bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparative phylogeography of Nearctic and Palearctic fishes
Authors: BERNATCHEZ LOUIS , WILSON CHRISTOPHER C.
Published: March 2003

Combining phylogeographic data from mitochondrial DNA (mtDNA) of Nearctic and Palearctic freshwater and anadromous fishes, we used a comparative approach to assess the influence of historical events on evolutionary patterns and processes in regional fish faunas. Specifically, we (i) determined whether regional faunas differentially affected by Pleistocene glaciations show predictable differences in phylogeographic patterns; (ii) evaluated how processes of divergence and speciation have been influenced by such differential responses; and (iii) assessed the general contribution of phylogeographic studies to conservation issues. Comparisons among case studies revealed fundamental differences in phylogeographic patterns among regional faunas. Tree topologies were typically deeper for species from nonglaciated regions compared to northern species, whereas species with partially glaciated ranges were intermediate in their characteristics. Phylogeographic patterns were strikingly similar among southern species, whereas species in glaciated areas showed reduced concordance. The extent and locations of secondary contact among mtDNA lineages varied greatly among northern species, resulting in reduced intraspecific concordance of genetic markers for some northern species. Regression analysis of phylogeographic data for 42 species revealed significant latitudinal shifts in intraspecific genetic diversity. Both relative nucleotide diversity and estimates of evolutionary effective population size showed significant breakpoints matching the median latitude for the southern limit of the Pleistocene glaciations. Similarly, analysis of clade depth of phylogenetically distinct lineages vs. area occupied showed that evolutionary dispersal rates of species from glaciated and nonglaciated regions differed by two orders of magnitude. A negative relationship was also found between sequence divergence among sister species as a function of their median distributional latitude, indicating that recent bursts of speciation events have occurred in deglaciated habitats. Phylogeographic evidence for parallel evolution of sympatric northern species pairs in postglacial times suggested that differentiation of cospecific morphotypes may be driven by ecological release. Altogether, these results demonstrate that comparative phylogeography can be used to evaluate not only phylogeographic patterns but also evolutionary processes. As well as having significant implications for conservation programs, this approach enables new avenues of research for examining the regional, historical, and ecological factors involved in shaping intraspecific genetic diversity.
Discriminating coho salmon (Oncorhynchus kisutch) populations within the Fraser River, British Columbia, using microsatellite DNA markers
Authors: SMALL M. P. , BEACHAM T. D. , WITHLER R. E. , NELSON R. J.
Published: March 2003

Three microsatellite loci were used to examine genetic variation among 16 coho salmon (Oncorhynchus kisutch) populations within the Fraser River drainage system, in British Columbia, Canada. Each locus was highly polymorphic with 30 alleles at the Ots101 locus, 15 alleles at the Ots3 locus and 38 alleles at the Ots103 locus. Average observed heterozygosities were 86.1%, 70%, and 56.1%, respectively. With the exception of the Dunn and Lemieux River populations, Chi‐square tests and FST values indicated that all populations had significantly different allele frequencies. Two distinct population groups within the Fraser River drainage were observed. Lower Fraser River populations were strongly differentiated from populations spawning in the upper Fraser River, which includes the Thompson River (a tributary flowing into the upper Fraser) and the portion of the Fraser River beyond the precipitous Fraser River canyon. This regional population structure may have resulted from colonization of the upper and lower Fraser River regions by different founder populations following Pleistocene glaciation, and be maintained by adaptive differences between the two groups of coho salmon. Coho salmon populations in the upper Fraser and Thompson River drainages form an evolutionarily significant unit (ESU) of importance for conservation of biodiversity in coho salmon. Microsatellite DNA loci show promise as technically simple and highly informative genetic markers for coho salmon population management.
Multiple mating in wild Drosophila melanogaster revisited by microsatellite analysis
Authors: IMHOF MARIANNE , HARR BETTINA , BREM GOTTFRIED , SCHLÖTTERER CHRISTIAN
Published: March 2003

The occurrence of multiple mating in Drosophila melanogaster is of particular interest to evolutionary biologists, as seminal fluid has some toxic effects for females. Thus, it has been predicted that the number of matings per females should be low. We have tested this prediction with seven highly polymorphic microsatellite loci in inseminated females from a Viennese D. melanogaster population. In contrast to the predicted low number of matings and previous studies in natural populations, we identified the genotypes of four to six different males fertilizing the offspring of each female tested. Potential causes and consequences are discussed.
Pocket gophers and chewing lice: a test of the maternal transmission hypothesis
Authors: DEMASTES J. W. , HAFNER M. S. , HAFNER D. J. , SPRADLING T. A.
Published: March 2003

The life‐history traits of pocket gophers and their chewing lice suggest that there is little opportunity for transmission of parasites among pocket gophers, with the exception of transmission from mother to offspring. Herein, we test the hypothesis that lice are transmitted maternally by using an indirect approach that compares the distribution of louse populations to the distribution of mitochondrial DNA haplotypes in the pocket gophers. Comparison of the chewing louse distributions to the distribution of mtDNA haplotypes for the gophers revealed no significant concordance, and thus falsifies the maternal transmission hypothesis.
Biodiversity of rhizobia isolated from a wide range of forest legumes in Brazil
Authors: MOREIRA F. M. S. , HAUKKA K. , YOUNG J. P. W.
Published: March 2003

