PAV-spotter: using signal cross-correlations to identify Presence/Absence Variation in target capture data

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

Published: Oct. 29, 2024

Abstract High throughput sequencing technologies have become essential in the fields of evolutionary biology and genomics. When dealing with non-model organisms or genomic gigantism, whole genomes is still relatively costly therefore reduced-genome representations are frequently obtained, for instance by ‘target capture’ approaches. While computational tools exist that can handle target capture data identify small-scale variants such as single nucleotide polymorphisms micro-indels, options to large scale structural limited. To meet this need, we introduce PAV-spotter: a tool presence/absence variation (PAV) data. PAV-spotter conducts signal cross-correlation calculation, which distribution read counts per between samples different priori defined classes – e.g. male versus female, diseased healthy compared. We apply test our methodology studying Triturus newts: salamanders gigantic currently lack an annotated reference genome. newts suffer from hereditary disease kills half their offspring during embryogenesis. compare two types embryos, characterized unique deletions, those embryos. Our findings show helps expose variants, even face medium low coverage levels, sample sizes, background noise due mis-mapped reads. be used study underlying supergene systems absence genome assemblies. The code, including further explanation on how use customize it, available through GitHub repository: https://github.com/Wielstra-Lab/PAVspotter .

Language: Английский

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Exploring chromosome evolution in 250 million year old groups of dragonflies and damselflies (Insecta:Odonata)

Molecular Ecology, Journal Year: 2023, Volume and Issue: 32(21), P. 5785 - 5797

Published: Oct. 3, 2023

Using recently published chromosome-length genome assemblies of two damselfly species, Ischnura elegans and Platycnemis pennipes, dragonfly Pantala flavescens Tanypteryx hageni, we demonstrate that the autosomes Odonata have undergone few fission, fusion, or inversion events, despite 250 million years separation. In four genomes discussed here, our results show all a clear ortholog in ancestral karyotype. Despite this chromosomal orthology, different factors, including concentration repeat dynamics, GC content, relative position on chromosome, proportion coding sequence influence density syntenic blocks across chromosomes. However, these factors do not interact to synteny same way any pairs nor is one factor retained species. Furthermore, it was previously unknown whether micro-chromosomes are descended from chromosome. structural rearrangements, evidence suggests sampled indeed descend an micro-chromosome P. lost through fusion with autosomes.

Language: Английский

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B Chromosomes in Psalidodon scabripinnis (Characiformes, Characidae) Species Complex

Animals, Journal Year: 2022, Volume and Issue: 12(17), P. 2174 - 2174

Published: Aug. 25, 2022

B chromosomes are extra-genomic components of cells found in individuals and populations some eukaryotic organisms. They have been described since the first observations chromosomes, but several aspects their biology remain enigmatic. Despite being present hundreds fungi, plants, animal species, only a small number investigated through high-throughput analyses, revealing remarkable mechanisms employed by these elements to ensure maintenance. Populations

Language: Английский

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Large X‐effects are absent in torrent frogs with nascent sex chromosomes

Molecular Ecology, Journal Year: 2023, Volume and Issue: 32(19), P. 5338 - 5349

Published: Aug. 21, 2023

Sex chromosomes are popularized as a special role in driving speciation. However, the empirical evidence from natural population processes has been limited to organisms with degenerated sex chromosomes, where hemizygosity is mainly considered act driver of reproductive isolation. Here, we examined several hybrid zones torrent frog Amolops mantzorum species complex, using an approach by mapping species-diagnostic loci onto reference genome compare sex-linked versus autosomal patterns introgression. We find little support incompatibilities for large X-effects these populations homomorphic due absence hemizygous effects. As expected, were not found those heteromorphic but newly evolved owing strong genetic differences between X and Y chromosomes. The available data so far on amphibians suggest genes nascent may be ubiquitous presumed across animal kingdom.

Language: Английский

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Does Haldane's rule speciation within mimetic Poison frogs?

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

Published: March 29, 2024

Abstract To explain how populations with distinct warning signals coexist in close parapatry, we experimentally assessed intrinsic mechanisms acting as reproductive barriers within three Ranitomeya poison-frog species. For all species, assortative mating did not occur, nor a survival disadvantage for inter-population hybrids. However, fantastica , these hybrids of the male sex are sterile, an outcome predicted by Haldane’s rule. Our results suggest possible XY determinism R. and show that this process is associated extraordinary diversity, leading to speciation. Graphical

Language: Английский

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Does Haldane’s rule speciation within mimetic Poison frogs?

