scholarly journals Contrasted histories of organelle and nuclear genomes underlying physiological diversification in a grass species

2020 ◽  
Vol 287 (1938) ◽  
pp. 20201960
Author(s):  
Matheus E. Bianconi ◽  
Luke T. Dunning ◽  
Emma V. Curran ◽  
Oriane Hidalgo ◽  
Robyn F. Powell ◽  
...  
Keyword(s):  
Gene Flow ◽  
Population Genomics ◽  
Nuclear Genome ◽  
Its Region ◽  
Grass Species ◽  
Region Of Origin ◽  
Ploidy Levels ◽  
Lower Elevation ◽  
Limited Dispersal ◽  
Genome Analyses

C 4 photosynthesis evolved multiple times independently in angiosperms, but most origins are relatively old so that the early events linked to photosynthetic diversification are blurred. The grass Alloteropsis semialata is an exception, as this species encompasses C 4 and non-C 4 populations. Using phylogenomics and population genomics, we infer the history of dispersal and secondary gene flow before, during and after photosynthetic divergence in A. semialata . We further analyse the genome composition of individuals with varied ploidy levels to establish the origins of polyploids in this species. Detailed organelle phylogenies indicate limited seed dispersal within the mountainous region of origin and the emergence of a C 4 lineage after dispersal to warmer areas of lower elevation. Nuclear genome analyses highlight repeated secondary gene flow. In particular, the nuclear genome associated with the C 4 phenotype was swept into a distantly related maternal lineage probably via unidirectional pollen flow. Multiple intraspecific allopolyploidy events mediated additional secondary genetic exchanges between photosynthetic types. Overall, our results show that limited dispersal and isolation allowed lineage divergence, with photosynthetic innovation happening after migration to new environments, and pollen-mediated gene flow led to the rapid spread of the derived C 4 physiology away from its region of origin.

scholarly journals Physiological diversity enhanced by recurrent divergence and secondary gene flow within a grass species

2020 ◽  
Author(s):  
Matheus E. Bianconi ◽  
Luke T. Dunning ◽  
Emma V. Curran ◽  
Oriane Hidalgo ◽  
Robyn F. Powell ◽  
...  
Keyword(s):  
Gene Flow ◽  
Population Genomics ◽  
Single Species ◽  
Grass Species ◽  
List Type ◽  
Physiological Diversity ◽  
Rapid Spread ◽  
Limited Dispersal ◽  
History Of ◽  
Lineage Divergence

SummaryC4 photosynthesis evolved multiple times independently in angiosperms, but most origins are relatively old so that the early events linked to photosynthetic diversification are blurred. The grass Alloteropsis semialata is an exception, as this single species encompasses C4 and non-C4 populations.Using phylogenomics and population genomics, we infer the history of dispersal and secondary exchanges before, during, and after photosynthetic divergence in A. semialata. We further establish the genetic origins of polyploids in this species.Organelle phylogenies indicate limited seed dispersal within the Central Zambezian region of Africa, where the species originated ∼ 2–3 Ma. Outside this region, the species spread rapidly across the paleotropics to Australia. Comparison of nuclear and organelle phylogenies and analyses of whole genomes reveal extensive secondary gene flow. In particular, the genomic group corresponding to the C4 trait was swept into seeds from distinct geographic regions. Multiple segmental allopolyploidy events mediated additional secondary genetic exchanges between photosynthetic types.Limited dispersal and isolation allowed lineage divergence, while episodic secondary exchanges led to the pollen-mediated, rapid spread of the derived C4 physiology. Overall, our study suggests that local adaptation followed by recurrent secondary gene flow promoted physiological diversification in this grass species.

scholarly journals The Evolution and Population Diversity of Bison in Pleistocene and Holocene Eurasia: Sex Matters

Diversity ◽  
2018 ◽  
Vol 10 (3) ◽  
pp. 65 ◽  
Author(s):  
Thierry Grange ◽  
Jean-Philip Brugal ◽  
Laurence Flori ◽  
Mathieu Gautier ◽  
Antigone Uzunidis ◽  
...  
Keyword(s):  
Gene Flow ◽  
Evolutionary History ◽  
Nuclear Genome ◽  
Population Diversity ◽  
Ecological Niches ◽  
Unified Framework ◽  
Putative Gene ◽  
Behavioral Studies ◽  
History Of ◽  
Genome Analyses