Tropical forests have a high diversity of plant species; are they associated with a correspondingly rich microbial flora? We addressed this question by examining the symbiotic rhizobium bacteria that nodulate a diverse pool of forest legume species in Brazil. The 44 strains studied had been isolated from 29 legume tree species representing 13 tribes including all three subfamilies of the Leguminosae, and were chosen to represent major groups from a larger sample that had previously been characterized by SDS–PAGE of total proteins. Partial 16S rRNA gene sequence was determined, corresponding to positions 44–303 in the Escherichia coli sequence. Fifteen sequences were found, including six novel ones. However, all but one of them could be assigned to a genus because they grouped closely with sequences from previously described rhizobial species. Fast‐growing strains had sequences similar to Rhizobium spp., Sinorhizobium spp. or Mesorhizobium spp., while the slow‐growing strains had sequences similar to Bradyrhizobium spp. One strain with an intermediate growth rate had a unique sequence which indicated that the strain might belong to the genus Azorhizobium. Although the strains showed a variety of sequences, it was surprising that these strains isolated from taxonomically very diverse host plants in previously unexplored environments were mostly very similar to strains described previously, largely from agricultural systems.
Genetic differentiation among local populations of the European hedgehog (Erinaceus europaeus) in mosaic habitats
Authors: BECHER S. A. , GRIFFITHS R.
Published: March 2003

Tissue samples from 160 European hedgehogs, Erinaceus europaeus, representing eight small populations from a highly fragmented landscape in Oxfordshire, UK, were screened for polymorphism at six microsatellite loci. Permutation analysis of allelic compositions revealed no evidence for linkage disequilibrium among loci. Genotype proportions within populations and at five loci did not differ from those expected at Hardy–Weinberg equilibrium. However, significant heterozygote deficit and amplification failure of several samples necessitated removal of one locus from the analysis. Mean observed heterozygosity was 0.70. Average RhoST was 0.079 and differed significantly from zero, suggesting restricted gene flow among local populations. Pairwise Nm values and geographical distance were not correlated, indicating that factors other than distance affected dispersal.
Geographical extent of Arctic char (Salvelinus alpinus) mtDNA introgression in brook char populations (S. fontinalis) from eastern Québec, Canada
Authors: GLÉMET H. , BLIER P. , BERNATCHEZ L.
Published: March 2003

The geographical extent of Arctic char (Salvelinus alpinus) mitochondrial DNA introgression into brook char (Salvelinus fontinalis) populations found in eastern Québec was determined by analysing a total of 598 fish from 29 lakes. The nuclear genome was analysed by protein electrophoresis, whereas the ND‐5,6 portion of the mitochondrial genome was analysed by restriction fragment length polymorphism. This survey revealed that introgressed S. fontinalis populations are restricted to only one river subdrainage of the Portneuf basin, where Arctic char is completely absent. Elsewhere, nonintrogressed pure S. fontinalis populations populate the lakes. These findings suggest that the initial hybridization event between the species is ancient and probably occurred shortly after recolonization of the area. At that time, the species would have been in contact and the chances of reproductive isolation mechanisms breaking down would have been high. We discuss the possibility that a combination of biogeographical conditions coupled with positive selection for mtDNA introgression led to the present‐day distribution of introgressed S. fontinalis in northeastern North America.
Intron size polymorphism of the Adh1 gene parallels the worldwide colonization history of the Mediterranean fruit fly, Ceratitis capitata
Authors: GOMULSKI L. M. , BOURTZIS K. , BROGNA S. , MORANDI P. A. , BONVICINI C. , SEBASTIANI F. , TORTI C. , GUGLIELMINO C. R. , SAVAKIS C. , GASPERI G. , MALACRIDA A. R.
Published: March 2003

The exon‐primed intron‐crossing (EPIC) PCR technique was used to analyse the size variation at the first intron of the Ceratitis capitata Adh1 gene. A total of 27 samples from 16 natural populations was analysed from five geographical regions in the species range: Africa, Mediterranean Basin, Latin America, Hawaii and Australia. The Adh1 first intron varies extensively in length with at least 18 size variants ranging from 1400 bp to 3450 bp. These variants can be grouped into four distinct size categories: short, medium, long and very long. The majority of these variants are present only in the African populations. Only a subset of the ancestral variants appear to have succeeded in migrating from Africa during the medfly colonization process. The medfly population structure inferred from the intron size polymorphism is congruent with that observed from the analysis of allozyme variation. The geographical dispersal of the medfly from its source area is associated with a gradual and great reduction in intron variability which parallels the trend of decreasing variability evaluated at 26 biochemical loci. The intron phylogenetic tree is in agreement with allozyme data in portraying the dynamic population history of the medfly. Stochastic evolutionary forces such as drift, bottleneck effects and migration seem to have played the major roles in the dispersion pattern of Adh1 intron variation during the colonization of the medfly.
Zoogeographical implications of variation in mitochondrial DNA of Arctic grayling (Thymallus arcticus)
Authors: Redenbach Z. , Taylor E. B.
Published: March 2003

