatellite-enriched genomic library of Labeobarbus intermedius from Lake Tana; the remaining four loci were obtained from a previous study. The genotypes of the 10 loci were analyzed to examine genetic diversity and population structure within Lake Tana Labeobarbus. Overall mean allelic richness (NA) was 17.6 alleles per locus and observed (Ho) and expected (He) heterozygosities were 0.84 ± 0.14 and 0.73 ± 0.09, respectively, across all Lake Tana Labeobarbus samples examined. Our analyses reveal that there is little genetic differentiation among species (FST = 0.020-0.099; only 10 of 91 species comparisons were significant), but moderate differentiation (FST = 0.11, p < 0.05) between lacustrine and riverine spawning populations. Relative to previous phylogenetic hypotheses, our phenetic analysis employing the R-based Analysis of Phylogenetics and Evolution (APE) program seems to perform marginally better in revealing lineages within Lake Tana Labeobarbus. Herein, our results are compared to a previous microsatellite-based study of the same populations.
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Affiliation(s)
- Kebede A Beshera
- Department of Biological Sciences and Chemistry; Southern University and Agricultural & Mechanical College; 801 Harding Blvd; Baton Rouge; LA 70807; USA.
| | - Phillip M Harris
- Biodiversity and Systematics; Department of Biological Sciences; The University of Alabama; Tuscaloosa; AL 35487-0345; USA.
| | - Semhar K Michael
- Department of Mathematics and Statistics; South Dakota State University; Box 2225; Brookings; SD.
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22
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Pérez-Alquicira J, Wehncke EV, García-Loza GA, Carstens BC, Domínguez CA, Pérez-Ishiwara R, Molina-Freaner FE, Zamora-Tavares MDP, Rico Y, Cabrera-Toledo D, Vargas-Ponce O, Rodríguez A, Ezcurra E. Geographic isolation and long-distance gene flow influence the genetic structure of the blue fan palm Brahea armata (Arecaceae). JOURNAL OF PLANT RESEARCH 2023; 136:277-290. [PMID: 36905462 DOI: 10.1007/s10265-023-01445-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
The formation of the Baja California Peninsula (BCP) has impacted the microevolutionary dynamics of different species in ways that depend on biological traits such as dispersal capacity. Plants with relatively low levels of vagility have exhibited high genetic divergence between the BCP and Continental mainland. Brahea armata (Arecaceae) is a palm species inhabiting the northern part of the BCP and Sonora; its distribution occurs in isolated oases of vegetation. We aimed to evaluate the influence of the formation of the BCP on the genetic structure of B. armata using nuclear microsatellites and chloroplast markers (cpDNA) to compare patterns of genetic diversity and structure with previous published studies. Because gene flow through seeds is usually more limited compared to pollen flow, we expect to find stronger genetic structure at (cpDNA) than at nuclear markers. Moreover, larger genetic structure might also be explained by the smaller effective population size of cpDNA. We analyzed six microsatellite markers and two cpDNA regions. The main results indicated high levels of genetic differentiation among isolated populations located in the BCP, while low genetic differentiation was found between southern populations of the BCP and Sonora, suggesting long distance gene flow. In contrast, chloroplast markers indicated high levels of genetic structure between BCP and Sonora populations, suggesting asymmetrical gene flow between pollen (measured by nuclear microsatellites) and seed (cpDNA markers). This study provides valuable information on genetic diversity of B. armata that can be relevant for conservation and management; and develops microsatellites markers that can be transferred to other Brahea species.
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Affiliation(s)
- Jessica Pérez-Alquicira
- Laboratorio Nacional de Identificación y Caracterización Vegetal, Departamento de Botánica y Zoología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Camino Ing. Ramón Sánchez Padilla 2100, Las Agujas, 45200, Zapopan, Jalisco, Mexico.
- CONACYT, Ciudad de Mexico, Mexico.
| | - Elisabet V Wehncke
- Centro de Investigación en Biodiversidad y Conservación, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, 62209, Cuernavaca, Morelos, Mexico
| | - Gustavo A García-Loza
- Laboratorio Nacional de Identificación y Caracterización Vegetal, Departamento de Botánica y Zoología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Camino Ing. Ramón Sánchez Padilla 2100, Las Agujas, 45200, Zapopan, Jalisco, Mexico
| | - Bryan C Carstens
- Department of Evolution, Ecology, and Organismal Biology and Museum of Biological Diversity, The Ohio State University, 1315 Kinnear Rd., Columbus, OH, 43212, USA
| | - César A Domínguez
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, 04510, Ciudad de Mexico, Mexico
| | - Rubén Pérez-Ishiwara
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, 04510, Ciudad de Mexico, Mexico
| | - Francisco E Molina-Freaner
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, 83250, Hermosillo, Sonora, Mexico
| | - María Del Pilar Zamora-Tavares
- Laboratorio Nacional de Identificación y Caracterización Vegetal, Departamento de Botánica y Zoología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Camino Ing. Ramón Sánchez Padilla 2100, Las Agujas, 45200, Zapopan, Jalisco, Mexico
| | - Yessica Rico
- CONACYT, Ciudad de Mexico, Mexico
- Red de Diversidad Biológica del Occidente Mexicano, Instituto de Ecología, A.C., Pátzcuaro, Michoacán, Mexico
| | - Dánae Cabrera-Toledo
- Departamento de Botánica Y Zoología, Instituto de Botánica, Centro Universitario de Ciencias Biológicas Y Agropecuarias, Universidad de Guadalajara, Ramón Padilla Sanchez 2100, Las Agujas, 45200, Zapopan, Jalisco, Mexico
| | - Ofelia Vargas-Ponce
- Departamento de Botánica Y Zoología, Instituto de Botánica, Centro Universitario de Ciencias Biológicas Y Agropecuarias, Universidad de Guadalajara, Ramón Padilla Sanchez 2100, Las Agujas, 45200, Zapopan, Jalisco, Mexico
| | - Aarón Rodríguez
- Departamento de Botánica Y Zoología, Instituto de Botánica, Centro Universitario de Ciencias Biológicas Y Agropecuarias, Universidad de Guadalajara, Ramón Padilla Sanchez 2100, Las Agujas, 45200, Zapopan, Jalisco, Mexico
| | - Exequiel Ezcurra
- Department of Botany and Plant Sciences, University of California, 2142 Batchelor Hall, Riverside, CA, 92521, USA
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23
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Infraspecific genetic diversity and seed fatty acid composition in Sesamum indicum L. populations (Pedaliaceae) in Iran. BIOCHEM SYST ECOL 2023. [DOI: 10.1016/j.bse.2023.104618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
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24
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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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25
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Nsabiyumva G, Mutegi CK, Wagacha JM, Mohamed AB, Njeru NK, Ndayihanzamaso P, Niyuhire MC, Atehnkeng J, Njukwe E, Callicott KA, Cotty PJ, Ortega-Beltran A, Bandyopadhyay R. Aflatoxin contamination of maize and groundnut in Burundi: Distribution of contamination, identification of causal agents and potential biocontrol genotypes of Aspergillus flavus. Front Microbiol 2023; 14:1106543. [PMID: 37065127 PMCID: PMC10093718 DOI: 10.3389/fmicb.2023.1106543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 02/21/2023] [Indexed: 03/14/2023] Open
Abstract
Aflatoxin contamination of the staples maize and groundnut is a concern for health and economic impacts across sub-Saharan Africa. The current study (i) determined aflatoxin levels in maize and groundnut collected at harvest in Burundi, (ii) characterized populations of Aspergillus section Flavi associated with the two crops, and (iii) assessed aflatoxin-producing potentials among the recovered fungi. A total of 120 groundnut and 380 maize samples were collected at harvest from eight and 16 provinces, respectively. Most of the groundnut (93%) and maize (87%) contained aflatoxin below the European Union threshold, 4 μg/kg. Morphological characterization of the recovered Aspergillus section Flavi fungi revealed that the L-morphotype of A. flavus was the predominant species. Aflatoxin production potentials of the L-morphotype isolates were evaluated in maize fermentations. Some isolates produced over 137,000 μg/kg aflatoxin B1. Thus, despite the relatively low aflatoxin levels at harvest, the association of both crops with highly toxigenic fungi poses significant risk of post-harvest aflatoxin contamination and suggests measures to mitigate aflatoxin contamination in Burundi should be developed. Over 55% of the L-morphotype A. flavus did not produce aflatoxins. These atoxigenic L-morphotype fungi were characterized using molecular markers. Several atoxigenic genotypes were detected across the country and could be used as biocontrol agents. The results from the current study hold promise for developing aflatoxin management strategies centered on biocontrol for use in Burundi to reduce aflatoxin contamination throughout the value chain.
