Arbuscular mycorrhizal fungi: genetics of multigenomic, clonal networks and its ecological consequences

Arbuscular mycorrhizal fungi are thought to have remained asexual for 400 million years, although recent studies have suggested that considerable genetic and phenotypic variation could potentially exist in populations. A brief discussion of these multigenomic organisms is presented.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 79 , 59–60.     

Mitochondrial and nuclear DNA analyses reveal population differentiation in Brazilian Creole sheep

Using ND5 sequences from mtDNA and 10 nuclear markers, we investigated the genetic differentiation of two South American Creole sheep phenotypes that historically have been bred in different biomes in southern Brazil. In total, 18 unique mtDNA haplotypes were detected, none of which was shared between the two phenotypes. Bayesian analysis also indicated two different groups (k = 2). Thus, these varieties are supported as being genotypically distinct. This situation could have resulted either from geographical isolation, associated with differences in the cultural habits of sheep farmers and in the way that flocks were managed, or more likely, from the introduction of different stocks four centuries ago.     

羊肚菌的多样性、演化历史及栽培研究进展

羊肚菌属Morchella真菌是一类珍稀食用和药用真菌,具有重要的经济和科研价值。从羊肚菌属的分类研究、物种多样性、物种分布与生态多样性、演化历史、人工栽培等方面,对新近的研究成果进行了综述,总结了世界羊肚菌研究中取得的主要成绩,指出了仍然存在的主要问题及解决这些问题的相应思路和对策。     

Testing hypotheses on the dispersal and evolutionary history of freshwater mussels (Mollusca: Bivalvia: Unionidae)

The relationship between dispersal and differentiation of the European freshwater mussel Unio pictorum (Linnaeus, 1758) was studied with molecular genetic methods. Forty‐two populations from France, Italy and central Europe were analysed. Genetic relationships were assessed from the geographical distribution of allele frequencies at 17 enzyme loci. Neighbouring groups of populations show small to moderate mean genetic distances (0.020 < D_mean < 0.263). With a few exceptions the genetic affinities of the populations are the closest within the same drainage basin. In central Europe and Northern Italy genetic differences between drainage systems are relatively large. Populations from north‐eastern Italy are genetically similar to Danubian populations. Mussels from the islands of Corsica and Sardinia are more closely related to populations from the Italian peninsula than to French populations from the Rhône drainage system. Genetic relationships within U. pictorum from central Europe reflect palaeogeographical relationships between river systems during the Pliocene and Pleistocene. Literature data on two North American unionid species and one European fish species show the same relationship between genetic diversity and the history of drainage systems, although the correlations are less strong. In France and Italy this correspondence is much less evident. Population dynamic processes and human activities leading to populational bottlenecks might have obscured it.     

Genetic differentiation and connectivity of morphological types of the broadcast‐spawning coral Galaxea fascicularis in the Nansei Islands,Japan

Population connectivity resulting from larval dispersal is essential for the maintenance or recovery of populations in marine ecosystems, including coral reefs. Studies of species diversity and genetic connectivity within species are essential for the conservation of corals and coral reef ecosystems. We analyzed mitochondrial DNA sequence types and microsatellite genotypes of the broadcast‐spawning coral, Galaxea fascicularis, from four regions in the subtropical Nansei Islands in the northwestern Pacific Ocean. Two types (soft and hard types) of nematocyst morphology are known in G. fascicularis and are significantly correlated with the length of a mitochondrial DNA noncoding sequence (soft type: mt‐L; hard type: mt‐S type). Using microsatellites, significant genetic differentiation was detected between the mitochondrial DNA sequence types in all regions. We also found a third genetic cluster (mt‐L+), and this unexpected type may be a cryptic species of Galaxea. High clonal diversity was detected in both mt‐L and mt‐S types. Significant genetic differentiation, which was found among regions within a given type (F_ST = 0.009–0.024, all Ps ≤ 0.005 in mt‐L; 0.009–0.032, all Ps ≤ 0.01 in mt‐S), may result from the shorter larval development than in other broadcast‐spawning corals, such as the genus Acropora. Nevertheless, intraspecific genetic diversity and connectivity have been maintained, and with both sexual and asexual reproduction, this species appears to have a potential for the recovery of populations after disturbance.     

