bluuebunny/crossref_metadata_2025 huggingface dataset:
To tree or not to tree
Authors: SMOUSE PETER E.
Published: March 2003

The practice of tracking geographical divergence along a phylogenetic tree has added an evolutionary perspective to biogeographic analysis within single species. In spite of the popularity of phylogeography, there is an emerging problem. Recurrent mutation and recombination both create homoplasy, multiple evolutionary occurrences of the same character that are identical in state but not identical by descent. Homoplasic molecular data are phylogenetically ambiguous. Converting homoplasic molecular data into a tree represents an extrapolation, and there can be myriad candidate trees among which to choose. Derivative biogeographic analyses of ‘the tree’ are analyses of that extrapolation, and the results depend on the tree chosen. I explore the informational aspects of converting a multicharacter data set into a phylogenetic tree, and then explore what happens when that tree is used for population analysis. Three conclusions follow: (i) some trees are better than others; good trees are true to the data, whereas bad trees are not; (ii) for biogeographic analysis, we should use only good trees, which yield the same biogeographic inference as the phenetic data, but little more; and (iii) the reliable biogeographic inference is inherent in the phenetic data, not the trees.
Molecular population genetics of the red kangaroo (Macropus rufus): mtDNA variation
Authors: CLEGG S. M. , HALE P. , MORITZ C.
Published: March 2003

The genetic population structure of a large, wide‐ranging marsupial, the red kangaroo (Macropus rufus) was assessed using sequence and haplotype frequency data of mitochondrial DNA (mtDNA) from locations across the species range in Australia. Results from sequence data revealed extensive haplotype diversity within the red kangaroo (32/34 sequences were unique). Sequence diversity was distributed within rather than between geographical regions across the species range. Genetic connectivity across the range of the species has therefore been maintained over the long term. On a smaller within‐region scale, significant genetic structuring was evident from heterogeneity of haplotype frequencies amongst sampling sites. The geographical scale of panmictic populations differed across the continent with more restricted genetic populations occurring in areas with greater topographic and habitat complexity. We propose that these differences in area of genetic populations are the result of population responses to limiting ecological factors during drought.
DNA fingerprinting reveals clonal nature of Vetiveria zizanioides (L.) Nash, Gramineae and sources of potential new germplasm
Authors: ADAMS R. P. , TURUSPEKOV M. ZHONG† Y. , DAFFORN M. R. , VELDKAMP J. F.
Published: March 2003

Random amplified polymorphic DNAs (RAPDs) were used to examine accessions of vetiver (Vetiveria zizanioides (L.) Nash, Gramineae) from around the world. It appears that only one genotype, ‘Sunshine’, accounts for almost all the germplasm utilized. Screening of numerous accessions of vetiver revealed only a few nonfertile germlines. Analysis of V. zizanioides and other Vetiveria species, Chrysopogon fulvus (Spreng.) Chiov., C. gryllus (L.) Trin., Sorghum bicolour (L.) Moench., and S. halepense (L.) Pers., revealed that Vetiveria and Chrysopogon are not separable by their RAPDs. This lends support to merging the genus Vetiveria with Chrysopogon. The lack of genetic diversity in this important cultivated plant is a critical factor and additional, suitable germplasm must be collected and introduced into erosion control projects around the world.
Conservation genetics of insular Podarcis lizards using partial cytochrome b sequences
Authors: CASTILLA A. M. , FERNÁNDEZ‐PEDROSA V. , BACKELJAU T. , GONZÁLEZ A. , LATORRE A. , MOYA A.
Published: March 2003

Sequence data derived from a 306 bp fragment of mitochondrial cytochrome b and molecular variance estimates were used to investigate the genetic population structure of the endangered and endemic lizard Podarcis atrata of the Columbretes archipelago (Mediterranean, Spain). Our results show a very high and significant among‐population genetic differentiation. FST values and phylogenetic analyses confirm the evolutionary distinctiveness of P. atrata populations, suggesting that the populations of these islands deserve special protection measures. The populations of the two islands Columbrete Grande and Mancolibre are less differentiated than those of Foradada and Lobo, and seem to have retained mainland haplotypes. This situation needs further attention as the origin of the mainland haplotypes is still unclear. If they are a result of recent introductions from mainland specimens, then they may represent a threat to the endemic lizards of the Columbretes islands.
Population structure and gene flow of the Atlantic walrus (Odobenus rosmarus rosmarus) in the eastern Atlantic Arctic based on mitochondrial DNA and microsatellite variation
Authors: ANDERSEN L. W. , BORN E. W. , GJERTZ I. , WIIG Ø. , HOLM L.‐E. , BENDIXEN C.
Published: March 2003