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Affiliation(s)
- Gedeon Nsabiyumva
- Institut des Sciences Agronomiques du Burundi (ISABU), Bujumbura, Burundi
| | - Charity K. Mutegi
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
| | - John M. Wagacha
- School of Biological Sciences, University of Nairobi, Nairobi, Kenya
| | - Asha B. Mohamed
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
| | - Nancy K. Njeru
- Kenya Agricultural and Livestock Research Organization (KALRO), Katumani, Nairobi, Kenya
| | | | | | | | | | - Kenneth A. Callicott
- United States Department of Agriculture, Agricultural Research Service, Tucson, AZ, United States
| | - Peter J. Cotty
- United States Department of Agriculture, Agricultural Research Service, Tucson, AZ, United States
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
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26
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Reproductive and Agronomic Characterization of Novel Apomictic Hybrids of Paspalum (Poaceae). Genes (Basel) 2023; 14:genes14030631. [PMID: 36980903 PMCID: PMC10047980 DOI: 10.3390/genes14030631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/18/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
The tetraploid germplasm of Paspalum contains a large diversity that can be used to generate better forages. The objective was to evaluate a group of Paspalum notatum and Paspalum simplex apomictic hybrids for a set of agronomic traits and apomixis expressivity. Forage yield, cold tolerance, winter regrowth, and seed yield were evaluated. The expressivity of apomixis was evaluated in P. simplex hybrids by flow cytometry. Progeny testing with molecular markers was used to determine the genotypic variability in the progeny. Differences within P. notatum and P. simplex hybrids were observed for all traits, and some of them were superior in comparison with the controls. The accumulated forage yield during three years was 988 g m−2 in the P. notatum hybrids, whereas, in P. simplex, the average forage yield per harvest (40 days of regrowth) was 180 g m−2. In P. simplex, the apomixis expressivity varied between 0 and 100%, and 65% of the hybrids showed high apomixis expressivity (superior to 70%). The genotypic mean homogeneity in the progeny was 76% and 85% in P. notatum and P. simplex, respectively. The generation of hybrids with high apomixis expressivity that combine good agronomic performance and homogeneity in the offspring is possible in tetraploid P. notatum and P. simplex.
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27
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Tong H, Deng H, Han Z. Genetic differentiation and genetic structure of mixed-ploidy Camellia hainanica populations. PeerJ 2023; 11:e14756. [PMID: 36852222 PMCID: PMC9961093 DOI: 10.7717/peerj.14756] [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: 09/12/2022] [Accepted: 12/27/2022] [Indexed: 02/24/2023] Open
Abstract
Camellia hainanica, which is common in China's Hainan Province, is an important woody olive tree species. Due to many years of geographic isolation, C. hainanica has not received the attention it deserves, which limits the exploitation of germplasm resources. Therefore, it is necessary to study population genetic characteristics for further utilization and conservation of C. hainanica. In this study, 96 individuals in six wild Camellia hainanica populations were used for ploidy analysis of the chromosome number, and the genetic diversity and population structure were investigated using 12 pairs of SSR primers. The results show complex ploidy differentiation in C. hainanica species. The ploidy of wild C. hainanica includes tetraploid, pentaploid, hexaploid, heptaploid, octoploid and decaploid species. Genetic analysis shows that genetic diversity and genetic differentiation among populations are low. Populations can be divided into two clusters based on their genetic structure, which matches their geographic location. Finally, to further maintain the genetic diversity of C. hainanica, ex-situ cultivation and in-situ management measures should be considered to protect it in the future.
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Affiliation(s)
- Hailang Tong
- Central South University of Forestry and Technology, The College of Forestry, Changsha, China,Central South University of Forestry and Technology, The Laboratory of Forestry Genetics, Changsha, China
| | - Hongda Deng
- Central South University of Forestry and Technology, The College of Forestry, Changsha, China,Central South University of Forestry and Technology, The Laboratory of Forestry Genetics, Changsha, China
| | - Zhiqiang Han
- Central South University of Forestry and Technology, The College of Forestry, Changsha, China,Central South University of Forestry and Technology, The Laboratory of Forestry Genetics, Changsha, China
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28
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Selz OM, Seehausen O. A taxonomic revision of ten whitefish species from the lakes Lucerne, Sarnen, Sempach and Zug, Switzerland, with descriptions of seven new species (Teleostei, Coregonidae). Zookeys 2023; 1144:95-169. [DOI: 10.3897/zookeys.1144.67747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 08/22/2022] [Indexed: 02/04/2023] Open
Abstract
The taxonomy of the endemic whitefish of the lakes of the Reuss River system (Lucerne, Sarnen, Zug) and Lake Sempach, Switzerland, is reviewed and revised. Lake Lucerne harbours five species. Coregonus intermundiasp. nov. and C. suspensussp. nov., are described. Coregonus nobilis Haack, 1882, C. suidteri Fatio, 1885, and C. zugensis Nüsslin, 1882, are redescribed. Genetic studies have shown that C. suidteri and C. zugensis are composed of several distinct species endemic to different lakes. The names C. suidteri and C. zugensis are restricted to the species of lakes Sempach and Zug, respectively. The whitefish populations previously referred to as C. suidteri and C. zugensis from Lake Lucerne are described as C. litoralissp. nov. and C. muellerisp. nov., respectively. Furthermore, the whitefish from Lake Zug that were previously referred to as C. suidteri are described as C. supersumsp. nov. A holotype is designated for C. supersum that was previously one of two syntypes of C. zugensis. The other syntype is retained for C. zugensis. Coregonus obliterussp. nov. is described from Lake Zug, and C. obliterus and C. zugensis from Lake Zug are extinct. Finally, we describe C. sarnensissp. nov. from lakes Sarnen and Alpnach. Coregonus suidteri from Lake Sempach shows strong signals of introgression from deliberately translocated non-native whitefish species, which questions if the extant population still carries a genetic legacy from the original species and thus may need to be considered extinct. Coregonus suspensus is genetically partially of allochthonous origin, closely related to the radiation of Lake Constance. It is therefore compared to all known and described species of Lake Constance: C. wartmanni Bloch, 1784, C. macrophthalmus Nüsslin, 1882, C. arenicolus Kottelat,1997, and C. gutturosus Gmelin, 1818.
