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Leal JL, Milesi P, Hodková E, Zhou Q, James J, Eklund DM, Pyhäjärvi T, Salojärvi J, Lascoux M. Complex Polyploids: Origins, Genomic Composition, and Role of Introgressed Alleles. Syst Biol 2024; 73:392-418. [PMID: 38613229 PMCID: PMC11282369 DOI: 10.1093/sysbio/syae012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 12/18/2023] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
Introgression allows polyploid species to acquire new genomic content from diploid progenitors or from other unrelated diploid or polyploid lineages, contributing to genetic diversity and facilitating adaptive allele discovery. In some cases, high levels of introgression elicit the replacement of large numbers of alleles inherited from the polyploid's ancestral species, profoundly reshaping the polyploid's genomic composition. In such complex polyploids, it is often difficult to determine which taxa were the progenitor species and which taxa provided additional introgressive blocks through subsequent hybridization. Here, we use population-level genomic data to reconstruct the phylogenetic history of Betula pubescens (downy birch), a tetraploid species often assumed to be of allopolyploid origin and which is known to hybridize with at least four other birch species. This was achieved by modeling polyploidization and introgression events under the multispecies coalescent and then using an approximate Bayesian computation rejection algorithm to evaluate and compare competing polyploidization models. We provide evidence that B. pubescens is the outcome of an autoploid genome doubling event in the common ancestor of B. pendula and its extant sister species, B. platyphylla, that took place approximately 178,000-188,000 generations ago. Extensive hybridization with B. pendula, B. nana, and B. humilis followed in the aftermath of autopolyploidization, with the relative contribution of each of these species to the B. pubescens genome varying markedly across the species' range. Functional analysis of B. pubescens loci containing alleles introgressed from B. nana identified multiple genes involved in climate adaptation, while loci containing alleles derived from B. humilis revealed several genes involved in the regulation of meiotic stability and pollen viability in plant species.
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Affiliation(s)
- J Luis Leal
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Pascal Milesi
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
- Science for Life Laboratory (SciLifeLab), Uppsala University, 75237 Uppsala, Sweden
| | - Eva Hodková
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, 16521 Prague, Czech Republic
| | - Qiujie Zhou
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Jennifer James
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - D Magnus Eklund
- Physiology and Environmental Toxicology, Department of Organismal Biology, Uppsala University, Norbyvägen 18A, 75236 Uppsala, Sweden
| | - Tanja Pyhäjärvi
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, and Viikki Plant Science Centre, University of Helsinki, P.O. Box 65 (Viikinkaari 1), 00014 Helsinki, Finland
- Department of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland
| | - Jarkko Salojärvi
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, and Viikki Plant Science Centre, University of Helsinki, P.O. Box 65 (Viikinkaari 1), 00014 Helsinki, Finland
| | - Martin Lascoux
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
- Science for Life Laboratory (SciLifeLab), Uppsala University, 75237 Uppsala, Sweden
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Reyna-Blanco CS, Caduff M, Galimberti M, Leuenberger C, Wegmann D. Inference of Locus-Specific Population Mixtures from Linked Genome-Wide Allele Frequencies. Mol Biol Evol 2024; 41:msae137. [PMID: 38958167 PMCID: PMC11255385 DOI: 10.1093/molbev/msae137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 07/04/2024] Open
Abstract
Admixture between populations and species is common in nature. Since the influx of new genetic material might be either facilitated or hindered by selection, variation in mixture proportions along the genome is expected in organisms undergoing recombination. Various graph-based models have been developed to better understand these evolutionary dynamics of population splits and mixtures. However, current models assume a single mixture rate for the entire genome and do not explicitly account for linkage. Here, we introduce TreeSwirl, a novel method for inferring branch lengths and locus-specific mixture proportions by using genome-wide allele frequency data, assuming that the admixture graph is known or has been inferred. TreeSwirl builds upon TreeMix that uses Gaussian processes to estimate the presence of gene flow between diverged populations. However, in contrast to TreeMix, our model infers locus-specific mixture proportions employing a hidden Markov model that accounts for linkage. Through simulated data, we demonstrate that TreeSwirl can accurately estimate locus-specific mixture proportions and handle complex demographic scenarios. It also outperforms related D- and f-statistics in terms of accuracy and sensitivity to detect introgressed loci.
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Affiliation(s)
- Carlos S Reyna-Blanco
- Department of Biology, University of Fribourg, Fribourg 1700, Switzerland
- Swiss Institute of Bioinformatics, Fribourg 1700, Switzerland
| | - Madleina Caduff
- Department of Biology, University of Fribourg, Fribourg 1700, Switzerland
- Swiss Institute of Bioinformatics, Fribourg 1700, Switzerland
| | - Marco Galimberti
- Department of Biology, University of Fribourg, Fribourg 1700, Switzerland
- Swiss Institute of Bioinformatics, Fribourg 1700, Switzerland
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- Veterans Affairs Connecticut Healthcare System, West Haven, CT, USA
| | | | - Daniel Wegmann
- Department of Biology, University of Fribourg, Fribourg 1700, Switzerland
- Swiss Institute of Bioinformatics, Fribourg 1700, Switzerland
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Dang Z, Li J, Liu Y, Song M, Lockhart PJ, Tian Y, Niu M, Wang Q. RADseq-based population genomic analysis and environmental adaptation of rare and endangered recretohalophyte Reaumuria trigyna. THE PLANT GENOME 2024; 17:e20303. [PMID: 36740755 DOI: 10.1002/tpg2.20303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/30/2022] [Indexed: 06/18/2023]
Abstract
Genetic diversity reflects the survival potential, history, and population dynamics of an organism. It underlies the adaptive potential of populations and their response to environmental change. Reaumuria trigyna is an endemic species in the Eastern Alxa and West Ordos desert regions in China. The species has been considered a good candidate to explore the unique survival strategies of plants that inhabit this area. In this study, we performed population genomic analyses based on restriction-site associated DNA sequencing to understand the genetic diversity, population genetic structure, and differentiation of the species. Analyses of 92,719 high-quality single-nucleotide polymorphisms (SNPs) indicated that overall genetic diversity of R. trigyna was low (HO = 0.249 and HE = 0.208). No significant genetic differentiation was observed among the investigated populations. However, a subtle population genetic structure was detected. We suggest that this might be explained by adaptive diversification reinforced by the geographical isolation of populations. Overall, 3513 outlier SNPs were located in 243 gene-coding sequences in the R. trigyna transcriptome. Potential sites under diversifying selection occurred in genes (e.g., AP2/EREBP, E3 ubiquitin-protein ligase, FLS, and 4CL) related to phytohormone regulation and synthesis of secondary metabolites which have roles in adaptation of species. Our genetic analyses provide scientific criteria for evaluating the evolutionary capacity of R. trigyna and the discovery of unique adaptions. Our findings extend knowledge of refugia, environmental adaption, and evolution of germplasm resources that survive in the Ordos area.
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Affiliation(s)
- Zhenhua Dang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Jiabin Li
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Yanan Liu
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Miaomiao Song
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Peter J Lockhart
- School of Natural Sciences, College of Sciences, Massey University, Palmerston North, New Zealand
| | - Yunyun Tian
- Ministry of Education Key Laboratory of Herbage & Endemic Crop Biotechnology, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Miaomiao Niu
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Qinglang Wang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
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de Tomás C, Vicient CM. The Genomic Shock Hypothesis: Genetic and Epigenetic Alterations of Transposable Elements after Interspecific Hybridization in Plants. EPIGENOMES 2023; 8:2. [PMID: 38247729 PMCID: PMC10801548 DOI: 10.3390/epigenomes8010002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/21/2023] [Accepted: 12/24/2023] [Indexed: 01/23/2024] Open
Abstract
Transposable elements (TEs) are major components of plant genomes with the ability to change their position in the genome or to create new copies of themselves in other positions in the genome. These can cause gene disruption and large-scale genomic alterations, including inversions, deletions, and duplications. Host organisms have evolved a set of mechanisms to suppress TE activity and counter the threat that they pose to genome integrity. These includes the epigenetic silencing of TEs mediated by a process of RNA-directed DNA methylation (RdDM). In most cases, the silencing machinery is very efficient for the vast majority of TEs. However, there are specific circumstances in which TEs can evade such silencing mechanisms, for example, a variety of biotic and abiotic stresses or in vitro culture. Hybridization is also proposed as an inductor of TE proliferation. In fact, the discoverer of the transposons, Barbara McClintock, first hypothesized that interspecific hybridization provides a "genomic shock" that inhibits the TE control mechanisms leading to the mobilization of TEs. However, the studies carried out on this topic have yielded diverse results, showing in some cases a total absence of mobilization or being limited to only some TE families. Here, we review the current knowledge about the impact of interspecific hybridization on TEs in plants and the possible implications of changes in the epigenetic mechanisms.
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Affiliation(s)
| | - Carlos M. Vicient
- Centre for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Cerdanyola del Vallès, 08193 Barcelona, Spain
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Yuan R, Li J, Ma X, Feng Z, Xing R, Chen S, Gao Q. Investigation of phylogenetic relationships within Saxifraga diversifolia complex (Saxifragaceae) based on restriction-site associated DNA sequence markers. Ecol Evol 2023; 13:e10675. [PMID: 37928197 PMCID: PMC10620575 DOI: 10.1002/ece3.10675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 09/28/2023] [Accepted: 10/16/2023] [Indexed: 11/07/2023] Open
Abstract
Subsect. Hirculoideae Engl. & Irmsch., belonging to Saxifraga sect. Ciliatae Haw., has high species richness. It can be divided into S. diversifolia, S. pseudohirculus, and S. sinomontana complexes based on morphological characteristics. The species with prominent leaf veins on the posterior leaf edge were placed in the S. diversifolia complex, which is mainly distributed on the eastern and southern margins of the Qinghai-Tibetan Plateau. In this study, 53 samples, representing 15 of the 33 described species in the S. diversifolia complex, were sequenced using the Restriction-site Associated DNA Sequence (RAD-seq) technique. A total of 111,938 high-quality SNP loci were screened to investigate the phylogenetic relationships within the S. diversifolia complex. The result of the neighbor-joining (NJ) tree shows that the S. diversifolia complex is a paraphyletic group. Despite of some inconsistencies as revealed by genetic structural analysis, clustering results of representative species reconstructed by both NJ and principal component analysis analyses support previous biogeographic and morphological evidences. In addition, long-distance gene flow events for 11 taxa were detected in the S. diversifolia complex, respectively from S. implicans 1 to S. implicans 2, S. diversifolia and S. maxionggouensis, and from S. maxionggouensis to S. nigroglandulifera. These findings may improve our comprehension of the phylogeny, classification, and evolution of the S. diversifolia complex.
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Affiliation(s)
- Rui Yuan
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology & Institute of Sanjiangyuan National Park Chinese Academy of Sciences Xining China
- University of Chinese Academy of Sciences Beijing China
| | - Jiaxin Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology & Institute of Sanjiangyuan National Park Chinese Academy of Sciences Xining China
- University of Chinese Academy of Sciences Beijing China
| | - Xiaolei Ma
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology & Institute of Sanjiangyuan National Park Chinese Academy of Sciences Xining China
- University of Chinese Academy of Sciences Beijing China
| | - Zhilin Feng
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology & Institute of Sanjiangyuan National Park Chinese Academy of Sciences Xining China
- University of Chinese Academy of Sciences Beijing China
| | - Rui Xing
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology & Institute of Sanjiangyuan National Park Chinese Academy of Sciences Xining China
| | - Shilong Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology & Institute of Sanjiangyuan National Park Chinese Academy of Sciences Xining China
| | - Qingbo Gao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology & Institute of Sanjiangyuan National Park Chinese Academy of Sciences Xining China
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology Chinese Academy of Sciences Xining China
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Liu H, Cheng H, Xu J, Hu J, Zhao C, Xing L, Wang M, Wu Z, Peng D, Yu N, Liu J. Genetic diversity and population structure of Polygonatum cyrtonema Hua in China using SSR markers. PLoS One 2023; 18:e0290605. [PMID: 37651363 PMCID: PMC10470896 DOI: 10.1371/journal.pone.0290605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 08/11/2023] [Indexed: 09/02/2023] Open
Abstract
Polygonatum cyrtonema Hua is a perennial herbaceous plant of the Polygonatum genus, belonging to the Liliaceae family, with significant medicinal and nutritional value. In China, this species is a traditional medicinal and edible herb with a long history of application and is widely appreciated by the people. However, as the demand for medicinal herbs continues to grow, excessive harvesting has led to the depletion of wild resources and the risk of genetic erosion. In addition, the chaotic cultivation of varieties and the lack of high quality germplasm resources have led to inconsistent quality of medical materials. Therefore, it is urgent to conduct genetic diversity evaluation of this species and establish a sound conservation plan. This study assessed the genetic diversity and population structure of 96 samples collected from seven regions in China using the simple sequence repeat (SSR) molecular marker technology. In this study, a total of 60 alleles (Na) were detected across the 10 polymorphic SSR markers used, with an average of 6.0 alleles generated per locus. The values of polymorphic information content (PIC) values ranged from 0.3396 to 0.8794, with an average value of 0.6430. The average value of the effective number of alleles (Ne) was 2.761, and the average value of the Shannon's information index (I) was 1.196. The population structure analysis indicates that the Polygonatum cyrtonema Hua germplasm can be classified into three subpopulations (JZ, QY, JD) at the molecular level, which corresponds to the previous subgroups identified based on individual plant phenotypic traits. Analysis of Molecular Variance (AMOVA) showed that 74% of the genetic variation was between individuals within populations in different regions. The phylogenetic analysis of the 96 germplasm samples divided them into three main populations. The QY and JD subpopulations are largely clustered together, which could be attributed to their mountainous distribution and the local climate environment. The genetic differentiation coefficient (Fst) value was low at 0.065, indicating relatively low population differentiation. The ratio of the genetic differentiation coefficient (Fst) between the JZ population and the other two populations (QY and JD) is much higher than the ratio between the QY and JD populations. Based on the clustering results and the ratio of the genetic differentiation coefficient (Fst), it can be inferred that the genetic relationship between the QY and JD subpopulations is closer, with a certain degree of genetic differentiation from the JZ subpopulation. This study supports the conservation of germplasm resources of Polygonatum cyrtonema Hua in China and provides new parental material for germplasm genetic improvement and breeding programs.
