Historic and modern genomes unveil a domestic introgression gradient in a wild red junglefowl population

Wu, Meng Yue; Low, Grace Kah Mun; Forcina, Antonio; Grouw, Hein van; Lee, Benjamin P. Y‐H.; Oh, Rachel Rui Ying; Rheindt, Frank E.

doi:10.1111/eva.13023

Cited by 21 publications

(24 citation statements)

References 106 publications

(141 reference statements)

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“…Aided by high-quality reference genomes, research projects now routinely use individual-level resequencing data to gain detailed insights into population structure, gene flow, inbreeding, genetic load, as well as admixture dynamics with closely related species ( Hu et al 2020 ; Wright et al 2020). DNA from historical and ancient samples is providing insights into historical levels of genetic diversity, inbreeding and introgression, enabling important benchmarks for assessing species statuses today ( Bi et al 2013 ; van der Valk et al 2019 ; Gauthier et al 2020 ; Wu et al 2020 ). Unfortunately, the vast majority of conservation genomic projects have been conducted with vertebrate systems, which have been the primary focus of many conservation management programs (Saremi et al 2019; Eldridge et al 2020 ).…”

Section: Introductionmentioning

confidence: 99%

The Genome Assembly and Annotation of the Apollo Butterfly Parnassius apollo, a Flagship Species for Conservation Biology

Podsiadłowski

Tunström

Espeland

et al. 2021

Genome Biology and Evolution

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Conservation genomics has made dramatic improvements over the past decade, leveraging the power of genomes to infer diverse parameters central to conservation management questions. However, much of this effort has focused upon vertebrate species, despite insects providing similar flagship status with the added benefit of smaller genomes, shorter generation times and extensive historical collections in museums. Here we present the genome of the Apollo butterfly (Parnassius apollo, Papilionidae), an iconic endangered butterfly, which like many species in this genus, needs conservation genomic attention yet lacks a genome. Using 68.7 Gb of long-read data (N50 = 15.2 kb) we assembled a 1.4 Gb genome for the Apollo butterfly, making this the largest sequenced Lepidopteran genome to date. The assembly was highly contiguous (N50 = 7.1 Mbp) and complete (97% of Lepidopteran BUSCOs were single-copy and complete) and consisted of 1707 contigs. Using RNAseq data and Arthropoda proteins, we annotated 28.3 K genes. Alignment with the closest related chromosome-level assembly, Papilio bianor, reveals a highly conserved chromosomal organization, albeit genome size is highly expanded in the Apollo butterfly, due primarily to a dramatic increase in repetitive element content. Using this alignment for super-scaffolding places the P. apollo genome in to 31 chromosomal scaffolds, and together with our functional annotation, provides an essential resource for advancing conservation genomics in a flagship species for insect conservation.

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Section: Introductionmentioning

confidence: 99%

The Genome Assembly and Annotation of the Apollo Butterfly Parnassius apollo, a Flagship Species for Conservation Biology

Podsiadłowski

Tunström

Espeland

et al. 2021

Genome Biology and Evolution

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“…Unlike its red jungle fowl predecessor, domestic chicken exhibit diverse types of plumage colours. The plumage colour variety rise through the domestication process [18].…”

Section: Resultsmentioning

confidence: 99%

Plumage colours Stability in Inbreed Pelung Chicken

Saragih

Perdamaian

Sadiman³

et al. 2021

BIO Web Conf.

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Pelung is one of the most importance local chicken in Indonesia. Genetic introgression and inbreeding depression were the major threat for local chicken gene pool. The objective of this research was to investigate the effect of serial inbreeding mating to plumage colours of Pelung chicken. Pure Pelung chicken which purchased from Cianjur sub-district was undergo full-sib mating through five generation. All offspring phenotypes was recorded. The results show gradual plumage phenotype change of inbreed Pelung chicken. Initially, adult male chicken had Black-red coloured as wildtype (WT) shifted to partridge and black-silver coloured in later generations. The current findings indicating that inbreeding made recessive traits to be expressed which some of them might had deleterious effect. Random mating should be maintained to preserve genetics stability of Pelung chicken

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“…Bidirectional matings between T. septentrionalis and T. sexlineatus have been observed several times in the laboratory (Figure 1), and an earlier study using the STRUCTURE analysis of nuclear and mitochondrial DNA data has shown that hybridization and introgression occur in the areas where the two species coexist and become increasingly pronounced as the geographical distance between heterospecific populations decreases (Guo, 2019). Hybridization and introgression may lead to morphological admixture (Milne et al, 1999;Olave et al, 2018;Wu et al, 2020;Yang et al, 2020), and this seems F I G U R E 5 Temporal shifts in the sympatric area of T. septentrionalis (Tsep) and T. sexlineatus (Tsex) under two scenarios at the 2021-2040, 2041-2060, 2061-2080, and 2081-2100 (Yu, 2014). Specifically, these individuals are similar in body size and shape to T. septentrionalis but have a mean number (4.4) of dorsal scales that is much close to that (4) of T. sexlineatus but fewer than that (6) of T. septentrionalis (Yu, 2014).…”

Section: Discussionmentioning

confidence: 99%

Climate warming will increase chances of hybridization and introgression between two Takydromus lizards (Lacertidae)

Guo

Zhong

Xie

et al. 2021

Ecology and Evolution

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Coexisting species may experience population and range changes alone or jointly in response to environmental change. Here, we used six climate variables and ten modeling algorithms to predict the distribution of two Takydromus species ( T . septentrionalis and T . sexlineatus ) in China. We identified the sympatric and allopatric areas by comparing projections between the two species based on habitat suitability under present and future climate scenarios. We constructed the hypervolumes of six climate variables for the two species and then evaluated overlaps between hypervolumes. From this study, we know the following. First, minimum temperature of coldest month contributes the most to the prediction of habitat suitability. Second, habitats suitable for the two species will shift northward in response to climate warming. Third, the range of T. sexlineatus will expand across the four future time intervals before 2,100, namely the 2021–2040, 2041–2060, 2061–2080, and 2081–2100 intervals, under both Shared socioeconomic pathway (SSP) 245 and SSP585 scenarios, and the range of T. septentrionalis will also expand in the future except at the 2081–2100 interval under the SSP585 scenario. Fourth, the sympatric areas will contract or expand under the SSP245 scenario and expand across the four future time intervals before 2,100 under the SSP585 scenario. Fifth, the niche hypervolumes of the two species partially overlapped, and the differences in niche centroid show some degree of niche differentiation between the two species. These results allow to conclude that climate warming will not only drive the northward drift of sympatric areas but also increase the size of these areas if nothing is done to limit the emission of greenhouse gases. Given the existence of hybridization and introgression between T. septentrionalis and T. sexlineatus in the field where they coexist, we also conclude that climate warming will increase chances of hybridization and introgression between the two species.

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Historic and modern genomes unveil a domestic introgression gradient in a wild red junglefowl population

Abstract: This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Cited by 21 publications

References 106 publications

The Genome Assembly and Annotation of the Apollo Butterfly Parnassius apollo, a Flagship Species for Conservation Biology

The Genome Assembly and Annotation of the Apollo Butterfly Parnassius apollo, a Flagship Species for Conservation Biology

Plumage colours Stability in Inbreed Pelung Chicken

Climate warming will increase chances of hybridization and introgression between two Takydromus lizards (Lacertidae)

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