Founder Genome Equivalents Research Articles

Population structure and genetic diversity of Polish Arabian horses based on pedigree data

With a history tracing back to at least the 18th century and a substantial global influence on various breeds, Polish Arabian horse population is of paramount importance for both breeders and conservationists. However, its genetic makeup and the population dynamics are still not well understood. This study presents an analysis of the modern Polish Arabian horse population using pedigree data, focusing on the breed's genetic diversity and population structure. Our analysis encompassed 1 498 individuals defined as the reference population (RP) and their 11 065 ancestors, which resulted in the dataset of 12 254 individuals (total population). We traced their genealogy to assess inbreeding coefficients (F), founder effects, and genetic variability measures such as the effective number of founders (fe), ancestors (fa), or founder genome equivalents (fge). The results indicated a good pedigree quality with an average of 28.1 maximum traced generations, revealing high pedigree completeness for initial generations with a decline beyond the seventh generation. The genetic diversity parameters showed a considerable bottleneck effect, with an effective number of founders at 73, which reflects a substantial loss of genetic diversity over time. Despite the vast total number of founders (852), only a few have had a lasting impact on the current population, signaling the need for revised breeding strategies to maintain diversity. The study identified a slight but consistent rise in inbreeding over the last century, with a marginal recent decline, and a significant difference in the contribution of various founders. The average F was 5.8%, with 99.6% of the reference population being inbred. The analysis of effective population size (Ne) highlighted potential risks for genetic diversity, urging for revision of breeding goals to consider a wider array of founder lineages. The study indicated that stallions belonging to RP can be attributed to 15 distinct sirelines, whereas mares to 45 unique damlines, more than considered in the current breeding program (8 and 15, respectively). Conclusively, the study underlines the need for ongoing monitoring and strategic breeding to maintain and enhance the genetic diversity of Polish Arabians, considering the breed's historical significance and contemporary genetic challenges.

Pedigree analysis in the mhorr gazelle (Nanger dama mhorr): Genetic variability evolution of the captive population.

Breeding programs have an essential role in the recovery of threatened populations through optimal genetic management and mating strategies. The dama gazelle (Nanger dama) is a North African ungulate listed as critically endangered. The mhorr subspecies is extinct in the wild and currently survives thanks to the creation in 1971 of an ex situ breeding program. The aim of the present study was to assess the evolution of genetic variability in this mhorr gazelle captive population, as well as the mating strategy used in two reference populations studied (Almeria and Europe). The entire pedigree, with 2739 animals, was analyzed to measure demographic characters, pedigree completeness level, probability of gene origin, level of relatedness and genetic structure of the population. The population size has been progressively increasing, with up to 264 individuals alive in Europe at the time of the study. The average number of equivalent complete generations was 5.55. The effective number of founders and ancestors was both 3, and the founder genome equivalent was 1.99. The genetic contributions of the four main ancestors were unbalanced. The average values of inbreeding and average relatedness for the whole pedigree were, respectively, 28.34% and 50.14%. The effective population size was 8.7 by individual increase in inbreeding and 9.8 by individual increase in coancestry. F-statistics evidenced a very small level of population subdivision (F ST = 0.033370). The mating strategy used, based on the minimum coancestry of the individuals, has minimized the losses of genetic variability and helped to balance the genetic contributions between ancestors. The strategy also avoided large subdivisions within the population and the appearance of new bottlenecks. This study shows how pedigree analysis can both be used to determine the genetic variability of the population and to assess the influence of the mating strategy used in the breeding program on such variability.

Genetic impact of external Targhee sires at the U.S. Sheep Experiment Station: a case study of introgression.

