Evaluation of the minimum sampling design for population genomic and microsatellite studies. An analysis based on wild maize

ABSTRACTMassive parallel sequencing is revolutionizing the field of molecular ecology by allowing to understand better the evolutionary history of populations and species, and to detect genomic regions that could be under selection. However, the needed economic and computational resources generate a tradeoff between the amount of loci that can be obtained and the number of populations or individuals that can be sequenced. In this work, we analyzed and compared two extensive genomic and one large microsatellite datasets consisting of empirical data. We generated different subsampling designs by changing the number of loci, individuals, populations and individuals per population to test for deviations in classic population genetics parameters (HS, FIS, FST) and landscape genetic tests (isolation by distance and environment, central abundance hypothesis). We also tested the effect of sampling different number of populations in the detection of outlier SNPs. We found that the microsatellite dataset is very sensitive to the number of individuals sampled when obtaining summary statistics. FIS was particularly sensitive to a low sampling of individuals in the genomic and microsatellite datasets. For the genomic datasets, we found that as long as many populations are sampled, few individuals and loci are needed. For all datasets we found that increasing the number of population sampled is important to obtain precise landscape genetic estimates. Finally, we corroborated that outlier tests are sensitive to the number of populations sampled. We conclude by proposing different sampling designs depending on the objectives.

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Haplotype threading: accurate polyploid phasing from long reads

Genome Biology ◽

10.1186/s13059-020-02158-1 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Sven D. Schrinner ◽

Rebecca Serra Mari ◽

Jana Ebler ◽

Mikko Rautiainen ◽

Lancelot Seillier ◽

...

Keyword(s):

Open Source ◽

Evolutionary History ◽

State Of The Art ◽

Regions Of Interest ◽

Breeding Strategies ◽

Polyploid Species ◽

Two Stage ◽

Long Reads ◽

History Of ◽

Genomic Regions

Abstract Resolving genomes at haplotype level is crucial for understanding the evolutionary history of polyploid species and for designing advanced breeding strategies. Polyploid phasing still presents considerable challenges, especially in regions of collapsing haplotypes.We present WhatsHap polyphase, a novel two-stage approach that addresses these challenges by (i) clustering reads and (ii) threading the haplotypes through the clusters. Our method outperforms the state-of-the-art in terms of phasing quality. Using a real tetraploid potato dataset, we demonstrate how to assemble local genomic regions of interest at the haplotype level. Our algorithm is implemented as part of the widely used open source tool WhatsHap.

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Phylogeography of the California Thrasher (Toxostoma Redivivum) Based on Nested-Clade Analysis of Mitochondrial-DNA Variation

The Auk ◽

10.1093/auk/120.2.346 ◽

2003 ◽

Vol 120 (2) ◽

pp. 346-361

Author(s):

Erik A. Sgariglia ◽

Kevin J. Burns

Keyword(s):

Mitochondrial Dna ◽

Range Expansion ◽

Evolutionary History ◽

Isolation By Distance ◽

Nested Clade Analysis ◽

Dna Variation ◽

History Of ◽

Past Fragmentation ◽

Intraspecific Relationships ◽

Geologic Data

Abstract Distribution of genealogical lineages within a species is likely the result of a complicated series of ecological and historical events. Nested-clade analysis is specifically designed as an objective phylogeographic approach for inferring evolutionary processes on a spatial and temporal scale for small subclades within a larger set of intraspecific relationships. Here, we use nested-clade analysis as well as other phylogeographic methods to investigate the evolutionary history of California Thrasher (Toxostoma redivivum) populations. Inferences resulting from nested clade analysis suggest a history that includes past fragmentation, range expansion, and isolation-by-distance. Along with root information, those inferences enable the construction of a biogeographic scenario for this species involving general southern ancestry, an early north–south division, northward range expansion, and a southward back-expansion into an already populated southern region. Isolation-by-distance is also identified, particularly in southern California, indicating that gene flow between localities does occur but is restricted. Many conclusions drawn from this study are concordant with geologic data as well as phylogeographic scenarios drawn for other codistributed California taxa.

