Mitonuclear co-introgression opposes genetic differentiation between phenotypically divergent songbirds

Comparisons of genomic variation among closely related species often show more differentiation in mitochondrial DNA (mtDNA) and sex chromosomes than in autosomes, a pattern expected due to the relative effective population sizes of these genomic components. Differential introgression can cause some species pairs to deviate dramatically from this pattern. The yellowhammer (Emberiza citrinella) and the pine bunting (E. leucocephalos) are hybridizing avian sister species that differ greatly in appearance but show no mtDNA differentiation. This discordance might be explained by mtDNA introgression-a process that can select for co-introgression at nuclear genes with mitochondrial functions (mitonuclear genes). We investigated genome-wide nuclear differentiation between yellowhammers and pine buntings and compared it to what was seen previously in the mitochondrial genome. We found clear nuclear differentiation that was highly heterogeneous across the genome, with a particularly wide differentiation peak on the sex chromosome Z. We further tested for preferential introgression of mitonuclear genes and detected evidence for such biased introgression in yellowhammers. Mitonuclear co-introgression can remove post-zygotic incompatibilities between species and may contribute to the continued hybridization between yellowhammers and pine buntings despite their clear morphological and genetic differences. As such, our results highlight the potential ramifications of co-introgression in species evolution.

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Evaluation of Four Methods to Identify the Homozygotic Sex Chromosome in Small Populations

10.21203/rs.3.rs-892602/v1 ◽

2021 ◽

Author(s):

Charles Christian Riis Hansen ◽

Kristen M. Westfall ◽

Snaebjörn Pálsson

Keyword(s):

Sex Chromosomes ◽

Sex Chromosome ◽

Read Depth ◽

Mapping Method ◽

Small Population ◽

Genomic Variation ◽

Z Chromosome ◽

Effective Population ◽

Organelle Genomes ◽

Heterogametic Sex

Abstract BackgroundWhole genomes are commonly assembled into a collection of scaffolds and often lack annotations of autosomes, sex chromosomes, and organelle genomes (i.e., mitochondrial and chloroplast). As these chromosome types differ in effective population size and can have highly disparate evolutionary histories, it is imperative to take this information into account when analysing genomic variation. Here we assessed the accuracy of four methods for identifying the homogametic sex chromosome in a small population using two whole genome sequences (WGS) and 133 RAD sequences of white-tailed eagles (Haliaeetus albicilla): i) difference in read depth per scaffold in a male and a female, ii) heterozygosity per scaffold in a male and a female, iii) mapping to a reference genome of a related species (chicken) with identified sex chromosomes, and iv) analysis of SNP-loadings from a principal components analysis (PCA), based on the low-depth RADseq data. ResultsThe best performing approach was the reference mapping (method iii), which identified 98.12% of the expected homogametic sex chromosome (Z). The read depth per scaffold (method i) identified 86.41% of the homogametic sex chromosome with few false positives. The SNP-loading scores (method iv) found 78.6% of the Z-chromosome and had a false positive discovery rate of more than 10%. The heterozygosity per scaffold (method ii) did not provide clear results due to a lack of diversity in both the Z and autosomal chromosomes, and potential interference from the heterogametic sex chromosome (W). The evaluation of these methods also revealed 10 Mb of likely PAR and gametologous regions.ConclusionIdentification of the homogametic sex chromosome in a small population is best accomplished by reference mapping or examining read depth differences between sexes.

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Ongoing production of low-fitness hybrids limits range overlap between divergent cryptic species

10.1101/2021.02.09.430089 ◽

2021 ◽

Author(s):

Else K. Mikkelsen ◽

Darren Irwin

Keyword(s):

