Detection of Ghost Introgression Requires Exploiting Topological and Branch Length Information

Systematic Biology, Journal Year: 2024, Volume and Issue: 73(1), P. 207 - 222

Published: Jan. 1, 2024

Abstract In recent years, the study of hybridization and introgression has made significant progress, with ghost introgression—the transfer genetic material from extinct or unsampled lineages to extant species—emerging as a key area for research. Accurately identifying introgression, however, presents challenge. To address this issue, we focused on simple cases involving 3 species known phylogenetic tree. Using mathematical analyses simulations, evaluated performance popular methods, including HyDe PhyloNet/MPL, full-likelihood method, Bayesian Phylogenetics Phylogeography (BPP), in detecting introgression. Our findings suggest that heuristic approaches relying site-pattern counts gene-tree topologies struggle differentiate between sampled non-sister species, frequently leading incorrect identification donor recipient species. The method BPP uses multilocus sequence alignments directly—hence taking into account both branch lengths, by contrast, is capable phylogenomic datasets. We analyzed real-world dataset 14 Jaltomata (Solanaceae) showcase potential methods accurate inference

Language: Английский

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Phylogenomics reveals patterns of ancient hybridization and differential diversification that contribute to phylogenetic conflict in willows, poplars, and close relatives

Systematic Biology, Journal Year: 2023, Volume and Issue: 72(6), P. 1220 - 1232

Published: July 14, 2023

Abstract Despite the economic, ecological, and scientific importance of genera Salix L. (willows) Populus (poplars, cottonwoods, aspens) Salicaceae, we know little about sources differences in species diversity between phylogenetic conflict that often confounds estimating trees. subgenera sections, particular, have been difficult to classify, with one recent attempt termed a “spectacular failure” due speculated radiation Vetrix Chamaetia. Here, use targeted sequence capture understand evolutionary history this portion Salicaceae plant family. Our hypothesis was based on 787 gene regions identified extensive among genes. analysis supported some previously described subgeneric relationships confirmed polyphyly others. Using an fbranch analysis, several cases hybridization deep branches phylogeny, which likely contributed discordance In addition, rapid increase diversification rate near origination Vetrix–Chamaetia clade Salix. This region tree coincided nodes lacked strong statistical support, indicating possible incomplete lineage sorting diversification. The extraordinary level both ancient played important roles these two genera.

Language: Английский

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Efficient Bayesian inference under the multispecies coalescent with migration

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(44)

Published: Oct. 23, 2023

Analyses of genome sequence data have revealed pervasive interspecific gene flow and enriched our understanding the role in speciation adaptation. Inference using genomic requires powerful statistical methods. Yet current likelihood-based methods involve heavy computation are feasible for small datasets only. Here, we implement multispecies-coalescent-with-migration model Bayesian program bpp , which can be used to test estimate migration rates, as well species divergence times population sizes. We develop Markov chain Monte Carlo algorithms efficient sampling from posterior, enabling analysis genome-scale with thousands loci. Implementation both introgression models same allows us whether occurred continuously over time or pulses. Anopheles mosquitoes demonstrate rich information typical about mode rate flow.

Language: Английский

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Interspecific transfer of genetic information through polyploid bridges

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(21)

Published: May 15, 2024

Hybridization blurs species boundaries and leads to intertwined lineages resulting in reticulate evolution. Polyploidy, the outcome of whole genome duplication (WGD), has more recently been implicated promoting facilitating hybridization between polyploid species, potentially leading adaptive introgression. However, because are usually ephemeral states evolutionary history life it is unclear whether WGD-potentiated any appreciable effect on their diploid counterparts. Here, we develop a model cytotype dynamics within mixed-ploidy populations demonstrate that polyploidy can fact serve as bridge for gene flow lineages, where introgression fully or partially hampered by barrier. Polyploid bridges emerge presence triploid organisms, which despite critically low levels fitness, still allow transfer alleles independently evolving species. Notably, while marked genetic divergence prevents polyploid-mediated interspecific flow, show increased recombination rates offset these constraints, allowing efficient sorting at higher-ploidy before into pools. Additionally, derive an analytical approximation rate tetraploid level necessary supersede diploids with nonzero rates, especially relevant plant complexes, ubiquitous. Altogether, our results illustrate potential impact (re)distribution material across ecological communities during evolution, representing force behind reticulation.

