Yufei Dai, Qingxian Lin, Wenzhen Fang, Xiaoping Zhou, Xiaolin Chen. 2015: Noninvasive and nondestructive sampling for avian microsatellite genotyping: a case study on the vulnerable Chinese Egret (Egretta eulophotes). Avian Research, 6(1): 24. DOI: 10.1186/s40657-015-0034-x
Citation: Yufei Dai, Qingxian Lin, Wenzhen Fang, Xiaoping Zhou, Xiaolin Chen. 2015: Noninvasive and nondestructive sampling for avian microsatellite genotyping: a case study on the vulnerable Chinese Egret (Egretta eulophotes). Avian Research, 6(1): 24. DOI: 10.1186/s40657-015-0034-x

Noninvasive and nondestructive sampling for avian microsatellite genotyping: a case study on the vulnerable Chinese Egret (Egretta eulophotes)

More Information
  • Corresponding author:

    Xiaoping Zhou. xpzhou@xmu.edu.cn

    Xiaolin Chen. xlchen@xmu.edu.cn

  • Received Date: 11 Feb 2015
  • Accepted Date: 21 Nov 2015
  • Available Online: 24 Apr 2022
  • Publish Date: 03 Sep 2015
  • Background 

    Noninvasive and nondestructive DNA sampling techniques are becoming more important in genetic studies because they can provide genetic material from wild animals with less or even without disturbance, which is particularly useful for the study of endangered species, i.e., birds. However, nondestructively and noninvasively sampled DNA may, in some cases, be inadequate in the amount and quality of the material collected, which can lead to low amplification success rates and high genotyping errors.

    Methods 

    In this study, noninvasive (eggshell swab, shed feather and feces), nondestructive (plucked feather and buccal swab) and invasive (blood) DNA samples were collected from the vulnerable Chinese Egret (Egretta eulophotes). DNA concentrations, PCR amplification success and microsatellite genotyping errors of different sample types were evaluated and compared to determine whether noninvasive and nondestructive samples performed as well as invasive samples in our experimental procedures.

    Results 

    A total of 159 samples were collected in the field. Among the different sample types, the highest DNA concentrations (154.0–385.5 ng/μL) were obtained from blood. Those extracted from fecal samples were the lowest, ranging from 1.25 to 27.5 ng/μL. Almost all of the DNA samples, i.e., 95.59 %, were successfully amplified for mtDNA (n = 152) and 92.76 % of mtDNA samples were successfully genotyped for at least five of the nine microsatellite loci tested (n = 141). Blood samples and buccal swabs produced reliable genotypes with no genotyping errors, but in feces, allelic dropouts and false alleles occurred in all nine loci, with error rates ranging from 6.67 to 38.10 % for the dropouts and from 6.06 to 15.15 % for the false alleles.

    Conclusions 

    These results indicate that both nondestructive and noninvasive samplings are suitable for avian microsatellite genotyping, save for fecal DNA. However, we should remain cautious of the appearance of genotyping errors, especially when using noninvasive material.

  • With complex geographical and climatic conditions, the forest areas in southeastern Tibet are home to many species of Galliformes. Previous fauna surveys in the region, either by foreigners during earlier times (Bailey, 1914; Battye, 1935; Ludlow and Kinnear, 1944) or by Chinese ornithologists since the 1960s (Cheng et al., 1983), only provided general information about the occurrence of Galliforme species. To understand the conservation status of these species in primary forests, we should have more quantitative data on habitat use and population abundance. Moreover, Galliforme species are susceptible to habitat change and are often treated as indicators of ecosystem health (Fuller et al., 2000; Fuller and Garson 2000; Storch, 2000). Data from areas with original ecosystems may provide a baseline for assessing the degree of habitat degradation in contrast to these highly human-disturbed areas.

    From May to October 1995, I investigated the habitat use of Galliformes in the upper Yigong Zangbu River, an area never explored by biologists. A further survey aimed at assessing the conservation status of the taxa in the area was made in May 2001.

    Fieldwork was carried out in the Sawang area (93°39′E, 32°24′N; Fig. 1), in Jiali county, southeastern Tibet, from May to October in 1995. Topographically, the study area is characterized by high mountains and deep canyons, with elevations ranging from 3700 to 6870 m, where most valley bottoms are less than 100 m wide. My survey area covered 32 km of the main valley and 14 km of three branches of the valley (Fig. 1). The vegetation is still original and varies vertically. On north-facing slopes < 4300 m in elevation, plant communities in the forest are dominated by Halfour spruce (Picea likiangensis) and between 4300–4800 m, by forests and scrubs of Rhododendron spp.; on south-facing slopes, between 3700–4300 m, the forest is dominated by Hollyleaf-like oak (Quercus aquifolioldes) between 4200–4700 m, by Tibetan juniper (Sabina tibetica) and at elevations > 4700 m, by alpine scrubs and meadows.

