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Mbo Nkoulou LF, Nkouandou YF, Ngalle HB, Cros D, Martin G, Molo T, Eya'a C, Essome C, Zandjanakou-Tachin M, Degbey H, Bell J, Achigan-Dako EG. Screening of Triploid Banana Population Under Natural and Controlled Black Sigatoka Disease for Genomic Selection. PLANT DISEASE 2024; 108:2006-2016. [PMID: 38243182 DOI: 10.1094/pdis-04-23-0741-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2024]
Abstract
Black sigatoka disease (BSD) is the most important foliar threat in banana production, and breeding efforts against it should take advantage of genomic selection (GS), which has become one of the most explored tools to increase genetic gain, save time, and reduce selection costs. To evaluate the potential of GS in banana for BSD, 210 triploid accessions were obtained from the African Banana and Plantain Research Center to constitute a training population. The variability in the population was assessed at the phenotypic level using BSD- and agronomic-related traits and at the molecular level using single-nucleotide polymorphisms (SNPs). The analysis of variance showed a significant difference between accessions for almost all traits measured, although at the genomic group level, there was no significant difference for BSD-related traits. The index of non-spotted leaves among accessions ranged from 0.11 to 0.8. The accessions screening in controlled conditions confirmed the susceptibility of all genomic groups to BSD. The principal components analysis with phenotypic data revealed no clear diversity partition of the population. However, the structure analysis and the hierarchical clustering analysis with SNPs grouped the population into four clusters and two subpopulations, respectively. The field and laboratory screening of the banana GS training population confirmed that all genomic groups are susceptible to BSD but did not reveal any genetic structure, whereas SNP markers exhibited clear genetic structure and provided useful information in the perspective of applying GS.
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Affiliation(s)
- Luther Fort Mbo Nkoulou
- Genetics, Biotechnology, and Seed Science Unit (GBioS), Laboratory of Crop Production, Physiology, Genetics and Plant Breeding (PAGEV), University of Abomey-Calavi, Abomey-Calavi, School of Plant Sciences, Cotonou, Republic of Benin
- Unit of genetics and plant Breeding (UGAP), Department of Plant Biology, Faculty of Science, University of Yaoundé 1, Yaoundé, Cameroon
- Institute of Agricultural Research for Development, Mbalmayo Agricultural Research Centre (CRA-MB) Mbalmayo, Mbalmayo, Cameroon
- Centre de Recherche et d'Accompagnement des Producteurs Agro-pastoraux du Cameroun, Boumyebel, Cameroun
| | - Yacouba Fifen Nkouandou
- Unit of genetics and plant Breeding (UGAP), Department of Plant Biology, Faculty of Science, University of Yaoundé 1, Yaoundé, Cameroon
| | - Hermine Bille Ngalle
- Unit of genetics and plant Breeding (UGAP), Department of Plant Biology, Faculty of Science, University of Yaoundé 1, Yaoundé, Cameroon
| | - David Cros
- Unité Mixte de Recherche (UMR), Amélioration Génétique et Adaptation des Plantes méditerranéennes et tropicales (AGAP) Institut, Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Montpellier, France
- Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Unité Mixte de Recherche (UMR), Amélioration Génétique et Adaptation des Plantes méditerranéennes et tropicales (AGAP) Institut, F-34398 Montpellier, France
| | - Guillaume Martin
- Unité Mixte de Recherche (UMR), Amélioration Génétique et Adaptation des Plantes méditerranéennes et tropicales (AGAP) Institut, Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Montpellier, France
- Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Unité Mixte de Recherche (UMR), Amélioration Génétique et Adaptation des Plantes méditerranéennes et tropicales (AGAP) Institut, F-34398 Montpellier, France
| | - Thierry Molo
- Unit of genetics and plant Breeding (UGAP), Department of Plant Biology, Faculty of Science, University of Yaoundé 1, Yaoundé, Cameroon
- Centre de Recherche et d'Accompagnement des Producteurs Agro-pastoraux du Cameroun, Boumyebel, Cameroun
| | - Clement Eya'a
- Unit of genetics and plant Breeding (UGAP), Department of Plant Biology, Faculty of Science, University of Yaoundé 1, Yaoundé, Cameroon
- Lipids analysis Laboratory, Institute of Agricultural Research for Development, Specialized Station for Oil Palm of La Dibamba, Douala, Cameroon
| | - Charles Essome
- Laboratory of Phytopathology and Crop Protection, Department of Plant Biology, University of Yaoundé I, 812, Yaoundé, Cameroon
| | - Martine Zandjanakou-Tachin
- School of Horticulture and Landscape Management (UNA), National University of Agriculture, Ketou, Republic of Benin
| | - Hervé Degbey
- Genetics, Biotechnology, and Seed Science Unit (GBioS), Laboratory of Crop Production, Physiology, Genetics and Plant Breeding (PAGEV), University of Abomey-Calavi, Abomey-Calavi, School of Plant Sciences, Cotonou, Republic of Benin
| | - Joseph Bell
- Unit of genetics and plant Breeding (UGAP), Department of Plant Biology, Faculty of Science, University of Yaoundé 1, Yaoundé, Cameroon
| | - Enoch G Achigan-Dako
- Genetics, Biotechnology, and Seed Science Unit (GBioS), Laboratory of Crop Production, Physiology, Genetics and Plant Breeding (PAGEV), University of Abomey-Calavi, Abomey-Calavi, School of Plant Sciences, Cotonou, Republic of Benin
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Ul Islam S, Ahmed Mangral Z, Tariq L, Ahmad Bhat B, Waseem Tantray W, Ahmad R, Ahmad Khuroo A, Ul Hassan Dar T. Conservation genetics of endangered Trillium govanianum Wall. ex D. Don - A pharmaceutically prized medicinal plant from the Himalaya and implications for species recovery. Gene 2023; 888:147748. [PMID: 37652171 DOI: 10.1016/j.gene.2023.147748] [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: 03/26/2023] [Revised: 08/20/2023] [Accepted: 08/28/2023] [Indexed: 09/02/2023]
Abstract
Understanding the genetic diversity and population structure of pharmaceutically important endangered plant species is crucial for their conservation and sustainable use. Despite the continuous population decline in Trillium govanianum Wall. ex D. Don, a highly prized medicinal plant endemic to the Himalaya, information regarding its conservation genetics has been lacking. Here, we employed a conservation genetics approach to investigate how drastically declining populations in natural habitats impact population genetic diversity and structure of this endangered species across the Kashmir Himalaya. We used Start codon targeted (SCoT) and Simple sequence repeat (SSR) markers to assess the intra- and inter-population genetic variation in seven sites across the study region. Based on these markers, we found a very low genetic diversity in T. govanianum populations. Very low levels of observed heterozygosity (Ho = 0.000) and that expected (He = 0.064) in the populations indicate high heterozygote deficiency and high levels of inbreeding depression (FIS = 1.000). A high genetic differentiation was observed among the populations for both SCoT (Gst = 0.719) and SSR (Fst = 0.707) markers. Both the markers showed low gene flow, SCoT (Nm = 0.195) and SSR (Nm = 0.119), depicting high among-population variation than within-population variation. Analysis of molecular variance also indicated a higher genetic variation between the populations than within populations. We also observed a significant positive correlation between genetic divergence and geographical distance, indicating that genetic differentiation in T. govanianum follows a pattern of isolation by distance. Bayesian structure and cluster analysis grouped the populations according to their geographical proximity. Further, redundancy analysis (RDA) revealed the presence of one polymorphic locus for each marker with high discriminatory power. Overall, our findings reveal a very low genetic diversity, high levels of inbreeding, and high genetic differentiation among the populations; likely resulting from habitat fragmentation, population isolation, bottleneck effect, low gene flow, and predominantly asexual reproduction currently operative in the species. Finally, based on the insights gained, we discuss the potential implications of our findings in guiding species recovery and habitat rehabilitation of T. govanianum in the Himalaya with conservation lessons for elsewhere in the world.
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Affiliation(s)
- Shahid Ul Islam
- Department of Biotechnology, School of Biosciences and Biotechnology, BGSB University, Rajouri, Jammu and Kashmir, India
| | - Zahid Ahmed Mangral
- Department of Biotechnology, School of Biosciences and Biotechnology, BGSB University, Rajouri, Jammu and Kashmir, India
| | - Lubna Tariq
- Department of Biotechnology, School of Biosciences and Biotechnology, BGSB University, Rajouri, Jammu and Kashmir, India
| | - Basharat Ahmad Bhat
- Department of Bioresources, Amar Singh College Campus, Cluster University Srinagar, Jammu and Kashmir, India
| | - Wajahat Waseem Tantray
- Department of Biotechnology, School of Biosciences and Biotechnology, BGSB University, Rajouri, Jammu and Kashmir, India
| | - Rameez Ahmad
- Centre for Biodiversity and Taxonomy, Department of Botany, University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Anzar Ahmad Khuroo
- Centre for Biodiversity and Taxonomy, Department of Botany, University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Tanvir Ul Hassan Dar
- Department of Biotechnology, School of Biosciences and Biotechnology, BGSB University, Rajouri, Jammu and Kashmir, India.
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Luan L, Shi G, Zhu G, Zheng J, Fan J, Dini-Andreote F, Sun B, Jiang Y. Biogeographical patterns of abundant and rare bacterial biospheres in paddy soils across East Asia. Environ Microbiol 2023; 25:294-305. [PMID: 36353981 DOI: 10.1111/1462-2920.16281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 11/08/2022] [Indexed: 11/11/2022]
Abstract
Soil bacterial communities play fundamental roles in ecosystem functioning and often display a skewed distribution of abundant and rare taxa. So far, relatively little is known about the biogeographical patterns and mechanisms structuring the assembly of abundant and rare biospheres of soil bacterial communities. Here, we studied the geographical distribution of different bacterial sub-communities by examining the relative influence of environmental selection and dispersal limitation on taxa distributions in paddy soils across East Asia. Our results indicated that the geographical patterns of four different bacterial sub-communities consistently displayed significant distance-decay relationships (DDRs). In addition, we found niche breadth and dispersal rates to significantly explain differences in community assembly of abundant and rare taxa, directly affecting the strength of DDRs. While conditionally rare and abundant taxa displayed the strongest DDR due to higher environmental filtering and dispersal limitation, moderate taxa sub-communities had the weakest DDR due to greater environmental tolerance and dispersal rate. Random forest models indicated that soil pH (9.13%-49.78%) and average annual air temperature (16.59%-46.49%) were the most important predictors of the variation in the bacterial community. This study advances our understanding of the intrinsic links between fundamental ecological processes and microbial biogeographical patterns in paddy soils.
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Affiliation(s)
- Lu Luan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Guangping Shi
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Guofan Zhu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Jie Zheng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Jianbo Fan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Francisco Dini-Andreote
- Department of Plant Science & Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Bo Sun
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Yuji Jiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
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4
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Ex situ versus in situ Eurasian lynx populations: implications for successful breeding and genetic rescue. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01494-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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5
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Ilves A, Kaljund K, Sild E, Münzbergová Z. High genetic variation of Trifolium alpestre at the northern margin: but for how long? CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01490-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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6
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Ishihara MA, Domingos FMCB, Gomides SC, Novelli IA, Colli GR, Vargas SM. Genetic structure of Enyalius capetinga (Squamata, Leiosauridae) in Central Cerrado and transitional areas between the Cerrado and the Atlantic forest, with updated geographic distribution. Genetica 2022; 150:367-377. [PMID: 36229707 DOI: 10.1007/s10709-022-00170-w] [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: 08/20/2021] [Accepted: 09/28/2022] [Indexed: 11/26/2022]
Abstract
The Brazilian Cerrado is considered a biodiversity hotspot highly threatened by human activities. Recently, many studies have demonstrated how underestimated is Cerrado's biodiversity considering squamate species, and the identification of divergent and cryptic lineages is essential for the formulation of effective conservation strategies. The transition areas between the Cerrado and the Atlantic Forest are even less known and, consequently, often dismissed in conservation policies. As previous studies suggested the presence of cryptic diversity within E. capetinga, we investigated patterns and processes in the geographic distribution of its genealogical lineages. We used DNA sequences from individuals collected in six localities and sequences publicly available from three mitochondrial markers (CYT-B, 16S and ND4) and one nuclear marker (C-Mos). We tested if the core and ecotone regions of the Cerrado show differences in biotic and abiotic characteristics that could promote genetic structure and divergence among lineages within E. capetinga. We found evidence for divergent lineages within the species, but not congruent with our hypothesis. Similar divergent patterns were observed in other Cerrado lizards, including interspecific divergences within the Enyalius genus. Molecular characterization of field-collected individuals (previously identified as E. bilineatus), allowed us to update the geographic distribution of the species to include the ecotone between the Cerrado and the Atlantic Forest, an area where species distribution overlap.
