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PubMed2005

The effects of habitat fragmentation on the social kin structure and mating system of the agile antechinus, Antechinus agilis.

Habitat fragmentation is one of the major contributors to the loss of biodiversity worldwide. However, relatively little is known about its more immediate impacts on within-patch population processes such as social structure and mating systems, whose alteration may play an important role in extinction risk. We investigated the impacts of habitat fragmentation due to the establishment of an exotic softwood plantation on the social kin structure and breeding system of the Australian marsupial carnivore, Antechinus agilis. Restricted dispersal by males in fragmented habitat resulted in elevated relatedness among potential mates in populations in fragments, potentially increasing the risk of inbreeding. Antechinus agilis nests communally in tree hollows; these nests are important points for social contact between males and females in the mating season. In response to elevated relatedness among potential mates in fragmented habitat, A. agilis significantly avoided sharing nests with opposite-sex relatives in large fragment sites (but not in small ones, possibly due to limited nest locations and small population sizes). Because opposite-sex individuals shared nests randomly with respect to relatedness in unfragmented habitat, we interpreted the phenomenon in fragmented habitat as a precursor to inbreeding avoidance via mate choice. Despite evidence that female A. agilis at high inbreeding risk selected relatively unrelated mates, there was no overall increased avoidance of related mates by females in fragmented habitats compared to unfragmented habitats. Simulations indicated that only dispersal, and not nonrandom mating, contributed to inbreeding avoidance in either habitat context. However, habitat fragmentation did influence the mating system in that the degree of multiple paternity was reduced due to the reduction in population sizes and population connectivity. This, in turn, reduced the number of males available to females in the breeding season. This suggests that in addition to the obvious impacts of reduced recruitment, patch recolonization and increased genetic drift, the isolation of populations in habitat patches may cause changes in breeding behaviour that contribute to the negative impacts of habitat fragmentation.

Animals↗
PubMed2005

Selfing and resource allocation in Schiedea salicaria (Caryophyllaceae), a gynodioecious species.

Abstract Levels of selfing and resource allocation patterns were investigated in Schiedea salicaria (Caryophyllaceae), a gynodioecious species with high levels of inbreeding depression and nuclear control of male sterility. Selfing levels were higher in hermaphrodites than females, especially when adjusted for early acting inbreeding depression. The sexes of S. salicaria were similar in most allocation patterns including number of flowers and capsules per inflorescence, seeds per flower, and seed mass. Seeds produced by females had higher levels of germination than seeds of hermaphrodites, a likely result of high selfing levels and the expression of inbreeding depression in the progeny of hermaphrodites. Invasion of females in populations of S. salicaria is probably related to the expression of inbreeding depression at germination and in later life history stages. Comparisons with related species of Schiedea that also have nuclear control of male sterility suggest that reallocation of resources in hermaphrodites to male function occurs as females increase in frequency, but that resource reallocation is not important for the success of females when they first invade populations.

Caryophyllaceae↗
PubMed2005

Microsatellite marker analysis of the genetic variability in Hanoverian Hounds.

Genetic variability of the dog breed Hanoverian Hound was analysed using a set of 16 microsatellites. The sample of 92 dogs was representative for the total current population [n=334, inbreeding coefficient 9.2%, relationship coefficient 11.2%] with respect to the level and distribution of the inbreeding and relationship coefficients. All microsatellites used were in Hardy-Weinberg equilibrium. The average number of alleles was 6.4. The average observed heterozygosity (H(O)) was slightly higher than the expected heterozygosity (H(E)). Dinucleotide microsatellites exhibited lower polymorphism information content (PIC) than tetranucleotide microsatellites (0.52 versus 0.66). The average PIC was 0.61. The individual inbreeding coefficient was negatively related to the average H(O) of all microsatellites, whereas the proportion of genes from introducing of Hanoverian Hounds from abroad showed no relationships to H(O). We found that the genetic variability in the Hanoverian Hounds analysed here was unexpectedly higher than that previously published for dog breeds of similar population size. Even in dog breeds of larger population size heterogyzosity was seldom higher than that observed here. The rather high genetic variability as quantified by polymorphic microsatellites in Hanoverian Hounds may be due to a large genetic variation in the founder animals of this breed and to the fact that this genetic diversity could be maintained despite genetic bottlenecks experienced by this breed in the 1920s and 1950s and despite the presence of high inbreeding and relationship coefficients for more than 50 years.

