Disrupted phylogeographical microsatellite and chloroplast DNA patterns indicate a vicariance rather than long‐distance dispersal origin for the disjunct distribution of the Chilean endemic Dioscorea biloba (Dioscoreaceae) around the Atacama Desert

Aim The Chilean endemic Dioscorea biloba (Dioscoreaceae) is a dioecious geophyte that shows a remarkable 600 km north–south disjunction in the peripheral arid area of the Atacama Desert. Its restricted present‐day distribution and probable Neogene origin indicate that its populations have a history linked to that of the Atacama Desert, making this an ideal model species with which to investigate the biogeography of the region. Location Chile, Atacama Desert and peripheral arid area. Methods Two hundred and seventy‐five individuals from nine populations were genotyped for seven nuclear microsatellite loci, and plastid trnL–F and trnT–L sequences were obtained for a representative subset of these. Analyses included the estimation of genetic diversity and population structure through clustering, Bayesian and analysis of molecular variance analyses, and statistical parsimony networks of chloroplast haplotypes. Isolation by distance was tested against alternative dispersal hypotheses. Results Microsatellite markers revealed moderate to high levels of genetic diversity within populations, with those from the southern Limarí Valley showing the highest values and northern populations showing less exclusive alleles. Bayesian analysis of microsatellite data identified three genetic groups that corresponded to geographical ranges. Chloroplast phylogeography revealed no haplotypes shared between northern and southern ranges, and little haplotype sharing between the two neighbouring southern valleys. Dispersal models suggested the presence of extinct hypothetical populations between the southern and northern ranges. Main conclusions Our results are consistent with prolonged isolation of the northern and southern groups, mediated by the life‐history traits of the species. Significant isolation was revealed at both large and moderate distances as gene flow was not evident even between neighbouring valleys. Bayesian analyses of microsatellite and chloroplast haplotype diversity identified the southern area of Limarí as the probable area of origin of the species. Our data do not support recent dispersal of D. biloba from the southern range into Antofagasta, but indicate the fragmentation of an earlier wider range, concomitant with the Pliocene–Pleistocene climatic oscillations, with subsequent extinctions of the Atacama Desert populations and the divergence of the peripheral ones as a consequence of genetic drift.     

Optimizing purebred selection for crossbred performance using QTL with different degrees of dominance

A method was developed to optimize simultaneous selection for a quantitative trait with a known QTL within a male and a female line to maximize crossbred performance from a two-way cross. Strategies to maximize cumulative discounted response in crossbred performance over ten generations were derived by optimizing weights in an index of a QTL and phenotype. Strategies were compared to selection on purebred phenotype. Extra responses were limited for QTL with additive and partial dominance effects, but substantial for QTL with over-dominance, for which optimal QTL selection resulted in differential selection in male and female lines to increase the frequency of heterozygotes and polygenic responses. For over-dominant QTL, maximization of crossbred performance one generation at a time resulted in similar responses as optimization across all generations and simultaneous optimal selection in a male and female line resulted in greater response than optimal selection within a single line without crossbreeding. Results show that strategic use of information on over-dominant QTL can enhance crossbred performance without crossbred testing.     

Isolation of microsatellite loci in the Capricorn silvereye,Zosterops lateralis chlorocephalus (Aves: Zosteropidae)

The Capricorn silvereye (Zosterops lateralis chlorocephalus) is ideally suited to investigating the genetic basis of body size evolution. We have isolated and characterized a set of microsatellite markers for this species. Seven out of 11 loci were polymorphic. The number of alleles detected ranged from two to five and observed heterozygosities between 0.12 and 0.67. One locus, ZL49, was found to be sex‐linked. This moderate level of diversity is consistent with that expected in an isolated, island population.     

Isolation of polymorphic tetranucleotide microsatellite markers for the ornate nursery frog Cophixalus ornatus

We have isolated 18 polymorphic microsatellite loci for Cophixalus ornatus from genomic libraries enriched for (AAAG)_n, (AACC)_n and (AAGG)_n repetitive elements. The number of alleles ranges from five to 22 per locus with the observed heterozygosity ranging from 0.10 to 0.92. These markers will be useful for the analysis of population structure in C. ornatus and testing alternative models of speciation.     

