Gene dispersal and outbreeding in a philopatric mammal

Extensive mark-recapture data from banner-tailed kangaroo rats, Dipodomys spectabilis, have shown that both males and females are highly philopatric and suggest the possibility of close inbreeding. However, indirect analyses based on genetic structure appear to contradict direct observations, suggesting longer dispersal distances. Using microsatellite genotypes from most members of a banner-tailed kangaroo rat population during five successive breeding seasons, we ask how relatedness is influenced by dispersal and how it in turn influences mating patterns. The data confirm that, because of philopatry, neighbours are often close relatives. However, patterns of parentage also show that the average distance between mates is large relative to natal dispersal distances and larger than the average distance between nearest opposite-sexed neighbours. Females' mates were often not their nearest male neighbour and many were less related than the nearest male neighbour. We detected multiple paternity in some females' litters; both sexes produce offspring with multiple mates within and between breeding seasons. At the population level, heterozygosities were high and estimates of F were low, indicating that levels of inbreeding were low. Using individual inbreeding coefficients of all juveniles to estimate their parents' relatedness, we found that parental relatedness was significantly lower than relatedness between nearest opposite-sexed adult neighbours. Thus in philopatric populations, long breeding forays can cause genes to move further than individuals disperse, and polyandry may serve to reduce relatedness between mates.     

A comparison of pedigree‐ and DNA‐based measures for identifying inbreeding depression in the critically endangered Attwater's Prairie‐chicken

The primary goal of captive breeding programmes for endangered species is to prevent extinction, a component of which includes the preservation of genetic diversity and avoidance of inbreeding. This is typically accomplished by minimizing mean kinship in the population, thereby maintaining equal representation of the genetic founders used to initiate the captive population. If errors in the pedigree do exist, such an approach becomes less effective for minimizing inbreeding depression. In this study, both pedigree‐ and DNA‐based methods were used to assess whether inbreeding depression existed in the captive population of the critically endangered Attwater's Prairie‐chicken (Tympanuchus cupido attwateri), a subspecies of prairie grouse that has experienced a significant decline in abundance and concurrent reduction in neutral genetic diversity. When examining the captive population for signs of inbreeding, variation in pedigree‐based inbreeding coefficients (f_pedigree) was less than that obtained from DNA‐based methods (f_DNA). Mortality of chicks and adults in captivity were also positively correlated with parental relatedness (r_DNA) and f_DNA, respectively, while no correlation was observed with pedigree‐based measures when controlling for additional variables such as age, breeding facility, gender and captive/release status. Further, individual homozygosity by loci (HL) and parental r_DNA values were positively correlated with adult mortality in captivity and the occurrence of a lethal congenital defect in chicks, respectively, suggesting that inbreeding may be a contributing factor increasing the frequency of this condition among Attwater's Prairie‐chickens. This study highlights the importance of using DNA‐based methods to better inform management decisions when pedigrees are incomplete or errors may exist due to uncertainty in pairings.     

What Happens after Inbreeding Avoidance? Inbreeding by Rejected Relatives and the Inclusive Fitness Benefit of Inbreeding Avoidance

Avoiding inbreeding, and therefore avoiding inbreeding depression in offspring fitness, is widely assumed to be adaptive in systems with biparental reproduction. However, inbreeding can also confer an inclusive fitness benefit stemming from increased relatedness between parents and inbred offspring. Whether or not inbreeding or avoiding inbreeding is adaptive therefore depends on a balance between inbreeding depression and increased parent-offspring relatedness. Existing models of biparental inbreeding predict threshold values of inbreeding depression above which males and females should avoid inbreeding, and predict sexual conflict over inbreeding because these thresholds diverge. However, these models implicitly assume that if a focal individual avoids inbreeding, then both it and its rejected relative will subsequently outbreed. We show that relaxing this assumption of reciprocal outbreeding, and the assumption that focal individuals are themselves outbred, can substantially alter the predicted thresholds for inbreeding avoidance for focal males. Specifically, the magnitude of inbreeding depression below which inbreeding increases a focal male’s inclusive fitness increases with increasing depression in the offspring of a focal female and her alternative mate, and it decreases with increasing relatedness between a focal male and a focal female’s alternative mate, thereby altering the predicted zone of sexual conflict. Furthermore, a focal male’s inclusive fitness gain from avoiding inbreeding is reduced by indirect opportunity costs if his rejected relative breeds with another relative of his. By demonstrating that variation in relatedness and inbreeding can affect intra- and inter-sexual conflict over inbreeding, our models lead to novel predictions for family dynamics. Specifically, parent-offspring conflict over inbreeding might depend on the alternative mates of rejected relatives, and male-male competition over inbreeding might lead to mixed inbreeding strategies. Making testable quantitative predictions regarding inbreeding strategies occurring in nature will therefore require new models that explicitly capture variation in relatedness and inbreeding among interacting population members.     

