Genetic structure of Mediterranean chukar (Alectoris chukar, Galliformes) populations as inferred by mitochondrial and microsatellite DNA markers: suggestions for their conservation.
Bibliographic record
Abstract
The chukar (Alectoris chukar, Galliformes) is a widespread, stantial game bird whose native distribution ranges from Greece and southeastern Bulgaria across mountainous areas of Middle East throughout central Asia until Manchuria, China. The chukar has been successfully introduced into North America (Canada and USA, Hawaii included), South Africa and New Zealand. Although most of the native chukar populations are not decreasing in their effective size, the survival of isolated groups is strongly threatened by genetically uncontrolled translocations for hunting purposes. Our study aimed to determine the genetic structure of the chukar populations colonizing a few Greek islands in the Aegean Sea such as, from north to south, Limnos, Lesvos, Chios and Crete as well as the Island of Cyprus. The final goal of this work was to provide useful information to game bird managers to bring the commercial exchange of Mediterranean chukar partridges into line with knowledge of their genetic kinship. A total of 143 samples (hunted birds: liver; captive birds: feathers) were collected. Particularly, they were obtained from wild partridges of Limnos (n = 22), Lesvos (n = 20), Chios (n = 21) and Crete (n = 27). From the last one some samples (n = 5) were also obtained from captive birds of “Game farm of Forest Service of Rethymno”. Finally, 48 samples were collected in Cyprus (12, from the only government farm; 24, from two wild geographically separated populations of the territory of the Republic; 12, from the Turkish-occupied part of the island). In order to determine whether genetically isolated groups do exist and need to be managed as distinct Management Units (MUs), the evolutionary relationships among populations were inferred by means of both mitochondrial (mtDNA) and microsatellite DNA markers. Two mtDNA segments were amplified by Polymerase Chain Reaction (PCR) and then directly sequenced on both strands for each specimen: the Cytochrome-b (Cyt-b) gene and the Control Region (CR) (2248 characters per specimen, total). A genetic comparison with a very large number of Asian and US introduced conspecific specimens: n = 118; feathers, blood, liver and scats; from 17 countries) was performed. Furthermore, eight microsatellite DNA loci originally isolated from either chicken (Gallus gallus, Wageningen University, The Netherlands: MCW 104, MCW 121, MCW 146, MCW 276, MCW 295) or red-legged partridge genome (A. rufa: Aru 1.23, Aru 1.27, Aru 1.29) were investigated only for the above-mentioned Greek and Cypriot chukars. Phylogenetic reconstructions (Neighbor-Joining, Maximum Parsimony, Maximum-Likelihood) obtained using Cyt-b + CR joined sequences showed that Greek and Cypriot populations all belong to a very large clade including Mediterranean, Middle East and Central Asian samples, which was clearly separated from a second clade to whom chukars from far East Asia as well as introduced US populations were assigned. A few Greek specimens (n = 13: from Crete, Lesvos and Chios) were included in the second clade suggesting their maternal origin from translocated specimens. Particularly, four out of five specimens from Cretan farm were assigned to the East Asia clade. The analysis of the population structure by means of microsatellite and mtDNA markers (Analysis of Molecular Variance, Fst, Bayesian inference, Principal Component Analysis, Factorial Correspondence Analysis) allowed suggesting that each island hosts a genetically isolated group. In Cyprus, two genetically isolated groups were found: the first, comprehending just the Turkish-occupied area’s population, and the second comprehending all of the others three populations, with low level of gene flow between them. These results suggest the existence of genetically (and, for Cyprus, also demographically) isolated populations that, in the absence of ecological data, should be treated as separate MUs. A wider genetic survey on Greek chukar farms is suggested to assess the level of admixture between native and allochthonous animals in order to establish genetically homogeneous reference stocks.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".