The population structure of the Atlantic walrus,Odobenus rosmarus rosmarus, was studied using 11 polymorphic microsatellites and restriction fragment length polymorphism detected in the NADH‐dehydrogenase ND1, ND2 and ND3/4 segments in mtDNA. A total of 105 walrus samples were analysed from northwest (NW) Greenland, east (E) Greenland, Svalbard and Franz Joseph Land. Two of the 10 haplotypes detected in the four samples were diagnostic for the NW Greenland sample, which implied that the group of walruses in this area is evolutionary distinct from walruses in the other three areas. One individual sampled in E Greenland exhibited a Pacific haplotype, which proved a connection between the Pacific walrus and walruses in eastern Greenland. The Franz Joseph Land, Svalbard and E Greenland samples shared the most common haplotype, indicating very little differentiation at the mtDNA level. Gene flow (Nm) estimates among the four areas indicated a very restricted exchange of female genes between NW Greenland and the more eastern Atlantic Arctic samples, and a closer relationship between the three samples composing the eastern Atlantic Arctic. The genetic variation at 11 polymorphic microsatellite loci grouped individuals into three populations, NW Greenland, E Greenland and a common Franz Joseph Land–Svalbard population, which were connected by moderate gene flow.
Microsatellite paternity analysis on captive Lake Malawi cichlids supports reproductive isolation by direct mate choice
Authors: KNIGHT M. E. , TURNER G. F. , RICO C. , VAN OPPEN M. J. H. , HEWITT G. M.
Published: March 2003

Three sympatrically occurring members of a cichlid fish species complex from Lake Malawi have previously been reported to show assortative mating in the field. Offspring from three experimental tanks each housing both sexes of all three members of this complex were screened at one to four microsatellite loci to determine paternity. Reproductive isolation was found to persist without exception under laboratory conditions, providing strong evidence for behavioural barriers to mating. Direct mate choice is suggested as the process preventing interbreeding. The results are interpreted with reference to the rapid and explosive evolution of the cichlid group.
Use of PCR for detection of subpatent infections of lizard malaria: implications for epizootiology
Authors: PERKINS SUSAN L. , OSGOOD SARAH M. , SCHALL JOS. J.
Published: March 2003

The estimated prevalence of a malaria parasite, Plasmodium mexicanum, of western fence lizards, Sceloporus occidentalis, was compared using two techniques: microscopic examination of blood smears, and nested PCR amplification of the 18S small subunit rRNA gene. Two sites in northern California, USA were investigated, one with known long‐term high prevalence of the parasite (30% by blood smear scanning), and one with low prevalence (6%). The nested PCR readily detected very low‐level infections (< 1 parasite per 10 000 erythrocytes); such infections are often subpatent by normal microscopic examination. False negatives (scored as not infected after scanning the blood smear, but found infected via PCR) were rare at both sites (4% at the high‐prevalence site, 6% at the low‐prevalence site). However, a greater proportion of infections was detected only by PCR at the low‐prevalence site (50% vs. 9%). If 50% of the infections sustain very weak parasitaemia where lizards are rarely infected, this would accord with hypotheses that predict that parasites should reduce infection growth when transmission is uncommon. The study demonstrates that PCR is a powerful tool to detect very low‐level malarial infections in vertebrate hosts, including those with nucleated erythrocytes.
Holarctic phylogeography of an asexual species complex – II. Allozymic variation and clonal structure in ArcticDaphnia
Authors: Weider Lawrence J. , Hobæk Anders , Hebert Paul D. N. , Crease Teresa J.
Published: March 2003

Previous mitochondrial (mt)DNA sequencing and restriction fragment length polymorphism (RFLP) studies have shown that the HolarcticDaphnia pulexcomplex is divisible into two major groups (pulicariaandtenebrosa) that exhibit distinct phylogeographic patterns. Here we examine allozymic variation at six polymorphic enzyme loci to ascertain clonal structure and clonal distribution patterns within each group. Specimens were collected from a total of 850 populations encompassing the Arctic. A significant negative relationship (Mantel test) between similarity of regional clonal arrays and geographical distance was observed. A small fraction of clones in each group was widespread (in the order of 1000s of kilometres). However, most clones were restricted to single regions, and were often found only in a single population. These data indicate that the population genetic structure is highly fragmented in this complex, but the potential for long‐distance passive dispersal exists. Further, ‘hot spots’ of high clonal richness and diversity were found in each group, which is concordant with earlier work. In addition, ≈ 20% ofpulicariagroup clones possess nuclear genes fromtenebrosa, while approximately 10% oftenebrosagroup clones harbourpulicarianuclear genes. These data indicate nuclear introgression between the two groups, which was found to be prominent in a broad zone of secondary contact encompassing parts of northwestern Russia, northern Fennoscandia, Svalbard, and extending into the high eastern Canadian Arctic.
Mitochondrial DNA population structure of roan and sable antelope: implications for the translocation and conservation of the species
Authors: MATTHEE CONRAD A. , ROBINSON TERENCE J.
Published: March 2003