Colony kin structure and host‐parasite relatedness in the barnacle goose

Conspecific brood parasitism (CBP), females laying eggs in the nest of other ‘host’ females of the same species, is a common alternative reproductive tactic among birds. For hosts there are likely costs of incubating and rearing foreign offspring, but costs may be low in species with precocial chicks such as waterfowl, among which CBP is common. Waterfowl show strong female natal philopatry, and spatial relatedness among females may influence the evolution of CBP. Here we investigate fine‐scale kin structure in a Baltic colony of barnacle geese, Branta leucopsis, estimating female spatial relatedness using protein fingerprints of egg albumen, and testing the performance of this estimator in known mother‐daughter pairs. Relatedness was significantly higher between neighbour females (nesting ≤ 40 metres from each other) than between females nesting farther apart, but there was no further distance trend in relatedness. This pattern may be explained by earlier observations of females nesting close to their mother or brood sisters, even when far from the birth nest. Hosts and parasites were on average not more closely related than neighbour females. In 25 of 35 sampled parasitized nests, parasitic eggs were laid after the host female finished laying, too late to develop and hatch. Timely parasites, laying eggs in the host’s laying sequence, had similar relatedness to hosts as that between neighbours. Females laying late parasitic eggs tended to be less related to the host, but not significantly so. Our results suggest that CBP in barnacle geese might represent different tactical life‐history responses.     

MHC‐disassortative mate choice and inbreeding avoidance in a solitary primate

Sexual selection theory suggests that choice for partners carrying dissimilar genes at the major histocompatibility complex (MHC) may play a role in maintaining genetic variation in animal populations by limiting inbreeding or improving the immunity of future offspring. However, it is often difficult to establish whether the observed MHC dissimilarity among mates drives mate choice or represents a by‐product of inbreeding avoidance based on MHC‐independent cues. Here, we used 454‐sequencing and a 10‐year study of wild grey mouse lemurs (Microcebus murinus), small, solitary primates from western Madagascar, to compare the relative importance on the mate choice of two MHC class II genes, DRB and DQB, that are equally variable but display contrasting patterns of selection at the molecular level, with DRB under stronger diversifying selection. We further assessed the effect of the genetic relatedness and of the spatial distance among candidate mates on the detection of MHC‐dependent mate choice. Our results reveal inbreeding avoidance, along with disassortative mate choice at DRB, but not at DQB. DRB‐disassortative mate choice remains detectable after excluding all related dyads (characterized by a relatedness coefficient r > 0), but varies slightly with the spatial distance among candidate mates. These findings suggest that the observed deviations from random mate choice at MHC are driven by functionally important MHC genes (like DRB) rather than passively resulting from inbreeding avoidance and further emphasize the need for taking into account the spatial and genetic structure of the population in correlative tests of MHC‐dependent mate choice.     

Studies on resources of genetic diversity in conservative flocks of geese using microsatellite DNA polymorphic markers

The studies conducted aimed at evaluating the genetic diversity within and between varieties of conservative flocks of geese, using the polymorphism of 14 microsatellite sequences. The experimental material included conservative flocks of geese the following indigenous breeds and varieties kept in Poland: Kielecka (Ki), Kartuska (Ka), Lubelska (Lu), Suvalska (Su), Rypinska (Ry), Sub-Carpathian (SC), Hunched Beak (HB) and Pomeranian (Po). Among the 14 microsatellite sequences a total of 97 microsatellite alleles were identified. The number of alleles at one locus ranged from 3 to 19. In the overall pool of 97 alleles, 26 (26.8%) were specific for individual breeds and varieties of geese. The values of the expected heterozygosity (He) for individual geese ranged from 0.38 (Sub-Carpathian) to 0.51 (HB). Similarly, the mean values for the observed heterozygosity (Ho) ranged from 0.45 (Po) to 0.55 (Ki and Su). The polymorphic information content reached the highest value of 0.80 at loci CKW21 (Ki) and TTUCG5 (Po and Su). The greatest genetic distance was observed between the HB and Ry (0.44) and between the HB and Po (0.39) varieties, while the smallest–between the Lu and Po as well as Lu and Ki (0.028) varieties. The phylogenetic tree, elaborated on the basis of the genetic distances, clearly confirms the specificity of the HB goose as compared to the remaining breeds and varieties.     

