scholarly journals New Insight into the Evolution of Symbiotic Genes in Black Locust-Associated Rhizobia

2019 ◽  
Vol 11 (7) ◽  
pp. 1736-1750 ◽  
Author(s):  
Zhenshan Liu ◽  
Weimin Chen ◽  
Shuo Jiao ◽  
Xinye Wang ◽  
Miaochun Fan ◽  
...  
Keyword(s):  
North America ◽  
Black Locust ◽  
Demographic History ◽  
Robinia Pseudoacacia ◽  
Geographic Origin ◽  
Symbiotic Genes ◽  
Plant Host ◽  
Rhizobial Species ◽  
History Of ◽  
Approximate Bayesian

Abstract Nitrogen fixation in legumes occurs via symbiosis with rhizobia. This process involves packages of symbiotic genes on mobile genetic elements that are readily transferred within or between rhizobial species, furnishing the recipient with the ability to interact with plant hosts. However, it remains elusive whether plant host migration has played a role in shaping the current distribution of genetic variation in symbiotic genes. Herein, we examined the genetic structure and phylogeographic pattern of symbiotic genes in 286 symbiotic strains of Mesorhizobium nodulating black locust (Robinia pseudoacacia), a cross-continental invasive legume species that is native to North America. We conducted detailed phylogeographic analysis and approximate Bayesian computation to unravel the complex demographic history of five key symbiotic genes. The sequencing results indicate an origin of symbiotic genes in Germany rather than North America. Our findings provide strong evidence of prehistoric lineage splitting and spatial expansion events resulting in multiple radiations of descendent clones from founding sequence types worldwide. Estimates of the timescale of divergence in North American and Chinese subclades suggest that black locust-specific symbiotic genes have been present in these continent many thousands of years before recent migration of plant host. Although numerous crop plants, including legumes, have found their centers of origin as centers of evolution and diversity, the number of legume-specific symbiotic genes with a known geographic origin is limited. This work sheds light on the coevolution of legumes and rhizobia.

scholarly journals Reconstructing the demographic history of Atlantic Salmon (Salmo salar) across its distribution range using Approximate Bayesian Computations

2017 ◽  
Author(s):  
Quentin Rougemont ◽  
Louis Bernatchez
Keyword(s):  
North America ◽  
Atlantic Salmon ◽  
Northern Hemisphere ◽  
Demographic History ◽  
Secondary Contact ◽  
Population Divergence ◽  
Isolated Populations ◽  
Quaternary Period ◽  
History Of ◽  
Approximate Bayesian

AbstractUnderstanding the dual roles of demographic and selective processes in the buildup of population divergence is one of the most challenging tasks in evolutionary biology. In the Northern hemisphere in particular, species genetic makeup has been largely influenced by severe climatic oscillations of the Quaternary Period. Here, we investigated the demographic history of Atlantic Salmon across the entire species range using 2035 anadromous individuals from 77 sampling sites from North America and Eurasia genotyped at 4,656 SNPs. By combining results from admixture graphs, geogenetic maps and an approximate Bayesian computation framework, we validate previous hypotheses pertaining to secondary contact between European and Northern American populations, but also demonstrate that European populations from different glacial refugia have been exchanging alleles in contemporary times. We further identify the major sources of admixture from the southern range of North America to more northern populations along with a strong signal of secondary gene flow between genetic regional groups. We hypothesize that these patterns reflects the spatial redistribution of ancestral variation across the entire American range. Results also point to a role for linked selection in the form of background selection and or positive hitchhiking. Altogether, differential introgression and linked selective effects likely played an underappreciated role in shaping the genomic landscape of species in the Northern hemisphere Therefore we conclude that such heterogeneity among loci should be systematically integrated into demographic inferences of the divergence process, even between incompletely reproductively isolated populations.

scholarly journals Population structure and demographic history of the chukar partridge Alectoris chukar in China

2013 ◽  
Vol 59 (4) ◽  
pp. 458-474 ◽  
Author(s):  
Sen Song ◽  
Shijie Bao ◽  
Ying Wang ◽  
Xinkang Bao ◽  
Bei An ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
North America ◽  
Demographic History ◽  
Population Expansion ◽  
Northwest China ◽  
Population History ◽  
Extant Species ◽  
History Of ◽  
Chukar Partridge

Abstract Pleistocene climate fluctuations have shaped the patterns of genetic diversity observed in extant species. Although the effects of recent glacial cycles on genetic diversity have been well studied on species in Europe and North America, genetic legacy of species in the Pleistocene in north and northwest of China where glaciations was not synchronous with the ice sheet development in the Northern Hemisphere or or had little or no ice cover during the glaciations’ period, remains poorly understood. Here we used phylogeographic methods to investigate the genetic structure and population history of the chukar partridge Alec-toris chukar in north and northwest China. A 1,152 – 1,154 bp portion of the mtDNA CR were sequenced for all 279 specimens and a total number of 91 haplotypes were defined by 113 variable sites. High levels of gene flow were found and gene flow estimates were greater than 1 for most population pairs in our study. The AMOVA analysis showed that 81% and 16% of the total genetic variability was found within populations and among populations within groups, respectively. The demographic history of chukar was examined using neutrality tests and mismatch distribution analyses and results indicated Late Pleistocene population expansion. Results revealed that most populations of chukar experienced population expansion during 0.027 ? 0.06 Ma. These results are at odds with the results found in Europe and North America, where population expansions occurred after Last Glacial Maximum (LGM, 0.023 to 0.018 Ma). Our results are not consistent with the results from avian species of Tibetan Plateau, either, where species experienced population expansion following the retreat of the extensive glaciation period (0.5 to 0.175 Ma).

