Total Inbreeding Research Articles

Inbreeding depression for producer-recorded udder, metabolic, and reproductive diseases in US dairy cattle

This study leveraged a growing dataset of producer-recorded phenotypes for mastitis, reproductive diseases (metritis and retained placenta), and metabolic diseases (ketosis, milk fever, and displaced abomasum) to investigate the potential presence of inbreeding depression for these disease traits. Phenotypic, pedigree, and genomic information were obtained for 354,043 and 68,292 US Holstein and Jersey cows, respectively. Total inbreeding coefficients were calculated using both pedigree and genomic information; the latter included inbreeding estimates obtained using a genomic relationship matrix and runs of homozygosity. We also generated inbreeding coefficients based on the generational inbreeding for recent and old pedigree inbreeding, for different run-of-homozygosity length classes, and for recent and old homozygous-by-descent segment-based inbreeding. Estimates on the liability scale revealed significant evidence of inbreeding depression for reproductive-disease traits, with an increase in total pedigree and genomic inbreeding showing a notable effect for recent inbreeding. However, we found inconsistent evidence for inbreeding depression for mastitis or any metabolic diseases. Notably, in Holsteins, the probability of developing displaced abomasum decreased with inbreeding, particularly for older inbreeding. Estimates of disease probability for cows with low, average, and high inbreeding levels did not significantly differ across any inbreeding coefficient and trait combination, indicating that although inbreeding may affect disease incidence, it likely plays a smaller role compared with management and environmental factors.

Historic Horse Family Displaying Malformations of the Cervicothoracic Junction and Their Connection to Modern German Warmblood Horses.

Malformations of the equine cervicothoracic junction affect the C6 and C7 cervical vertebrae, the T1 thoracic vertebra and in variable extent the first and second sternal ribs. To date, the clinical impact of this malformation, its prevalence and mode of inheritance in equine populations are not yet determined. We examined five skeletons for signs of malformation of the cervicothoracic junction, including three skeletons from widely used Thoroughbred stallions affected with the malformation and two skeletons serving as a comparison. The three affected historical horses were the Thoroughbred stallions Der Loewe XX, Birkhahn XX and their common great grandsire Dark Ronald XX. Malformations of C6 and C7 showed a large variation between the three stallions, as Dark Ronald XX, Der Loewe XX and Birkhahn XX were affected uni-laterally at C6 and C7, uni-laterally at C6 and bi-laterally at C6 and C7, respectively, with varying grades. In order to evaluate whether or not these malformations are incidental, we took a random sample of 20 living German Warmblood horses, which are distant descendants of these stallions. This sample consisted of ten controls and ten horses with malformations of C6/C7. Blood proportions of the historical sires in the modern Warmblood horses ranged from 0.10 to 6.25%. The contribution to inbreeding in each individual horse of our selected horse group by those sires was expressed as a percentage of the total inbreeding coefficient and ranged from 0.01 to 17.96%, demonstrating their influence on the modern Warmblood. In the present study, we were able to describe the variability of the malformation of C6/C7 within a horse family including historic and modern horses. Additionally, we detected variations appearing in connection with malformations of the cervicothoracic junction that have not been described in the literature yet. This is the first time that the malformations of C6 and C7 have been described within a familial context, providing hints on inheritance in Thoroughbreds and Warmbloods. It is worthwhile to carry out further studies in a larger setting to gain more comprehensive insights into the inheritance of the malformation and the role of important ancestors.

Interpopulation variation in inbreeding is primarily driven by tolerance of mating with relatives in a spermcasting invertebrate.