Methods to estimate effective population size using pedigree data: Examples in dog,sheep, cattle and horse

Background

Effective population sizes of 140 populations (including 60 dog breeds, 40 sheep breeds, 20 cattle breeds and 20 horse breeds) were computed using pedigree information and six different computation methods. Simple demographical information (number of breeding males and females), variance of progeny size, or evolution of identity by descent probabilities based on coancestry or inbreeding were used as well as identity by descent rate between two successive generations or individual identity by descent rate.

Results

Depending on breed and method, effective population sizes ranged from 15 to 133 056, computation method and interaction between computation method and species showing a significant effect on effective population size (P < 0.0001). On average, methods based on number of breeding males and females and variance of progeny size produced larger values (4425 and 356, respectively), than those based on identity by descent probabilities (average values between 93 and 203). Since breeding practices and genetic substructure within dog breeds increased inbreeding, methods taking into account the evolution of inbreeding produced lower effective population sizes than those taking into account evolution of coancestry. The correlation level between the simplest method (number of breeding males and females, requiring no genealogical information) and the most sophisticated one ranged from 0.44 to 0.60 according to species.

Conclusions

When choosing a method to compute effective population size, particular attention should be paid to the species and the specific genetic structure of the population studied.     

A genetic perspective on mating systems and sex ratios of parasitoid wasps

Parasitoid sex ratios are influenced by mating systems, whether complete inbreeding, partial inbreeding, complete inbreeding avoidance, or production of all-male broods by unmated females. Population genetic theory demonstrates that inbreeding is possible in haplodiploids because the purging of deleterious and lethal mutations through haploid males reduces inbreeding depression. However, this purging does not act quickly for deleterious mutations or female-limited traits (e.g., fecundity, host searching, sex ratio). The relationship between sex ratio, inbreeding, and inbreeding depression has not been explored in depth in parasitoids. The gregarious egg parasitoid, Trichogramma pretiosum Riley, collected from Riverside, CA (USA) produced a female-biased sex ratio of 0.24 (proportion of males). Six generations of sibling mating in the laboratory uncovered considerable inbreeding depression (∼ 20%) in fecundity and sex ratio. A population genetic study (based upon allozymes) showed the population was inbred (F _it = 0.246), which corresponds to 56.6% sib-mating. However, average relatedness among females emerging from the same host egg was only 0.646, which is less than expected (0.75) if ovipositing females mate randomly. This lower relatedness could arise from inbreeding avoidance, multiple mating by females, or superparasitism. A review of the literature in general shows relatively low inbreeding depression in haplodiploid species, but indicates that inbreeding depression can be as high as that found in Drosophila. Finally, mating systems and inbreeding depression are thought to evolve in concert (in plants), but similar dynamic models of the joint evolution of sex ratio, mating systems, and inbreeding depression have not been developed for parasitoid wasps. Received: November 13, 1998 /Accepted: January 8, 1999     

Mating structure and genetic relatedness among gynes in the primitively eusocial wasp Polistes snelleni (Hymenoptera: Vespidae)

Mating structure and genetic relatedness among gynes (potential reproductive females) of the paper wasp Polistes snelleni were investigated using DNA microsatellite markers. All colonies had one foundress inseminated by a single male, and no sign of inbreeding was detected. The mean genetic relatedness among gynes was 0.734 ± 0.028 (SE), which is not significantly different from the expected value of 0.75 for full sisters.     