Most of the northern half of North America’s freshwater fish survived the last glacial period in unfrozen refugia peripheral to the ice sheets. In our study, the question of which refugia Arctic grayling (Thymallus arcticus) inhabited during the Wisconsinan Ice Age, and how they subsequently dispersed to their present geographical range, was examined using mitochondrial DNA (mtDNA) analysis. mtDNA from 12 T. arcticus populations was analysed by direct sequencing and restriction fragment length polymorphism analysis (RFLP). Our data support the hypotheses that T. arcticus had a large refugial population in the Bering Refuge (shown by high mtDNA diversity in extant Alaskan populations) and that British Columbia was colonized from the Bering Refuge (shown by mtDNA haplotype similarities). Our data also show that a disjunct southern set of populations in Montana is significantly different from the northern grayling, in terms of restriction haplotype frequency and distinguishing sequence characteristics. Sequence results yielded an estimated divergence time of 370 000 years between the northern and Montana grayling haplotypes. We conclude that T. arcticus survived the Wisconsinan glaciation in at least two refugia: (i) the Bering Refuge north of the ice sheets; and (ii) either the Upper Missouri or the southwest Alberta Refuge, south of the ice sheet.
Intrasporal variability of ribosomal sequences in the endomycorrhizal fungus Gigaspora margarita
Authors: Lanfranco L. , Delpero M. , Bonfante P.
Published: March 2003

The sequence variability of the ribosomal internal transcribed spacer (ITS) region, which comprises the 5.8 gene and the flanking regions ITS1 and ITS2, was investigated in the arbuscular mycorrhizal fungus Gigaspora margarita. DNA analysis of a multispore preparation and three single spores led to the identification of 11 slightly different sequences (three variants within a single spore), indicating substantial intersporal and intrasporal genetic variability (up to 9% sequence divergence). The sequence variations inside a single spore may be higher than that observed between spores. Even so, primers designed on the ITS1 and ITS2 regions identified Gi. margarita isolates and detected the endophyte during colonization.
Population genetic analysis of Elliottiaracemosa (Ericaceae), a rare Georgia shrub
Authors: Godt M. J. W. , Hamrick J. L.
Published: March 2003

Genetic and genotypic diversity found within populations of threatened plant species can have important implications for their conservation and management. In this study we describe genetic and genotypic diversity found within 10 populations of the endemic shrub Elliottiaracemosa (Ericaceae), the Georgia plume. E. racemosa is a threatened species known from fewer than 50 locations, all within the state of Georgia, USA. Seedset is limited to nonexistent in some E. racemosa populations and sexual recruitment has not been documented. However, the species is known to spread vegetatively via root‐sprouts. Twenty‐one allozyme loci were resolved for E. racemosa, nine of which were polymorphic. Compared with other woody taxa, E. racemosa has low genetic (i.e. allelic) diversity within populations (Hep = 0.063) and at the species level (Hes = 0.091). Most of the genetic variation (82%) was found within populations, and genetic identities between populations were high (mean I = 0.96). However, genotypic diversity (i.e. the number of multilocus genotypes) differed markedly among populations. Two of the 10 populations consisted almost entirely of single multilocus genotypes, whereas more than 20 multilocus genotypes (in samples of 48 stems) were detected at three sites. Sites in which few multilocus genotypes were detected have low seedset, suggesting that the lack of clonal diversity limits reproduction in some populations of this reportedly self‐incompatible species.
Multiple origins of polyploidy and the geographic structure ofHeuchera grossulariifolia
Authors: SEGRAVES K. A. , THOMPSON J. N. , SOLTIS P. S. , SOLTIS D. E.
Published: March 2003

Multiple origins of polyploidy from an ancestral diploid plant species were investigated using restriction site polymorphism and sequence variation in the chloroplast DNA (cpDNA) ofHeuchera grossulariifolia(Saxifragaceae). Phylogenetic analysis indicated that autopolyploidy has arisen at least twice in the evolutionary history of this species and potentially up to as many as seven times. These results suggest a greater range of independent polyploid origins as compared to a previous study ofH. grossulariifoliausing cpDNA restriction sites that indicated a minimum of three independent origins. Moreover, most polyploid populations did not contain cpDNA haplotypes from a single origin, but rather combined haplotypes from at least two polyploid origins. Past migration among polyploid populations of independent origin or localized polyploid formation may explain the distribution of polyploid haplotypes within and among populations. The analysis also revealed a discrepancy between relatedness and geographical location. In nearly all sympatric populations of diploids and polyploids, polyploids had the same cpDNA haplotypes as diploids from a geographically remote population. This geographical discordance has several possible explanations, including small sample sizes, extinction of parental diploid haplotypes, chloroplast introgression, and homoplasy in the cpDNA sequence data. We conclude that the recurrent formation of polyploids is an important evolutionary mechanism in the diversification ofH. grossulariifolia.
Amplified fragment length polymorphism (AFLP) analysis of genetic variation in Moringa oleifera Lam.
Authors: MULUVI G. M. , SPRENT J. I. , SORANZO N. , PROVAN J. , ODEE D. , FOLKARD G. , McNICOL J. W. , POWELL W.
Published: March 2003