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Affiliation(s)
- M A Ishihara
- Departamento de Ciências Biológicas, Laboratório de Genética E Evolução Molecular, Universidade Federal Do Espírito Santo, Vitória, ES, 29075-910, Brazil.
- Universidade Federal Do Espírito Santo, Vitória, ES, 29075-910, Brazil.
| | - F M C B Domingos
- Departamento de Zoologia, Universidade Federal Do Paraná, Curitiba, PR, 81531-980, Brazil
| | - S C Gomides
- Programa de Pós-Graduação em Biodiversidade, Universidade Federal do Oeste do Pará, Campus Oriximiná, Rodovia PA-254, 257, Oriximiná, PA, 68270-000, Brazil
| | - I A Novelli
- Laboratório de Zoologia, Centro Universitário de Lavras - UNILAVRAS, Lavras, MG, 37203-593, Brazil
| | - G R Colli
- Departamento de Zoologia, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - S M Vargas
- Departamento de Ciências Biológicas, Laboratório de Genética E Evolução Molecular, Universidade Federal Do Espírito Santo, Vitória, ES, 29075-910, Brazil
- Universidade Federal Do Espírito Santo, Vitória, ES, 29075-910, Brazil
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Kusuma YWC, Matsuo A, Suyama Y, Wanke S, Isagi Y. Conservation genetics of three Rafflesia species in Java Island, Indonesia using SNP markers obtained from MIG-seq. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01470-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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8
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Abstract
The ways in which genetic variation is distributed within and among populations is a key determinant of the evolutionary features of a species. However, most comprehensive studies of these features have been restricted to studies of subdivision in settings known to have been driven by local adaptation, leaving our understanding of the natural dispersion of allelic variation less than ideal. Here, we present a geographic population-genomic analysis of 10 populations of the freshwater microcrustacean Daphnia pulex, an emerging model system in evolutionary genomics. These populations exhibit a pattern of moderate isolation-by-distance, with an average migration rate of 0.6 individuals per generation, and average effective population sizes of ∼650,000 individuals. Most populations contain numerous private alleles, and genomic scans highlight the presence of islands of excessively high population subdivision for more common alleles. A large fraction of such islands of population divergence likely reflect historical neutral changes, including rare stochastic migration and hybridization events. The data do point to local adaptive divergence, although the precise nature of the relevant variation is diffuse and cannot be associated with particular loci, despite the very large sample sizes involved in this study. In contrast, an analysis of between-species divergence highlights positive selection operating on a large set of genes with functions nearly nonoverlapping with those involved in local adaptation, in particular ribosome structure, mitochondrial bioenergetics, light reception and response, detoxification, and gene regulation. These results set the stage for using D. pulex as a model for understanding the relationship between molecular and cellular evolution in the context of natural environments.
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Affiliation(s)
- Takahiro Maruki
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287, USA
| | - Zhiqiang Ye
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287, USA
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287, USA
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Cortazar-Chinarro M, Meurling S, Schroyens L, Siljestam M, Richter-Boix A, Laurila A, Höglund J. Major Histocompatibility Complex Variation and Haplotype Associated Survival in Response to Experimental Infection of Two Bd-GPL Strains Along a Latitudinal Gradient. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.915271] [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
While both innate and adaptive immune system mechanisms have been implicated in resistance against the chytrid fungus Batrachochytrium dendrobatidis (Bd), studies on the role of specific MHC haplotypes on Bd infection are rare. Here, we studied variation in MHC Class IIB loci in the common toad Bufo bufo along a latitudinal gradient across Sweden. In general, Swedish toad populations had few MHC Class IIB haplotypes and MHC diversity declined from south (13 haplotypes) to the north (four haplotypes). The low diversity may compromise the ability of northern populations to fight emerging disease, such as Bd. In a laboratory experiment, we infected newly metamorphosed toads with two strains of the Global Pandemic Lineage of the fungus (Bd-GPL) and compared survival with sham controls. Bd-infected toads had lower survival compared to controls. Moreover, survival was dependent on the Bd-strain and northern toads had lower Bd-mediated survival than southern individuals. MHC diversity was lower in northern toads. All northern experimental animals were monomorphic for a single MHC haplotype, whereas we found seven different haplotypes in southern experimental animals. In southern toads, survival was dependent on both Bd-strain and MHC haplotype suggesting differential infection dynamics depending on both Bd-strain and host immune system characteristics.
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Ranathunge C, Chimahusky ME, Welch ME. A comparative study of population genetic structure reveals patterns consistent with selection at functional microsatellites in common sunflower. Mol Genet Genomics 2022; 297:1329-1342. [PMID: 35786764 DOI: 10.1007/s00438-022-01920-3] [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: 12/25/2021] [Accepted: 06/16/2022] [Indexed: 10/17/2022]
Abstract
Microsatellites, also known as short tandem repeats (STRs), have long been considered non-functional, neutrally evolving regions of the genome. Recent findings suggest that they can function as drivers of rapid adaptive evolution. Previous work on the common sunflower identified 479 transcribed microsatellites where allele length significantly correlates with gene expression (eSTRs) in a stepwise manner. Here, a population genetic approach is used to test whether eSTR allele length variation is under selection. Genotypic variation among and within populations at 13 eSTRs was compared with that at 19 anonymous microsatellites in 672 individuals from 17 natural populations of sunflower from across a cline running from Saskatchewan to Oklahoma (distance of approximately 1600 km). Expected heterozygosity, allelic richness, and allelic diversity were significantly lower at eSTRs, a pattern consistent with higher relative rates of purifying selection. Further, an analysis of variation in microsatellite allele lengths (lnRV), and heterozygosities (lnRH), indicate recent selective sweeps at the eSTRs. Mean microsatellite allele lengths at four eSTRs within populations are significantly correlated with latitude consistent with the predictions of the tuning-knob model which predicts stepwise relationships between microsatellite allele length and phenotypes. This finding suggests that shorter or longer alleles at eSTRs may be favored in climatic extremes. Collectively, our results imply that eSTRs are likely under selection and that they may be playing a role in facilitating local adaptation across a well-defined cline in the common sunflower.
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Affiliation(s)
- Chathurani Ranathunge
- Department of Biological Sciences, Mississippi State University, Starkville, MS, 39762, USA.
- School of Health Professions, Eastern Virginia Medical School, Norfolk, VA, 23507, USA.
| | - Melody E Chimahusky
- Department of Biological Sciences, Mississippi State University, Starkville, MS, 39762, USA
| | - Mark E Welch
- Department of Biological Sciences, Mississippi State University, Starkville, MS, 39762, USA
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11
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Schmidt C, Muñoz G, Lancaster LT, Lessard JP, Marske KA, Marshall KE, Garroway CJ. Population demography maintains biogeographic boundaries. Ecol Lett 2022; 25:1905-1913. [PMID: 35753949 DOI: 10.1111/ele.14058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 05/11/2022] [Accepted: 05/24/2022] [Indexed: 11/27/2022]
Abstract
Global biodiversity is organised into biogeographic regions that comprise distinct biotas. The contemporary factors maintaining differences in species composition between regions are poorly understood. Given evidence that populations with sufficient genetic variation can adapt to fill new habitats, it is surprising that more homogenisation of species assemblages across regions has not occurred. Theory suggests that expansion across biogeographic regions could be limited by reduced adaptive capacity due to demographic variation along environmental gradients, but this possibility has not been empirically explored. Using three independently curated data sets describing continental patterns of mammalian demography and population genetics, we show that populations near biogeographic boundaries have lower effective population sizes and genetic diversity, and are more genetically differentiated. These patterns are consistent with reduced adaptive capacity in areas where one biogeographic region transitions into the next. That these patterns are replicated across mammals suggests they are stable and generalisable in their contribution to long-term limits on biodiversity homogenisation. Understanding the contemporary processes that maintain compositional differences among regional biotas is crucial for our understanding of the current and future organisation of global biodiversity.
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Affiliation(s)
- Chloé Schmidt
- Department of Biological Sciences, University of Manitoba, Winnipeg, Canada
| | - Gabriel Muñoz
- Faculty of Arts and Sciences, Department of Biology, Concordia University, Montréal, Canada
| | | | - Jean-Philippe Lessard
- Faculty of Arts and Sciences, Department of Biology, Concordia University, Montréal, Canada
| | | | - Katie E Marshall
- Department of Zoology, University of British Columbia, Vancouver, Canada
| | - Colin J Garroway
- Department of Biological Sciences, University of Manitoba, Winnipeg, Canada
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Alcala N, Rosenberg NA. Mathematical constraints on FST: multiallelic markers in arbitrarily many populations. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200414. [PMID: 35430885 PMCID: PMC9014193 DOI: 10.1098/rstb.2020.0414] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/23/2021] [Indexed: 11/12/2022] Open
Abstract
Interpretations of values of the FST measure of genetic differentiation rely on an understanding of its mathematical constraints. Previously, it has been shown that FST values computed from a biallelic locus in a set of multiple populations and FST values computed from a multiallelic locus in a pair of populations are mathematically constrained as a function of the frequency of the allele that is most frequent across populations. We generalize from these cases to report here the mathematical constraint on FST given the frequency M of the most frequent allele at a multiallelic locus in a set of multiple populations. Using coalescent simulations of an island model of migration with an infinitely-many-alleles mutation model, we argue that the joint distribution of FST and M helps in disentangling the separate influences of mutation and migration on FST. Finally, we show that our results explain a puzzling pattern of microsatellite differentiation: the lower FST in an interspecific comparison between humans and chimpanzees than in the comparison of chimpanzee populations. We discuss the implications of our results for the use of FST. This article is part of the theme issue 'Celebrating 50 years since Lewontin's apportionment of human diversity'.
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Affiliation(s)
- Nicolas Alcala
- Rare Cancers Genomics Team (RCG), Genetic Epidemiology Branch (GEM), International Agency for Research on Cancer/World Health Organization, Lyon 69008, France
| | - Noah A. Rosenberg
- Department of Biology, Stanford University, Stanford, CA 94305-5020, USA
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Wang X, Tong L, Deng J, Li L, Xiang P, Xu L, Luo Z, Yang K, Song Z. Insights into historical drainage evolution based on the phylogeography of Schizopygopsis malacanthus Herzenstein (Cypriniformes, Cyprinidae) across the upper and middle Yalong River drainage in the Hengduan Mountains region, southwest China. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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14
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Otolith Microchemistry and Demographic History Provide New Insight into the Migratory Behavior and Heterogeneous Genetic Divergence of Coilia grayii in the Pearl River. FISHES 2022. [DOI: 10.3390/fishes7010023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Coilia grayii is the anadromous form of anchovy that is distributed in the East and South China Seas. It is a common fish species in the estuarine area of the Pearl River. Nevertheless, freshwater populations appear upstream in the Pearl River, but the migratory pathway has been mostly impeded by dam construction. Behavioral differences and constrained habitat within tributaries are suspected of promoting genetic divergence in these populations. In this study, we investigated the migratory behavior and genetic divergence of six populations of C. grayii fragmented by dams based on the otolith strontium/calcium (Sr/Ca) ratio, mitochondrial DNA, and microsatellite genotyping. All populations were in freshwater with low Sr/Ca ratios, except the estuarine population (Humen population) hatched in brackish water. Reduced nucleotide diversity corresponding to distance was observed. Populations from distant hydrological regions exhibited a decline in genetic diversity and a significant difference with the remaining populations after fitting the isolation by distance model. Pairwise fixation indices confirmed these results and moderate and significant differentiation was found between Hengxian site and downstream sites. Furthermore, STRUCTURE analyses revealed that all separated populations exhibited an admixed phylogenetic pattern except for individuals from the Hengxian locality. The upstream sites showed significantly increased resistance to gene flow from the estuarine population because of isolation by the dam. The results of the neutrality test and Bayesian skyline plots demonstrated complex demography—individuals’ experienced historical expansion and partial upper-dam populations had recently undergone a colonization, forming a new genetic structure. Accordingly, this study demonstrates differences in the migration pattern and genetic differentiation of C. grayii as a consequence of demographic history and current processes (habitat fragmentation and colonization).