scholarly journals Large-scale geographic survey provides insights into the colonization history of a major aphid pest on its cultivated apple host in Europe, North America and North Africa

2020 ◽  
Author(s):  
S.G. Olvera-Vazquez ◽  
C. Remoue ◽  
A. Venon ◽  
A. Rousselet ◽  
O. Grandcolas ◽  
...  
Keyword(s):  
Gene Flow ◽  
North America ◽  
Genetic Differentiation ◽  
North Africa ◽  
Large Scale ◽  
Demographic History ◽  
High Genetic Diversity ◽  
The North ◽  
The Us ◽  
History Of

With frequent host shifts involving the colonization of new hosts across large geographical ranges, crop pests are good models for examining the mechanisms of rapid colonization. The microbial partners of pest insects may be involved or affected by colonization, which has been little studied so far. We investigated the demographic history of the rosy apple aphid, Dysaphis plantaginea, a major pest of the cultivated apple (Malus domestica) in Europe, North Africa and North America, as well as the diversity of its endosymbiotic bacterial community. We genotyped a comprehensive sample of 714 colonies from Europe, Morocco and the US using mitochondrial (CytB and CO1), bacterial (16s rRNA and TrnpB), and 30 microsatellite markers. We detected five populations spread across the US, Morocco, Western and Eastern Europe, and Spain. Populations showed weak genetic differentiation and high genetic diversity, except the Moroccan and the North American that are likely the result of recent colonization events. Coalescent-based inferences releaved high levels of gene flow among populations during the colonization, but did not allow determining the sequence of colonization of Europe, America and Morroco by D. plantaginea, likely because of the weak genetic differentiation and the occurrence of gene flow among populations. Finally, we found that D. plantaginea rarely hosts any other endosymbiotic bacteria than its obligate nutritional symbiont Buchnera aphidicola. This suggests that secondary endosymbionts did not play any role in the rapid spread of the rosy apple aphid. These findings have fundamental importance for understanding pest colonization processes and implications for sustainable pest control programs.

scholarly journals Reconstructing the demographic history of divergence between European river and brook lampreys using approximate Bayesian computations

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1910 ◽  
Author(s):  
Quentin Rougemont ◽  
Camille Roux ◽  
Samuel Neuenschwander ◽  
Jerome Goudet ◽  
Sophie Launey ◽  
...  
Keyword(s):  
Gene Flow ◽  
Life Histories ◽  
Evolutionary Biology ◽  
Demographic History ◽  
Secondary Contact ◽  
Isolation With Migration ◽  
Genome Wide Data ◽  
History Of ◽  
Parameterized Model ◽  
Approximate Bayesian

Inferring the history of isolation and gene flow during species divergence is a central question in evolutionary biology. The European river lamprey (Lampetra fluviatilis) and brook lamprey(L. planeri)show a low reproductive isolation but have highly distinct life histories, the former being parasitic-anadromous and the latter non-parasitic and freshwater resident. Here we used microsatellite data from six replicated population pairs to reconstruct their history of divergence using an approximate Bayesian computation framework combined with a random forest model. In most population pairs, scenarios of divergence with recent isolation were outcompeted by scenarios proposing ongoing gene flow, namely the Secondary Contact (SC) and Isolation with Migration (IM) models. The estimation of demographic parameters under the SC model indicated a time of secondary contact close to the time of speciation, explaining why SC and IM models could not be discriminated. In case of an ancient secondary contact, the historical signal of divergence is lost and neutral markers converge to the same equilibrium as under the less parameterized model allowing ongoing gene flow. Our results imply that models of secondary contacts should be systematically compared to models of divergence with gene flow; given the difficulty to discriminate among these models, we suggest that genome-wide data are needed to adequately reconstruct divergence history.

scholarly journals Moose genomes reveal past glacial demography and the origin of modern lineages

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Nicolas Dussex ◽  
Federica Alberti ◽  
Matti T. Heino ◽  
Remi-Andre Olsen ◽  
Tom van der Valk ◽  
...  
Keyword(s):  
North America ◽  
De Novo ◽  
Demographic History ◽  
Glacial Refugia ◽  
Population Declines ◽  
Glacial Cycles ◽  
Climate Fluctuations ◽  
Northern Latitudes ◽  
Genomic Studies ◽  
History Of