Animals↗
PubMed2005

Estimates of genetic diversity in the brown cattle population of Switzerland obtained from pedigree information.

The study investigates the genetic diversity present as well as its development in the Brown Cattle population of Switzerland from pedigree information. The population consisted of three subpopulations, the Braunvieh (BV), the original Braunvieh (OB) and the US-Brown Swiss (BS). The BV is a cross of OB with BS where crossing still continues. The OB is without any genetic influence of BS. The diversity measures effective population size, effective number of ancestors (explaining 99% of reference genome) and founder genome equivalents were calculated for 11 reference populations of animals born in a single year from 1992 onwards. The BS-subpopulation consisted of animals and their known ancestors which were used in the crossing scheme and was, therefore, quite small. The youngest animals were born in 2002, the oldest ones in the 1920s. Average inbreeding was by far the highest in BS, in spite of the lowest quality of pedigrees, and lowest in OB. Effective population size obtained from the difference between average inbreeding of offspring and their parents was, mostly due to the heavy use of few highly inbred BS-sires, strongly overestimated in some BV-reference populations. If this parameter was calculated from the yearly rate of inbreeding and a generation interval of 5 years, no bias was observed and ranking of populations from high to low was OB-BV-BS, i.e. equal to the other diversity parameters. The high genetic diversity found in OB was a consequence of the use of many natural service sires. Rate of decrease of effective number of ancestors was steeper in BV than OB was, however, equal for founder genome equivalents. Founder genome equivalents were more stable than effective population sizes calculated from the difference between average inbreeding of offspring and parents. The five most important ancestors contributed one-third of the 2002-reference genomes of BV and OB, in BV all were BS-sires. The relative amount of BS-genes in the BV-genome increased from 59.2% to 78.5% during the 11 years considered.

Animals↗
PubMed1999

Conservation genetics of Nordic carnivores: lessons from zoos.

This paper summarizes results from genetic studies of Nordic carnivore populations bred in captivity. The conservation genetic implications of those results for the management of wild populations of the same species are discussed. Inbreeding depression has been documented in the brown bear (Ursus arctos), wolf (Canis lupus), and lynx (Lynx lynx) populations held in Nordic zoos. The characters negatively affected by inbreeding include litter size (brown bear and wolf), longevity (lynx and wolf), female reproduction, and weight (wolf). In addition, hereditary defects caused by single autosomal alleles occur in the wolf and brown bear populations. These deleterious alleles cause blindness (wolf) and albinism (brown bear) in the homozygous state. The amount of inbreeding depression observed in Nordic carnivores are similar to that documented in other species. The captive populations have the same genetic background as the current wild ones and inbreeding depression is therefore a potential threat to wild carnivore populations in Sweden. This threat is presently not being adequately recognized in the management of these species. Frequently occurring misunderstandings regarding the kind of conclusions that can be drawn from the presented genetic observations are also discussed.

Animal Husbandry↗
PubMed2025

Persistent Genomic Erosion in Whooping Cranes Despite Demographic Recovery.

Integrating in-situ (wild) and ex-situ (captive) conservation efforts can mitigate genetic diversity loss and help prevent extinction of endangered wild populations. The whooping crane (Grus americana) experienced severe population declines in the 18th century, culminating in a collapse to ~20 individuals by 1944. Legal protections and conservation actions have since increased the census population from a stock of 16 individuals to approximately 840 individuals, yet the impact on genomic diversity remains unclear. We analysed the temporal dynamics of genomic erosion by sequencing a high-quality reference genome, and re-sequencing 16 historical (years 1867-1893) and 37 modern (2007-2020) genomes, including wild individuals and four generations of captive-bred individuals. Genomic demographic reconstructions reveal a steady decline, accelerating over the past 300 years with the European settlement of North America. Temporal genomic analyses show that despite demographic recovery, the species has lost 70% of its historical genetic diversity and has increased its inbreeding. Although the modern population bottleneck reduced the ancestral genetic load, modern populations possess more realised load than masked load, possibly resulting in a chronic loss of fitness. Integrating pedigree and genomic data, we underscore the role of breeding management in reducing recent inbreeding. Yet ongoing heterozygosity loss, load accumulation, and persistent effects of historical inbreeding (i.e., background inbreeding) argue against the species' downlisting from its current Endangered status on the IUCN Red List and the Endangered Species Act. The presence of private genetic variation in wild and captive populations suggests that wild-captive crosses could enhance genetic diversity and reduce the realised load. Our findings emphasise the role of genomics in informing conservation management and policy.