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15
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Åkesson M, Flagstad Ø, Aspi J, Kojola I, Liberg O, Wabakken P, Sand H. Genetic signature of immigrants and their effect on genetic diversity in the recently established Scandinavian wolf population. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01423-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
AbstractTransboundary connectivity is a key component when conserving and managing animal species that require large areas to maintain viable population sizes. Wolves Canis lupus recolonized the Scandinavian Peninsula in the early 1980s. The population is geographically isolated and relies on immigration to not lose genetic diversity and to maintain long term viability. In this study we address (1) to what extent the genetic diversity among Scandinavian wolves has recovered during 30 years since its foundation in relation to the source populations in Finland and Russia, (2) if immigration has occurred from both Finland and Russia, two countries with very different wolf management and legislative obligations to ensure long term viability of wolves, and (3) if immigrants can be assumed to be unrelated. Using 26 microsatellite loci we found that although the genetic diversity increased among Scandinavian wolves (n = 143), it has not reached the same levels found in Finland (n = 25) or in Russia (n = 19). Low genetic differentiation between Finnish and Russian wolves, complicated our ability to determine the origin of immigrant wolves (n = 20) with respect to nationality. Nevertheless, based on differences in allelic richness and private allelic richness between the two countries, results supported the occurrence of immigration from both countries. A priori assumptions that immigrants are unrelated is non-advisable, since 5.8% of the pair-wise analyzed immigrants were closely related. To maintain long term viability of wolves in Northern Europe, this study highlights the potential and need for management actions that facilitate transboundary dispersal.
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16
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Errbii M, Keilwagen J, Hoff KJ, Steffen R, Altmüller J, Oettler J, Schrader L. Transposable elements and introgression introduce genetic variation in the invasive ant Cardiocondyla obscurior. Mol Ecol 2021; 30:6211-6228. [PMID: 34324751 DOI: 10.1111/mec.16099] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 07/22/2021] [Accepted: 07/26/2021] [Indexed: 12/11/2022]
Abstract
Introduced populations of invasive organisms have to cope with novel environmental challenges, while having reduced genetic variation caused by founder effects. The mechanisms associated with this "genetic paradox of invasive species" has received considerable attention, yet few studies have examined the genomic architecture of invasive species. Populations of the heart node ant Cardiocondyla obscurior belong to two distinct lineages, a New World lineage so far only found in Latin America and a more globally distributed Old World lineage. In the present study, we use population genomic approaches to compare populations of the two lineages with apparent divergent invasive potential. We find that the strong genetic differentiation of the two lineages began at least 40,000 generations ago and that activity of transposable elements (TEs) has contributed significantly to the divergence of both lineages, possibly linked to the very unusual genomic distribution of TEs in this species. Furthermore, we show that introgression from the Old World lineage is a dominant source of genetic diversity in the New World lineage, despite the lineages' strong genetic differentiation. Our study uncovers mechanisms underlying novel genetic variation in introduced populations of C. obscurior that could contribute to the species' adaptive potential.
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Affiliation(s)
- Mohammed Errbii
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Jens Keilwagen
- Institute for Biosafety in Plant Biotechnology, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Quedlinburg, Germany
| | - Katharina J Hoff
- Institute of Mathematics and Computer Science, University of Greifswald, Greifswald, Germany.,Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Raphael Steffen
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Janine Altmüller
- Cologne Center for Genomics, Institute of Human Genetics, University of Cologne, Cologne, Germany.,Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Core Facility Genomics, Berlin, Germany.,Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Jan Oettler
- Lehrstuhl für Zoologie/Evolutionsbiologie, University Regensburg, Regensburg, Germany
| | - Lukas Schrader
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
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17
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Neto JM, Viturino MG, Ananina G, Bajano FF, Costa SMDS, Roque AB, Borges GF, Franchi R, Rim PH, Medina FM, Costa FF, Melo MBD, de Vasconcellos JP. Association of genetic variants rs641153 ( CFB), rs2230199 ( C3), and rs1410996 ( CFH) with age-related macular degeneration in a Brazilian population. Exp Biol Med (Maywood) 2021; 246:2290-2296. [PMID: 34233521 DOI: 10.1177/15353702211024543] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
This study aimed to investigate the association among genetic variants of the complement pathway CFB R32Q (rs641153), C3 R102G (rs2230199), and CFH (rs1410996) with age-related macular degeneration (AMD) in a sample of the Brazilian population. In a case-control study, 484 AMD patients were classified according to the clinical age-related maculopathy grading system (CARMS) and compared to 479 unrelated controls. The genetic variants rs1410996 of complement H (CFH), rs641153 of complement factor B (CFB), and rs2230199 of complement 3 (C3) were evaluated through polymerase chain reaction (PCR) and direct sequencing. The associations between single nucleotide polymorphisms (SNPs) and AMD, adjusted by age, were assessed by using logistic regression models. A statistically significant association was observed between AMD risk and rs2230199 variant with an OR of 2.01 (P = 0.0002) for CG individuals compared to CC individuals. Regarding the comparison of advanced AMD versus the control group, the OR was 2.12 (P = 0.0036) for GG versus AA genotypes for rs1410996 variant. Similarly, the OR for rs2230199 polymorphism was 2.3034 (P = 5.47e-05) when comparing CG individuals to CC carriers. In contrast, the rs641153 variant showed a significant protective effect against advanced AMD for GA versus GG genotype (OR = 0.4406; P = 0.0019). When comparing wet AMD versus controls, a significant association was detected for rs1410996 variant (OR = 2.16; P = 0.0039) comparing carriers of the homozygous GG versus AA genotype, as well as in the comparisons of GG (OR = 3.0713; P = 0.0046) and CG genotypes (OR = 2.2249; P = 0.0002) versus CC genotype for rs2230199 variant, respectively. The rs641153 variant granted a significant protective effect against wet AMD for GA versus GG genotypes (OR = 0.4601; P = 0.0044). Our study confirmed the risk association between rs2230199 and rs1410996 variants and AMD, and the protective role against AMD for rs641153 variant.
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Affiliation(s)
- Jamil M Neto
- Department of Ophthalmology, Faculty of Medical Sciences - University of Campinas - Campinas, SP 13083-887, Brazil
| | - Marina Gm Viturino
- Department of Ophthalmology, Faculty of Medical Sciences - University of Campinas - Campinas, SP 13083-887, Brazil
| | - Galina Ananina
- Laboratory of Human Genetics, Center for Molecular Biology and Genetic Engineering (CBMEG) - University of Campinas - Campinas, SP 13083-875, Brazil
| | - Flávia F Bajano
- Laboratory of Human Genetics, Center for Molecular Biology and Genetic Engineering (CBMEG) - University of Campinas - Campinas, SP 13083-875, Brazil
| | - Sueli M da S Costa
- Laboratory of Human Genetics, Center for Molecular Biology and Genetic Engineering (CBMEG) - University of Campinas - Campinas, SP 13083-875, Brazil
| | - Alicia B Roque
- Department of Ophthalmology, Faculty of Medical Sciences - University of Campinas - Campinas, SP 13083-887, Brazil
| | - Gessica Fs Borges
- Department of Ophthalmology, Faculty of Medical Sciences - University of Campinas - Campinas, SP 13083-887, Brazil
| | - Raissa Franchi
- Laboratory of Human Genetics, Center for Molecular Biology and Genetic Engineering (CBMEG) - University of Campinas - Campinas, SP 13083-875, Brazil
| | - Priscila Hh Rim
- Department of Ophthalmology, Faculty of Medical Sciences - University of Campinas - Campinas, SP 13083-887, Brazil
| | - Flávio M Medina
- Department of Ophthalmology, Faculty of Medical Sciences, University of State of Rio de Janeiro - Rio de Janeiro, RJ 20551-030, Brazil
| | - Fernando F Costa
- Hematology and Hemotherapy Center - University of Campinas - Campinas, SP 13083-878, Brazil
| | - Mônica B de Melo
- Laboratory of Human Genetics, Center for Molecular Biology and Genetic Engineering (CBMEG) - University of Campinas - Campinas, SP 13083-875, Brazil
| | - José Pc de Vasconcellos
- Department of Ophthalmology, Faculty of Medical Sciences - University of Campinas - Campinas, SP 13083-887, Brazil
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18
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Rönkä N, Pakanen VM, Pauliny A, Thomson RL, Nuotio K, Pehlak H, Thorup O, Lehikoinen P, Rönkä A, Blomqvist D, Koivula K, Kvist L. Genetic differentiation in an endangered and strongly philopatric, migrant shorebird. BMC Ecol Evol 2021; 21:125. [PMID: 34147062 PMCID: PMC8214799 DOI: 10.1186/s12862-021-01855-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 06/08/2021] [Indexed: 11/24/2022] Open
Abstract
Background Populations living in fragmented habitats may suffer from loss of genetic variation and reduced between-patch dispersal, which are processes that can result in genetic differentiation. This occurs frequently in species with reduced mobility, whereas genetic differentiation is less common among mobile species such as migratory birds. The high dispersal capacity in the latter species usually allows for gene flow even in fragmented landscapes. However, strongly philopatric behaviour can reinforce relative isolation and the degree of genetic differentiation. The Southern Dunlin (Calidris alpina schinzii) is a philopatric, long-distance migratory shorebird and shows reduced dispersal between isolated breeding patches. The endangered population of the Southern Dunlin breeding at the Baltic Sea has suffered from habitat deterioration and fragmentation of coastal meadows. We sampled DNA across the entire population and used 12 polymorphic microsatellite loci to examine whether the environmental changes have resulted in genetic structuring and loss of variation. Results We found a pattern of isolation-by-distance across the whole Baltic population and genetic differentiation between local populations, even within the southern Baltic. Observed heterozygosity was lower than expected throughout the range and internal relatedness values were positive indicating inbreeding. Conclusions Our results provide long-term, empirical evidence for the theoretically expected links between habitat fragmentation, population subdivision, and gene flow. They also demonstrate a rare case of genetic differentiation between populations of a long-distance migratory species. The Baltic Southern Dunlin differs from many related shorebird species that show near panmixia, reflecting its philopatric life history and the reduced connectivity of its breeding patches. The results have important implications as they suggest that reduced connectivity of breeding habitats can threaten even long-distance migrants if they show strong philopatry during breeding. The Baltic Southern Dunlin warrants urgent conservation efforts that increase functional connectivity and gene flow between breeding areas. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01855-0.
