bluuebunny/crossref_metadata_2025 huggingface dataset:
Characterization of root colonization profiles by a microcosm community of arbuscular mycorrhizal fungi using 25S rDNA‐targeted nested PCR
Authors: VAN TUINEN D. , JACQUOT E. , ZHAO B. , GOLLOTTE A. , GIANINAZZI‐PEARSON V.
Published: March 2003

The aim of the present work was to study colonization patterns in roots by different arbuscular mycorrhizal fungi developing from a mixed community in soil. As different fungi cannot be distinguished with certainty in planta on the basis of fungal structures, taxon‐discriminating molecular probes were developed. The 5′ end of the large ribosomal subunit containing the variable domains D1 and D2 was amplified by PCR from Glomus mosseae (BEG12), G. intraradices (LPA8), Gigaspora rosea (BEG9) and Scutellospora castanea (BEG1) using newly designed eukaryote‐specific primers. Sequences of the amplification products showed high interspecies variability and PCR taxon‐discriminating primers were designed to distinguish between each of these four fungi. A nested PCR, using universal eukaryotic primers for the first amplification and taxon‐discriminating primers for the second, was performed on individual trypan blue‐stained mycorrhizal root fragments of onion and leek, and root colonization by four fungi inoculated together in a microcosm experiment was estimated. More than one fungus was detected in the majority of root fragments and all four fungi frequently co‐existed within the same root fragment. Root colonization by G. mosseae and G. intraradices was similar from individual and mixed inoculum, whilst the frequency of S. castanea and Gig. rosea increased in the presence of the two Glomus species, suggesting that synergistic interactions may exist between some arbuscular mycorrhizal fungi.
Assessing hybridization in natural populations of Penstemon (Scrophulariaceae) using hypervariable intersimple sequence repeat (ISSR) bands
Authors: WOLFE ANDREA D. , XIANG QIU‐YUN , KEPHART SUSAN R.
Published: March 2003

Inferences regarding hybridization rely on genetic markers to differentiate parental taxa from one another. Intersimple sequence repeat (ISSR) markers are based on single‐primer PCR reactions where the primer sequence is derived from di‐ and trinucleotide repeats. These markers have successfully been used to assay genetic variability among cultivated plants, but have not yet been tested in natural populations. We used genetic markers generated from eight ISSR primers to examine patterns of hybridization and purported examples of hybrid speciation in Penstemon (Scrophulariaceae) in a hybrid complex involving P. centranthifolius, P. grinnellii, P. spectabilis and P. clevelandii. This hybrid complex has previously been studied using three molecular data sets (allozymes, and restriction‐site variation of nuclear rDNA and chloroplast DNA). These studies revealed patterns of introgression involving P. centranthifolius, but were unsuccessful in determining whether gene flow occurs among the other species, and support for hypotheses of diploid hybrid speciation was also lacking. In this study, we were able to fingerprint each DNA accession sampled with one to three ISSR primers and most accessions could be identified with a single primer. We found population‐ and species‐specific markers for each taxon surveyed. Our results: (i) do not support the hybrid origin of P. spectabilis; (ii) do support the hypothesis that P. clevelandii is a diploid hybrid species derived from P. centranthifolius and P. spectabilis; and (iii) demonstrate that pollen‐mediated gene flow via hummingbird vectors is prevalent in the hybrid complex.
Mitochondrial DNA phylogeography of European hedgehogs
Authors: SANTUCCI F. , EMERSON B. C. , HEWITT G. M.
Published: March 2003