The degree to which individuals inbreed is a fundamental aspect of population biology shaped by both passive and active processes. Yet, the relative influences of random and non-random mating on the overall magnitude of inbreeding are not well characterized for many taxa. We quantified variation in inbreeding among qualitatively accessible and isolated populations of a sessile marine invertebrate (the colonial ascidian Lissoclinum verrilli) in which hermaphroditic colonies cast sperm into the water column for subsequent uptake and internal fertilization. We compared estimates of inbreeding to simulations predicting random mating within sites to evaluate if levels of inbreeding were (1) less than expected because of active attempts to limit inbreeding, (2) as predicted by genetic subdivision and passive inbreeding tolerance, or (3) greater than simulations due to active attempts to promote inbreeding via self-fertilization or a preference for related mates. We found evidence of restricted gene flow and significant differences in the genetic diversity of L. verrilli colonies among sites, indicating that on average colonies were weakly related in accessible locations, but their levels of relatedness matched that of first cousins or half-siblings on isolated substrates. Irrespective of population size, progeny arrays revealed variation in the magnitude of inbreeding across sites that tracked with the mean relatedness of conspecifics. Biparental reproduction was confirmed in most offspring (86%) and estimates of total inbreeding largely overlapped with simulations of random mating, suggesting that interpopulation variation in mother-offspring resemblance was primarily due to genetic subdivision and passive tolerance of related mates. Our results highlight the influence of demographic isolation on the genetic composition of populations, and support theory predicting that tolerance of biparental inbreeding, even when mates are closely related, may be favoured under a broad set of ecological and evolutionary conditions.

Genetic variation of LEI0258 locus at major histocompatibility complex (MHC) region in Ethiopian indigenous village chicken


 Indigenous chickens are locally adapted to environmental challenges and provide subsistence to millions of farmers in Africa. However, their productivity remains low compared to exotic strains. Efforts are being made to combine the local adaptation of indigenous chicken with productive traits of exotic chicken. Understanding the link between genetic diversity and environmental challenges leads to marker-assisted breed improvement programs for sustainable chicken production at smallholder level. Genetic variation at LEI0258 VNTR locus located within the MHC region has been linked to infectious disease resistance/susceptibility in commercial breeds. The aim of this study was to investigate allelic variability, genetic diversity and genetic relationships of 24 chicken populations in Ethiopia. Here, the diversity at LEI0258 in 236 chickens from 24 Ethiopian indigenous chicken populations using the major Histo-compatibility Complex linked LEI0258 marker is reported. A total of 236 DNA samples were genotyped by capillary electrophoresis from 24 chicken populations. The number of alleles, allele frequency, and heterozygosity levels were used to measure genetic variation at LEI0258 locus in Ethiopian indigenous village chicken. Twenty-nine LEI0258 alleles were observed using capillary electrophoresis that ranged from 185 to 569 bp with no significant difference in allele frequencies between populations. The number of alleles ranged from 179 (Meseret) to 569 (Batambie), with an average of 9.6 alleles per population. Allelic polymorphism was further evaluated through genotyping by Sanger sequencing. Twenty-three DNA samples with different fragment sizes were re-amplified and their alleles sequenced to depict polympormisms based on the combination of two repeat regions at 12 bp and 13 bp, respectively, and flanking regions with SNP and indels. The repeat region at 12 bp appeared 2 to 18 times, whereas the region at 13 bp appeared invariant in all populations. Sequence relationships revealed two distinct groups of alleles. The number of indels and mutations were 33 and 17, respectively. From capillary electrophoresis, the fixation coefficient of the sub-population within the total population (FST), inbreeding/fixation/ coefficient of an individual in a sub population (FIS) and total inbreeding /heterozygosity deficit/ coefficient of an individual within the total population (FIT) in the locus was 0.03, 0.08 and 0.11, respectively. Three percent of the genetic diversity was due to differences among populations, where as 8% and 89% were variations among individuals and variations within individuals, respectively. Despite the overall low genetic differentiation, both fragment and sequencing analysis revealed high allelic and genetic variability across the 24 populations. The high diversity at LEI0258 in Ethiopian indigenous village chicken populations supports the importance of the MHC region in relation to the disease challenges faced by smallholder poultry farmers across Ethiopia. We recommend that breed improvement programs ensure the maintenance of this diversity by selecting breeding stock as diverse as possible at the LEI0258 locus.