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Affiliation(s)
- Nelli Rönkä
- Ecology and Genetics Research Unit, University of Oulu, P.O. Box 3000, 90014, Oulu, Finland
| | - Veli-Matti Pakanen
- Ecology and Genetics Research Unit, University of Oulu, P.O. Box 3000, 90014, Oulu, Finland.,Department of Biological and Environmental Sciences, University of Gothenburg, P.O. Box 463, 405 30, Gothenburg, Sweden
| | - Angela Pauliny
- Department of Biological and Environmental Sciences, University of Gothenburg, P.O. Box 463, 405 30, Gothenburg, Sweden
| | - Robert L Thomson
- Section of Ecology, Department of Biology, University of Turku, 20014, Turku, Finland.,Percy FitzPatrick Institute of African Ornithology, DST-NRF Centre of Excellence, University of Cape Town, Rondebosch, 7701, South Africa
| | - Kimmo Nuotio
- Environmental Agency, Valtakatu 11, 28100, Pori, Finland
| | - Hannes Pehlak
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 5, 51014, Tartu, Estonia.,OÜ Xenus, Koguva, 94724, Muhu Island, Saare, Estonia
| | - Ole Thorup
- , V. Vedsted Byvej 32, Vester Vedsted, 6760, Ribe, Denmark
| | - Petteri Lehikoinen
- The Helsinki Lab of Ornithology, Finnish Museum of Natural History, University of Helsinki, 00014, Helsinki, Finland
| | - Antti Rönkä
- Ecology and Genetics Research Unit, University of Oulu, P.O. Box 3000, 90014, Oulu, Finland
| | - Donald Blomqvist
- Department of Biological and Environmental Sciences, University of Gothenburg, P.O. Box 463, 405 30, Gothenburg, Sweden.
| | - Kari Koivula
- Ecology and Genetics Research Unit, University of Oulu, P.O. Box 3000, 90014, Oulu, Finland
| | - Laura Kvist
- Ecology and Genetics Research Unit, University of Oulu, P.O. Box 3000, 90014, Oulu, Finland
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19
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Hanson JO, Veríssimo A, Velo‐Antón G, Marques A, Camacho‐Sanchez M, Martínez‐Solano Í, Gonçalves H, Sequeira F, Possingham HP, Carvalho SB. Evaluating surrogates of genetic diversity for conservation planning. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2021; 35:634-642. [PMID: 32761662 PMCID: PMC8048567 DOI: 10.1111/cobi.13602] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 07/16/2020] [Accepted: 07/23/2020] [Indexed: 05/13/2023]
Abstract
Protected-area systems should conserve intraspecific genetic diversity. Because genetic data require resources to obtain, several approaches have been proposed for generating plans for protected-area systems (prioritizations) when genetic data are not available. Yet such surrogate-based approaches remain poorly tested. We evaluated the effectiveness of potential surrogate-based approaches based on microsatellite genetic data collected across the Iberian Peninsula for 7 amphibian and 3 reptilian species. Long-term environmental suitability did not effectively represent sites containing high genetic diversity (allelic richness). Prioritizations based on long-term environmental suitability had similar performance to random prioritizations. Geographic distances and resistance distances based on contemporary environmental suitability were not always effective surrogates for identification of combinations of sites that contain individuals with different genetic compositions. Our results demonstrate that population genetic data based on commonly used neutral markers can inform prioritizations, and we could not find an adequate substitute. Conservation planners need to weigh the potential benefits of genetic data against their acquisition costs.
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Affiliation(s)
- Jeffrey O. Hanson
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoCampus de Vairão, Rua Padre Armando Quintas, no. 7Vairão4485‐661Portugal
| | - Ana Veríssimo
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoCampus de Vairão, Rua Padre Armando Quintas, no. 7Vairão4485‐661Portugal
| | - Guillermo Velo‐Antón
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoCampus de Vairão, Rua Padre Armando Quintas, no. 7Vairão4485‐661Portugal
| | - Adam Marques
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoCampus de Vairão, Rua Padre Armando Quintas, no. 7Vairão4485‐661Portugal
| | - Miguel Camacho‐Sanchez
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoCampus de Vairão, Rua Padre Armando Quintas, no. 7Vairão4485‐661Portugal
| | - Íñigo Martínez‐Solano
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoCampus de Vairão, Rua Padre Armando Quintas, no. 7Vairão4485‐661Portugal
- Museo Nacional de Ciencias Naturales‐CSICCalle de José Gutiérrez Abascal2Madrid28006Spain
| | - Helena Gonçalves
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoCampus de Vairão, Rua Padre Armando Quintas, no. 7Vairão4485‐661Portugal
- Museu de História Natural e da CiênciaUniversidade do PortoPraça Gomes TeixeiraPorto4099‐002Portugal
| | - Fernando Sequeira
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoCampus de Vairão, Rua Padre Armando Quintas, no. 7Vairão4485‐661Portugal
| | - Hugh P. Possingham
- The Nature ConservancyMinneapolisMN55415U.S.A.
- Centre for Biodiversity and Conservation Science, School of Biological SciencesThe University of QueenslandBrisbaneQLD 4072Australia
| | - Silvia B. Carvalho
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoCampus de Vairão, Rua Padre Armando Quintas, no. 7Vairão4485‐661Portugal
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20
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Hedrén M, Birkedal S, de Boer H, Ghorbani A, Gravendeel B, Hansson S, Svensson Å, Zarre S. Asymmetric contributions of seed and pollen to gene dispersal in the marsh orchid Dactylorhiza umbrosa in Asia Minor. Mol Ecol 2021; 30:1791-1805. [PMID: 33587812 DOI: 10.1111/mec.15848] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 07/25/2020] [Accepted: 08/05/2020] [Indexed: 11/29/2022]
Abstract
Orchids differ from other plants in their extremely small and partly air-filled seeds that can be transported long distances by wind. Seed dispersal in orchids is expected to contribute strongly to overall gene flow, and orchids generally express low levels of genetic differentiation between populations and low pollen to seed flow ratios. However, studies in orchids distributed in northern Europe have often found a poor geographic structuring of genetic variation. Here, we studied geographic differentiation in the marsh orchid Dactylorhiza umbrosa, which is widely distributed in upland regions from Asia Minor to Central Asia. These areas were less affected by Pleistocene ice ages than northern Europe and the orchid should have been able to survive the last ice age in local refugia. In the plastid genome, which is dispersed by seeds, populations at close distance were clearly divergent, but the differentiation still increased with geographic distance, and a significant phylogeographic structure had developed. In the nuclear genome, which is dispersed by both seeds and pollen, populations showed an even stronger correlation between genetic and geographic distance, but average levels of differentiation were lower than in the plastid genome, and no phylogeographic structure was evident. Combining plastid and nuclear data, we found that the ratio of pollen to seed dispersal (mp/ms) decreases with physical distance. Comparison with orchids that grow in parts of Europe that were glaciated during the last ice suggests that a balanced structure of genetic diversity develops only slowly in many terrestrial orchids, despite efficient seed dispersal.
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Affiliation(s)
- Mikael Hedrén
- Department of Biology, University of Lund, Lund, Sweden
| | | | - Hugo de Boer
- Natural History Museum, University of Oslo, Oslo, Norway.,Department of Organismal Biology, Uppsala University, Uppsala, Sweden.,Endless Forms Group, Naturalis Biodiversity Center, Leiden, The Netherlands
| | | | - Barbara Gravendeel
- Endless Forms Group, Naturalis Biodiversity Center, Leiden, The Netherlands
| | | | - Åke Svensson
- Department of Dermatology, Malmö University Hospital SUS, Malmö, Sweden
| | - Shahin Zarre
- Department of Plant Sciences, School of Biology, College of Science, University of Tehran, Tehran, Iran
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21
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do Amaral TS, Dos Santos JS, Rosa FF, Pessôa MB, Chaves LJ, Ribeiro MC, Collevatti RG. Agricultural Landscape Heterogeneity Matter: Responses of Neutral Genetic Diversity and Adaptive Traits in a Neotropical Savanna Tree. Front Genet 2021; 11:606222. [PMID: 33613620 PMCID: PMC7890196 DOI: 10.3389/fgene.2020.606222] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 12/31/2020] [Indexed: 11/27/2022] Open
Abstract
Plants are one of the most vulnerable groups to fragmentation and habitat loss, that may affect community richness, abundance, functional traits, and genetic diversity. Here, we address the effects of landscape features on adaptive quantitative traits and evolutionary potential, and on neutral genetic diversity in populations of the Neotropical savanna tree Caryocar brasiliense. We sampled adults and juveniles in 10 savanna remnants within five landscapes. To obtain neutral genetic variation, we genotyped all individuals from each site using nine microsatellite loci. For adaptive traits we measured seed size and mass and grown seeds in nursery in completely randomized experimental design. We obtained mean, additive genetic variance (Va) and coefficient of variation (CVa%), which measures evolvability, for 17 traits in seedlings. We found that landscapes with higher compositional heterogeneity (SHDI) had lower evolutionary potential (CVa%) in leaf length (LL) and lower aboveground dry mass (ADM) genetic differentiation (QST). We also found that landscapes with higher SHDI had higher genetic diversity (He) and allelic richness (AR) in adults, and lower genetic differentiation (FST). In juveniles, SHDI was also positively related to AR. These results are most likely due to longer dispersal distance of pollen in landscapes with lower density of flowering individuals. Agricultural landscapes with low quality mosaic may be more stressful for plant species, due to the lower habitat cover (%), higher cover of monocropping (%) and other land covers, and edge effects. However, in landscapes with higher SHDI with high quality mosaic, forest nearby savanna habitat and the other environments may facilitate the movement or provide additional habitat and resources for seed disperses and pollinators, increasing gene flow and genetic diversity. Finally, despite the very recent agriculture expansion in Central Brazil, we found no time lag in response to habitat loss, because both adults and juveniles were affected by landscape changes.
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Affiliation(s)
- Tatiana Souza do Amaral
- Laboratório de Genética & Biodiversidade, ICB, Universidade Federal de Goiás (UFG), Goiânia, Brazil
| | - Juliana Silveira Dos Santos
- Laboratório de Genética & Biodiversidade, ICB, Universidade Federal de Goiás (UFG), Goiânia, Brazil.,Laboratório de Ecologia Espacial e Conservação (LEEC), Departamento de Biodiversidade, Universidade Estadual Paulista (UNESP), Rio Claro, Brazil
| | - Fernanda Fraga Rosa
- Laboratório de Genética & Biodiversidade, ICB, Universidade Federal de Goiás (UFG), Goiânia, Brazil
| | - Marcelo Bruno Pessôa
- Laboratório de Metacomunidades e Paisagem, ICB, Universidade Federal de Goiás (UFG), Goiânia, Brazil
| | - Lázaro José Chaves
- Escola de Agronomia, Universidade Federal de Goiás (UFG), Goiânia, Brazil
| | - Milton Cezar Ribeiro
- Laboratório de Ecologia Espacial e Conservação (LEEC), Departamento de Biodiversidade, Universidade Estadual Paulista (UNESP), Rio Claro, Brazil
| | - Rosane Garcia Collevatti
- Laboratório de Genética & Biodiversidade, ICB, Universidade Federal de Goiás (UFG), Goiânia, Brazil
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22
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Abstract
Cultivated peanut (Arachis hypogaea) is an important oil, food, and feed crop worldwide. The USDA peanut germplasm collection currently contains 8,982 accessions. In the 1990s, 812 accessions were selected as a core collection on the basis of phenotype and country of origin. The present study reports genotyping results for the entire available core collection. Each accession was genotyped with the Arachis_Axiom2 SNP array, yielding 14,430 high-quality, informative SNPs across the collection. Additionally, a subset of 253 accessions was replicated, using between two and five seeds per accession, to assess heterogeneity within these accessions. The genotypic diversity of the core is mostly captured in five genotypic clusters, which have some correspondence with botanical variety and market type. There is little genetic clustering by country of origin, reflecting peanut’s rapid global dispersion in the 18th and 19th centuries. A genetic cluster associated with the hypogaea/aequatoriana/peruviana varieties, with accessions coming primarily from Bolivia, Peru, and Ecuador, is consistent with these having been the earliest landraces. The genetics, phenotypic characteristics, and biogeography are all consistent with previous reports of tetraploid peanut originating in Southeast Bolivia. Analysis of the genotype data indicates an early genetic radiation, followed by regional distribution of major genetic classes through South America, and then a global dissemination that retains much of the early genetic diversity in peanut. Comparison of the genotypic data relative to alleles from the diploid progenitors also indicates that subgenome exchanges, both large and small, have been major contributors to the genetic diversity in peanut.
