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      Deciphering the Patterns of Genetic Admixture and Diversity in the Ecuadorian Creole Chicken

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          Abstract

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          In Ecuador, the production of Ecuadorian Creole chicken is of crucial importance in the economy and for the nutrition of families. These chickens represent a focal point in scientific research for three main reasons: (1) they are an unknown genetic resource derived from 500 years of environmental and human selection and represent an important reservoir of genetic variability and adaptability; (2) Ecuadorian Creole chicken production is normally familiar, in a marginal dimension, and it is an important source of economic input for medium–low income communities; and (3) being a local genetic resource, it is available to local communities without intermediary international enterprises and represents the starting point for food sovereignty. We aimed to measure the level of genetic diversity and its phylogenetic position compared with other outgroup breeds using information from microsatellite and mitochondrial markers. Our results showed that these chicken populations represent a great reservoir of genetic variability; however, the genetic fragmentation owing to the high geographical diversity of the country could compromise the conservation status and, therefore, the establishment of an official breeding program is needed for the conservation and valuation of these avian populations, with this genetic characterization being a first step.

          Abstract

          Latin American Creole chickens are generally not characterized; this is the case in Ecuador, where the lack of scientific information is contributing to their extinction. Here, we developed a characterization of the genetic resources of Ecuadorian chickens located in three continental agroecosystems (Pacific coastal, Andean, and Amazonian). Blood samples of 234 unrelated animals were collected in six provinces across Ecuador: Bolívar, Chimborazo, Cotopaxi, Guayas, Morona Santiago, and Tungurahua, in order to perform a genetic characterization and population structure assessment using the AVIANDIV project microsatellites panel (30 loci) and D-loop sequences of mitochondrial DNA and comparing with reference data from other breeds or genetic lines. The results indicate that Ecuadorian Creole chickens are the result of the admixture of different genetic groups that occurred during the last five centuries. While the influence of South Spanish breeds is demonstrated in the colonial age, genetic relationships with other breeds (Leghorn, Spanish fighter cock) cannot be discarded. The geographical configuration of the country and extreme climate variability have influenced the genetic isolation of groups constituting a homogeneous genetic status into the whole population. This is not only a source of genetic variation, but also a critical point because genetic drift produces a loss of genetic variants.

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          Counting Alleles with Rarefaction: Private Alleles and Hierarchical Sampling Designs

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            Bayesian clustering using hidden Markov random fields in spatial population genetics.

            We introduce a new Bayesian clustering algorithm for studying population structure using individually geo-referenced multilocus data sets. The algorithm is based on the concept of hidden Markov random field, which models the spatial dependencies at the cluster membership level. We argue that (i) a Markov chain Monte Carlo procedure can implement the algorithm efficiently, (ii) it can detect significant geographical discontinuities in allele frequencies and regulate the number of clusters, (iii) it can check whether the clusters obtained without the use of spatial priors are robust to the hypothesis of discontinuous geographical variation in allele frequencies, and (iv) it can reduce the number of loci required to obtain accurate assignments. We illustrate and discuss the implementation issues with the Scandinavian brown bear and the human CEPH diversity panel data set.
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              Chicken domestication: an updated perspective based on mitochondrial genomes.

              Domestic chickens (Gallus gallus domesticus) fulfill various roles ranging from food and entertainment to religion and ornamentation. To survey its genetic diversity and trace the history of domestication, we investigated a total of 4938 mitochondrial DNA (mtDNA) fragments including 2843 previously published and 2095 de novo units from 2044 domestic chickens and 51 red junglefowl (Gallus gallus). To obtain the highest possible level of molecular resolution, 50 representative samples were further selected for total mtDNA genome sequencing. A fine-gained mtDNA phylogeny was investigated by defining haplogroups A-I and W-Z. Common haplogroups A-G were shared by domestic chickens and red junglefowl. Rare haplogroups H-I and W-Z were specific to domestic chickens and red junglefowl, respectively. We re-evaluated the global mtDNA profiles of chickens. The geographic distribution for each of major haplogroups was examined. Our results revealed new complexities of history in chicken domestication because in the phylogeny lineages from the red junglefowl were mingled with those of the domestic chickens. Several local domestication events in South Asia, Southwest China and Southeast Asia were identified. The assessment of chicken mtDNA data also facilitated our understanding about the Austronesian settlement in the Pacific.
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                Author and article information

                Journal
                Animals (Basel)
                Animals (Basel)
                animals
                Animals : an Open Access Journal from MDPI
                MDPI
                2076-2615
                11 September 2019
                September 2019
                : 9
                : 9
                : 670
                Affiliations
                [1 ]Escuela Superior Politécnica de Chimborazo, Panamericana Sur Km 1 ½, EC060155, Riobamba, Ecuador; paulasol37@ 123456yahoo.es (P.A.T.V.); luisfior@ 123456yahoo.es (L.R.F.O.); dralexvillafuerte@ 123456hotmail.com (A.A.V.G.)
                [2 ]Centro Agropecuario Provincial de Córdoba, Diputación Provincial de Córdoba, 14071 Córdoba, Spain; jomalejur@ 123456yahoo.es
                [3 ]Department of Genetics, Faculty of Veterinary Sciences, University of Cordoba, 14071 Cordoba, Spain; amparomartinezuco@ 123456gmail.com (A.M.); id1debej@ 123456uco.es (J.V.D.)
                [4 ]Animal Breeding Consulting sl., C/. Astrónoma Cecilia Payne, ID-1, 8-PE, Rabanales 21, 14014 Cordoba, Spain
                Author notes
                [* ]Correspondence: landivincenzo@ 123456yahoo.it ; Tel.: +34-630639439
                Article
                animals-09-00670
                10.3390/ani9090670
                6770841
                31514349
                65b92fae-c7e3-406a-ae98-887e18acb5fb
                © 2019 by the authors.

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

                History
                : 14 August 2019
                : 06 September 2019
                Categories
                Article

                creole chicken,microsatellites markers,d-loop,conservation

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