Pengcheng Wang, Ping Hu, Jinping Zhang, Lixia Zhang, Jing Zhang, Zhengwang Zhang. 2023: Using non-destructive sampling to evaluate the population genomic status of captive Brown Eared Pheasants. Avian Research, 14(1): 100078. DOI: 10.1016/j.avrs.2023.100078
Citation: Pengcheng Wang, Ping Hu, Jinping Zhang, Lixia Zhang, Jing Zhang, Zhengwang Zhang. 2023: Using non-destructive sampling to evaluate the population genomic status of captive Brown Eared Pheasants. Avian Research, 14(1): 100078. DOI: 10.1016/j.avrs.2023.100078

Using non-destructive sampling to evaluate the population genomic status of captive Brown Eared Pheasants

Funds: The project was funded by the National Natural Science Foundation of China (Grant No. 31872244 to Z.Z.), Priority Academic Program Development of Jiangsu Higher Education Institutions, Beijing Zoo Management Office (No. zx2019016 to J.Z.), and the Biodiversity Survey, Monitoring and Assessment Project (2019–2023) of the Ministry of Ecology and Environment, China (No. 2019HB2096001006 to Z.Z.)
More Information
  • Corresponding author:

    E-mail address: zhangjing0468@126.com (J. Zhang)

    E-mail address: zzw@bnu.edu.cn (Z. Zhang)

  • Received Date: 16 Aug 2022
  • Rev Recd Date: 27 Dec 2022
  • Accepted Date: 27 Dec 2022
  • Available Online: 14 Jun 2023
  • Publish Date: 12 Jan 2023
  • Evaluating the genetic status of threatened species is an essential task in conservation genetics. However, the genetic status of threatened species has been mostly evaluated through techniques that fail to estimate genetic diversity at the whole genomic level. Next generation sequencing can meet this demand, but high quality samples such as blood or muscle tissues are required. However, it is difficult to collect such samples from threatened species because sampling work may impact their health. Therefore, it is essential to design a workflow to evaluate the whole genomic status of threatened species using non-destructive sampling. Even though non-destructive sampling has been used in traditional barcoding technique, the barcoding technique cannot evaluate the whole genomic status. Brown Eared Pheasant (Crossoptilon mantchuricum) is an endangered species, with captive populations maintained in Taiyuan Zoo, China, and Europe. However, the genetic diversity, inbreeding pattern, and mutation load of these two populations are unclear. To uncover the genetic status of these two captive populations, we applied 2b-RAD technology to evaluate the genomic status of these populations using feathers as samples. The feathers could be collected by non-destructive sampling. The results indicate that the Taiyuan Zoo population has a lower genetic diversity and higher inbreeding coefficient than the European population. The Taiyuan Zoo population has lethal mutations when homozygous. The current project uses a non-destructive sampling technique to evaluate the whole genomic status of the two captive populations, providing a paradigm for conservation genetics, which will facilitate the development of conservation biology.

  • Among the four species of ground jays (Podoces) in the world, two are found in the west of China (Qian et al., 1965; Cheng, 1987): the Xinjiang Ground Jay (P. biddulphi) (Fig. 1) and the Mongolian Ground Jay (P. hendersoni). Xinjiang Ground Jays occur only in the Taklimakan Desert, the southern part of Xinjiang. Since the species was established by A. Hume in 1874, little has been known of its status and ecology. The current essay describes such information based on a long-term field survey.

    Figure  1.  The Xinjiang Ground Jay in the Lopnur Desert (Photo by Ming Ma)

    The ground jays are residents at the center of the Taklimakan Desert (37–42°N, 77–94°E, 790–1500 m elevations; Fig. 2). Most of distribution range of the species falls within Xinjiang, with a few extending to the east, e.g. the Qaidam Basin in Qinghai Province and Dunhuang in Gansu Province (Collar et al., 2001; Sun and Li, 2009). Interestingly, Mongolian Ground Jays are distributed around the range of Xinjiang Ground Jays (Fig. 2). Such a pattern should be a result of inter-species competition. There is evidence showing that the ground jays are expanding their range from west to east during recent decades (Ma, 2010).