Mitochondrial DNA (mtDNA) control region sequences were analysed to determine the geographical genetic structure ofHippotragus niger(sable antelope) andH. equinus(roan antelope). Analyses byAMOVA, minimum evolution networks, parsimony, neighbour joining and maximum likelihood show that the roan antelope populations are geographically partitioned and that their phylogeography corresponds well with subspecific boundaries. In sharp contrast, however, our sequence data group all the sable antelope into two well‐delineated maternal clades. One comprising specimens from the strictly east AfricanH.n. roosevelti, and a second geographically diverse group which includesH.n. niger(South Africa, Zimbabwe),H.n. variani(Angola), andH.n. kirkii(Zambia, Malawi). The differences in the genetic population structure suggest that distinct extrinsic and intrinsic factors have shaped the phylogeography of these two closely related antelope species. In the absence of obvious extrinsic barriers to gene flow, we suggest that behavioural differences may be responsible, at least in part, for the contrasting spatial patterns detected among geographical localities. Although our data reflect only the maternal phylogeny of these important game species, they nonetheless suggest that different management strategies should be applied. We recommend that roan antelope be translocated only within the currently defined subspecies boundaries, while in the case of sable antelope, conservation measures should focus on preserving the genetic integrity of the east African and southern African sable populations. Implicit in this is that translocations of animals between populations comprising these two distinct maternal genetic clades should be actively discouraged.
Low genetic variation in muskoxen (Ovibos moschatus) from western Greenland using microsatellites
Authors: Holm L.‐E. , Forchhammer M. C. , Boomsma J. J.
Published: March 2003

Muskoxen are large herbivores living in Arctic environments. Lack of genetic variation in allozymes has made it difficult to study the social and genetic structure of this species. In this study, we have tried to find polymorphic microsatellite loci using both cattle‐derived microsatellite primers and primers developed from a genomic plasmid library of muskoxen. Only limited variation was found for both sets of microsatellite loci. We conclude that this consistent low genetic variation is probably due to demographic features of the muskoxen populations rather than to methodological constraints caused by the transfer of microsatellites between species.
A population genetic comparison of large‐ and small‐bodied sage grouse in Colorado using microsatellite and mitochondrial DNA markers
Authors: Oyler‐mccance S. J. , Kahn N. W. , Burnham K. P. , Braun C. E. , Quinn T. W.
Published: March 2003

Sage grouse (Centrocercus urophasianus) from southwestern Colorado and southeastern Utah (United States) are 33% smaller than all other sage grouse and have obvious plumage and behavioural differences. Because of these differences, they have been tentatively recog—nized as a separate ‘small‐bodied’ species. We collected genetic evidence to further test this proposal, using mitochondrial sequence data and microsatellite markers to determine whether there was gene flow between the two proposed species. Significant differences in the distribution of alleles between the large‐ and small‐bodied birds were found in both data sets. Analysis of molecular variance (amova) revealed that 65% of the variation in mitochondrial DNA (mtDNA) haplotypes could be explained by the large‐ vs. small‐bodied distinction. Genetic distances and neighbour‐joining trees based on allelic frequency data showed a distinct separation between the proposed species, although cladistic analysis of the phylogenetic history of the mitochondrial sequence haplotypes has shown a lack of reciprocal monophyly. These results further support the recognition of the small‐bodied sage grouse as a distinct species based on the biological species concept, providing additional genetic evidence to augment the morphological and behavioural data. Furthermore, small‐bodied sage grouse had much less genetic variation than large‐bodied sage grouse, which may have implications for conservation issues.
Distribution of Gymnostoma spp. microsymbiotic Frankia strains in New Caledonia is related to soil type and to host‐plant species
Authors: Navarro E. , Jaffre T. , Gauthier D. , Gourbiere F. , Rinaudo G. , Simonet P. , Normand P.
Published: March 2003

The diversity of the Frankia strains that are naturally in symbiosis with plants belonging to the Gymnostoma genus in New Caledonia was investigated. A direct molecular characterization of DNA extracted from nodules was performed, followed by characterization by restriction fragment length polymorphism (RFLP) of the ribosomal rrs–rrl (16S–23S) intergenic spacer (IGS) polymerase chain reaction (PCR)‐amplified region. Seventeen different patterns were identified among the 358 microsymbiotic strains studied in the eight species of host plant present in New Caledonia. This genotypical approach permitted us to show that a large diversity existed among the patterns and that these did not exhibit a strict specificity to any host‐plant species comparable with that previously found in the Casuarina and Allocasuarina symbioses in Australia. Despite this lack of specificity, a correspondence analysis nevertheless showed that the distribution of these patterns was related to soil type and to host‐plant species. Furthermore, several Frankia strains were exclusively associated with the ultramafic soils.
Interaction between the endophytic fungus Epichloë bromicola and the grass Bromus erectus: effects of endophyte infection, fungal concentration and environment on grass growth and flowering
Authors: Groppe K. , Steinger T. , Sanders I. , Schmid B. , Wiemken A. , Boller T.
Published: March 2003

Epichloë bromicola is an endophytic fungal species that systemically and perennially colonizes intercellular spaces of leaf blades, leaf sheaths and culms of Bromus grass species. E. bromicola causes choke disease in B. erectus, suppressing maturation of most, if not all, host inflorescences. In an investigation of the interaction between fungus and host, we used a quantitative polymerase chain reaction technique to estimate the amount of fungal DNA, and thereby fungal concentration, in host plants. Fungal concentration was directly correlated with vegetative vigour of the plant, as measured by longest leaf length, number of tillers and vegetative above‐ground biomass, suggesting that, during vegetative growth, the endophytic fungus is most beneficial for the plant when present in high concentrations. In contrast, the reproduction of the plant, as measured by the number of functional inflorescences, was inversely correlated with fungal concentration: the majority of infected plants, and all that were associated with high concentrations of fungi, were diseased. Thus, the benefit of endophyte infection for the plant is coupled with the disadvantages of infertility. Fungal concentration was shown to be at least in part genetically determined because fungal concentration differed significantly in different plant–endophyte genotype combinations (symbiotum). In a field experiment with normal and CO2‐enriched environments, elevated CO2 levels favoured fungal reproductive vigour over host reproductive vigour, suggesting that these plant endophytes would be at a selective advantage in a corresponding environmental‐change scenario. We conclude that a dynamic and complex relationship between fungal endophyte infection, fungal concentration, genotype and environment affects growth and fecundity of B. erectus and should contribute to the evolution of these plant–fungal interactions.
The use of random amplified polymorphic DNA (RAPD) markers to identify strawberry varieties: a forensic application
Authors: Congiu L. , Chicca M. , Cella R. , Rossi R. , Bernacchia G.
Published: March 2003