Knowledge about the origin and evolutionary history of the bison has been improved recently owing to several genomic and paleogenomic studies published in the last two years, which elucidated large parts of the evolution of bison populations during the Upper Pleistocene and Holocene in Eurasia. The produced data, however, were interpreted in contradicting manners. Here, we have gathered, reanalyzed and compared previously published or unpublished morphometric and genetic data that have not yet been integrated and that we synthesize in a unified framework. In particular, we re-estimate dates of divergence of mitogenome lineages based on an extended dataset comprising 81 complete ancient bison mitogenomes and we revisit putative gene flow between the Bos and Bison genera based on comparative analyses of ancient and modern bison genomes, thereby questioning published conclusions. Morphometric analyses taking into account sexual dimorphism invalidate a previous claim that Bison schoetensacki was present in France during the Late Pleistocene. Both morphometric and genome analyses reveal that Eurasian bison belonging to different Bison priscus and Bison bonasus lineages maintained parallel evolutionary paths with gene flow during a long period of incomplete speciation that ceased only upon the migration of B. priscus to the American continent establishing the American bison lineage. Our nuclear genome analysis of the evolutionary history of B. bonasus allows us to reject the previous hypothesis that it is a hybrid of B. priscus and Bos primigenius. Based on present-day behavioral studies of European and American bison, we propose that apparently conflicting lines of evidence can be reconciled by positing that female bison drove the specialization of bison populations to different ecological niches while male bison drove regular homogenizing genetic exchanges between populations.

scholarly journals Hybridisation boosts dispersal of two contrasted ecotypes in a grass species

2021 ◽  
Author(s):  
Emma V Curran ◽  
Matilda S Scott ◽  
Jill K Olofsson ◽  
Florence Nyirenda ◽  
Graciela Sotelo ◽  
...  
Keyword(s):  
Population Genomics ◽  
Nuclear Genome ◽  
The Other ◽  
Grass Species ◽  
Reproductive Barriers ◽  
Miombo Woodlands ◽  
Ecological Strategies ◽  
Chloroplast Genomes ◽  
New Locations ◽  
African Grass

In the absence of strong reproductive barriers, 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 hybridisation. How these dynamics affect the emergence and spread of novel ecological strategies remains only partially understood. We use phylogenomics and population genomics to retrace the origin of two geographically overlapping ecotypes of the African grass Alloteropsis angusta. We report the existence of a previously undescribed ecotype inhabiting miombo woodlands and grasslands. The two ecotypes have divergent nuclear genomes. 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 reach the seeds of the other via pollen movements, with strong selection subsequently sorting nuclear alleles by habitat. The contrasting ecotypes of A. angusta can use each other as a gateway to new locations across a large part of Africa. Coupled with newly discovered hybridisation with the sister species A. semialata, our results show that hybridisation can facilitate the geographical dispersal of distinct ecotypes of the same grass species.

Population genomics reveals high gene flow in grass rockfish ( Sebastes rastrelliger )

2017 ◽  
Vol 33 ◽  
pp. 57-63 ◽  
Author(s):  
Edith Martinez ◽  
Vincent Buonaccorsi ◽  
John R. Hyde ◽  
Andres Aguilar
Keyword(s):  
Gene Flow ◽  
Population Genomics ◽  
High Gene Flow ◽  
High Gene

scholarly journals Spatial population genomics of a recent mosquito invasion

2020 ◽  
Author(s):  
Thomas L Schmidt ◽  
T. Swan ◽  
Jessica Chung ◽  
Stephan Karl ◽  
Samuel Demok ◽  
...  
Keyword(s):  
Gene Flow ◽  
Population Genomics ◽  
Isolation By Distance ◽  
Spatial Genetic Structure ◽  
Nucleotide Polymorphisms ◽  
Discrete Events ◽  
Long Distance ◽  
Population Genomic ◽  
Asian Tiger ◽  
Study Designs

