Ghost Lineages Highly Influence the Interpretation of Introgression Tests

Tricou, Théo; Tannier, Éric; Vienne, Damien M. de

doi:10.1093/sysbio/syac011

Cited by 63 publications

(74 citation statements)

References 71 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…A number of authors have discussed the impact of ghost species on detection of between-species gene flow ( Beerli 2004 ; Ottenburghs 2020 ). Tricou et al (2022) used simulations to demonstrate that D -statistics can be misled to detect false signals of introgression when the model involved an unsampled (ghost) species. In our simulations, the impact of ghost species on Bayesian estimation of introgression rate and time was minor provided we considered the rate of gene flow in the migration and introgression models to reflect both indirect gene flow via intermediate species and direct gene flow.…”

Section: Discussionmentioning

confidence: 99%

“…Alternatively, introgression may involve species that have since gone extinct or are not included in the data sample. The presence of such ghost species is known to mislead inference of the history of gene flow for the sampled species ( Beerli 2004 ; Tricou et al 2022 ). Thus we conducted simulation to examine the impact of unsampled species on the inference of gene flow.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Inference of Gene Flow between Species under Misspecified Models

Huang

Thawornwattana

Flouri

et al. 2022

Molecular Biology and Evolution

View full text Add to dashboard Cite

Genomic sequence data provide a rich source of information about the history of species divergence and interspecific hybridization or introgression. Despite recent advances in genomics and statistical methods, it remains challenging to infer gene flow, and as a result, one may have to estimate introgression rates and times under misspecified models. Here we use mathematical analysis and computer simulation to examine estimation bias and issues of interpretation when the model of gene flow is misspecified in analysis of genomic datasets, for example, if introgression is assigned to the wrong lineages. In the case of two species, we establish a correspondence between the migration rate in the continuous migration model and the introgression probability in the introgression model. When gene flow occurs continuously through time but in the analysis is assumed to occur at a fixed time point, common evolutionary parameters such as species divergence times are surprisingly well estimated. However, the time of introgression tends to be estimated towards the recent end of the period of continuous gene flow. When introgression events are assigned incorrectly to the parental or daughter lineages, introgression times tend to collapse onto species divergence times, with introgression probabilities underestimated. Overall, our analyses suggest that the simple introgression model is useful for extracting information concerning between-specific gene flow and divergence even when the model may be misspecified. However, for reliable inference of gene flow it is important to include multiple samples per species, in particular, from hybridizing species.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Inference of Gene Flow between Species under Misspecified Models

Huang

Thawornwattana

Flouri

et al. 2022

Molecular Biology and Evolution

View full text Add to dashboard Cite

show abstract

“…The past introgression between C. robusta and C. intestinalis is puzzling given natural transoceanic migration was impossible during glacial periods. The signal of introgression we detected might come from a ghost (extinct or unsampled) lineage (Tricou et al 2022) related to C. robusta that colonized the Altlantic at the previous interglacial and came into contact with C. intestinalis during the last glacial maximum. Indeed cryptic lineages are often found in the genus Ciona (Zhan et al 2010;Mastrototaro et al 2020) that may prove better candidates for a 30 Ky old introgression event.…”

Section: Introgression Between Highly Divergent Sea Squirt Genomesmentioning

confidence: 91%

Introgression between highly divergent sea squirt genomes: an adaptive breakthrough?

Fraïssé¹,

Moan²,

Roux³

et al. 2022

Peer Community Journal

View full text Add to dashboard Cite

Human-mediated introductions are reshuffling species distribution on a global scale. Consequently, an increasing number of allopatric taxa are now brought into contact, promoting introgressive hybridization between incompletely isolated species and new adaptive gene transfer. The broadcast spawning marine species, Ciona robusta, has been recently introduced in the native range of its sister taxa, Ciona intestinalis, in the English Channel and North-East Atlantic. These sea squirts are highly divergent, yet hybridization has been reported by crossing experiments and genetic studies in the wild. Here, we examined the consequences of secondary contact between C. intestinalis and C. robusta in the English Channel. We produced genomes phased by transmission to infer the history of divergence and gene flow, and analyzed introgressed genomic tracts. Demographic inference revealed a history of secondary contact with a low overall rate of introgression. Introgressed tracts were short, segregating at low frequency, and scattered throughout the genome, suggesting traces of past contacts during the last 30 ky. However, we also uncovered a hotspot of introgression on chromosome 5, characterized by several hundred kb-long C. robusta haplotypes segregating in C. intestinalis, that introgressed during contemporary times the last 75 years. Although locally more frequent than the baseline level of introgression, C. robusta alleles are not fixed, even in the core region of the introgression hotspot. Still, linkage-disequilibrium patterns and haplotype-based tests suggest this genomic region is under recent positive selection. We further detected in the hotspot an over-representation of candidate SNPs lying on a cytochrome P450 gene with a high copy number of tandem repeats in the introgressed alleles. Cytochromes P450 are a superfamily of enzymes involved in detoxifying exogenous compounds, constituting a promising avenue for functional studies. These findings support that introgression of an adaptive allele is possible between very divergent genomes and that anthropogenic hybridization can provide the raw material for adaptation of native lineages in the Anthropocene.

show abstract

“…Other assumptions of the D -statistic include infinite sites (no saturation of bases), no ancestral population structure, a single historical introgression event under the alternative hypothesis, no introgression between the outgroup and ingroups, and that all introgressed taxa are sampled. This last assumption has been the focus of a recent study where “ghost” lineages (unsampled or extinct populations) can result in incorrect interpretations of donors and recipients of gene flow [Tricou et al, 2022a].…”

Section: Introductionmentioning

confidence: 99%

Summary tests of introgression are highly sensitive to rate variation across lineages

Frankel

Ané

2023

Preprint

View full text Add to dashboard Cite

The evolutionary implications and frequency of hybridization and introgression are increasingly being recognized across the tree of life. To detect hybridization from multi-locus and genome-wide sequence data, a popular class of methods are based on summary statistics from subsets of 3 or 4 taxa. However, these methods often carry the assumption of a constant substitution rate across lineages and genes, which is commonly broken in many groups. In this work, we quantify the effects of rate variation on theD-statistic (also known as ABBA-BABA test), theD3statistic, and HyDe. All three tests are used widely across a range of taxonomic groups, in part because they are very fast to compute. We consider rate variation across species lineages, across genes, their lineage-by-gene interaction, and rate variation across gene-tree edges. We simulated species networks according to a birth-death-hybridization process so as to capture a range of realistic species phylogenies. For all three methods tested, we found a marked increase in the false discovery of reticulation (type-1 error rate) when there is rate variation across species lineages. TheD3statistic was the most sensitive, with around 80% type-1 error, such thatD3appears to more sensitive to a departure from the clock than to the presence of reticulation. For all three tests, the power to detect hybridization events decreased as the number of hybridization events increased, indicating that multiple hybridization events can "hide" one another if they occur within a small subset of taxa. Our study highlights the need to consider rate variation when using site-based summary statistics, and points to the advantages of methods that do not require assumptions on evolutionary rates across lineages or across genes.

show abstract

Ghost Lineages Highly Influence the Interpretation of Introgression Tests

Cited by 63 publications

References 71 publications

Inference of Gene Flow between Species under Misspecified Models

Inference of Gene Flow between Species under Misspecified Models

Introgression between highly divergent sea squirt genomes: an adaptive breakthrough?

Summary tests of introgression are highly sensitive to rate variation across lineages

Contact Info

Product

Resources

About