Asian water buffalo: domestication, history and genetics.

The domestic Asian water buffalo (Bubalus bubalis) is found on all five continents, with a global population of some 202 million. The livelihoods of more people depend on this species than on any other domestic animal. The two distinct types (river and swamp) descended from different wild Asian water buffalo (Bubalus arnee) populations that diverged some 900 kyr BP and then evolved in separate geographical regions. After domestication in the western region of the Indian subcontinent (ca. 6300 years BP), the river buffalo spread west as far as Egypt, the Balkans and Italy. Conversely, after domestication in the China/Indochina border region ca. 3000-7000 years BP, swamp buffaloes dispersed through south-east Asia and China as far as the Yangtze River valley. Molecular and morphological evidence indicates that swamp buffalo populations have strong geographic genetic differentiation and a lack of gene flow, but strong phenotypic uniformity. In contrast, river buffalo populations show a weaker phylogeographic structure, but higher phenotypic diversity (i.e. many breeds). The recent availability of a high-quality reference genome and of a medium-density marker panel for genotyping has triggered a number of genome-wide investigations on diversity, evolutionary history, production traits and functional elements. The growing molecular knowledge combined with breeding programmes should pave the way to improvements in production, environmental adaptation and disease resistance in water buffalo populations worldwide.

Genetic variation for resistance to high temperature stress of mature sperm - a study in Drosophila.

Genetic variation for resistance to heat stress has been found for a number of life-history components in Drosophila species. For male and female fertility (or sterility), stress resistance of the parents is confounded with stress resistance of the haploid gametes. Many genes are known to influence male fertility in Drosophila melanogaster. Some may carry temperature sensitive alleles that reduce fertility through effects on mature sperm when exposed to heat stress. In this study, sperm from each of 320 males were either not heat shocked (control) or exposed to a heat shock (36.9°C for 2 hours) either in the male testes or in the female reproductive tract. We did not detect any temperature sensitive sterility alleles. These results are relevant in relation to haploid gene expression and the findings of considerable amounts of mRNA in mature sperm, potentially important for sperm function and fertilization.

Effective population size of natural populations of Drosophila buzzatii, with a comparative evaluation of nine methods of estimation.

Allozyme and microsatellite data from numerous populations of Drosophila buzzatii have been used (i) to determine to what degree N(e) varies among generations within populations, and among populations, and (ii) to evaluate the congruence of four temporal and five single-sample estimators of N(e) . Effective size of different populations varied over two orders of magnitude, most populations are not temporally stable in genetic composition, and N(e) showed large variation over generations in some populations. Short-term N(e) estimates from the temporal methods were highly correlated, but the smallest estimates were the most precise for all four methods, and the most consistent across methods. Except for one population, N(e) estimates were lower when assuming gene flow than when assuming populations that were closed. However, attempts to jointly estimate N(e) and immigration rate were of little value because the source of migrants was unknown. Correlations among the estimates from the single-sample methods generally were not significant although, as for the temporal methods, estimates were most consistent when they were small. These single-sample estimates of current N(e) are generally smaller than the short-term temporal estimates. Nevertheless, population genetic variation is not being depleted, presumably because of past or ongoing migration. A clearer picture of current and short-term effective population sizes will only follow with better knowledge of migration rates between populations. Different methods are not necessarily estimating the same N(e) , they are subject to different bias, and the biology, demography and history of the population(s) may affect different estimators differently.

Genetic differentiation of water buffalo (Bubalus bubalis) populations in China, Nepal and south-east Asia: inferences on the region of domestication of the swamp buffalo.

