Genomic investigation refutes record of most diverged avian hybrid

Alfieri, James M.; Johnson, Taryn; Linderholm, Anna; Blackmon, Heath; Athrey, Giridhar

doi:10.1002/ece3.9689

Cited by 2 publications

(4 citation statements)

References 39 publications

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“…The range of parameters used in our simulations was selected to be comparable with some of the study systems to which we referred in the Introduction as cases of highly divergent hybridizing lineages. In terms of numbers of generations, recombination rate, and mutation rate, our simulations are comparable to the interfamilial hybridization events between helmeted guineafowl N. meleagris and chicken G. gallus (Alfieri et al, 2023). The divergence of these two lineages can be placed around 30 million generations ago, assuming a generation time of 1 year (Mariadassou et al, 2021;Sanchez-Donoso et al, 2014) and a divergence about 30 million years ago (Prum et al, 2015).…”

Section: Simulationsmentioning

confidence: 53%

“…3 fowl hybrids are crosses between helmeted guineafowl Numida meleagris and chicken G. gallus, two species from the families Numididae and Phasanidae that diverged about 30 million years ago (Prum et al, 2015). Putative hybrids between those two taxa have been recorded already since the 1930s (Ghigi, 1936) and an F1-hybrid was recently identified genetically (Alfieri et al, 2023).…”

Section: Rate Variation Produces False Signals Of Introgressionmentioning

confidence: 99%

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Towards reliable detection of introgression in the presence of among-species rate variation

Koppetsch

Malinsky

Matschiner

2023

Preprint

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The role of interspecific hybridization in the context of diversification dynamics has recently seen increasing attention. Genomic research has now made it abundantly clear that both hybridization and introgression - the exchange of genetic material through hybridization - are far more common than previously thought. Moreover, even highly divergent species were found to hybridize and backcross. These findings raise the question whether commonly used methods for the detection of introgression are applicable to such divergent hybridizing species, given that most of these methods were originally developed for analyses at the level of populations and recently diverged species. In particular, the assumption of constant evolutionary rates, which is implicit in many commonly used approaches, is more likely to be violated as evolutionary divergence increases. To test the limitations of introgression detection methods when being applied to divergent species, we simulated thousands of genomic datasets under a wide range of settings, with varying degrees of among-species rate variation and introgression. Using these simulated datasets, we were able to show that commonly applied statistical methods, including the D-statistic and tests based on sets of phylogenetic trees, produce false-positive signals of introgression between highly divergent taxa when these have different rates of evolution. These misleading signals are caused by the presence of homoplasies that occur at different rates when rate variation is present. To distinguish between the patterns caused by rate variation and genuine introgression, we developed a new test that is based on the expected clustering of introgressed sites and implemented this test in the program Dsuite.

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Section: Simulationsmentioning

confidence: 53%

Section: Rate Variation Produces False Signals Of Introgressionmentioning

confidence: 99%

Towards reliable detection of introgression in the presence of among-species rate variation

Koppetsch

Malinsky

Matschiner

2023

Preprint

View full text Add to dashboard Cite

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“…Additionally, we performed forward and backward literature searches for references within the Handbook of Avian Hybrids of the World ( McCarthy 2006 ) and Bird Hybrids: A Checklist with Bibliography ( Gray 1958 ). We attempted to access the original reports within these databases to confirm the accuracy of the information regarding the referenced cross, as Gray has been noted to include dubious crosses ( Wu and Davis 1993 ; Alfieri et al 2023 ). When present, we recorded F1 fertility information (sterile, only males fertile, and both sexes fertile).…”

Section: Methodsmentioning

confidence: 99%

“…For example, while the most diverged species pair that can still hybridize and result in viable offspring in mammals is Camelus dromedarius (dromedary camel) and Lama guanicoe (guanaco) (~20 MY), in fish, it is Acipenser gueldenstaedtii (Russian sturgeon) and Polyodon spathula (American paddlefish) (~150 MY). In birds, the most diverged hybrid is between Numida meleagris (Helmeted guineafowl) and Gallus gallus (chicken) (51 to 65 MY) ( Alfieri et al 2023 ). To our knowledge, in plants, the most diverged hybrid is between Gymnocarpium sp.…”

Section: Introductionmentioning

confidence: 99%

Domestication is associated with increased interspecific hybrid compatibility in landfowl (order: Galliformes)

Alfieri,

Hingoranee,

Athrey

et al. 2023

Journal of Heredity

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Some species are able to hybridize despite being exceptionally diverged. The causes of this variation in accumulation of reproductive isolation remain poorly understood, and domestication as an impetus or hindrance to reproductive isolation remains to be characterized. In this study, we investigated the role of divergence time, domestication, and mismatches in morphology, habitat, and clutch size among hybridizing species on reproductive isolation in the bird order Galliformes. We compiled and analyzed hybridization occurrences from literature and recorded measures of postzygotic reproductive isolation. We used a text-mining approach leveraging a historical aviculture magazine to quantify the degree of domestication across species. We obtained divergence time, morphology, habitat, and clutch size data from open sources. We found 123 species pairs (involving 77 species) with known offspring fertility (sterile, only males fertile, or both sexes fertile). We found that divergence time and clutch size were significant predictors of reproductive isolation (McFadden's Pseudo-R 2 = 0.59), but not habitat or morphological mismatch. Perhaps most interesting, we found a significant relationship between domestication and reproductive compatibility after correcting for phylogeny, removing extreme values, and addressing potential biases (F1,74 = 5.43, R 2 = 0.06, p-value = 0.02). We speculate that the genetic architecture and disruption in selective reproductive regimes associated with domestication may impact reproductive isolation, causing domesticated species to be more reproductively labile.

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Genomic investigation refutes record of most diverged avian hybrid

Abstract: Hybridization between species is an important evolutionary event that generates genomic and phenotypic diversity and affects speciation (Moran et al., 2021). Most contemporary hybridization records rely on phenotypic observations, which can be controversial

Cited by 2 publications

References 39 publications

Towards reliable detection of introgression in the presence of among-species rate variation

Towards reliable detection of introgression in the presence of among-species rate variation

Domestication is associated with increased interspecific hybrid compatibility in landfowl (order: Galliformes)

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