The random amplified polymorphic DNA (RAPD) technique was applied to settle a lawsuit involving unauthorized commercialization of a patented strawberry variety of high economical relevance (‘Marmolada’®). Because of economical involvements, the molecular approach was added to the more traditional morphological examination in a double‐blind test. All plants belonging to the patented variety were unambiguously identified (13 plants among a total of 31 plants examined). The results were accepted as evidence in the court. This study confirms that the RAPD technique is especially suitable for identification of asexually reproduced plant varieties for forensic or agricultural purposes.
Screening of Mhc variation in Atlantic salmon (Salmo salar): a comparison of restriction fragment length polymorphism (RFLP), denaturing gradient gel electrophoresis (DGGE) and sequencing
Authors: Langefors Åsa , Lohm Jakob , Von Schantz Torbjörn , Grahn Mats
Published: March 2003

We compared three different molecular methods currently used for screening of Mhc variation in population studies of Atlantic salmon. Restriction fragment length polymorphism (RFLP) of the entire class II gene detected 22 haplotypes. Seventeen exon 2 sequences were obtained from individuals carrying the 22 haplotypes, two of which had not been detected by RFLP. The six alleles (27%) detected by RFLP and not by exon 2 sequencing probably resulted from sequence variation outside exon 2. Within exon 2, RFLP differentiated 88% of the sequences. Alternatively, denaturing gradient gel electrophoresis (DGGE) performed under two run conditions detected 94% of the sequence variation. Both RFLP using different probes, and the two PCR‐based methods using three different primer pairs, suggest that there is only a single Mhc class II B gene in the Baltic populations of Atlantic salmon.
Genetic divergence between Atlantic and Indo‐Pacific stocks of bigeye tuna (Thunnus obesus) and admixture around South Africa
Authors: Chow Seinen , Okamoto Hiroaki , Miyabe Naozumi , Hiramatsu Kazuhiko , Barut Noel
Published: March 2003

Two mitochondrial DNA segments of the bigeye tuna (Thunnus obesus) were amplified by polymerase chain reaction (PCR), and restriction fragment length polymorphism (RFLP) analyses of these segments were used for the genetic stock study. The variation in a segment flanking the ATPase and COIII genes was low; only two genotypes (α and β) were detected by RsaI digestion. Yet a large difference in the genotype distribution was observed between ocean basin samples. The α type predominated in four Atlantic samples, where 178 of 244 individuals were the α type. In contrast, only one of 195 individuals collected in the Indo‐Pacific was the α type? The frequency of the α type varied considerably from 0 to 80% among seven samples collected off the Cape of Good Hope. The variation found in the other segment, containing the D‐loop region, was much higher; two endonucleases (DpnII and RsaI) detected five genotypes each and 15 composite genotypes. A highly significant difference in genotype frequencies was observed between the Atlantic and Indo‐Pacific samples, but no heterogeneity was observed among the four Atlantic or among four Indo‐Pacific samples. These results clearly indicate that not only gene flow, but also fish migration, between the Atlantic and Indian Oceans are severely restricted, and that fishes from these distinct stocks are intermingling around South Africa. The simple and diagnostic genetic marker found in this study can be used to estimate mixing ratios between Atlantic and Indian stocks around South Africa.
Ecological determinants and temporal stability of the within‐river population structure in Atlantic salmon (Salmo salarL.)*
Authors: Garant Dany , Dodson Julian J. , Bernatchez Louis
Published: March 2003

A gene diversity analysis was performed using microsatellite loci in order to (i) describe the extent and pattern of population structure in Atlantic salmon (Salmo salarL.) within a river system; (ii) establish the importance of quantifying the signal:noise ratio in accurately estimating population structure; and (iii) assess the potential usefulness of two evolutionary models in explaining within‐river population structure from the ecological and habitat characteristics of Atlantic salmon. We found weak, yet highly significant microscale spatial patterning after accounting for variance among temporal replicates within sites. Lower genetic distances were observed among temporal samples at four sampling sites whereas no evidence for temporal stability was observed at the other three locations. The component of genetic variance attributable to either temporal instability and/or random sampling errors was almost three times more important than the pure spatial component. This indicates that not considering signal:noise ratio may lead to an important overestimation of genetic substructuring in situations of weak genetic differentiation. This study also illustrates the usefulness of the member–vagrant hypothesis to generate a priori predictions regarding the number of subpopulations that should compose a species, given its life‐history characteristics and habitat structure. On the other hand, a metapopulation model appears better suited to explain the extent of genetic divergence among subpopulations, as well as its temporal persistence, given the reality of habitat patchiness and environment instability. We thus conclude that the combined use of both models may offer a promising avenue for studies aiming to understand the dynamics of genetic structure of species found in unstable environments.
Hydrography and population genetic structure in brook charr (Salvelinus fontinalis, Mitchill) from eastern Canada
Authors: Hébert C. , Danzman R. G. , Jones M. W. , Bernatchez L.
Published: March 2003