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Affiliation(s)
- Heng Liu
- Department of Biopharmaceuticals, College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui Province, China
| | - He Cheng
- Department of Biopharmaceuticals, College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui Province, China
| | - Jun Xu
- Department of Biopharmaceuticals, College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui Province, China
| | - Jiayi Hu
- Department of Biopharmaceuticals, College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui Province, China
| | - Chenchen Zhao
- Department of Biopharmaceuticals, College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui Province, China
| | - Lihua Xing
- Department of Biopharmaceuticals, College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui Province, China
- MOE-Anhui Joint Collaborative Innovation Center for Quality Improvement of Anhui Genuine Chinese Medicinal Materials, Hefei, Anhui Province, China
| | - Mengjin Wang
- Department of Biopharmaceuticals, College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui Province, China
| | - Zhendong Wu
- Anhui Qingyang County Jiuhua traditional Chinese Medicinal Materials Technology Co., Ltd, Chizhou City, Anhui Province, China
| | - Daiyin Peng
- Department of Biopharmaceuticals, College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui Province, China
- MOE-Anhui Joint Collaborative Innovation Center for Quality Improvement of Anhui Genuine Chinese Medicinal Materials, Hefei, Anhui Province, China
| | - Nianjun Yu
- Department of Biopharmaceuticals, College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui Province, China
- MOE-Anhui Joint Collaborative Innovation Center for Quality Improvement of Anhui Genuine Chinese Medicinal Materials, Hefei, Anhui Province, China
| | - Junling Liu
- Department of Biopharmaceuticals, College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui Province, China
- Anhui Provincial Institutes for Food and Drug Control, Hefei, Anhui Province, China
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Gonçalves-Dias J, Singh A, Graf C, Stetter MG. Genetic Incompatibilities and Evolutionary Rescue by Wild Relatives Shaped Grain Amaranth Domestication. Mol Biol Evol 2023; 40:msad177. [PMID: 37552934 PMCID: PMC10439364 DOI: 10.1093/molbev/msad177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/20/2023] [Accepted: 08/02/2023] [Indexed: 08/10/2023] Open
Abstract
Crop domestication and the subsequent expansion of crops have long been thought of as a linear process from a wild ancestor to a domesticate. However, evidence of gene flow from locally adapted wild relatives that provided adaptive alleles into crops has been identified in multiple species. Yet, little is known about the evolutionary consequences of gene flow during domestication and the interaction of gene flow and genetic load in crop populations. We study the pseudo-cereal grain amaranth that has been domesticated three times in different geographic regions of the Americas. We quantify the amount and distribution of gene flow and genetic load along the genome of the three grain amaranth species and their two wild relatives. Our results show ample gene flow between crop species and between crops and their wild relatives. Gene flow from wild relatives decreased genetic load in the three crop species. This suggests that wild relatives could provide evolutionary rescue by replacing deleterious alleles in crops. We assess experimental hybrids between the three crop species and found genetic incompatibilities between one Central American grain amaranth and the other two crop species. These incompatibilities might have created recent reproductive barriers and maintained species integrity today. Together, our results show that gene flow played an important role in the domestication and expansion of grain amaranth, despite genetic species barriers. The domestication of plants was likely not linear and created a genomic mosaic by multiple contributors with varying fitness effects for today's crops.
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Affiliation(s)
| | - Akanksha Singh
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - Corbinian Graf
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - Markus G Stetter
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
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Tomowski M, Lozada-Gobilard S, Jeltsch F, Tiedemann R. Recruitment and migration patterns reveal a key role for seed banks in the meta-population dynamics of an aquatic plant. Sci Rep 2023; 13:11269. [PMID: 37438408 DOI: 10.1038/s41598-023-37974-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 06/30/2023] [Indexed: 07/14/2023] Open
Abstract
Progressive habitat fragmentation threatens plant species with narrow habitat requirements. While local environmental conditions define population growth rates and recruitment success at the patch level, dispersal is critical for population viability at the landscape scale. Identifying the dynamics of plant meta-populations is often confounded by the uncertainty about soil-stored population compartments. We combined a landscape-scale assessment of an amphibious plant's population structure with measurements of dispersal complexity in time to track dispersal and putative shifts in functional connectivity. Using 13 microsatellite markers, we analyzed the genetic structure of extant Oenanthe aquatica populations and their soil seed banks in a kettle hole system to uncover hidden connectivity among populations in time and space. Considerable spatial genetic structure and isolation-by-distance suggest limited gene flow between sites. Spatial isolation and patch size showed minor effects on genetic diversity. Genetic similarity found among extant populations and their seed banks suggests increased local recruitment, despite some evidence of migration and recent colonization. Results indicate stepping-stone dispersal across adjacent populations. Among permanent and ephemeral demes the resulting meta-population demography could be determined by source-sink dynamics. Overall, these spatiotemporal connectivity patterns support mainland-island dynamics in our system, highlighting the importance of persistent seed banks as enduring sources of genetic diversity.
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Affiliation(s)
- Maxi Tomowski
- Unit of Evolutionary Biology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Plant Ecology and Nature Conservation, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | | | - Florian Jeltsch
- Plant Ecology and Nature Conservation, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Ralph Tiedemann
- Unit of Evolutionary Biology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
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Cai XX, Wang Z, Yuan Y, Pang LH, Wang Y, Lu BR. Crop-Weed Introgression Plays Critical Roles in Genetic Differentiation and Diversity of Weedy Rice: A Case Study of Human-Influenced Weed Evolution. BIOLOGY 2023; 12:biology12050744. [PMID: 37237556 DOI: 10.3390/biology12050744] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023]
Abstract
As an important driving force, introgression plays an essential role in shaping the evolution of plant species. However, knowledge concerning how introgression affects plant evolution in agroecosystems with strong human influences is still limited. To generate such knowledge, we used InDel (insertion/deletion) molecular fingerprints to determine the level of introgression from japonica rice cultivars into the indica type of weedy rice. We also analyzed the impact of crop-to-weed introgression on the genetic differentiation and diversity of weedy rice, using InDel (insertion/deletion) and SSR (simple sequence repeat) molecular fingerprints. Results based on the STRUCTURE analysis indicated an evident admixture of some weedy rice samples with indica and japonica components, suggesting different levels of introgression from japonica rice cultivars to the indica type of weedy rice. The principal coordinate analyses indicated indica-japonica genetic differentiation among weedy rice samples, which was positively correlated with the introgression of japonica-specific alleles from the rice cultivars. In addition, increased crop-to-weed introgression formed a parabola pattern of dynamic genetic diversity in weedy rice. Our findings based on this case study provide evidence that human activities, such as the frequent change in crop varieties, can strongly influence weed evolution by altering genetic differentiation and genetic diversity through crop-weed introgression in agroecosystems.
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Affiliation(s)
- Xing-Xing Cai
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Zhi Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ye Yuan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Li-Hao Pang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ying Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Bao-Rong Lu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
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Evans A, de Kort H, Brys R, Duffy KJ, Jersáková J, Kull T, Selosse MA, Tsiftsis S, Minasiewicz J, Jacquemyn H. Historical biogeography and local adaptation explain population genetic structure in a widespread terrestrial orchid. ANNALS OF BOTANY 2023; 131:623-634. [PMID: 36680796 PMCID: PMC10147325 DOI: 10.1093/aob/mcad010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 01/11/2023] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS Historical changes in environmental conditions and colonization-extinction dynamics have a direct impact on the genetic structure of plant populations. However, understanding how past environmental conditions influenced the evolution of species with high gene flow is challenging when signals for genetic isolation and adaptation are swamped by gene flow. We investigated the spatial distribution and genetic structure of the widespread terrestrial orchid Epipactis helleborine to identify glacial refugia, characterize postglacial population dynamics and assess its adaptive potential. METHODS Ecological niche modelling was used to locate possible glacial refugia and postglacial recolonization opportunities of E. helleborine. A large single-nucleotide polymorphism (SNP) dataset obtained through genotyping by sequencing was used to define population genetic diversity and structure and to identify sources of postglacial gene flow. Outlier analyses were used to elucidate how adaptation to the local environment contributed to population divergence. KEY RESULTS The distribution of climatically suitable areas was restricted during the Last Glacial Maximum to the Mediterranean, south-western Europe and small areas in the Alps and Carpathians. Within-population genetic diversity was high in E. helleborine (mean expected heterozygosity, 0.373 ± 0.006; observed heterozygosity, 0.571 ± 0.012; allelic richness, 1.387 ± 0.007). Italy and central Europe are likely to have acted as important genetic sources during postglacial recolonization. Adaptive SNPs were associated with temperature, elevation and precipitation. CONCLUSIONS Forests in the Mediterranean and Carpathians are likely to have acted as glacial refugia for Epipactis helleborine. Postglacial migration northwards and to higher elevations resulted in the dispersal and diversification of E. helleborine in central Europe and Italy, and to geographical isolation and divergent adaptation in Greek and Italian populations. Distinguishing adaptive from neutral genetic diversity allowed us to conclude that E. helleborine has a high adaptive potential to climate change and demonstrates that signals of adaptation and historical isolation can be identified even in species with high gene flow.
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Affiliation(s)
- Alexandra Evans
- Department of Biology, Plant Conservation and Population Biology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Hanne de Kort
- Department of Biology, Plant Conservation and Population Biology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Rein Brys
- Research Institute for Forest and Nature, Geraardsbergen, Belgium
| | - Karl J Duffy
- Department of Biology, University of Naples Federico II, Complesso Monte Sant’Angelo, Naples 80126, Italy
| | - Jana Jersáková
- Department of Biology of Ecosystems, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Tiiu Kull
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, 5 Kreutzwaldi, 51014 Tartu, Estonia
| | - Marc-André Selosse
- Institut Systématique Evolution Biodiversité, Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, Paris, France
- Department of Plant Taxonomy and Nature Conservation, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Spyros Tsiftsis
- Department of Forest and Natural Environment Sciences, International Hellenic University, GR-66132, Drama, Greece
| | - Julita Minasiewicz
- Department of Plant Taxonomy and Nature Conservation, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Hans Jacquemyn
- Department of Biology, Plant Conservation and Population Biology, Katholieke Universiteit Leuven, Leuven, Belgium
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11
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Murphy AM, Jiang S, Elderfield JA, Pate AE, Halliwell C, Glover BJ, Cunniffe NJ, Carr JP. Biased pollen transfer by bumblebees favors the paternity of virus-infected plants in cross-pollination. iScience 2023; 26:106116. [PMID: 36994192 PMCID: PMC10040881 DOI: 10.1016/j.isci.2023.106116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/14/2022] [Accepted: 01/30/2023] [Indexed: 03/19/2023] Open
Abstract
We used a green fluorescent protein marker gene for paternity analysis to determine if virus infection affected male reproductive success of tomato in bumblebee-mediated cross-pollination under glasshouse conditions. We found that bumblebees that visited flowers of infected plants showed a strong preference to subsequently visit flowers of non-infected plants. The behavior of the bumblebees to move toward non-infected plants after pollinating virus-infected plants appears to explain the paternity data, which demonstrate a statistically significant ∼10-fold bias for fertilization of non-infected plants with pollen from infected parents. Thus, in the presence of bumblebee pollinators, CMV-infected plants exhibit enhanced male reproductive success.