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23
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Cheng J, Zhang N, Sha Z. Nuclear microsatellites reveal population genetic structuring and fine-scale pattern of hybridization in the Japanese mantis shrimp Oratosquilla oratoria. PeerJ 2020; 8:e10270. [PMID: 33194430 PMCID: PMC7649012 DOI: 10.7717/peerj.10270] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 10/08/2020] [Indexed: 11/27/2022] Open
Abstract
The interplay between historical and contemporary processes can produce complex patterns of genetic differentiation in the marine realm. Recent mitochondrial and nuclear sequence analyses revealed cryptic speciation in the Japanese mantis shrimp Oratosquilla oratoria. Herein, we applied nuclear microsatellite markers to examine patterns and causes of genetic differentiation in this morphotaxon. Population structure analyses revealed two genetically divergent and geographically structured clades in O. oratoria, one dominating the temperate zone of the Northwestern (NW) Pacific and the other occurring in the subtropical and tropical waters where are influenced by the Kuroshio Current. Two sympatric zones, one around the Changjiang Estuary in China coast and the other in the northern Japan Sea, were demonstrated to be hybrid zones where introgressive hybridization occurred asymmetrically. The interaction between historical climate shifts and contemporary factors (e.g., freshwater discharge, temperature gradient and isolation by distance) may contribute to the present-day genetic architecture in the Japanese mantis shrimp. Range shift induced by climate changes and oceanographic factors may promote hybridization and gene flow between the O. oratoria complex. Our results provide insights into the interacting mechanisms that give rise to diversification and speciation of coastal species in the NW Pacific.
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Affiliation(s)
- Jiao Cheng
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Nan Zhang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Zhongli Sha
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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24
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Prentice MB, Bowman J, Murray DL, Khidas K, Wilson PJ. Spatial and environmental influences on selection in a clock gene coding trinucleotide repeat in Canada lynx (Lynx canadensis). Mol Ecol 2020; 29:4637-4652. [PMID: 32989809 DOI: 10.1111/mec.15652] [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: 03/27/2020] [Accepted: 09/09/2020] [Indexed: 11/30/2022]
Abstract
Clock genes exhibit substantial control over gene expression and ultimately life-histories using external cues such as photoperiod, and are thus likely to be critical for adaptation to shifting seasonal conditions and novel environments as species redistribute their ranges under climate change. Coding trinucleotide repeats (cTNRs) are found within several clock genes, and may be interesting targets of selection due to their containment within exonic regions and elevated mutation rates. Here, we conduct inter-specific characterization of the NR1D1 cTNR between Canada lynx and bobcat, and intra-specific spatial and environmental association analyses of neutral microsatellites and our functional cTNR marker, to investigate the role of selection on this locus in Canada lynx. We report signatures of divergent selection between lynx and bobcat, with the potential for hybrid-mediated gene flow in the area of range overlap. We also provide evidence that this locus is under selection across Canada lynx in eastern Canada, with both spatial and environmental variables significantly contributing to the explained variation, after controlling for neutral population structure. These results suggest that cTNRs may play an important role in the generation of functional diversity within some mammal species, and allow for contemporary rates of adaptation in wild populations in response to environmental change. We encourage continued investment into the study of cTNR markers to better understand their broader relevance to the evolution and adaptation of mammals.
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Affiliation(s)
- Melanie B Prentice
- Department of Environmental & Life Sciences, Trent University, Peterborough, ON, Canada
| | - Jeff Bowman
- Wildlife Research and Monitoring Section, Ontario Ministry of Natural Resources and Forestry, Peterborough, ON, Canada
| | - Dennis L Murray
- Biology Department, Trent University, Peterborough, ON, Canada
| | - Kamal Khidas
- Vertebrate Zoology and Beaty Centre for Species Discovery, Canadian Museum of Nature, Ottawa, ON, Canada
| | - Paul J Wilson
- Biology Department, Trent University, Peterborough, ON, Canada
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Boca SM, Huang L, Rosenberg NA. On the heterozygosity of an admixed population. J Math Biol 2020; 81:1217-1250. [PMID: 33034736 DOI: 10.1007/s00285-020-01531-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 08/04/2020] [Indexed: 01/18/2023]
Abstract
In this study, we consider admixed populations through their expected heterozygosity, a measure of genetic diversity. A population is termed admixed if its members possess recent ancestry from two or more separate sources. As a result of the fusion of source populations with different genetic variants, admixed populations can exhibit high levels of genetic diversity, reflecting contributions of their multiple ancestral groups. For a model of an admixed population derived from K source populations, we obtain a relationship between its heterozygosity and its proportions of admixture from the various source populations. We show that the heterozygosity of the admixed population is at least as great as that of the least heterozygous source population, and that it potentially exceeds the heterozygosities of all of the source populations. The admixture proportions that maximize the heterozygosity possible for an admixed population formed from a specified set of source populations are also obtained under specific conditions. We examine the special case of [Formula: see text] source populations in detail, characterizing the maximal admixture in terms of the heterozygosities of the two source populations and the value of [Formula: see text] between them. In this case, the heterozygosity of the admixed population exceeds the maximal heterozygosity of the source groups if the divergence between them, measured by [Formula: see text], is large enough, namely above a certain bound that is a function of the heterozygosities of the source groups. We present applications to simulated data as well as to data from human admixture scenarios, providing results useful for interpreting the properties of genetic variability in admixed populations.
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Affiliation(s)
- Simina M Boca
- Department of Oncology, Department of Biostatistics, Bioinformatics and Biomathematics, Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC, 20007, USA.
| | - Lucy Huang
- Bioinformatics Graduate Program, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Noah A Rosenberg
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
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Camacho-Sanchez M, Velo-Antón G, Hanson JO, Veríssimo A, Martínez-Solano Í, Marques A, Moritz C, Carvalho SB. Comparative assessment of range-wide patterns of genetic diversity and structure with SNPs and microsatellites: A case study with Iberian amphibians. Ecol Evol 2020; 10:10353-10363. [PMID: 33072264 PMCID: PMC7548196 DOI: 10.1002/ece3.6670] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 07/22/2020] [Indexed: 11/11/2022] Open
Abstract
Reduced representation genome sequencing has popularized the application of single nucleotide polymorphisms (SNPs) to address evolutionary and conservation questions in nonmodel organisms. Patterns of genetic structure and diversity based on SNPs often diverge from those obtained with microsatellites to different degrees, but few studies have explicitly compared their performance under similar sampling regimes in a shared analytical framework. We compared range‐wide patterns of genetic structure and diversity in two amphibians endemic to the Iberian Peninsula: Hyla molleri and Pelobates cultripes, based on microsatellite (18 and 14 loci) and SNP (15,412 and 33,140 loci) datasets of comparable sample size and spatial extent. Model‐based clustering analyses with STRUCTURE revealed minor differences in genetic structure between marker types, but inconsistent values of the optimal number of populations (K) inferred. SNPs yielded more repeatable and less admixed ancestries with increasing K compared to microsatellites. Genetic diversity was weakly correlated between marker types, with SNPs providing a better representation of southern refugia and of gradients of genetic diversity congruent with the demographic history of both species. Our results suggest that the larger number of loci in a SNP dataset can provide more reliable inferences of patterns of genetic structure and diversity than a typical microsatellite dataset, at least at the spatial and temporal scales investigated.
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Affiliation(s)
- Miguel Camacho-Sanchez
- CIBIO/InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto Vairão Portugal
| | - Guillermo Velo-Antón
- CIBIO/InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto Vairão Portugal
| | - Jeffrey O Hanson
- CIBIO/InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto Vairão Portugal
| | - Ana Veríssimo
- CIBIO/InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto Vairão Portugal
| | | | - Adam Marques
- CIBIO/InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto Vairão Portugal
| | - Craig Moritz
- Centre for Biodiversity Analysis and Research School of Biology The Australian National University Canberra ACT Australia
| | - Sílvia B Carvalho
- CIBIO/InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto Vairão Portugal
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Arnaud-Haond S, Stoeckel S, Bailleul D. New insights into the population genetics of partially clonal organisms: When seagrass data meet theoretical expectations. Mol Ecol 2020; 29:3248-3260. [PMID: 32613610 DOI: 10.1111/mec.15532] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/30/2020] [Accepted: 06/11/2020] [Indexed: 01/23/2023]
Abstract
Seagrass meadows are among the most important coastal ecosystems in terms of both spatial extent and ecosystem services, but they are also declining worldwide. Understanding the drivers of seagrass meadow dynamics is essential for designing sound management, conservation and restoration strategies. However, poor knowledge of the effect of clonality on the population genetics of natural populations severely limits our understanding of the dynamics and connectivity of meadows. Recent modelling approaches have described the expected distributions of genotypic and genetic descriptors under increasing clonal rates, which may help us better understand and interpret population genetics data obtained for partial asexuals. Here, in the light of these recent theoretical developments, we revisited population genetics data for 165 meadows of four seagrass species. Contrasting shoot lifespan and rhizome turnover led to the prediction that the influence of asexual reproduction would increase along a gradient from Zostera noltii to Zostera marina, Cymodocea nodosa and Posidonia oceanica, with increasing departure from Hardy-Weinberg equilibrium (Fis ), mostly towards heterozygote excess, and decreasing genotypic richness (R). This meta-analysis provides a nested validation of this hypothesis at both the species and meadow scales through a significant relationship between Fis and R within each species. By empirically demonstrating the theoretical expectations derived from recent modelling approaches, this work calls for the use of Hardy-Weinberg equilibrium (Fis ) rather than only the strongly sampling-sensitive R to assess the importance of clonal reproduction (c), at least when the impact of selfing on Fis can be neglected. The results also emphasize the need to revise our appraisal of the extent of clonality and its influence on the dynamics, connectivity and evolutionary trajectory of partial asexuals in general, including in seagrass meadows, to develop the most accurate management strategies.
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Affiliation(s)
| | - Solenn Stoeckel
- IGEPP INRAE, Institut Agro, University of Rennes, Le Rheu, France
| | - Diane Bailleul
- Université de Montpellier, Ifremer, CNRS, IRD, MARBEC, Sète, France
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Lefèvre F, Gallais A. Partitioning heterozygosity in subdivided populations: Some misuses of Nei's decomposition and an alternative probabilistic approach. Mol Ecol 2020; 29:2957-2962. [PMID: 32594582 DOI: 10.1111/mec.15527] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 06/12/2020] [Accepted: 06/12/2020] [Indexed: 01/05/2023]
Abstract
Nei's decomposition of total expected heterozygosity in subdivided populations into within- and between-subpopulation components, HS and DST , respectively, is a classical tool in the conservation and management of genetic resources. Reviewing why this is not a decomposition into independent terms of within- and between-subpopulation gene diversity, we illustrate how this approach can be misleading because it overemphasizes the within-subpopulation component compared to Jost's nonadditive decomposition based on gene diversity indices. Using probabilistic partitioning of the total expected heterozygosity into independent within- and between-subpopulation contributions, we show that the contribution of the within-subpopulation expected heterozygosity to the total expected heterozygosity is not HS , as suggested by Nei's decomposition, but HS /s, with s being the number of subpopulations. Finally, we compare three possible approaches of decomposing total heterozygosity in subdivided populations (i.e., Nei's decomposition, Jost's approach, and probabilistic partitioning) with regard to independence between terms and sensitivity to unequal subpopulation sizes. For the conservation and management of genetic resources, we recommend using probabilistic partitioning and Jost's differentiation parameter rather than Nei's decomposition.