Animals↗
PubMed2004

Population structure of a colony of dog guides.

The objective of this study was to describe changes in genetic diversity in a colony of dog guides since its founding. Two breeds, German Shepherds (GS) and Labrador Retrievers (LR), were evaluated. Data were pedigrees of 4,699 GS and 3,573 LR dogs bred for use as guides by The Seeing Eye, Inc., Morristown, NJ. Rapid increases in average pairwise numerator relationships occurred in both breeds, although the average was approximately one-third higher in the GS population than in the LR population. A similar trend was observed for average inbreeding. The rate of increase in inbreeding has slowed in recent generations. In the current generation, relationship and inbreeding for all animals averaged 25.3 and 26.2% in GS, and 15.5 and 22.0% in LR, respectively. Effective founder numbers initially decreased in GS until Generation 3, and then increased steadily. Effective founder number in LR constantly increased. There was a constant increase in effective founder number in LR. A similar pattern was noted for effective ancestor number as well. Founder genome equivalents were initially higher in GS but decreased over time in both breeds. Generation intervals averaged 23.7 mo in GS and 23.2 mo in LR. Sires had average service lives of 2.7 and 2.2 generations in GS and LR, respectively. Dams had average service lives of 2.1 generations in both breeds. Litter sizes averaged 5.1 and 7.4 pups per litter for GS and LR, respectively. Effective founder and ancestor numbers have slowly increased over time, and heterozygosity as measured by the number of founder genome equivalents in the population has increased. Limitations on the number of matings permitted for sires and service life of dams has led to a plateau for inbreeding and relationships. The importation of germplasm from other working dog colonies is desirable.

Animals↗
PubMed1984

Growth patterns of Angus, Hereford and shorthorn cattle. II. Relationship of growth patterns of dams with progeny performance.

Relationships between estimated growth curve parameters of dams and performance traits of their progeny were studied in Angus, Hereford and Shorthorn herds, each divided into four inbred and two noninbred lines. Growth curve parameters were calculated from the growth function Yt=A(1-Be-Kt), where Yt was weight at age t, A was estimated mature weight, B was an estimate related to early life weight changes and provided for a Y-intercept term and K was estimated general rate of maturing. Least-squares analyses of progeny variables were calculated separately for each breed and sex. Line differences did not influence any of the progeny variables except weaning type score of Shorthorn males (P less than .01). Birth year exerted a curvilinear effect on birth weights of Angus female progeny (P less than .01), a linear influence on 205-d weights of Shorthorn male progeny (P less than .05) and a curvilinear effect on weaning type scores of Angus and Shorthorn male progeny (P less than .01). Regression coefficients on weaning age indicated that calves born earlier in the calving season had lighter birth weights and that older calves at weaning received higher type scores. Inbreeding of the progeny negatively influenced (P less than .05) birth weights of Angus male and Hereford female progeny. Hereford male and Shorthorn female 205-d weights were negatively affected (P less than .05) by inbreeding, while weaning type scores of Shorthorn female progeny were negatively influenced (P less than .001) by inbreeding. Regression coefficients of all progeny variables on inbreeding in all analyses indicated negative trends.(ABSTRACT TRUNCATED AT 250 WORDS)

Analysis of Variance↗
PubMed1997

Dominance models with method R for stature of Holsteins.