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Affiliation(s)
- Alex M. Murphy
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA United Kingdom
- Corresponding author
| | - Sanjie Jiang
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA United Kingdom
| | - James A.D. Elderfield
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA United Kingdom
| | - Adrienne E. Pate
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA United Kingdom
| | - Chay Halliwell
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA United Kingdom
| | - Beverley J. Glover
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA United Kingdom
| | - Nik J. Cunniffe
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA United Kingdom
| | - John P. Carr
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA United Kingdom
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12
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Ma C, Liu L, Liu T, Jia Y, Jiang Q, Bai H, Ma S, Li S, Wang Z. QTL Mapping for Important Agronomic Traits Using a Wheat55K SNP Array-Based Genetic Map in Tetraploid Wheat. PLANTS (BASEL, SWITZERLAND) 2023; 12:847. [PMID: 36840195 PMCID: PMC9964379 DOI: 10.3390/plants12040847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 01/31/2023] [Accepted: 02/07/2023] [Indexed: 06/18/2023]
Abstract
Wheat yield is highly correlated with plant height, heading date, spike characteristics, and kernel traits. In this study, we used the wheat55K single nucleotide polymorphism array to genotype a recombinant inbred line population of 165 lines constructed by crossing two tetraploid wheat materials, Icaro and Y4. A genetic linkage map with a total length of 6244.51 cM was constructed, covering 14 chromosomes of tetraploid wheat. QTLs for 12 important agronomic traits, including plant height (PH), heading date (HD), awn color (AC), spike-branching (SB), and related traits of spike and kernel, were mapped in multiple environments, while combined QTL-by-environment interactions and epistatic effects were analyzed for each trait. A total of 52 major or stable QTLs were identified, among which may be some novel loci controlling PH, SB, and kernel length-width ratio (LWR), etc., with LOD values ranging from 2.51 to 54.49, thereby explaining 2.40-66.27% of the phenotypic variation. Based on the 'China Spring' and durum wheat reference genome annotations, candidate genes were predicted for four stable QTLs, QPH.nwafu-2B.2 (165.67-166.99 cM), QAC.nwafu-3A.1 (419.89-420.52 cM), QAC.nwafu-4A.1 (424.31-447.4 cM), and QLWR.nwafu-7A.1 (166.66-175.46 cM). Thirty-one QTL clusters and 44 segregation distortion regions were also detected, and 38 and 18 major or stable QTLs were included in these clusters and segregation distortion regions, respectively. These results provide QTLs with breeding application potential in tetraploid wheat that broadens the genetic basis of important agronomic traits such as PH, HD, AC, SB, etc., and benefits wheat breeding.
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Affiliation(s)
- Chao Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Le Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Tianxiang Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Yatao Jia
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Qinqin Jiang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Haibo Bai
- Agricultural Bio-Technology Research Center, Ningxia Academy of Agriculture and Forestry Science, Yinchuan 750002, China
| | - Sishuang Ma
- Agricultural Bio-Technology Research Center, Ningxia Academy of Agriculture and Forestry Science, Yinchuan 750002, China
| | - Shuhua Li
- Agricultural Bio-Technology Research Center, Ningxia Academy of Agriculture and Forestry Science, Yinchuan 750002, China
| | - Zhonghua Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
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13
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Diaz-Martin Z, Browne L, Cabrera D, Olivo J, Karubian J. Impacts of Flowering Density on Pollen Dispersal and Gametic Diversity Are Scale Dependent. Am Nat 2023; 201:52-64. [PMID: 36524929 DOI: 10.1086/721918] [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] [Indexed: 11/03/2022]
Abstract
AbstractPollen dispersal is a key evolutionary and ecological process, but the degree to which variation in the density of concurrently flowering conspecific plants (i.e., coflowering density) shapes pollination patterns remains understudied. We monitored coflowering density and corresponding pollination patterns of the insect-pollinated palm Oenocarpus bataua in northwestern Ecuador and found that the influence of coflowering density on these patterns was scale dependent: high neighborhood densities were associated with reductions in pollen dispersal distance and gametic diversity of progeny arrays, whereas we observed the opposite pattern at the landscape scale. In addition, neighborhood coflowering density also impacted forward pollen dispersal kernel parameters, suggesting that low neighborhood densities encourage pollen movement and may promote gene flow and genetic diversity. Our work reveals how coflowering density at different spatial scales influences pollen movement, which in turn informs our broader understanding of the mechanisms underlying patterns of genetic diversity and gene flow within populations of plants.
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14
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Escobar S, Vigouroux Y, Karubian J, Zekraoui L, Balslev H, Montúfar R. Limited seed dispersal shapes fine‐scale spatial genetic structure in a Neotropical dioecious large‐seeded palm. Biotropica 2022. [DOI: 10.1111/btp.13172] [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]
Affiliation(s)
- Sebastián Escobar
- Ecoinformatics and Biodiversity, Department of Biology Aarhus University Aarhus Denmark
- Grupo de Investigación en Biodiversidad, Medio Ambiente, y Salud Universidad de Las Américas Quito Ecuador
| | - Yves Vigouroux
- Diversité, Adaptation, Développement des Plantes Institut de Recherche pour le Développement, University of Montpellier Montpellier France
| | - Jordan Karubian
- Department of Ecology and Evolutionary Biology Tulane University New Orleans USA
| | - Leila Zekraoui
- Diversité, Adaptation, Développement des Plantes Institut de Recherche pour le Développement, University of Montpellier Montpellier France
| | - Henrik Balslev
- Ecoinformatics and Biodiversity, Department of Biology Aarhus University Aarhus Denmark
| | - Rommel Montúfar
- Facultad de Ciencias Exactas y Naturales Pontificia Universidad Católica del Ecuador Quito Ecuador
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15
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Hopley T, Byrne M. Implications of climate change on a floodplain shrub: associations between genomic and environmental variation. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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16
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Imwattana K, Aguero B, Duffy A, Shaw AJ. Demographic history and gene flow in the peatmosses Sphagnum recurvum and Sphagnum flexuosum (Bryophyta: Sphagnaceae). Ecol Evol 2022; 12:e9489. [PMID: 36407896 PMCID: PMC9667404 DOI: 10.1002/ece3.9489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 09/28/2022] [Accepted: 10/19/2022] [Indexed: 11/18/2022] Open
Abstract
Population size changes and gene flow are processes that can have significant impacts on evolution. The aim of this study was to investigate the relationship of geography to patterns of gene flow and population size changes in a pair of closely related Sphagnum (peatmoss) species: S. recurvum and S. flexuosum. Both species occur in eastern North America, and S. flexuosum also occurs in Europe. Genetic data from restriction-site-associated DNA sequencing (RAD-seq) were used in this study. Analyses of gene flow were accomplished using coalescent simulations of site frequency spectra (SFSs). Signatures of gene flow were confirmed by f 4 statistics. For S. flexuosum, genetic diversity of plants in glaciated areas appeared to be lower than that in unglaciated areas, suggesting that glaciation can have an impact on effective population sizes. There is asymmetric gene flow from eastern North America to Europe, suggesting that Europe might have been colonized by plants from eastern North America after the last glacial maximum. The rate of gene flow between S. flexuosum and S. recurvum is lower than that between geographically disjunct S. flexuosum populations. The rate of gene flow between species is higher among sympatric plants of the two species than between currently allopatric S. flexuosum populations. There was also gene flow from S. recurvum to the ancestor S. flexuosum on both continents which occurred through secondary contact. These results illustrate a complex history of interspecific gene flow between S. flexuosum and S. recurvum, which occurred in at least two phases: between ancestral populations after secondary contact and between currently sympatric plants.
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Affiliation(s)
- Karn Imwattana
- Department of Biology & L. E. Anderson Bryophyte HerbariumDuke UniversityDurhamNorth CarolinaUSA
| | - Blanka Aguero
- Department of Biology & L. E. Anderson Bryophyte HerbariumDuke UniversityDurhamNorth CarolinaUSA
| | - Aaron Duffy
- Department of Biology & L. E. Anderson Bryophyte HerbariumDuke UniversityDurhamNorth CarolinaUSA
| | - A. Jonathan Shaw
- Department of Biology & L. E. Anderson Bryophyte HerbariumDuke UniversityDurhamNorth CarolinaUSA
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17
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Feigs JT, Holzhauer SIJ, Huang S, Brunet J, Diekmann M, Hedwall PO, Kramp K, Naaf T. Pollinator movement activity influences genetic diversity and differentiation of spatially isolated populations of clonal forest herbs. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.908258] [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
In agricultural landscapes, forest herbs live in small, spatially isolated forest patches. For their long-term survival, their populations depend on animals as genetic linkers that provide pollen- or seed-mediated gene flow among different forest patches. However, whether insect pollinators serve as genetic linkers among spatially isolated forest herb populations in agricultural landscapes remains to be shown. Here, we used population genetic methods to analyze: (A) the genetic diversity and genetic differentiation of populations of two common, slow-colonizing temperate forest herb species [Polygonatum multiflorum (L.) All. and Anemone nemorosa L.] in spatially isolated populations within three agricultural landscapes in Germany and Sweden and (B) the movement activity of their most relevant associated pollinator species, i.e., the bumblebee Bombus pascuorum (Scopoli, 1,763) and the hoverfly Melanostoma scalare (Fabricus, 1,794), respectively, which differ in their mobility. We tested whether the indicated pollinator movement activity affected the genetic diversity and genetic differentiation of the forest herb populations. Bumblebee movement indicators that solely indicated movement activity between the forest patches affected both genetic diversity and genetic differentiation of the associated forest herb P. multiflorum in a way that can be explained by pollen-mediated gene flow among the forest herb populations. In contrast, movement indicators reflecting the total movement activity at a forest patch (including within-forest patch movement activity) showed unexpected effects for both plant-pollinator pairs that might be explained by accelerated genetic drift due to enhanced sexual reproduction. Our integrated approach revealed that bumblebees serve as genetic linkers of associated forest herb populations, even if they are more than 2 km apart from each other. No such evidence was found for the forest associated hoverfly species which showed significant genetic differentiation among forest patches itself. Our approach also indicated that a higher within-forest patch movement activity of both pollinator species might enhance sexual recruitment and thus diminishes the temporal buffer that clonal growth provides against habitat fragmentation effects.
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18
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Brooks E, Slender AL, Cu S, Breed MF, Stangoulis JCR. A range-wide analysis of population structure and genomic variation within the critically endangered spiny daisy (Acanthocladium dockeri). CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01468-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractUnderstanding population structure and genetic diversity is important for designing effective conservation strategies. As a critically endangered shrub, the six remaining extant populations of spiny daisy (Acanthocladium dockeri) are restricted to country roadsides in the mid-north of South Australia, where the species faces many ongoing abiotic and biotic threats to survival. Currently the spiny daisy is managed by selecting individuals from the extant populations and translocating them to establish insurance populations. However, there is little information available on the genetic differentiation between populations and diversity within source populations, which are essential components of planning translocations. To help fill this knowledge gap, we analysed population structure within and among all six of its known wild populations using 7,742 SNPs generated by a genotyping-by-sequencing approach. Results indicated that each population was strongly differentiated, had low levels of genetic diversity, and there was no evidence of inter-population gene flow. Individuals within each population were generally closely related, however, the Melrose population consisted entirely of clones. Our results suggest genetic rescue should be applied to wild spiny daisy populations to increase genetic diversity that will subsequently lead to greater intra-population fitness and adaptability. As a starting point, we suggest focussing on improving seed viability via inter-population crosses such as through hand pollination experiments to experimentally assess their sexual compatibility with the hope of increasing spiny daisy sexual reproduction and long-term reproductive fitness.
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Heredia-Pech M, Chávez-Pesqueira M, Ortiz-García MM, Andueza-Noh RH, Chacón-Sánchez MI, Martínez-Castillo J. Consequences of introgression and gene flow on the genetic structure and diversity of Lima bean ( Phaseolus lunatus L.) in its Mesoamerican diversity area. PeerJ 2022; 10:e13690. [PMID: 35811827 PMCID: PMC9266586 DOI: 10.7717/peerj.13690] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 06/16/2022] [Indexed: 01/17/2023] Open
Abstract
We evaluated the role of gene flow and wild-crop introgression on the structure and genetic diversity of Lima bean (Phaseolus lunatus) in the Yucatan Peninsula, an important Mesoamerican diversity area for this crop, using a genotyping-by-sequencing approach (15,168 SNP markers) and two scales. At the local scale, STRUCTURE and NGSEP analyses showed predominantly crop-to-wild introgression, but also evidence of a bidirectional gene flow in the two wild-weedy-crop complexes studied (Itzinté and Dzitnup). The ABBA-BABA tests showed a higher introgression in Itzinté (the older complex) than in Dzitnup (the younger one); at the allelic level, the wild-crop introgression in Itzinté was similar in both directions, in Dzitnup it was higher from crop-to-wild; and at the chromosomal level, introgression in Itzinté was from wild-to-crop, whereas in Dzitnup it occured in the opposite direction. Also, we found H E values slightly higher in the domesticated accessions than in the wild ones, in both complexes (Itzinté: wild = 0.31, domesticated = 0.34; Dzinup: wild = 0.27, domesticated = 0.36), but %P and π estimators were higher in the wild accessions than in the domesticated ones. At a regional scale, STRUCTURE and MIGRATE showed a low gene flow, predominantly from crop-to-wild; and STRUCTURE, Neighbor-Joining and PCoA analyses indicated the existence of two wild groups and one domesticated group, with a marked genetic structure based in the existence of domesticated MI and wild MII gene pools. Also, at the regional scale, we found a higher genetic diversity in the wild accessions than in the domesticated ones, in all estimators used (e.g., H E = 0.27 and H E = 0.17, respectively). Our results indicate that gene flow and introgression are playing an important role at the local scale, but its consequences on the structure and genetic diversity of the Lima bean are not clearly reflected at the regional scale, where diversity patterns between wild and domesticated populations could be reflecting historical events.
