Comparison of different genetic distances to test isolation by distance between populations.

Studying isolation by distance can provide useful demographic information. To analyze isolation by distance from molecular data, one can use some kind of genetic distance or coalescent simulations. Molecular markers can often display technical caveats, such as PCR-based amplification failures (null alleles, allelic dropouts). These problems can alter population parameter inferences that can be extracted from molecular data. In this simulation study, we analyze the behavior of different genetic distances in Island (null hypothesis) and stepping stone models displaying varying neighborhood sizes. Impact of null alleles of increasing frequency is also studied. In stepping stone models without null alleles, the best statistic to detect isolation by distance in most situations is the chord distance DCSE. Nevertheless, for markers with genetic diversities HS<0.4-0.5, all statistics tend to display the same statistical power. Marginal sub-populations behave as smaller neighborhoods. Metapopulations composed of small sub-population numbers thus display smaller neighborhood sizes. When null alleles are introduced, the power of detection of isolation by distance is significantly reduced and DCSE remains the most powerful genetic distance. We also show that the proportion of null allelic states interact with the slope of the regression of FST/(1-FST) as a function of geographic distance. This can have important consequences on inferences that can be made from such data. Nevertheless, Chapuis and Estoup's FreeNA correction for null alleles provides very good results in most situations. We finally use our conclusions for reanalyzing and reinterpreting some published data sets.

Effect of genetic European taurine ancestry on milk yield of Ankole-Holstein crossbred dairy cattle in mixed smallholders system of Burundi highlands.

Different breeding systems associated with specific bovine genetic resources have coexisted in Burundi. To prepare for the development of a national action plan for the improvement of bovine genetic resources in Burundi, we aimed at performing genetic characterization of Ankole and Ankole × European crossbred individuals and assessing the effect of European ancestry on milk productivity of cows kept under the mixed crops livestock system. To that end, we genotyped 37 Ankole and 138 crossbred individuals on 42 636 SNPs and combined these genotypes with those from 21 cattle breeds, representative of the bovine genetic diversity. We also measured milk yield not suckled and estimated suckled milk. Given the results, we confirmed the indicine × African taurine admixed origin of the Ankole in Burundi and showed that crossbred individuals present a high proportion of European ancestry (i.e. 57% on average). As the proportion of European ancestry increased, milk yield increased by 0.03 ± 0.01 l/day, at a lower extent than expected. We also observed that breeders were unable to correctly evaluate the European proportion in their livestock. Our results may provide useful information for objective dairy breeding in Burundi. As an example, an ex-situ conservation program of Ankole within the framework of value chains is proposed as an accompanying strategy to improve the sustainability of the crossbreeding program.

Association studies in QTL regions linked to bovine trypanotolerance in a West African crossbred population.

African animal trypanosomosis is a parasitic blood disease transmitted by tsetse flies and is widespread in sub-Saharan Africa. West African taurine breeds have the ability, known as trypanotolerance, to limit parasitaemia and anaemia and remain productive in enzootic areas. Several quantitative trait loci (QTL) underlying traits related to trypanotolerance have been identified in an experimentally infected F(2) population resulting from a cross between taurine and zebu cattle. Although this information is highly valuable, the QTL remain to be confirmed in populations subjected to natural conditions of infection, and the corresponding regions need to be refined. In our study, 360 West African cattle were phenotyped for the packed cell volume control under natural conditions of infection in south-western Burkina Faso. Phenotypes were assessed by analysing data from previous cattle monitored over 2 years in an area enzootic for trypanosomosis. We further genotyped for 64 microsatellite markers mapping within four previously reported QTL on BTA02, BTA04, BTA07 and BTA13. These data enabled us to estimate the heritability of the phenotype using the kinship matrix between individuals computed from genotyping data. Thus, depending on the estimators considered and the method used, the heritability of anaemia control ranged from 0.09 to 0.22. Finally, an analysis of association identified an allele of the MNB42 marker on BTA04 as being strongly associated with anaemia control, and a candidate gene, INHBA, as being close to that marker.

No more cold-chain failures, using dehydrated reagents in ELISA antibody-detection against animal trypanosomes of African origin.