Despite the abundance of studies of genetic diversity in freshwater fishes, few have specifically addressed the role of habitat structure in partitioning genetic variance within and among populations. In this study, we analysed the variability of six microsatellite loci among 24 brook charr population samples in order to correlate hydrographic structure with genetic organization. These populations originated from three Canadian National parks (Kouchibouguac, Fundy and Forillon) that showed distinct hydrographic structure. Considering the general characteristics of these habitats, we formulated specific hypotheses in regard to genetic structure, which were principally based on the potential for gene flow and population size associated with each habitat. The hierarchical analysis of molecular variance and the genetic distances computed among populations revealed that habitat structure analyses constitute an important, but insufficient, predictor of genetic structure. We discuss the importance of habitat complexity on genetic structure in the context of management and conservation.
Marker‐inferred relatedness as a tool for detecting heritability in nature
Authors: Ritland Kermit
Published: March 2003

This paper presents a perspective of how inferred relatedness, based on genetic marker data such as microsatellites or amplified fragment length polymorphisms (AFLPs), can be used to demonstrate quantitative genetic variation in natural populations. Variation at two levels is considered: among pairs of individuals within populations, and among pairs of subpopulations within a population. In the former, inferred pairwise relatedness, combined with trait measures, allow estimates of heritability ‘in the wild’. In the latter, estimates ofQSTare obtained, in the absence of known heritabilities, via estimates of pairwiseFST. Estimators of relatedness based on the ‘Kronecker operator’ are given. Both methods require actual variation of relationship, a rarely studied aspect of population structure, and not necessarily present. Some conditions for appropriate population structures in the wild are identified, in part through a review of recent studies.
Chloroplast diversity in Vouacapoua americana (Caesalpiniaceae), a neotropical forest tree
Authors: Dutech C. , Maggia L. , Joly H. I.
Published: March 2003

The chloroplast genome has been widely used to describe genetic diversity in plant species. Its maternal inheritance in numerous angiosperm species and low mutation rate are suitable characters when inferring historical events such as possible recolonization routes. Here we have studied chloroplast DNA variation using PCR–RFLP (polymerase chain reaction–restriction fragment length polymorphism) with seven pairs of primers and four restriction enzymes in 14 populations of Vouacapoua americana (Caesalpiniaceae) a neotropical tree sampled throughout French Guiana. Population diversity (Hs), total gene diversity (Ht) and differentiation among populations (GST) were estimated using Nei’s method as 0.09, 0.87 and 0.89, respectively. This is consistent with the limited gene flow associated with synzoochory in this species. The genetic structure observed in the north of French Guiana suggests that historical events such as contractions and recent recolonizations have had a large impact on the distribution of genetic diversity in this species.
Experimental evaluation of the usefulness of microsatellite DNA for detecting demographic bottlenecks
Authors: Spencer C. C. , Neigel J. E. , Leberg P. L.
Published: March 2003

Evolutionary and conservation biologists often use molecular markers to evaluate whether populations have experienced demographic bottlenecks that resulted in a loss of genetic variation. We evaluated the utility of microsatellites for detection of recent, severe bottlenecks and compared the amounts of genetic diversity lost in bottlenecks of different sizes. In experimental mesocosms, we established replicate populations by releasing 1, 2, 4 or 8 pairs of the western mosquitofish,Gambusia affinis(Poeciliidae). Using eight polymorphic microsatellite loci, we quantified seven indices of genetic diversity or change that have been used to assess the effects of demographic bottlenecks on populations. We compared indices for the experimentally bottlenecked populations to those for the source population and examined differences between populations established with different numbers of founders. Direct count heterozygosity and the proportion of polymorphic loci were not very sensitive to genetic changes that resulted from the experimental bottlenecks. Heterozygosity excess and expected heterozygosity were useful to varying degrees in the detection of bottlenecks. Allelic diversity and temporal variance in allele frequencies were most sensitive to genetic changes that resulted from the bottlenecks, and the temporal variance method was slightly more correlated with bottleneck size than was allelic diversity. Based on comparisons to a previous study with allozymes, heterozygosity, temporal variance in allele frequencies and allelic diversity, but not proportion of polymorphic loci, appear to be more sensitive to demographic bottlenecks when quantified using microsatellites. We found that analysis of eight highly polymorphic loci was sufficient to detect a recent demographic bottleneck and to obtain an estimate of the magnitude of bottleneck severity.
Genetic variation and population structure in Scandinavian wolverine (Gulo gulo) populations
Authors: Walker C. W. , Vilà C. , Landa A. , Lindén M. , Ellegren H.
Published: March 2003