Data from three published studies of genetic variation at 18 microsatellite loci in water buffalo populations in China (18 swamp type, two river type), Nepal (one wild, one domestic river, one hybrid) and south-east Asia (eight swamp, three river) were combined so as to gain a broader understanding of genetic relationships among the populations and their demographic history. Mean numbers of alleles and expected heterozygosities were significantly different among populations. Estimates of θ (a measure of population differentiation) were significant among the swamp populations for all loci and among the river populations for most loci. Differentiation among the Chinese swamp populations (which was due primarily to just one population) was much less than among the south-east Asian. The Nepal wild animals, phenotypically swamp type but genetically like river type, are significantly different from all the domestic river populations and presumably represent the ancestral Bubalus arnee (possibly with some river-type introgression). Relationships among the swamp populations (D(A) genetic distances, principal component analysis and structure analyses) show the south-east Asian populations separated into two groups by the Chinese populations. Given these relationships and the patterns of genetic variability, we postulate that the swamp buffalo was domesticated in the region of the far south of China, northern Thailand and Indochina. Following domestication, it spread south through peninsular Malaysia to Sumatra, Java and Sulawesi, and north through China, and then to Taiwan, the Philippines and Borneo.

Altitudinal and seasonal variation in microsatellite allele frequencies of Drosophila buzzatii.

Variation in climate, particularly temperature, is known to affect the genetic composition of populations. Although there have been many studies of latitudinal variation, comparisons of populations across altitudes or seasons, particularly for animal species, are less common. Here, we study genetic variation (microsatellite markers) in populations of Drosophila buzzatii collected along altitudinal gradients and in different seasons. We found no differences in genetic variation between 2 years or between seasons within years. However, there were numerous cases of significant associations between allele frequencies or expected heterozygosities and altitude, with more than half showing nonlinear relationships. While these associations indicate possible selection and local altitudinal adaptation, direct tests gave strong evidence for selection affecting two loci and weaker evidence for five other loci. Two loci that are located within an inversion (including the one with strongest evidence for selection) show a linear increase in genetic diversity with altitude, likely due to thermal selection. Parallel associations with altitude here and with latitude in Australian populations indicate that selection is operating on chromosomal regions marked by some of the loci.

Bottlenecks, population differentiation and apparent selection at microsatellite loci in Australian Drosophila buzzatii.

Species colonizing new areas disjunct from their original habitat may be subject to novel selection pressures, and exhibit adaptive genetic changes. However, if colonization occurs through a small number of founders, the genetic composition of the colonized population may differ from that of the original population simply due to genetic drift. Disentangling the effects of founder drift and selection after colonization is crucial to understanding the adaptive process. Drosophila buzzatii colonized Australia some 600-700 generations ago, and spread rapidly over a wide geographical range. Genetic variation for 15 microsatellite loci in each of nine populations in eastern Australia was used to estimate the size of the bottleneck, and to determine if any of these microsatellites marked genomic regions subject to recent selection. We estimate that on its introduction to Australia, D. buzzatii went through a moderate bottleneck (approximately 30-40 founders). Linkage disequilibrium was common, both intrachromosomal and between loci on different chromosomes. Of the 15 loci, 2 showed evidence of selection, one exhibiting local adaptation in different populations and the other balancing selection. We conclude that linkage disequilibria may be far more common in natural populations than is generally assumed, and the loci apparently affected by selection may well be marking selection in large genome regions including many loci that are not necessarily closely linked.

Interleukin (IL)-1 regulates ozone-enhanced tracheal smooth muscle responsiveness by increasing substance P (SP) production in intrinsic airway neurons of ferret.

Exposure to ozone induces airway hyperresponsiveness (AHR) mediated partly by substance P (SP) released from nerve terminals of intrinsic airway neurons. Our recent studies showed that interleukin (IL)-1, an important multifunctional proinflammatory cytokine, increases synthesis and release of SP from intrinsic airway neurons. The purpose of this study is to investigate the possible involvement of endogenous IL-1 in modulating neural responses associated with ozone-enhanced airway responsiveness. Ferrets were exposed to 2ppm ozone or filtered air for 3h. IL-1 in the bronchoalveolar lavage (BAL) fluid was significantly increased in ozone-exposed animals and responses of tracheal smooth muscle to methacholine (MCh) and electrical field stimulation (EFS) were elevated significantly. Both the SP nerve fiber density in tracheal smooth muscle and the number of SP-containing neurons in airway ganglia were significantly increased following ozone exposure. Pretreatment with IL-1 receptor antagonist (IL-1 Ra) significantly diminished ozone-enhanced airway responses to EFS as well as ozone-increased SP in the airway. To selectively investigate intrinsic airway neurons, segments of ferret trachea were maintained in culture conditions for 24h to eliminate extrinsic contributions from sensory nerves. The segments were then exposed to 2ppm ozone in vitro for 3h. The changes of ozone-induced airway responses to MCh and EFS, and the SP levels in airway neurons paralleled those observed with in vivo ozone exposure. The ozone-enhanced airway responses and neuronal SP levels were inhibited by pretreatment with IL-1 Ra. These findings show that IL-1 is released during ozone exposure enhances airway responsiveness by modulating SP expression in airway neurons.