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Updates in the Language ofHistoplasmaBiodiversity

mBio ◽

10.1128/mbio.00181-18 ◽

2018 ◽

Vol 9 (3) ◽

Author(s):

Pierre Gladieux

Keyword(s):

Evolutionary History ◽

Species Recognition ◽

Fungal Species ◽

Species Status ◽

Genome Resequencing ◽

Intraspecific Divergence ◽

Testing Framework ◽

Population Genomic ◽

History Of ◽

Whole Genome Resequencing

ABSTRACTIn a recent article, Sepúlveda et al. (mBio 8:e01339-17, 2017, https://doi.org/10.1128/mBio.01339-17) investigated the genetic structure and evolutionary history of the human pathogenHistoplasma. Using whole-genome resequencing data, Sepúlveda et al. found that theHistoplasmagenus is composed of at least four strongly differentiated lineages. Their tour de force is to use a smart combination of population genomic approaches to show that the advanced stage of intraspecific divergence observed withinHistoplasmadoes not simply reflect population structure, but instead results from previously unidentified speciation events. The four independently evolvingHistoplasmalineages are elevated to the species status and assigned names. The newly described species exhibit medically important differences in phenotype, and these findings, therefore, have important epidemiological implications. This work provides a blueprint for phylogenomic species recognition in fungi, opening the way for a new age of enlightenment in which fungal species are diagnosed using highly discriminatory tools within a hypothesis-testing framework.

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Linked-read sequencing enables haplotype-resolved resequencing at population scale

10.1101/2020.01.15.907261 ◽

2020 ◽

Cited By ~ 2

Author(s):

Dave Lutgen ◽

Raphael Ritter ◽

Remi-André Olsen ◽

Holger Schielzeth ◽

Joel Gruselius ◽

...

Keyword(s):

Evolutionary History ◽

Sequencing Data ◽

Sequencing Technology ◽

Genome Resequencing ◽

High Coverage ◽

Population Genomic ◽

Genomic Analyses ◽

History Of ◽

Population Scale ◽

Haplotype Information

AbstractThe feasibility to sequence entire genomes of virtually any organism provides unprecedented insights into the evolutionary history of populations and species. Nevertheless, many population genomic inferences – including the quantification and dating of admixture, introgression and demographic events, and the inference of selective sweeps – are still limited by the lack of high-quality haplotype information. In this respect, the newest generation of sequencing technology now promises significant progress. To establish the feasibility of haplotype-resolved genome resequencing at population scale, we investigated properties of linked-read sequencing data of songbirds of the genus Oenanthe across a range of sequencing depths. Our results based on the comparison of downsampled (25x, 20x, 15x, 10x, 7x, and 5x) with high-coverage data (46-68x) of seven bird genomes suggest that phasing contiguities and accuracies adequate for most population genomic analyses can be reached already with moderate sequencing effort. At 15x coverage, phased haplotypes span about 90% of the genome assembly, with 50 and 90 percent of the phased sequence located in phase blocks longer than 1.25-4.6 Mb (N50) and 0.27-0.72 Mb (N90), respectively. Phasing accuracy reaches beyond 99% starting from 15x coverage. Higher coverages yielded higher contiguities (up to about 7 Mb/1Mb (N50/N90) at 25x coverage), but only marginally improved phasing accuracy. Finally, phasing contiguity improved with input DNA molecule length; thus, higher-quality DNA may help keeping sequencing costs at bay. In conclusion, even for organisms with gigabase-sized genomes like birds, linked-read sequencing at moderate depth opens an affordable avenue towards haplotype-resolved genome resequencing data at population scale.

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A distinct expression profile in the cerebellum and striatum for genes under selection within introgression deserts

10.1101/2021.03.26.437167 ◽

2021 ◽

Author(s):

Raul Buisan ◽

Juan Moriano ◽

Alejandro Andirko ◽

Cedric Boeckx

Keyword(s):

Positive Selection ◽

Evolutionary History ◽

Developmental Stages ◽

Homo Sapiens ◽

Transcriptomic Data ◽

Functional Differences ◽

History Of ◽

Genomic Regions ◽

Cerebral Neocortex

Analyses of ancient DNA from extinct hominins have provided unique insights into the complex evolutionary history of Homo sapiens, intricately related to that of the Neanderthals and the Denisovans as revealed by several instances of admixture events. These analyses have also allowed the identification of introgression deserts: genomic regions in our species that are depleted of `archaic' haplotypes. The presence of genes like FOXP2 in these deserts has been taken to be suggestive of brain-related functional differences between Homo species. Here, we seek a deeper characterization of these regions, taking into account signals of positive selection in our lineage. Analyzing publicly available transcriptomic data from the human brain at different developmental stages, we found that structures outside the cerebral neocortex, and especially the cerebellum and the striatum at prenatal stages, show the most divergent transcriptomic profiles when considering genes under positive selection within introgression deserts.