Animal trypanosomoses due to trypanosomes of African origin (ATAO), mainly caused by Trypanosoma congolense type Savannah (TCS), T. brucei brucei (TBB), T. vivax (TV), and T. evansi, are widespread diseases that affect domestic and wild mammals and have a huge economic impact. ATAO clinical suspicions are usually confirmed by parasitological and molecular methods, while sero-epidemiological surveys are generally carried out using the OIE-recommended ELISA method based on whole cell lysate soluble antigens (WCLSA) from purified trypanosomes; this reagent is usually stored frozen. With a view to expanding this ELISA test, we assessed, standardized, and validated the use of dehydrated rather than frozen WCLSA and serum samples. For the three ELISA assays (TV, TCS & TBB), a repeatability study revealed no significant difference between repeats. The results obtained using frozen rather than freeze-dried antigen and serum strongly correlated for Pearson's correlation values (>0.93) and Lin's measure ("very good" to "excellent"). Reproducibility was robust, with Pearson's correlation values >0.97 for inter technician effects, and 0.87 (TV) to 0.97 (TBB & TCS) for inter-laboratory tests; their combination was "very satisfactory" to "excellent" according to Lin's measure and there was no impact on qualitative test results. Dehydrated reagents offer the advantage of shipment at room temperature, allowing the secured provision of reagents to regional laboratories. Together with a compendium of standard diagnostic protocols for ATAO (/OIE), dehydrated reagents will enable the serological diagnosis of ATAO at regional level in endemic countries. This very welcome improvement in the context of the Progressive Control Pathway for trypanosomes, recently launched by African countries, will possibly be extended to Latin America in the near future.

Population sizes and dispersal pattern of tsetse flies: rolling on the river?

The West African trypanosomoses are mostly transmitted by riverine species of tsetse fly. In this study, we estimate the dispersal and population size of tsetse populations located along the Mouhoun river in Burkina Faso where tsetse habitats are experiencing increasing fragmentation caused by human encroachment. Dispersal estimated through direct (mark and recapture) and indirect (genetic isolation by distance) methods appeared consistent with one another. In these fragmented landscapes, tsetse flies displayed localized, small subpopulations with relatively short effective dispersal. We discuss how such information is crucial for designing optimal strategies for eliminating this threat. To estimate ecological parameters of wild animal populations, the genetic measures are both a cost- and time-effective alternative to mark-release-recapture. They can be applied to other vector-borne diseases of medical and/or economic importance.

Detection of selection signatures within candidate regions underlying trypanotolerance in outbred cattle populations.

Breeding indigenous African taurine cattle tolerant to trypanosomosis is a straightforward approach to control costs generated by this disease. A recent study identified quantitative trait loci (QTL) underlying trypanotolerance traits in experimental crosses between tolerant N'Dama and susceptible Boran zebu cattle. As trypanotolerance is thought to result from local adaptation of indigenous cattle breeds, we propose an alternative and complementary approach to study the genetic architecture of this trait, based on the identification of selection signatures within QTL or candidate genes. A panel of 92 microsatellite markers was genotyped on 509 cattle belonging to four West African trypanotolerant taurine breeds and 10 trypanosusceptible European or African cattle breeds. Some of these markers were located within previously identified QTL regions or candidate genes, while others were chosen in regions assumed to be neutral. A detailed analysis of the genetic structure of these different breeds was carried out to confirm a priori grouping of populations based on previous data. Tests based on the comparison of the observed heterozygosities and variances in microsatellite allelic size among trypanotolerant and trypanosusceptible breeds led to the identification of two significantly less variable microsatellite markers. BM4440, one of these two outlier loci, is located within the confidence interval of a previously described QTL underlying a trypanotolerance-related trait. Detection of selection signatures appears to be a straightforward approach for unravelling the molecular determinism of trypanosomosis pathogenesis. We expect that a whole genome approach will help confirm these results and achieve a higher resolving power.

How does farmer connectivity influence livestock genetic structure? A case-study in a Vietnamese goat population.

Assessing how genes flow across populations is a key component of conservation genetics. Gene flow in a natural population depends on ecological traits and the local environment, whereas for a livestock population, gene flow is driven by human activities. Spatial organization, relationships between farmers and their husbandry practices will define the farmer's network and so determine farmer connectivity. It is thus assumed that farmer connectivity will affect the genetic structure of their livestock. To test this hypothesis, goats reared by four different ethnic groups in a Vietnamese province were genotyped using 16 microsatellites. A Bayesian approach and spatial multivariate analysis (spatial principal component analysis, sPCA) were used to identify subpopulations and spatial organization. Ethnic group frequencies, husbandry practices and altitude were used to create cost maps that were implemented in a least-cost path approach. Genetic diversity in the Vietnamese goat population was low (0.508) compared to other local Asian breeds. Using a Bayesian approach, three clusters were identified. sPCA confirmed these three clusters and also that the genetic structure showed a significant spatial pattern. The least-cost path analysis showed that genetic differentiation was significantly correlated (0.131-0.207) to ethnic frequencies and husbandry practices. In brief, the spatial pattern observed in the goat population was the result of complex gene flow governed by the spatial distribution of ethnic groups, ethnicity and husbandry practices. In this study, we clearly linked the livestock genetic pattern to farmer connectivity and showed the importance of taking into account spatial information in genetic studies.