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Affiliation(s)
- François Lefèvre
- Ecologie des Forêts Méditerranéennes, URFM, INRAE, Avignon, France
| | - André Gallais
- UMR Génétique Quantitative et Evolution, INRAE-UPS-CNRS, Gif-sur-Yvette, France
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Wirgin I, Maceda L, Tozer M, Stabile J, Waldman J. Atlantic Coastwide Population Structure of Striped Bass Morone saxatilis Using Microsatellite DNA Analysis. FISHERIES RESEARCH 2020; 226:105506. [PMID: 34987272 PMCID: PMC8726014 DOI: 10.1016/j.fishres.2020.105506] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Striped bass Morone saxatilis support one of the most popular and important inshore recreational and commercial fisheries along the Atlantic Coast of North America. Populations at both extremes of its distribution are largely resident while those in the center of its range (Hudson River, New York, to Roanoke River, North Carolina) are seasonally migratory, ranging from the Bay of Fundy, Canada, to the Outer Banks of North Carolina. Historically, population abundances of striped bass fluctuated widely, sometimes resulting in the imposition of severe management measures to restrict their harvest. Detailed knowledge of its rangewide population structure would aid in more effective management; however, most genetic studies addressing the structure of the migratory coastal stock have largely failed to achieve this goal. To address this need, we used multi-loci microsatellite DNA analysis. We identified six genetically distinct populations across the species' distribution, including the Miramichi, Shubenacadie, Hudson, Delaware-Chesapeake, Roanoke, and Santee-Cooper rivers. We also report significant genetic differentiation between the Nanticoke and Choptank rivers along the eastern shore of the Chesapeake Bay and collections from tributaries along the western shore of the Bay. The Annapolis and Saint John rivers, tributaries of the Bay of Fundy, historically hosted striped bass aggregations that were extirpated, or nearly so, by anthropogenic stressors in the late 20th century. No specimens with unique genotypes were found in collections from either river; instead the vast majority were admixed with genotypes of Shubenacadie River, Hudson River, Chesapeake Bay, and Roanoke River lineage. Finally, we show in simulations that these genetic markers should be informative in quantifying the contributions of the Hudson River, Chesapeake Bay-Delaware, and Roanoke River to mixed-stock harvests that occur within the range of the coastal migratory stock.
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Affiliation(s)
- Isaac Wirgin
- Department of Environmental Medicine, NYU School of Medicine, 341 East 25 Street, New York, New York 10010, USA
| | - Lorraine Maceda
- Department of Environmental Medicine, NYU School of Medicine, 341 East 25 Street, New York, New York 10010, USA
| | - Matt Tozer
- Department of Biology, Queens College, 65-30 Kissena Boulevard, Queens, New York 11367, and Graduate Program in Biology City University of New York, New York, NY 10016, USA
| | - Joseph Stabile
- Department of Biology, Iona College, 715 North Avenue, New Rochelle, New York 10801, USA
| | - John Waldman
- Department of Biology, Queens College, 65-30 Kissena Boulevard, Queens, New York 11367, and Graduate Program in Biology City University of New York, New York, NY 10016, USA
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Vargas Arboleda AF, Cuadrado-Rios S, Mantilla-Meluk H. Systematic considerations on two species of nectarivorous bats (<i>Anoura caudifer</i> and <i>A. geoffroyi</i>) based on barcoding sequences. ACTA BIOLÓGICA COLOMBIANA 2020. [DOI: 10.15446/abc.v25n2.75848] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
As a product of recent revisions of the nectivore bat genus Anoura (Glossophaginae: Anourina), new species have been described, and several taxa have been elevated to the specific level in the so-called Anoura caudifer and A. geoffroyi species complexes in the last four decades. The genus has a wide distribution across regions of high ecological complexity, including geographic features, such as the Andes and the Isthmus of Panamá, previously identified as natural barriers that restrict gene flow in other phyllostomid bat genera. Up to date, no analyses have been conducted to investigate the contribution of biogeographic factors on the genetic divergence of the genus. In this work, we analyze barcoding DNA sequences (cytochrome oxidase subunit I, COI) to test for geographic structure among Central and South American populations of the A. caudifer and A. geoffroyi complexes. Our analyses show geographic structure for populations previously identified as the A. geoffroyi lasiopyga, suggesting an independent evolutionary fate for Central American representatives of the genus. We also highlight the presence of unrecognized diversity within the A. caudifer complex from the Pacific coast of northern Ecuador.
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Ding C, Hamann A, Yang RC, Brouard JS. Genetic parameters of growth and adaptive traits in aspen (Populus tremuloides): Implications for tree breeding in a warming world. PLoS One 2020; 15:e0229225. [PMID: 32126110 PMCID: PMC7053761 DOI: 10.1371/journal.pone.0229225] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 01/31/2020] [Indexed: 11/18/2022] Open
Abstract
Aspen (Populus tremuloides Michx) is a widespread commercial forest tree of high economic importance in western Canada and has been subject to tree improvement efforts over the past two decades. Such improvement programs rely on accurate estimates of the genetic gain in growth traits and correlated response in adaptive traits that are important for forest health. Here, we estimated genetic parameters in 10 progeny trials containing >30,000 trees with pedigree structures based on a partial factorial mating design that includes 60 half-sibs, 100 full-sib families and 1,400 clonally replicated genotypes. Estimated narrow-sense and broad-sense heritabilities were low for height and diameter (~0.2), but moderate for the dates of budbreak and leaf senescence (~0.4). Furthermore, estimated genetic correlations between growth and phenology were moderate to strong with tall trees being associated with early budbreak (r = -0.3) and late leaf senescence (r = -0.7). Survival was not compromised, but was positively associated with early budbreak or late leaf senescence, indicating that utilizing the growing season was more important for survival and growth than avoiding early fall or late spring frosts. These result suggests that populations are adapted to colder climate conditions and lag behind environmental conditions to which they are optimally adapted due to substantial climate warming observed over the last several decades for the study area.
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Affiliation(s)
- Chen Ding
- Department of Renewable Resources, University of Alberta, Edmonton, Alberta, Canada
- * E-mail:
| | - Andreas Hamann
- Department of Renewable Resources, University of Alberta, Edmonton, Alberta, Canada
| | - Rong-Cai Yang
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Jean S. Brouard
- Isabella Point Forestry Ltd., Salt Spring Island, British Columbia, Canada
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Chen Z, Li H, Zhai X, Zhu Y, He Y, Wang Q, Li Z, Jiang J, Xiong R, Chen X. Phylogeography, speciation and demographic history: Contrasting evidence from mitochondrial and nuclear markers of the Odorrana graminea sensu lato (Anura, Ranidae) in China. Mol Phylogenet Evol 2020; 144:106701. [DOI: 10.1016/j.ympev.2019.106701] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 11/21/2019] [Accepted: 12/03/2019] [Indexed: 10/25/2022]
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Derouiche L, Irzagh A, Rahmouni R, Tahri R, Hadjeloum M, Bouhadad R, Fernandes C. Deep mitochondrial DNA phylogeographic divergence in the threatened aoudad Ammotragus lervia (Bovidae, Caprini). Gene 2020; 739:144510. [PMID: 32109559 DOI: 10.1016/j.gene.2020.144510] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 02/20/2020] [Accepted: 02/24/2020] [Indexed: 12/13/2022]
Abstract
The aoudad or Barbary sheep (Ammotragus lervia) is a threatened ungulate emblematic of North Africa, whose population structure and subspecific taxonomy have not been examined genetically. This knowledge is essential and urgently needed to inform ongoing conservation and management efforts. We analysed the mitochondrial cytochrome b gene and four nuclear genes (casein kappa, spectrin beta nonerythrocytic 1, thyroglobulin, thyrotropin subunit beta) for the first phylogeographic survey of the aoudad, and uncovered a deep Mediterranean-Saharan mitochondrial split separating two highly distinct evolutionary lineages. Their level of divergence is greater than or comparable to those observed between several pairs of congeneric species of different caprine genera. The split was estimated to have occurred in the Early Pleistocene, about 1.3 million years ago. None of the four nuclear genes surveyed, chosen because they have been used in phylogeographic and species-level phylogenetic studies of bovids, allowed us to detect, likely due to their slow evolutionary rate, the substantial and geographically coherent subdivision revealed by mitochondrial DNA. This study is evidence and testament to the ability of mitochondrial DNA, probably unrivalled by any other single-locus marker, as an exploratory tool for investigating population genealogy and history and identifying potential evolutionarily significant units for conservation in animals.
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Affiliation(s)
- Louiza Derouiche
- LBEIG, Population Genetics & Conservation Unit, Faculté des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumediene, BP 32 El-Alia, Bab Ezzouar, 16111, Algiers, Algeria.
| | - Ahmed Irzagh
- Département de Biotechnologie, Faculté des Sciences de la Nature et de la Vie, Université Saad Dahlab de Blida, route de Soumâa, BP 270, 09000 Blida, Algeria
| | - Rafiq Rahmouni
- Réserve de Chasse de Tlemcen, Direction Générale des Forêts (DGF), Boulevard de Lala Sitti, Tlemcen, Algeria
| | | | - Mohamed Hadjeloum
- Bureau de la Gestion et Protection de la Faune, Direction Générale des Forêts (DGF), Algiers, Algeria
| | - Rachid Bouhadad
- LBEIG, Population Genetics & Conservation Unit, Faculté des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumediene, BP 32 El-Alia, Bab Ezzouar, 16111, Algiers, Algeria
| | - Carlos Fernandes
- CE3C - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal.
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Tajchman K, Sawicka-Zugaj W, Greguła-Kania M, Drozd L, Czyżowski P. Effect of Translocations on the Genetic Structure in Populations of the Red Deer (Cervus elaphus) in Poland. RUSS J GENET+ 2020. [DOI: 10.1134/s102279541912010x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Rocha de Almeida T, Alix M, Le Cam A, Klopp C, Montfort J, Toomey L, Ledoré Y, Bobe J, Chardard D, Schaerlinger B, Fontaine P. Domestication may affect the maternal mRNA profile in unfertilized eggs, potentially impacting the embryonic development of Eurasian perch (Perca fluviatilis). PLoS One 2019; 14:e0226878. [PMID: 31891603 PMCID: PMC6938363 DOI: 10.1371/journal.pone.0226878] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 12/06/2019] [Indexed: 12/18/2022] Open
Abstract
Domestication is an evolutionary process during which we expect populations to progressively adapt to an environment controlled by humans. It is accompanied by genetic and presumably epigenetic changes potentially leading to modifications in the transcriptomic profile in various tissues. Reproduction is a key function often affected by this process in numerous species, regardless of the mechanism. The maternal mRNA in fish eggs is crucial for the proper embryogenesis. Our working hypothesis is that modifications of maternal mRNAs may reflect potential genetic and/or epigenetic modifications occurring during domestication and could have consequences during embryogenesis. Consequently, we investigated the trancriptomic profile of unfertilized eggs from two populations of Eurasian perch. These two populations differed by their domestication histories (F1 vs. F7+-at least seven generations of reproduction in captivity) and were genetically differentiated (FST = 0.1055, p<0.05). A broad follow up of the oogenesis progression failed to show significant differences during oogenesis between populations. However, the F1 population spawned earlier with embryos presenting an overall higher survivorship than those from the F7+ population. The transcriptomic profile of unfertilized eggs showed 358 differentially expressed genes between populations. In conclusion, our data suggests that the domestication process may influence the regulation of the maternal transcripts in fish eggs, which could in turn explain differences of developmental success.