    Figure  1.  Spatial patterns of habitat in t survey area. Vertical lines: oak forests; crossed lines: spruce forests; circles: juniper forests; dots: Rhododendron shrubs; short oblique lines: alpine shrub-meadows; white sections: rocky zones; black sections: glaciers; thick lines: rivers and streams; black squares: villages.

    Along the entire valley of 50 km, there are only five Tibetan villages, with a very low population density (one person per 100 km2). Farmland is restricted to the bottom of the mountains. The villagers cut the oaks near the foot of the mountains for firewood, resulting in secondary scrub oak forests.

    Because the birds are shy in dense cover, I had few opportunities to catch sight of them. However, I found that feathers, fallen from their plumage, could survive for at least one month and were easy to identify in the field and distinguishable among species. The detection rate of feathers of each species in a defined habitat should be positively related with the number of birds and the time they spent in their habitat. Thus, encounter rates of molted feather samples were used as indicators of the relative abundance of Galliformes. The methodology of feather-counting was described by Lu and Zheng (2001). When collecting feather samples along the transects, I also noted individual birds, their flock size and membership. The data on individual sightings were provided in contrast to the results of feather-counting. I compared the flock size of each Galliforme species during the nesting period (late May to early July) to that in the chick-rearing period (mid-July to mid-October).

    All of seven species of Galliformes in the study area were found on south-facing slopes and only two species, the Chinese Grouse (Bonasa sewerzowi) and the Blood Pheasant (Ithaginis cruentus) also appeared on north-facing slopes (Table 1). A hybrid of the White Eared-pheasant (Crossoptilon crossoptilon) × the Tibetan Eared-pheasant (C. harmani) was the most predominant component of the Galliforme community, followed by Blood Pheasants and Chinese Grouse. These three species were relatively well adapted to the various types of vegetation in the area. Two other forest-dependent species, the Snow Partridge (Lerwa lerwa) and the Pheasant Grouse (Tetraophasis obscurus), were limited to the upper part of the forests with relatively low population densities, while a third species, the Crimson-bellied Tragopan (Tragopan temminckii) was only rarely sighted. Two meadow-dependent species, the Tibetan Snow Cock (Tetraogallus tibetanus) and the Tibetan Partridge (Perdix hodgsoniae), were relatively uncommon.

    Table  1.  Mean hourly encounter rates of Galliforme feather and individual (in parentheses) samples from the study area in summer
    Habitat Elevation (m) Survey time (h) Chinese Grouse Snow Partridge Tibetan Snow Cock Pheasant Grouse Tibetan Partridge Blood Pheasant Crimson-bellied Tragopan Hybrid Eared-pheasant
    Farmland 3700−3800 46.0 (0.04)
    South-facing slopes
    Secondary oak shrubs 3700−3900 39.6 0.05 (0.03) 0.81 (0.15)
    Oak forest 3800−4300 82.2 0.02 (0.02) 0.09 (0.04) 0.02 (0.01) 3.21 (0.34)
    Shrub-meadow above tree line 4300−4500 19.5 0.92
    Juniper forests 4200−4700 62.0 0.70 (0.13) 0.03 (0.03) 1.00 (1.00) 0.03 (0.02) 1.69 (0.27)
    Shrub-meadows above tree line 4600−4900 25.5 (0.04) (0.04) 0.75 (0.24)
    North-facing slopes
    Spruce forests 3700−4300 16.6 0.12 (0.12) 0.18 (0.18)
    Rhododendron 4300−4800 8.5 0.12
    Shrub-meadows above tree line 4600−4900 7.0
     | Show Table
    DownLoad: CSV

    The following provides further information about each species.

    The Chinese Grouse: This survey discovered a new distribution of the species, which extends its range from 98°40′ to 93°39′E. In the survey area, often 2–5 birds (3.4 ± 0.3, n = 11) were encountered in their preferred habitat with streams and dense scrub, sometimes in small open plots in the forest, feeding or dusting. If suddenly disturbed, the birds fly up to nearby trees.

    The Snow Partridge: In late June, three groups with five, five and six birds respectively were flushed from a juniper woodland close to the tree line, where their dusting sites were located. In late July, two birds were found in a scrub-grassland above the tree line.