PCR primers for polymorphic microsatellite loci in the desert locust,Schistocerca gregaria (Orthoptera: Acrididae)

Nine pairs of polymerase chain reaction (PCR) primers that amplify polymorphic microsatellite loci in the desert locust, Schistocerca gregaria (Forskal), were developed using a magnetic bead‐based enrichment protocol. A sample of 48 locusts collected during the 1993 and 1995 upsurge periods in Eritrea, East Africa, were genotyped. The number of alleles per locus ranged from six to 20; the average was 12.67. Allelic distributions were significantly different between samples from different localities.     

Isolation and characterization of polymorphic microsatellite loci in the gudgeon,Gobio gobio (Cyprinidae)

A total of seven polymorphic microsatellite loci from Gobio gobio were isolated and characterized. A preliminary population survey of 82 specimens from four populations, located in a downstream pollution gradient of cadmium and zinc, demonstrated the usefulness of these primers both in population genetic studies in general, as well as in evaluating the effects of anthropogenic pollution on genetic structure. Overall locus polymorphism ranged from two to 13 alleles. Observed heterozygosity per locus ranged from 0.39 to 0.73.     

Highly polymorphic microsatellite loci in the bank vole (Clethrionomys glareolus)

We describe seven polymorphic, dinucleotide microsatellite loci isolated from bank voles (Clethrionomys glareolus, Rodentia: Muridae) collected from the Wirral Peninsula, United Kingdom. Microsatellites were isolated as part of a long‐term study on the wider effects of host–pathogen interactions of an endemic viral disease. These microsatellites showed between five and 13 alleles per locus in these populations. Observed and expected heterozygosities varied between 0.275 to 0.777 and 0.487 to 0.794, respectively. These markers will allow us to investigate the structure of this bank vole population.     

“A cleaner break”: Genetic divergence between geographic groups and sympatric phenotypes revealed in ballan wrasse (Labrus bergylta)

Capture and long‐distance translocation of cleaner fish to control lice infestations on marine salmonid farms has the potential to influence wild populations via overexploitation in source regions, and introgression in recipient regions. Knowledge of population genetic structure is therefore required. We studied the genetic structure of ballan wrasse, a phenotypically diverse and extensively used cleaner fish, from 18 locations in Norway and Sweden, and from Galicia, Spain, using 82 SNP markers. We detected two very distinct genetic groups in Scandinavia, northwestern and southeastern. These groups were split by a stretch of sandy beaches in southwest Norway, representing a habitat discontinuity for this rocky shore associated benthic egg‐laying species. Wrasse from Galicia were highly differentiated from all Scandinavian locations, but more similar to northwestern than southeastern locations. Distinct genetic differences were observed between sympatric spotty and plain phenotypes in Galicia, but not in Scandinavia. The mechanisms underlying the geographic patterns between phenotypes are discussed, but not identified. We conclude that extensive aquaculture‐mediated translocation of ballan wrasse from Sweden and southern Norway to western and middle Norway has the potential to mix genetically distinct populations. These results question the sustainability of the current cleaner fish practice.     

Molecular phylogeny of Heritiera Ait on (Sterculiaceae), a tree mangrove: variations in RAPD markers and nuclear DNA content

Random amplified polymorphic DNA (RAPD) markers are used to estimate interspecific variation among mangrove and non-mangrove Heritiera fomes, H. littoralis and H. macrophylla. All the species have 2n = 38 chromosomes, with minute structural changes distinguishing the karyotype of each species. Significant variation of 4C DNA content occurs at the interspecific level. Interspecific polymorphism ranged from 14.09% between H. fomes and H. littoralis to 52.73% between H. fomes and H. macrophylla. H. macrophylla showed wide polymorphism in the RAPD marker with H. littoralis (51.23%) and H. fomes (52.73%). Two distinct RAPD products obtained from OPA-10 (1000 bp) and OPD-15 (900 bp) found characteristic molecular markers in H. macrophylla , a species from a non-mangrove habitat. H. macrophylla was more distantly related to H. fomes [genetic distance (1-F) = 0.305] than to H. littoralis [genetic distance (1-F) = 0.273]. H. littoralis was of a closer affinity to H. fomes [genetic distance (1-F) = 0.218] than to H. macrophylla.