Estimates of variance components were obtained with method R for several additive and dominance models. The data included 301,960 records for first parity and 280,040 records for later parities of Holsteins. The single-record model included effects of management, regression on inbreeding percentage, age at calving, stage of lactation, and additive and dominance effects. The repeatability model included these effects in addition to permanent environment. For the single-record model, estimates were 46% of the total variance for additive variance, 12% of total variance for dominance variance, and -0.06 for the regression coefficient on inbreeding. In the repeatability model, the variance for permanent environment was estimated at 5%; other estimates were similar. When the dominance effect was eliminated, the estimate of the variance for permanent environment increased to 17% for the repeatability model. Elimination of stage of lactation increased regression on inbreeding to 0.09 and the estimate of dominance variance to 17% in the single-record model. The same change increased the estimate of additive variance to 64% for the repeatability model. Elimination of regression on inbreeding or stage of lactation had a small effect on the estimates. The presence or absence of the dominance effect had little influence on additive variance. In the absence of dominance, the estimate of the permanent environment effect included the dominance effect. Estimates of variances with method R are very sensitive to age adjustments. With the adjustments, the estimates of the dominance and additive variances are consistent.

Aging↗
PubMed1998

Optimizing pure line breeding strategies utilizing reproductive technologies.

The development of new reproductive techniques has had a great effect on schemes for dairy cattle improvement; AI resulted in progeny-testing schemes, and, more recently, multiple ovulation and embryo transfer has resulted in nucleus breeding schemes. In traditional breeding schemes, the use of multiple ovulation and embryo transfer resulted in only small increases of genetic gains because the selection intensity of bull dams was already high, but the selection intensity of cows in nucleus breeding schemes increased considerably. This increase makes nucleus schemes very competitive, especially when in vitro maturation and fertilization is used to increase female reproductive rates further. The increased genetic gain results in the selection of young females (i.e., optimal generation intervals are shortened). The combined effect of multiple ovulation and embryo transfer and shorter generation intervals increases the rate of gain by approximately 15% but also increases the rate of inbreeding and variances of the selection response (i.e., the risk of the breeding scheme) by about 80%. Recently, selection methods have been developed to reduce the rates of inbreeding or the variance of the selection response in breeding schemes. A scheme that maximized the selection differential while constraining the rate of inbreeding yielded about 30 to 60% more selection response than selection for BLUP estimated breeding value at the same rate of inbreeding. For the future, the combination of juvenile predictors of genetic merit (e.g., DNA markers) and techniques that further increase female reproductive rates seem very promising methods to increase the rates of genetic gain. As an example, the genetic gain of an optimized hybrid nucleus scheme could be increased 24% by the combined use of juvenile predictors and in vitro maturation and fertilization. Fertilization of fetal embryos was predicted to increase rates of gain by up to 18%.

Animals↗
PubMed1999

Evaluation of genetic, common-litter, and within-litter effects on preweaning mortality in a birth cohort of puppies.

OBJECTIVE: To determine relative impact of genetic, common-litter, and within-litter factors on puppy mortality. ANIMALS: 2,622 Boxer puppies of 413 litters born during a 14-month period. PROCEDURE: For each puppy, pedigree was determined, and litter in which it was born was registered. Overall mortality and mortality per specific cause of death were analyzed by use of a model that included an additive genetic effect, common-litter effect, within-litter effect, and regression of mortality on inbreeding coefficient. Relative importance of the effects was determined from estimates of the variance in mortality explained by each factor. RESULTS: 22% of the puppies died before reaching 7 weeks old. Stillbirth was the most frequent cause of death, followed by infection. Most observed differences were attributable to within-litter factors, which explained 67% of the variance in death attributable to infection and < or = 96% of the variance in death attributable to asphyxia. Common-litter factors were more important than additive genetic factors. Variance attributed to common-litter factors ranged from 2% for cheiloschisis, palatoschisis, or cheilopalatoschisis to 30% for death attributable to infection, and variance attributed to additive genetic factors ranged from 0% for asphyxia to 14% for euthanatized because of white color. Inbreeding coefficient had a significant effect on death attributable to infection, which increased 0.26% for each percentage increase of inbreeding. CONCLUSIONS AND CLINICAL RELEVANCE: Additive genetic factors have less impact on preweaning mortality than common-litter factors, which in turn have less impact than within-litter factors. Mortality attributable to infection increases significantly with increases in inbreeding.

Animals↗
PubMedDate not supplied

[Analysis of the population structure of the South German coldblood in Bavaria, Germany].