Sheep breeders requested that the U.S. Sheep Experiment Station (USSES) to participate in national genetic evaluation through the National Sheep Improvement Program (NSIP). The reasons included the need for (1) a comparison of the productivity of industry and United States Department of Agriculture (USDA) lines, (2) transparency of USDA flocks, (3) genetic ties for NSIP by sampling of industry flocks, and (4) development of premium genetic lines for public release. In response, USSES began to incorporate external sires from NSIP participating flocks into the USSES Targhee flock. Our objective, based on a pedigree analysis, was to test if introgression of external genetics into the flock was achieved. The pedigree included 13,189 animals with mean maximum generations, mean complete generations, and mean equivalent complete generations of 4.2, 1.8, and 2.6, respectively. The mean generation interval was 3.1 yr. The reference population was defined as lambs born from 2021 to 2023 (n = 792). Two additional populations were defined as the current mature ewe flock (n = 123) and the current mature rams (n = 14). The Genetic Conservation Index averaged 7.7 for the full population and 25.7 for the reference population. Overall inbreeding was 0.003 for the full population and 0.006 for the reference population. The rate of inbreeding was 0.0003 per generation. Average relatedness was 0.015 for the full population and 0.018 for the reference population. The effective number of founders, effective number of ancestors, and founder genome equivalents contributing to the reference population were 60, 39, and 19.1, respectively. The ratio of the effective number of founders to the effective number of ancestors was 1.5, indicating the presence of genetic bottlenecks. Measures of effective population size ranged from 102 to 547. Of the 704 offspring produced by external sires, 17 ram lambs and 132 ewe lambs were retained for breeding. The USSES sires produced 299 offspring with 2 ram lambs and 51 ewe lambs retained. Incorporating external sires resulted in a cumulative percentage of genetic variance of 48.8, 49.1, and 44.2 of external genetics for the reference population, current mature ewe flock, and current mature rams, respectively. Stakeholder needs were addressed by introgression of external sires and participation in NSIP, but future selection practices need to be modified to maintain a minimum of 50% USSES core genetics in the flock.

Applying genomics to metapopulation management in North American insurance populations of southern sable antelope (Hippotragus niger niger) and addra gazelle (Nanger dama ruficollis)

Insurance populations can provide a short-term safeguard for at-risk species. The goal for all insurance populations should be to maintain a high welfare, genetically diverse, self-sustaining population that is available for eventual reintroduction of animals back into the wild when it is safe to do so. However, many insurance populations in zoos are not meeting sustainability goals, and there is a need for larger conservation centers and sanctuaries, a greater focus on threatened species, and metapopulation management between independently managed populations. Within North America, privately-owned ranches frequently maintain large populations of threatened ungulates that are presently managed independently from AZA-accredited zoos. Using a large set of single nucleotide polymorphisms, we generated empirical kinship and genetic distance estimates for AZA and private ranch populations of southern sable antelope ( Hippotragus niger niger ) and critically endangered addra gazelle ( Nanger dama ruficollis ). We used stochastic population models to project population mean kinship ( mk ) and founder genome equivalents (FGE) over time with and without genetic metapopulation management, using empirical kinships and genetic distances to guide transfers. Mean kinship-guided transfers were consistently beneficial for all study populations, for both species. Genetic distance-guided transfers, however, resulted in modest population mk increases for AZA populations, but predicted remarkable decreases in population mk for ranch populations. Although predicted benefits varied depending on management approach, our results show that a metapopulation management plan, whether mutually beneficial or altruistic, best supports species conservation by mitigating the loss of genetic diversity, minimizing the possibility of inbreeding, and yielding genetically diverse animals.

Pedigree analysis of a red fox (Vulpes vulpes) population

Abstract Fur animal breeding has a long history. In many countries several fur animal species (including the red fox) have been recognized as livestock. The aim of this study was to estimate the pedigree parameters in the population of red fox on a Polish breeding farm. The data set consisted of information on 39 434 individuals, including 18 697 females and 20 004 males (733 animals were of unknown sex), from the years 1956–2016. The following pedigree parameters were estimated: average number of discrete generation equivalents, individual inbreeding coefficient, total and effective number of founders, effective population size, average relationship, founder genome equivalent, effective number of non-founders, and genetic diversity coefficient. The population size changed in successive years. The average inbreeding level was 5.34% for the population as a whole, and 6.04% for the inbred population. The estimated effective number of founders of the population was 84.18. The founder genome equivalent, which indicates the anticipated loss of genetic diversity caused by genetic drift, reached 9.59 in 2016 from an initial value of 34.22 in 1956. The loss of genetic diversity caused by the unequal contribution of the founder alleles did not change significantly over the years. Generally, the results indicate the good pedigree structure (including pedigree completeness) of the population studied. This implies reliable estimation of the inbreeding level, as one of the most important parameters in the genetic improvement programme.