Wolverine (Gulo gulo) numbers in Scandinavia were significantly reduced during the early part of the century as a result of predator removal programmes and hunting. Protective legislation in both Sweden and Norway in the 1960s and 1970s has now resulted in increased wolverine densities in Scandinavia. We report here the development of 15 polymorphic microsatellite markers in wolverine and their use to examine the population sub‐structure and genetic variability in free‐ranging Scandinavian wolverine populations as well as in a sample of individuals collected before 1970. Significant subdivision between extant populations was discovered, in particular for the small and isolated population of southern Norway, which represents a recent recolonization. Overall genetic variability was found to be lower than previously reported for other mustelids, with only two to five alleles per locus and observed heterozygosities (HO) ranging from 0.269 to 0.376 across the examined populations, being lowest in southern Norway. Analysis of the mitochondrial DNA control region revealed no variation throughout the surveyed populations. As the historical sample did not show higher levels of genetic variability, our results are consistent with a reduction in the genetic variation in Scandinavian wolverines that pre‐dates the demographic bottleneck observed during the last century. The observed subdivision between populations calls for management caution when issuing harvest quotas, especially for the geographically isolated south Norwegian population.
The root rot fungus Armillaria mellea introduced into South Africa by early Dutch settlers
Authors: Coetzee Martin P. A. , Wingfield Brenda D. , Harrington Thomas C. , Steimel Joe , Coutinho Teresa A. , Wingfield Michael J.
Published: March 2003

Dead and dying oak (Quercus) and numerous other woody ornamental trees and shrubs showing signs and symptoms of Armillaria root rot were identified in the Company Gardens, Cape Town, South Africa, which were established in the mid‐1600s by the Dutch East Indies Trading Company. Nineteen isolates from dying trees or from mushrooms were collected and analysed to identify and characterize the Armillaria sp. responsible for the disease. The AluI digestion of the amplified product of the first intergenic spacer region (IGS‐1) of the rRNA operon of 19 isolates from the Company Gardens was identical to that of some of the European isolates of A. mellea s. s. The IGS‐1 region and the internal transcribed spacers (ITS) were sequenced for some of the Cape Town isolates. Phylogenetic analyses placed the Cape Town isolates in the European clade of A. mellea, which is distinct from the Asian and North American clades of this species. Identification based on sexual compatibility was conducted using A. mellea tester strains in diploid–haploid pairings, which showed some compatibility between the Cape Town isolates and testers from Europe. Somatic compatibility tests (diploid–diploid pairings) and DNA fingerprinting with multilocus, microsatellite probes indicated that the Cape Town isolates were genetically identical and may have resulted from vegetative (clonal) spread from a single focus in the centre of the original Company Gardens (c. 1652). The colonized area is at least 345 m in diameter. Assuming a linear spread rate underground of 0.3 m/year to 1.6 m/year, the genet (clone) was estimated to be between 108 and 575 years old. These data suggest that A. mellea was introduced into Cape Town from Europe, perhaps on potted plants, such as grapes or citrus, planted in the Company Gardens more than 300 years ago.
Reconciling patterns of inter‐ocean molecular variance from four classes of molecular markers in blue marlin (Makaira nigricans)
Authors: Buonaccorsi V. P. , Mcdowell J. R. , Graves J. E.
Published: March 2003

Different classes of molecular markers occasionally yield discordant views of population structure within a species. Here, we examine the distribution of molecular variance from 14 polymorphic loci comprising four classes of molecular markers within ≈ 400 blue marlin individuals (Makaira nigricans). Samples were collected from the Atlantic and Pacific Oceans over 5 years. Data from five hypervariable tetranucleotide microsatellite loci and restriction fragment length polymorphism (RFLP) analysis of whole molecule mitochondrial DNA (mtDNA) were reported and compared with previous analyses of allozyme and single‐copy nuclear DNA (scnDNA) loci. Temporal variance in allele frequencies was nonsignificant in nearly all cases. Mitochondrial and microsatellite loci revealed striking phylogeographic partitioning among Atlantic and Pacific Ocean samples. A large cluster of alleles was present almost exclusively in Atlantic individuals at one microsatellite locus and for mtDNA, suggesting that, if gene flow occurs, it is likely to be unidirectional from Pacific to Atlantic oceans. Mitochondrial DNA inter‐ocean divergence (FST) was almost four times greater than microsatellite or combined nuclear divergences including allozyme and scnDNA markers. Estimates of Neuvaried by five orders of magnitude among marker classes. Using mathematical and computer simulation approaches, we show that substantially different distributions ofFSTare expected from marker classes that differ in mode of inheritance and rate of mutation, without influence of natural selection or sex‐biased dispersal. Furthermore, divergentFSTvalues can be reconciled by quantifying the balance between genetic drift, mutation and migration. These results illustrate the usefulness of a mitochondrial analysis of population history, and relative precision of nuclear estimates of gene flow based on a mean of several loci.
Genetic variation and structure of fisher (Martes pennanti) populations across North America
Authors: Kyle C. J. , Robitaille J. F. , Strobeck C.
Published: March 2003