First Generation ◽

Sex Chromosome ◽

Genomic Variation ◽

F1 Hybrids ◽

The Pacific ◽

Species Pairs ◽

Genetic Clusters ◽

Range Overlap ◽

Female Specific

AbstractContact zones between recently-diverged taxa provide opportunities to examine the causes of reproductive isolation and to examine the processes that determine whether two species can coexist over a broad region. The Pacific Wren (Troglodytes pacificus) and the Winter Wren (Troglodytes hiemalis) are two morphologically similar songbird species that started diverging about 4 million years ago, older than most sister species pairs. The ranges of these species come into narrow contact in western Canada, where the two species remain distinct in sympatry. To assess evidence for differentiation, hybridization, and introgression in this system, we examined variation in over 250,000 single nucleotide polymorphism markers distributed across the genomes of the two species. The two species formed highly divergent genetic clusters, consistent with long-term differentiation. In a set of 75 individuals from allopatry and sympatry, two first-generation hybrids (i.e., F1’s) were detected, indicating only moderate levels of assortative mating between these taxa. We found no recent backcrosses or F2’s or other evidence of recent breeding success of F1 hybrids, indicating very low or zero fitness of F1 hybrids. Examination of genomic variation shows evidence for only a single backcrossing event in the distant past. The sizeable rate of hybridization combined with very low fitness of F1 hybrids is expected to result in a population sink in the contact zone, largely explaining the narrow overlap of the two species. If such dynamics are common in nature, they could explain the narrow range overlap often observed between pairs of closely related species. Additionally, we present evidence for a rare duplication of a large chromosomal segment from an autosome to the W chromosome, the female-specific sex chromosome in birds.

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The formation of avian montane diversity across barriers and along elevational gradients

Nature Communications ◽

10.1038/s41467-021-27858-5 ◽

2022 ◽

Vol 13 (1) ◽

Author(s):

José Martín Pujolar ◽

Mozes P. K. Blom ◽

Andrew Hart Reeve ◽

Jonathan D. Kennedy ◽

Petter Zahl Marki ◽

...

Keyword(s):

Gene Flow ◽

Population Differentiation ◽

Bird Species ◽

Geographic Area ◽

Effective Population ◽

Tropical Mountains ◽

Mountainous Regions ◽

Pleistocene Climate ◽

Genome Wide ◽

Population Sizes

AbstractTropical mountains harbor exceptional concentrations of Earth’s biodiversity. In topographically complex landscapes, montane species typically inhabit multiple mountainous regions, but are absent in intervening lowland environments. Here we report a comparative analysis of genome-wide DNA polymorphism data for population pairs from eighteen Indo-Pacific bird species from the Moluccan islands of Buru and Seram and from across the island of New Guinea. We test how barrier strength and relative elevational distribution predict population differentiation, rates of historical gene flow, and changes in effective population sizes through time. We find population differentiation to be consistently and positively correlated with barrier strength and a species’ altitudinal floor. Additionally, we find that Pleistocene climate oscillations have had a dramatic influence on the demographics of all species but were most pronounced in regions of smaller geographic area. Surprisingly, even the most divergent taxon pairs at the highest elevations experience gene flow across barriers, implying that dispersal between montane regions is important for the formation of montane assemblages.

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Evaluation of Linkage Disequilibrium, Effective Population Size and Haplotype Block Structure in Chinese Cattle

Animals ◽

10.3390/ani9030083 ◽

2019 ◽

Vol 9 (3) ◽

pp. 83 ◽

Cited By ~ 6

Author(s):

Lei Xu ◽

Bo Zhu ◽

Zezhao Wang ◽

Ling Xu ◽

Ying Liu ◽

...

Keyword(s):

Linkage Disequilibrium ◽

Genomic Selection ◽

Haplotype Block ◽

Block Structure ◽

Effective Population ◽

Chinese Cattle ◽

Genome Wide ◽

Population Sizes ◽

Haplotype Block Structure ◽

Selection For

Understanding the linkage disequilibrium (LD) across the genome, haplotype structure, and persistence of phase between breeds can enable us to appropriately design and implement the genome-wide association (GWAS) and genomic selection (GS) in beef cattle. We estimated the extent of genome-wide LD, haplotype block structure, and the persistence of phase in 10 Chinese cattle population using high density BovinHD BeadChip. The overall LD measured by r2 between adjacent SNPs were 0.60, 0.67, 0.58, 0.73, and 0.71 for South Chinese cattle (SCHC), North Chinese cattle (NCC), Southwest Chinese cattle (SWC), Simmental (SIM), and Wagyu (WAG). The highest correlation (0.53) for persistence of phase across groups was observed for SCHC vs. SWC at distances of 0–50 kb, while the lowest correlation was 0.13 for SIM vs. SCHC at the same distances. In addition, the estimated current effective population sizes were 27, 14, 31, 34, and 43 for SCHC, NCC, SWC, SIM, and WAG, respectively. Our result showed that 58K, 87K, 95K, 52K, and 52K markers were required for implementation of GWAS and GS in SCHC, NCC, SWC, SIM, and WAG, respectively. Also, our findings suggested that the implication of genomic selection for multipopulation with high persistence of phase is feasible for Chinese cattle.

