Uncovering Ghost Introgression Through Genomic Analysis of a Distinct East Asian Hickory Species DOI Creative Commons
Wei‐Ping Zhang, Ya‐Mei Ding, Yu Cao

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: June 27, 2023

ABSTRACT Although the possibility of introgression from ghost lineages (all unsampled extant and extinct taxa) is now widely recognized, detecting characterizing remains a challenge. Here, we propose combined use popular D -statistic method, which tests for presence introgression, full-likelihood method BPP, determines possible gene-flow scenarios, including truly responsible. We illustrate utility this approach by investigating reticulation bifurcation history genus Carya (Juglandaceae), beaked hickory sinensis . To achieve goal, generated two chromosome-level reference genomes respectively C. cathayensis Furthermore, re-sequenced whole 43 individuals one individual each 11 diploid species The latter dataset with per used to reconstruct phylogenetic networks estimate divergence time Our results unambiguously demonstrate an lineage into hickory, dispelling certain misconceptions about also discuss profound implications historical biogeography species. [BPP; ; -statistic; gene flow; introgression]

Language: Английский

Genomic data reveal a north-south split and introgression history of blood fluke populations across Africa DOI Creative Commons
Roy N. Platt, Egie E. Enabulele,

Ehizogie Adeyemi

et al.

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: April 13, 2025

Language: Английский

Citations

0
A complex interplay of genetic introgression and local adaptation during the evolutionary history of three closely related spruce species DOI Creative Commons
Shuo Feng,

Hai-Xia Ma,

Yu Yin

et al.

Plant Diversity, Journal Year: 2025, Volume and Issue: unknown

Published: May 1, 2025

Language: Английский

Citations

0
Widespread introgression of MHC genes in Iberian Podarcis lizards DOI
Tomasz S. Gaczorek, Mateusz Chechetkin, Katarzyna Dudek

et al.

Molecular Ecology, Journal Year: 2023, Volume and Issue: 32(14), P. 4003 - 4017

Published: May 4, 2023

Abstract Major histocompatibility complex (MHC) genes are crucial for the adaptive immune response of jawed vertebrates. Their variation, reaching extreme levels, is driven mainly by an arms race between hosts and pathogens. One hypothesised mechanism contributing to MHC polymorphism introgression, exchange genetic variants hybridising species favoured selection, yet its effect on variation poorly understood. Detection though challenging, may be facilitated analysis complexes forming multiple hybrid zones. Here, we investigated introgression in six zones formed seven Podarcis lizards inhabiting Iberian Peninsula. To differentiate from neutral compared patterns gene genome‐wide markers. We found elevated sharing alleles proximity contact beyond areas detectable admixture most and, half them, asymmetric exchange. In general, allele pairs with abutting ranges geographically isolated also supports prevalence introgression. Collectively, our results demonstrate widespread suggest adaptiveness. Contrary previous Triturus newts, did not observe differences rate classes. Our work adds support emerging view as a key shaping diversity. It raises questions about factors leading asymmetry

Language: Английский

Citations

8
Predicting the potential impacts of climate change on the endangered endemic annonaceae species in east africa DOI Creative Commons
Elijah Mbandi Mkala, Virginia M. Mwanzia, John M. Nzei

et al.

Heliyon, Journal Year: 2023, Volume and Issue: 9(6), P. e17405 - e17405

Published: June 1, 2023

Globally, endemic species and natural habitats have been significantly impacted by climate change, further considerable impacts are predicted. Therefore, understanding how change can aid in advancing the necessary conservation initiatives. The use of niche modeling is becoming a popular topic biological to forecast changes distributions under various scenarios. This study used Australian Community Climate Earth System Simulator version 1 (ACCESS-CM2) general circulation model coupled intercomparison project phase 6 (CMIP6) current distribution suitable habitat for four threatened Annonaceae East Africa (EA), determine impact on their years 2050 (average 2041-2060) 2070 2061-2080). Two shared socio-economic pathways (SSPs) SSP370 SSP585 were contraction expansion Uvariodendron kirkii, Uvaria dzomboense Asteranthe asterias Kenya Tanzania EA. all highly influenced precipitation, temperature, environmental factors (population, potential evapotranspiration, aridity index). Although loss original anticipated be significant, appropriate projections species. More than 70% 40% dzombense kirkii predicted destroyed respectively. Based our research, we suggest that areas expected shrink owing classified as important protection zones preservation

Language: Английский

Citations

7
Genomic data reveal a north-south split and introgression history of blood fluke (Schistosoma haematobium) populations from across Africa DOI Creative Commons
Roy N. Platt, Egie E. Enabulele,

Ehizogie Adeyemi

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 8, 2024

Abstract The human parasitic fluke, Schistosoma haematobium hybridizes with the livestock parasite S. bovis in laboratory, but extent of hybridization nature is unclear. We analyzed 34.6 million single nucleotide variants 162 samples from 18 African countries, revealing a sharp genetic discontinuity between northern and southern . found no evidence for recent hybridization. Instead data reveal admixture events that occurred 257-879 generations ago populations. Fifteen introgressed genes are approaching fixation four potentially driving adaptation. identified 19 regions were resistant to introgression; these enriched on sex chromosomes. These results (i) demonstrate strong barriers gene flow species, (ii) indicate may be less common than currently envisaged, (iii) profound genomic consequences interspecific schistosomes medical veterinary importance.