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29
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Gervais L, Mouginot P, Gibert A, Salles O, Latutrie M, Piquet J, Archambeau J, Pujol B. Wild snapdragon plant pedigree sheds light on limited connectivity enhanced by higher migrant reproductive success in a fragmented landscape. OPEN RESEARCH EUROPE 2023; 1:145. [PMID: 37645181 PMCID: PMC10446054 DOI: 10.12688/openreseurope.14281.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/16/2022] [Indexed: 08/31/2023]
Abstract
Background: In contrast with historical knowledge, a recent view posits that a non-negligible proportion of populations thrive in a fragmented landscape. One underlying mechanism is the maintenance of functional connectivity, i.e., the net flow of individuals or their genes moving among suitable habitat patches. Alternatively, functional connectivity might be typically limited but enhanced by a higher reproductive success of migrants. Methods: We tested for this hypothesis in wild snapdragon plants inhabiting six patches separated by seawater in a fragmented Mediterranean scrubland landscape. We reconstructed their pedigree by using a parentage assignment method based on microsatellite genetic markers. We then estimated functional connectivity and the reproductive success of plants resulting from between-patch dispersal events. Results: We found that wild snapdragon plants thrived in this fragmented landscape, although functional connectivity between habitat patches was low (i.e. 2.9%). The progeny resulting from between-patch dispersal events had a higher reproductive success than residents. Conclusion: Our findings imply that low functional connectivity in a fragmented landscapes may have been enhanced by higher reproductive success after migration. This original mechanisms might be partly compensating the negative impact of fragmentation.
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Affiliation(s)
- Laura Gervais
- CRIOBE PSL Université Paris : EHPE-UPVD-CNRS, Université de Perpignan, USR 3278, CNRS, Perpignan, France
| | - Pierick Mouginot
- CRIOBE PSL Université Paris : EHPE-UPVD-CNRS, Université de Perpignan, USR 3278, CNRS, Perpignan, France
| | - Anais Gibert
- CRIOBE PSL Université Paris : EHPE-UPVD-CNRS, Université de Perpignan, USR 3278, CNRS, Perpignan, France
| | - Oceane Salles
- CRIOBE PSL Université Paris : EHPE-UPVD-CNRS, Université de Perpignan, USR 3278, CNRS, Perpignan, France
| | - Mathieu Latutrie
- CRIOBE PSL Université Paris : EHPE-UPVD-CNRS, Université de Perpignan, USR 3278, CNRS, Perpignan, France
| | - Jesaelle Piquet
- CRIOBE PSL Université Paris : EHPE-UPVD-CNRS, Université de Perpignan, USR 3278, CNRS, Perpignan, France
| | | | - Benoit Pujol
- CRIOBE PSL Université Paris : EHPE-UPVD-CNRS, Université de Perpignan, USR 3278, CNRS, Perpignan, France
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30
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Gamba D, Muchhala N. Pollinator type strongly impacts gene flow within and among plant populations for six Neotropical species. Ecology 2023; 104:e3845. [PMID: 36224746 DOI: 10.1002/ecy.3845] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 06/13/2022] [Accepted: 06/23/2022] [Indexed: 02/01/2023]
Abstract
Animal pollinators directly affect plant gene flow by transferring pollen grains between individuals. Pollinators with restricted mobility are predicted to limit gene flow within and among populations, whereas pollinators that fly longer distances are likely to promote genetic cohesion. These predictions, however, remain poorly tested. We examined population genetic structure and fine-scale spatial genetic structure (FSGS) in six perennial understory angiosperms in Andean cloud forests of northwestern Ecuador. Species belong to three families (Gesneriaceae, Melastomataceae, and Rubiaceae), and within each family we paired one insect-pollinated with one hummingbird-pollinated species, predicting that insect-pollinated species have greater population differentiation (as quantified with the FST statistic) and stronger FSGS (as quantified with the SP statistic) than hummingbird-pollinated species. We confirmed putative pollinators through a literature review and fieldwork, and inferred population genetic parameters with a genome-wide genotyping approach. In two of the three species pairs, insect-pollinated species had much greater (>2-fold) population-level genetic differentiation and correspondingly steeper declines in fine-scale genetic relatedness. In the Gesneriaceae pair, however, FST and SP values were similar between species and to those of the other hummingbird-pollinated plants. In this pair, the insect pollinators are euglossine bees (as opposed to small bees and flies in the other pairs), which are thought to forage over large areas, and therefore may provide similar levels of gene flow as hummingbirds. Overall, our results shed light on how different animal pollination modes influence the spatial scale of plant gene flow, suggesting that small insects strongly decrease genetic cohesion.
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Affiliation(s)
- Diana Gamba
- Department of Biology, University of Missouri at Saint Louis, Saint Louis, Missouri, USA
| | - Nathan Muchhala
- Department of Biology, University of Missouri at Saint Louis, Saint Louis, Missouri, USA
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31
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Vallier M, Suwandi A, Ehrhardt K, Belheouane M, Berry D, Čepić A, Galeev A, Johnsen JM, Grassl GA, Baines JF. Pathometagenomics reveals susceptibility to intestinal infection by Morganella to be mediated by the blood group-related B4galnt2 gene in wild mice. Gut Microbes 2023; 15:2164448. [PMID: 36683151 PMCID: PMC9872957 DOI: 10.1080/19490976.2022.2164448] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 12/15/2022] [Accepted: 12/28/2022] [Indexed: 01/24/2023] Open
Abstract
Infectious disease is widely considered to be a major driver of evolution. A preponderance of signatures of balancing selection at blood group-related genes is thought to be driven by inherent trade-offs in susceptibility to disease. B4galnt2 is subject to long-term balancing selection in house mice, where two divergent allele classes direct alternative tissue-specific expression of a glycosyltransferase in the intestine versus blood vessels. The blood vessel allele class leads to prolonged bleeding times similar to von Willebrand disease in humans, yet has been maintained for millions of years. Based on in vivo functional studies in inbred lab strains, it is hypothesized that the cost of prolonged bleeding times may be offset by an evolutionary trade-off involving susceptibility to a yet unknown pathogen(s). To identify candidate pathogens for which resistance could be mediated by B4galnt2 genotype, we here employed a novel "pathometagenomic" approach in a wild mouse population, which combines bacterial 16S rRNA gene-based community profiling with histopathology of gut tissue. Through subsequent isolation, genome sequencing and controlled experiments in lab mice, we show that the presence of the blood vessel allele is associated with resistance to a newly identified subspecies of Morganella morganii, a clinically important opportunistic pathogen. Given the increasing importance of zoonotic events, the approach outlined here may find useful application in the detection of emerging diseases in wild animal populations.