Pedigree analysis of the racing line Quarter Horse: Genetic diversity and most influential ancestors

The aims of this study were to evaluate the genetic diversity of the racing line Quarter Horse breed in Brazil and to provide data on the most influential ancestors by pedigree analysis. All horses that had participated in sprint races in Brazil between 1978 and 2016 were evaluated. There were 5,861 athletes horses (2,474 males and 3,387 females) born between 1971 and 2014. These animals were referred to as the racing population (Pr), which was divided into three subpopulations to evaluate three complete decades (84.5% of Pr). These subpopulations consisted of 1,712, 1,604 and 1,461 animals born in the 1980s (sP80), 1990s (sP90) and 2000s (sP00), respectively. The quality of the pedigree was assessed based on the number of complete equivalent generation traced. There were 5.4 (Pr), 4.7 (sP80), 5.7 (sP90) and 6.3 (sP00) generations, which permitted accuracy of the conclusions reported. The generation intervals were long, with 13.2 (sire-son/daughter) and 10.6 (dams-son/daughter) years (Pr). The coefficients of inbreeding and average relatedness were 0.95% and 1.84% for Pr and 1.60% and 2.56% for sP00, respectively. In Pr and sP00, the effective population size (Ne) based on ΔFi was 215 and 144, respectively, with 68 and 41 animals per generation. The probability of gene origin given by the effective number of founders (fe), ancestors (fa) and founder genome equivalents (fge) was 192, 61 and 34, respectively, for Pr, with considerable losses of genetic diversity over the last decades evaluated. The number of ancestors (founders or not) that explained the total genetic diversity was 1,587. This number is considered high; however, only 32 and 9 ancestors explained 50% of the genetic diversity of Pr and sP00, respectively. The 10 most influential ancestors of sP00 explained 52.2% of the total genetic diversity. The loss of genetic diversity and concentration in a reduced number of breeding animals indicate failures in the breeding and conservation programs of the racing line. Mating designs in conjunction with the selection of breeding animals should be promoted and goals should be defined for racing line of the Quarter Horse breed in Brazil.

Statistical analysis in support of maintaining a healthy traditional Siamese cat population

BackgroundFor many years, breeders of companion animals have applied inbreeding or line breeding to transfer desirable genetic traits from parents to their offspring. Simultaneously, this resulted in a considerable spread of hereditary diseases and phenomena associated with inbreeding depression.ResultsOur cluster analysis of kinship and inbreeding coefficients suggests that the Thai or traditional Siamese cat could be considered as a subpopulation of the Siamese cat, which shares common ancestors, although they are considered as separate breeds. In addition, model-based cluster analysis could detect regional differences between Thai subpopulations. We show that by applying optimal contribution selection and simultaneously limiting the contributions by other breeds, the genetic diversity within subpopulations can be improved.ConclusionIn principle, the European mainland Thai cat population can achieve a genetic diversity of about 26 founder genome equivalents, a value that could potentially sustain a genetically diverse population. However, reaching such a target will be difficult in the absence of a supervised breeding program. Suboptimal solutions can be obtained by minimisation of kinships within regional subpopulations. Exchanging animals between different regions on a small scale might be already quite useful to reduce the kinship, by achieving a potential diversity of 23 founder genome equivalents. However, contributions by other breeds should be minimised to preserve the original Siamese gene pool.

Genetic diversity of the Polish Hunting Dog population based on pedigree analyses and molecular studies

The aim of the study was to determine the degree of relatedness between individuals in the Polish Hunting Dog population and to assess the genetic variability of the population based on pedigree analysis and molecular DNA testing. Pedigree data on Polish Hunting Dogs provided by the Polish Kennel Club was used. In total, data on 2783 individuals were obtained. DNA was obtained from cheek swabs taken from 177 dogs of the tested breed. A panel of 21 markers (Short Tandem Repeat - STR) was used. On the basis of genotypes in microsatellite loci, assessment of the Hardy-Weinberg genetic equilibrium was also carried out in the analyzed dog population using the χ2 test. The pedigree data contributed to identification of 26 founders. The Founder Genome Equivalent was 4.17, Founder Genomes Surviving was 17.03 and effective population size (Mean Ne) was estimated at 28.51. The gene diversity was 0.8802, the population mean kinship was 0.1198, and the mean inbreeding was 0.1151. Studies of STR markers revealed polymorphic information content – PIC = 0.56, and the estimated values of expected heterozygosity were generally close to the observed heterozygosity values and on average amounted to 0.6050 and 0.6142, respectively. The calculated average inbreeding coefficient (FIS) value was negative −0.012, which suggests a low level of inbreeding in the examined breed as well as avoidance of related animals in mates.

Managing genomes of conserved livestock breeds with historical introgression to decrease genetic overlap with other breeds.