Moringa oleifera is an important multipurpose tree introduced to Africa from India at the turn of this century. Despite limited knowledge of the levels of genetic diversity and relatedness of introduced populations, their utilization as a source of seed for planting is widespread. In order to facilitate reasoned scientific decisions on its management and conservation and prepare for a selective breeding programme, genetic analysis of seven populations was performed using amplified fragment length polymorphism (AFLP) markers. The four pairs of AFLP primers (PstI/MseI) generated a total of 236 amplification products of which 157 (66.5%) were polymorphic between or within populations. Analysis of molecular variance (AMOVA) revealed significant differences between regions and populations, even though outcrossing perennial plants are expected to maintain most variation within populations. A phenetic tree illustrating relationships between populations suggested at least two sources of germplasm introductions to Kenya. The high levels of population differentiation detected suggest that provenance source is an important factor in the conservation and exploitation of M. oleifera genetic resources.
Phylogeography of the canyon treefrog, Hyla arenicolor (Cope) based on mitochondrial DNA sequence data
Authors: Barber PAUL H.
Published: March 2003

Patterns of phylogeography and gene flow were examined in the canyon treefrog, Hyla arenicolor. A total of 973 bp of mitochondrial cytochrome b sequence data were obtained for 65 individuals from 53 populations, yielding 50 unique haplotypes. Interpopulation sequence variation ranged from 0 to 13.7%. Phylogenetic analysis revealed three deeply divergent mtDNA lineages. These three Clades were mapped onto geography and found to represent completely concordant, nonoverlapping, geographical regions. Levels of sequence divergence between the three Clades were equal to or greater than published levels of divergence found in other vertebrate species and genera. Furthermore, one Clade of H. arenicolor was found to be more closely related to the outgroup H. eximia than to other H. arenicolor, suggesting that the taxonomy of this species may require revision.
Genetic diversity and dispersal of the moss Sarconeurum glaciale on Ross Island, East Antarctica
Authors: Skotnicki  , Ninham  , Selkirk
Published: March 2003

The extent of genetic variation and dispersal mechanisms were investigated over short distances of 1–100 m, and up to 3 km, by the random amplified polymorphic DNA (RAPD) technique, for the moss Sarconeurum glaciale, at three locations on Ross Island, Antarctica. At Arrival Heights, genetic variation occurred within single colonies, and the relationships between clumps indicated that they were dispersed down small, meltwater drainage channels by water. The genetic similarities between the colonies from Arrival Heights and others from Scott Base and Crater Hill, a few km away, together with the prevailing wind direction and absence of this moss in the intervening snow‐covered area, suggested longer‐distance dispersal by wind. Overall, the Ross Island samples appeared to form a single, polymorphic population that was distinct from another population at Canada Glacier, 110 km distant. Somatic mutation, rather than immigration of genetically different propagules from elsewhere, appeared to be the most probable cause of genetic variability in these haploid, vegetatively reproducing Antarctic moss populations. Initiation of recolonization of S. glaciale across a dirt track at Arrival Heights was also investigated by RAPDs, to investigate how regrowth of mosses in disturbed areas occurred in the extreme environment of Antarctica.
Genetic variation inFitzroya cupressoides(alerce), a threatened South American conifer
Authors: Allnutt T. R. , Newton A. C. , Lara A. , Premoli A. , Armesto J. J. , Vergara R. , Gardner M.
Published: March 2003

Fitzroya cupressoides(alerce, Cupressaceae) is a large and exceptionally long‐lived conifer, endemic to a restricted area of southern Chile and neighbouring areas of Argentina. As a result of its high economic value, the species has been severely exploited for timber, and remnant populations are fragmented and often highly disturbed. The species is thought to have undergone a major range contraction during the last glaciation. In order to assess the extent of genetic variation using DNA markers within and between populations of this species, samples were obtained from throughout the natural range and analysed for random amplified polymorphic DNA (RAPD) variation. Eight 10‐mer and three 15‐mer primers were used to produce a total of 54 polymorphic bands. Shannon's diversity estimates were calculated to provide an estimate of the degree of variation within each population. Values varied from 0.343 to 0.636 with only the lowest value differing significantly from the others (Spop= 0.547). This indicated that there is a significant degree of variation within each population, and did not provide evidence for genetic ‘bottleneck’ effects within the species. A pairwise distance measure calculated from the RAPD data was used as an input for principal coordinate (PCO) andamovaanalyses. The first three principal coordinates of RAPD distances described 8.3, 5.9 and 5.4% of the total variance, respectively, and a degree of clustering of samples according to their geographical origin was detectable.amovaanalysis indicated that although most of the variation (85.6%) was found within populations, a significant proportion (P < 0.002) was attributable to differences between populations. Anupgmadendrogram constructed using ΦSTvalues derived fromamovaproduced a pattern broadly similar to that produced by the PCO, highlighting differences between three main groups of populations within Chile: those from the northern Coastal Range, the southern Coastal Range and Central Depression, and the Andes. Populations from Argentina also emerged as significantly different from those in Chile. These results are interpreted in the context of the postglacial history of the species, and their implications for the development of conservation strategies forFitzroyaare discussed.
Effects of natural habitat fragmentation on an endemic scrub lizard (Sceloporus woodi): an historical perspective based on a mitochondrial DNA gene genealogy
Authors: Clark A. M. , Bowen B. W. , Branch L. C.
Published: March 2003