Fine-tuning genomic and pedigree inbreeding rates in equine population with a deep and reliable stud book: the case of the Pura Raza Española horse

BackgroundEstimating inbreeding, which is omnipresent and inevitable in livestock populations, is a primary goal for management and animal breeding especially for those interested in mitigating the negative consequences of inbreeding. Inbreeding coefficients have been historically estimated by using pedigree information; however, over the last decade, genome-base inbreeding coefficients have come to the forefront in this field. The Pura Raza Española (PRE) horse is an autochthonous Spanish horse breed which has been recognised since 1912. The total PRE population (344,718 horses) was used to estimate Classical (F), Ballou’s ancestral, Kalinowski’s ancestral, Kalinowski’s new and the ancestral history coefficient values. In addition, genotypic data from a selected population of 805 PRE individuals was used to determine the individual inbreeding coefficient using SNP-by-SNP-based techniques (methods of moments -FHOM-, the diagonal elements of the genomic -FG-, and hybrid matrixes -FH-) and ROH measures (FRZ). The analyse of both pedigree and genomic based inbreeding coefficients in a large and robust population such as the PRE horse, with proven parenteral information for the last 40 years and a high degree of completeness (over 90% for the last 70 years) will allow us to understand PRE genetic variability better and the correlations between the estimations will give the data greater reliability.ResultsThe mean values of the pedigree-based inbreeding coefficients ranged from 0.01 (F for the last 3 generations -F3-) to 0.44 (ancestral history coefficient) and the mean values of genomic-based inbreeding coefficients varied from 0.05 (FRZ for three generations, FH and FHOM) to 0.11 (FRZ for nine generations). Significant correlations were also found between pedigree and genomic inbreeding values, which ranged between 0.58 (F3 with FHOM) and 0.79 (F with FRZ). In addition, the correlations between FRZ estimated for the last 20 generations and the pedigree-based inbreeding highlight the fact that fewer generations of genomic data are required when comparing total inbreeding values, and the opposite when ancient values are calculated.ConclusionsUltimately, our results show that it is still useful to work with a deep and reliable pedigree in pedigree-based genetic studies with very large effective population sizes. Obtaining a satisfactory parameter will always be desirable, but the approximation obtained with a robust pedigree will allow us to work more efficiently and economically than with massive genotyping.

Low Genetic Connectivity of Strongly Inbred Ruppia brevipedunculata in Aquaculture Dominated Lagoons (Viet Nam)

Lagoonal environments exhibit high levels of instability depending on hydrological, climatic and ecological factors, thereby influencing the distribution and structure of submerged plant communities. Conditions typically fluctuate widely due to the interaction of freshwater from rivers with saltwater from the sea, as well as from aquaculture activities that together influence submerged hydrophyte community spatial and temporal variability depending on plant survival strategies. Ruppia species feature either underwater pollination mediated by an air bubble or by the release of pollen floating at the water surface, the former promoting self-pollination. Tropical Asian Ruppia brevipedunculata Yu and den Hartog was assumed to pollinate below the water surface and identified as a separate lineage among selfed Ruppia taxa. We used nine nuclear microsatellites to estimate inbreeding levels and connectivity of R. brevipedunculata within a large SE Asian lagoon complex. Ruppia brevipedunculata meadows were strongly inbred as could be derived from the many monomorphic or totally fixed loci for unique alleles in different parts of the lagoon, which appears consistent with selfing behavior. Those from aquaculture ponds were highly inbred (FIS = 0.620), though less than open lagoon sites that showed nearly total inbreeding (FIS = 0.942). Ruppia brevipedunculata from two major lagoon parts were highly differentiated with spatially structured gene pools and a strong barrier between parts of the lagoon over a 30 km distance. Migration-n analysis indicated unidirectional though limited gene flow and following potential hydrological connectivity. Overall, private alleles under homozygote conditions explained a stronger genetic differentiation of populations situated inside aquaculture ponds than of open lagoon populations. Kinship values were only relevant up to 5 km distance in the open lagoon. Within a confined area of aquaculture ponds featuring dense vegetation in stagnant water, there would be opportunity for mixed pollination, thereby explaining the higher diversity of unique multilocus genotypes of aquaculture pond habitats. Low connectivity prevents gene pools to homogenize however promoted sites with private alleles across the lagoon. Complex hydrodynamic systems and human-made habitats enclosed by physical structures impose barriers for propagule dispersal though may create refugia and contribute to conserving regional genetic diversity.