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: April 25, 2024

To explain how populations with distinct warning signals coexist in close parapatry, we experimentally assessed intrinsic mechanisms acting as reproductive barriers within three Ranitomeya poison-frog species. For all species, assortative mating did not occur, nor a survival disadvantage for inter-population hybrids. However, Ranitomeya fantastica, these hybrids of the male sex are sterile, an outcome predicted by Haldane’s rule. Our results suggest possible XY determinism R. and show that this process is associated extraordinary diversity, leading to speciation.

Language: Английский

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Comparative genomics supports ecologically induced selection as a putative driver of banded penguin diversification

Molecular Biology and Evolution, Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 16, 2024

Abstract The relative importance of genetic drift and local adaptation in facilitating speciation remains unclear. This is particularly true for seabirds, who can disperse over large geographic distances, providing opportunities intermittent gene flow among distant colonies that span the temperature salinity gradients oceans. Here, we delve into genomic basis banded penguins, Galápagos (Spheniscus mendiculus), Humboldt (S. humboldti), Magellanic magellanicus) African penguins demersus), by analyzing 114 genomes from main 16 breeding colonies. We aim to identify molecular mechanism adaptive traits have facilitated their diversifications. Through positive selection family expansion analyses, identified candidate genes may be related reproductive isolation processes mediated ecological thermal niche divergence. recover signals on key loci associated with spermatogenesis, especially during recent peripatric divergence penguin penguin. High temperatures tropical habitats favored spermatogenesis maintain sperm viability, leading young species. Our results suggest genome-wide pathways underpin thermoregulation, osmoregulation, hypoxia, social behavior appear been crucial penguins. Overall, these contribute our understanding how complexity biotic, but abiotic, factors, along high dispersal capabilities marine species, promote both neutral lineage even presence flow.

Language: Английский

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The importance of reproductive isolation in driving diversification and speciation within Peruvian mimetic poison frogs (Dendrobatidae)

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

Published: Aug. 27, 2024

To explain how populations with distinct warning signals coexist in close parapatry, we experimentally assessed intrinsic mechanisms acting as reproductive barriers within three poison-frog species from the Peruvian Amazon belonging to a Müllerian mimetic ring (Ranitomeya variabilis, Ranitomeya imitator and fantastica). We tested role of prezygotic postzygotic isolation between phenotypically different ecotypes each species, using no-choice mating experiments offspring survival analysis. Our results show that preference did not occur except for one specific ecotype R. imitator, all were able produce viable inter-population F1 hybrids. However, while variabilis hybrids F2 generations, found fantastica, every hybrid males sterile females remained fertile. This unexpected result, echoing Haldane's rule speciation, validated phylogenetic studies which tentatively diagnose these fantastica two species. work suggests genetic likely participate extraordinary phenotypic diversity observed populations, by maintaining boundaries.

Language: Английский

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Genome Survey of Male Rana dybowskii to Further Understand the Sex Determination Mechanism

Animals, Journal Year: 2024, Volume and Issue: 14(20), P. 2968 - 2968

Published: Oct. 14, 2024

is one of the important aquaculture species in Northeast China. The fallopian tubes female

Language: Английский

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Contrast and Genomic Characterisation of Ancient and Recent Interspecific Introgression Between Deeply Diverged Moustache Toads (Leptobrachium)

Molecular Ecology, Journal Year: 2024, Volume and Issue: 33(23)

Published: Oct. 28, 2024

Recent genomic analyses have provided new insights into the process of interspecific introgression and its consequences on species evolution. Most recent studies, however, focused hybridization between recently radiated species, with few examining outcomes ancient across deeply diverged species. Using whole genome data moustache toads (Leptobrachium), we identified signals three events among nine that at Eocene. An from L. leishanense to ancestral branch (C1) liui introduced adaptive variants. The highly introgressed regions include genes important functions in odorant detection immune responses. These are preserved all descendent populations liui_C1, these likely been positively selected over a long filtering process. A occurred huashen tengchongense, being mostly neutral. Furthermore, one F1 hybrid individual was detected sympatric ailaonicum promustache. largely disappeared after removing individual, indicating an occasional but minimal introgression. Further examination divergent low revealed both pre-mating isolation genetic incompatibility as potential mechanisms resisting maintaining boundaries. Additionally, no large X-effect found events. Hybridization amphibian may be common, detectable introgressions less so, neutral rare potentially adaptive. Our findings complement work, together they provide better understanding characteristics significance adaptation

Language: Английский

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