The Florida scrub lizard, Sceloporus woodi, is endemic to scrub habitat patches along the central portion of the Florida peninsula and xeric coastal regions. Scrub ecosystems are the patchily distributed remnants of previously widespread habitats formed during the Pleiocene and early Pleistocene. Scrub lizards appear to have limited dispersal capabilities due to high habitat specificity and low mobility. To assess the population structure and phylogeography of S. woodi, 135 samples were collected from 16 patches on five major ridges in Florida, USA. Analysis of 273 bp of mitochondrial DNA (mtDNA) cytochrome b reveals a very strong geographic distribution of genetic diversity. Haplotype frequencies are significantly different in 63 of 66 comparisons between patches. With one exception, samples from the five major ridges are characterized by fixed differences in haplotype distribution and deep evolutionary separations (3–10%). Fixed genetic differences were also observed between northern and southern segments of several ridges. Analysis of molecular variance (amova) shows an estimated 10.4% total genetic variation within patches, 17.5% among patches (within ridges), and 72.1% among ridges. This strong population structure among patches within ridges indicates that the distribution of S. woodi is tightly linked to sandy scrub habitat and that the discontinuous distribution of scrub habitats significantly inhibits dispersal and gene flow. Phylogeographic analyses indicate a pattern of dispersal down the Florida peninsula during the late Pliocene–early Pleistocene, followed by habitat fragmentation and vicariant isolation events. Therefore, the deep genetic structuring among scrub lizard populations on separate ridges is attributed to ancient isolation events induced by a shift from dry (xeric) to wet (mesic) conditions on the Florida peninsula. These findings indicate that some scrub lizard populations have persisted in isolation for time frames in excess of 1 Myr, providing a case history on the genetic consequences of habitat fragmentation.
Cleistogamy in Scutellaria indica (Labiatae): effective mating system and population genetic structure
Authors: Sun M.
Published: March 2003

Scutellaria indica is a perennial herb with both chasmogamous (CH) and cleistogamous (CL) flowers on the same plant in some populations, and only CL flowers in other populations. Actual seed production by CH and CL flowers was investigated in populations of S. indica. The average seed set of CL flowers was 19 times higher than CH flowers, indicating much greater fertilization success. The CL seeds were also significantly heavier than the CH seeds. However, the resource cost of producing a CH flower was much higher than that of producing a CL flower. The CH flower was approximately seven times larger, and its pollen/ovule ratio was approximately five times higher than that of CL flowers. The level and pattern of genetic diversity at both allozyme and random amplified polymorphic DNA (RAPD) levels were consistent with a predominantly selfing system in the species. The average amount of within‐population genetic variation was extremely low (A = 1.025, P = 2.36%, HO = 0.001 and HE = 0.008 based on allozyme data, and P = 8.94% and HE = 0.03 based on RAPD data). At the species level, the estimates of total gene diversity (HT) were 0.101 based on allozyme data and 0.139 based on RAPD data. A very high level of genetic differentiation occurred between populations (allozyme GST = 0.92 and RAPD GST = 0.81). Genetic drift coupled with predominant cleistogamous selfing apparently played the major role in determining the population genetic structure in S. indica. Although the features associated with CH and CL flower and seed production seem to be sufficient for the evolution of complete cleistogamy in S. indica, random fixation of alternative alleles for dimorphic or complete cleistogamy in small populations could maintain the multiple strategy of chasmogamous and cleistogamous reproduction in the species.
Genetic variation in postfire aspen seedlings in Yellowstone National Park
Authors: Stevens Michael T. , Turner Monica G. , Tuskan Gerald A. , Romme William H. , Gunter Lee E. , Waller Donald M.
Published: March 2003