Molecular population genetics of the alpha-esterase5 gene locus in original and colonized populations of Drosophila buzzatii and its sibling Drosophila koepferae.

Several studies have suggested that esterase-2 (EST-2) may be the target of natural selection in the cactophilic fly Drosophila buzzatii. In this work, we analyzed nucleotide variation in a fragment of alpha-esterase5 (alphaE5), the gene encoding EST-2, in original (Argentinian) and colonized (Australian) populations of D. buzzatii and in its sibling D. koepferae. Estimates of nucleotide heterozygosity in D. buzzatii were similar in Australia and Argentina, although we detected a loss of singletons in colonized populations, suggesting a moderate founder effect. Interspecific comparisons revealed that D. buzzatii was more polymorphic for nonsynonymous variation, whereas D. koepferae was more variable for synonymous and noncoding sites. The two major chromosomal arrangements (2st and 2j) in D. buzzatii displayed similar levels of nucleotide variation, whereas 2jz3 was monomorphic. The sequenced region allowed the discrimination of a greater number of EST-2 protein variants in the Australian sample than in the Argentinean sample. In D. koepferae, nucleotide variation in alphaE5 does not depart from neutral expectations, although tests of population structure were significant for silent variation. In contrast, D. buzzatii has probably undergone a recent population expansion in its South American range. In addition, the McDonald and Kreitman test revealed an excess of nonsynonymous polymorphism in both original and colonized populations of this species.

Climatic adaptation of Drosophila buzzatii populations in southeast Australia.

Variation in 19 traits possibly relevant for thermal adaptation was studied in 11 populations of Drosophila buzzatii collected in southeast Australia. Using stepwise multiple regression, the variation was compared to variation in geographic coordinates and to a set of climatic variables estimated for each collection site. For 13 of the traits, a significant part of the variation was explained by climatic variables and/or geographic coordinates, suggesting directional selection for adaptation to the environment in the majority of traits studied. In 10 of the traits, both geographic coordinates and climatic variables explained significant proportions of the variation, with R2 ranging from 0.075 to 0.58. Although larvae, pupae and adults of D. buzzatii share a common habitat, the measured traits were not correlated across life stages and gender. Also, there seemed to be special conditions in marginal populations near species borders, giving rise to nonlinear relations with latitude. Climate apparently does influence the adaptive evolution of the traits studied, but they also are affected by other factors that vary with latitude, longitude and distance to coast. These results highlight the complex challenges imposed by the environment on the adaptive process.

Microsatellites reveal male recombination and neo-sex chromosome formation in Scaptodrosophila hibisci (Drosophilidae).

In drosophilid flies, male recombination and neo-sex chromosome formation are rare. Following the genotyping of full-sib families with 20 microsatellite markers and subsequent cytological work, we found evidence of both male recombination and neo-sex chromosome formation in Scaptodrosophila hibisci. As far as we are aware, this is the first report of male recombination and neo-sex chromosome formation co-occurring in a drosophilid fly. Two autosomal loci, Sh29c and Sh90, showed aberrant segregation of male parental alleles. We describe how an autosomal fission followed by fusion of one of the autosomal fragments to the Y chromosome to create a Y1Y2X1X2/X1X1X2X2 sex determination system provides the most parsimonious explanation of the patterns we observe. Male recombination was observed in three families, including autosomal linkage groups and the Y1/X2 linkage group. In addition to the X1 linkage group, two autosomal linkage groups were identified.