Bayesian inference of the inbreeding load variance for fertility traits in Brown Swiss cattle

Our study investigated the inbreeding load for fertility traits in the Italian Brown Swiss dairy cattle breed. Fertility traits included continuous traits (i.e., interval from calving to first service, days open, and calving interval) and categorical traits (i.e., calving rate at first insemination and nonreturn date at d 56). We included only records of the first 3 parities of cows that calved between 2010 and 2018. We traced up the pedigree of the cows with records as far as possible, ending up with a total of 73,246 animals. The final data set consisted of 59,864 records from 34,921 cows. We analyzed all models using a Bayesian approach that included a covariate with total inbreeding in addition to systematic, permanent environment, additive genetic, and inbreeding load effects. We then evaluated the trends in heritabilities and ratios of the inbreeding load using a continuum of partial inbreeding coefficients from 0.001 to 0.100 as reference. Posterior estimates of heritabilities tended to decrease across the continuum, whereas ratios of the inbreeding load tended to increase, more noticeably in categorical traits (calving rate at first insemination and nonreturn date at d 56). From the results obtained, we confirmed the presence of heterogeneity in inbreeding depression. We then predicted the inbreeding load effects, which had a low reliability of prediction, explained by having only 513 ancestors generating inbreeding. However, reliability of prediction was high enough for some of the individuals, obtaining a favorable prediction of inbreeding load for a relevant percentage, which improved the phenotypic performance of their inbred descendants. These results make it feasible to implement breeding and management strategies that select ancestors with a favorable inbreeding load prediction. In addition, it opens the possibility to define a global index for the expected consequences of the inbreeding generated by each individual.

Genetic diversity and the application of runs of homozygosity-based methods for inbreeding estimation in German White-headed Mutton sheep.

The German White-headed Mutton (GWM) sheep is a monitoring population believed to have been improved through crosses with other breeds, e.g., Texel (TXL) and French Berrichone du Cher (BDC). The primary aim of the study was to analyse genetic diversity and breed composition of GWM sheep. Furthermore, different measures of computing inbreeding from the runs of homozygosity (ROH) were investigated. Data for GWM consisted of pedigree information on 19,000 animals and 40,753 quality filtered SNPs on 46 individuals. Additionally, publicly available genotype data on 209 individuals belonging to nine sheep breeds were included in the analysis. Due to evenness of SNPs spacing and proportionality of the number of SNPs in each autosome to autosome length, a high correlation (rp = 0.99) was found between genomic inbreeding coefficients computed based on the length of ROH (FROH_L) and those computed relative to the number of SNPs in ROH (FROH_N). Total inbreeding was partitioned into values for individual chromosomes revealing the highest levels of inbreeding on chromosomes 1, 2 and 3. Correlations between the ROH-based inbreeding measures and pedigree inbreeding reached 0.82. The observed heterozygosity estimate in GWM was high (0.39), however, the breed suffered low level of effective population size (~50) from a genomic viewpoint. Moreover, effective number of founders (186), and effective number of ancestors (144) implied disequilibrium of founder contribution and a genetic bottleneck in the breed. Multidimensional scaling and network visualisation analyses revealed close connectedness of GWM to BDC and German Texel (GTX). A model-based admixture analysis consistently indicated the flow of genes from other breeds, particularly BDC to GWM. Our analyses highlight the mixed genetic background of GWM sheep and furthermore, suggest a close monitoring of the breed to consolidate its genetic diversity while averting further reduction in the effective population size.