Population genetic structure of wild and farmed rusa deer (Cervus timorensis russa) in New-Caledonia inferred from polymorphic microsatellite loci.

Historical records indicate that 12 rusa deer (Cervus timorensis russa) were introduced in New-Caledonia during the 1870s. We used eight polymorphic microsatellite DNA loci to assess the genetic differentiation and diversity of farmed and wild deer populations. Past genetic bottlenecks were detected in both sub-populations, although higher genetic diversity was maintained in farmed populations, probably due to the regular introduction of reproducers from wild populations and from other farms. The genetic structure of farmed and wild populations differed significantly. There was a significant isolation by distance for wild populations, whereas farmed populations were significantly differentiated between farms independently from their geographical proximity. Wild rusa deer consisted of small populations (with effective population sizes ranging between 7 and 19 individuals depending on the methods used), with a low parent-offspring dispersion range (0.20-2.02 km). Genetic tools and direct observations provided congruent estimates of dispersion and population sizes. We discuss the relevance of our results for management purposes.

First outbreak of Trypanosoma evansi in camels in metropolitan France.

The first outbreak of trypanosomosis caused by Trypanosoma evansi in camels in France was reported on a farm in the Aveyron Department. Five camels were imported from the Canary Islands to the farm in early July 2006, and trypanosomes were observed on a stained blood smear from one of them, which died in October. On further investigations, trypanosomes were observed in the blood of five camels, three of them indigenous to the farm and two that had been imported. On the basis of microscopical examination (morphological criteria and measurements) and serological results based on the card agglutination T evansi test and PCR typing, the parasites were identified as T evansi. After treatment with melarsomine, the infected camels rapidly became negative by parasitological tests and were negative two to four months later by serological tests. The parasite was probably transmitted by tabanids and Stomoxys calcitrans, which were abundant in July to September 2006. No parasites were observed in other animals on the farm or on neighbouring farms, but some of the sheep on these farms were positive by PCR or serology.

The extent of linkage disequilibrium in a large cattle population of western Africa and its consequences for association studies.

Several previous studies concluded that linkage disequilibrium (LD) in livestock populations from developed countries originated from the impact of strong selection. Here, we assessed the extent of LD in a cattle population from western Africa that was bred in an extensive farming system. The analyses were performed on 363 individuals in a Bos indicus x Bos taurus population using 42 microsatellite markers on BTA04, BTA07 and BTA13. A high level of expected heterozygosity (0.71), a high mean number of alleles per locus (9.7) and a mild shift in Hardy-Weinberg equilibrium were found. Linkage disequilibrium extended over shorter distances than what has been observed in cattle from developed countries. Effective population size was assessed using two methods; both methods produced large values: 1388 when considering heterozygosity (assuming a mutation rate of 10(-3)) and 2344 when considering LD on whole linkage groups (assuming a constant population size over generations). However, analysing the decay of LD as a function of marker spacing indicated a decreasing trend in effective population size over generations. This decrease could be explained by increasing selective pressure and/or by an admixture process. Finally, LD extended over small distances, which suggested that whole-genome scans will require a large number of markers. However, association studies using such populations will be effective.

Karyotype identity of two subspecies of Eld's deer [Cervus eldi (Cervinae, Artiodactyla)] and its consequences for conservation.

Among the three subspecies generally recognized within the Eld's deer (Cervus eldi)--C. e. eldi, C. e. thamin, and C. e. siamensis--C. e. siamensis is considered to be particularly endangered following its disappearance from a major portion of its original range. The only captive breeding population of this subspecies is in the zoological parks at the Paris Museum of Natural History. Taking into account its low effective population size (Ne = 7) and the increasing levels of inbreeding, the continued breeding of this "micropopulation" in isolation from closely related subspecies and in particular from C. e. thamin, which is much more common in zoos as well as in the nature, is questioned. As an initial step in determining if crosses between these subspecies could be performed without risk of outbreeding depression due, in part, to gross differences in their karyotypes, a comparative chromosome banding analysis (RBG-bands) of C. e. siamensis and C. e. thamin was undertaken. No chromosomal differences were identified between the taxa at the level of resolution obtained. The study suggests that, at least from a karyotypic perspective, no obvious differences delimit the two subspecies, and hybridization between endangered C. e. siamensis and C. e. thamin is not likely to lead to impaired fertility in hybrid animals.

Efficiency of semi-automated fluorescent multiplex PCRs with 11 microsatellite markers for genetic studies of deer populations.