Population structure and host-plant specialization in two Scaptodrosophila flower-breeding species.

In contrast to phytophagous insect species, little attention has been paid to the possibility of host races in the Drosophilidae, although flower-breeding species, where courtship and mating take place on the flowers, are likely candidates. Two species of Scaptodrosophila, S. hibisci and S. aclinata, are restricted to flowers of Hibiscus species (section Furcaria), and the Furcaria specialization likely predated the separation of S. hibisci and S. aclinata. In all, 20 microsatellite loci were analysed in nine populations of S. hibisci and five of S. aclinata. For two pairs of S. hibisci populations in close proximity, but breeding on different Hibiscus species, differentiation between the populations of each of these pairs was similar to that between the populations that were from the same Hibiscus species, but geographically distant, suggesting the early stages of host-race formation. Genetic variability was significantly less in S. aclinata than in S. hibisci, suggesting greater drift effects in the former. However, of 253 alleles detected, 82 were present in both species, 160 in S. hibisci only and 11 in S. aclinata only, indicating that S. aclinata was derived from S. hibisci, following a strong bottleneck at the time of separation--possibly 40,000 years BP. Analyses and interpretation of Hardy-Weinberg equilibrium and F statistics needed to account for null alleles known to be present at eight loci in S. hibisci, and possibly present at other loci. The results emphasize the need for caution in studies where the presence of null alleles is inferred only from population data.

Remating and sperm displacement in a natural population of Drosophila buzzatii inferred from mother-offspring analysis of microsatellite loci.

Prospects for estimation of parameters of models of sperm competition from field data have improved recently with the development of methods that employ multilocus genotype data from brood-structured samples. Sperm competition in Drosophila buzzatii is of special interest because it is possible to directly observe the breeding behaviour of this species in its natural habitat of rotting cactus. Previous laboratory experiments showed that this species exhibits an unusual pattern of frequent remating and sperm partitioning. This paper reports the first attempt to estimate the frequency of female remating and sperm competition in natural populations of D. buzzatii. For the Australian population studied, the mean remating frequency was lower (alpha = 2.12-2.20) than previously estimated in laboratory experiments with the same population, whereas mean sperm displacement (beta = 0.69-0.71) fell within the limits of previous laboratory results. The evolution of the D. buzzatii mating system is discussed.

Biogeography of the yeasts of ephemeral flowers and their insects.

We studied specific yeast communities vectored by beetles, drosophilids, and bees that visit ephemeral flowers, mostly in the genus Hibiscus and in the families Convolvulaceae and Cactaceae, in the Neotropical, Nearctic, and Australian biogeographic regions. The communities consist mostly of yeasts in four clades centered around the genera Metschnikowia, Kodamaea, Wickerhamiella, and Starmerella. The largest geographic discontinuity occurs as a function of the nitidulid beetle species that dominate the non-pollinator insect visitors of the flowers. This partitions the New World, where the dominant beetle is in the genus Conotelus, from the Australian biogeographic region, dominated by species of Aethina. Distinct but sympatric insects may also carry radically different yeast communities.

Variation in body size and life history traits in Drosophila aldrichi and D. buzzatii from a latitudinal cline in eastern Australia.