A rare episode of regeneration of aspen (Populus tremuloides Michx.) by seeds occurred in Yellowstone National Park (YNP), Wyoming, USA, following extensive fires that occurred in 1988. In 1997, we sampled 410 aspen seedlings from 23 local populations distributed widely across YNP to determine how genetic diversity varies with elevation, substrate, plant competition, ungulate browsing, and geographical location. We employed 132 randomly amplified polymorphic DNA (RAPD) markers based on six primers to show genetic relationships within and among the postfire aspen seedling populations. Measures of genetic variation, including estimates of percentage polymorphic loci, expected heterozygosity, and Nei’s FST, indicated that most of the variation occurred within rather than among local populations. There was no indication of geographical differentiation among sampled populations based on hierarchal estimates of Nei’s FST, neighbour‐joining, or correlations between genetic distance and geographical distance. Even genetically distant populations shared nearly 90% of the same markers. Within plots, the amount of genetic variation decreased slightly in response to increased percentage vegetative cover, mean seedling basal diameter, and mean seedling height. Geological substrate, density of lodgepole pine (Pinus contorta var. latifolia Dougl.) seedlings, browsing intensity, and elevation were not significantly related to levels of genetic variation within the seedling plots. These data suggest that genetic variation and geographical structure among seedling populations may occur over time as the transition from seedling‐dominated stands to clone‐dominated stands occurs.
Phylogeography and mitochondrial DNA (mtDNA) diversity in North American collared lemmings (Dicrostonyx groenlandicus)
Authors: Ehrich D. , Fedorov V. B. , Stenseth N. C. , Krebs C. J. , Kenney A.
Published: March 2003

Variation in the nucleotide sequence of the mitochondrial control region (250 bp) and the cytochrome b region (870 bp) was examined in collared lemmings (Dicrostonyx groenlandicus) from 19 localities in northern Alaska and the Canadian Arctic. The division of D. groenlandicus in two phylogeographical groups with limited divergence across the Mackenzie River is consistent with the separation of this species in more than one refugial area located to the northwest of the Laurentide ice sheet during the last glaciation. Populations of D.groenlandicus from formerly glaciated areas are no less variable than those in nonglaciated areas. Instead, the low intrapopulation and intraregional diversity estimates in D. groenlandicus are probably a result of regional bottleneck events due to range contractions during Holocene warming events. These results are consistent with findings previously reported on collared lemmings (D. torquatus) from the Eurasian Arctic.
Comparison of microsatellites and amplified fragment length polymorphism markers for parentage analysis
Authors: Gerber S. , Mariette S. , Streiff R. , Bodénès C. , Kremer A.
Published: March 2003

This study compares the properties of dominant markers, such as amplified fragment length polymorphisms (AFLPs), with those of codominant multiallelic markers, such as microsatellites, in reconstructing parentage. These two types of markers were used to search for both parents of an individual without prior knowledge of their relationships, by calculating likelihood ratios based on genotypic data, including mistyping. Experimental data on 89 oak trees genotyped for six microsatellite markers and 159 polymorphic AFLP loci were used as a starting point for simulations and tests. Both sets of markers produced high exclusion probabilities, and among dominant markers those with dominant allele frequencies in the range 0.1–0.4 were more informative. Such codominant and dominant markers can be used to construct powerful statistical tests to decide whether a genotyped individual (or two individuals) can be considered as the true parent (or parent pair). Gene flow from outside the study stand (GFO), inferred from parentage analysis with microsatellites, overestimated the true GFO, whereas with AFLPs it was underestimated. As expected, dominant markers are less efficient than codominant markers for achieving this, but can still be used with good confidence, especially when loci are deliberately selected according to their allele frequencies.
Highly reliable genetic identification of individual northern hairy‐nosed wombats from single remotely collected hairs: a feasible censusing method
Authors: Sloane M. A. , Sunnucks P. , Alpers D. , Beheregaray L. B. , Taylor A. C.
Published: March 2003

The highly endangered northern hairy‐nosed wombat (Lasiorhinus krefftii) is extremely difficult to study in the wild, and its numbers correspondingly difficult to estimate. Disturbance to the animals caused by trapping and radio‐tracking may not only constitute an excessive risk to the population’s viability, but may also yield biased data. The results of a pilot study are presented, which clearly show noninvasive genotyping to be a highly feasible and reliable alternative censusing method forL. krefftii. The protocol can identify individual wombats from single hairs collected remotely at burrow entrances, using: (i) a panel of microsatellite markers giving individual‐specific genotypes; and (ii) a Y‐linked sexing marker in combination with a single‐copy X‐linked amplification control. Using just the eight most variable microsatellites (of 20 available), only one in 200 pairs of full‐sibs are predicted to share the same genotype. From 12 wombat hair samples collected on tape suspended over burrow entrances, three known female, two known male and an unknown wombat of each sex were identified. The approach will allow censusing of individuals that evade capture, and will also reveal some otherwise problematic aspects of the behaviour of this elusive animal.
Testing models of diversification in mice in the Abrothrix olivaceus/xanthorhinus complex in Chile and Argentina
Authors: Smith M. F. , Kelt D. A. , Patton J. L.
Published: March 2003