Recovering the native genetic background of a breed and increasing the founder genome equivalent (FGE) that is contributed by a breed to the gene pool of the species can increase its value for conservation. The suitability of several strategies was compared, whereby a hypothetical multi-breed population, the core set, was used to approximate the genetic diversity of the species. Twenty-five generations of management were simulated based on genotypes of German Angler cattle. The scenarios were compared when the kinship reached 0.10. The native contribution (NC) increased in a population with 400 births per generation from 0.317 to 0.706, whereas 1,000 births enabled to reach 0.894. This scenario maximized the NC, constrained the native kinship, and the kinship of the core set so that its genetic diversity could not decrease. It increased the proportions of mainstream breeds because their genes were removed from the target breed. A substantial increase of the FGE was achieved in some other scenarios, which arose from reduced genetic overlap and from increased diversity within the breed. The latter factor is especially important for breeds with high contributions to the core set.

Evaluation of selection program by assessing the genetic diversity and inbreeding effects on Nellore sheep growth through pedigree analysis.

ObjectiveThe main objectives of the present study were to assess the genetic diversity, population structure and to appraise the efficiency of ongoing selective breeding program in the closed nucleus herd of Nellore sheep through pedigree analysis.MethodsInformation utilized in the study was collected from the pedigree records of Livestock Research Station, Palamaner during the period from 1989 to 2016. Genealogical parameters like generation interval, pedigree completeness, inbreeding level, average relatedness among the animals and genetic conservation index were estimated based on gene origin probabilities. Lambs born during 2012 and 2016 were considered as reference population. Two animal models either with the use of Fi or ΔFi as linear co-variables were evaluated to know the effects of inbreeding on the growth traits of Nellore sheep.ResultsAverage generation interval and realized effective population size for the reference cohort were estimated as 3.38±0.10 and 91.56±1.58, respectively and the average inbreeding coefficient for reference population was 3.32%. Similarly, the effective number of founders, ancestors and founder genome equivalent of the reference population were observed as 47, 37, and 22.48, respectively. Fifty per cent of the genetic variability was explained by 14 influential ancestors in the reference cohort. The ratio fe/fa obtained in the study was 1.21, which is an indicator of bottlenecks in the population. The number of equivalent generations obtained in the study was 4.23 and this estimate suggested the fair depth of the pedigree.ConclusionStudy suggested that the population had decent levels of genetic diversity and a non-significant influence of inbreeding coefficient on growth traits of Nellore lambs. However, small portion of genetic diversity was lost due to a disproportionate contribution of founders and bottlenecks. Hence, breeding strategies which improve the genetic gain, widens the selection process and with optimum levels of inbreeding are recommended for the herd.

Analysis of founders and performance test effects on an autochthonous horse population through pedigree analysis: structure, genetic variability and inbreeding

The Maremmano is an autochthonous Italian horse breed, which probably descended from the native horses of the Etruscans (VI century B.C.); the Studbook was acknowledged in 1980, and it includes 12 368 horses born from that year up to 2015. The aim of this study was to evaluate the effect of the selection program on the genetic variability of the Maremmano population; the analysis was performed using both the ‘Endog v 4.8’ program available at http://webs.ucm.es/info/prodanim/html/JP_Web.htm and in-house software on official pedigree data. Four Reference Populations were considered, and the most important one was the population of the 12 368 Maremmano horses officially registered in the National Studbook. The pedigree completeness of this population was very good because it was more than 90% at the third parental generation and more than 70% at the fifth generation; the pedigree traced back to a maximum of 10.50 generations with an average of 3.30 complete generations and 5.70 equivalent complete generations. The average generation interval was 10.65±4.72 years, with stallions used for longer periods than mares. The intervals ranged from 10.15±4.45 (mother–daughter) to 10.99±4.93 (father–daughter). The effective number of founders (fe) was 74 and the effective number of ancestors (fa) was 30 so that the ratio fe/fa was 2.47. The founder genome equivalents (fg) was 13.72 with a ratio fg/fe equal to 0.18. The mean of the genetic conservation index was 5.55±3.37, and it ranged from 0.81 to 21.32. The average inbreeding coefficient was 2.94%, with an increase of 0.1%/year, and the average relatedness coefficient was 5.52%. The effective population size (Ne) computed by an individual increase in inbreeding was 68.1±13.00; the Ne on equivalent generations was 42.00, and this value slightly increased to 42.20 when computed by Log regression on equivalent generations. The analysis confirmed the presence of seven traditional male lines. The percentage of Thoroughbred blood in the foals born in 2015 was 20.30% and has increased 0.21%/year since 1980; in particular, it increased more than twice (0.51%/year) until 1993 and afterwards slightly fluctuated. The pedigree analysis confirmed the completeness of genealogical information and the traditional importance that breeders gave to the male lines; although the genetic diversity of Maremmano seemed to be not endangered by the selection program, some effects on the population structure were found and a more scientific approach to genetic conservation should be incorporated in the selection plans.