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Affiliation(s)
- Marie Vallier
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
- Guest Group Evolutionary Medicine, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Abdulhadi Suwandi
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), Hannover, Germany
| | - Katrin Ehrhardt
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), Hannover, Germany
| | - Meriem Belheouane
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
- Guest Group Evolutionary Medicine, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - David Berry
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
| | - Aleksa Čepić
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
- Guest Group Evolutionary Medicine, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Alibek Galeev
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
- Guest Group Evolutionary Medicine, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Jill M. Johnsen
- Bloodworks Research Institute, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Guntram A. Grassl
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), Hannover, Germany
| | - John F. Baines
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
- Guest Group Evolutionary Medicine, Max Planck Institute for Evolutionary Biology, Plön, Germany
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32
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Kang H, An SM, Park YJ, Lee YB, Lee JH, Cheon KS, Kim KA. Population Genomics Study and Implications for the Conservation of Zabelia tyaihyonii Based on Genotyping-By-Sequencing. PLANTS (BASEL, SWITZERLAND) 2022; 12:171. [PMID: 36616299 PMCID: PMC9823854 DOI: 10.3390/plants12010171] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/26/2022] [Accepted: 12/26/2022] [Indexed: 06/17/2023]
Abstract
Zabelia tyaihyonii (Nakai) Hisauti and H. Hara is a perennial shrub endemic to Republic of Korea that grows naturally in only a very limited region of the dolomite areas of Gangwon-do and Chungcheongbuk-do Provinces in the Republic of Korea. Given its geographical characteristics, it is more vulnerable than more widely distributed species. Despite the need for comprehensive information to support conservation, population genetic information for this species is very scarce. In this study, we analyzed the genetic diversity and population structure of 94 individuals from six populations of Z. tyaihyonii using a genotyping-by-sequencing (GBS) approach to provide important information for proper conservation and management. Our results, based on 3088 single nucleotide polymorphisms (SNPs), showed a mean expected heterozygosity (He) of 0.233, no sign of within-population inbreeding (GIS that was close to or even below zero in all populations), and a high level of genetic differentiation (FST = 0.170). Analysis of molecular variance (AMOVA) indicated that the principal molecular variance existed within populations (84.5%) rather than among populations (17.0%). We suggested that six management units were proposed for conservation considering Bayesian structure analysis and phylogenetic analysis, and given the various current situations faced by Z. tyaihyonii, it is believed that not only the in situ conservation but also the ex situ conservation should be considered.
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Affiliation(s)
- Halam Kang
- Department of Biological Science, Sangji University, Wonju 26339, Republic of Korea
| | - Sung-Mo An
- Department of Biological Science, Sangji University, Wonju 26339, Republic of Korea
| | - Yoo-Jung Park
- Department of Biological Science, Sangji University, Wonju 26339, Republic of Korea
| | - Yoo-Bin Lee
- Department of Biological Science, Sangji University, Wonju 26339, Republic of Korea
| | - Jung-Hyun Lee
- Department of Biology Education, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Kyeong-Sik Cheon
- Department of Biological Science, Sangji University, Wonju 26339, Republic of Korea
| | - Kyung-Ah Kim
- Environmental Research Institute, Kangwon National University, Chuncheon 24341, Republic of Korea
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Worth JRP, Shitara T, Kitamura K, Kikuchi S, Kanetani S, Matsui T, Uchiyama K, Tomaru N. Low‐elevation warm‐edge
Fagus crenata
populations in the core of the species range are glacial relicts with high conservation value. Ecol Res 2022. [DOI: 10.1111/1440-1703.12378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- James R. P. Worth
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute Forest Research and Management Organization Matsunosato, Ibaraki Japan
| | - Takuto Shitara
- Institute of Agriculture Tokyo University of Agriculture and Technology Fuchu‐shi, Tokyo Japan
| | - Keiko Kitamura
- Hokkaido Research Centre, Forestry and Forest Products Research Institute Forest Research and Management Organization Sapporo, Hokkaido Japan
| | - Satoshi Kikuchi
- Hokkaido Research Centre, Forestry and Forest Products Research Institute Forest Research and Management Organization Sapporo, Hokkaido Japan
| | - Seiichi Kanetani
- Kyushu Research Center Forestry and Forest Products Research Institute Chuo‐ku, Kumamoto Japan
| | - Tetsuya Matsui
- Center for Biodiversity and Climate Change, Forestry and Forest Products Research Institute Forest Research and Management Organization Matsunosato, Ibaraki Japan
- Faculty of Life and Environmental Sciences University of Tsukuba Tsukuba, Ibaraki Japan
| | - Kentaro Uchiyama
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute Forest Research and Management Organization Matsunosato, Ibaraki Japan
| | - Nobuhiro Tomaru
- Graduate School of Bioagricultural Sciences Nagoya University Chikusa‐ku, Nagoya Japan
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Juhasz CC, Avargues N, Humeau L, Ringler D, Pinet P, Hollinger C, Beaulieu R, Faulquier L, Choeur A, Bureau S, Da Silva D, Dubos J, Soulaimana-Mattoir Y, Le Corre M. Application of genetic and Spatially Explicit Capture-Recapture analyses to design adaptive feral cat control in a large inhabited island. NEOBIOTA 2022. [DOI: 10.3897/neobiota.79.87726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Faunas of oceanic islands have a high proportion of endemic species which contribute to the uniqueness of island communities. Island species are particularly naïve and vulnerable to alien predators, such as cats (Felis catus). On large, inhabited islands, where the complete eradication of feral cat populations is not considered feasible, control represents the best management option to lower their detrimental effects on native fauna. The first objective of our study was to investigate population genetics of feral cats of Réunion Island. The second objective was to understand the space use of feral cats established near the breeding colonies of the two endemic and endangered seabirds of Réunion Island, the Barau’s Petrel (Pterodroma baraui) and the Mascarene Petrel (Pseudobulweria aterrima). We evaluated genetic diversity, population structure and gene flow amongst six groups of feral cats located at a maximum of 10 km from known petrel colonies. We also analysed the behaviour and space use of one of these feral cat groups using camera-trap data and Spatially Explicit Capture-Recapture (SECR) models. Genetic analyses revealed that feral cats were structured in three genetic clusters explained mostly by the island topography. Two clusters were observed at five sampled sites, suggesting high connectivity amongst these sites. The last cluster was found in only one site, suggesting high isolation. This site was a remote mountain area located in the vicinity of one of the main Barau’s Petrel colonies. The behavioural study was conducted on this isolated feral cat population. Mark recapture analysis suggested that feral cats were present at low density and had large home ranges, which is probably explained by reduced food availability. Finally, we make several recommendations for refining feral cat management programmes on inhabited islands.
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Kitamura K, Namikawa K, Tsuda Y, Kobayashi M, Matsui T. Possible northern persistence of Siebold's beech, Fagus crenata, at its northernmost distribution limit on an island in Japan Sea: Okushiri Island, Hokkaido. FRONTIERS IN PLANT SCIENCE 2022; 13:990927. [PMID: 36589061 PMCID: PMC9797532 DOI: 10.3389/fpls.2022.990927] [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: 07/11/2022] [Accepted: 11/16/2022] [Indexed: 06/17/2023]
Abstract
Siebold's beech, Fagus crenata, is widely distributed across the Japanese Archipelago and islands in Japan Sea. Similar to the northern limit of the geographical distribution of F. crenata on the mainland of Hokkaido, the northern limit of the distribution of F. crenata on islands in the Japan Sea is observed on Okushiri Island (ca 42°N). To understand the genetic relationships of F. crenata on Okushiri Island, we examined chloroplast (cp) DNA haplotypes and 11 nuclear microsatellite (SSR) loci among 1,838 individuals from 44 populations from Okushiri Island, mainland Hokkaido, and the northern part of the Tohoku region on Honshu Island. We identified 2 cpDNA haplotypes, which represent not only populations on the Japan Sea coast but also those on the Pacific coast and this suggested the Okushiri Island populations might not be formed by single colonization. Genetic diversity of the Okushiri Island populations of nuclear SSR was not lower than the mainland and the STRUCTURE analysis revealed the Okushiri Island individuals were admixed between Hokkaido and Tohoku clusters. Approximate Bayesian computation inferred that divergence between Tohoku and Hokkaido, and admixture between two populations which generated Okushiri populations occurred before the last glacial maximum (LGM), that is, 7,890 (95% hyper probability density (HPD): 3,420 - 9,910) and 3,870 (95% HPD: 431- 8,540) generations ago, respectively. These inferences were well supported by a geological history which suggested an isolation of Okushiri Island from Hokkaido started prior to the Middle Pleistocene. We discuss the possible persistence of F. crenata during the last glacial maximum on northern islands in the Japan Sea such as Okushiri Island.