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Evolutionary history of a relict conifer, Pseudotaxus chienii (Taxaceae), in south-east China during the late Neogene: old lineage, young populations

Annals of Botany ◽

10.1093/aob/mcz153 ◽

2019 ◽

Vol 125 (1) ◽

pp. 105-117 ◽

Cited By ~ 2

Author(s):

Yixuan Kou ◽

Li Zhang ◽

Dengmei Fan ◽

Shanmei Cheng ◽

Dezhu Li ◽

...

Keyword(s):

Dna Sequences ◽

Genetic Divergence ◽

Evolutionary History ◽

Isolation By Distance ◽

Demographic History ◽

East China ◽

Population Divergence ◽

Isolation By Environment ◽

Late Neogene ◽

History Of

Abstract Background and Aims Many monotypic gymnosperm lineages in south-east China paradoxically remain in relict status despite long evolutionary histories and ample opportunities for allopatric speciation, but this paradox has received little attention and has yet to be resolved. Here, we address this issue by investigating the evolutionary history of a relict conifer, Pseudotaxus chienii (Taxaceae). Methods DNA sequences from two chloroplast regions and 14 nuclear loci were obtained for 134 samples. The demographic history was inferred and the contribution of isolation by environment (IBE) in patterning genetic divergence was compared with that of isolation by distance (IBD). Key Results Three genetic clusters were identified. Approximate Bayesian computation analyses showed that the three clusters diverged in the late Pliocene (~3.68 Ma) and two admixture events were detected. Asymmetric gene flow and similar population divergence times (~ 3.74 Ma) were characterized using the isolation with migration model. Neither IBD nor IBE contributed significantly to genetic divergence, and the contribution of IBE was much smaller than that of IBD. Conclusions These results suggest that several monotypic relict gymnosperm lineages like P. chienii in south-east China did not remain in situ and undiversified for millions of years. On the contrary, they have been evolving and the extant populations have become established more recently, having insufficient time to speciate. Our findings provide a new perspective for understanding the formation and evolution of the relict gymnosperm flora of China as well as of the Sino-Japanese Flora.

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Phylogeographic Approaches to Characterize the Emergence of Plant Pathogens

Phytopathology ◽

10.1094/phyto-07-20-0319-fi ◽

2020 ◽

pp. PHYTO-07-20-031

Author(s):

David A. Rasmussen ◽

Niklaus J. Grünwald

Keyword(s):

Evolutionary History ◽

Plant Pathogens ◽

Geographic Information ◽

Geographic Context ◽

Population Genomic ◽

History Of

Phylogeography combines geographic information with phylogenetic and population genomic approaches to infer the evolutionary history of a species or population in a geographic context. This approach has been instrumental in understanding the emergence, spread, and evolution of a range of plant pathogens. In particular, phylogeography can address questions about where a pathogen originated, whether it is native or introduced, and when and how often introductions occurred. We review the theory, methods, and approaches underpinning phylogeographic inference and highlight applications providing novel insights into the emergence and spread of select pathogens. We hope that this review will be useful in assessing the power, pitfalls, and opportunities presented by various phylogeographic approaches.

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Minimal-assumption inference from population-genomic data

eLife ◽

10.7554/elife.24836 ◽

2017 ◽

Vol 6 ◽

Cited By ~ 15

Author(s):

Daniel B Weissman ◽

Oskar Hallatschek

Keyword(s):

Evolutionary History ◽

Simulated Data ◽

Large Samples ◽

Minimal Assumption ◽

Population Genomic ◽

Human Genomes ◽

History Of ◽

Or Gene ◽

Linked Selection ◽

Genomic Length

Samples of multiple complete genome sequences contain vast amounts of information about the evolutionary history of populations, much of it in the associations among polymorphisms at different loci. We introduce a method, Minimal-Assumption Genomic Inference of Coalescence (MAGIC), that reconstructs key features of the evolutionary history, including the distribution of coalescence times, by integrating information across genomic length scales without using an explicit model of coalescence or recombination, allowing it to analyze arbitrarily large samples without phasing while making no assumptions about ancestral structure, linked selection, or gene conversion. Using simulated data, we show that the performance of MAGIC is comparable to that of PSMC’ even on single diploid samples generated with standard coalescent and recombination models. Applying MAGIC to a sample of human genomes reveals evidence of non-demographic factors driving coalescence.