Pedigree analysis of Brazilian Morada Nova hair sheep

The aim of this study was to describe the population structure of Morada Nova sheep breed using pedigree analysis to support development strategies for conservation and breeding programs. Data was available on 10,015 Morada Nova animals born between 1973 and 2014, registered by ARCO (Brazilian Association of Sheep Breeders). The animals were divided into three categories: (1) Base: animals of unknown origin showing strong breed morphology; (2) Prov: animals with genealogy control for one (Prov I), two (Prov II) or three (Prov III) complete generations; (3) PO: animals with four or more complete generations of controlled genealogy. Data was analyzed using the ENDOG software v4.8 to determine individual inbreeding (F), effective population size (Ne), effective number of founders (fe), effective number of ancestors (fa) and number of founder genome equivalents (fg), generation intervals (Int) and genetic conservation index (GCI), of the Morada Nova sheep breed. The Base population (one or more unknown parents) contained 4,709 animals. Only 53.03% and 52.98% had known sire and dam, respectively. Most animals were found in the Brazilian Northeast, but in recent years numbers have increased in São Paulo State. Generation interval in this breed was approximately 3.6 years. Most farms buy rams or semen which helps maintain low inbreeding levels, as well as using their own rams. There is a need to increase registration beyond Base animals and use pedigree to avoid crosses between related animals. Nevertheless, no immediate problems were seen for maintenance of genetic diversity within the Morada Nova sheep breed.

Genetic analysis of the Hungarian population of endangered Hucul horses

The population genetic evaluation of the Hungarian Hucul horse population was performed based on pedigree records. Herd book data of registered Hucul horses available up to 2016 were analysed using ENDOG (Gutierrez and Goyache 2005) and POPREP (Groeneveld et al. 2009) on the whole population (WP) as well as on the reference stock (RS) (breeding stock registered in 2016). Inbreeding coefficients were 5.57% (WP) and 7.18% (RS). Average relatedness was 10.39% in WP and higher in RS (12.67%). Effective population size was 52.32. Generation interval was 13.01 years for WP and 10.99 years for RS. The values for equivalent complete generations were 6.07 and 8.75, for the maximum number of generations 14.11 and 19.16, and for the number of full generations traced 3.77 and 5.50 for WP and RS, respectively. The effective number of founders (f<sub>e</sub>) was 23 both for WP and RS. The effective number of ancestors (f<sub>a</sub>) was 20 in WP and lower in RS (16). The f<sub>a</sub>/f<sub>e</sub> ratio was 0.869 in WP and 0.696 in RS. Founder genome equivalent (f<sub>g</sub>) was 9.618 in WP and 5.790 in RS. The f<sub>g</sub>/f<sub>e</sub> ratio was 0.481 in WP and 0.361 in RS. The study revealed that both the inbreeding coefficient and the average relatedness were high. The above mentioned ratios indicated loss of genetic diversity in the Hungarian Hucul population.

Genetic diversity of Brazilian Brahman cattle by pedigree analysis

Abstract: The objective of this work was to evaluate the genetic diversity of Brahman cattle in Brazil with pedigree analysis. Genealogical records of a subpopulation were used considering all pedigree information (Pt) and the pedigree information divided into two periods (P1, from 1994 to 2004; and P2, from 2005 to 2012) or according to the raising system (Ppt, animals on pasture; or Pst, on stable). Estimates were obtained for average inbreeding coefficients, generation intervals (GI), number of equivalent known generation (CGE), number of founders (Nf), effective number of founders (fe), effective number of ancestors (fa), and founder genome equivalents (fg). The average inbreeding coefficients were 11.97, 7.79, 11.95, 11.74, and 11.31% for Pt, P1, P2, Ppt, and Pst, respectively. Average GI was 4.4 years, whereas CGE was 3.18. The fe values were similar to those of fa, which were greater than those of fg. The fe/fa and fg/fe ratios were close to 1, which indicates no genetic bottleneck and small losses by genetic drift. The genetic diversity in the Brazilian population of Brahman breed is not significantly reduced.