Latitudinal variation in thorax and wing size traits was studied in wild-caught flies of the cactophilic Drosophila species, D. aldrichi and D. buzzatii, and their laboratory-reared progeny. The flies originated from five populations in Queensland, Australia, spanning an 800-km transect. The laboratory flies were reared at controlled densities and three temperatures, 20, 25, and 30 degrees C. We measured the same traits for the laboratory-reared flies as for the wild-caught flies, plus developmental time and viability. Latitudinal variation in wild-caught flies of both species followed a similar pattern for all linear size traits, with size generally increasing from north to south, but with flies from one intermediate locality markedly smaller. A drier environment at this locality and weather conditions immediately prior to collection, most likely explain the reduced size. Laboratory-reared D. aldrichi from this locality also were smaller than those from other localities, and had the fastest developmental time and highest viability. In laboratory-reared flies, body size traits did not show any clear trend to increase with latitude. The patterns of change with latitude were different between species, with D. aldrichi more similar in pattern to that of the natural populations. D. aldrichi had comparatively higher coefficients of variation in the laboratory-reared flies and lower viability at all temperatures. However, fluctuating asymmetry was lower in D. aldrichi in both wild-caught and laboratory-reared flies. The differences among populations of D. aldrichi for all traits were much larger than for D. buzzatii. As these differences in the laboratory-reared flies are expected to be largely genetic, they most likely reflect adaptation to specific (unknown) environmental factors that do not show linear latitudinal variation on the geographical scale studied.

Reproductive characteristics of the flower-breeding Drosophila hibisci Bock (Drosophilidae) in eastern Australia: within-population genetic determinants of ovariole number.

Genetic variation for ovariole number in the flower-breeding Drosophila hibisci was studied within populations obtained from three separate sites in the centre of the species distribution along the east coast of Australia. Heritability for ovariole number (adjusted for body size), derived from isofemale lines from each site, was estimated to be h2+/-SE = 0.564+/-0.160. The variance of ovariole number within sites (sigma2(within) = 2.039) was comparable to the variance between sites (sigma2(between) = 2.048) obtained from an earlier study of populations sampled over 14 degrees of latitude. Two isofemale lines (from within one site) that differed by an average of 4.6 ovarioles were used to generate F1, F2 and backcross generations. Analysis of mean ovariole number for these generations showed that only additive gene effects were important and that dominance, digenic epistasis and maternal effects were not significant. This within-population result contrasted with earlier results between populations that revealed additive and digenic epistasis for the same trait. High heritability within populations and the relatively large within-population variation for ovariole number suggest that substantial microhabitat variation is influencing this fitness-related trait.

Genetic architecture of a wing size measure in Drosophila hibisci from two populations in eastern Australia.

Two models of evolutionary change invoke either additive genetic contributions to phenotypic traits (Fisher) or epistatic as well as additive effects (Wright). An earlier study of the flower-breeding Drosophila hibisci from two sites in eastern Australia reported additive and epistatic genetic effects as well as environmental effects on ovariole number. The present study of the same flies examines the genetic architecture of wing width, a trait that is correlated phenotypically with ovariole number and body size. A generation means analysis of flies reared at 25 degrees C indicated additive and epistatic genetic effects, but no consistent maternal effects, whereas for flies reared at three temperatures (18 degrees C, 21.5 degrees C, and 25 degrees C) linear and nonlinear environmental effects interacted with additive genetic effects. The genetic correlation matrix for ovariole number and wing width suggested negative genetic correlations between additive effects on one trait and epistatic effects on the other. Both traits provide evidence of genetic effects consistent with assumptions of Wright's shifting balance theory of evolution.

Kodamaea kakaduensis and Candida tolerans, two new ascomycetous yeast species from Australian Hibiscus flowers.

Two new yeast species were isolated from flowers of Hibiscus species in Eastern and Northern Australia. Kodamaea kakaduensis is heterothallic, haploid, and similar to other Kodamaea species and to Candida restingae. Buds are often produced on short protuberances, and a true mycelium is formed. The new species differs from others by the assimilation of trehalose, melezitose, and xylitol, and is reproductively isolated. The cells of Candida tolerans are small and a pseudomycelium is formed. The carbon and nitrogen assimilation pattern is reminiscent of that of Zygosaccharomyces rouxii but the two are not closely related. Sequences of the D1/D2 domain of large subunit ribosomal DNA confirm the membership of K. kakaduensis in the genus Kodamaea and indicate that C. tolerans belongs to the Clavispora-Metschnikowia clade, with a moderate relatedness to Candida mogii. The type strains are: K. kakaduensis, UWO(PS)98-119.2 (h+, holotype, CBS 8611) and UWO(PS)98-117.1 (h-, isotype, CBS 8612); and C. tolerans, UWO(PS)98-115.5 (CBS 8613).