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High density genome scan for selection signatures in French sheep reveals allelic heterogeneity and introgression at adaptive loci

10.1101/103010 ◽

2017 ◽

Cited By ~ 4

Author(s):

Christina Marie Rochus ◽

Flavie Tortereau ◽

Florence Plisson-Petit ◽

Gwendal Restoux ◽

Carole Moreno ◽

...

Keyword(s):

Environmental Conditions ◽

Evolutionary History ◽

Coat Colour ◽

Phenotypic Trait ◽

Southern Population ◽

Selection Signatures ◽

Adaptive Mutations ◽

Livestock Species ◽

History Of ◽

Genomic Regions

AbstractSheep was one of the first domesticated livestock species in the Anatolia region of contemporary Iran and eventually spread world-wide. Previous studies have shown that French sheep populations likely harbour a large part of European domesticated sheep diversity in a relatively small geographical region, offering a powerful model for the study of adaptation. We studied the diversity of 27 French sheep populations by genotyping 542 individuals for more than 500 000 SNPs. We found that French sheep breeds were divided into two main groups, corresponding to northern and southern origins and additionally we identified admixture events between northern and southern populations. The genetic diversity of domesticated animals results from adaptation of populations to constraints imposed by farmers and environmental conditions. We identified 126 genomic regions likely affected by selection. In many cases, we found evidence for parallel selection events in different genetic backgrounds, most likely for different mutations. Some of these regions harbour genes potentially involved in morphological traits (SOCS2, NCAPG/LCORL, MSRB3), coat colour (MC1R) and adaptation to environmental conditions (ADAMTS9). Closer inspection of two of these regions clarified their evolutionary history: at the LCORL/NCAPG locus we found evidence for introgression of an adaptive allele from a southern population into northern populations and by resequencing MC1R in some breeds we confirmed different mutations in this gene are responsible for the same phenotypic trait. Our study illustrates how dense genetic data in multiple populations allows the deciphering of evolutionary history of populations and of their adaptive mutations.

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Diversity patterns of subterranean invertebrate fauna in calcretes of the Yilgarn Region, Western Australia

Marine and Freshwater Research ◽

10.1071/mf17005 ◽

2018 ◽

Vol 69 (1) ◽

pp. 114 ◽

Cited By ~ 4

Author(s):

Josephine Hyde ◽

Steven J. B. Cooper ◽

William F. Humphreys ◽

Andrew D. Austin ◽

Pablo Munguia

Keyword(s):

Western Australia ◽

Evolutionary History ◽

Taxon Richness ◽

Abundance Distribution ◽

Internal Factors ◽

Rainfall Events ◽

Diversity Patterns ◽

History Of ◽

Episodic Fluctuations ◽

Number Of Individuals

Calcrete aquifers are unique groundwater habitats containing stygobiontic species endemic to each calcrete. The evolutionary history of stygofauna suggests the calcretes in Western Australia contain multiple ancient lineages, yet populations experience episodic variation in rainfall patterns, with little-known ecological consequences. The aim of the present study was to document stygofaunal diversity patterns and determine whether they are influenced by rainfall events. The average taxon richness in boreholes peaked shortly after periods of high rainfall, and when dominant taxa were excluded, evenness decreased after periods of both high and low rainfall, indicating that dominant taxa are an important factor in driving the system. Strong abundance–distribution relationships reflected the commonality of taxon groups; common taxon groups had broad distributions and high abundance levels, whereas rare taxon groups had small distributions and low abundance. After periods of intermediate and low rainfall, taxon groups had narrower distributions and the maximum number of individuals per borehole was lower. Finally, the majority of boreholes did not show changes in evenness over the 11-year study period, suggesting a reasonably stable ecosystem with episodic fluctuations that can be attributed to rainfall events. The results of the present study indicate that diversity patterns within boreholes are driven episodically by both external and internal factors, such as rainfall and rapid borehole dominance respectively.

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