Pedigree analysis of the Turkish Arab horse population: structure, inbreeding and genetic variability

The aim of this study was to evaluate genetic variability in the Turkish Arab horse population using pedigree information. This study is the first detailed pedigree analysis of the breed in Turkey. Pedigree data were collected from the National Studbook. The pedigree data for 23 668 horses, born between 1904 and 2014, were used in the analysis. From this data set, a reference population (RP) of 14 838 animals symbolising the last generation was defined. Demographic parameters, the inbreeding level (F), the average relatedness (AR), the effective population size (Ne), the effective number of founders (fe), the effective number of ancestors (fa) and the number of founder genome equivalents (fg) were calculated for the population. The average generation interval for the RP was 12.2±4.6 years, whereas the calculated pedigree completeness levels were 98.2%, 96.6% and 95.0% for the first, second and third known generations. The mean equivalent generations (t), the average complete generations and the mean maximum generations for the RP were 7.8, 5.4 and 12.2, respectively, whereas the meanFand AR were 4.6% and 9.5% for the RP. The rate of inbred animals was 94.2% for the RP, whereas the number of founders, the number of ancestors and thefe,faandfgwere 342, 223, 40, 22 and 9.6 for the RP. The large differences observed betweenfe, and the number of founders demonstrates that genetic diversity decreased between the founder and the RP. Contribution of the 14 most influential founder to the RP was 50.0%, whereas just eight ancestral horses can account for 50% of the genetic variability.Neestimated via an individual increase in inbreeding per generation (N¯e), and paired increase in coancestry(​N¯eC), were 74.4±3.9 and 73.5±0.58, respectively. The inbreeding increases with the pedigree knowledge. In addition, the decrease in inbreeding in last years is more noticeable.

Genetic diversity of Iranian Lori-Bakhtiari sheep assessed by pedigree analysis

In this study a pedigree analysis was conducted to characterize the genetic structure and diversity of the closed nucleus of Iranian Lori-Bakhtiari sheep. Herdbook information collected between 1992 and 2014, was used to estimate generation interval, pedigree completeness level, inbreeding and its evolution during the studied years. Animals born between 2011 and 2014 were selected as a reference population for estimating parameters derived from probability of gene origins. The mean generation interval was 3.42 year in the studied period. Average inbreeding coefficient of the animals in the reference population was 1.02%. The rate of inbreeding was 0.17% per generation (P<0.01) in the studied period. Realized effective population size estimated from individual increase in coancestry was 101. The effective number of founders, effective number of ancestors and founder genome equivalent of the reference population were 77, 43 and 21 respectively. The results indicated that population under study has fairly good genetic diversity. However, population has lost a part of its genetic diversity due to unbalanced contribution of founders, bottlenecks and genetic drift. For continued genetic gain, enlarging the selection basis and implementation of methods that maximize the selection response at an acceptable level of inbreeding are recommended.

Equivalent effective population size mating as a useful tool in the genetic management of the Ibicenco rabbit breed (Conill Pages d'Eivissa)

The Ibicenco rabbit (Conill Pages D'Eivissa) is a rare breed mainly located on Ibiza Island, in rural areas. Today breeders are looking for a sustainable use and alternative routes for profitability of the population to avoid its extinction. The breed presents some variety in coat colour (brown, black, orange, and grey), and breeders would like to maintain these characteristics. The objectives of this study were to develop a method to design matings in a population with unbalanced pedigree depth in a scenario of maintaining the variety of coat colours, and to analyze the genealogical information of the Ibicenco rabbit to ascertain the genetic structure of the population. Equivalent effective population size mating was developed as a useful parameter to design the mating in this particular scenario. Results obtained by the initial application showed that this population was properly managed for maintaining the maximum genetic variability. This mating method is recommended to manage the genetic variability of this small rabbit population in a scenario of partial permanent colour structure. For the pedigree analysis, a reference population formed by 143 animals available for reproduction was used. A demographic study, a probability gene origin analysis, computation of inbreeding and effective size, and an analysis of genetic structure were done. The generation interval was approximately one year (11.8 months). The average number of equivalent generations was 3.4. The effective numbers of founders and ancestors were 10 and 11, respectively, and the founder genome equivalent was 6. The average inbreeding was 10.8%, but the mean inbreeding seems to have stopped increasing as a consequence of deeper monitoring in the mating design. The realized effective size was 9.6 (via inbreeding) and 17.5 (via coancestry). Regarding the genetic structure, the orange and black groups are the most distant genetically while grey and blacks are closer.