Samples of the forest‐dwelling mouse Abrothrix olivaceus and the steppe‐dwelling A. xanthorhinus across a transect between 45 and 47° S in southern Chile were analysed using the mitochondrial cytochrome b (cyt b) sequence, substantially adding to the data presented previously for these taxa from Argentina and Chile. The level of variation in the cyt b sequence throughout the entire olivaceus/xanthorhinus complex is comparable to that seen within a single species in many South American sigmodontine rodents, consistent with a previous conclusion that both taxa are sub‐species of A. olivaceus. Haplotypes of xanthorhinus have not yet achieved reciprocal monophyly relative to those of olivaceus. We evaluate competing hypotheses for the morphological divergence of xanthorhinus and olivaceus by allopatry in Pleistocene refuges versus postglacial diversification across ecological gradients. Two contrasting patterns are predicted for plots of the distribution of pairwise genetic differences, depending on whether the taxa diverged in allopatric refuges or through selection across a gradient. Examples of both modes of diversification are found in this complex.
Phylogeography and conservation of impala and greater kudu
Authors: Nersting Louise Grau , Arctander Peter
Published: March 2003

The phylogeography of the bush habituated African bovid species impala (Aepyceros melampus) and greater kudu (Tragelaphus strepsiceros) is investigated using mitochondrial DNA (mtDNA) markers. Combined analysis of individual lineages, relationships and population genetics suggest a colonization process from Southern Africa toward Eastern regions in the greater kudu. Results are less clear for the impala, although remaining consistent with a similar pattern of historical dispersion. The study reveals a similar pattern, that is a marked divergence of lineages from South‐western Africa relative to other regions. This pattern is opposed to previously published findings in other African bovid species. In the impala, the genetically isolated region is consistent with morphology because it is recognized as the subspecies A. m. petersi, the black‐faced impala. In contrast, the similar split of South‐western mitochondrial lineages was not expected in the greater kudu on the basis of morphology. Both species show a significant population genetic differentiation. Beyond their phylogeographical value, our results should raise conservation concerns about South‐western populations of both species. The black‐faced impala is categorized as vulnerable and our data show indications of hybridization with common impala A. m. melampus. The previously unrecognized genetic status of the South‐western kudus could also imply conservation regulations.
Immunological analysis of phloem sap of Bacillus thuringiensis corn and of the nontarget herbivore Rhopalosiphum padi (Homoptera: Aphididae) for the presence of Cry1Ab
Authors: Raps A. , Kehr J. , Gugerli P. , Moar W. J. , Bigler F. , Hilbeck A.
Published: March 2003

Phloem sap of transgenic Bacillus thuringiensis (Bt) corn expressing a truncated form of the B. thuringiensisδ‐endotoxin Cry1Ab, sap sucking aphids feeding on Bt corn and their honeydew were analysed for presence of Cry1Ab using ELISA. Phloem sap of Bt and non‐Bt corn was collected using a newly developed technique with a microcapillary being directly inserted into the phloem tubes. Using this technique, no Cry1Ab was detected in the phloem sap. In contrast, measurable concentrations of Cry1Ab in the range of 1 ppb were detected when phloem sap of pooled leaf samples was extracted using EDTA buffer. This was probably because of Cry1Ab toxin released from damaged cells. When analysing apterous adults of Rhopalosiphum padi L. and their honeydew, no Cry1Ab could be detected. In contrast, Cry1Ab was clearly detected in both larvae of the leaf chewing herbivore Spodoptera littoralis (Boisduval) and their faeces, showing that Cry1Ab is detectable after ingestion and excretion by herbivores. These results suggest that R. padi ingests or contains no or only very low concentrations of Cry1Ab in the range of the detection limit. In consequence it is hypothesized that R. padi as an important prey for beneficial insects in corn is unlikely to cause any harm to its antagonists due to mediating Bt toxin.
Speciation in rapidly diverging systems: lessons from Lake Malawi
Authors: Danley Patrick D. , Kocher Thomas D.
Published: March 2003

Rapid evolutionary radiations provide insight into the fundamental processes involved in species formation. Here we examine the diversification of one such group, the cichlid fishes of Lake Malawi, which have radiated from a single ancestor into more than 400 species over the past 700 000 years. The phylogenetic history of this group suggests: (i) that their divergence has proceeded in three major bursts of cladogenesis; and (ii) that different selective forces have dominated each cladogenic event. The first episode resulted in the divergence of two major lineages, the sand‐ and rock‐dwellers, each adapted to a major benthic macrohabitat. Among the rock‐dwellers, competition for trophic resources then drove a second burst of cladogenesis, which resulted in the differentiation of trophic morphology. The third episode of cladogenesis is associated with differentiation of male nuptial colouration, most likely in response to divergent sexual selection. We discuss models of speciation in relation to this observed pattern. We advocate a model, divergence with gene flow, which reconciles the disparate selective forces responsible for the diversification of this group and suggest that the nonadaptive nature of the tertiary episode has significantly contributed to the extraordinary species richness of this group.
Chloroplast microsatellites and mitochondrial nad1 intron 2 sequences indicate congruent phylogenetic relationships among Swiss stone pine (Pinus cembra), Siberian stone pine (Pinus sibirica), and Siberian dwarf pine (Pinus pumila)
Authors: Gugerli F. , Senn J. , Anzidei M. , Madaghiele A. , Büchler U. , Sperisen C. , Vendramin G. G.
Published: March 2003