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Affiliation(s)
| | - Maud Alix
- UR AFPA, University of Lorraine, INRA, Nancy, France
| | - Aurélie Le Cam
- LPGP, UR1037 Fish Physiology and Genomics, INRA, Rennes, France
| | | | - Jérôme Montfort
- LPGP, UR1037 Fish Physiology and Genomics, INRA, Rennes, France
| | - Lola Toomey
- UR AFPA, University of Lorraine, INRA, Nancy, France
| | | | - Julien Bobe
- LPGP, UR1037 Fish Physiology and Genomics, INRA, Rennes, France
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Dou C, Muhammad F, Liu L, Gong L, Chen Y, Guo B, Lü Z. Population diversity ofCistopus indicusinferred from mitochondrial DNA (Cytochrome b) variation from China and Vietnam. MOLLUSCAN RESEARCH 2019. [DOI: 10.1080/13235818.2019.1688635] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Canfeng Dou
- National Engineering Research Centre of Maricultural Facilities of China, Zhejiang Ocean University, Zhoushan, People’s Republic of China
| | - Faiz Muhammad
- National Engineering Research Centre of Maricultural Facilities of China, Zhejiang Ocean University, Zhoushan, People’s Republic of China
- Centre of Excellence in Marine Biology, University of Karachi, Karachi, Pakistan
| | - Liqin Liu
- National Engineering Research Centre of Maricultural Facilities of China, Zhejiang Ocean University, Zhoushan, People’s Republic of China
| | - Li Gong
- National Engineering Research Centre of Maricultural Facilities of China, Zhejiang Ocean University, Zhoushan, People’s Republic of China
| | - Yongjiu Chen
- National Engineering Research Centre of Maricultural Facilities of China, Zhejiang Ocean University, Zhoushan, People’s Republic of China
| | - Baoying Guo
- National Engineering Research Centre of Maricultural Facilities of China, Zhejiang Ocean University, Zhoushan, People’s Republic of China
| | - Zhenming Lü
- National Engineering Research Centre of Maricultural Facilities of China, Zhejiang Ocean University, Zhoushan, People’s Republic of China
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Haines ML, Luikart G, Amish SJ, Smith S, Latch EK. Evidence for adaptive introgression of exons across a hybrid swarm in deer. BMC Evol Biol 2019; 19:199. [PMID: 31684869 PMCID: PMC6827202 DOI: 10.1186/s12862-019-1497-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 08/22/2019] [Indexed: 12/21/2022] Open
Abstract
Background Secondary contact between closely related lineages can result in a variety of outcomes, including hybridization, depending upon the strength of reproductive barriers. By examining the extent to which different parts of the genome introgress, it is possible to infer the strength of selection and gain insight into the evolutionary trajectory of lineages. Following secondary contact approximately 8000 years ago in the Pacific Northwest, mule deer (Odocoileus hemionus hemionus) and black-tailed deer (O. h. columbianus) formed a hybrid swarm along the Cascade mountain range despite substantial differences in body size (up to two times) and habitat preference. In this study, we examined genetic population structure, extent of introgression, and selection pressures in freely interbreeding populations of mule deer and black-tailed deer using mitochondrial DNA sequences, 9 microsatellite loci, and 95 SNPs from protein-coding genes. Results We observed bi-directional hybridization and classified approximately one third of the 172 individuals as hybrids, almost all of which were beyond the F1 generation. High genetic differentiation between black-tailed deer and mule deer at protein-coding genes suggests that there is positive divergent selection, though selection on these loci is relatively weak. Contrary to predictions, there was not greater selection on protein-coding genes thought to be associated with immune function and mate choice. Geographic cline analyses were consistent across genetic markers, suggesting long-term stability (over hundreds of generations), and indicated that the center of the hybrid swarm is 20-30 km to the east of the Cascades ridgeline, where there is a steep ecological transition from wet, forested habitat to dry, scrub habitat. Conclusions Our data are consistent with a genetic boundary between mule deer and black-tailed deer that is porous but maintained by many loci under weak selection having a substantial cumulative effect. The absence of clear reproductive barriers and the consistent centering of geographic clines at a sharp ecotone suggests that ecology is a driver of hybrid swarm dynamics. Adaptive introgression in this study (and others) promotes gene flow and provides valuable insight into selection strength on specific genes and the evolutionary trajectory of hybridizing taxa. Electronic supplementary material The online version of this article (10.1186/s12862-019-1497-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Margaret L Haines
- Behavioral and Molecular Ecology Research Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, 53211, USA
| | - Gordon Luikart
- Montana Conservation Genomics Laboratory, Division of Biological Sciences, The University of Montana, 32 Campus Drive, Missoula, MT, 59812, USA.,Montana Conservation Genomics Laboratory, Flathead Lake Biological Station, Division of Biological Sciences, The University of Montana, 32125 Bio Station Lane, Polson, MT, 59860, USA
| | - Stephen J Amish
- Montana Conservation Genomics Laboratory, Division of Biological Sciences, The University of Montana, 32 Campus Drive, Missoula, MT, 59812, USA
| | - Seth Smith
- Montana Conservation Genomics Laboratory, Division of Biological Sciences, The University of Montana, 32 Campus Drive, Missoula, MT, 59812, USA
| | - Emily K Latch
- Behavioral and Molecular Ecology Research Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, 53211, USA.
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Magnúsdóttir H, Pálsson S, Westfall KM, Jónsson ZO, Örnólfsdóttir EB. Morphological variation in genetically divergent populations of the common whelk, Buccinum undatum (Gastropoda: Buccinidae), across the North Atlantic. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz095] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
The variation in shelled marine gastropod morphology across small spatial scales can reflect restricted population connectivity, resulting in evolution or plastic responses to environmental heterogeneity. The common whelk, Buccinum undatum, is a subtidal gastropod, ubiquitous in the North Atlantic, that exhibits considerable spatial variation in shell morphology and colour. Given that species delimitation in shelled marine gastropods is often based on shell characteristics, such morphological variation can lead to taxonomic confusion. Phylogeographical analysis based on mitochondrial DNA and microsatellites suggested cryptic species composed of Western and Eastern North Atlantic common whelk populations, the separation of which dates to the onset of the Pleistocene glaciation ~2.1 Mya. Divergence within the Eastern North Atlantic is more recent and characterized by isolation by distance. In the present study, phenotypic variation in shell morphology across the North Atlantic range is analysed and compared with molecular divergence. The morphological variation of B. undatum populations reflected the pattern observed for the molecular markers only for certain comparisons of populations and might, in other cases, reflect larger constraints on the morphological variation and, possibly, the impact of environmental influences.
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Affiliation(s)
- Hildur Magnúsdóttir
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
- Department of Aquaculture and Fish Biology, Hólar University College, Sauðárkrókur, Iceland
| | - Snæbjörn Pálsson
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
| | | | - Zophonías O Jónsson
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
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39
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Stone BW, Ward A, Farenwald M, Lutz AW, Wolfe AD. Genetic diversity and population structure in Cary’s Beardtongue Penstemon caryi (Plantaginaceae), a rare plant endemic to the eastern Rocky Mountains of Wyoming and Montana. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01204-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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40
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Novel microsatellite markers discovery in Patagonian toothfish (Dissostichus eleginoides) using high-throughput sequencing. Mol Biol Rep 2019; 46:5525-5530. [PMID: 31209744 DOI: 10.1007/s11033-019-04912-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 06/07/2019] [Indexed: 10/26/2022]
Abstract
Patagonian toohfish (Dissostichus eleginoides), is a sub Antartic notothenioid fish key in the marine ecosystem that sustains fishery of higher commercial value in the world. However, there are a scarce knowledge or information about its population genetic background, product of the almost null information of molecular markers available for this species. Here, we use high-throughput sequencing technology (Illumina platform) to develop 1071 microsatellite loci, of which 22 loci were selected to evaluation. Polymorphism and genetic diversity of each locus was assessed in two locations distant by 2370 km. Considering both locations, a mean PIC value of 0.748 was estimated. Selected microsatellite loci showed among two to seventeen alleles by locus in the first location and two to twelve in the second. The observed heterozygosity varied from 0.18 to 0.91 and from 0.12 to 0.87 for the first and second location, respectively. While, the expected heterozygosity ranged from 0.15 to 0.92 and from 0.11 to 0.90. Three loci were monomorphic in only one location. Microsatellite markers developed here will be useful in future studies on conservation, fishery and population genetics of this species.
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Albinsky D, Wham D, Shinzato N, Reimer JD. Population Connectivity in the Common Reef Zoantharian Zoanthus sansibaricus (Anthozoa: Hexacorallia) in Southern Japan. Zoolog Sci 2019; 35:321-329. [PMID: 30079838 DOI: 10.2108/zs180007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Tropical and subtropical shallow benthic marine communities are highly diverse and balanced systems that constitute an important natural resource. Knowledge of the genetic diversity, connectivity and reproduction mode of each population is critical to understanding the fate of whole assemblages in times of disturbances. Importantly, the capability of populations to adapt to environmental challenges will be crucial to determining their survival. Here, we report on the population structure of the common reef zoantharian Zoanthus sansibaricus in the northwestern Pacific, by examining populations at three different locations in southern Japan using five highly variable microsatellite markers. Analyses of a population at the species' northern distribution limit combined with analyses of two subtropical populations suggest that habitat characteristics and ocean currents influence the connectivity and genetic diversity of this species. Our findings emphasize the adaptive ability of Z. sansibaricus to different environmental conditions and may help explain the wide distribution and generalist nature of this species.
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Affiliation(s)
- Doris Albinsky
- 1 Molecular Invertebrate Systematics and Ecology Laboratory, Graduate School of Engineering and Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, Japan.,2 Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, United Kingdom
| | - Drew Wham
- 3 Department of Biology, Pennsylvania State University, 214 Mueller Laboratory, University Park, PA 16802, USA
| | - Naoya Shinzato
- 1 Molecular Invertebrate Systematics and Ecology Laboratory, Graduate School of Engineering and Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, Japan.,4 Tropical Biosphere Research Center, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, Japan
| | - James Davis Reimer
- 1 Molecular Invertebrate Systematics and Ecology Laboratory, Graduate School of Engineering and Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, Japan.,4 Tropical Biosphere Research Center, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, Japan
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42
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Berner D. Allele Frequency Difference AFD⁻An Intuitive Alternative to FST for Quantifying Genetic Population Differentiation. Genes (Basel) 2019; 10:genes10040308. [PMID: 31003563 PMCID: PMC6523497 DOI: 10.3390/genes10040308] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 04/08/2019] [Accepted: 04/12/2019] [Indexed: 01/19/2023] Open
Abstract
Measuring the magnitude of differentiation between populations based on genetic markers is commonplace in ecology, evolution, and conservation biology. The predominant differentiation metric used for this purpose is FST. Based on a qualitative survey, numerical analyses, simulations, and empirical data, I here argue that FST does not express the relationship to allele frequency differentiation between populations generally considered interpretable and desirable by researchers. In particular, FST (1) has low sensitivity when population differentiation is weak, (2) is contingent on the minor allele frequency across the populations, (3) can be strongly affected by asymmetry in sample sizes, and (4) can differ greatly among the available estimators. Together, these features can complicate pattern recognition and interpretation in population genetic and genomic analysis, as illustrated by empirical examples, and overall compromise the comparability of population differentiation among markers and study systems. I argue that a simple differentiation metric displaying intuitive properties, the absolute allele frequency difference AFD, provides a valuable alternative to FST. I provide a general definition of AFD applicable to both bi- and multi-allelic markers and conclude by making recommendations on the sample sizes needed to achieve robust differentiation estimates using AFD.
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Affiliation(s)
- Daniel Berner
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, CH-4051 Basel, Switzerland.