The assignment success for 22 horse breeds registered in the Czech Republic: The machine learning perspective

The paper demonstrates the dependability of assignment testing in the identification of an appropriate breed to monitor comprehensive genetic information from molecular markers to analyse the collection of real population data covering 22 horse breeds registered in the Czech Republic, including native breeds and genetic resources. If 17 microsatellites are used, the mean number of alleles per locus corresponds to 10.4. The count of alleles at the individual loci ranges between five (HTG07) and 17 (ASB17). The loci ASB02, ASB23, HMS03, HTG10, and VHL20 exhibit the highest gene diversity and observed heterozygosity (both above 80%), with the mean value of 0.77 and 0.73, respectively. The moderate total inbreeding coefficient (5.2%) is estimated across all the loci and breeds. The levels of apparent breed differentiation span from zero between the Czech Warmblood and Slovak Warmblood to 0.15 between the Shetland Pony and Standardbred. The phylogenetic breed relationships are revealed via the NeighbourNet dendrogram constructed from Reynolds’ genetic distances, which clearly separate the Coldblood draught, Hot/Warmblood, and Pony horses. Our results reveal that the Bayesian approach (the Rannala and Mountain technique) provides the most intensive prediction power (83.6%) out of the GeneClass tools and that the Bayes Net algorithm exhibits the best efficiency (78.4%) from the WEKA machine learning workbench options, considering the use of the five-fold cross validation technique. The algorithms could be trained on large real reference data sets, and thus there appears another viable perspective for machine learning in horse ancestry testing. In this context, it is also important to stress the fact that innovated computational tools will potentially lead towards structuring a novel web server to allow the identification of horse breeds.

Litter Size of Sheep (Ovis aries): Inbreeding Depression and Homozygous Regions.

Ovine litter size (LS) is an important trait showing variability within breeds. It remains largely unknown whether inbreeding depression on LS exists based on genomic homozygous regions, and whether the homozygous regions resulted from inbreeding are significantly associated with LS in sheep. We here reanalyze a set of single nucleotide polymorphism (SNP) chip of six breeds to characterize the patterns of runs of homozygosity (ROH), to evaluate inbreeding levels and inbreeding depressions on LS, and to identify candidate homozygous regions responsible for LS. Consequently, unique ROH patterns were observed among six sheep populations. Inbreeding depression on LS was only found in Hu sheep, where a significant reduction of 0.016, 0.02, and 0.02 per 1% elevated inbreeding FROH4–8, FROH > 8 and the total inbreeding measure was observed, respectively. Nine significantly homozygous regions were found for LS in Hu sheep, where some promising genes for LS possibly via regulation of the development of oocytes (NGF, AKT1, and SYCP1), fertilization (SPAG17, MORC1, TDRD9, ZFYVE21, ADGRB3, and CKB), embryo implantation (PPP1R13B, INF2, and VANGL1) and development (DPPA2, DPPA4, CDCA4, CSDE1, and ADSSL1), and reproductive health (NRG3, BAG5, CKB, and XRCC3) were identified. These results from the present study would provide insights into the genetic management and complementary understandings of LS in sheep.

Preferencias matrimoniales en Tulumba (Córdoba). Primer tercio del siglo XX

El principal objetivo de este trabajo fue comparar las tres primeras décadas del siglo XX, en cuanto a preferencias matrimoniales, en la pedanía Parroquia del departamento Tulumba del norte de Córdoba (Argentina). Se utilizaron como fuente las actas de nacimientos de entre 1901 y 1930 y, como principales métodos, la isonimia y los pares repetidos. No se observaron diferencias notables entre las décadas, manifestando más particularidades la segunda, 1911-1920, con mayor consanguinidad aleatoria y total y mínimo parentesco intrapoblacional. A su vez, la frecuencia en los casamientos entre linajes fue en todos los casos muy elevada. Los resultados de la segunda década se interpretaron como un paliativo contra recién arribados, pero más aún contra el efecto de la emigración hacia la región pampeana en forma creciente, al menos hasta comienzos de la Primera Guerra Mundial. Del mismo modo, el menor parentesco en 1911-1920 pudo deberse a cierta inmigración de corta distancia, pero también transoceánica. En suma, pese a lo antedicho, caben destacar las semejanzas entre las tres décadas, no viéndose reflejados cambios profundos en el comportamiento de la población de casados. Esto último sí podría esperarse en la región pampeana de la misma época, que contó con un desarrollo productivo e incremento demográfico, particulamente inmigración, notorios.