Genetic characterisation of the endangered Gochu Asturcelta pig breed using microsatellite and mitochondrial markers: Insights for the composition of the Iberian native pig stock

The extremely endangered Gochu Asturcelta pig breed was analysed to document its genetic background and to ascertain if the traditional classification of native pig of the Iberian Peninsula into the Celtic-Iberian and the Iberian groups has genetic support. Two populations of Gochu Asturcelta pig (initial and present, including 31 and 124 individuals, respectively) were typed for 17 microsatellites together with 137 individuals of four domestic pig populations (eight breeds) and Wild Boar. Gochu Asturcelta populations showed a noticeable genetic distance with the other populations analysed due to the extreme bottleneck suffered by the breed. In any case, differentiation between the two Gochu Asturcelta populations analysed was very low (FST=0.021±0.005). Morever, the two Gochu Asturcelta populations took basically the same values (1.14 and 1.13, respectively) for parameter Ng (founder genome equivalents) suggesting that the Gochu Asturcelta breed has not suffered additional genetic losses of genetic variability due to drift after the implementation of the breeding scheme. A total of 174 mtDNA control region fragments (647bp) were analysed allowing the identification of 30 different haplotypes. Gochu Asturcelta had only three different haplotypes. The most frequent haplotypes H3 (18% of the samples; assigned to Larson et al.'s haplogropup A) and H5 (25% of the samples; assigned to Larson et al.'s haplogropup C) could be identified in all the Celtic-Iberian, Iberian and Cosmopolitan pig breeds analysed. This makes difficult to ensure that the classical hypothesis explaining different origins for the native pig strains of the Iberian Peninsula has genetic support. Projection of the mitochondrial DNA genetic variability (summarised via Principal Component Analysis) on geographical maps informed that the mtDNA composition of domestic pig native of the Iberian Peninsula depicts the recent rather than the ancient history of the analysed populations.

The influence of captive breeding management on founder representation and inbreeding in the ‘Alalā, the Hawaiian crow

The ‘Alalā (Corvus hawaiiensis), or the Hawaiian crow, was historically only found on the island of Hawai‘i, declined greatly in the twentieth century, and was last seen in the wild in 2002. A captive breeding program was initiated in the 1970s and 113 individuals were in captivity in 2014. All of the present day individuals are descended from nine founders. From pedigree analysis, 50 % of the initial ancestry was from a single founder pair and as of 2014, 45 % of the ancestry was still from this pair. Six other founders have also contributed substantially to the population and managed breeding has increased and evened out their contributions in recent years. Managed breeding has also kept the inbreeding level at the relatively low level of 0.120 in 2014. However, for most of the history of the population, all of the inbreeding was from the single founder pair and in 2014, 76 % of the inbreeding was still from this pair. As a result, the high inbreeding depression previously seen in this population appears to descend from this single pair. Breeding management to maximize founder genome equivalents, which takes into account loss of variation from genetic drift, could increase the genetic representation from the founders, particularly if ancestry from the single founder with only one living descendant is increased.

Genetic contribution from a zoo population can increase genetic variation in the highly inbred wild Swedish wolf population

The Swedish wolf population (Canis lupus) descends from five individuals and is isolated and highly inbred with an average inbreeding coefficient of 0.27. In addition, inbreeding depression has led to reduced litter size and a high frequency of spinal disorders. To achieve the management goal of reducing the mean level of inbreeding, introductions into the wild population from a zoo conservation breeding program have been proposed by authorities. We used pedigree data of the wild and zoo populations to evaluate the extent to which the captive population can contribute genetic variation to the wild one. We measure genetic variation as founder alleles and founder genome equivalents. The two populations have three founders in common, but in spite of this common ancestry, our results show a potential to almost double genetic variation from 11.2 to 21.1 founder alleles. Similarly, the number of founder genome equivalents in the wild population can increase from the present 1.8 to 3.2, but this requires that almost 50 % of the wild gene pool consists of genes from the zoo population. Average kinship in the joint zoo and wild population is 0.15, which is above the management target of 0.1. Genetic contribution from the zoo has the potential to improve, but not solve, the genetically precarious situation of the wild population.