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Genetic structure of Mediterranean chukar (Alectoris chukar, Galliformes) populations: conservation and management implications

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Abstract

The chukar (Alectoris chukar, Galliformes) is a species hunted throughout its native range from the East Mediterranean to Manchuria and in the USA, which hosts the world’s largest introduced population. This study aims to investigate the genetic structure of Mediterranean chukar populations to aid management decisions. We genotyped 143 specimens at two regions of the mitochondrial DNA (mtDNA: cytochrome b, control region) and eight loci of the microsatellite DNA. Samples were collected in northern (Limnos, Lesvos, Chios) and southern (Crete) Aegean islands (Greece) and Cyprus. We also carried out mtDNA-based comparison with chukars (n = 124) from Asia (16 countries) and the USA (five states). We propose six management units for Mediterranean populations. Given their genetic integrity, Limnos and Cyprus, which host different subspecies, proved to be of primary conservation interest. We found exotic A. chukar mtDNA lineages in Lesvos, Chios and Crete and produced definitive genetic evidence for the Asian origin of the US chukars.

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Acknowledgements

Chukar samples were provided by: P. Birtsas (Hunting Federation of Macedonia-Thrace), G. Arnellos and A. Sakoulis (Hunting Federation of Crete), P. Lemanis (Hunting Federation of Archipelago) and C. Barboutis (University of Crete) from Greece; L. Gilbertson (Nevada Department of Wildlife, Reno, Nevada) and R. Kaholoaa (Resources Management Division, Haleakala National Park, Maui, Hawaii) from USA; Natural History Museum of Crete (Heraklion, Greece, NHMC samples: from 80.4.59.11 to 80.4.59.23); University of Washington Burke Museum (Seattle, Washington, UWBM samples: 46402, 46516, 57853, 57857, 57859, 66692). We deeply thank G. Paoli and L. Taglioli (Department of Biology, University of Pisa) for their valuable support in the statistical analyses as well as Alan Crabtree (Cyprus) and Peter Wilkinson (UK) for their helpful linguistic revision of the paper and for their constructive comments. The Cypriot Game Fund Service, Ministry of the Interior, Nicosia (Cyprus) granted this research.

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Authors and Affiliations

  1. Department of Biology, Protistology–Zoology Unit, Via A. Volta 6, 56126, Pisa, Italy

    Filippo Barbanera, Chiara Marchi & Monica Guerrini

  2. National Environmental Research Institute, Department of Wildlife Ecology and Biodiversity, University of Aarhus, Grenåvej 14, 8410, Rønde, Denmark

    Chiara Marchi

  3. Cypriot Game Fund Service, Ministry of the Interior, 1453, Nicosia, Cyprus

    Panicos Panayides & Pantelis Hadjigerou

  4. Hunting Federation of Macedonia-Thrace, Ethnikis Antistaseos 173–175, 55134, Thessaloniki, Greece

    Christos Sokos

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  1. Filippo Barbanera
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Correspondence to Filippo Barbanera.

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S1

Chukar sampling localities are indicated for each island (a–e). a Limnos (477 km2): (1) Agios Dimitrios, (2) Papias Ormos, (3) Gomati, (4) Paradisi. b Lesvos (1,630 km2): (1) Mesotopus, (2) Lapsarna, (3) Tsichlioda. c Chios (840 km2): (1) Trypes, (2) Amades, (3) Kardamyla, (4) Agia Markella. d Cyprus (9,250 km2): (1) Paphos forest, (2) Karpasia, (3) Larnaka coastal area, (4) Stavrouvoni farm; dotted line marks out the border between the government-controlled area and the Turkish-occupied territory. e Crete (8,400 km2): (1) Lefka mountains, (2) Rethymno farm, (3) Psiloreitis, (4) Heraklion, (5) Dikti, (6) Ierapetra, (7) Sitia (DOC 4392 kb)

S2

Chukar sample size (n = 267). Geographic reference is reported together with population type, number of samples, type of tissue, number of haplotypes (Cyt-b + CR sequences) and literature record. *: with samples of Natural History Museum of Crete (acronym NHMC: from 80.4.59.11 to 80.4.59.23); **: with samples of University of Washington Burke Museum (acronym UWBM: 46402, 46516, 57853, 57857, 57859, 66692). One wild A. graeca specimen (Southern Apennines, Italy; type of tissue: liver; haplotype: H113) was used as out-group. Abbreviations: Prov., Province; NP, National Park (DOC 106 kb)

S3

The STR primers. Legend: F, forward; R, reverse; Ta (°C), first/second annealing temperature in touchdown (TD) PCR (DOC 33 kb)

S4

The frequency distribution of A. chukar specimens belonging to the A (white) or B (black) mtDNA clades of Fig. 1 is reported for all populations (S2). a Europe and Asia. For both Crete and Cyprus, the percentage was calculated by pooling together all wild and captive specimens. Triangles mark out the main mountain chains in Asia. b USA: the study areas are indicated (five states) (DOC 592 kb)

S5

The principal components analysis performed using the pairwise ϕST distances calculated for the ingroup of the mtDNA reconstructions. Specimens are grouped according to each population (S2) (DOC 164 kb)

S6

The outcome (t value, degrees of freedom or df, P value) of the Student t test for all pairs of populations (Pop. 1 vs. Pop. 2) as obtained for nucleotide diversity (π), haplotype diversity (h), mean number of pairwise differences (k) and index of Nei (I N). No significant differences were found after application of the Bonferroni correction (α = 0.05: for π, h and k, \( \alpha \prime = \alpha /28 = 0.001786 \); for I N, \( \alpha \prime = \alpha /36 = 0.001389 \)). Abbreviations: Cyprus-Paphos, Paphos forest; Cyprus-Larnaka, Larnaka coastal area; Cyprus-Karpasia, Karpasia; Cyprus-Farm, Stavrouvoni farm; Crete-Farm, Rethymno farm. −: Crete-Farm mtDNA data not computed, see “Material and methods” (DOC 84 kb)

S7

STR variability for each population: n, sample size; nA, number of alleles per locus; na, number of unique alleles; Ar, allelic richness; I n, Nei’s index with standard deviation (SD); H O, observed heterozygosity; H E, expected heterozygosity; P, probability value for the HWE test; χ 2 test with relative degrees of freedom (df; Fisher global test, all loci). Mono., monomorphic locus; *: significant departure from HWE after application of the Bonferroni correction (α = 0.05, \( \alpha \prime = \alpha /8 = 0.006 \)). Abbreviations: Cyprus-Paphos, Paphos forest; Cyprus-Larnaka, Larnaka coastal area; Cyprus-Karpasia, Karpasia; Cyprus-Farm, Stavrouvoni farm; Crete-Farm, Rethymno farm (DOC 139 kb)

S8

Fisher global test for departure from linkage disequilibrium (LE) with application of the Bonferroni correction (α = 0.05, \( \alpha \prime = \alpha /28 = 0.0018 \)). Significant departure was found only in the Lesvos population (see data in bold); –: comparison not possible as one locus was monomorphic (DOC 57 kb)

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Barbanera, F., Marchi, C., Guerrini, M. et al. Genetic structure of Mediterranean chukar (Alectoris chukar, Galliformes) populations: conservation and management implications. Naturwissenschaften 96, 1203–1212 (2009). https://doi.org/10.1007/s00114-009-0586-x

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