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Affiliation(s)
- Mauricio Heredia-Pech
- Unidad de Recursos Naturales, Centro de Investigación Científica de Yucatán, A.C., Mérida, Yucatán, México
| | - Mariana Chávez-Pesqueira
- Unidad de Recursos Naturales, Centro de Investigación Científica de Yucatán, A.C., Mérida, Yucatán, México
| | - Matilde M. Ortiz-García
- Unidad de Recursos Naturales, Centro de Investigación Científica de Yucatán, A.C., Mérida, Yucatán, México
| | - Rubén Humberto Andueza-Noh
- División de Estudios de Posgrado e Investigación, Instituto Tecnológico de Conkal, Conkal, Yucatán, México
| | - María Isabel Chacón-Sánchez
- Departamento de Agronomía, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Bogotá, D.C., Colombia
| | - Jaime Martínez-Castillo
- Unidad de Recursos Naturales, Centro de Investigación Científica de Yucatán, A.C., Mérida, Yucatán, México
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Pollen-mediated transfer of herbicide resistance between johnsongrass (Sorghum halepense) biotypes. Sci Rep 2022; 12:7663. [PMID: 35538136 PMCID: PMC9091218 DOI: 10.1038/s41598-022-11713-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 04/18/2022] [Indexed: 11/23/2022] Open
Abstract
Johnsongrass (Sorghum halepense) is a troublesome weed in row crop production in the United States. Herbicide resistance is a growing concern in this species, with resistance to ACCase-, ALS-, and EPSPS-inhibitors already reported. Pollen-mediated gene flow (PMGF) is capable of spreading herbicide resistance, but the extent of PMGF has not yet been studied in johnsongrass. Field experiments were conducted in a Nelder-wheel design to quantify the distance and frequency of PMGF from ALS-inhibitor-resistant (AR) to -susceptible (AS) johnsongrass across three environments (summer 2018, fall 2018, and fall 2019). The AR biotype (pollen donor) was established at the center of the wheel (5-m diameter), and a naturally occurring johnsongrass (AS) infestation was utilized as the pollen recipient, in eight directions and at nine distances (5, 10, 15, 20, 25, 35, 40, 45, and 50 m) within each direction. Seeds collected from the AS plants in each distance and direction were screened for survival to the ALS-inhibitor herbicide nicosulfuron (Accent Q) at 95 g ai ha−1 under greenhouse conditions. The survivors (i.e. hybrids) were further confirmed based on the presence of the Trp574Leu mutation. At the closest distance of 5 m, PMGF was 9.6–16.2% across the directions and environments, which progressively declined to 0.8–1.2% at 50 m. The exponential decay model predicted 50% reduction in PMGF at 2.2 m and 90% reduction at 5.8 m from the pollen donor block. Results demonstrate that herbicide resistance can spread between adjacent field populations of johnsongrass through PMGF, which necessitates sound monitoring and management.
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The Genetics and Ecology of Post-Fire Eucalyptus globulus Recruitment in an Isolated Stand in Central Portugal. FORESTS 2022. [DOI: 10.3390/f13050680] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Eucalyptus globulus Labill. is a widespread forest tree species, reported as naturalized across the introduced range, often showing abundant natural regeneration after wildfires. This paper studies a post-fire cohort of seedlings derived from a small, isolated E. globulus stand in central Portugal. The aim is to better understand the genetic dynamics and dispersal mechanisms of naturally established E. globulus populations in the introduced range. The seedling density at 55 m from adult trees was 12,000 ha−1, the farthest seedling being registered at 101 m. Post-fire expansion occurred in a southward direction, in accordance with predominant wind. Seedlings had significantly lower levels of genetic diversity (Ae = 5.8.; He = 0.8) than adult trees (Ae = 6.5; He = 0.8). Crossings were strongly unbalanced, with only eight trees contributing to the sampled seedlings, and one single tree contributing to 52% of these seedlings. Moreover, the co-ancestry amongst seedlings more than doubled (from θ = 0.03 to 0.076), and the population status number was around one third of the value registered for the adult population (from Ns = 16.2 to 6.6). Despite its isolation, external pollen was detected in the stand, and appears to have travelled at least 700 m, contributing to 22% of the offspring. Overall, the seedling cohort is much less diverse than the parent trees, with expected lower resilience and persistence to environmental stresses.
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Wu X, Liu Y, Luo H, Shang L, Leng C, Liu Z, Li Z, Lu X, Cai H, Hao H, Jing HC. Genomic footprints of sorghum domestication and breeding selection for multiple end uses. MOLECULAR PLANT 2022; 15:537-551. [PMID: 34999019 DOI: 10.1016/j.molp.2022.01.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 12/01/2021] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
Domestication and diversification have had profound effects on crop genomes. Originating in Africa and subsequently spreading to different continents, sorghum (Sorghum bicolor) has experienced multiple onsets of domestication and intensive breeding selection for various end uses. However, how these processes have shaped sorghum genomes is not fully understood. In the present study, population genomics analyses were performed on a worldwide collection of 445 sorghum accessions, covering wild sorghum and four end-use subpopulations with diverse agronomic traits. Frequent genetic exchanges were found among various subpopulations, and strong selective sweeps affected 14.68% (∼107.5 Mb) of the sorghum genome, including 3649, 4287, and 3888 genes during sorghum domestication, improvement of grain sorghum, and improvement of sweet sorghum, respectively. Eight different models of haplotype changes in domestication genes from wild sorghum to landraces and improved sorghum were observed, and Sh1- and SbTB1-type genes were representative of two prominent models, one of soft selection or multiple origins and one of hard selection or an early single domestication event. We also demonstrated that the Dry gene, which regulates stem juiciness, was unconsciously selected during the improvement of grain sorghum. Taken together, these findings provide new genomic insights into sorghum domestication and breeding selection, and will facilitate further dissection of the domestication and molecular breeding of sorghum.
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Affiliation(s)
- Xiaoyuan Wu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yuanming Liu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hong Luo
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Li Shang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Chuanyuan Leng
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Zhiquan Liu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Zhigang Li
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Xiaochun Lu
- Institute of Sorghum Research, Liaoning Academy of Agricultural Sciences, Shenyang 110161, China
| | - Hongwei Cai
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China
| | - Huaiqing Hao
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
| | - Hai-Chun Jing
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; Engineering Laboratory for Grass-Based Livestock Husbandry, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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23
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Curran EV, Scott MS, Olofsson JK, Nyirenda F, Sotelo G, Bianconi ME, Manzi S, Besnard G, Pereira L, Christin PA. Hybridization boosts dispersal of two contrasted ecotypes in a grass species. Proc Biol Sci 2022; 289:20212491. [PMID: 35078363 PMCID: PMC8790336 DOI: 10.1098/rspb.2021.2491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 12/23/2021] [Indexed: 11/12/2022] Open
Abstract
Genetic exchanges between closely related groups of organisms with different adaptations have well-documented beneficial and detrimental consequences. In plants, pollen-mediated exchanges affect the sorting of alleles across physical landscapes and influence rates of hybridization. How these dynamics affect the emergence and spread of novel phenotypes remains only partially understood. Here, we use phylogenomics and population genomics to retrace the origin and spread of two geographically overlapping ecotypes of the African grass Alloteropsis angusta. In addition to an ecotype inhabiting wetlands, we report the existence of a previously undescribed ecotype inhabiting Miombo woodlands and grasslands. The two ecotypes are consistently associated with different nuclear groups, which represent an advanced stage of divergence with secondary low-level gene flow. However, the seed-transported chloroplast genomes are consistently shared by distinct ecotypes inhabiting the same region. These patterns suggest that the nuclear genome of one ecotype can enter the seeds of the other via occasional pollen movements with sorting of nuclear groups in subsequent generations. The contrasting ecotypes of A. angusta can thus use each other as a gateway to new locations across a large part of Africa, showing that hybridization can facilitate the geographical dispersal of distinct ecotypes of the same grass species.
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Affiliation(s)
- Emma V. Curran
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Matilda S. Scott
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Jill K. Olofsson
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Florence Nyirenda
- Department of Biological Sciences, University of Zambia, Lusaka, Zambia
| | - Graciela Sotelo
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Matheus E. Bianconi
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Sophie Manzi
- Laboratoire Evolution and Diversité Biologique (EDB UMR5174), Université de Toulouse III – Paul Sabatier, CNRS, IRD, 118 route de Narbonne, 31062 Toulouse, France
| | - Guillaume Besnard
- Laboratoire Evolution and Diversité Biologique (EDB UMR5174), Université de Toulouse III – Paul Sabatier, CNRS, IRD, 118 route de Narbonne, 31062 Toulouse, France
| | - Lara Pereira
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Pascal-Antoine Christin
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
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24
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Holmes KH, Lindquist JL, Rebarber R, Werle R, Yerka M, Tenhumberg B. Modeling the evolution of herbicide resistance in weed species with a complex life cycle. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2022; 32:e02473. [PMID: 34652876 DOI: 10.1002/eap.2473] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 02/17/2021] [Accepted: 04/21/2021] [Indexed: 06/13/2023]
Abstract
A growing number of weed species have evolved resistance to herbicides in recent years, which causes an immense financial burden to farmers. An increasingly popular method of weed control is the adoption of crops that are resistant to specific herbicides, which allows farmers to apply the herbicide during the growing season without harming the crop. If such crops are planted in the presence of closely related weed species, it is possible that resistance genes could transfer from the crop species to feral populations of the wild species via gene flow and become stably introgressed under ongoing selective pressure by the herbicide. We use a density-dependent matrix model to evaluate the effect of planting such crops on the evolution of herbicide resistance under a range of management scenarios. Our model expands on previous simulation studies by considering weed species with a more complex life cycle (perennial, rhizomatous weed species), studying the effect of environmental variation in herbicide effectiveness, and evaluating the role of common simplifying genetic assumptions on resistance evolution. Our model predictions are qualitatively similar to previous modeling studies using species with a simpler life cycle, which is, crop rotation in combination with rotation of herbicide site of action effectively controls weed populations and slows the evolution of herbicide resistance. We find that ignoring the effect of environmental variation can lead to an over- or under-prediction of the speed of resistance evolution. The effect of environmental variation in herbicide effectiveness depends on the resistance allele frequency in the weed population at the beginning of the simulation. Finally, we find that degree of dominance and ploidy level have a much larger effect on the predicted speed of resistance evolution compared to the rate of gene flow.
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Affiliation(s)
- K Harrison Holmes
- Department of Mathematics, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA
| | - John L Lindquist
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA
| | - Richard Rebarber
- Department of Mathematics, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA
| | - Rodrigo Werle
- Department of Agronomy, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Melinda Yerka
- Department of Agriculture, Nutrition and Veterinary Sciences, University of Nevada-Reno, Reno, Nevada, 89557, USA
| | - Brigitte Tenhumberg
- School of Biological Sciences and Department of Mathematics, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA
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25
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Zhao X, Fu X, Yin C, Lu F. Wheat speciation and adaptation: perspectives from reticulate evolution. ABIOTECH 2021; 2:386-402. [PMID: 36311810 PMCID: PMC9590565 DOI: 10.1007/s42994-021-00047-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 04/27/2021] [Indexed: 12/16/2022]
Abstract
Reticulate evolution through the interchanging of genetic components across organisms can impact significantly on the fitness and adaptation of species. Bread wheat (Triticum aestivum subsp. aestivum) is one of the most important crops in the world. Allopolyploid speciation, frequent hybridization, extensive introgression, and occasional horizontal gene transfer (HGT) have been shaping a typical paradigm of reticulate evolution in bread wheat and its wild relatives, which is likely to have a substantial influence on phenotypic traits and environmental adaptability of bread wheat. In this review, we outlined the evolutionary history of bread wheat and its wild relatives with a highlight on the interspecific hybridization events, demonstrating the reticulate relationship between species/subspecies in the genera Triticum and Aegilops. Furthermore, we discussed the genetic mechanisms and evolutionary significance underlying the introgression of bread wheat and its wild relatives. An in-depth understanding of the evolutionary process of Triticum species should be beneficial to future genetic study and breeding of bread wheat.