Gene contributions of foreign populations as well as coefficients of inbreeding and relationship were calculated in 1918 South German Coldblood horses registered in Bavaria in 2003. Based on nearly complete 8-generation-pedigrees (index of pedigree completeness: 76%) the mean coefficient of inbreeding was 23%. After considering missing pedigree data, the mean coefficient of inbreeding was 3%. The rates of inbreeding per generation in the current population amount to about 0.43% over the last eight generations and to about 0.15% in the forthcoming generation. In the total current population, the mean degree of relationship was 6%. The proportion of purebred South German Coldblood horses in the current population is about 43%. As the Noric horse is of same origin as the South German Coldblood, these two breeds can be considered as an entity and thus the proportion of purebred genes in the current Bavarian South German Coldblood population reaches more than 93%. The Suffolk Punch and Thoroughbred Horse were the most important contributors to the current South German Coldblood population, whereas the Rhenish-German and Black Forest Draught Horse as well as the Percheron had neglectable influences. The effective population size in the current Bavarian South German Coldblood population is Ne = 332.

Animals↗
PubMed2004

Consanguinity and endogamy in Northern Tunisia and its impact on non-syndromic deafness.

Deafness is an important health problem in the Tunisian population, especially in isolates where the prevalence ranges from 2 to 8%. To evaluate the effect of inbred unions on deafness, a study was conducted on 5,020 individuals (160 are deaf) between 2000 and 2002 in the North of Tunisia. The coefficient of inbreeding for all individuals and the levels of inbreeding in ten districts were computed. The higher levels were obtained in the rural districts. Our study revealed that geographic isolation, social traditions, and parental involvement in mode selection all contribute to increase consanguinity in these regions. The mean inbreeding seems to be similar to those estimated in highly inbred isolates in the world. The relative risk of the 35delG mutation, the single most frequent allele for non-syndromic recessive deafness in Tunisia, was estimated from the observed inbreeding coefficient and found to be 10.76 (SD 7.74) for first-cousin marriages, which are the most common form of consanguineous marriage encountered. Our knowledge of the risk rate of deafness and our understanding of consanguinity is required for the prevention of genetic deafness in the Tunisian population.

Case-Control Studies↗
PubMed1997

Surname and consanguineous marriages in Japan.

A survey of consanguineous marriages in Japan was conducted on 1 September 1983, by questionnaires. The total number of couples surveyed was 9225. They were chosen from six widely different areas and the inbreeding coefficients from isonymy and pedigrees were estimated for each area. Random inbreeding remained constant with the marriage year whereas total (F) and non-random (Fn) inbreeding from isonymy and inbreeding from pedigrees (alpha) decreased with the marriage year in each area. Estimates of genetic microdifferentiation from surnames were obtained; estimates of the reduced variance indicated low microdifferentiation (0.000014-0.000081) in five areas and a higher value in Fukue City (0.0004). The ratio of FST (the average within-group a priori kinship) to alpha-value ranged from 0.42 in Kawanishi City to 3.9 in Minobu-Cho.

Consanguinity↗
PubMed1998

Population genetic structure in a Robertsonian race of house mice: evidence from microsatellite polymorphism.

Genetic evidence was assessed for inbreeding and population subdivision in a Robertsonian fusion (Rb) race of the western European form of house mouse, Mus musculus domesticus, in central Belgium. Inbreeding, and the factors responsible for subdivision (genetic drift and extinction-recolonization) can theoretically influence the fixation of underdominant Rb variants. The data consisted of allele frequencies of eight microsatellite loci and of the Rb(4.12) and Rb(5.10) chromosomes. Six populations were sampled once, and a seventh was sampled successively over 3 years. No evidence for inbreeding within populations was found. Levels of between-population subdivision were high (theta = 0.15-0.39), and showed no association with either karyotype or geographical distance over 8-60 km. In addition, low values of effective size were found in the successively sampled population (Ne = 5-20). Cases of significant two-locus disequilibria were associated with the most closely linked pair of microsatellite loci (r = 0.15): also consistent with small effective sizes. These results suggest that both the lack of inbreeding, and the combined effects of genetic drift and extinction-recolonization, may promote Rb polymorphism in M. m. domesticus.

Animals↗
PubMed2000

F1 hybrid inviability in eucalyptus: the case of E. ovata x E. globulus.