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Genome-Wide Linkage Disequilibrium and the Extent of Effective Population Sizes in Six Chinese Goat Populations Using a 50K Single Nucleotide Polymorphism Panel

Animals ◽

10.3390/ani9060350 ◽

2019 ◽

Vol 9 (6) ◽

pp. 350 ◽

Cited By ~ 4

Author(s):

Haile Berihulay ◽

Rabiul Islam ◽

Lin Jiang ◽

Yuehui Ma

Keyword(s):

Linkage Disequilibrium ◽

Genetic Parameter ◽

Genetic Selection ◽

Chromosome 1 ◽

Effective Population ◽

Genome Wide ◽

Population Sizes ◽

Trait Locus ◽

D Values ◽

Genome Wide Linkage Disequilibrium

Genome-wide linkage disequilibrium is a useful parameter to study quantitative trait locus (QTL) mapping and genetic selection. In many genomic methodologies, effective population size is an important genetic parameter because of its relationship to the loss of genetic variation, increases in inbreeding, the accumulation of mutations, and the effectiveness of selection. In this study, a total of 193 individuals were genotyped to assess the extent of LD and Ne in six Chinese goat populations using the SNP 50K BeadChip. Across the determined autosomal chromosomes, we found an average of 0.02 and 0.23 for r2 and D’ values, respectively. The average r2 between all the populations varied little and ranged from 0.055 r2 for the Jining Grey to 0.128 r2 for the Guangfeng, with an overall mean of 0.083. Across the 29 autosomal chromosomes, minor allele frequency (MAF) was highest on chromosome 1 (0.321) and lowest on chromosome 25 (0.309), with an average MAF of 0.317, and showing the lowest (25.5% for Louping) and highest (28.8% for Qingeda) SNP proportions at MAF values > 0.3. The inbreeding coefficient ranged from 0.064 to 0.085, with a mean of 0.075 for all the autosomes. The Jining Grey and Qingeda populations showed higher Ne estimates, highlighting that these animals could have been influenced by artificial selection. Furthermore, a declining recent Ne was distinguished for the Arbas Cashmere and Guangfeng populations, and their estimated values were closer to 64 and 95, respectively, 13 generations ago, which indicates that these breeds were exposed to strong selection. This study provides an insight into valuable genetic information and will open up the opportunity for further genomic selection analysis of Chinese goat populations.

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Modeling the Multiple Facets of Speciation-with-Gene-Flow Towards Inferring the Divergence History of Lake Whitefish Species Pairs (Coregonus Clupeaformis)

10.1101/068932 ◽

2016 ◽

Cited By ~ 4

Author(s):

Clément Rougeux ◽

Louis Bernatchez ◽

Pierre-Alexandre Gagnaire

Keyword(s):