European hedgehog populations belonging to Erinaceus europaeus and E. concolor have been investigated by mitochondrial DNA analysis. A 383 bp fragment of the cytochrome b gene has been sequenced and maximum parsimony and neighbour‐joining trees of Tamura–Nei genetic distance values have been constructed. Similar topologies have been produced by both methods, showing a deep divergence between E. europaeus and E. concolor and a further subdivision of each species into a western and an eastern clade. A comparison with previously published allozyme data is made, and concordant and discordant patterns are discussed. The influence of Pleistocene glaciations on the observed pattern of divergence is inferred.
Mapping the geographical distribution of genetic variation in the genusLensfor the enhanced conservation of plant genetic diversity
Authors: FERGUSON M. E. , FORD‐LLOYD B. V. , ROBERTSON L. D. , MAXTED N. , NEWBURY H. J.
Published: March 2003

Plant genetic resource conservation strategies, informed by an understanding of the geographical distribution of genetic variation within species, are likely to result in a wider representation of conserved diversity inex situgene banks andin situgenetic reserves. The main objective of this study was to map the geographical distribution of genetic variation, as revealed by randomly amplified polymorphic DNA (RAPDs), in four wild relatives of the cultivated lentil, namelyLens culinarisssp.orientalis, L. odemensis, L. ervoidesandL. nigricans. Areas of high diversity and unique diversity were located for each taxon, and regions where further germplasm collection was most likely to yield novel genetic variation were identified. There were centres of diversity forL. culinarisssp.orientalisin southeast Turkey and northwest Syria, and in south Syria and Jordan. A centre of diversity was found to exist in Sweida province, south Syria, forL. odemensis, and forL. ervoidesalong the coastal border region between Syria and Turkey stretching down along the Syrian coast. There was a centre of diversity forL. nigricansin west Turkey. Analytical techniques previously used at the species level were found to be useful at the genotypic level to objectively target areas for future collection missions, to increase diversity inex situcollections and to target areas forin situconservation.
Random amplified polymorphic DNA (RAPD) analysis reveals extensive natural chimerism in a marine protochordate
Authors: Dorothea Sommerfeldt  , Bishop John D. D.
Published: March 2003

Random amplified polymorphic DNA (RAPD) analysis was applied to individual modules (zooids) of a colonial ascidian to investigate the presence and extent of chimerism, the parabiotic association of different genetic entities. The technique proved to be rapid and efficient for distinguishing different genotypes present in a colony, and revealed genetic mosaicism in wild material, as well as in laboratory cultures following planned fusion. Approximately one‐third of colonies in the natural population studied possessed multiple genotypes, presumably as the result of fusion of different colonies. Furthermore, individual zooids of different genetic origin often intermingled after colony fusion, spreading each genotype throughout a larger total area.
Estimating genetic drift and effective population size from temporal shifts in dominant gene marker frequencies
Authors: Jorde P. E. , Palm S. , Ryman N.
Published: March 2003

Measurement of temporal change in allele frequencies represents an indirect method for estimating the genetically effective size of populations. When allele frequencies are estimated for gene markers that display dominant gene expression, such as, e.g. random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) markers, the estimates can be seriously biased. We quantify bias for previous allele frequency estimators and present a new expression that is generally less biased and provides a more precise assessment of temporal allele frequency change. We further develop an estimator for effective population size that is appropriate when dealing with dominant gene markers. Comparison with estimates based on codominantly expressed genes, such as allozymes or microsatellites, indicates that about twice as many loci or sampled individuals are required when using dominant markers to achieve the same precision.
DNA fingerprinting reveals polygyny in the subterranean rodent Ctenomys talarum
Authors: Zenuto Roxana R. , Lacey Eileen A. , Busch Cristina
Published: March 2003

DNA fingerprinting was used to characterize patterns of paternity in two populations of Ctenomys talarum from Buenos Aires Province, Argentina. The multilocus probe PV47–2 was used to detect variation in genomic DNA extracted from 12 females, their 32 offspring, and 14 putative sires. For 11 out of 12 litters examined, a single male capable of providing all nonmaternal bands was identified. Within each study population, individual males sired more than one litter, suggesting that C. talarum is polygynous. No evidence of multiple paternity of litters was found. High band‐sharing values among females suggest that further research is needed to assess the population genetic structure of this species.
The use of genetic markers in the identification and characterization of three recently discovered populations of a threatened plant species
Authors: Martín C. , González‐Benito M. E. , Iriondo J. M.
Published: March 2003