The impact of inbreeding and hybridization on fitness was compared in the two co-occurring forest tree species, Eucalyptus ovata and E. globulus, aimed at explaining the rarity of their hybrids in nature. The success of selfing, open-pollination and outcrossing of both species and interspecific hybridization was monitored from seed-set to 10-year's growth in a field trial. There was a unilateral barrier to hybridization with seed-set obtained only with E. ovata females. The F1 hybrids exhibited reduced viability compared to intraspecific cross-types at virtually all stages of the life cycle and are clearly at a selective disadvantage compared with their open-pollinated E. ovata half-sibs with which they would directly compete in nature. Eucalyptus ovata and E. globulus overlap in their flowering time but the F1 hybrids flowered later with virtually no overlap with either species. The asynchronous flowering and reduced reproductive fitness of F1 hybrids would markedly limit the opportunity for advanced generation hybridization. Inbreeding similarly had a deleterious effect on the fitness of both species, and the F1 hybrids were most competitive with the E. ovata selfs. It is argued that changes in inbreeding levels of parental populations may be a key factor affecting the relative fitness of hybrids and their potential to impact on the pure species gene pool. Reduced fitness of the pure species through inbreeding may result in hybridization having its greatest evolutionary impact in small founder or relict populations.

Biological Evolution↗
PubMed2001

Population genetic structure of the endangered tropical tree species Caryocar brasiliense, based on variability at microsatellite loci.

We report the population genetic structure of the endangered tropical tree species Caryocar brasiliense, based on variability at 10 microsatellite loci. Additionally, we compare heterozygosity and inbreeding estimates for continuous and fragmented populations and discuss the consequences for conservation. For a total of 314 individuals over 10 populations, the number of alleles per locus ranged from 20 to 27 and expected and observed heterozygosity varied from 0.129 to 0.924 and 0.067 to 1.000, respectively. Significant values of theta and R(ST) showed important genetic differentiation among populations. theta was much lower than R(ST), suggesting that identity by state and identity by descent have diverged in these populations. Although a significant amount of inbreeding was found under the identity by descent model (f = 0.11), an estimate of inbreeding for microsatellite markers based on a more adequate stepwise mutation model showed no evidence of nonrandom mating (R(IS) = 0.04). Differentiation (pairwise F(ST)) was positively correlated with geographical distance, as expected under the isolation by distance model. No effect of fragmentation on heterozygosity or inbreeding could be detected. This is most likely due to the fact that Cerrado fragmentation is a relatively recent event (approximately 60 years) compared to the species life cycle. Also, the populations surveyed from both fragmented and disturbed areas were composed mainly of adult individuals, already present prior to ecosystem fragmentation. Adequate hypothesis testing of the effect of habitat fragmentation will require the recurrent analysis of juveniles across generations in both fragmented and nonfragmented areas.

Brazil↗
PubMedDate not supplied

Marriage behaviour in the Alpine Non Valley from 1825 to 1923.

BACKGROUND: The study is part of a research project on the marital structure of mountain populations from the Eastern Italian Alps. Little is known about marriage patterns in this Alpine area. AIM: The aim of the study is to evaluate the extent of reproductive isolation in some communities of the Non Valley (Trentino, Italy) and to investigate its microgeographic and temporal changes over the period 1825-1923. SUBJECTS AND METHODS: 4518 microfilmed marriage records from registers of seven parishes of the Non Valley were used to analyse the following: endogamy rate, inbreeding calculated both from dispensations and from isonymy, repeating pairs of surnames in marriages, isonymic relationships. RESULTS: The results show notable variability among parishes in the levels of endogamy (40-73%), inbreeding (alpha: 1.9-4.57; Ft: 0.0073-0.019) and subdivision (RPr/RP: 0.5-1.3). The values are relatively stable over the course of a century, apart from a rise in inbreeding indicated by dispensations and a slight decrease of endogamy at the beginning of the 20th century. Isonymic relationships reflect geographic proximity between populations, with minimum changes through time. CONCLUSIONS: Variations in the level of reproductive isolation within the Non Valley are consistent with the different geographic characteristics and population sizes of the settlements. Comparison with data obtained from previous studies in the Eastern Italian Alps shows that the values of the investigated biodemographic indicators are in line with the geography and altitude of the area. The slight differences in temporal trend of endogamy and inbreeding can be correlated with different migration patterns.

Consanguinity↗