Thirty bovine and eight ovine microsatellite primer pairs were tested on four tropical deer species: Eld's and Swamp deer (highly threatened) and Rusa and Vietnamese Sika deer (economically important). Thirty markers gave an amplified product in all four species (78.9%). The number of polymorphic microsatellite markers varied among the species from 14 in Eld's deer (47%) to 20 in Swamp deer (67%). Among them, 11 microsatellite loci were multiplexed in three polymerase chain reactions (PCRs) and labelled with three different fluorochromes that can be loaded in one gel-lane. To test the efficiency of the multiplex, primary genetic studies (mean number of alleles, expected heterozygosities and Fis values) were carried out on four deer populations. Parentage exclusion probability and probability of identity were computed and discussed on a Swamp deer population. These multiplexes PCRs were also tested on several other deer species and subspecies. The aim of this study is to establish a tool useful for genetic studies of population structure and diversity in four tropical deer species which with few modifications can be applied to other species of the genus Cervus.

Cytogenetic comparison between Vietnamese sika deer and cattle: R-banded karyotypes and FISH mapping.

R-banded chromosomes of Vietnamese sika (VS) deer (Cervus nippon pseudaxis, 2N = 66), a threatened subspecies of sika deer endemic to Vietnam, are presented for the first time and were compared with bovine R-banded chromosomes to define a standard karyotype. Nineteen VS deer autosomes (CNP) were identified on the basis of the banding pattern relative to bovine chromosomes (BTA), while hypotheses for the remaining thirteen were proposed from comparisons with the published deer genetic map, BTA 1, 2, 5, 6, 8 and 9 each equivalent to two separate acrocentric CNP chromosomes and BTA 26 and 28 associated in a tandem fusion. To confirm these hypotheses, probes for the twenty-nine Texas nomenclature type I markers specific for each cattle autosome, sixteen other type I and fourteen microsatellite markers were used in FISH experiments on VS deer chromosomes. CNP7 presented the most complex rearrangement as compared with cattle chromosomes. A complete correspondence between VS deer and cattle chromosomes was established and it was extended with a comparison with the human karyotype to transfer human map information to this species of scientific and economic interest. Moreover, this work anchors the deer genetic linkage map to chromosome-specific markers.

Identification by R-banding and FISH of chromosome arms involved in Robertsonian translocations in several deer species.

We constructed and analyzed the RBG-banded karyotype of five deer species: Chital (Axis axis), White-lipped deer (Cervus albirostris), Rusa deer (Cervus timorensis russa), Sambar deer (Cervus unicolor) and Eld's deer (Cervus eldi siamensis). Among these five species, only Eld's deer had been previously karyotyped using R-banding. In order to identify all the chromosome correspondences with cattle and precisely which chromosome arms are involved in Robertsonian translocations, we compared the karyotypes of these five species with those of the closely related and well-characterized species, cattle (Bos taurus) and Vietnamese Sika deer (Cervus nippon pseudaxis). Among these six deer species (the five above plus the Vietnamese Sika deer), we found thirteen different Robertsonian translocations involving nineteen different chromosome arms. Thirteen chromosome arms were identified by comparison of R-banding patterns only and the remaining six were either confirmed or identified by FISH-mapping of bovine or caprine probes previously localized in cattle. Finally, we observed that five of the thirteen Robertsonian translocations are shared by at least two species and that some chromosome arms are more frequently involved in Robertsonian translocations than others.

Microsatellite analysis of genetic diversity of the Vietnamese sika deer (Cervus nippon pseudaxis).

The Vietnamese sika deer (Cervus nippon pseudaxis) is an endangered subspecies of economic and traditional value in Vietnam. Most living individuals are held in traditional farms in central Vietnam, others being found in zoos around the world. Here we study the neutral genetic diversity and population structure of this subspecies using nine microsatellite loci in order to evaluate the consequences of the limited number of individuals from which this population was initiated and of the breeding practices (i.e., possible inbreeding). Two hundred individuals were sampled from several villages. Our data show both evidence for limited local inbreeding and isolation by distance with a mean F(ST) value of 0.02 between villages. This suggests that exchange of animals occurs at a local scale, at a rate such that highly inbred mating is avoided. However, the genetic diversity, with an expected heterozygosity (H(e)) of 0.60 and mean number of alleles (k) of 5.7, was not significantly larger than that estimated from zoo populations of much smaller census size (17 animals sampled; H(e) = 0.65, k = 4.11). Our results also suggest that the Vietnamese population might have experienced a slight bottleneck. However, this population is sufficiently variable to constitute a source of individuals for reintroduction in the wild in Vietnam.