Language: Английский

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Uncovering ghost introgression through genomic analysis of a distinct eastern Asian hickory species

The Plant Journal, Journal Year: 2024, Volume and Issue: 119(3), P. 1386 - 1399

Published: June 6, 2024

SUMMARY Ghost introgression, or the transfer of genetic material from extinct unsampled lineages to sampled species, has attracted much attention. However, conclusive evidence for ghost especially in plant remains scarce. Here, we newly assembled chromosome‐level genomes both Carya sinensis and cathayensis , additionally re‐sequenced whole 43 C. individuals as well 11 representing diploid hickory species. These genomic datasets were used investigate reticulation bifurcation patterns within genus (Juglandaceae), with a particular focus on beaked . By combining D ‐statistic BPP methods, obtained compelling that supports occurrence introgression an ancestral lineage. This conclusion was reinforced through phylogenetic network analysis genome scan method VolcanoFinder, latter which can detect signatures adaptive unknown donors. Our results not only dispel certain misconceptions about history but also further refine our understanding 's biogeography via divergence estimates. Moreover, successful integration methods demonstrates their efficacy facilitating more precise identification types.

Language: Английский

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Inferring the Direction of Introgression Using Genomic Sequence Data

Molecular Biology and Evolution, Journal Year: 2023, Volume and Issue: 40(8)

Published: Aug. 1, 2023

Abstract Genomic data are informative about the history of species divergence and interspecific gene flow, including direction, timing, strength flow. However, flow in opposite directions generates similar patterns multilocus sequence data, such as reduced between hybridizing species. As a result, inference direction is challenging. Here, we investigate information present genomic using likelihood-based methods under multispecies-coalescent-with-introgression model. We analyze case two species, use simulation to examine cases with three or four find that it easier infer from small population large one than inflow (gene outgroup an ingroup species) outflow species). It also if there longer time separate evolution initial subsequent introgression. When introgression assumed occur wrong tends be correctly estimated Bayesian test often significant, while estimates probability can even greater true probability. sequences Heliconius butterflies demonstrate typical datasets well its timing strength.

Language: Английский

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Phylogenomics of Psammodynastes and Buhoma (Elapoidea: Serpentes), with the description of a new Asian snake family

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: April 25, 2024

Abstract Asian mock vipers of the genus Psammodynastes and African forest snakes Buhoma are two genera belonging to snake superfamily Elapoidea. The phylogenetic placements within Elapoidea has been extremely unstable which resulted in their uncertain debated taxonomy. We used ultraconserved elements traditional nuclear mitochondrial markers infer relationships these with other elapoids. , for a reference genome sequenced, were found, strong branch support, be relatively early diverging split that is sister clade consisting Elapidae, Micrelapidae Lamprophiidae. Hence, we allocate its own family, Psammodynastidae new family . However, position could not resolved high degree confidence. Attempts identify possible sources conflict rapid radiation elapoid suggest both hybridisation/introgression during diversification, including ghost introgression, as well incomplete lineage sorting likely have had confounding role. usual practice combining loci genomic data appears mislead phylogeny reconstructions scenarios, especially absence scale data.