Abstract Background Numerous megafauna species from northern latitudes went extinct during the Pleistocene/Holocene transition as a result of climate-induced habitat changes. However, several ungulate species managed to successfully track their habitats during this period to eventually flourish and recolonise the holarctic regions. So far, the genomic impacts of these climate fluctuations on ungulates from high latitudes have been little explored. Here, we assemble a de-novo genome for the European moose (Alces alces) and analyse it together with re-sequenced nuclear genomes and ancient and modern mitogenomes from across the moose range in Eurasia and North America. Results We found that moose demographic history was greatly influenced by glacial cycles, with demographic responses to the Pleistocene/Holocene transition similar to other temperate ungulates. Our results further support that modern moose lineages trace their origin back to populations that inhabited distinct glacial refugia during the Last Glacial Maximum (LGM). Finally, we found that present day moose in Europe and North America show low to moderate inbreeding levels resulting from post-glacial bottlenecks and founder effects, but no evidence for recent inbreeding resulting from human-induced population declines. Conclusions Taken together, our results highlight the dynamic recent evolutionary history of the moose and provide an important resource for further genomic studies.

scholarly journals Declining Growth Rate of West Nile Virus in North America

2006 ◽  
Vol 81 (5) ◽  
pp. 2531-2534 ◽  
Author(s):  
Katherine W. Snapinn ◽  
Edward C. Holmes ◽  
David S. Young ◽  
Kristen A. Bernard ◽  
Laura D. Kramer ◽  
...  
Keyword(s):  
Growth Rate ◽  
West Nile Virus ◽  
North America ◽  
Demographic History ◽  
Data Sets ◽  
Coding Region ◽  
West Nile ◽  
Region Data ◽  
History Of ◽  
The Mean

ABSTRACT To determine the demographic history of West Nile virus (WNV) in North America, we employed a coalescent method to envelope coding region data sets for the NY99 and WN02 genotypes. Although the observed genetic diversities in both genotypes were of approximately the same age, the mean rate of epidemiological growth of the WN02 population was approximately three times that of the NY99 population, a finding compatible with the recent dominance of the former genotype. However, there has also been a marked decrease in the recent growth rate of WN02, suggesting that WNV has reached its peak prevalence in North America.

scholarly journals Reconstructing the demographic history of orang-utans using Approximate Bayesian Computation

2015 ◽  
Vol 24 (2) ◽  
pp. 310-327 ◽  
Author(s):  
Alexander Nater ◽  
Maja P. Greminger ◽  
Natasha Arora ◽  
Carel P. van Schaik ◽  
Benoit Goossens ◽  
...  
Keyword(s):  
Approximate Bayesian Computation ◽  
Demographic History ◽  
Bayesian Computation ◽  
History Of ◽  
Approximate Bayesian

scholarly journals Erratum to: Insight into the evolutionary history of symbiotic genes of Robinia pseudoacacia rhizobia deriving from Poland and Japan

2010 ◽  
Vol 192 (6) ◽  
pp. 505-505
Author(s):  
Bożena Mierzwa ◽  
Barbara Łotocka ◽  
Sylwia Wdowiak-Wróbel ◽  
Michał Kalita ◽  
Sebastian Gnat ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Robinia Pseudoacacia ◽  
Symbiotic Genes ◽  
History Of ◽  
Insight Into

Connection, isolation and reconnection: Quaternary climatic oscillations and the Andes shaped the phylogeographical patterns of the Patagonian bee Centris cineraria (Apidae)

2020 ◽  
Vol 131 (2) ◽  
pp. 396-416 ◽  
Author(s):  
María Sosa-Pivatto ◽  
Gonzalo A Camps ◽  
Matías C Baranzelli ◽  
Anahí Espíndola ◽  
Alicia N Sérsic ◽  
...  
Keyword(s):  
Demographic History ◽  
Joint Effect ◽  
Secondary Contact ◽  
Glacial Refugium ◽  
Distribution Models ◽  
Climatic Oscillations ◽  
The Andes ◽  
History Of ◽  
Spatio Temporal ◽  
Approximate Bayesian

Abstract The joint effect of the Andes as a geographical barrier and the Quaternary glaciations as promoters of genetic divergence remains virtually unexplored in southern South America. To help fill this knowledge gap, in this study we investigated the demographic history of Centris cineraria, a solitary bee mainly distributed in Patagonia. We used mitochondrial and nuclear markers and performed phylogeographical and dating analyses, adjusted spatio-temporal diffusion and species distribution models, and used Approximate Bayesian Computation to identify likely historical demographic scenarios. Our results revealed that during glacial periods the Andes represented a barrier due to the extent of the ice-sheets and the occurrence of unsuitable habitats, while interglacials allowed for gene flow across the Andes. Secondary contact between previously isolated lineages was evident across at least two low-altitude Andean areas, the northern one being a putative glacial refugium. Our findings also suggest that C. cineraria has persisted in situ in four periglacial refugia located along a north–south transect, congruent with the maximum extent of the ice sheet during the Greatest Patagonian Glaciation. As the first phylogeographical study of Patagonian insects, our work reveals that the interaction between Quaternary climatic oscillations and the Andes as a barrier was the main driver of the spatial and demographic history of C. cineraria.

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