Resolving the conundrum of inbreeding depression but no inbreeding avoidance: Estimating sex‐specific selection on inbreeding by song sparrows (Melospiza melodia)

Inbreeding avoidance among interacting females and males is not always observed despite inbreeding depression in offspring fitness, creating an apparent “inbreeding paradox.” This paradox could be resolved if selection against inbreeding was in fact weak, despite inbreeding depression. However, the net magnitude and direction of selection on the degree to which females and males inbreed by pairing with relatives has not been explicitly estimated. We used long‐term pedigree data to estimate phenotypic selection gradients on the degree of inbreeding that female and male song sparrows (Melospiza melodia) expressed by forming socially persistent breeding pairs with relatives. Fitness was measured as the total numbers of offspring and grand offspring contributed to the population, and as corresponding expected numbers of identical‐by‐descent allele copies, thereby accounting for variation in offspring survival, reproduction, and relatedness associated with variation in parental inbreeding. Estimated selection gradients on the degree to which individuals paired with relatives were weakly positive in females, but negative in males that formed at least one socially persistent pairing. However, males that paired had higher mean fitness than males that remained socially unpaired. These analyses suggest that net selection against inbreeding may be weak in both sexes despite strong inbreeding depression, thereby resolving the “inbreeding paradox.”     

Relatedness measured by oligonucleotide probe DNA fingerprints and an estimate of the mating system of Sea Lavender (Limonium carolinianum)

Using DNA fingerprint markers within species and populations of wild plants requires information on the relationship between fingerprint similarity and relatedness. We identified a hypervariable marker based on oliog(GATA)₄-hybridization of DpnII-cut genomic DNA from Sea Lavender (Limonium carolinianum). Banding patterns were somatically stable and highly variable among unrelated individuals. Band molecular-weight sizing errors (as a percent of band molecular weight) were estimated at 0.44%±0.003 within gels and 0.76%±0.964 between gels. Band sizing errors defined a 99% confidence bin of ±0.95% (1.90% total) of molecular weight. Band-sharing estimates were based on this bin size and on variance estimates that compensate for non-independent comparisons. Band-sharing among nine unrelated individuals () was 0.198±0.O11. Experimental pollinations designed to produce selfed, fulland half-sib progeny groups led to five selfed progeny groups and no outcrossed progeny (mean band-sharing, ovS=0.468±0.074). A linear regression between band-sharing (S) and relatedness (r) assuming 17% inbreeding was r=0.006+0.914*S (R²=0.973) and established the maximum amount of inbreeding. ovS(0.392±0.022) estimated from wild pollinated seeds from four maternal families was intermediate to unrelated individuals and experimental selfed progeny, giving evidence for mixed mating in wild plants. More extensive plant pedigrees with known levels of inbreeding will be needed to measure variation in the relationship between S and r among populations and families.     

A New Enzyme,d-Fructose Dehydrogenase

Genetic relatedness of 14 yeast strains and 2 mold strains was studied by the DNA-DNA hybridization method. The hybridization was performed between mitochondrial-DNA-free, ³²p-labeled DNA of Saccharomyces cerevisiae IAM 4009 and cold DNA of other strains. The DNA homology indices deviated considerably even among S. cerevisiae strains having similar GC contents, but, in general, yeast strains known to be able to mate with S. cerevisiae, showed high homology indices (35∽70%). Other species of Saccharomycetaceae and 6 asporogenous yeast strains exhibited values of 10∽20%. The relatedness suggested from these results was confirmed by the competition experiments and also by the hybridization with ³²P-DNA of Candida pulcherrima IFO 0561. DNA’s of Aspergillus oryzae I and Neurospora crassa IFO 6067 also exhibited low but appreciable homology indices (5∽7%). These results were discussed from the aspects of phylogenetics and also of gene conservation in microorganisms.     

Genetic structure and admixture in sheep from terminal breeds in the United States

Selection for performance in diverse production settings has resulted in variation across sheep breeds worldwide. Although sheep are an important species to the United States, the current genetic relationship among many terminal sire breeds is not well characterized. Suffolk, Hampshire, Shropshire and Oxford (terminal) and Rambouillet (dual purpose) sheep (n = 248) sampled from different flocks were genotyped using the Applied Biosystems Axiom Ovine Genotyping Array (50K), and additional Shropshire sheep (n = 26) using the Illumina Ovine SNP50 BeadChip. Relationships were investigated by calculating observed heterozygosity, inbreeding coefficients, eigenvalues, pairwise Wright’s F_ST estimates and an identity by state matrix. The mean observed heterozygosity for each breed ranged from 0.30 to 0.35 and was consistent with data reported in other US and Australian sheep. Suffolk from two different regions of the United States (Midwest and West) clustered separately in eigenvalue plots and the rectangular cladogram. Further, divergence was detected between Suffolk from different regions with Wright’s F_ST estimate. Shropshire animals showed the greatest divergence from other terminal breeds in this study. Admixture between breeds was examined using admixture , and based on cross-validation estimates, the best fit number of populations (clusters) was K = 6. The greatest admixture was observed within Hampshire, Suffolk, and Shropshire breeds. When plotting eigenvalues, US terminal breeds clustered separately in comparison with sheep from other locations of the world. Understanding the genetic relationships between terminal sire breeds in sheep will inform us about the potential applicability of markers derived in one breed to other breeds based on relatedness.     