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Affiliation(s)
- Keiko Kitamura
- Hokkaido Research Centre, Forestry and Forest Products Research Institute, Sapporo, Japan
| | - Kanji Namikawa
- Biological Laboratory, Hokkaido University of Education, Sapporo, Japan
| | - Yoshiaki Tsuda
- Sugadaira Montane Research Center, University of Tsukuba, Ueda, Japan
| | - Makoto Kobayashi
- Department of Education and Culture, Echigo-Matsunoyama Museum of Natural Science, Tokamachi, Japan
| | - Tetsuya Matsui
- Center of Biodiversity and Climate Change, Forestry and Forest Products Research Institute, Tsukuba, Japan
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
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Horreo JL, Ucero A, Palacín C, López‐Solano A, Abril‐Colón I, Alonso JC. Human decimation caused bottleneck effect, genetic drift, and inbreeding in the Canarian houbara bustard. J Wildl Manage 2022. [DOI: 10.1002/jwmg.22342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jose L. Horreo
- Department of Genetics, Physiology and Microbiology Universidad Complutense Madrid Spain
| | - Alberto Ucero
- Department of Evolutionary Ecology Museo Nacional de Ciencias Naturales (CSIC) Madrid Spain
| | - Carlos Palacín
- Department of Evolutionary Ecology Museo Nacional de Ciencias Naturales (CSIC) Madrid Spain
| | - Alfonso López‐Solano
- Department of Biodiversity and Evolutionary Biology Museo Nacional de Ciencias Naturales (CSIC) Madrid Spain
| | - Inmaculada Abril‐Colón
- Department of Evolutionary Ecology Museo Nacional de Ciencias Naturales (CSIC) Madrid Spain
| | - Juan C. Alonso
- Department of Evolutionary Ecology Museo Nacional de Ciencias Naturales (CSIC) Madrid Spain
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Huang K, Li W, Yang B, Wang D, He S, Shen Y, Ao J, Li Y, Cui Y, Kong Y, Li W, Li N, Dunn DW, Li B. vcfpop: Performing population genetics analyses for autopolyploids and aneuploids based on next-generation sequencing data sets. Mol Ecol Resour 2022. [PMID: 36458971 DOI: 10.1111/1755-0998.13744] [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: 04/09/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/05/2022]
Abstract
Polyploids are cells or organisms with a genome consisting of more than two sets of homologous chromosomes. Polyploid plants have important traits that facilitate speciation and are thus often model systems for evolutionary, molecular ecology and agricultural studies. However, due to their unusual mode of inheritance and double-reduction, diploid models of population genetic analysis cannot properly be applied to autopolyploids. To overcome this problem, we developed a software package entitled vcfpop to perform a variety of population genetic analyses for autopolyploids, such as parentage analysis, analysis of molecular variance, principal coordinates analysis, hierarchical clustering analysis and Bayesian clustering. We used three data sets to evaluate the capability of vcfpop to analyse large data sets on a desktop computer. This software is freely available at http://github.com/huangkang1987/vcfpop.
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Affiliation(s)
- Kang Huang
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Wenkai Li
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Bing Yang
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Dan Wang
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Shujun He
- Shaanxi Key Laboratory for Animal Conservation, Institute of Zoology, Shaanxi Academy of Sciences, Xi'an, China
| | - Yujia Shen
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Jincuo Ao
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Yuhang Li
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Yunxia Cui
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Yuchen Kong
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Wei Li
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Nianlong Li
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Derek W Dunn
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Baoguo Li
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
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Seascape genomics of common dolphins (Delphinus delphis) reveals adaptive diversity linked to regional and local oceanography. BMC Ecol Evol 2022; 22:88. [PMID: 35818031 PMCID: PMC9275043 DOI: 10.1186/s12862-022-02038-1] [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: 03/02/2022] [Accepted: 06/14/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
High levels of standing genomic variation in wide-ranging marine species may enhance prospects for their long-term persistence. Patterns of connectivity and adaptation in such species are often thought to be influenced by spatial factors, environmental heterogeneity, and oceanographic and geomorphological features. Population-level studies that analytically integrate genome-wide data with environmental information (i.e., seascape genomics) have the potential to inform the spatial distribution of adaptive diversity in wide-ranging marine species, such as many marine mammals. We assessed genotype-environment associations (GEAs) in 214 common dolphins (Delphinus delphis) along > 3000 km of the southern coast of Australia.
Results
We identified 747 candidate adaptive SNPs out of a filtered panel of 17,327 SNPs, and five putatively locally-adapted populations with high levels of standing genomic variation were disclosed along environmentally heterogeneous coasts. Current velocity, sea surface temperature, salinity, and primary productivity were the key environmental variables associated with genomic variation. These environmental variables are in turn related to three main oceanographic phenomena that are likely affecting the dispersal of common dolphins: (1) regional oceanographic circulation, (2) localised and seasonal upwellings, and (3) seasonal on-shelf circulation in protected coastal habitats. Signals of selection at exonic gene regions suggest that adaptive divergence is related to important metabolic traits.
Conclusion
To the best of our knowledge, this represents the first seascape genomics study for common dolphins (genus Delphinus). Information from the associations between populations and their environment can assist population management in forecasting the adaptive capacity of common dolphins to climate change and other anthropogenic impacts.
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Genetic diversity, asexual reproduction and conservation of the edible fruit tree Spondias purpurea L. (Anacardiaceae) in the Costa Rican tropical dry forest. PLoS One 2022; 17:e0277439. [PMID: 36395193 PMCID: PMC9671346 DOI: 10.1371/journal.pone.0277439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/26/2022] [Indexed: 11/19/2022] Open
Abstract
The term circa situm has been used to describe different conservation strategies within agricultural landscapes. Circa situm conserves planted or remnant species in farmlands, where natural vegetation has been modified through anthropogenic intervention. It has been proposed that trees planted or retained under circa situm conditions may contribute to maintaining genetic diversity, however information on the role of this strategy in preserving genetic diversity is scarce. The aim of this study was to determine the levels of genetic diversity and structure, and mating patterns in planted and unmanaged stands of the tropical fruit tree Spondias purpurea L. in north western Costa Rica. In three localities, we used seven polymorphic microsatellite loci and genotyped 201 adults and 648 seeds from planted and wild stands. We found no differences in genetic diversity among planted and wild stands. Genetic structure analysis revealed that gene flow occurs among planted and wild stands within localities. Clones were present and their diversity and evenness were both high and similar between planted and wild stands. The number of pollen donors per progeny array was low (Nep = 1.01) which resulted in high levels of correlated paternity (rp = 0.9). Asexual seeds were found in 4.6% of the progeny arrays, which had multilocus genotypes that were identical to the maternal trees. Our results show that although planted stands under circa situm conditions can maintain similar levels of genetic diversity than wild stands, the low number of sires and asexual seed formation could threaten the long term persistence of populations.