    Figure  2.  Distribution of the Xinjiang Ground Jay and the Mongolian Ground Jay in the Taklimakan Desert

    Ground jays are well adapted to desert and semi-desert regions (Ludlow and Kinnear, 1933). Compared with crows or choughs, ground jays are sandy in plumage, presumably providing protection from desert predators (Londei, 2004). As their names indicate, ground jays spend much of their time on the ground. The strong legs should be adaptive to the habit. However, ground jays nest in shrubs and trees, a characteristic similar to that followed by the Corvids species.

    Information on breeding ecology of Xinjiang Ground Jays is very limited. A total of 20 ground jay nests were recorded in Niya and Qarqan from 2003 to 2004. The birds placed their nests on the small desert-poplar tree Populus diversifolia and Tamarix spp. bushes, averaging 1.09 ± 0.15 m (range = 0–2.30 m, n = 18) above the ground (Fig. 3). The nests were composed of sheep wool, camel's wool, horse's hair, dead leaves, dry grass, and the soft cottony growth of reeds, with poplar skin, twigs and small sticks being lined at the base. The external diameter of the nest is 35.75 ± 2.30 cm (range = 16–55 cm, n = 16), the internal diameter of the nest is 12.82 ± 0.85 cm (range = 9–20 cm, n = 14), and depth of the nest is 9.50 ± 1.00 cm (range = 5–16 cm, n = 13) and the height is 20.88 ± 1.33 cm (range = 12–35 cm, n = 16) (Fig. 4a). Clutch size varied between 1 and 3 eggs (1.89 ± 0.31 eggs, n = 9), the diameters of the eggs are 32.88 ± 0.83 mm × 23.48 ± 0.09 mm, and the weight of egg is 8.33 ± 0.88 g (n = 4). The color of egg is pale green and grayish white with brown spots scattered all over the surface, rather more densely at the broad end (Fig. 4b). The parents fed the young (Fig. 4c) more than 42 times during one day for one nest located in the middle March (Ma, 2004). After fledging, family flocks of 4 to 6 birds were encountered between early May and July. These data suggested that the ground jays laid eggs from late February to April.

    Figure  3.  Nest height above the ground in relation to nesting bush height of the Xinjiang Ground Jays
    Figure  4.  Breeding ecoloty of the Xinjiang Ground Jay. (a) The local guide in the field work, showing the nest built on a Tamarix bush; (b) The egg; (c) Feeding the chicks; (d) Nearly fledging chicks (photos by Ming Ma).

    Based on the transect counting conducted from 1988 to 2011, the density of ground jays was to be 3–5 pairs per 100 km2. It was estimated to have 4100–6700 pairs of ground jays over the species' range of 135000 km2.

    The ground jay populations seemed to drop during recent decades (Grimmett, 1991; Madge and Burn, 1994; Ma, 1998). However, with the intensified desertification in western China, the jays have a tendency to expand to the east.For example, there were some of new records in Gansu and Qinghai provinces (Collar et al., 2001; Sun and Li, 2009; Ma, 2010). Arguably, this bird is an indicator species of desertification and climate change.

    Human activities such as oil industry, ecotourism, land exploitation and overgrazing should be responsible for the population decline (Ma, 2001; Ma and Kwok, 2004). The restricted range and special requirements for nesting habitats suggest an urgent conservation need for this species. Now, although the bird is classified as "near-threatened" (Collar et al., 2001), no protection measures have been in practice (Zheng and Wang, 1998).

    The research is supported by the Science Supporting Project of National Ministry of Science and Technology (2008BAC39B04) and the National Natural Science Foundation of China (30270211, 30470262, 30970340). Sincere thanks are due to all participants in the field work, especially to Jinghe Gu, Kwok Hon Kai, Zexin Jia, Batuerhan, Eugene Potapov, Chuanbo Wang, Feng Xu, Yiqun Wu, Mike Kilburn, Geoff Carey, Richard Lewthwaite, Sebastien Lepetz and Paul Leader. Gratitudes are also given to Prof. Xin Lu from Wuhan University who helps revise the earlier manuscript very carefully.

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