Role of male‐biased dispersal in inbreeding avoidance in the grey‐sided vole (Myodes rufocanus)

Effects of male‐biased dispersal on inbreeding avoidance were investigated in a semi‐natural population of Myodes (formerly Clethrionomys) rufocanus using a large outdoor enclosure (3 ha). Parentage of 918 voles weaned from 215 litters and relatedness of mates were analysed using microsatellite loci, and dispersal distances were obtained from mark–recapture live‐trapping data. Natal and breeding male‐biased dispersal was observed. There remained, however, chances that incestuous mating could occur, because not all males dispersed from their natal site, and 51 matings occurred between relatives (relatedness r > 0). The number of weaned juveniles from inbred litters was significantly smaller than that from non‐inbred litters. Fourteen incestuous matings occurred between close relatives (r ≥ 0.25), most of which were those between non‐littermate maternal half siblings (four cases) and those between paternal half siblings (seven cases). When comparing the observed frequencies to the expected ones generated by combining every oestrous female with a male randomly chosen from her surroundings, the observed values for inbreeding of r ≥ 0.25 were significantly smaller than the expectations, while no difference was observed for inbreeding of 0 < r < 0.25. These results suggest that male‐biased dispersal is partly effective to avoid incestuous mating, but it does not provide complete separation of male and female close relatives. Additional mechanisms such as kin discrimination based on familiarity may work in inbreeding avoidance of the vole.     

A spatial genetic structure and effects of relatedness on mate choice in a wild bird population

Inbreeding depression, as commonly found in natural populations, should favour the evolution of inbreeding avoidance mechanisms. If natal dispersal, the first and probably most effective mechanism, does not lead to a complete separation of males and females from a common origin, a small-scale genetic population structure may result and other mechanisms to avoid inbreeding may exist. We studied the genetic population structure and individual mating patterns in blue tits (Parus caeruleus). The population showed a local genetic structure in two out of four years: genetic relatedness between individuals (estimated from microsatellite markers) decreased with distance. This pattern was mainly caused by immigrants to the study area; these, if paired with fellow immigrants, were more related than expected by chance. Since blue tits did not avoid inbreeding with their social partner, we examined if individuals preferred less related partners at later stages of the mate choice process. We found no evidence that females or males avoided inbreeding through extra-pair copulations or through mate desertion and postbreeding dispersal. Although the small-scale genetic population structure suggests that blue tits could use a simple rule of thumb to select less related mates, females did not generally prefer more distantly breeding extra-pair partners. However, the proportion of young fathered by an extra-pair male in mixed paternity broods depended on the genetic relatedness with the female. This suggests that there is a fertilization bias towards less related copulation partners and that blue tits are able to reduce the costs of inbreeding through a postcopulatory process.     

Relationships between nuclear DNA content and seed and leaf size in soybean

 A correlation between genome size and agronomically important traits has been observed in many plant species. The goal of the present research was to determine the relationship between genome size, seed size, and leaf width and length in soybean [Glycine max (L.) Merr.] Twelve soybean strains, representing three distinct seed size groups, were analyzed. Flow cytometry was used to estimate their 2C nuclear DNA contents. Data on seed size and leaf size of the 12 strains were obtained from 1994 and 1995 field experiments. Variation of 2C nuclear DNA among the 12 soybean strains was 4.6%, ranging from 2.37 pg for a small-seed strain to 2.48 pg for a large-seed strain. Strain seed size was positively associated with leaf width (r=0.92) and leaf length (r=0.93). Genome size was highly correlated with seed size (r=0.97), leaf width (r=0.90) , and leaf length (r=0.93). The results of our study indicate that there is a significant correlation between genome size and leaf and seed size in soybean. It is possible that selection for greater seed size either leads to, or results from, greater genome size. If so, this relationship might be worth exploring at a more fundamental level. Received: 5 April 1997 / Accepted: 9 January 1998     