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Affiliation(s)
- Xuebo Zhao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiangdong Fu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Changbin Yin
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Fei Lu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
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26
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Key Roles of De-Domestication and Novel Mutation in Origin and Diversification of Global Weedy Rice. BIOLOGY 2021; 10:biology10090828. [PMID: 34571705 PMCID: PMC8472751 DOI: 10.3390/biology10090828] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/16/2021] [Accepted: 08/17/2021] [Indexed: 11/17/2022]
Abstract
Simple Summary Weedy rice is a noxious weed infesting rice fields worldwide and causing tremendous losses of rice yield and quality. The control of this conspecific weed is difficult owing to abundant genetic diversity associated with its complex origins and evolution. Applying different molecular methods, we demonstrate the multiple origins of weedy rice with the major pathway from its cultivar progenitors. The origin and diversification of weedy rice are also closely associated with differentiation of indica-japonica rice varieties. In addition, novel mutations are identified, which may promote continued evolution and genetic diversity of weedy rice. Knowledge generated from this study provides deep insights into the origin and evolution of conspecific weeds, in addition to the design of effective measures to control these weeds. Abstract Agricultural weeds pose great challenges to sustainable crop production, owing to their complex origins and abundant genetic diversity. Weedy rice (WD) infests rice fields worldwide causing tremendous losses of rice yield/quality. To explore WD origins and evolution, we analyzed DNA sequence polymorphisms of the seed shattering genes (sh4 and qsh1) in weedy, wild, and cultivated rice from a worldwide distribution. We also used microsatellite and insertion/deletion molecular fingerprinting to determine their genetic relationship and structure. Results indicate multiple origins of WD with most samples having evolved from their cultivated progenitors and a few samples from wild rice. WD that evolved from de-domestication showed distinct genetic structures associated with indica and japonica rice differentiation. In addition, the weed-unique haplotypes that were only identified in the WD samples suggest their novel mutations. Findings in this study demonstrate the key role of de-domestication in WD origins, in which indica and japonica cultivars stimulated further evolution and divergence of WD in various agroecosystems. Furthermore, novel mutations promote continued evolution and genetic diversity of WD adapting to different environments. Knowledge generated from this study provides deep insights into the origin and evolution of conspecific weeds, in addition to the design of effective measures to control these weeds.
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27
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Gompert Z, Springer A, Brady M, Chaturvedi S, Lucas LK. Genomic time-series data show that gene flow maintains high genetic diversity despite substantial genetic drift in a butterfly species. Mol Ecol 2021; 30:4991-5008. [PMID: 34379852 DOI: 10.1111/mec.16111] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 07/09/2021] [Accepted: 07/19/2021] [Indexed: 11/29/2022]
Abstract
Effective population size affects the efficacy of selection, rate of evolution by drift, and neutral diversity levels. When species are subdivided into multiple populations connected by gene flow, evolutionary processes can depend on global or local effective population sizes. Theory predicts that high levels of diversity might be maintained by gene flow, even very low levels of gene flow, consistent with species long-term effective population size, but tests of this idea are mostly lacking. Here, we show that Lycaeides buttery populations maintain low contemporary (variance) effective population sizes (e.g., ~200 individuals) and thus evolve rapidly by genetic drift. In contrast, populations harbored high levels of genetic diversity consistent with an effective population size several orders of magnitude larger. We hypothesized that the differences in the magnitude and variability of contemporary versus long-term effective population sizes were caused by gene flow of sufficient magnitude to maintain diversity but only subtly affect evolution on generational time scales. Consistent with this hypothesis, we detected low but non-trivial gene flow among populations. Furthermore, using short-term population-genomic time-series data, we documented patterns consistent with predictions from this hypothesis, including a weak but detectable excess of evolutionary change in the direction of the mean (migrant gene pool) allele frequencies across populations, and consistency in the direction of allele frequency change over time. The documented decoupling of diversity levels and short-term change by drift in Lycaeides has implications for our understanding of contemporary evolution and the maintenance of genetic variation in the wild.
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Affiliation(s)
- Zachariah Gompert
- Department of Biology, Utah State University, Logan, UT, 84322, USA.,Ecology Center, Utah State University, Logan, UT, 84322, USA
| | - Amy Springer
- Department of Biology, Utah State University, Logan, UT, 84322, USA
| | - Megan Brady
- Department of Biology, Utah State University, Logan, UT, 84322, USA
| | - Samridhi Chaturvedi
- Department of Biology, Utah State University, Logan, UT, 84322, USA.,Department of Organismic & Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Lauren K Lucas
- Department of Biology, Utah State University, Logan, UT, 84322, USA
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28
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Diaz-Martin Z, Karubian J. Forest cover at landscape scales increases male and female gametic diversity of palm seedlings. Mol Ecol 2021; 30:4353-4367. [PMID: 34216497 DOI: 10.1111/mec.16060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 05/19/2021] [Accepted: 06/11/2021] [Indexed: 11/28/2022]
Abstract
Genetic diversity shapes the evolutionary potential of plant populations. For outcrossing plants, genetic diversity is influenced by effective population size and by dispersal, first of paternal gametes through pollen, and then of paternal and maternal gametes through seeds. Forest loss often reduces genetic diversity, but the degree to which it differentially impacts the paternal and maternal contributions to genetic diversity and the spatial scale at which these impacts are most pronounced are poorly understood. To address these questions, we genotyped 504 seedlings of the animal-dispersed palm Oenocarpus bataua collected from 29 widely distributed sites across Ecuador and decomposed the contribution of paternal and maternal gametes to overall genetic diversity. The amount of forest cover at a landscape scale (>10 km radius) had an equally significant positive association with both male and female gametic diversity. In addition, there was a significant positive association between forest cover and effective population size. Stronger fine-scale spatial genetic structure for female versus male gametes was observed at sites with low forest cover, but this did not scale up to differences in male versus female gametic diversity. These findings show that reductions in forest cover at spatial scales much larger than those typically evaluated in ecological studies lead to significant, and equivalent, decreases of diversity in both male and female gametes, and that this association between landscape level forest loss and genetic diversity may be driven directly by reductions in effective population size of O. bataua, rather than by indirect disruptions to local dispersal processes.
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Affiliation(s)
- Zoe Diaz-Martin
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, Louisiana, USA.,Foundation for the Conservation of the Tropical Andes (FCAT), Quito, Ecuador
| | - Jordan Karubian
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, Louisiana, USA.,Foundation for the Conservation of the Tropical Andes (FCAT), Quito, Ecuador
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29
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Wenzell KE, McDonnell AJ, Wickett NJ, Fant JB, Skogen KA. Incomplete reproductive isolation and low genetic differentiation despite floral divergence across varying geographic scales in Castilleja. AMERICAN JOURNAL OF BOTANY 2021; 108:1270-1288. [PMID: 34289081 DOI: 10.1002/ajb2.1700] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/18/2021] [Indexed: 06/13/2023]
Abstract
PREMISE Divergence depends on the strength of selection and frequency of gene flow between taxa, while reproductive isolation relies on mating barriers and geographic distance. Less is known about how these processes interact at early stages of speciation. Here, we compared population-level differentiation in floral phenotype and genetic sequence variation among recently diverged Castilleja to explore patterns of diversification under different scenarios of reproductive isolation. METHODS Using target enrichment enabled by the Angiosperms353 probe set, we assessed genetic distance among 50 populations of four Castilleja species. We investigated whether patterns of genetic divergence are explained by floral trait variation or geographic distance in two focal groups: the widespread C. sessiliflora and the more restricted C. purpurea species complex. RESULTS We document that C. sessiliflora and the C. purpurea complex are characterized by high diversity in floral color across varying geographic scales. Despite phenotypic divergence, groups were not well supported in phylogenetic analyses, and little genetic differentiation was found across targeted Angiosperms353 loci. Nonetheless, a principal coordinate analysis of single nucleotide polymorphisms revealed differentiation within C. sessiliflora across floral morphs and geography and less differentiation among species of the C. purpurea complex. CONCLUSIONS Patterns of genetic distance in C. sessiliflora suggest species cohesion maintained over long distances despite variation in floral traits. In the C. purpurea complex, divergence in floral color across narrow geographic clines may be driven by recent selection on floral color. These contrasting patterns of floral and genetic differentiation reveal that divergence can arise via multiple eco-evolutionary paths.
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Affiliation(s)
- Katherine E Wenzell
- Program in Plant Biology and Conservation, Northwestern University, O.T. Hogan Hall, Room 6-140B, 2205 Tech Drive, Evanston, IL, 60208, USA
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, Glencoe, IL, 60022, USA
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - Angela J McDonnell
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, Glencoe, IL, 60022, USA
| | - Norman J Wickett
- Program in Plant Biology and Conservation, Northwestern University, O.T. Hogan Hall, Room 6-140B, 2205 Tech Drive, Evanston, IL, 60208, USA
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, Glencoe, IL, 60022, USA
| | - Jeremie B Fant
- Program in Plant Biology and Conservation, Northwestern University, O.T. Hogan Hall, Room 6-140B, 2205 Tech Drive, Evanston, IL, 60208, USA
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, Glencoe, IL, 60022, USA
| | - Krissa A Skogen
- Program in Plant Biology and Conservation, Northwestern University, O.T. Hogan Hall, Room 6-140B, 2205 Tech Drive, Evanston, IL, 60208, USA
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, Glencoe, IL, 60022, USA
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30
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Goulet-Scott BE, Garner AG, Hopkins R. Genomic analyses overturn two long-standing homoploid hybrid speciation hypotheses. Evolution 2021; 75:1699-1710. [PMID: 34101168 DOI: 10.1111/evo.14279] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/27/2021] [Accepted: 05/11/2021] [Indexed: 01/21/2023]
Abstract
The importance of hybridization in generating biological diversity has been historically controversial. Previously, inference about hybridization was limited by dependence on morphological data; with the advent of the next-generation sequencing tools for nonmodel organisms, the evolutionary significance of hybridization is more evident. Here, we test classic hypotheses of hybrid origins of two species in the Phlox pilosa complex. Morphological intermediacy motivated the hypotheses that Phlox amoena lighthipei and Phlox pilosa deamii were independent homoploid hybrid lineages derived from P. amoena amoena and P. pilosa pilosa. We use double-digest restriction site-associated DNA sequencing of individuals from throughout the range of these taxa to conduct the most thorough analysis of evolutionary history in this system to date. Surprisingly, we find no support for the hybrid origin of P. pilosa deamii or P. amoena lighthipei. Our data do identify a history of admixture in individuals collected at a contemporary hybrid zone between the putative parent lineages. We show that three very different evolutionary histories, only one of which involves hybrid origin, have produced intermediate or recombinant morphological traits between P. amoena amoena and P. pilosa pilosa. Although morphological data are still an efficient means of generating hypotheses about past gene flow, genomic data are now the standard of evidence for elucidating evolutionary history.
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Affiliation(s)
- Benjamin E Goulet-Scott
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, 02138
| | - Austin G Garner
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, 02138
| | - Robin Hopkins
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, 02138.,Arnold Arboretum of Harvard University, Boston, Massachusetts, 02131
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31
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Serrato-Capuchina A, Schwochert TD, Zhang S, Roy B, Peede D, Koppelman C, Matute DR. Pure species discriminate against hybrids in the Drosophila melanogaster species subgroup. Evolution 2021; 75:1753-1774. [PMID: 34043234 DOI: 10.1111/evo.14259] [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] [Received: 03/01/2020] [Revised: 01/20/2021] [Accepted: 02/09/2021] [Indexed: 12/11/2022]
Abstract
Introgression, the exchange of alleles between species, is a common event in nature. This transfer of alleles between species must happen through fertile hybrids. Characterizing the traits that cause defects in hybrids illuminates how and when gene flow is expected to occur. Inviability and sterility are extreme examples of fitness reductions but are not the only type of defects in hybrids. Some traits specific to hybrids are more subtle but are important to determine their fitness. In this report, we study whether F1 hybrids between two species pairs of Drosophila are as attractive as the parental species. We find that in both species pairs, the sexual attractiveness of the F1 hybrids is reduced and that pure species discriminate strongly against them. We also find that the cuticular hydrocarbon (CHC) profile of the female hybrids is intermediate between the parental species. Perfuming experiments show that modifying the CHC profile of the female hybrids to resemble pure species improves their chances of mating. Our results show that behavioral discrimination against hybrids might be an important component of the persistence of species that can hybridize.