Erodium paularense Fern. Gonz. & Izco (Geraniaceae) is a perennial, narrow endemic species of central Spain. Recently, three new populations have been found 160 km northwest of the first site, although the taxonomic status of the new populations has not yet been published. Random amplified polymorphic DNA (RAPD) markers were used to confirm that the new populations belong to E. paularense, and to evaluate the genetic diversity among individuals, populations and regions. The two regions were clearly differentiated through
upgma, whereas significant φST distances between all pairs of populations were obtained by
amova. Genetic distances between populations were partially explained by geographical distances. The clear genetic differentiation among regions, on top of the geographical distance and differences in geological substratum, supports a taxonomical discrimination of the regions at a subspecific level.
Mitochondrial phylogeography of the European pond turtle, Emys orbicularis (Linnaeus 1758)
Authors: Lenk P. , Fritz U. , Joger U. , Wink M.
Published: March 2003

The phylogeny and phylogeography of Emys orbicularis was inferred from mitochondrial nucleotide sequences of the cytochrome b gene analysed by DNA sequencing and RNA heteroduplex analysis. Within the family Emydidae the monotypic genus Emys is affiliated with the nearctic taxa Emydoidea blandingii and Clemmys marmorata. The analysis of 423 individuals of E. orbicularis, originating throughout its distribution range, revealed a remarkable intraspecific differentiation in 20 different haplotypes with distinct geographical ranges. Maximum parsimony analysis produced a star‐like phylogeny with seven main lineages which may reflect separations in the late Pliocene. The haplotype distribution examined by partial Mantel tests and analysis of molecular variance revealed a substantial effect of glacial periods. This historical perspective suggests the existence of multiple glacial refugia and considerable Holocene range expansion which was modulated by climatic traits. Further support is gained for the occurrence of long‐term parapatry in glacial refugia.
Disparate phylogeographic patterns of molecular genetic variation in four closely related South American small cat species
Authors: Johnson Warren E. , Slattery Jill Pecon , Eizirik Eduardo , Kim Jae‐Heup , Menotti Raymond Marilyn , Bonacic Cristian , Cambre Richard , Crawshaw Peter , Nunes Adauto , Seuánez Héctor N. , Martins Moreira Miguel Angelo , Seymour Kevin L. , Simon Faiçal , Swanson William , O’Brien Stephen J.
Published: March 2003

Tissue specimens from four species of Neotropical small cats (Oncifelis geoffroyi, N = 38; O. guigna, N = 6; Leopardus tigrinus, N = 32; Lynchailurus colocolo, N = 22) collected from throughout their distribution were examined for patterns of DNA sequence variation using three mitochondrial genes, 16S rRNA, ATP8, and NADH‐5. Patterns between and among O. guigna and O. geoffroyi individuals were assessed further from size variation at 20 microsatellite loci. Phylogenetic analyses using mitochondrial DNA sequences revealed monophyletic clustering of the four species, plus evidence of natural hybridization between L. tigrinus and L. colocolo in areas of range overlap and discrete population subdivisions reflecting geographical isolation. Several commonly accepted subspecies partitions were affirmed for L. colocolo, but not for O. geoffroyi. The lack of geographical substructure in O. geoffroyi was recapitulated with the microsatellite data, as was the monophyletic clustering of O. guigna and O. geoffroyi individuals. L. tigrinus forms two phylogeographic clusters which correspond to L.t. oncilla (from Costa Rica) and L.t. guttula (from Brazil) and which have mitochondrial DNA (mtDNA) genetic distance estimates comparable to interspecific values between other ocelot lineage species. Using feline‐specific calibration rates for mitochondrial DNA mutation rates, we estimated that extant lineages of O. guigna diverged 0.4 million years ago (Ma), compared with 1.7 Ma for L. colocolo, 2.0 Ma for O. geoffroyi, and 3.7 Ma for L. tigrinus.
Captive breeding, reintroduction, and the conservation genetics of black and white ruffed lemurs, Varecia variegata variegata
Authors: Wyner Yael M. , Amato George , DeSalle Rob
Published: March 2003