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40
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Cohen JI, Ruane LG. Conservation genetics of Phlox hirsuta, a serpentine endemic. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01478-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Gloria-Soria A, Faraji A, Hamik J, White G, Amsberry S, Donahue M, Buss B, Pless E, Cosme LV, Powell JR. Origins of high latitude introductions of Aedes aegypti to Nebraska and Utah during 2019. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 103:105333. [PMID: 35817397 DOI: 10.1016/j.meegid.2022.105333] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 06/27/2022] [Accepted: 07/05/2022] [Indexed: 06/15/2023]
Abstract
Aedes aegypti (L.), the yellow fever mosquito, is also an important vector of dengue and Zika viruses, and an invasive species in North America. Aedes aegypti inhabits tropical and sub-tropical areas of the world and in North America is primarily distributed throughout the southern US states and Mexico. The northern range of Ae. aegypti is limited by cold winter months and establishment in these areas has been mostly unsuccessful. However, frequent introductions of Ae. aegypti to temperate, non-endemic areas during the warmer months can lead to seasonal activity and disease outbreaks. Two Ae. aegypti incursions were reported in the late summer of 2019 into York, Nebraska and Moab, Utah. These states had no history of established populations of this mosquito and no evidence of previous seasonal activity. We genotyped a subset of individuals from each location at 12 microsatellite loci and ~ 14,000 single nucleotide polymorphic markers to determine their genetic affinities to other populations worldwide and investigate their potential source of introduction. Our results support a single origin for each of the introductions from different sources. Aedes aegypti from Utah likely derived from Tucson, Arizona, or a nearby location. Nebraska specimen results were not as conclusive, but point to an origin from southcentral or southeastern US. In addition to an effective, efficient, and sustainable control of invasive mosquitoes, such as Ae. aegypti, identifying the potential routes of introduction will be key to prevent future incursions and assess their potential health threat based on the ability of the source population to transmit a particular virus and its insecticide resistance profile, which may complicate vector control.
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Affiliation(s)
- Andrea Gloria-Soria
- Department of Entomology, Center for Vector Biology & Zoonotic Diseases, The Connecticut Agricultural Experiment Station, 123 Huntington Street, P.O. Box 1106, New Haven, CT 06511, USA; Yale University, Department of Ecology and Evolutionary Biology, 21 Sachem Street, New Haven, CT 06511, USA.
| | - Ary Faraji
- Salt Lake City Mosquito Abatement District, 2215 North 2200 West, Salt Lake City, UT 84116-1108, USA.
| | - Jeff Hamik
- Nebraska Department of Health and Human Services, Epidemiology and Informatics Unit, 301 Centennial Mall South, Lincoln, NE 68509, USA; University of Nebraska-Lincoln, Department of Educational Psychology, 114 Teachers College Hall, Lincoln, NE 68588, USA.
| | - Gregory White
- Salt Lake City Mosquito Abatement District, 2215 North 2200 West, Salt Lake City, UT 84116-1108, USA.
| | - Shanon Amsberry
- Moab Mosquito Abatement District, 1000 Sand Flats Rd, Moab, UT 84532, USA.
| | - Matthew Donahue
- Nebraska Department of Health and Human Services, Epidemiology and Informatics Unit, 301 Centennial Mall South, Lincoln, NE 68509, USA; Epidemic Intelligence Service, CDC, USA.
| | - Bryan Buss
- Nebraska Department of Health and Human Services, Epidemiology and Informatics Unit, 301 Centennial Mall South, Lincoln, NE 68509, USA; Career Epidemiology Field Officer Program, Division of State and Local Readiness, Center for Preparedness and Response, CDC, USA.
| | | | - Luciano Veiga Cosme
- Yale University, Department of Ecology and Evolutionary Biology, 21 Sachem Street, New Haven, CT 06511, USA.
| | - Jeffrey R Powell
- Yale University, Department of Ecology and Evolutionary Biology, 21 Sachem Street, New Haven, CT 06511, USA.
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Kinship and Breeding Site Philopatry Drive Fine-Scale Genetic Structure in Fragmented Populations of the Gopher Frog (Rana capito) in North Carolina. J HERPETOL 2022. [DOI: 10.1670/20-140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Wagutu GK, Fan X, Fu W, Tengwer MC, Li W, Chen Y. Genetic structure of wild rice Zizania latifolia in an expansive heterogeneous landscape along a latitudinal gradient. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.929944] [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] Open
Abstract
Global aquatic habitats are undergoing rapid degradation and fragmentation as a result of climate change and changes in land use. Understanding the genetic variability and adaptive potential of aquatic plant species is thus important for conservation purposes. In this study, we investigated the genetic diversity and structure of the extant natural populations of Zizania latifolia from five river basins in China based on 46 microsatellite markers. We tested isolation by environment (IBE), isolation by resistance (IBR), and isolation by distance (IBD) patterns using a reciprocal causal model (RCM). Furthermore, we elucidated the impact of the environment on Z. latifolia genetic diversity using generalized linear models (GLMs) and spatially explicit mixed models. Low genetic diversity (HE = 0.125–0.433) and high genetic differentiation (FST = 0.641, Øpt = 0.654) were found. Higher historical gene flow (MH = 0.212–2.354) than contemporary gene flow (MC = 0.0112–0.0247) and significant bottlenecks in almost all populations were identified, highlighting the negative impact of wetland fragmentation. The IBE model was exclusively supported for all populations and in three river basins. The IBD and IBR models were supported in one river basin each. The maximum temperature of the warmest month and precipitation seasonality were the plausible environmental parameters responsible for the observed pattern of genetic diversity. Local adaptation signatures were found, with nine loci identified as outliers, four of which were gene-linked and associated with environmental variables. Based on these findings, IBE is more important than IBD and IBR in shaping the genetic structure of Z. latifolia.
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Addis BR, Lowe WH. Environmentally associated variation in dispersal distance affects inbreeding risk in a stream salamander. Am Nat 2022; 200:802-814. [DOI: 10.1086/721763] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Yakimowski SB, Southcott L, Barrett SCH. Contrasting patterns of genetic diversity and differentiation across the continental disjunct range of a sexually polymorphic aquatic plant. ANNALS OF BOTANY 2022; 130:27-40. [PMID: 35511701 PMCID: PMC9295920 DOI: 10.1093/aob/mcac056] [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: 12/08/2021] [Accepted: 04/28/2022] [Indexed: 05/05/2023]
Abstract
BACKGROUND AND AIMS Reproductive systems enabling opportunities for self-fertilization influence population genetic structure and play a key role in colonization and genetic differentiation during range expansion. Because of their well-developed powers of dispersal, aquatic plants often have widespread disjunct geographical distributions, providing opportunities to investigate the role of reproductive systems in structuring genetic variation between parts of the range that differ in migration history and ecology. METHODS We compared reproductive systems and spatial genetic structure of the freshwater aquatic macrophyte Sagittaria latifolia between disjunct western and eastern ranges of North America (NA). Populations of this species are most commonly either monoecious or dioecious. We examined chloroplast DNA haplotype variation to test the hypothesis that the western range of this species represents a secondary colonization from the east, and evaluated the roles of reproductive system differences and geography in structuring contemporary patterns of genetic variation at 11 polymorphic SSR (simple sequence repeat) loci. KEY RESULTS Chloroplast haplotyping revealed a single haplotype in western NA compared to numerous haplotypes in eastern NA, consistent with a genetic bottleneck during westward migration. Estimates of genetic diversity in eastern NA populations differed significantly between reproductive systems, but this pattern was not evident in the western range. Eastern populations could be reliably assigned to genetic clusters based on their reproductive systems, whereas western populations clustered primarily by geographical location. CONCLUSIONS The sparser distribution of aquatic habitats in the drier western range of S. latifolia, combined with secondary colonization of this region, probably cause the lower genetic diversity and increased differentiation among populations, possibly overriding the effects of reproductive system evident in the eastern portion of the range. Our findings demonstrate that the complex interplay between migratory history, reproductive systems and habitat availability plays an important role in structuring spatial patterns of genetic variation in disjunct plant populations.