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Fourdrilis S, Backeljau T. Highly polymorphic mitochondrial DNA and deceiving haplotypic differentiation: implications for assessing population genetic differentiation and connectivity. BMC Evol Biol 2019; 19:92. [PMID: 30999853 PMCID: PMC6472099 DOI: 10.1186/s12862-019-1414-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 03/26/2019] [Indexed: 11/11/2022] Open
Abstract
Background Hyperdiverse mtDNA with more than 5% of variable synonymous nucleotide sites can lead to erroneous interpretations of population genetic differentiation patterns and parameters (φST, DEST). We illustrate this by using hyperdiverse mtDNA markers to infer population genetic differentiation and connectivity in Melarhaphe neritoides, a NE Atlantic (NEA) gastropod with a high dispersal potential. We also provide a recent literature example of how mtDNA hyperdiversity may have misguided the interpretation of genetic connectivity in the crab Opecarcinus hypostegus. Results mtDNA variation surveyed throughout the NEA showed that nearly all M. neritoides specimens had haplotypes private to populations, suggesting at first glance a lack of gene flow and thus a strong population genetic differentiation. Yet, the bush-like haplotype network, though visually misleading, showed no signs of phylogeographic or other haplotype structuring. Coalescent-based gene flow estimates were high throughout the NEA, irrespective of whether or not mtDNA hyperdiversity was reduced by removing hypervariable sites. Conclusions Melarhaphe neritoides seems to be panmictic over the entire NEA, which is consistent with its long-lived pelagic larval stage. With hyperdiverse mtDNA, the apparent lack of shared haplotypes among populations does not necessarily reflect a lack of gene flow and/or population genetic differentiation by fixation of alternative haplotypes (DEST ≈ 1 does not a fortiori imply φST ≈ 1), but may be due to (1) a too low sampling effort to detect shared haplotypes and/or (2) a very high mutation rate that may conceal the signal of gene flow. Hyperdiverse mtDNA can be used to assess connectivity by coalescent-based methods. Yet, the combined use of φST and DEST can provide a reasonable inference of connectivity patterns from hyperdiverse mtDNA, too.
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Affiliation(s)
- S Fourdrilis
- Royal Belgian Institute of Natural Sciences, Rue Vautier 29, B-1000, Brussels, Belgium.
| | - T Backeljau
- Royal Belgian Institute of Natural Sciences, Rue Vautier 29, B-1000, Brussels, Belgium.,Evolutionary Ecology Group, University of Antwerp, Universiteitsplein 1, B-2610, Antwerp, Belgium
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Erichsen EO, Wolff K, Hansen OK. Genetic and clonal structures of the tree species
Tilia cordata
mill. in remnants of ancient forests in Denmark. POPUL ECOL 2019. [DOI: 10.1002/1438-390x.12002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Eva Ortvald Erichsen
- Department of Geosciences and Natural Resource ManagementUniversity of Copenhagen Frederiksberg Denmark
| | - Kirsten Wolff
- School of Natural and Environmental SciencesNewcastle University Newcastle UK
| | - Ole K. Hansen
- Department of Geosciences and Natural Resource ManagementUniversity of Copenhagen Frederiksberg Denmark
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Njoroge AW, Andersson B, Lees AK, Mutai C, Forbes GA, Yuen JE, Pelle R. Genotyping of Phytophthora infestans in Eastern Africa Reveals a Dominating Invasive European Lineage. PHYTOPATHOLOGY 2019; 109:670-680. [PMID: 30253119 DOI: 10.1094/phyto-07-18-0234-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Strains of Phytophthora infestans, the pathogen causing late blight of potato and tomato, are thought to be moved around the world through infected planting material. Since its first appearance in 1941, late blight has caused important losses to potato production in the eastern-Africa region (EAR). In the current study, the genetic structure of the population in Kenya, Uganda, Tanzania, Burundi, and Rwanda was characterized using 12-plex microsatellite markers with the aim of testing the hypothesis that a strain originating from Europe, 2_A1, has recently dominated the population in EAR. Analyses of 1,093 potato and 165 tomato samples collected between 2013 and 2016 revealed the dominance on potato in all countries of the 2_A1 clonal lineage. On tomato, a host-specialized form of the US-1 lineage appears to persist in Rwanda, Uganda, and Tanzania whereas, in Kenya, most samples from tomato (72.5%) were 2_A1. The US-1 lineage in Tanzania had two private alleles at the Pi02 marker, suggesting a possible independent introduction into the region. US-1 had higher genetic variability than 2_A1, consistent with the earlier establishment of the former. Continuous tracking of P. infestans population changes should help identify new virulent and aggressive strains, which would inform strategic disease management options.
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Affiliation(s)
- Anne W Njoroge
- 1 International Potato Center (CIP), PO Box 25171-00603 Nairobi, Kenya
- 2 Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, PO Box 7026, S-750 07 Uppsala, Sweden
| | - Björn Andersson
- 2 Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, PO Box 7026, S-750 07 Uppsala, Sweden
| | - Alison K Lees
- 3 Cell and Molecular Sciences, The James Hutton Institute, Dundee, DD2 5DA, United Kingdom
| | - Collins Mutai
- 4 Biosciences eastern and central Africa-International Livestock Research Institute Hub, PO Box 30709-00100, Nairobi, Kenya; and
| | | | - Jonathan E Yuen
- 2 Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, PO Box 7026, S-750 07 Uppsala, Sweden
| | - Roger Pelle
- 4 Biosciences eastern and central Africa-International Livestock Research Institute Hub, PO Box 30709-00100, Nairobi, Kenya; and
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Alcala N, Rosenberg NA. GST' , Jost's D, and F ST are similarly constrained by allele frequencies: A mathematical, simulation, and empirical study. Mol Ecol 2019; 28:1624-1636. [PMID: 30589985 PMCID: PMC6821915 DOI: 10.1111/mec.15000] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 12/11/2018] [Accepted: 12/17/2018] [Indexed: 01/15/2023]
Abstract
Statistics GST' and Jost's D have been proposed for replacing FST as measures of genetic differentiation. A principal argument in favour of these statistics is the independence of their maximal values with respect to the subpopulation heterozygosity HS , a property not shared by FST . Nevertheless, it has been unclear if these alternative differentiation measures are constrained by other aspects of the allele frequencies. Here, for biallelic markers, we study the mathematical properties of the maximal values of GST' and D, comparing them to those of FST . We show that GST' and D exhibit the same peculiar frequency-dependence phenomena as FST , including a maximal value as a function of the frequency of the most frequent allele that lies well below one. Although the functions describing GST' , D, and FST in terms of the frequency of the most frequent allele are different, the allele frequencies that maximize them are identical. Moreover, we show using coalescent simulations that when taking into account the specific maximal values of the three statistics, their behaviours become similar across a large range of migration rates. We use our results to explain two empirical patterns: the similar values of the three statistics among North American wolves, and the low D values compared to GST' and FST in Atlantic salmon. The results suggest that the three statistics are often predictably similar, so that they can make quite similar contributions to data analysis. When they are not similar, the difference can be understood in relation to features of genetic diversity.
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Affiliation(s)
- Nicolas Alcala
- Department of Biology, Stanford University, Stanford, California
| | - Noah A Rosenberg
- Department of Biology, Stanford University, Stanford, California
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Serin A, Ay M, Sevay H, Gurkan C, Canan H. Genetic characterisation of 13 rapidly mutating Y-STR loci in 100 father and son pairs from South and East Turkey. Ann Hum Biol 2019; 45:506-515. [DOI: 10.1080/03014460.2018.1559353] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Ayse Serin
- Department of Forensic Medicine, Faculty of Medicine, University of Cukurova, Adana, Turkey
| | - Mustafa Ay
- Department of Forensic Medicine, Institute of Health Science, University of Cukurova, Adana, Turkey
| | - Huseyin Sevay
- Department of Information Systems Engineering, Near East University, Nicosia (North Cyprus), Turkey
| | - Cemal Gurkan
- Turkish Cypriot DNA Laboratory, Committee on Missing Persons in Cyprus Turkish Cypriot Member Office, Nicosia (North Cyprus), Turkey
- Dr. Fazıl Küçük Faculty of Medicine, Eastern Mediterranean University, Famagusta (North Cyprus), Turkey
| | - Husniye Canan
- Department of Forensic Medicine, Faculty of Medicine, University of Cukurova, Adana, Turkey
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Pérez-Espona S, Goodall-Copestake WP, Savirina A, Bobovikova J, Molina-Rubio C, Pérez-Barbería FJ. First assessment of MHC diversity in wild Scottish red deer populations. EUR J WILDLIFE RES 2019. [DOI: 10.1007/s10344-019-1254-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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49
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Belinchón R, Ellis CJ, Yahr R. Climate-woodland effects on population genetics for two congeneric lichens with contrasting reproductive strategies. FEMS Microbiol Ecol 2018; 94:5069390. [PMID: 30107505 DOI: 10.1093/femsec/fiy159] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 08/09/2018] [Indexed: 01/08/2023] Open
Abstract
Genetic variation is expected to be influenced by the interaction between reproductive mode and dispersal traits on the one hand and environmental and habitat setting affecting establishment success on the other. We evaluated how environmental/habitat setting affects population genetic variation (i.e. variation in genetic diversity and structure) when regulated by contrasting dispersal traits. We used fungus-specific microsatellite markers to examine genetic diversity and structure of two closely related epiphytic lichen fungi that differ in their primary reproductive mode: Nephroma laevigatum (sexually reproducing, n = 191, 10 microsatellites) and N. parile (asexually reproducing, n = 182, 12 microsatellites), along a steep climatic gradient in Scotland. Despite their reproductive differences, we found a high proportion of clones in both species and a background pattern of genetic structure related to climatic gradients. We also demonstrated that woodland connectivity, rather than geographic distance, explained genetic diversity in both species. Environmental/habitat setting, modulated by the reproductive mode of the species, affects genetic diversity and structure, but the putative dissimilarity in their reproductive mode is less important than has been previously assumed. We reinforce the importance of protecting highly connected populations, positioned along a gradient capturing the segregation of gene pool differences in response to climatic variation.
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Affiliation(s)
- Rocío Belinchón
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, EH3 5LR, Edinburgh, UK
| | | | - Rebecca Yahr
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, EH3 5LR, Edinburgh, UK
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Golkar P, Mokhtari N. Molecular diversity assessment of a world collection of safflower genotypes by SRAP and SCoT molecular markers. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2018; 24:1261-1271. [PMID: 30425439 PMCID: PMC6214440 DOI: 10.1007/s12298-018-0545-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 03/06/2018] [Accepted: 05/02/2018] [Indexed: 05/05/2023]
Abstract
Safflower (Carthamus tinctorius L.) is considered as an oil crop that is rich in medicinal and industrial properties. In this study, the genetic diversity of safflower was assessed using 12 polymorphic sequence-related amplified polymorphism (SRAPs) and 11 polymorphic start codon targeted (SCoT) markers in 100 genotypes of safflower gathered from different geographical regions of the world. The 23 primers generated a total of 227 polymorphism fragments with a mean of 68.2% within the range of 3 (SCoT 31 and SCoT 35) to 13 (SCoT 35) bands per primer. Polymorphism per primer ranged between 100% (in Me4-Em1) and 18.1% (in SCoT19), with an average of 36.76%. The polymorphism information contents of the SRAP and SCoT markers were 0.35 and 0.30, respectively, indicating that SRAP markers were more effective than SCoT markers for assessing the degree of genetic diversity of the safflower. The results of the analysis of molecular variance showed a significant difference across cultivated safflower genotypes possessing a high intra-population variation. The examined accessions were categorized into five clusters based on similarity centers: the Middle East containing Iran, Iraq, Turkey, and Tajikistan; the Far East, including India, Pakistan, and Korea; Europe; the American continent; and Africa, including Egypt, Sudan and Libya. The present study shows the effectiveness of employing the mixture of SRAP and SCoT markers in the identification of safflower genetic diversity that would be useful for conservation and population genetics of safflower improvement in further studies.
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Affiliation(s)
- Pooran Golkar
- Research Institute for Biotechnology and Bioengineering, Isfahan University of Technology, Isfahan, 84156 83111 Iran
| | - Niloofar Mokhtari
- Department of Agricultural Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, 84156 83111 Iran
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