Genetic diversity and genetic structure of the Daurian Partridge (Perdix dauuricae) in China, assessed by microsatellite variation

Cao, Man; Liu, Naifa; Wang, Xiaoli; Guan, Ming

doi:10.5122/cbirds.2009.0005

Cited by 3 publications

(4 citation statements)

References 23 publications

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“…We found a considerable amount of genetic diversity within each population, in the range of 1.06 × 10 −3 to 2.31 × 10 −3 ( supplementary table S5, Supplementary Material online), similar to that reported in other bird populations ( Ellegren 2013 ). The genetic diversity was highest in P. dauurica , which is consistent with previous findings of high genetic diversity in this species based on microsatellite variation ( Cao et al 2010 ).…”

Section: Resultssupporting

confidence: 92%

Genomic Variation, Population History, and Long-Term Genetic Adaptation to High Altitudes in Tibetan Partridge (Perdix hodgsoniae)

Palacios,

Wang,

Wang

et al. 2023

Molecular Biology and Evolution

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Species residing across elevational gradients display adaptations in response to environmental changes such as oxygen availability, ultraviolet (UV) radiation, and temperature. Here we study genomic variation, gene expression, and long-term adaptation in Tibetan Partridge (Perdix hodgsoniae) populations residing across the elevational gradient of the Tibetan Plateau. We generated a high-quality draft genome and used it to carry out downstream population genomic and transcriptomic analysis. The P. hodgsoniae populations residing across various elevations were genetically distinct and their phylogenetic clustering was consistent with their geographic distribution. We identified possible evidence of gene flow between populations residing in < 3,000 and > 4,200 m elevation that is consistent with known habitat expansion of high-altitude populations of P. hodgsoniae to a lower elevation. We identified a 60-kilobase haplotype encompassing the Estrogen Receptor 1 (ESR1) gene, showing strong genetic divergence between populations of P. hodgsoniae. We identified six SNPs within the ESR1 gene fixed for derived alleles in high-altitude populations that are strongly conserved across vertebrates. We also compared blood transcriptome profiles and identified differentially expressed genes (such as GAPDH, LDHA, and ALDOC) that correlated with differences in altitude among populations of P. hodgsoniae. These candidate genes from population genomics and transcriptome analysis were enriched for neutrophil degranulation and glycolysis pathways, which are known to respond to hypoxia and hence may contribute to long-term adaptation to high altitudes in P. hodgsoniae. Our results highlight Tibetan Partridges as a useful model to study molecular mechanisms underlying long-term adaptation to high altitudes.

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Section: Resultssupporting

confidence: 92%

Genomic Variation, Population History, and Long-Term Genetic Adaptation to High Altitudes in Tibetan Partridge (Perdix hodgsoniae)

Palacios,

Wang,

Wang

et al. 2023

Molecular Biology and Evolution

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“…Genetic diversity was considerably high in all three species, with the highest in P. daurica, which is consistent with the wider distribution range of this species 122 and the effects of the Tibetan Plateau uplift and environmental changes on its phylogeographic structure 110 . The whole-genome phylogenetic tree indicated that P. perdix is a sister clade to P. dauurica, and P.…”

Section: Discussionsupporting

confidence: 81%

“…We found a considerable amount of genetic diversity within each population, in the range of 1.06 x 10 -3 to 2.31 x 10 -3 (Supplementary Table 5), similar to that reported in other bird populations 121 . The genetic diversity was highest in P. daurica, which is consistent with previous findings of high genetic diversity based on microsatellite variation 122 , possibly due to the wider distribution range of this species.…”

Section: Population-scale Sequencingsupporting

confidence: 91%

Long-term adaptation and short-term acclimation to high-altitudes in Tibetan Partridges (Perdix hodgsoniae)