Genetic Analysis and Estimation of Genetic Diversity in East-European Breeds of Windhounds (Canis familiaris L.) Based on the Data of Genomic Studies Using RAPD Markers

The method of polymerase chain reaction with a set of arbitrary primers (RAPD–PCR) was used to describe genetic variation and to estimate genetic diversity in East-European windhounds, Russian Borzoi and Russian Chortai. For comparison, windhounds of two West-European breeds (Whippet and Greyhound) and single dogs of other breed types (shepherd, terriers, mastiffs, and bird dogs) were examined. For all dog groups, their closest related species, the wolf Canis lupus, was used as an outgroup. Variation of RAPD markers was studied at several hierarchic levels: intra- and interfamily (for individual families of Russian Psovyi and Chortai windhounds), intra- and interbreed (for ten dog breeds), and interspecific (C. familiaris–C. lupus). In total, 57 dogs and 4 wolves were studied. Using RAPD–PCR with three primers, 93 DNA fragments with a length of 150–1500 bp were detected in several Windhound families with known filiation. These fragments were found to be inherited as dominant markers and to be applicable for estimation of genetic differences between parents and their offspring and for comparison of individuals and families with different level of inbreeding. A high level of intra- and interbreed diversity was found in Russian Borzoi and Russian Chortai. In these dogs, genetic similarity indices varied in a range of 72.2 to 93.4% (parents–offspring) and 68.0 to 94.5 (sibs). Based on the patterns of RAPD markers obtained using six primers, a dendrogram of genetic similarity between the wolf and different dog breeds was constructed, and indices of intragroup diversity were calculated. All studied breeds grouped into two clusters, windhounds (Borzoi-like dogs) and other dog breeds. Russian windhounds represent a very heterogeneous group, in which the Russian Borzoi is closer to Greyhound than the Russian Chortai. All studied wolves constituted a separate cluster. Significant differences were found between the wolf and dogs by the number of RAPD markers (92.8 and 86.1, respectively) and by the indices of genetic diversity (54.3 and 64.8%, respectively). The reason for the high intraspecific variation of dogs (including Russian windhounds) and the prospects of using the studied group of markers for genetic analysis and differentiation in C. familiaris are discussed.     

Natal dispersal and parental escorting predict relatedness between mates in a passerine bird

Although relatedness between mates is of considerable evolutionary and ecological significance, the way in which the level of relatedness is determined by different behavioural processes remains largely unknown. We investigated the role of behaviour in predicting mate relatedness in great tits using genotypic markers and detailed observations. We studied how mate relatedness is influenced by natal dispersal, inbreeding/outbreeding avoidance after natal dispersal and a behaviour not previously considered that influences membership to social aggregations, namely family escorting behaviour by parents. Among locally born individuals, the level of mate relatedness decreased with natal dispersal distance for females, but not for males. In contrast, mate relatedness was negatively related to the extent of family movements for males, but not for females. However, family movements did not predict dispersal distance for either sex. Local recruits were more related to their mates than immigrants, but this was only significant for females. No evidence was found for inbreeding/outbreeding avoidance after dispersal. Our results suggest that, in highly mobile species, mating options are spatially and/or socially limited, and that parents influence mating options of their offspring before dispersal.     

The use of <Emphasis Type="Italic">gyrB</Emphasis> sequence analysis in the phylogeny of the genus <Emphasis Type="Italic">Amycolatopsis</Emphasis>

Partial gyrB sequences (>1 kb) were obtained from 34 type strains of the genus Amycolatopsis. Phylogenetic trees were constructed to determine the effectiveness of using this gene to predict taxonomic relationships within the genus. The use of gyrB sequence analysis as an alternative to DNA–DNA hybridization was also assessed for distinguishing closely related species. The gyrB based phylogeny mostly confirmed the conventional 16S rRNA gene-based phylogeny and thus provides additional support for certain of these 16S rRNA gene-based phylogenetic groupings. Although pairwise gyrB sequence similarity cannot be used to predict the DNA relatedness between type strains, the gyrB genetic distance can be used as a means to assess quickly whether an isolate is likely to represent a new species in the genus Amycolatopsis. In particular a genetic distance of >0.02 between two Amycolatopsis strains (based on a 315 bp variable region of the gyrB gene) is proposed to provide a good indication that they belong to different species (and that polyphasic taxonomic characterization of the unknown strain is worth undertaking). Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. The GenBank accession numbers for the gyrB gene sequences obtained in this study are shown in Table 1.