Language: Английский

Citations

2
Genetic Incompatibilities and Evolutionary Rescue by Wild Relatives Shaped Grain Amaranth Domestication DOI Creative Commons
José Gonçalves-Dias, Akanksha Singh, Corbinian Graf

et al.

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

Published: Aug. 1, 2023

Crop domestication and the subsequent expansion of crops have long been thought as a linear process from wild ancestor to domesticate. However, evidence gene flow locally adapted relatives that provided adaptive alleles into has identified in multiple species. Yet, little is known about evolutionary consequences during interaction genetic load crop populations. We study pseudo-cereal grain amaranth domesticated three times different geographic regions Americas. quantify amount distribution along genome species their two relatives. Our results show ample between Gene decreased This suggests could provide rescue by replacing deleterious crops. assess experimental hybrids found incompatibilities one Central American other These might created recent reproductive barriers maintained integrity today. Together, our played an important role amaranth, despite barriers. The plants was likely not genomic mosaic contributors with varying fitness effects for today's

Language: Английский

Citations

5
The recombination landscape of introgression in yeast DOI Creative Commons
Enrique J. Schwarzkopf, Nathan Brandt, Caiti Smukowski Heil

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 5, 2024

Meiotic recombination is an evolutionary force that acts by breaking up genomic linkage, increasing the efficacy of selection. Recombination initiated with a double-strand break which resolved via crossover, involves reciprocal exchange genetic material between homologous chromosomes, or non-crossover, results in small tracts non-reciprocal material. Crossover and non-crossover rates vary species, populations, individuals, across genome. In recent years, rate has been associated distribution ancestry derived from past interspecific hybridization (introgression) variety species. We explore this interaction introgression sequencing spores detecting crossovers non-crossovers two crosses yeast

Language: Английский

Citations

1
Resolving Relationships of Bolbitis sinensis Species Complex Using RAD Sequencing DOI Open Access
Liyun Nie, Yuhan Fang, Zeng‐Qiang Xia

et al.

Published: June 3, 2024

Species identification and phylogenetic relationships clarification are fundamental goals in species delimitation. Yet these tasks pose challenges when based on morphologies, geographic distribution, genomic data. Previously, two new of fern genus Bolbitis, B. × multipinna longiaurita, were described morphological traits, phylogenetically intertwined with sinensis fail to form monophyletic groups. To address the unclear within complex, RAD sequencing was performed 65 individuals from five populations. Our integrated analysis tree, neighbor net, genetic structure, indicate that complex should not be considered as separate species. Moreover, our findings reveal differences degree differentiation among populations, ranged low moderate, which might influenced by geographical distance gene flow. The Fst values also confirmed intensifies increasing distance. Collectively, this study clarifies elucidates diversity across studied offers valuable insights contribute broader evolutionary population genetics Bolbitis

Language: Английский

Citations

1
Big Epidemiology: The Birth, Life, Death, and Resurgence of Diseases on a Global Timescale DOI Creative Commons
Nicola Luigi Bragazzi, Thorsten Lehr

Epidemiologia, Journal Year: 2024, Volume and Issue: 5(4), P. 669 - 691

Published: Nov. 6, 2024

Big Epidemiology represents an innovative framework that extends the interdisciplinary approach of History to understand disease patterns, causes, and effects across human history on a global scale. This comprehensive methodology integrates epidemiology, genetics, environmental science, sociology, history, data science address contemporary future public health challenges through broad historical societal lens. The foundational research agenda involves mapping occurrence diseases their impact societies over time, utilizing archeological findings, biological data, records. By analyzing skeletal remains, ancient DNA, artifacts, researchers can trace origins spread diseases, such as

Language: Английский

Citations

1
Phenotypically wild barley shows evidence of introgression from cultivated barley DOI
Chaochih Liu, Lei Li, Mingqin Shao

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: July 3, 2024

Abstract Plant conservation hinges on preserving biodiversity, which is crucial for long-term adaptation. Multiple studies have reported genetic evidence of crop-to-wild introgression in phenotypically wild accessions barley ( Hordeum vulgare ssp. spontaneum ). We examined 318 Wild Barley Diversity Collection (WBDC) from cultivated barley. Using SNP genotype and exome capture data, we performed local ancestry inference between the WBDC to identify genomic regions with introgression. intervals well-characterized genes involved domestication improvement, at potentially important maintaining a phenotype. Our analysis revealed that nearly 16% (48 318) showed barley, up 16.6% genome has been introgressed. All identified as introgressed based domestication-related phenotypes show clear The size runs identity by state suggests most did not occur recently. This study long history exchange highlighting potential influence makeup future adaptation populations, implications plant strategies.

Language: Английский

Citations

1