Language: Английский

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Phylogenomics, historical biogeography, and diversification of leaf traits in the Malagasy‐endemic genus Uncarina (Pedaliaceae)

American Journal of Botany, Journal Year: 2025, Volume and Issue: unknown

Published: April 2, 2025

Uncarina contains 14 species of woody plants endemic to Madagascar. Its occurrence across dryland biomes on the island make it an interesting system study diversification flora. Using samples all and 512 nuclear loci, we reconstructed phylogenetic trees examine relationships assess their monophyly. We also studied historical biogeography genus combined leaf trait data derived from SEM photography trichomes geometric morphometric analysis shape better understand its biomes. is monophyletic, major clades showed a clear biogeographical signal. Leaf traits corroborated among clades. Although most are at least one cryptic exists. Uncarina, like many arid-adapted plant lineages in Madagascar originated Miocene or Pleistocene. Geographic movement has been primarily along south-north axis, with river basins apparently acting as barriers gene flow. The evolution spiny thicket dry forest biome. As Malagasy lemurs other animals, riverine may have involved apply more broadly epizoochorous angiosperms suggest either loss adaptations extremely arid, high irradiance environments release herbivores. likely needed lineages, thorough population-level sampling specimen collecting fully taxonomic morphological diversity genus.

Language: Английский

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Detecting cryptic ghost lineage introgression in four-taxon genomic datasets

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: April 29, 2025

Abstract Premise Hybridization and introgression are pervasive evolutionary forces that have played fundamental roles in shaping the diversity of wild domesticated plants. Four-taxon tests for provide a reliable framework detecting signatures ancient from genomic data, which an important role revealing reticulate nature plant evolution; however, there is emerging evidence cryptic process known as ghost lineage has potential to dramatically skew interpretations four-taxon statistics, particularly our ability determine lineages involved introgression. This ambiguity limits resolve mechanisms functional implications because it means we can neither donor nor recipient introgressed alleles with confidence. Methods Here, develop ghostbuster , statistical test designed detect data based on patterns sequence divergence. We employ coalescent simulations method ascertain conditions under accurately identifies ingroup versus Finally, demonstrate utility apply previously identified event family Brassicaceae. Result Our reveal distinguishes across wide range scenarios, errors arising only when divergence events closely spaced. analysis empirical reveals likely constitutes and, thus, was misinterpreted. Discussion analyses simulated will be helpful tool resolving evolution plants other taxa. biological insights provides by presenting updated model Brassicaceae, impacting understanding molecular crop species this lineage. Ghostbuster code freely available at: https://github.com/EvanForsythe/Ghost_introgression .

Language: Английский

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Evolutionary History and Vocal Differentiation in Two Cryptic Neotropical Suboscines (Pseudocolopteryx citreola and P. flaviventris)

Zoologica Scripta, Journal Year: 2025, Volume and Issue: unknown

Published: May 24, 2025

ABSTRACT The speciose family Tyrannidae harbours numerous morphologically cryptic species that differ most notably in their innate vocalisations. Among these, five belong to the Neotropical genus Pseudocolopteryx , including a pair of sister species, P. flaviventris and citreola which markedly vocalisations exhibit an extremely low mitochondrial divergence. Using genome‐wide ddRADseq data, we reconstructed phylogenetic relationships assessed population structure within evaluated four speciation scenarios for sibling using coalescent‐based demographic simulations. Phylogenomic analyses found no mito‐nuclear discordance tree topologies disagreement between Z‐linked autosomal locus trees genus. was monophyletic embedded potentially paraphyletic whilst (PCA, ADMIXTURE) recovered both as different units. Coalescent‐based simulations estimated divergence ~550,000 generations ago (~0.55 ~1.15 mya), with minor gene flow starting ca. ~935 (~935 ~1965 ya), without eroding separate evolutionary trajectories. Therefore, previously reported differentiation could stem from past hybridization. Vocal differences are key traits specific mate recognition systems evolved context plumage stasis were likely influenced by concomitant habitat switches, playing fundamental role early process. In non‐learner such tyrant flycatchers, minimal genetic changes may suffice produce acoustic innovations critical recognition. Exploring morphological developmental processes underlying vocal tract anatomy provide deeper insights into how distinctions arise lead flycatchers.

Language: Английский

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