We studied the phylogenetic relationships among the three stone pine species, Pinus cembra, P. sibirica, and P. pumila, using chloroplast microsatellites and mitochondrial nad1 intron 2 sequences. The three chloroplast microsatellite loci combined into a total of 18 haplotypes. Fourteen haplotypes were detected in 15 populations of P. cembra and one population of P. sibirica, five of which were shared between the two species, and the two populations of P. pumila comprised four species‐specific haplotypes. Mitochondrial intron sequences confirmed this grouping of species. Sequences of P. cembra and P. sibirica were identical, but P. pumila differed by several nucleotide substitutions and insertions/deletions. A repeat region found in the former two species showed no intraspecific variation. These results indicate a relatively recent evolutionary separation of P. cembra and P. sibirica, despite their currently disjunct distributions. The species‐specific chloroplast and mitochondrial markers of P. sibirica and P. pumila should help to trace the hybridization in their overlapping distribution area and to identify fossil remains with respect to the still unresolved postglacial re‐colonization history of these two species.
Molecular investigations in populations of Spartina anglica C.E. Hubbard (Poaceae) invading coastal Brittany (France)
Authors: Baumel A. , Ainouche M. L. , Levasseur J. E.
Published: March 2003

Spartina anglica is a classical example of recent alloploid speciation. It arose during the end of the nineteenth century in England by hybridization between the indigenous Spartina maritima and the introduced East‐American Spartina alterniflora. Duplication of the hybrid genome (Spartina × townsendii) gave rise to a vigorous allopolyploid involved in natural and artificial invasions on different continents. Spartina anglica was first recorded in France in 1906, and since then, it has spread all along the western French coast. Earlier studies revealed that native British populations display consistent morphological plasticity and lack of isozyme variation. In this paper, we use different molecular markers (randomly amplified polymorphic DNA, intersimple sequence repeats and restriction patterns from nuclear and chloroplast DNA sequences) to analyse the genetic patterns of the French populations of S. anglica. Our results show that French populations are mainly composed of one ‘major’ multilocus genotype. This genotype is identical to the first‐generation hybrid S. × townsendii from England. Losses of few markers from this genotype are observed but are restricted to a few populations from Brittany; it is likely that they appeared independently, subsequent to their introduction. In southern Brittany, no hybrids between S. anglica and S. maritima have been found where the two species co‐occur. All French populations of S. anglica display the same chloroplast DNA sequences as S. alterniflora, the maternal genome donor. These findings are consistent with a severe genetic bottleneck at the time of the species formation, as a consequence of a unique origin of the species. Both parental nuclear sequences are present in the allopolyploid populations, revealing that for the markers investigated, no extensive changes have occurred in this young species.
Glacial biogeography of North American coho salmon (Oncorhynchus kisutch)
Authors: Smith Christian T. , Nelson R. John , Wood Chris C. , Koop Ben F.
Published: March 2003

To study the glacial biogeography of coho we examined 20 microsatellite loci and mitochondrial DNA D‐loop sequence in samples from Alaska to California. Microsatellite data divided our samples among five biogeographic regions: (1) Alaska and northern coastal British Columbia; (2) the Queen Charlotte Islands; (3) the mainland coast of British Columbia and northern Washington State; (4) the Thompson River; and (5) Oregon and California. The D‐loop sequence data suggested three geographical regions: (1) Oregon and California; (2) the Thompson River; and (3) all the other sites north of the southern ice margin. Microsatellite data revealed no difference in the number of alleles in different regions, but mitochondrial DNA data revealed a cline of decreasing diversity from south to north. We suggest that the two signals presented by these different marker types illuminate two time frames in the history of this species. Endemic microsatellite diversity in Alaska and on the Queen Charlotte Islands provides evidence in favour of Fraser Glaciation refugia in these regions. The loss of mitochondrial variation from south to north suggests that one of the earlier, more extensive, Pleistocene glaciations eliminated coho from its northern range.
Statistical properties of population differentiation estimators under stepwise mutation in a finite island model
Authors: Balloux F. , Goudet J.
Published: March 2003

Microsatellite loci mutate at an extremely high rate and are generally thought to evolve through a stepwise mutation model. Several differentiation statistics taking into account the particular mutation scheme of the microsatellite have been proposed. The most commonly used is , which is independent of the mutation rate under a generalized stepwise mutation model.

and

are commonly reported in the literature, but often differ widely. Here we compare their statistical performances using individual‐based simulations of a finite island model. The simulations were run under different levels of gene flow, mutation rates, population number and sizes. In addition to the per locus statistical properties, we compare two ways of combining

over loci. Our simulations show that even under a strict stepwise mutation model, no statistic is best overall. All estimators suffer to different extents from large bias and variance. While

better reflects population differentiation in populations characterized by very low gene‐exchange,

gives better estimates in cases of high levels of gene flow. The number of loci sampled (12, 24, or 96) has only a minor effect on the relative performance of the estimators under study. For all estimators there is a striking effect of the number of samples, with the differentiation estimates showing very odd distributions for two samples.