Kodamaea nitidulidarum, Candida restingae and Kodamaea anthophila, three new related yeast species from ephemeral flowers.

Three new yeast species were discovered during studies of yeasts associated with ephemeral flowers in Brazil, Australia and Hawaii. Their physiological and morphological similarity to Kodamaea (Pichia) ohmeri suggested a possible relationship to that species, which was confirmed by rDNA sequencing. Kodamaea nitidulidarum and Candida restingae were found in cactus flowers and associated nitidulid beetles in sand dune ecosystems (restinga) of South-eastern Brazil. Over 350 strains of Kodamaea anthophila were isolated from Hibiscus and morning glory flowers (Ipomoea spp.) in Australia, and from associated nitidulid beetles and Drosophila hibisci. A single isolate came from a beach morning glory in Hawaii. Expansion of the genus Kodamaea to three species modified the existing definition of the genus only slightly. The type and isotype strains are as follows: K. nitidulidarum strains UFMG96-272T (h+; CBS 8491T) and UFMG96-394I (h-; CBS 8492I); Candida restingae UFMG96-276T (CBS 8493T); K. anthophila strains UWO(PS)95-602.1T (h+; CBS 8494T), UWO(PS)91-893.2I (h-; CBS 8495I) and UWO(PS)95-725.1I (h-; CBS 8496I).

Transposable DNA elements and life history traits: II. Transposition of P DNA elements in somatic cells reduces fitness, mating activity, and locomotion of Drosophila melanogaster.

Some transposable DNA elements in higher organisms are active in somatic cells, as well as in germinal cells. What effect does the movement of DNA elements in somatic cells have on life history traits? It has previously been reported that somatically active P and mariner elements in Drosophila induce genetic damage and significantly reduce lifespan. In this study, we report that the movement of P elements in somatic cells also significantly reduces fitness, mating activity, and locomotion of Drosophila melanogaster. If other elements cause similar changes in life history traits, it is doubtful if transposable DNA elements remain active for long in somatic cells in natural populations.

Wickerhamiella australiensis, Wickerhamiella cacticola, Wickerhamiella occidentalis, Candida drosophilae and Candida lipophila, five new related yeast species from flowers and associated insects.

Five new yeast species, Wickerhamiella australiensis, Wickerhamiella cacticola, Wickerhamiella occidentalis, Candida drosophilae and Candida lipophila, are described to accommodate isolates recovered from flowers and floricolous insects of Australian Hibiscus trees, cosmopolitan morning glories (Ipomoea spp.) and Brazilian cereoid cacti. The new Wickerhamiella species are heterothallic, occur in the haploid condition and are clearly separated reproductively from one another. Although they exhibit little physiological variation, they are easily delineated from Wickerhamiella domercqiae, the only species known previously, by their resistance to cycloheximide and the production of strong extracellular lipases. C. drosophilae and C. lipophila share the latter property, but unlike the Wickerhamiella species, they fail to utilize nitrate as sole nitrogen source. PFGE indicates that these yeasts have an unusually low number of chromosomes. The large-subunit rDNA (D1/D2) sequences demonstrate a close relationship between the five species and Candida vanderwaltii and Candida azyma. Their relationship with W. domercqiae is more distant, but all share, with some other Candida species, a single monophyletic clade. The type and isotype strains are as follows: W. australiensis strains UWO(PS)95-604.3T (h+; CBS 8456T) and UWO(PS)95-631.3I (h-; CBS 8457I); W. cacticola strains UFMG96-267T (h+; CBS 8454T) and UFMG96-381I (h-; CBS 8455I); W. occidentalis strains UWO(PS)91-698.4T (h+; CBS 8452T) and UFMG96-212I (h-; CBS 8453I); C. drosophilae UWO(PS)91-716.3T (CBS 8459T); and C. lipophila UWO(PS)91-681.3T (CBS 8458T).