AbstractPopulation genomic approaches can characterise dispersal across a single generation through to many generations in the past, bridging the gap between individual movement and intergenerational gene flow. These approaches are particularly useful when investigating dispersal in recently altered systems, where they provide a way of inferring long-distance dispersal between newly established populations and their interactions with existing populations. Human-mediated biological invasions represent such altered systems which can be investigated with appropriate study designs and analyses. Here we apply temporally-restricted sampling and a range of population genomic approaches to investigate dispersal in a 2004 invasion of Aedes albopictus (the Asian tiger mosquito) in the Torres Strait Islands (TSI) of Australia. We sampled mosquitoes from 13 TSI villages simultaneously and genotyped 373 mosquitoes at genome-wide single nucleotide polymorphisms (SNPs): 331 from the TSI, 36 from Papua New Guinea (PNG), and 4 incursive mosquitoes detected in uninvaded regions. Within villages, spatial genetic structure varied substantially but overall displayed isolation by distance and a neighbourhood size of 232–577. Close kin dyads revealed recent movement between islands 31–203 km apart, and deep learning inferences showed incursive Ae. albopictus had travelled to uninvaded regions from both adjacent and non-adjacent islands. Private alleles and a coancestry matrix indicated direct gene flow from PNG into nearby islands. Outlier analyses also detected four linked alleles introgressed from PNG, with the alleles surrounding 12 resistance-associated cytochrome P450 genes. By treating dispersal as both an intergenerational process and a set of discrete events, we describe a highly interconnected invasive system.

scholarly journals Significant cross-species gene flow detected in the Tamias quadrivittatus group of North American chipmunks

2021 ◽  
Author(s):  
Jiayi Ji ◽  
Donavan J. Jackson ◽  
Adam D. Leaché ◽  
Ziheng Yang
Keyword(s):  
Gene Flow ◽  
Sequence Data ◽  
Nuclear Genome ◽  
Likelihood Method ◽  
Recent Analysis ◽  
The Past ◽  
Rapid Speciation ◽  
Full Likelihood ◽  
Nuclear Loci ◽  
Robust Evidence

In the past two decades genomic data have been widely used to detect historical gene flow between species in a variety of plants and animals. The Tamias quadrivittatus group of North America chipmunks, which originated through a series of rapid speciation events, are known to undergo massive amounts of mitochondrial introgression. Yet in a recent analysis of targeted nuclear loci from the group, no evidence for cross-species introgression was detected, indicating widespread cytonuclear discordance. The study used heuristic methods that analyze summaries of the multilocus sequence data to detect gene flow, which may suffer from low power. Here we use the full likelihood method implemented in the Bayesian program BPP to reanalyze these data. We take a stepwise approach to constructing an introgression model by adding introgression events onto a well-supported binary species tree. The analysis detected robust evidence for multiple ancient introgression events affecting the nuclear genome, with introgression probabilities reaching 65%. We estimate population parameters and highlight the fact that species divergence times may be seriously underestimated if ancient cross-species gene flow is ignored in the analysis. Our analyses highlight the importance of using adequate statistical methods to reach reliable biological conclusions concerning cross-species gene flow.

Assessment of gene flow using tetraploid genotypes of perennial ryegrass (Lolium perenne L.)

2004 ◽  
Vol 55 (4) ◽  
pp. 389 ◽  
Author(s):  
K. V. Cunliffe ◽  
A. C. Vecchies ◽  
E. S. Jones ◽  
G. A. Kearney ◽  
J. W. Forster ◽  
...  
Keyword(s):  
Gene Flow ◽  
Seed Production ◽  
Lolium Perenne ◽  
Perennial Ryegrass ◽  
Grass Species ◽  
Numerical Representation ◽  
Pasture Grass ◽  
Important Species ◽  
Lolium Perenne L ◽  
Total Seed

Ryegrass species are among the most important species in sown pastures, turf settings, and weed populations worldwide. Perennial ryegrass (Lolium perenne L.) is an outcrossing, wind-pollinated grass. Recent research has demonstrated the feasibility of developing transgenic perennial ryegrass varieties. In order to model the consequences of gene flow from transgenic grass genotypes in a field situation, the model non-transgenic trait of fertility among autotetraploid genotypes was chosen. Gene flow over distance and direction from a donor plot to surrounding sexually compatible recipient plants was studied. Reproductive isolation was achieved through the fertility barrier that arises between tetraploid and diploid ryegrass genotypes, despite the presence of diploid plants in a meadow situation. Fertility was used as an indication of effective gene flow over distance and direction. Measures of the fertility of recipient plants included total seed production (TSP), floret site utilisation (FSU), and relative fertility of recipient plants as a percentage of those within the donor plot (RF%). A leptokurtic distribution for gene flow was identified, with differences in the rate of decline over distance depending on direction. Simple sequence repeat (SSR) polymorphism was used to identify the paternity of progeny plants. The proportional representation of parents among the progeny was not significantly different from that expected due to the numerical representation of the different donor parent genotypes. The results of this research will have important implications for risk analysis prior to the field release of transgenic ryegrasses, fescues, and other pasture grass species, and for seed production in terms of cultivar purity and optimum isolation distance.

