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

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.

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

PeerJ ◽

10.7717/peerj.1910 ◽

2016 ◽

Vol 4 ◽

pp. e1910 ◽

Cited By ~ 17

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.

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

Biological Journal of the Linnean Society ◽

10.1093/biolinnean/blaa116 ◽

2020 ◽

Vol 131 (2) ◽

pp. 396-416 ◽

Cited By ~ 1

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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The demographic history of Atlantic salmon (Salmo salar ) across its distribution range reconstructed from approximate Bayesian computations*

Evolution ◽

10.1111/evo.13486 ◽

2018 ◽

Vol 72 (6) ◽

pp. 1261-1277 ◽

Cited By ~ 30

Author(s):

Quentin Rougemont ◽

Louis Bernatchez

Keyword(s):

Atlantic Salmon ◽

Salmo Salar ◽

Demographic History ◽

Distribution Range ◽

Atlantic Salmon Salmo Salar ◽

History Of ◽

Approximate Bayesian

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

Genome Biology and Evolution ◽

10.1093/gbe/evz116 ◽

2019 ◽

Vol 11 (7) ◽

pp. 1736-1750 ◽

Cited By ~ 1

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.

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Fossil flower of Staphylea L. from the Miocene amber of Mexico: New evidence of the Boreotropical Flora in low-latitude North America

Earth and Environmental Science Transactions of the Royal Society of Edinburgh ◽

10.1017/s1755691018000701 ◽

2017 ◽

Vol 108 (4) ◽

pp. 471-478 ◽

Cited By ~ 1

Author(s):

Ana L. Hernández-Damián ◽

Sergio R. S. Cevallos-Ferriz ◽

Alma R. Huerta-Vergara

Keyword(s):

North America ◽

Northern Hemisphere ◽

Fossil Record ◽

First Record ◽

High Latitudes ◽

Low Latitude ◽

Southern Mexico ◽

Apparent Lack ◽

History Of ◽

New Evidence

ABSTRACTA new flower preserved in amber in sediments of Simojovel de Allende, México, is identified as an extinct member of Staphyleaceae, a family of angiosperms consisting of only three genera (Staphylea, Turpinia and Euscaphis), which has a large and abundant fossil record and is today distributed over the Northern Hemisphere. Staphylea ochoterenae sp. nov. is the first record of a flower for this group, which is small, pedicelled, pentamer, bisexual, with sepals and petals with similar size, dorsifixed anthers and superior ovary. Furthermore, the presence of stamens with pubescent filaments allows close comparison with extant flowers of Staphylea bulmada and S. forresti, species currently growing in Asia. However, their different number of style (one vs. three) and the apparent lack of a floral disc distinguish them from S. ochoterenae. The presence of Staphyleaceae in southern Mexico ca. 23 to 15My ago is evidence of the long history of integration of vegetation in low-latitude North America, in which some lineages, such as Staphylea, could move southwards from high latitudes of the Northern Hemisphere, as part of the Boreotropical Flora. In Mexico it grew in association with tropical elements, as suggested by the fossil record of the area.

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

Current Zoology ◽

10.1093/czoolo/59.4.458 ◽

2013 ◽

Vol 59 (4) ◽

pp. 458-474 ◽

Cited By ~ 2

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).

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Gondwana and Pangea

Continents and Supercontinents ◽

10.1093/oso/9780195165890.003.0010 ◽

2004 ◽

Author(s):

John J. W. Rogers ◽

M. Santosh

Keyword(s):

North America ◽

South America ◽

Southern Hemisphere ◽

Northern Hemisphere ◽

Late Paleozoic ◽

Northern Asia ◽

Pan African ◽

History Of ◽

Single Block ◽

Orogenic Belts

Pangea, the most recent supercontinent, attained its condition of maximum packing at ~250 Ma. At this time, it consisted of a northern part, Laurasia, and a southern part, Gondwana. Gondwana contained the southern continents—South America, Africa, India, Madagascar, Australia, and Antarctica. It had become a coherent supercontinent at ~500 Ma and accreted to Pangea largely as a single block. Laurasia consisted of the northern continents—North America, Greenland, Europe, and northern Asia. It accreted during the Late Paleozoic and became a supercontinent when fusion of these continental blocks with Gondwana occurred near the end of the Paleozoic. The configuration of Pangea, including Gondwana, can be determined accurately by tracing the patterns of magnetic stripes in the oceans that opened within it (chapters 1 and 9). The history of accretion of Laurasia is also well known, but the development of Gondwana is highly controversial. Gondwana was clearly a single supercontinent by ~500 Ma, but whether it formed by fusion of a few large blocks or the assembly of numerous small blocks is uncertain. Figure 8.1 shows Gondwana divided into East and West parts, but the boundary between them is highly controversial (see below). We start this chapter by investigating the history of Gondwana, using appendix SI to describe detailed histories of orogenic belts of Pan-African age (600–500-Ma). Then we continue with the development of Pangea, including the Paleozoic orogenic belts that led to its development. The next section summarizes the paleomagnetically determined movement of blocks from the accretion of Gondwana until the assembly of Pangea, and the last section discusses the differences between Gondwana and Laurasia in Pangea. The patterns of dispersal and development of modern oceans are left to chapter 9, and the histories of continents following dispersal to chapter 10. By the later part of the 1800s, geologists working in the southern hemisphere realized that the Paleozoic fossils that occurred there were very different from those in the northern hemisphere. They found similar fossils in South America, Africa, Madagascar, India, and Australia, and in 1913 they added Antarctica when identical specimens were found by the Scott expedition.

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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

10.1101/2020.12.11.421644 ◽

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.

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Blockwise Site Frequency Spectra for Inferring Complex Population Histories and Recombination

10.1101/077958 ◽

2016 ◽

Cited By ~ 3

Author(s):

Champak R. Beeravolu ◽

Michael J. Hickerson ◽

Laurent A.F. Frantz ◽

Konrad Lohse

Keyword(s):

Demographic History ◽

Composite Likelihood ◽

Model Organisms ◽

Secondary Contact ◽

Parameter Estimates ◽

Genome Sequences ◽

Frequency Spectra ◽

Genome Wide ◽

Complex Population ◽

History Of

AbstractWe introduce ABLE (Approximate Blockwise Likelihood Estimation), a novel composite likelihood framework based on a recently introduced summary of sequence variation: the blockwise site frequency spectrum (bSFS). This simulation-based framework uses the the frequencies of bSFS configurations to jointly model demographic history and recombination and is explicitly designed to make inference using multiple whole genomes or genome-wide multi-locus data (e.g. RADSeq) catering to the needs of researchers studying model or non-model organisms respectively. The flexible nature of our method further allows for arbitrarily complex population histories using unphased and unpolarized whole genome sequences. In silico experiments demonstrate accurate parameter estimates across a range of divergence models with increasing complexity, and as a proof of principle, we infer the demographic history of the two species of orangutan from multiple genome sequences (over 160 Mbp in length) from each species. Our results indicate that the two orangutan species split approximately 650-950 thousand years ago but experienced a pulse of secondary contact much more recently, most likely during a period of low sea-level South East Asia (∼300,000 years ago). Unlike previous analyses we can reject a history of continuous gene flow and co-estimate genome-wide recombination. ABLE is available for download at https://github.com/champost/ABLE.

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