A character‐based phylogenetic species concept approach was used to examine conservation unit status for three wild populations of black and white ruffed lemurs, Varecia vareigata variegata, from Betampona (N = 3), Manombo (N = 6), and Ranomafana (N = 14), Madagascar. Population aggregation analysis was performed on 548 bp from the control region (D‐loop) of the mitochondrial DNA (mtDNA). Twenty‐one diagnostic sites were found to differentiate the Betampona (northern) population from the Manombo/Ranomafana (southern) populations. Additionally, individuals from the North American captive population (N = 11) and from Parc Ivoloina, Madagascar (N = 6) were examined for the same mtDNA fragment. The captive animals more closely resembled the southern populations and the Parc Ivoloina animals were more similar to the northern population. However, the inclusion of these ex situ animals reduced the number of diagnostic sites differentiating the northern and southern populations. Our genetic data were used to assess the ongoing management strategy for reintroducing individuals into the Betampona population and for introducing new founders into the ex situ population. This study demonstrates the utility of combining genetic information with a consideration of conservation priorities in evaluating the implementation of management strategies.
Nuclear DNA microsatellite analysis of genetic diversity and gene flow in the Scandinavian brown bear (Ursus arctos)
Authors: Waits Lisette , Taberlet Pierre , Swenson Jon E. , Sandegren Finn , Franzén Robert
Published: March 2003

In the 1930s, the Scandinavian brown bear was close to extinction due to vigorous extermination programmes in Norway and Sweden. Increased protection of the brown bear in Scandinavia has resulted in the recovery of four subpopulations, which currently contain close to 1000 individuals. Effective conservation and management of the Scandinavian brown bear requires knowledge of the current levels of genetic diversity and gene flow among the four subpopulations. Earlier studies of mitochondrial DNA (mtDNA) diversity revealed extremely low levels of genetic variation, and population structure that grouped the three northern subpopulations in one genetic clade and the southernmost subpopulation in a second highly divergent clade. In this study, we extended the analysis of genetic diversity and gene flow in the Scandinavian brown bear using data from 19 nuclear DNA microsatellite loci. Results from the nuclear loci were strikingly different than the mtDNA results. Genetic diversity levels in the four subpopulations were equivalent to diversity levels in nonbottlenecked populations from North America, and significantly higher than levels in other bottlenecked and isolated brown bear populations. Gene flow levels between subpopulations ranged from low to moderate and were correlated with geographical distance. The substantial difference in results obtained using mtDNA and nuclear DNA markers stresses the importance of collecting data from both types of genetic markers before interpreting data and making recommendations for the conservation and management of natural populations. Based on the results from the mtDNA and nuclear DNA data sets, we propose one evolutionarily significant unit and four management units for the brown bear in Scandinavia.
Microsatellite and mitochondrial DNA polymorphism reveals life‐history dependent interbreeding between hatchery and wild brown trout (Salmo truttaL.)
Authors: Hansen Michael M. , Ruzzante Daniel E. , Nielsen Einar E. , Mensberg Karen‐lise D.
Published: March 2003