Microsatellite-Based Genetic Diversity among Egyptian Sheep Breeds

Sheep represent one of the most important domestic animals in Egypt, where meat and coarse wool production are the basic breeding objectives for Egyptian sheep. Therefore, evaluation of genetic diversity of sheep breeds is necessary for implementing the most suitable breed-region conservation programs. Animals from the three major Egyptian sheep breeds (Ossimi, Rahmani and Barki) were genotyped for 14 microsatellite markers. All loci tested were highly polymorphic. Various measures of genetic variation were calculated. The total observed number of alleles per microsatellite ranged from 6 to 12 for markers MAF65 and OarHH47, respectively. Estimates of effective number of alleles were between 3.11 for TGLA53 and 6.12 for OarHH47. The mean of polymorphism information content was 0.73. Overall gene diversity for all microsatellites analyzed was 0.66, 0.69 and 0.75 for Ossimi, Rahmani and Barki, respectively. For all breeds studied, estimates of observed heterozygosity were significantly lower than the expected heterozygosity. Average observed and expected heterozygosity estimates were 0.55 and 0.67, respectively. Significant departures from Hardy-Weinberg Equilibrium (HWE) due to heterozygote deficiency were observed for all the markers analyzed. The three breeds revealed significant deviation from HWE. The overall indicator of population subdivision (FST) was calculated to be 0.071; pointing out that about 7% of genetic diversity is due to genetic variation between breeds. Estimates of total inbreeding (FIT) and within-breed inbreeding (FIS) coefficients were 0.187 and 0.118, respectively. The estimates of pair-wise genetic differentiation were 0.039, 0.051 and 0.056 for Ossimi-Rahmani, Barki-Rahmani and Ossimi-Barki pairs, respectively. Measures of genetic distance between pairs of sheep breeds ranged from 0.423 to 0.615 for Rahmani-Ossimi and Barki-Ossimi sheep breed pairs. The results obtained in this study may be useful in sustainable breeding programs of Egyptian sheep breeds.

Seed germination in cleistogamous species: theoretical considerations and a literature survey of experimental results

AbstractA cleistogamous species consists of individuals that produce both chasmogamous (open, CH) and cleistogamous (permanently closed, CL) flowers, which facilitates a mixed-mating system. In contrast to what one might expect, CL (obligately selfed) seeds and the plants derived from them can be more fit than CH (potentially outcrossed) seeds and the plants they give rise to. Our aim was to review some theoretical aspects of mixed mating in relation to retention of both CH and CL in cleistogamous species and to determine if data on germination support the notion that CL is advantageous over that of CH. Based on germination (or seedling emergence) of CHvsCL seeds in 29 species in 21 genera and 11 families of monocots and eudicots, CL seeds germinated better in 107 and equally well as in 64 of 252 case studies as CH seeds (67.9%), and the (CH < CL):(CH > CL) ratio was 107/81 (1.32). We conclude that our study lends support to the notion that production of CL seeds by cleistogamous species is advantageous over that of CH seeds. Retention of CH by CL species may be due to the need to prevent complete selfing (s= 1.0) and thus total inbreeding depression (δ), which theory predicts would decrease reproductive success. Some caveats concerning the results of comparative studies on the germination biology of CHvsCL seeds of amphicarpicsensu strictoFabaceae species andCommelina benghalensisand the aerial cleistogamous grassDanthonia spicataare discussed.