    The Tibetan Snow Cock: Because of limited time of investigation in its preferred habitat, i.e., high-elevation meadows with rocks, I only saw one group of seven birds. One young bird, caught, weighted 0.53 kg, suggesting that the date of egg-laying of this bird was early April.

    The Pheasant Grouse: This bird limited its activities to the upper part of the forest dominated by oak but never moved out of the forest into the scrub-grassland above the tree line. If disturbed by dogs, this bird flew up to the top of trees. Its microhabitats consisted often of rocks and streams. Dusting sites beside a path visited by the birds were found at least three times.

    The Tibetan Partridge: Despite considerable efforts in investigating this species in the alpine scrub-meadows, believed suitable for this bird, I did not manage to find a single bird there. Only one pair was continuously seen at the foot of the mountains from June through July.

    The Blood Pheasant: The birds occurred in various habitats but their densities on south-facing slopes were higher than on north-facing slopes. They preferred microhabitats close to streams. Usually two birds (46.5%) (2.0 ± 0.3, ranging from 1–4, n = 11) remained together during the breeding season. I found in late September that these birds and Hybrid Eared-pheasants used the same dusting hollows. In winter, according to the villagers, flocks are formed of more than 10 individual birds, appearing at lower elevations.

    The Crimson-bellied Tragopan: Only two single birds were found in an oak woodland and a dusting site in the juniper forest.

    The Hybrid Eared-pheasant: This bird has the largest population among the Galliformes in the area and appeared in various habitats on south-facing slopes, with oak forests as its most preferred habitat. During the nesting period (May to July), flock size varied between 1 to 7 birds (2.9 ± 0.3, n = 43) and then increased (7.0 ± 1.0, 2–15, n = 14) during the brood-rearing period (August to October).

    My results showed that the Galliforme species in the study area tended to avoid coniferous forests dominated by Balfour spruce, an environment widely encountered on the eastern Qinghai-Tibet plateau and preferred by many species of Galliformes (Cheng et al., 1978; Johnsgard, 1999). The reason is thought to be that the climate in the woodland is so humid that ground-dwellers have difficulties in breeding and foraging (Lu and Zheng, 2001).

    Before the 1980s, rifles were available to local people. It is generally known that game animals, including Galliformes, were frequently killed during that period. In the mid 1990's, the Firearm Law of the People's Republic of China was issued, forbidding anybody to own and keep any kind of gun privately. As a result, pressure from hunting of wildlife has declined considerably. However, trapping, especially by people from outside Tibet, has not been entirely prohibited, causing a certain loss of Galliformes. Oak-cutting in nearby villages has led to the emergence of second scrub oak forests, not suitable to Galliformes. To encourage local people to use firewood in more effective ways (for example by promoting more efficient stoves), is one means of reducing the loss of oak forests.

    However, overall, because of low population densities, poor communication and less developed economies, as well as protection by local religious and government policies, Galliformes in the region have been facing relatively fewer threats. But it should be kept in mind that developing local economies and improved communication will inevitably pose a threat to wildlife. Therefore, development plans for unexplored areas should be carefully made, because once loss of biodiversity, derived from a long-term evolutionary trend, reestablishment is almost impossible.

    I suggest for government agencies to establish a nature reserve in the region. This will prevent large-scale landscape use in the future and also provide a foundation for enhancing public conservation awareness. To aid conservation, further studies on the biology and ecology of the Galliformes are needed.

    I would like to thank Duojicipei and his family for accommodation in the area. I am grateful to Bingyuan Gu, Soulong Ciren and Cangjue Zhuoma for their assistance in the survey. The field survey was supported by the Tibetan Bureau of Science and Technology, the National Natural Science Foundation of China (Grant No. 39800016) and the Tibet Important Bird Area Survey Programme organized by BirdLife International.