Palacios

Wang

et al. 2022

Preprint

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Short-term phenotypic plasticity and long-term genetic adaptation are two key evolutionary processes that mediate organismal persistence in a new environment. But generally, there are few vertebrate systems where the molecular architecture of such plastic and genetic changes has been simultaneously characterized. Birds residing across elevational gradients are known to thrive in rapid and long-term environmental stimuli, demonstrate quantifiable plastic and adaptive traits, and thus can be a suitable model system to study molecular mechanisms of phenotypic plasticity and genetic adaptation. Here, we studied three species from the genus Perdix (Phasianidae, Galliformes): Tibetan Partridge (Perdix hodgsoniae), Daurian Partridge (Perdix dauurica), and Grey Partridge (Perdix perdix) by using an integrative approach of population and comparative genomics, transcriptomics, and field-based transplantation experiments. We identified a 60-kilobase haplotype encompassing the ESR1 gene, a ligand-activated transcription factor, showing strong genetic divergence between populations of Tibetan partridges adapted to different altitudes. We identified six SNPs in the ESR1 gene fixed for derived alleles in high-altitude populations that are strongly conserved across vertebrates, which are likely key genetic changes associated with high-altitude adaptation in Tibetan partridge. We also identified strong genetic divergence in additional genes associated with the regulation of apoptosis pathways, possibly indicating genetic adaptation to long-term chronic hypoxia in a high-altitude environment. Transcriptome analysis identified regulation of apoptosis, glycolysis, and response to hypoxia as key pathways among differentially expressed genes between populations of Tibetan partridges residing across the elevational gradient. Similarly, transcriptome analysis in birds transplanted from high to low elevation have identified differential expressed genes related to the immune system, and to stress response (mainly heat). Comparative transcriptomics analyses among Tibetan partridges in their “native” and “transplanted” habitats indicated that there are different suites of genes responding to short-term physiological acclimation or long-term adaptation in this species. However, we found two genes associated with the HIF-1 signaling pathway; Lactate Dehydrogenase-A (LDHA) and Aldolase C (ALDOC) were differentially expressed both (a) across the native populations along the elevational gradient and (b) after experimental transplantation from high to low elevation. Our results highlight Tibetan partridges as a useful study system to explore the genetic architecture associated with short-term acclimation and long-term genetic adaptation to high altitudes.

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“…The microsatellite results also indicated that E. jankowskii had a higher degree of genetic diversity than all passerines birds (H e = 0.24-0.59), which were listed in the article of Jamieson et al (2006), and also higher than N. nippon (H e = 0.50, H o = 0.47) (He 2007), and M. palustris sinensis (H e = 0.53, H o = 0.38) (Zhao 2012). The observed heterozygosity of E. jankowskii was higher than Gallus gallus (H o = 0.37-0.41) and Perdix dauuricae (H o = 0.58), but the expected heterozygosity of E. jankowskii was a little lower than Gallus gallus (H e = 0.72-0.77) and Perdix dauuricae (H e = 0.72) (Cao et al 2010;Masroor et al 2012). It is well established that decreases in genetic variation may reduce fitness and adaptability (Allentoft and O'Brien 2010).…”

Section: High-level Genetic Diversity and Inbreedingmentioning

confidence: 96%

High levels of genetic diversity and an absence of genetic structure among breeding populations of the endangered Rufous-backed Bunting in Inner Mongolia, China: implications for conservation

Zhang

et al. 2021

Avian Res

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Background The Rufous-backed Bunting, Emberiza jankowskii, is an endangered species that is primarily distributed in Inner Mongolia, China. The main threats to the continued persistence of this species are habitat loss and degradation. However, the impact of population loss on genetic diversity remains unclear. To support future conservation and management efforts, we assessed the genetic diversity and population structure of E. jankowskii using mitochondrial DNA and microsatellites. Methods Blood samples were collected from 7‒8-day-old nestlings in Inner Mongolia, China between May and August of 2012 and 2013. Mitochondrial DNA sequences and microsatellite markers were used to assess the genetic diversity, genetic structure and inbreeding of E. jankowskii. The results of genetic diversity and inbreeding were compared to other avian species. Results We found an unexpectedly high level of genetic diversity in terms of mitochondrial DNA and microsatellite compared to other avian species. However, there were high levels of gene flow and minimal genetic structuring, among the fragmented breeding populations of E. jankowskii in Inner Mongolia. These findings suggest that E. jankowskii in Inner Mongolia is a metapopulation. Despite the high genetic diversity of E. jankowskii, local populations in each small patch remain at risk of extinction due to habitat loss. In addition, the E. jankowskii population has a high risk of inbreeding. Conclusions To minimize further loss of genetic diversity of this endangered species, we suggest that the E. jankowskii in Inner Mongolia should be considered as a protected species for management purposes. Conservation efforts should concentrate on E. jankowskii habitat management. This may be most effectively achieved by protecting the current breeding habitats and prohibiting over-grazing.

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Genetic diversity and genetic structure of the Daurian Partridge (Perdix dauuricae) in China, assessed by microsatellite variation

Cited by 3 publications

References 23 publications

Genomic Variation, Population History, and Long-Term Genetic Adaptation to High Altitudes in Tibetan Partridge (Perdix hodgsoniae)

Genomic Variation, Population History, and Long-Term Genetic Adaptation to High Altitudes in Tibetan Partridge (Perdix hodgsoniae)

Long-term adaptation and short-term acclimation to high-altitudes in Tibetan Partridges (Perdix hodgsoniae)

High levels of genetic diversity and an absence of genetic structure among breeding populations of the endangered Rufous-backed Bunting in Inner Mongolia, China: implications for conservation

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