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Affiliation(s)
- Antonio Serrato-Capuchina
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599
| | - Timothy D Schwochert
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599
| | - Stephania Zhang
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599
| | - Baylee Roy
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599
| | - David Peede
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599
| | - Caleigh Koppelman
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599
| | - Daniel R Matute
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599
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32
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Santa‐Martinez E, Cardoso Castro C, Flick A, Sullivan M, Riday H, Clayton MK, Brunet J. Bee species visiting Medicago sativa differ in pollen deposition curves with consequences for gene flow. AMERICAN JOURNAL OF BOTANY 2021; 108:1016-1028. [PMID: 34114219 PMCID: PMC8362063 DOI: 10.1002/ajb2.1683] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 01/25/2021] [Indexed: 06/12/2023]
Abstract
PREMISE Pollinator foraging behavior can influence pollen dispersal and gene flow. In many plant species a pollinator trips a flower by applying pressure to release its sexual organs. We propose that differences in tripping rate among grooming pollinators could generate distinct pollen deposition curves, the pattern of pollen deposition over successive flowers visited. This study compares the pollen deposition curves of two grooming pollinators, a social bumble bee and a solitary leafcutting bee, with distinct tripping rates on Medicago sativa flowers. We predict a steeper deposition curve for pollen moved by leafcutting bees, the pollinator with the higher tripping rate. METHODS Medicago sativa plants carrying a gene (GUS) whose product is easily detected by staining, were used as pollen donors. After visiting the GUS plants, a bee was released on a linear array of conventional M. sativa plants. The number of GUS pollen grains deposited over successive flowers visited or over cumulative distances was examined. Distinct mixed effect Poisson regression models, illustrating different rates of decay in pollen deposition, were fitted to the pollen data for each bee species. RESULTS Pollen decay was steeper for leafcutting bees relative to bumble bees for both models of flowers visited and cumulative distance, as predicted by their higher tripping rate. CONCLUSIONS This is the first report of a difference in pollen deposition curves between two bee species, both grooming pollinators. Such differences could lead to distinct impacts of bee species on gene flow, genetic differentiation, introgression, and ultimately speciation.
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Affiliation(s)
- Emmanuel Santa‐Martinez
- Department of EntomologyUniversity of WisconsinMadisonWisconsin53706USA
- Biology DepartmentSalt Lake Community CollegeSalt Lake CityUtah84123USA
| | - Cibele Cardoso Castro
- Unidade Acadêmica de GaranhunsUniversidade Federal Rural de PernambucoGaranhuns, Pernambuco5292‐272Brazil
| | - Andrew Flick
- Agricultural Research Service Research Participation Program – Oak Ridge Institute for Science and Education (ORISE)MadisonWisconsin53706USA
| | - Michael Sullivan
- United States Department of AgricultureAgricultural Research ServiceMadisonWisconsin53706USA
| | - Heathcliffe Riday
- United States Department of AgricultureAgricultural Research ServiceMadisonWisconsin53706USA
| | - Murray K. Clayton
- Department of StatisticsUniversity of WisconsinMadisonWisconsin53706USA
| | - Johanne Brunet
- United States Department of AgricultureAgricultural Research ServiceMadisonWisconsin53706USA
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33
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Feres JM, G Nazareno A, Borges LM, Corbo Guidugli M, Bonifacio-Anacleto F, Alzate-Marin AL. Depicting the mating system and patterns of contemporary pollen flow in trees of the genus Anadenanthera (Fabaceae). PeerJ 2021; 9:e10579. [PMID: 33868794 PMCID: PMC8035892 DOI: 10.7717/peerj.10579] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 11/24/2020] [Indexed: 12/11/2022] Open
Abstract
Anadenanthera (Fabaceae) is endemic to the Neotropics and consists of two tree species: A. colubrina (Vell.) Brenan and A. peregrina (L.) Speg. This study examined the mating system and contemporary gene flow of A. colubrina (Acol) and A. peregrina (Aper) in a highly fragmented area of the Atlantic Forest to provide valuable information that informs conservation strategies. Reproductive adults from forest remnants [n A. colubrina = 30 (2.7 ha), n A. peregrina = 55 (4.0 ha)] and progeny-arrays (n A. colubrina = 322, n A. peregrina = 300) were genotyped for seven nuclear microsatellite markers. Mating system analyses revealed that A. colubrina is a mixed mating species (tm = 0.619) while A. peregrina is a predominantly outcrossing species (tm = 0.905). For both Anadenanthera species, high indices of biparental inbreeding were observed (Acol = 0.159, Aper = 0.216), resulting in low effective pollination neighborhood sizes. Categorical paternity analysis revealed different scales of pollen dispersal distance: the majority of crossings occurring locally (i.e., between nearby trees within the same population), with moderate pollen dispersal coming from outside the forest fragments boundaries (Acol mp = 30%, Aper mp = 35%). Nevertheless, pollen immigration from trees outside the populations for both species suggests that the populations are not reproductively isolated. This study highlights the importance of evaluating both mating system and contemporary gene flow for a better understanding of the biology of Anadenanthera species. This information should be considered to ensure the effective conservation and management practices of these plant species.
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Affiliation(s)
- Juliana Massimino Feres
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Alison G Nazareno
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Leonardo M Borges
- Departamento de Botânica, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Marcela Corbo Guidugli
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Fernando Bonifacio-Anacleto
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Ana Lilia Alzate-Marin
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Ribeirão Preto, SP, Brazil
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Kesoju SR, Kramer M, Brunet J, Greene SL, Jordan A, Martin RC. Gene flow in commercial alfalfa (Medicago sativa subsp. sativa L.) seed production fields: Distance is the primary but not the sole influence on adventitious presence. PLoS One 2021; 16:e0248746. [PMID: 33765070 PMCID: PMC7993763 DOI: 10.1371/journal.pone.0248746] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 03/04/2021] [Indexed: 11/18/2022] Open
Abstract
In insect-pollinated crops, gene flow is affected by numerous factors including crop characteristics, mating system, life history, pollinators, and planting management practices. Previous studies have concentrated on the impact of distance between genetically engineered (GE) and conventional fields on adventitious presence (AP) which represents the unwanted presence of a GE gene. Variables other than distance, however, may affect AP. In addition, some AP is often present in the parent seed lots used to establish conventional fields. To identify variables that influence the proportion of AP in conventional alfalfa fields, we performed variable selection regression analyses. Analyses based on a sample-level and a field-level analysis gave similar, though not identical results. For the sample-level model, distance from the GE field explained 66% of the variance in AP, confirming its importance in affecting AP. The area of GE fields within the pollinator foraging range explained an additional 30% of the variation in AP in the model. The density of alfalfa leafcutting bee domiciles influenced AP in both models. To minimize AP in conventional alfalfa seed fields, management practices should focus on optimizing isolation distances while also considering the size of the GE pollen pool within the pollinator foraging range, and the foraging behavior of pollinators.
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Affiliation(s)
- Sandya R. Kesoju
- Department of Agriculture, Columbia Basin College, Pasco, Washington, United States of America
| | - Matthew Kramer
- Statistics Group, Beltsville Agricultural Research Center, USDA Agricultural Research Service, Beltsville, Maryland, United States of America
| | - Johanne Brunet
- Vegetable Crops Research Unit, USDA, Agricultural Research Service, Madison, Wisconsin, United States of America
| | - Stephanie L. Greene
- Agricultural Genetic Resources Preservation Research Unit, USDA, Agricultural Research Service, Fort Collins, Colorado, United States of America
| | - Amelia Jordan
- Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, Washington, United States of America
| | - Ruth C. Martin
- Forage Seed and Cereal Research, USDA, Agricultural Research Service, Corvallis, Oregon, United States of America
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Spengler RN, Petraglia M, Roberts P, Ashastina K, Kistler L, Mueller NG, Boivin N. Exaptation Traits for Megafaunal Mutualisms as a Factor in Plant Domestication. FRONTIERS IN PLANT SCIENCE 2021; 12:649394. [PMID: 33841476 PMCID: PMC8024633 DOI: 10.3389/fpls.2021.649394] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 02/25/2021] [Indexed: 05/26/2023]
Abstract
Megafaunal extinctions are recurring events that cause evolutionary ripples, as cascades of secondary extinctions and shifting selective pressures reshape ecosystems. Megafaunal browsers and grazers are major ecosystem engineers, they: keep woody vegetation suppressed; are nitrogen cyclers; and serve as seed dispersers. Most angiosperms possess sets of physiological traits that allow for the fixation of mutualisms with megafauna; some of these traits appear to serve as exaptation (preadaptation) features for farming. As an easily recognized example, fleshy fruits are, an exaptation to agriculture, as they evolved to recruit a non-human disperser. We hypothesize that the traits of rapid annual growth, self-compatibility, heavy investment in reproduction, high plasticity (wide reaction norms), and rapid evolvability were part of an adaptive syndrome for megafaunal seed dispersal. We review the evolutionary importance that megafauna had for crop and weed progenitors and discuss possible ramifications of their extinction on: (1) seed dispersal; (2) population dynamics; and (3) habitat loss. Humans replaced some of the ecological services that had been lost as a result of late Quaternary extinctions and drove rapid evolutionary change resulting in domestication.
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Affiliation(s)
- Robert N. Spengler
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Michael Petraglia
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- Department of Anthropology, Smithsonian Institution, National Museum of Natural History, Washington, DC, United States
- School of Social Science, The University of Queensland, Brisbane, QLD, Australia
| | - Patrick Roberts
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Kseniia Ashastina
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Logan Kistler
- Department of Anthropology, Smithsonian Institution, National Museum of Natural History, Washington, DC, United States
| | - Natalie G. Mueller
- Department of Archaeology, Washington University in St. Louis, St. Louis, MO, United States
| | - Nicole Boivin
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- Department of Anthropology, Smithsonian Institution, National Museum of Natural History, Washington, DC, United States
- School of Social Science, The University of Queensland, Brisbane, QLD, Australia
- Department of Anthropology and Archaeology, University of Calgary, Calgary, AB, Canada
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Rivest S, Lajoie G, Watts DA, Vellend M. Earlier spring reduces potential for gene flow via reduced flowering synchrony across an elevational gradient. AMERICAN JOURNAL OF BOTANY 2021; 108:538-545. [PMID: 33733494 DOI: 10.1002/ajb2.1627] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 11/02/2020] [Indexed: 06/12/2023]
Abstract
PREMISE One of the best-documented ecological responses to climate warming involves temporal shifts of phenological events. However, we lack an understanding of how phenological responses to climate change vary among populations of the same species. Such variability has the potential to affect flowering synchrony among populations and hence the potential for gene flow. METHODS To test whether an earlier start of the growing season affects the potential for gene flow among populations, we quantified the distributions of flowering times of two spring-flowering plants (Trillium erectum and Erythronium americanum) over 6 years along an elevational gradient. We developed a novel model-based metric of potential gene flow between pairs of populations to quantify the potential for pollen-mediated gene flow based on flowering phenology. RESULTS Earlier onset of spring led to greater separation of peak flowering dates across the elevational gradient for both species investigated, but was only associated with a reduction in potential gene flow in T. erectum, not E. americanum. CONCLUSIONS Our study suggests that climate change could decrease gene flow via phenological separation among populations along climatic gradients. We also provide a novel method for quantifying potential pollen-mediated gene flow using data on flowering phenology, based on a quantitative, more biologically interpretable model than other available metrics.
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Affiliation(s)
- Sébastien Rivest
- Department of Biology, University of Ottawa, K1N 6N5, Ottawa, Ontario, Canada
| | - Geneviève Lajoie
- Département des Sciences Biologiques, Université du Québec à Montréal, H2X 1Y4, Montréal, Québec, Canada
| | - David A Watts
- Département de Biologie, Université de Sherbrooke, J1K 2R1, Sherbrooke, Québec, Canada
| | - Mark Vellend
- Département de Biologie, Université de Sherbrooke, J1K 2R1, Sherbrooke, Québec, Canada
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Chybicki IJ, Oleksa A, Dering M. Identification of determinants of pollen donor fecundity using the hierarchical neighborhood model. Mol Ecol Resour 2020; 21:781-800. [PMID: 33290637 DOI: 10.1111/1755-0998.13307] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 11/24/2020] [Accepted: 12/01/2020] [Indexed: 11/30/2022]
Abstract
Individual differences in male reproductive success drive genetic drift and natural selection, altering genetic variation and phenotypic trait distributions in future generations. Therefore, identifying the determinants of reproductive success is important for understanding the ecology and evolution of plants. Here, based on the spatially explicit mating model (the neighborhood model), we develop a hierarchical probability model that links co-dominant genotypes of offspring and candidate parents with phenotypic determinants of male reproductive success. The model accounts for pollen dispersal, genotyping errors as well as individual variation in selfing, pollen immigration, and differentiation of immigrant pollen pools. Unlike the classic neighborhood model approach, our approach is specially designed to account for excessive variation (overdispersion) in male fecundity. We implemented a Bayesian estimation method (the Windows computer program available at: https://www.ukw.edu.pl/pracownicy/plik/igor_chybicki/1806/) that, among others, allows for selecting phenotypic variables important for male fecundity and assessing the fraction of variance in fecundity (R2 ) explained by selected variables. Simulations showed that our method outperforms both the classic neighborhood model and the two-step approach, where fecundities and the effects of phenotypic variables are estimated separately. The analysis of two data examples showed that in wind-pollinated trees, male fecundity depends on both the amount of produced pollen and the ability to pollen spread. However, despite that the tree size was positively correlated with male fecundity, it explained only a fraction of the total variance in fecundity, indicating the presence of additional factors. Finally, case studies highlighted the importance of accounting for pollen dispersal in the estimation of fecundity determinants.