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Affiliation(s)
| | - Laura Southcott
- Department of Ecology and Evolutionary Biology, 25 Willcocks Street, University of Toronto, Toronto, ON, Canada
- Committee on Evolutionary Biology, Chicago, IL, USA
| | - Spencer C H Barrett
- Department of Ecology and Evolutionary Biology, 25 Willcocks Street, University of Toronto, Toronto, ON, Canada
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Nouri-Aiin M, Connolly S, Keough C, Smigelsky AJ, Wen Y, Howland J, Schall JJ, Görres JH. Genetic population structure and reproductive system of two invasive Asian earthworms, Amynthas tokioensis and Amynthas agrestis. PeerJ 2022; 10:e13622. [PMID: 35855901 PMCID: PMC9288164 DOI: 10.7717/peerj.13622] [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: 03/14/2022] [Accepted: 06/02/2022] [Indexed: 01/17/2023] Open
Abstract
The invasive Asian earthworms, Amynthas tokioensis and A. agrestis, have been successful in entering North American forests in recent decades, with significant damage to both soils and above-ground environments. This success could be driven in part by a polyploid genetic system and parthenogenetic reproduction, often suggested as benefits for invasive species. Therefore, we assessed the genetic population structure, genetic diversity, and reproductive system of both species using morphological traits and panels of microsatellite markers. A total of 216 A. tokioensis and 196 A. agrestis from six sites in Vermont USA were analyzed. Although all worms were morphologically hermaphroditic, all the A. agrestis lacked the male pore (the structure allowing pass of sperm between individuals), and only 19% of the A. tokioensis possessed the male pore. All A. tokioensis earthworms were triploid (scored for three alleles for at least 1 locus, and usually several), and A. agrestis was a mix of triploid and diploid individuals. Notable was the high proportion (80%) of A. agrestis earthworms that were diploid at one site. There was clearly clonal reproduction, with identical seven- locus genotypes observed for earthworms from each site, with as many as 45 individuals with the identical genotype at one site. However, the earthworms were also genetically diverse, with 14 genotypes observed for A. tokioensis and 54 for A. agrestis, and with many singleton genotypes (a single individual). Most genotypes (71% for A. tokioensis and 92% for A. agrestis) were found at a single site. The greatest number of genotypes was found at a commercial nursery where fully 23/26 A. agrestis earthworms were singleton genotypes. As expected for the pattern of private clone alleles at sites, several measures of geographic genetic differentiation were positive, and as expected for triploid systems, an AMOVA analysis showed high within-individual genetic diversity. The paradox of clear clonal reproduction, but with a great number of genotypes for each species, and the mix of triploid and diploid individuals could be explained if the worms have been sexually reproductive, with the switch to the uniparental system only recently (or even if sexual reproduction is episodic). Last, a large number of microsatellite loci were recovered for each species and there sequence and suggested PCR primers are provided for free use by other researchers.
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Affiliation(s)
- Maryam Nouri-Aiin
- Plant and Soil Science Department, University of Vermont, Burlington, VT, United States of America
| | - Samantha Connolly
- Plant Biology Department, University of Vermont, Burlington, VT, United States of America
| | - Cheryl Keough
- Plant and Soil Science Department, University of Vermont, Burlington, VT, United States of America
| | - Annie Jean Smigelsky
- Plant and Soil Science Department, University of Vermont, Burlington, VT, United States of America
| | - Yiyi Wen
- Environmental Science, Rubinstein School of the Environment, University of Vermont, Burlington, VT, United States of America
| | - Jeremy Howland
- Plant and Soil Science Department, University of Vermont, Burlington, VT, United States of America
| | - Jos. J. Schall
- Department of Biology, University of Vermont, Burlington, VT, United States of America
| | - Josef H. Görres
- Plant and Soil Science Department, University of Vermont, Burlington, VT, United States of America
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Jones FA, Hadley AS, Bonner K, Zahawi RA, Robinson WD, Kormann U, Betts MG. Elevated inbreeding in Heliconia tortuosa is determined by tropical forest stand age, isolation, and loss of hummingbird functional diversity. Mol Ecol 2022; 31:4465-4477. [PMID: 35808851 DOI: 10.1111/mec.16607] [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: 02/19/2021] [Revised: 06/10/2022] [Accepted: 06/29/2022] [Indexed: 11/27/2022]
Abstract
Forest conversion and habitat loss are major threats to biological diversity. Forest regeneration can mitigate the negative effects of old growth forest loss on species diversity, but less is known about the extent to which forest loss reduces genetic diversity in remnant populations and whether secondary forests play a role in the maintenance of genetic diversity. We quantified genetic diversity in a tropical hummingbird-pollinated understory herb, Heliconia tortuosa, across a landscape mosaic of primary and secondary forest regrowth. Using microsatellite genotypes from >850 adult and juvenile plants within 33 forest patches and extensive bird surveys, we examined the effect of contemporary and historical landscape features including forest age (primary vs. secondary forest), stand isolation, and pollinator assemblages on genetic diversity and levels of inbreeding in H. tortuosa. We found that inbreeding was up to 3x higher in secondary forest, and this effect was amplified with reductions in primary forest in the surrounding landscape through reduced observed heterozygosity in isolated fragments. Inbreeding in forest patches was negatively correlated with the local frequency of specialist long-distance foraging traplining hummingbirds. Traplining hummingbirds therefore appear to facilitate mating among unrelated plants - an inference we tested using empirically parameterized simulations. Higher levels of inbreeding in H. tortuosa are therefore associated with reduced functional diversity of hummingbirds in secondary forests and forest patches isolated from primary forests. Our findings suggest a cryptic consequence of primary forest loss and secondary forest regeneration through the disruption of mutualistic interactions resulting in the erosion of genetic diversity in a common understory plant.