Fishers are mid‐sized forest carnivores indigenous to North America that experienced sharp population declines from the early 1800s through to the mid‐1900s. To evaluate levels of genetic variation within and subdivision among northern fisher populations 459 individuals were genotyped using 13 microsatellite loci. Genetic diversity was found to be slightly lower in re‐introduced populations than in adjacent indigenous populations. Furthermore, fisher populations revealed much more genetic structuring than two closely related mustelids. Further investigation is needed to determine if fishers are more philopatric than martens and wolverines or if barriers to dispersal explain the levels of structure identified in this study.
Clonal mixing in the soldier‐producing aphidPemphigus spyrothecae(Hemiptera: Aphididae)
Authors: Johnson Paul C. D. , Whitfield John A. , Foster William A. , Amos William
Published: March 2003

Illuminating the genetic relationships within soldier‐producing aphid colonies is an essential element of any attempt to explain the evolution of the altruistic soldier caste.Pemphigus spyrothecaeis a soldier‐producing aphid that induces galls on the leaf petioles of its host (trees of the genusPopulus). At least a quarter of the aphids within the clonally produced gall population are morphologically and behaviourally distinct first‐instar soldiers that defend the gall population from predation. Using field trapping and microsatellites, we investigated the degree of clonal mixing within natural gall populations. Field trapping in the UK showed that all the migrants ofP. spyrothecaeand of two otherPemphigusspecies were wingless first‐instar soldiers. The average degree of mixing estimated from trappingP. spyrothecaemigrants was 0.68% (range = 0–15%). Microsatellite genotyping of 277 aphids from 13 galls collected in Italy revealed an average mixing level of 10.4% (range = 0–59%). Six galls contained more than one clone (range = 2–5 clones). Non‐kin aphids were not restricted to the soldier caste but were evenly distributed across instars. An additional gall, from which 527 occupants were genotyped, contained 12 non‐kin aphids distributed among nine clones, showing that clonal diversity can be high even when mixing is very low. These observations suggest that although soldiers migrate regularly and can moult and reproduce within foreign galls, clonal mixing in this species is generally low and is unlikely to provide a barrier to the evolution of investment by the aphid clones in an altruistic soldier caste.
Complex patterns of colonization and refugia revealed for European grayling Thymallus thymallus, based on complete sequencing of the mitochondrial DNA control region
Authors: Weiss S. , Persat H. , Eppe R. , Schlötterer C. , Uiblein F.
Published: March 2003

The complete mitochondrial DNA (mtDNA) control region (1043 base pairs) and 162‐bp of flanking transfer RNA genes were sequenced in 316 European grayling, Thymallus thymallus, from 44 populations throughout the Western European range of the species. A total of 58 haplotypes were revealed with pairwise divergence ranging from 0.001 to 0.038. An inferred intraspecific phylogenetic tree revealed two well‐supported clades within the Danube basin, one highly divergent clade in the Adriatic basin, and one large, diverse group representing most other populations. A deeply divergent haplotype fixed in the Loire basin in central France, more groups of haplotypes from distinct Danubian tributaries, and a relatively ancestral haplotype fixed in former tributaries of the Elbe in Denmark all suggest a complex pattern of interglacial and postglacial expansions originating from disjunct refugia throughout central Europe. Despite some evidence of human‐mediated stock transfers, parsimony‐network‐based nested‐clade analysis (NCA) supported specific inferences relating to corridors of postglacial expansion such as the lower Rhine (Moselle) and Elbe systems (Danish populations) serving as sources for expansion into the Baltic to the north as well as the upper Rhine and Danube to the south; and specific Rhine populations (Doller, Orbe and Reuss) serving as sources for colonization of the Rhone. The multiple divergent clades representing populations in the upper Danube, as well as the deeply divergent haplotypes found in the Adriatic and Loire basins (> 5% divergence from Asian outgroups) support the theory that European grayling have had a long history in Western Europe, pre‐dating Pleistocene glacial cycles. The patterns of mtDNA divergence shown here support a perspective of rich inter‐ and intrabasin genetic diversity that should be protected from current trends to translocate brood stocks for rearing and release in response to declining populations, especially in southern European basins.
Phylogeography of western PacificLeucetta ‘chagosensis’(Porifera: Calcarea) from ribosomal DNA sequences: implications for population history and conservation of the Great Barrier Reef World Heritage Area (Australia)
Authors: Wörheide Gert , Hooper John N. A. , Degnan Bernard M.
Published: March 2003

Leucetta ‘chagosensis’is a widespread calcareous sponge, occurring in shaded habitats of Indo‐Pacific coral reefs. In this study we explore relationships among 19 ribosomal DNA sequence types (the ITS1‐5.8S–ITS2 region plus flanking gene sequences) found among 54 individuals from 28 locations throughout the western Pacific, with focus on the Great Barrier Reef (GBR). Maximum parsimony analysis revealed phylogeographical structuring into four major clades (although not highly supported by bootstrap analysis) corresponding to the northern/central GBR with Guam and Taiwan, the southern GBR and subtropical regions south to Brisbane, Vanuatu and Indonesia. Subsequent nested clade analysis (NCA) confirmed this structure with a probability of > 95%. After NCA of geographical distances, a pattern of range expansion from the internal Indonesian clade was inferred at the total cladogram level, as the Indonesian clade was found to be the internal and therefore oldest clade. Two distinct clades were found on the GBR, which narrowly overlap geographically in a line approximately from the Whitsunday Islands to the northern Swain Reefs. At various clade levels, NCA inferred that the northern GBR clade was influenced by past fragmentation and contiguous range expansion events, presumably during/after sea level low stands in the Pleistocene, after which the northern GBR might have been recolonized from the Queensland Plateau in the Coral Sea. The southern GBR clade is most closely related to subtropicalL. ‘chagosensis’, and we infer that the southern GBR probably was recolonized from there after sea level low stands, based on our NCA results and supported by oceanographic data. Our results have important implications for conservation and management of the GBR, as they highlight the importance of marginal transition zones in the generation and maintenance of species rich zones, such as the Great Barrier Reef World Heritage Area.
The role of ecologic diversification in sibling speciation ofEmpidonaxflycatchers (Tyrannidae): multigene evidence from mtDNA
Authors: Johnson N. K. , Cicero C.
Published: March 2003