Gene Flow ◽

Genomic Variation ◽

Secondary Contact ◽

Lake Whitefish ◽

Lineage Sorting ◽

Effective Population ◽

Modeling Framework ◽

Species Pairs ◽

History Of ◽

And Migration

AbstractParallel divergence patterns across replicated species pairs occurring in similar environmental contrasts may arise through distinct evolutionary scenarios. Deciphering whether such parallelism actually reflects repeated parallel divergence driven by divergent selection or a single divergence event with subsequent gene flow needs to be ascertained. Reconstructing historical gene flow is therefore of fundamental interest to understand how demography and selection jointly shaped genomic divergence during speciation. Here, we use an extended modeling framework to explore the multiple facets of speciation-with-gene-flow with demo-genetic divergence models that capture both temporal and genomic variation in effective population size and migration rate. We investigate the divergence history of five sympatric Lake Whitefish limnetic (dwarf) and benthic (normal) species pairs characterized by variable degrees of ecological divergence and reproductive isolation. Genome-wide SNPs were used to document the extent of genetic differentiation in each species pair, and 26 divergence models were fitted and compared to the unfolded joint allele frequency spectrum of each pair. We found evidence that a recent (circa 3000-4000 generations) asymmetrical secondary contact between expanding post-glacial populations has accompanied Whitefish diversification. Our results suggest that heterogeneous genomic differentiation patterns have emerged through the combined effects of linked selection generating variable rates of lineage sorting across the genome during geographical isolation, and heterogeneous introgression eroding divergence at different rates across the genome upon secondary contact. This study thus provides a new retrospective insight into the historical demographic and selective processes that shaped a continuum of divergence associated with ecological speciation.

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Adaptation in outbred sexual yeast is repeatable, polygenic, and favors rare haplotypes

10.1101/2021.08.27.457900 ◽

2021 ◽

Cited By ~ 1

Author(s):

Robert A. Linder ◽

Behzad Zabanavar ◽

Arundhati Majumder ◽

Hannah Chiao-Shyan Hoang ◽

Vanessa Genesaret Delgado ◽

...

Keyword(s):

Rare Variants ◽

Intermediate Frequency ◽

Effective Population ◽

Entire Genome ◽

Frequency Shifts ◽

Haplotype Blocks ◽

Genome Wide ◽

Population Sizes ◽

Drug Treatments ◽

Per Gene

AbstractWe describe the results of a 200 generation Evolve and Resequence (E&R) study initiated from an outbred dipliod recombined synthetic base population derived from 18 genetically diverse founders. Replicate populations were maintained at large effective population sizes (>105 individuals), exposed to several different chemical challenges over 12 weeks of evolution, and whole-genome resequenced. Weekly forced outcrossing implies a per gene per cell-division recombination rate higher than that achieved in Drosophila E&R studies. In 55 sexual populations we observe large fitness gains and highly repeatable patterns of genome-wide haplotype change within each chemical challenge. There was little evidence for pervasive pleiotropy, as evidenced by patterns of haplotype change between drug treatments. Within treatment adaptation appears highly polygenic with almost the entire genome showing significant consistent haplotype change. Finally, adaptation was almost always associated with only one of the 18 founder alleles, suggesting selection primarily acts on rare variants private to a founder or haplotype blocks harboring multiple mutations. This observation contradicts the notion that adaptation is often due to subtle frequency shifts at intermediate frequency variants.

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Dissecting the Effects of Selection and Mutation on Genetic Diversity in Three Wood White (Leptidea) Butterfly Species

Genome Biology and Evolution ◽

10.1093/gbe/evz212 ◽

2019 ◽

Vol 11 (10) ◽

pp. 2875-2886 ◽

Cited By ~ 1

Author(s):

Venkat Talla ◽

Lucile Soler ◽

Takeshi Kawakami ◽

Vlad Dincă ◽

Roger Vila ◽

...

Keyword(s):

Genetic Diversity ◽

Natural Selection ◽

Nucleotide Diversity ◽

Gene Annotation ◽

Rate Variation ◽

Butterfly Species ◽

Relative Role ◽

Effective Population ◽

Genome Wide ◽

Population Sizes

Abstract The relative role of natural selection and genetic drift in evolution is a major topic of debate in evolutionary biology. Most knowledge spring from a small group of organisms and originate from before it was possible to generate genome-wide data on genetic variation. Hence, it is necessary to extend to a larger number of taxonomic groups, descriptive and hypothesis-based research aiming at understanding the proximate and ultimate mechanisms underlying both levels of genetic polymorphism and the efficiency of natural selection. In this study, we used data from 60 whole-genome resequenced individuals of three cryptic butterfly species (Leptidea sp.), together with novel gene annotation information and population recombination data. We characterized the overall prevalence of natural selection and investigated the effects of mutation and linked selection on regional variation in nucleotide diversity. Our analyses showed that genome-wide diversity and rate of adaptive substitutions were comparatively low, whereas nonsynonymous to synonymous polymorphism and substitution levels were comparatively high in Leptidea, suggesting small long-term effective population sizes. Still, negative selection on linked sites (background selection) has resulted in reduced nucleotide diversity in regions with relatively high gene density and low recombination rate. We also found a significant effect of mutation rate variation on levels of polymorphism. Finally, there were considerable population differences in levels of genetic diversity and pervasiveness of selection against slightly deleterious alleles, in line with expectations from differences in estimated effective population sizes.