Short-tandem repeat analysis in seven Chinese regional populations

In the present study, we investigated the application of 13 short tandem repeat (STR) loci (D13S317, D7S820, TH01, D16S539, CSFIPO, VWA, D8S1179, TPOX, FGA, D3S1358, D21S11, D18S51 and D5S818) routinely used in forensic analysis, for delineating population relationships among seven human populations representing the two major geographic groups, namely the southern and northern Chinese. The resulting single topology revealed pronounced geographic and population partitioning, consistent with the differences in geographic location, languages and eating habits. These findings suggest that forensic STR loci might be particularly powerful tools in providing the necessary fine resolution for reconstructing recent human evolutionary history.     

VNTR loci reveal differentiation between and structure within populations of the eastern barred bandicoot Perameles gunnii

The Eastern Barred Bandicoot Perameles gunnii has declined in abundance within mainland south-eastern Australia, to a relict wild population of less than 100 individuals in Hamilton, Victoria. It is more common, but is also declining in Tasmania. Genomic DN A variability was compared within and between surviving populations of P. gunnii using variable number of tandem repeat (VNTR) markers in one of two ways. First, average percentage differences (APDs) were determined between profiles for two VNTR probe—endonuclease combinations. Secondly, because one of these combinations revealed two multiallelic VNTR loci, genotypes were assigned and analysed for homogeneity of allele frequencies among subpopulations, for deviation of heterozygosity from Hardy-Weinberg equilibrium within populations and for genetic structuring among individuals from different subpopulations. The results of both the APD and defined locus approaches showed consistent trends within and between populations. Genetic variability was higher among mainland P. gunnii than in Tasmanian populations (higher APDs, number of alleles, and heterozygosity at one locus), despite the known decline and subdivision of the Hamilton population. Eleven per cent of the variability detected in Hamilton was attributed to genetic differentiation between east and west subdivisions of the population. Departure from random mating indicating local inbreeding within collecting localities was evident for one locus in both north and south Tasmania, particularly at one locality. AH alleles at both loci were unique to either Hamilton or Tasmanian P. gunnii. The initial captive colony contains high heterozygosity for these loci. It is concluded that VNTR markers can be of benefit for use in studies of population differentiation and for conservation management.     

Michael Ruse and His Fifteen Years of Booknotes – For Better or for Worse

In this paper I trace Michael Ruse's Booknotes from the first volumeof Biology and Philosophy in 1986 to the present. I deal withboth the style and the content of these booknotes. Ruse paid specialattention to authors outside of the traditional English axis as wellas to feminist writers. He complained that too much attention wasbeing paid to certain topics (e.g., evolutionary ethics, evolutionaryepistemology, the species problem and reduction) while other, moreimportant topics were all but ignored (e.g., natural selection,population genetics, levels of selection and extraterrestrial life).He also dealt with the Darwin Industry. Creationism, his love-haterelationships with several authors and his undiluted love of CharlesDickens.     

Pervasive selection or is it…? why are FST outliers sometimes so frequent?

It is now common for population geneticists to estimate F_ST for a large number of loci across the genome, before testing for selected loci as being outliers to the F_ST distribution. One surprising result of such F_ST scans is the often high proportion (>1% and sometimes >10%) of outliers detected, and this is often interpreted as evidence for pervasive local adaptation. In this issue of Molecular Ecolog, Fourcade et al. ( 2013 ) observe that a particularly high rate of F_ST outliers has often been found in river organisms, such as fishes or damselflies, despite there being no obvious reason why selection should affect a larger proportion of the genomes of these organisms. Using computer simulations, Fourcade et al. ( 2013 ) show that the strong correlation in co‐ancestry produced in long one‐dimensional landscapes (such as rivers, valleys, peninsulas, oceanic ridges or coastlines) greatly increases the neutral variance in F_ST, especially when the landscape is further reticulated into fractal networks. As a consequence, outlier tests have a high rate of false positives, unless this correlation can be taken into account. Fourcade et al.'s study highlights an extreme case of the general problem, first noticed by Robertson ( 1975a , b ) and Nei & Maruyama ( 1975 ), that correlated co‐ancestry inflates the neutral variance in F_ST when compared to its expectation under an island model of population structure. Similar warnings about the validity of outlier tests have appeared regularly since then but have not been widely cited in the recent genomics literature. We further emphasize that F_ST outliers can arise in many different ways and that outlier tests are not designed for situations where the genetic architecture of local adaptation involves many loci.