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Affiliation(s)
- F Andrew Jones
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA.,Smithsonian Tropical Research Institute, Panama City, Panama
| | - Adam S Hadley
- Forest Biodiversity Research Network, Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA
| | - Kaitlin Bonner
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA.,Department of Biology, St. John Fisher College, Rochester, NY, USA
| | - Rakan A Zahawi
- School of Life Sciences and Lyon Arboretum, University of Hawai'i at Mānoa, Honolulu, HI, USA.,Charles Darwin Foundation, Puerto Ayora, Galapagos, Ecuador
| | - W Douglas Robinson
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, USA
| | - Urs Kormann
- Forest Biodiversity Research Network, Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA.,Division of Forest Sciences, School of Agricultural, Forest & Food Sciences, Bern University of Applied Sciences, Zollikofen, Switzerland.,Swiss Ornithological Institute, Sempach, Switzerland
| | - Matthew G Betts
- Forest Biodiversity Research Network, Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA
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Radačovská A, Čisovská Bazsalovicsová E, Šoltys K, Štefka J, Minárik G, Gustinelli A, Chugunova JK, Králová-Hromadová I. Unique genetic structure of the human tapeworm Dibothriocephalus latus from the Alpine lakes region - a successful adaptation? Parasitology 2022; 149:1106-1118. [PMID: 35570686 PMCID: PMC11010471 DOI: 10.1017/s0031182022000634] [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: 01/13/2022] [Revised: 04/22/2022] [Accepted: 04/29/2022] [Indexed: 11/07/2022]
Abstract
Dibothriocephalus latus is the most frequent causative agent of fish-borne zoonosis (diphyllobothriosis) in Europe, where it is currently circulating mainly in the Alpine lakes region (ALR) and Russia. Three mitochondrial genes (cox1, cob and nad3) and 6 microsatellite loci were analysed to determine how is the recently detected triploidy/parthenogenesis in tapeworms from ALR displayed at the DNA level. A geographically distant population from the Krasnoyarsk Reservoir in Russia (RU-KR) was analysed as a comparative population. One or 2 alleles of each microsatellite locus was detected in plerocercoids from RU-KR, corresponding to the microsatellite pattern of a diploid organism. In contrast, 1–3 alleles were observed in tapeworms from ALR, in accordance with their triploidy. The high diversity of mitochondrial haplotypes in D. latus from RU-KR implied an original and relatively stable population, but the identical structure of mitochondrial genes of tapeworms from ALR was probably a consequence of a bottleneck typical of introduced populations. These results indicated that the diploid/sexually reproducing population from RU-KR was ancestral, located within the centre of the distribution of the species, and the triploid/parthenogenetically reproducing subalpine population was at the margin of the distribution. The current study revealed the allelic structure of the microsatellite loci in the triploid tapeworm for the first time.
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Affiliation(s)
- Alžbeta Radačovská
- Institute of Parasitology, Slovak Academy of Sciences, Hlinkova 3, 04001 Košice, Slovakia
| | | | - Katarína Šoltys
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 84215 Bratislava, Slovakia
| | - Jan Štefka
- Biology Centre CAS, Institute of Parasitology, Branišovská 31, 37005 České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, Branišovská 1760, 37005 České Budějovice, Czech Republic
| | - Gabriel Minárik
- Medirex, a.s., Galvaniho 17/C, P.O. Box 143, 82016 Bratislava, Slovakia
| | - Andrea Gustinelli
- Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra 50, 40064 Ozzano Emilia, BO, Italy
| | - Julia K. Chugunova
- Krasnoyarsk Branch of the Russian Federal Research Institute of Fisheries and Oceanography ‘VNIRO’, Parizhskoi Kommuny, 33, 660097 Krasnoyarsk, Russia
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49
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Baker CM, Ballesteros JA, Aharon S, Gainett G, Armiach Steinpress I, Wizen G, Sharma PP, Gavish-Regev E. Recent speciation and phenotypic plasticity within a parthenogenetic lineage of Levantine whip spiders (Chelicerata: Amblypygi: Charinidae). Mol Phylogenet Evol 2022; 175:107560. [PMID: 35779767 DOI: 10.1016/j.ympev.2022.107560] [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: 03/21/2022] [Revised: 05/25/2022] [Accepted: 06/02/2022] [Indexed: 10/17/2022]
Abstract
Caves constitute ideal study systems for investigating adaptation and speciation, as the abiotic conditions shared by aphotic habitats exert a set of environmental filters on their communities. Arachnids constitute an important component of many cave ecosystems worldwide. We investigated the population genomics of two whip spider species: Sarax ioanniticus, a widely distributed parthenogenetic species found across the eastern Mediterranean; and S. israelensis, a recently described troglomorphic species that is endemic to caves in Israel. Here, we show that S. israelensis is completely genetically distinct from S. ioanniticus and most likely also constitutes a parthenogen. Counterintuitively, despite the lack of genetic variability within S. ioanniticus and S. israelensis, we discovered considerable variation in the degree of median eye reduction, particularly in the latter species. Natural history data from captive-bred specimens of S. israelensis validated the interpretation of parthenogenesis. Our results are most consistent with a scenario of a sexual ancestral species that underwent speciation, followed by independent transitions to apomictic parthenogenesis in each of the two daughter species. Moreover, the lack of genetic variability suggests that variation in eye morphology in S. israelensis is driven exclusively by epigenetic mechanisms.
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Affiliation(s)
- Caitlin M Baker
- Department of Integrative Biology, University of Madison-Wisconsin, Madison, WI 53706, United States
| | | | - Shlomi Aharon
- The National Natural History Collections, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel; Department of Ecology, Evolution & Behavior, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Guilherme Gainett
- Department of Integrative Biology, University of Madison-Wisconsin, Madison, WI 53706, United States
| | - Igor Armiach Steinpress
- The National Natural History Collections, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel; Department of Ecology, Evolution & Behavior, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Gil Wizen
- 602-52 Park St. E, Mississauga, Ontario, L5G 1M1, Canada
| | - Prashant P Sharma
- Department of Integrative Biology, University of Madison-Wisconsin, Madison, WI 53706, United States
| | - Efrat Gavish-Regev
- The National Natural History Collections, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel.
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50
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Colihueque N, Cabello J, Fuentes-Moliz A. Genetic divergence and demography of pudu deer (Pudu puda) in five provinces of southern Chile, analyzed through latitudinal and longitudinal ranges. NEOTROPICAL BIOLOGY AND CONSERVATION 2022. [DOI: 10.3897/neotropical.17.e81324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Pudu deer (Pudu puda) is endemic to the temperate rainforests of Chile. Genetic studies at different geographic scales for this species are required to better determine the genetic divergence within and among populations and their demography across the distribution range. These data can provide unique insights into the species or population status for conservation plans and decision-makers. We analyzed the mtDNA control region (CR) and cytochrome b (Cyt b) sequences of pudu deer in five provinces of southern Chile located at different latitudinal locations (Cautín, Valdivia, Osorno, Llanquihue and Chiloé Island) and three geographic areas within the studied provinces, representative of different longitudinal sites (Andes range, Central Valley and Coastal Range), to understand their genetic divergence and demography. The haplotype (H) and nucleotide (Π) diversities of CR and Cyt b ranged from 0.64286 to 0.98333 and from 0.00575 to 0.01022, respectively. CR diversity was significantly different among provinces, with Valdivia showing higher values than Llanquihue and Chiloé Island (H = 0.98333 vs. 0.64286–0.92727, P < 0.05). Cyt b variation also showed significant differences among provinces, particularly, among Cautín and Llanquihue (H = 1.000 vs. 0.222, P < 0.05). Genetic structuring among provinces was relatively high, as indicated by the FST index (FST = 0.41905). Clustering analysis indicated the presence of a distinctive cluster for Chiloé Island individuals. Fu’s FS and Tajima’s D based on CR revealed significant, negative deviations from equilibrium for Chiloé Island (D = -1.65898), Valdivia (Fs = -7.75335) and Llanquihue (Fs = -3.93267), suggesting population expansion in these provinces. Analysis at the longitudinal range showed significant differences among areas based on Π (P < 0.05), with the Andes range and Central Valley showing higher diversity than the Coastal Range. Neither population structuring (FST = 0.01360, P > 0.05) nor distinctive clusters in the longitudinal range were observed. Fu’s Fs and Tajima’s D were negative and significant for the Coastal Range based on CR (Fs = -6.64752, P < 0.001) and Cyt b (D = -1.74110, P < 0.05), suggesting the existence of population expansion. Our results suggest that pudu deer in the analyzed provinces is a genetically structured species, which could be associated with reduced panmixia among populations. The genetic divergence pattern and the population expansion recorded are likely to be associated with past processes of recolonization after Pleistocene glaciation events.
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