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Exploring the Legacy of Central European Historical Winter Wheat Landraces

10.21203/rs.3.rs-637988/v1 ◽

2021 ◽

Author(s):

András Cseh ◽

Péter Poczai ◽

Tibor Kiss ◽

Krisztina Balla ◽

Zita Berki ◽

...

Keyword(s):

Genetic Diversity ◽

Genome Wide Association Study ◽

Snp Array ◽

Genetic Erosion ◽

Effective Population ◽

Low Frequencies ◽

Central European ◽

Genome Wide ◽

Population Sizes ◽

Wheat Landraces

Abstract Historical wheat landraces are rich sources of genetic diversity offering untapped reservoirs for broadening the genetic base of modern varieties. Using a 20K SNP array, we investigated the accessible genetic diversity in a Central European bread wheat landrace collection with great drought, heat stress tolerance and higher tillering capacity. We discovered distinct differences in the number of average polymorphisms between Central and Western European collections, and identified a set of novel rare alleles present at low frequencies in the historical collection. The detected polymorphisms were unevenly distributed along the wheat genome, and polymorphic markers co-localized with genes of great agronomic importance. The efficiency of the highly diverse population for Genome-Wide Association study was confirmed and two significant marker trait associations with seed hardness were identified on the 5DS chromosome arm. The geographical distribution of the inferred Bayesian clustering revealed six genetically homogenous ancestral groups among the collection, where the Central European core bared an admixed background originating from four ancestral groups. We evaluated the effective population sizes (Ne) of the Central European collection and assessed changes in diversity over time, which revealed a dramatic ~97% genetic erosion between 1955 and 2015.

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Conserved genomic landscapes of differentiation across Populus speciation continuum

10.1101/2021.08.26.457771 ◽

2021 ◽

Author(s):

Huiying Shang ◽

Martha Rendón-Anaya ◽

Ovidiu Paun ◽

David L Field ◽

Jaqueline Hess ◽

...

Keyword(s):

Substantial Contribution ◽

Species Variation ◽

Effective Population ◽

Species Pairs ◽

Population Sizes ◽

Speciation Continuum ◽

Positive Correlations ◽

Multiple Species ◽

Demographic Trajectories ◽

Species Specific

AbstractInvestigating genome-wide variation patterns along a speciation continuum is of central importance to understand the evolutionary processes contributing to lineage diversification. To identify which forces have shaped the genomic landscapes in Populus, we resequenced 201 whole-genomes from eight closely related species, with pairs of species at different stages along the speciation continuum. Using population structure and identity by descent analyses, we show extensive introgression between some species pairs, especially those with parapatric distributions. Inference of historical changes in effective population sizes support species-specific demographic trajectories, including recent population expansions in species characterized by broad present-day distributions. We observe highly conserved genomic landscapes, either focusing on within-species (genetic diversity: π and recombination rate: ρ) or among-species variation (relative divergence: FST and absolute divergence: DXY). Independent of the stage across the divergence continuum, we recovered positive correlations between the pair π and ρ and the pair DXY and ρ across all species pairs, which is consistent with a substantial contribution of linked selection in shaping these genomic landscapes. However, the positive correlations between π and DXY became weaker as the overall divergence level (da) increased, suggesting that background selection is not the only factor at play. Positive correlations between FST and DXY in all species pairs, regardless of the rate of gene flow, also indicates the high FST could be due to divergent sorting of ancient polymorphism before speciation. Our study showcases the importance of investigating genomic patterns on multiple species across the speciation continuum to better understand the genomic landscapes of diversity and differentiation.

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