  • Baumgardt JA, Goldberg CS, Reese KP, Connelly JW, Musil DD, Garton EO, Waits LP. A method for estimating population sex ratio for sage-grouse using noninvasive genetic samples. Mol Ecol Resour. 2013;13:393–402.
    BirdLife International. Species factsheet: Egretta eulophotes. 2014. [].
    Bonin A, Bellemain E, Bronken Eidesen P, Pompanon F, Brochmann C, Taberlet P. How to track and assess genotyping errors in population genetics studies. Mol Ecol. 2004;13:3261–73.
    Brooks R, Williamson J, Hensley A, Butler E, Touchton G, Smith E. Buccal cells as a source of DNA for comparative animal genomic analysis. Biotech Lett. 2003;25:451–4.
    Broquet T, Petit E. Quantifying genotyping errors in noninvasive population genetics. Mol Ecol. 2004;13:3601–8.
    Brown MB, Brown CR. Blood sampling reduces annual survival in cliff swallows (Petrochelidon pyrrhonota). Auk. 2009;126:853–61.
    Bush KL, Vinsky MD, Aldridge CL, Paszkowski CA. A comparison of sample types varying in invasiveness for use in DNA sex determination in an endangered population of greater Sage-Grouse (Centrocercus uropihasianus). Conserv Genet. 2005;6:867–70.
    Costantini V, Guaricci AC, Laricchiuta P, Rausa F, Lacalandra GM. DNA sexing in Humboldt Penguins (Spheniscus humboldti) from feather samples. Anim Reprod Sci. 2008;106:162–7.
    Criscuolo F. Does blood sampling during incubation induce nest desertion in the female common eider Somateria mollissima. Mar Ornithol. 2001;29:47–50.
    Dai Y, Zhou X, Fang W, Lin Q, Chen X. Development and cross-species transferability of 23 microsatellite markers from the vulnerable Chinese Egret (Egretta eulophotes) using 454 sequencing. Conserv Genet Resour. 2013;5:1035–8.
    Deagle BE, Eveson JP, Jarman SN. Quantification of damage in DNA recovered from highly degraded samples—a case study on DNA in faeces. Front Zool. 2006;3:11.
    Egloff C, Labrosse A, Hebert C, Crump D. A nondestructive method for obtaining maternal DNA from avian eggshells and its application to embryonic viability determination in herring gulls (Larus argentatus). Mol Ecol Resour. 2009;9:19–27.
    Gagneux P, Boesch C, Woodruff DS. Microsatellite scoring errors associated with noninvasive genotyping based on nuclear DNA amplified from shed hair. Mol Ecol. 1997;6:861–8.
    Gebhardt KJ, Waits LP. High error rates for avian molecular sex identification primer sets applied to molted feathers. J Field Ornithol. 2008;79:286–92.
    Handel CM, Pajot LM, Talbot SL, Sage GK. Use of buccal swabs for sampling DNA from nestling and adult birds. Wildl Soc Bull. 2006;34:1094–100.
    Horvâth MB, Martìnez CB, Negro JJ, Kalmâr L, Godoy JA. An overlooked DNA source for non-invasive genetic analysis in birds. J Avian Biol. 2005;36:84–8.
    Huang X, Zhou X, Chen M, Fang W, Chen X. Isolation and characterization of microsatellite loci in vulnerable Chinese egret (Egretta eulophotes: Aves). Conserv Genet. 2010;11:1211–4.
    Huang X, Zhou X, Lin Q, Peng Z, Fang W, Chen X. A novel multiplex PCR assay for species identification in the Chinese Egret (Egretta eulophotes) and Little Egret (E. garzetta). Conserv Genet Resour. 2012a;4:31–3.
    Huang X, Zhou X, Lin Q, Fang W, Chen X. An efficient molecular sexing of the vulnerable Chinese egret (Egretta eulophotes) from faeces samples. Conserv Genet Resour. 2012b;4:391–3.
    Huang X, Zhou X, Lin Q, Fang W, Chen X. PCR-RFLP technique for species identification of molted feathers in six species of co-occurring Ardeids. Conserv Genet Resour. 2013;5:817–9.
    Idaghdour Y, Broderick D, Korrida A. Faeces as a source of DNA for molecular studies in a threatened population of great bustards. Conserv Genet. 2003;4:789–92.
    Isabel MC, Del Lama Sn. Molted feathers as a source of DNA for genetic studies in waterbird populations. Waterbirds. 2009;32:322–9.
    Johansson MP, Mcmahon BJ, Höglund J, Segelbacher G. Amplification success of multilocus genotypes from feathers found in the field compared with feathers obtained from shot birds. Ibis. 2012;154:15–20.
    Kalinowski ST, Taper ML, Marshall TC. Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol Ecol. 2007;16:1099–106.