scholarly journals Speciation in the presence of gene flow: population genomics of closely related and diverging Eucalyptus species

Heredity ◽  
2018 ◽  
Vol 121 (2) ◽  
pp. 126-141 ◽  
Author(s):  
Susan Rutherford ◽  
Maurizio Rossetto ◽  
Jason G. Bragg ◽  
Hannah McPherson ◽  
Doug Benson ◽  
...  
Keyword(s):  
Gene Flow ◽  
Population Genomics ◽  
Eucalyptus Species

scholarly journals Genetic Diversity and Population Structure of Bermudagrass [Cynodon dactylon (L.) Pers.] along Latitudinal Gradients and the Relationship with Polyploidy Level

Diversity ◽  
2019 ◽  
Vol 11 (8) ◽  
pp. 135 ◽  
Author(s):  
Jingxue Zhang ◽  
Miaoli Wang ◽  
Zhipeng Guo ◽  
Yongzhuo Guan ◽  
Jianyu Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Flow ◽  
Population Genetic ◽  
Cynodon Dactylon ◽  
Latitudinal Gradients ◽  
Wind Pollination ◽  
Ploidy Levels ◽  
Sexual And Asexual Reproduction ◽  
Genetic Pattern

Understanding the population genetic pattern and process of gene flow requires a detailed knowledge of how landscape characteristics structure populations. Although Cynodon dactylon (L.) Pers. (common bermudagrass) is widely distributed in the world, information on its genetic pattern and population structure along latitudinal gradients is limited. We tried to estimate the genetic diversity and genetic structure of C. dactylon along a latitudinal gradient across China. Genetic diversity among different ploidy levels was also compared in the study. The material used consisted of 296 C. dactylon individuals sampled from 16 geographic sites from 22°35′ N to 36°18′ N. Genetic diversity was estimated using 153 expressed sequence tag-derived simple sequence repeat (EST-SSR) loci. Higher within-population genetic diversity appeared at low-latitude, as well as having positive correlation with temperature and precipitation. The genetic diversity increased with the ploidy level of C. dactylon, suggesting polyploidy creates higher genetic diversity. No isolation by distance and notable admixture structure existed among populations along latitudes. Both seed dispersal (or vegetative organs) and extrinsic pollen played important roles for gene flow in shaping the spatial admixture population structure of C. dactylon along latitudes. In addition, populations were separated into three clusters according to ploidy levels. C. dactylon has many such biological characters of perennial growth, wind-pollination, polyploidy, low genetic differentiation among populations, sexual and asexual reproduction leading to higher genetic diversity, which gives it strong adaptability with its genetic patterns being very complex across all the sampled latitudes. The findings of this study are related to landscape population evolution, polyploidy speciation, preservation, and use of bermudagrass breeding.

scholarly journals Population genomics in two cave-obligate invertebrates confirms extremely limited dispersal between caves

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Andras Balogh ◽  
Lam Ngo ◽  
Kirk S. Zigler ◽  
Groves Dixon
Keyword(s):  
Genetic Divergence ◽  
Population Genomics ◽  
Sample Sizes ◽  
Dense Region ◽  
Evolutionary Processes ◽  
Cumberland Plateau ◽  
Selective Pressures ◽  
Genome Wide ◽  
Good Sample ◽  
Limited Dispersal

Abstract Caves offer selective pressures that are distinct from the surface. Organisms that have evolved to exist under these pressures typically exhibit a suite of convergent characteristics, including a loss or reduction of eyes and pigmentation. As a result, cave-obligate taxa, termed troglobionts, are no longer viable on the surface. This circumstance has led to an understanding of highly constrained dispersal capabilities, and the prediction that, in the absence of subterranean connections, extreme genetic divergence between cave populations. An effective test of this model would involve (1) common troglobionts from (2) nearby caves in a cave-dense region, (3) good sample sizes per cave, (4) multiple taxa, and (5) genome-wide characterization. With these criteria in mind, we used RAD-seq to genotype an average of ten individuals of the troglobiotic spider Nesticus barri and the troglobiotic beetle Ptomaphagus hatchi, each from four closely located caves (ranging from 3 to 13 km apart) in the cave-rich southern Cumberland Plateau of Tennessee, USA. Consistent with the hypothesis of highly restricted dispersal, we find that populations from separate caves are indeed highly genetically isolated. Our results support the idea of caves as natural laboratories for the study of parallel evolutionary processes.

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