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Affiliation(s)
- Igor J Chybicki
- Department of Genetics, Kazimierz Wielki University, Bydgoszcz, Poland
| | - Andrzej Oleksa
- Department of Genetics, Kazimierz Wielki University, Bydgoszcz, Poland
| | - Monika Dering
- Institute of Dendrology, Polish Academy of Sciences, Kórnik, Poland.,Department of Silviculture, Poznań University of Life Sciences, Poznań, Poland
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Vasiliev D, Greenwood S. Pollinator biodiversity and crop pollination in temperate ecosystems, implications for national pollinator conservation strategies: Mini review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 744:140880. [PMID: 32693283 DOI: 10.1016/j.scitotenv.2020.140880] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/03/2020] [Accepted: 07/09/2020] [Indexed: 05/11/2023]
Abstract
Pollinator biodiversity and biomass are in decline globally. This fact accompanied by shortage and collapses of domesticated pollinator colonies, puts human food security under unprecedented threat. Many countries worldwide have adopted or intend to introduce national pollinator conservation strategies. Decisions of policy makers and other involved stakeholders are often driven by pragmatic considerations, rather than biodiversity conservation per se. At the same time, different opinions exist in the literature on the role of pollinator biodiversity versus abundance of few dominant species in crop pollination. This article critically evaluates the literature in order to understand the importance of biodiversity over abundance and to examine the effectiveness of conservation strategies. Results of this review suggest that pollinator biodiversity is critical for crop pollination quality, magnitude and resilience. Most current national pollinator conservation strategies lack comprehensive measures for maintaining pollinator biodiversity at a landscape scale.
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Affiliation(s)
- Denis Vasiliev
- Biodiversity, Wildlife and Ecosystem Health MSc, Biomedical Sciences, The University of Edinburgh, 1 George Square, Edinburgh EH8 9JZ, United Kingdom of Great Britain and Northern Ireland.
| | - Sarah Greenwood
- Biodiversity, Wildlife and Ecosystem Health MSc, Biomedical Sciences, The University of Edinburgh, 1 George Square, Edinburgh EH8 9JZ, United Kingdom of Great Britain and Northern Ireland
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Gamba D, Muchhala N. Global patterns of population genetic differentiation in seed plants. Mol Ecol 2020; 29:3413-3428. [PMID: 32743850 DOI: 10.1111/mec.15575] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 06/06/2020] [Accepted: 07/23/2020] [Indexed: 01/07/2023]
Abstract
Evaluating the factors that drive patterns of population differentiation in plants is critical for understanding several biological processes such as local adaptation and incipient speciation. Previous studies have given conflicting results regarding the significance of pollination mode, seed dispersal mode, mating system, growth form and latitudinal region in shaping patterns of genetic structure, as estimated by FST values, and no study to date has tested their relative importance together across a broad scale. Here, we assembled a 337-species data set for seed plants from publications with data on FST from nuclear markers and species traits, including variables pertaining to the sampling scheme of each study. We used species traits, while accounting for sampling variables, to perform phylogenetic multiple regressions. Results demonstrated that FST values were higher for tropical, mixed-mating, non-woody species pollinated by small insects, indicating greater population differentiation, and lower for temperate, outcrossing trees pollinated by wind. Among the factors we tested, latitudinal region explained the largest portion of variance, followed by pollination mode, mating system and growth form, while seed dispersal mode did not significantly relate to FST . Our analyses provide the most robust and comprehensive evaluation to date of the main ecological factors predicted to drive population differentiation in seed plants, with important implications for understanding the basis of their genetic divergence. Our study supports previous findings showing greater population differentiation in tropical regions and is the first that we are aware of to robustly demonstrate greater population differentiation in species pollinated by small insects.
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Affiliation(s)
- Diana Gamba
- Biology Department, University of Missouri, Saint Louis, MO, USA
| | - Nathan Muchhala
- Biology Department, University of Missouri, Saint Louis, MO, USA
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Nieto Feliner G, Casacuberta J, Wendel JF. Genomics of Evolutionary Novelty in Hybrids and Polyploids. Front Genet 2020; 11:792. [PMID: 32849797 PMCID: PMC7399645 DOI: 10.3389/fgene.2020.00792] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/03/2020] [Indexed: 12/15/2022] Open
Abstract
It has long been recognized that hybridization and polyploidy are prominent processes in plant evolution. Although classically recognized as significant in speciation and adaptation, recognition of the importance of interspecific gene flow has dramatically increased during the genomics era, concomitant with an unending flood of empirical examples, with or without genome doubling. Interspecific gene flow is thus increasingly thought to lead to evolutionary innovation and diversification, via adaptive introgression, homoploid hybrid speciation and allopolyploid speciation. Less well understood, however, are the suite of genetic and genomic mechanisms set in motion by the merger of differentiated genomes, and the temporal scale over which recombinational complexity mediated by gene flow might be expressed and exposed to natural selection. We focus on these issues here, considering the types of molecular genetic and genomic processes that might be set in motion by the saltational event of genome merger between two diverged species, either with or without genome doubling, and how these various processes can contribute to novel phenotypes. Genetic mechanisms include the infusion of new alleles and the genesis of novel structural variation including translocations and inversions, homoeologous exchanges, transposable element mobilization and novel insertional effects, presence-absence variation and copy number variation. Polyploidy generates massive transcriptomic and regulatory alteration, presumably set in motion by disrupted stoichiometries of regulatory factors, small RNAs and other genome interactions that cascade from single-gene expression change up through entire networks of transformed regulatory modules. We highlight both these novel combinatorial possibilities and the range of temporal scales over which such complexity might be generated, and thus exposed to natural selection and drift.
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Affiliation(s)
- Gonzalo Nieto Feliner
- Department of Biodiversity and Conservation, Real Jardín Botánico, CSIC, Madrid, Spain
| | - Josep Casacuberta
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Barcelona, Spain
| | - Jonathan F. Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, United States
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Riaz S, Menéndez CM, Tenscher A, Pap D, Walker MA. Genetic mapping and survey of powdery mildew resistance in the wild Central Asian ancestor of cultivated grapevines in Central Asia. HORTICULTURE RESEARCH 2020; 7:104. [PMID: 32637132 PMCID: PMC7326912 DOI: 10.1038/s41438-020-0335-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 04/01/2020] [Accepted: 05/01/2020] [Indexed: 05/21/2023]
Abstract
Cultivated grapevines (Vitis vinifera) lack resistance to powdery mildew (PM) with few exceptions. Resistance to this pathogen within V. vinifera has been reported in earlier studies and identified as the Ren1 locus in two Central Asian table grape accessions. Other PM-resistant cultivated varieties and accessions of the wild ancestor V. vinifera subsp. sylvestris were soon identified raising questions regarding the origin of the resistance. In this study, F1 breeding populations were developed with a PM susceptible V. vinifera subsp. vinifera breeding line and a PM-resistant subsp. sylvestris accession. Genotyping was carried out with five Ren1 locus linked SSR markers. A PM resistance locus explaining up to 96% of the phenotypic variation was identified in the same genomic position, where the Ren1 locus was previously reported. New SSR marker alleles linked with the resistance locus were identified. We report results of PM resistance in multiple accessions of subsp. sylvestris collected as seed lots or cuttings from five countries in the Caucasus and Central Asia. A total of 20 females from 11 seed lots and 19 males from nine seed lots collected from Georgia, Armenia, and Azerbaijan were resistant to PM. Three male and one female plant collected as cuttings from Afghanistan and Iran were also resistant to PM. Allelic analysis of markers linked with the Ren1 locus in conjunction with disease evaluation data found a high diversity of allelic haplotypes, which are only possible via recombination events occurring over a long time period. Sequence analysis of two alleles of the SSR marker that cosegregates with the resistance found SNPs that were present in the wild progenitor and in cultivated forms. Variable levels of PM resistance among the tested accessions were also observed. These lines of evidence suggest that the powdery mildew fungus may have been present in Asia for a longer time than currently thought, giving the wild progenitor V. vinifera subsp. sylvestris time to coevolve with and develop resistance to this pathogen.
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Affiliation(s)
- Summaira Riaz
- Department of Viticulture and Enology, University of California, Davis, CA 95616 USA
| | - Cristina M. Menéndez
- Instituto de Ciencias de la Vid y del Vino (ICVV), Universidad de La Rioja-CSIC-Gobierno de La Rioja, Carretera de Burgos Km, 6, Finca La Grajera, Logroño, La Rioja 26007 Spain
| | - Alan Tenscher
- Department of Viticulture and Enology, University of California, Davis, CA 95616 USA
| | - Daniel Pap
- Department of Viticulture and Enology, University of California, Davis, CA 95616 USA
| | - M. Andrew Walker
- Department of Viticulture and Enology, University of California, Davis, CA 95616 USA
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Binelli G, Montaigne W, Sabatier D, Scotti‐Saintagne C, Scotti I. Discrepancies between genetic and ecological divergence patterns suggest a complex biogeographic history in a Neotropical genus. Ecol Evol 2020; 10:4726-4738. [PMID: 32551056 PMCID: PMC7297752 DOI: 10.1002/ece3.6227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 03/04/2020] [Indexed: 11/19/2022] Open
Abstract
Phylogenetic patterns and the underlying speciation processes can be deduced from morphological, functional, and ecological patterns of species similarity and divergence. In some cases, though, species retain multiple similarities and remain almost indistinguishable; in other cases, evolutionary convergence can make such patterns misleading; very often in such cases, the "true" picture only emerges from carefully built molecular phylogenies, which may come with major surprises. In addition, closely related species may experience gene flow after divergence, thus potentially blurring species delimitation. By means of advanced inferential methods, we studied molecular divergence between species of the Virola genus (Myristicaceae): widespread Virola michelii and recently described, endemic V. kwatae, using widespread V. surinamensis as a more distantly related outgroup with different ecology and morphology-although with overlapping range. Contrary to expectations, we found that the latter, and not V. michelii, was sister to V. kwatae. Therefore, V. kwatae probably diverged from V. surinamensis through a recent morphological and ecological shift, which brought it close to distantly related V. michelii. Through the modeling of the divergence process, we inferred that gene flow between V. surinamensis and V. kwatae stopped soon after their divergence and resumed later, in a classical secondary contact event which did not erase their ecological and morphological differences. While we cannot exclude that initial divergence occurred in allopatry, current species distribution and the absence of geographical barriers make complete isolation during speciation unlikely. We tentatively conclude that (a) it is possible that divergence occurred in allopatry/parapatry and (b) secondary contact did not suppress divergence.
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Affiliation(s)
| | - William Montaigne
- UMR EcoFoGUniversité des Antilles et de la GuyaneKourouFrench Guiana
| | - Daniel Sabatier
- AMAPIRDCIRADCNRSINRAEUniversité de MontpellierMontpellierFrance
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Spengler RN. Anthropogenic Seed Dispersal: Rethinking the Origins of Plant Domestication. TRENDS IN PLANT SCIENCE 2020; 25:340-348. [PMID: 32191870 DOI: 10.1016/j.tplants.2020.01.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 01/03/2020] [Accepted: 01/21/2020] [Indexed: 05/26/2023]
Abstract
It is well documented that ancient sickle harvesting led to tough rachises, but the other seed dispersal properties in crop progenitors are rarely discussed. The first steps toward domestication are evolutionary responses for the recruitment of humans as dispersers. Seed dispersal-based mutualism evolved from heavy human herbivory or seed predation. Plants that evolved traits to support human-mediated seed dispersal express greater fitness in increasingly anthropogenic ecosystems. The loss of dormancy, reduction in seed coat thickness, increased seed size, pericarp density, and sugar concentration all led to more-focused seed dispersal through seed saving and sowing. Some of the earliest plants to evolve domestication traits had weak seed dispersal processes in the wild, often due to the extinction of animal dispersers or short-distance mechanical dispersal.
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Affiliation(s)
- Robert N Spengler
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany.