Characterization of six cross-species microsatellite markers suitable for estimating the population parameters of the black-backed jackal (Canis mesomelas) using a non-invasive genetic recovery protocol

AbstractThe black-backed jackal has proven difficult to study in the wild due to its elusive behaviour. As a rabies vector and predator of livestock, understanding dispersal patterns and population structure is of importance when considering the management of this species in South Africa’s rural areas. We have characterised a suite of six cross-species microsatellite markers suitable for this purpose and present a method to isolate suitable quantities of host DNA from faeces in order to undertake endpoint PCR. Allelic dropout and null allele frequencies were shown to be negligible for all loci. No evidence of selection could be detected at any of the loci examined. The genotype frequencies of the total sampled population were tested for concordance with Hardy–Weinberg equilibrium. No significant deficit of heterozygote individuals was detected globally when tested by locus and marker set. An excess of heterozygosity was recorded at three loci within a single study site. The total inbreeding coefficient FS...

Genome-wide inbreeding estimation within Lebanese communities using SNP arrays.

Consanguineous marriages have been widely practiced in several global communities with varying rates depending on religion, culture, and geography. In consanguineous marriages, parents pass to their children autozygous segments known as homozygous by descent segments. In this study, single-nucleotide polymorphisms were analyzed in 165 unrelated Lebanese people from Greek Orthodox, Maronite, Shiite and Sunni communities. Runs of homozygosity, total inbreeding levels, remote consanguinity, and population admixture and structure were estimated. The inbreeding coefficient value was estimated to be 1.61% in offspring of unrelated parents over three generations and 8.33% in offspring of first cousins. From these values, remote consanguinity values, resulting from genetic drift or recurrent consanguineous unions, were estimated in offspring of unrelated and first-cousin parents to be 0.61 and 1.2%, respectively. This remote consanguinity value suggests that for any unrelated marriages in Lebanon, the mates could be related as third cousins or as second cousins once removed. Under the assumption that 25% of marriages occur between first cousins, the mean inbreeding value of 2.3% may explain the increased incidence of recessive disease in offspring. Our analysis reveals a common ancestral population in the four Lebanese communities we studied.

Surnames in Honduras: A Study of the Population of Honduras through Isonymy

In this work, we investigated surname distribution in 4,348,021 Honduran electors with the aim of detecting population structure through the study of isonymy in three administrative levels: the whole nation, the 18 departments, and the 298 municipalities. For each administrative level, we studied the surname effective number, α, the total inbreeding, FIT , the random inbreeding, FST , and the local inbreeding, FIS . Principal components analysis, multidimensional scaling, and cluster analysis were performed on Lasker's distance matrix to detect the direction of surname diffusion and for a graphic representation of the surname relationship between different locations. The values of FIT , FST , and FIS display a variation of random inbreeding between the administrative levels in the Honduras population, which is attributed to the "Prefecture effect." Multivariate analyses of department data identified two main clusters, one south-western and the second north-eastern, with the Bay Islands and the eastern Gracias a Dios out of the main clusters. The results suggest that currently the population structure of this country is the result of the joint action of short-range directional migration and drift, with drift dominating over migration, and that population diffusion may have taken place mainly in the NW-SE direction.

English

The objectives of this study were to analyze genetic diversity and population structure of Sudanese native chicken breeds involved in a conservation program. Five Sudanese native chicken breeds were compared with populations studied previously, which included six purebred lines, six African populations and one Sudanese chicken population. Twenty-nine (29) microsatellite markers were genotyped individually in these five populations. Expected and observed heterozygosity, mean number of alleles per locus and inbreeding coefficient were calculated. A model based cluster analysis was carried out and a Neighbor net was constructed based on marker estimated kinships. Two hundred and one alleles were detected in all populations, with a mean number of 6.93 ± 3.52 alleles per locus. The mean observed and expected heterozygosity across 29 loci was 0.524 and 0.552, respectively. Total inbreeding coefficient (FIT) was 0.069±0.112, while differentiation of subpopulations (FST 0.026±0.049) was low indicating the absence of clear sub-structuring of the Sudanese native chicken populations. The inbreeding coefficient (FIS) was 0.036±0.076. STRUCTURE software was used to cluster individuals to 2 ≤ k ≤ 7 assumed clusters. Solutions with the highest similarity coefficient were found at K=5 and K=6, in which Malawian, Zimbabwean, and purebred lines split from Sudanese gene pool. The six Sudanese native chicken populations formed one heterogeneous cluster. We concluded that Sudanese native chickens are highly diverse, and are genetically separated from Malawian, Zimbabwean chickens and six purebred lines. Our study reveals the absence of population sub-structuring of the Sudanese indigenous chicken populations.   Key words: Genetic diversity, microsatellites, population structure, Sudanese native chickens.