    Kang JH, Kim IK, Lee H, Rhim SJ. Distribution and Breeding Status of Chinese Egret Egretta eulophotes in South Korea. J Anim Vet Adv. 2013;12:618–20.
    Litvinenko NM, Shibaev YV. Importance of Furugelm Island in the Sea of Japan for wetland birds: the first record of a breeding colony of the Chinese egret Egretta eulophotes. Oryx. 2000;34:335–7.
    Martín-Gálvez D, Peralta SJ, Dawson D, Martín PA, Martínez BM, Burke T, Soler JJ. DNA sampling from eggshell swabbing is widely applicable in wild bird populations as demonstrated in 23 species. Mol Ecol Resour. 2011;11:481–93.
    Matysioková B, Remeš V. The importance of having a partner: male help releases females from time limitation during incubation in birds. Front Zool. 2014;11:24.
    Miquel C, Bellemain E, Poillot C, Bessiere J, Durand A, Taberlet P. Quality indexes to assess the reliability of genotypes in studies using noninvasive sampling and multiple-tube approach. Mol Ecol Notes. 2006;6:985–8.
    Pompanon F, Bonin A, Bellemain E, Taberlet P. Genotyping errors: causes, consequences and solutions. Nat Rev Genet. 2005;6:846–7.
    Regnaut S, Lucas FS, Fumagalli L. DNA degradation in avian faecal samples and feasibility of non-invasive genetic studies of threatened capercaillie populations. Conserv Genet. 2006;7:449–53.
    Renan S, Speyer E, Shahar N, Gueta T, Templeton AR, Bar D. A factorial design experiment as a pilot study for noninvasive genetic sampling. Mol Ecol Resour. 2012;12:1040–7.
    Rousset F. GENEPOP'007: a complete re-implementation of the genepop software for Windows and Linux. Mol Ecol Resour. 2008;8:103–6.
    Sacchi P, Soglia D, Maione S, Meneguz G, Campora M, Rasero R. A non-invasive test for sex identification in Short-toed Eagle (Circaetus gallicus). Mol Cell Probe. 2004;18:193–6.
    Schmaltz G, Somers CM, Sharma P, Quinn JS. Non-destructive sampling of maternal DNA from the external shell of bird eggs. Conserv Genet. 2006;7:543–9.
    Shen Z, Qu W, Wang W, Lu Y, Wu Y, Li Z, Zhang C. MPprimer: a program for reliable multiplex PCR primer design. BMC Bioinformatics. 2010;11:143.
    Skutch AF. The incubation patterns of birds. Ibis. 1957;99:69–93.
    Taberlet P, Bouvet J. A single plucked feather as a source of DNA for bird genetic studies. Auk. 1991;108:959–60.
    Taberlet P, Griffin S, Goossens B, Questiau S, Manceau V, Escaravage N, Bouvet J. Reliable genotyping of samples with very low DNA quantities using PCR. Nucleic Acids Res. 1996;24:3189–94.
    Taberlet P, Waits LP, Luikart G. Noninvasive genetic sampling: look before you leap. Trends Ecol Evol. 1999;14:323–7.
    Van Oosterhout C, Hutchinson WF, Wills DP, Shipley P. MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes. 2004;4:535–8.
    Wang Z, Zhou X, Lin Q, Fang W, Chen X. New primers for sex identification in the Chinese Egret and other ardeid species. Mol Ecol Resour. 2011;11:176–9.
    Wang Z, Zhou X, Lin Q, Fang W, Chen X. Characterization, polymorphism and selection of major histocompatibility complex (MHC) DAB genes in vulnerable Chinese egret (Egretta eulophotes). PLoS One. 2013;8:e74185.
    Wellbrock AH, Bauch C, Rozman J, Witte K. Buccal swabs as a reliable source of DNA for sexing young and adult Common Swifts (Apus apus). J Ornithol. 2012;153:991–4.
    Yannic G, Sermier R, Aebischer A, Gavrilo MV, Gilg O, Miljeteig C, Broquet T. Description of microsatellite markers and genotyping performances using feathers and buccal swabs for the ivory gull (Pagophila eburnea). Mol Ecol Resour. 2011;11:877–89.
    Zhou X, Wang Y, Chen X, Lin Q, Fang W, Wei D. A set of primer pairs for amplifying the complete mitochondrial DNA of endangered Chinese egret (Aves, Ardeidae, Egretta eulophotes). Mol Ecol Resour. 2008;8:412–4.
    Zhou X, Fang W, Chen X. Mitochondrial DNA diversity of the vulnerable Chinese Egret (Egretta eulophotes) from China. J Ornithol. 2010;151:409–14.
    Zhou X, Lin Q, Fang W, Chen X. The complete mitochondrial genomes of sixteen ardeid birds revealing the evolutionary process of the gene rearrangements. BMC Genom. 2014;15:573.
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