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Souto‐Vilarós D, Houadria M, Michalek J, Sisol M, Isua B, Kuyaiva T, Weiblen GD, Novotny V, Segar ST. Contrasting patterns of fig wasp communities along Mt. Wilhelm, Papua New Guinea. Biotropica 2020. [DOI: 10.1111/btp.12763] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Daniel Souto‐Vilarós
- Biology Centre of the Czech Academy of Sciences Institute of Entomology South Bohemia Czech Republic
- Faculty of Science University of South Bohemia South Bohemia Czech Republic
- Department of Ecology Faculty of Science Charles University Prague Czech Republic
| | - Mickal Houadria
- Biology Centre of the Czech Academy of Sciences Institute of Entomology South Bohemia Czech Republic
| | - Jan Michalek
- Biology Centre of the Czech Academy of Sciences Institute of Entomology South Bohemia Czech Republic
| | - Mentap Sisol
- New Guinea Binatang Research Centre Madang Papua New Guinea
| | - Brus Isua
- New Guinea Binatang Research Centre Madang Papua New Guinea
| | - Thomas Kuyaiva
- New Guinea Binatang Research Centre Madang Papua New Guinea
| | - George D. Weiblen
- Institute on the Environment University of Minnesota Saint Paul MN USA
| | - Vojtech Novotny
- Biology Centre of the Czech Academy of Sciences Institute of Entomology South Bohemia Czech Republic
- Faculty of Science University of South Bohemia South Bohemia Czech Republic
| | - Simon T. Segar
- Biology Centre of the Czech Academy of Sciences Institute of Entomology South Bohemia Czech Republic
- Department of Crop and Environment Sciences Harper Adams University New Port UK
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Borges D, Mariano-Neto E, Caribé D, Corrêa R, Gaiotto F. Changes in fine-scale spatial genetic structure related to protection status in Atlantic Rain Forest fragment. J Nat Conserv 2020. [DOI: 10.1016/j.jnc.2019.125784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Zhang Z, Gale SW, Li JH, Fischer GA, Ren MX, Song XQ. Pollen-mediated gene flow ensures connectivity among spatially discrete sub-populations of Phalaenopsis pulcherrima, a tropical food-deceptive orchid. BMC PLANT BIOLOGY 2019; 19:597. [PMID: 31888488 PMCID: PMC6937714 DOI: 10.1186/s12870-019-2179-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 11/29/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND Gene flow in plants via pollen and seeds is asymmetrical at different geographic scales. Orchid seeds are adapted to long-distance wind dispersal but pollinium transfer is often influenced by pollinator behavior. We combined field studies with an analysis of genetic diversity among 155 physically mapped adults and 1105 F1 seedlings to evaluate the relative contribution of pollen and seed dispersal to overall gene flow among three sub-populations of the food-deceptive orchid Phalaenopsis pulcherrima on Hainan Island, China. RESULTS Phalaenopsis pulcherrima is self-sterile and predominantly outcrossing, resulting in high population-level genetic diversity, but plants are clumped and exhibit fine-scale genetic structuring. Even so, we detected low differentiation among sub-populations, with polynomial regression analysis suggesting gene flow via seed to be more restricted than that via pollen. Paternity analysis confirmed capsules of P. pulcherrima to each be sired by a single pollen donor, probably in part facilitated by post-pollination stigma obfuscation, with a mean pollen flow distance of 272.7 m. Despite limited sampling, we detected no loss of genetic diversity from one generation to the next. CONCLUSIONS Outcrossing mediated by deceptive pollination and self-sterility promote high genetic diversity in P. pulcherrima. Long-range pollinia transfer ensures connectivity among sub-populations, offsetting the risk of genetic erosion at local scales.
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Affiliation(s)
- Zhe Zhang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Hainan University), Ministry of Education, College of Forestry, Hainan University, Haikou, People's Republic of China
- Key Laboratory of Germplasm Resources of Tropical Special Ornamental Plants of Hainan Province, College of Forestry, Hainan University, Haikou, People's Republic of China
| | - Stephan W Gale
- Kadoorie Farm & Botanic Garden, Lam Kam Road, Tai Po, Hong Kong, People's Republic of China.
| | - Ji-Hong Li
- Kadoorie Farm & Botanic Garden, Lam Kam Road, Tai Po, Hong Kong, People's Republic of China
| | - Gunter A Fischer
- Kadoorie Farm & Botanic Garden, Lam Kam Road, Tai Po, Hong Kong, People's Republic of China
| | - Ming-Xun Ren
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Hainan University), Ministry of Education, College of Forestry, Hainan University, Haikou, People's Republic of China
- Center for Terrestrial Biodiversity of the South China Sea, Hainan University, Haikou, People's Republic of China
| | - Xi-Qiang Song
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Hainan University), Ministry of Education, College of Forestry, Hainan University, Haikou, People's Republic of China.
- Key Laboratory of Germplasm Resources of Tropical Special Ornamental Plants of Hainan Province, College of Forestry, Hainan University, Haikou, People's Republic of China.
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Nazareno AG, Dick CW, Lohmann LG. A Biogeographic Barrier Test Reveals a Strong Genetic Structure for a Canopy-Emergent Amazon Tree Species. Sci Rep 2019; 9:18602. [PMID: 31819128 PMCID: PMC6901565 DOI: 10.1038/s41598-019-55147-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 10/31/2019] [Indexed: 11/09/2022] Open
Abstract
Wallace's (1854) Riverine Barrier hypothesis is one of the earliest explanations for Amazon biotic diversification. Despite the importance of this hypothesis for explaining speciation in some animal groups, it has not been studied extensively for plant species. In this study we use a prominent Amazon tree, Buchenavia oxycarpa (Mart.) Eichler (Combretaceae), to evaluate Wallace's hypothesis along the Rio Negro, a major Amazon tributary that has driven allopatric speciation for several animal taxa. We sampled six individuals from sixteen localities along both river banks, and used a modified ddRADseq protocol to identify SNP markers. Our population genomic data revealed strong genetic structure for B. oxycarpa sampled across banks of the Rio Negro (ϕCT = 0.576, P < 0.001), supporting the hypothesis that the Rio Negro acted as a significant genetic barrier for B. oxycarpa. Our study shows that gene flow for this large and well-dispersed Amazon tree is impeded by riverine barriers, though this has not yet resulted in speciation. Future studies focused on species with different life histories, including species restricted to non-flooded forests, are needed to further advance our understanding of Amazon rivers as drivers of biotic diversification.
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Affiliation(s)
- Alison G Nazareno
- Departamento de Botânica, Universidade de São Paulo, São Paulo, SP, Brazil.
| | - Christopher W Dick
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Lúcia G Lohmann
- Departamento de Botânica, Universidade de São Paulo, São Paulo, SP, Brazil.
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Moreira-Hernández JI, Muchhala N. Importance of Pollinator-Mediated Interspecific Pollen Transfer for Angiosperm Evolution. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2019. [DOI: 10.1146/annurev-ecolsys-110218-024804] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Understanding how pollen moves between species is critical to understanding speciation, diversification, and evolution of flowering plants. For co-flowering species that share pollinators, competition through interspecific pollen transfer (IPT) can profoundly impact floral evolution, decreasing female fitness via heterospecific pollen deposition on stigmas and male fitness via pollen misplacement during visits to heterospecific flowers. The pollination literature demonstrates that such reproductive interference frequently selects for reproductive character displacement in floral traits linked to pollinator attraction, pollen placement, and mating systems and has also revealed that IPT between given pairs of species is typically asymmetric. More recent work is starting to elucidate its importance to the speciation process, clarifying the link between IPT and current and historical patterns of hybridization, the evolution of phenotypic novelty through adaptive introgression, and the rise of reproductive isolation. Our review aims to stimulate further research on IPT as a ubiquitous mechanism that plays a central role in angiosperm diversification.
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Affiliation(s)
- Juan Isaac Moreira-Hernández
- Department of Biology and Whitney R. Harris World Ecology Center, University of Missouri–St. Louis, St. Louis, Missouri 63121, USA;,
| | - Nathan Muchhala
- Department of Biology and Whitney R. Harris World Ecology Center, University of Missouri–St. Louis, St. Louis, Missouri 63121, USA;,
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49
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Ayre BM, Roberts DG, Phillips RD, Hopper SD, Krauss SL. Near-neighbour optimal outcrossing in the bird-pollinated Anigozanthos manglesii. ANNALS OF BOTANY 2019; 124:423-436. [PMID: 31115446 PMCID: PMC6798840 DOI: 10.1093/aob/mcz091] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 05/20/2019] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS In plants, the spatial and genetic distance between mates can influence reproductive success and offspring fitness. Negative fitness consequences associated with the extremes of inbreeding and outbreeding suggest that there will be an intermediate optimal outcrossing distance (OOD), the scale and drivers of which remain poorly understood. In the bird-pollinated Anigozanthos manglesii (Haemodoraceae) we tested (1) for the presence of within-population OOD, (2) over what scale it occurs, and (3) for OOD under biologically realistic scenarios of multi-donor deposition associated with pollination by nectar-feeding birds. METHODS We measured the impact of mate distance (spatial and genetic) on seed set, fruit size, seed mass, seed viability and germination success following hand pollination from (1) single donors across 0 m (self), <1 m, 1-3 m, 7-15 m and 50 m, and (2) a mix of eight donors. Microsatellite loci were used to quantify spatial genetic structure and test for the presence of an OOD by paternity assignment after multi-donor deposition. KEY RESULTS Inter-mate distance had a significant impact on single-donor reproductive success, with selfed and nearest-neighbour (<1 m) pollination resulting in only ~50 seeds per fruit, lower overall germination success and slower germination. Seed set was greatest for inter-mate distance of 1-3 m (148 seeds per fruit), thereafter plateauing at ~100 seeds per fruit. Lower seed set following nearest-neighbour mating was associated with significant spatial genetic autocorrelation at this scale. Paternal success following pollination with multiple sires showed a significantly negative association with increasing distance between mates. CONCLUSIONS Collectively, single- and multi-donor pollinations indicated evidence for a near-neighbour OOD within A. manglesii. A survey of the literature suggests that within-population OOD may be more characteristic of plants pollinated by birds than those pollinated by insects.
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Affiliation(s)
- Bronwyn M Ayre
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
- Kings Park Science, Department of Biodiversity, Conservation and Attractions, Perth, WA, Australia
| | - David G Roberts
- Kings Park Science, Department of Biodiversity, Conservation and Attractions, Perth, WA, Australia
- Centre for Excellence in Natural Resource Management, School of Agriculture and Environment, University of Western Australia, Albany, WA, Australia
| | - Ryan D Phillips
- Kings Park Science, Department of Biodiversity, Conservation and Attractions, Perth, WA, Australia
- Department of Ecology, Environment and Evolution, La Trobe University, Melbourne, VIC, Australia
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Stephen D Hopper
- Centre for Excellence in Natural Resource Management, School of Agriculture and Environment, University of Western Australia, Albany, WA, Australia
| | - Siegfried L Krauss
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
- Kings Park Science, Department of Biodiversity, Conservation and Attractions, Perth, WA, Australia
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50
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Grant EL, Conroy GC, Lamont RW, Reddell PW, Wallace HM, Ogbourne SM. Short distance pollen dispersal and low genetic diversity in a subcanopy tropical rainforest tree, Fontainea picrosperma (Euphorbiaceae). Heredity (Edinb) 2019; 123:503-516. [PMID: 31076650 PMCID: PMC6781113 DOI: 10.1038/s41437-019-0231-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 03/28/2019] [Accepted: 04/24/2019] [Indexed: 11/09/2022] Open
Abstract
Gene flow via pollen movement affects genetic variation in plant populations and is an important consideration in plant domestication. Fontainea picrosperma is a subcanopy rainforest tree that is of commercial interest because it is the source of tigilanol tiglate, a natural product used for the treatment of solid tumors. We identify patterns of pollen-mediated gene flow within natural populations of F. picrosperma and estimate genetic parameters and genetic structure between adult and juvenile groups using microsatellite markers. Our results show pollination events occur over much shorter distances than reported for tropical canopy species. At least 63% of seeds are sired by male trees located within 30 m of the mother. On average, 27% of the local male population contributed to successful reproduction of F. picrosperma with most fathers siring a single seed, however, the contributions to reproduction were uneven. Larger male trees with more flowers had greater reproductive success than those with less flowers (P < 0.05). There were comparatively low levels of genetic variation across the species (HE = 0.405 for adult trees and 0.379 for juveniles) and we found no loss of genetic diversity between adult and juvenile trees. Short distance pollen flow and low genetic diversity is theoretically a prelude to genetic impoverishment, however F. picrosperma has persisted through multiple significant climatic oscillations. Nevertheless, the remaining low genetic diversity is of concern for domestication programs which require maximal genetic diversity to facilitate efficient selective breeding and genetic improvement of this commercially significant species.
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Affiliation(s)
- Elektra L Grant
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Gabriel C Conroy
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Robert W Lamont
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | | | - Helen M Wallace
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Steven M Ogbourne
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, QLD, Australia.
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