Avian genera characterized by sibling species with distinctive habitat preferences present an evolutionary enigma in view of the more commonplace occurrence of syntopic congeners that differ strikingly in colour and pattern. No existing theory has explained the evolutionary background that led to these differences. Here we propose that great phenotypic similarity among some groups of sibling species limits their coexistence and that clues to their radiation can be seen in patterns of geographical occurrence. To illustrate our thesis we focused on the New World flycatcher genusEmpidonax, a group of 15 species notorious for their great phenotypic similarity. Using 3069 base pairs of mitochondrial DNA from four genes, we produced a complete molecular phylogeny that identified four clades, three of which represent close relatives. The fourth clade includes onlyE. virescens, which apparently has no close living relatives. The majority of species, including many distant relatives, are completely (58.1%) or essentially (6.7%) allopatric in breeding distribution and exhibit striking ecological segregation into distinctive climate–vegetation zones. Even where ranges overlap, occupancy of the same habitat by different species is rare. Phylogenetic and distributional patterns inEmpidonaxsuggest a peripatric model of stepwise colonization and then range expansion of small groups of pioneers during glacial periods into initially enlarging, distinctive habitats destined to be widespread during interglacials. Vicariance is not indicated in the absence of barriers of appropriate age and geographical position. Rapoport's rule that northern species have larger ranges than southern species is strongly supported.
Population genetic structure and male‐biased dispersal in the queenless antDiacamma cyaneiventre
Authors: Doums Claudie , Cabrera Humberto , Peeters Christian
Published: March 2003

In this study we investigated the population genetic structure of the queenless antDiacamma cyaneiventre. This species, lacking winged queens, is likely to have a restricted female dispersal. We used both mitochondrial and microsatellite markers to assess the consequence of such restricted female dispersal at three geographical scales: within a given locality (< 1 km), between localities within a given region (< 10 km) and between regions (> 36 km). Within a locality, a strong population structure was observed for mitochondrial DNA (mtDNA) whereas weak or nonexistent population genetic structure was observed for the microsatellites (around 5% of the value for mtDNA). Male gene flow was estimated to be about 20–30 times higher than female gene flow at this scale. At a larger spatial scale, very strong genetic differentiation for both markers was observed between localities — even within a single region. Female dispersal is nonexistent at these scales and male dispersal is very restricted, especially between regions. The phylogeographical structure of the mtDNA haplotypes as well as the very low genetic diversity of mtDNA within localities indicate that new sites are colonized by a single migration event from adjacent localities, followed by successive colony fissions. These patterns of genetic variability and differentiation agree with what is theoretically expected when colonization events are kin‐structured and when, following colonization, dispersion is mainly performed by males.
The clonal structure of Quercus geminata revealed by conserved microsatellite loci
Authors: Ainsworth E. A. , Tranel P. J. , Drake B. G. , Long S. P.
Published: March 2003

The scrub oak communities of the southeastern USA may have existed at their present locations for thousands of years. These oaks form suckers, and excavations of root systems suggest that clones may occupy very large areas. Resolution of the clonal nature of scrub oaks is important both to manage the tracts of this ecosystem that remain, and in conducting long‐term ecological studies, where the study area must substantially exceed the area occupied by any single clone. Microsatellites were used to determine the genetic diversity of a dominant oak species within a 2‐ha long‐term experimental site on Merritt Island at the Kennedy Space Center. This area contains a long‐term study of the effects of elevated CO2 on the ecosystem. Conservation of seven microsatellite loci, previously identified in the sessile oak, Quercus petraea, was tested in two Florida scrub oak species, Q. geminata and Q. myrtifolia. Sequence analysis revealed that all seven microsatellite loci were conserved in Q. geminata and five loci were conserved in Q. myrtifolia. Six microsatellite loci were polymorphic in Q. geminata and these were subsequently used to investigate the clonal structure of the Q. geminata population. Twenty‐one unique combinations of microsatellites, or haplotypes, occurred only once, whereas the remaining 26 individuals belonged to a total of seven different haplotypes. Trees with identical haplotypes were in close proximity, supporting the interpretation that they were clones. The results showed that there is significant genetic diversity within the 2‐ha experimental site. Microsatellites provided a powerful and noninvasive tool for distinguishing individual genotypes and determining an adequate area for long‐term ecosystem studies.