Isonymy and repeated pairs of surnames among the Muslims of Manipur, India

Surnames have been used for studying population structure in different parts of the globe. The present study is aimed at indirectly estimating the degree of inbreeding from surnames and understanding the influences of the clan-like structure on mate selection among Manipuri Muslims. The proportion of isonymy I was found to be 0.0144. The non-random and random components were −0.0226 and 0.0239, respectively. The total inbreeding coefficient was estimated to be 0.0018. The scores of random pairs (RP) and random repeated pairs (RPr) were 0.026 and 0.010, respectively. The score of RP was higher than the RPr which gives a ratio of 0.38, indicating that Manipuri Muslims have a tendency of acquiring mates from within a given set of surnames while not in favour of isonymy. To conclude, surname/clan is a criterion for mate selection for various reasons among this population.

Microsatellite DNA markers indicate three genetic lineages in East Asian indigenous goat populations

The genetic differentiation and phylogenetic relationships of 18 indigenous goat populations from seven East Asian countries were analysed based on data obtained from 26 microsatellite DNA markers. The mean number of alleles (MNA) per population ranged from 2.5 to 7.6, with an average of 5.8. Genetic variability estimated from MNA and heterozygosity (H(E) and H(O) ) were relatively low in coastal and island populations. A heterozygous deficiency within populations (F(IS) = 0.054, P < 0.001) and total inbreeding (F(IT) = 0.181, P < 0.01) were observed, and genetic differentiation in the populations (F(ST) ) was 13.4%. The results of Bayesian model-based clustering and a neighbour-joining tree based on Nei's genetic distance showed that Asian goat populations could be subdivided into at least the following three genetic clusters: East Asian, Southeast Asian and Mongolian. These results are in close accordance with conventional morphological and geographical classifications and migration history.

Genetic Diversity of Wild and Cultured Populations of Penaeus monodon using Microsatellite Markers

Information on the genetic diversity of Penaeus monodon throughout its natural range in Malaysia is still Hmited even though it is a highly exploited species, thus this study was undertaken to genetically characterize the prawn populations. The P. monodon samples were randomly collected from Malaysian waters and were characterized using thirty polymorphic primer pairs which showed high level of polymorphism. The total number of alleles per locus ranged from 3 to 36 with allele size ranging from 100 to 275 base pairs. The mean observed heterozygosity (0.5166) was less than the expected (0.5552), highly significant deficiencies in heterozygotes were detected in total inbreeding (F IS = 0.5500) and pair-wise genetic differentiation (F ST = 0.6308) among the populations. Both the (χ 2) chi-square and (G 2) likelihood ratio tests detected significant differences (p<0.05) which showed a deviation from the Hardy-Weinberg equilibrium, indicating a probable inbreeding might have occurred in the populations. A Cluster analysis based on genetic distance revealed a fair genetic relationship among all the populations and the pattern was in accordance to the populations' geographical origins. The highest genetic distance (0.7588) was observed between Law as and Bulau Sayak populations while the lowest genetic distance (0.1191) was recorded between the Endau Rompin and Sedili populations. Various levels of genetic diversity of the P. monodon reported in this study indicated their genetic status in Malaysian waters and suitability for breeding and culture purposes. This information provides a basis for improvement through selective breeding and in the design of suitable management guidelines for this genetic material.