The effects of stocking hatchery trout into wild populations were studied in a Danish river, using microsatellite and mitochondrial DNA (mtDNA) markers. Baseline samples were taken from hatchery trout and wild trout assumed to be unaffected by previous stocking. Also, samples were taken from resident and sea trout from a stocked section of the river. Genetic differentiation between the hatchery strain and the local wild population was modest (microsatelliteFST = 0.06). Using assignment tests, more than 90% of individuals from the baseline samples were classified correctly. Assignment tests involving samples from the stocked river section suggested that the contribution by hatchery trout was low among sea trout (< 7%), but high (46%) among resident trout. Hybrid index analysis and a high percentage of mtDNA haplotypes specific to indigenous trout observed among resident trout that were assigned to the hatchery strain suggested that interbreeding took place between hatchery and wild trout. The latter result also indicated that male hatchery trout contributed more to interbreeding than females. We suggest that stronger selection acts against stocked hatchery trout that become anadromous compared to hatchery trout that become resident. As most resident trout are males this could also explain why gene flow from hatchery to wild trout appeared to be male biased. The results show that even despite modest differentiation at neutral loci domesticated trout may still perform worse than local populations and it is important to be aware of differential survival and reproductive success both between life‐history types and between sexes.
Spatial and temporal distribution of chloroplast DNA polymorphism in a tropical tree species
Authors: Caron H. , Dumas S. , Marque G. , Messier C. , Bandou E. , Petit R. J. , Kremer A.
Published: March 2003

The level and the spatial organization of chloroplast DNA polymorphism were investigated in Dicorynia guianensis Hamshoff (Caesalpiniaceae) at different spatial and temporal scales. D. guianensis is a canopy tree of the rain forest that is distributed throughout the Guiana plateau in small aggregates. Twelve different haplotypes were identified using restriction analysis of polymerase chain reaction (PCR) amplified fragments of the chloroplast genome. When populations from different areas of French Guiana were compared, a clear geographical pattern of haplotype frequencies was identified along the Atlantic coast. This pattern is most likely the result of the restriction–expansion dynamics of the tropical forest during the Quaternary. At the local level, D. guianensis was characterized by a high level of within population diversity. Maintenance of within population diversity results from the dynamics of the aggregates; stochastic demography associated with the turnover of aggregates generates genetic differentiation among them. At the stand level, a strong spatial aggregation of haplotypes persisted from the adult to the seedling cohort indicating limited seed flow. There was also a strong difference in levels of diversity between the cohorts which suggested that recruitment over several years is needed in order to maintain genetic diversity during regeneration.
Extra‐pair paternity in waved albatrosses
Authors: Huyvaert Kathryn P. , Anderson David J. , Jones Thomas C. , Duan Wenrui , Parker Patricia G.
Published: March 2003

We estimated the rate of extra‐pair fertilizations (EPFs) in waved albatrosses (Phoebastria irrorata) on Isla Española, Galápagos, Ecuador, using multilocus minisatellite DNA fingerprinting. Waved albatrosses are socially monogamous, long‐lived seabirds whose main population is on Española. Aggressive extra‐pair copulation (EPC) attempts have been observed in the breeding colony during the days preceding egg‐laying. Our genetic analyses of 16 families (single chicks and their attending parents) revealed evidence of EPFs in four families. In all cases males were the excluded parent. These data suggest that waved albatrosses have an unusually high rate of EPF relative to taxa with similar life histories. Future behavioural observations will determine the extent to which forced vs. unforced EPCs contribute to this high EPF rate.
Phylogeography of colonially nesting seabirds, with special reference to global matrilineal patterns in the sooty tern (Sterna fuscata)
Authors: Avise John C. , Nelson William S. , Bowen Brian W. , Walker Deette
Published: March 2003

Sooty tern (Sterna fuscata) rookeries are scattered throughout the tropical oceans. When not nesting, individuals wander great distances across open seas, but, like many other seabirds, they tend to be site‐faithful to nesting locales in successive years. Here we examine the matrilineal history of sooty terns on a global scale. Assayed colonies within an ocean are poorly differentiated in mitochondrial DNA sequence, a result indicating tight historical ties. However, a shallow genealogical partition distinguishes Atlantic from Indo‐Pacific rookeries. Phylogeographic patterns in the sooty tern are compared to those in other colonially nesting seabirds, as well as in the green turtle (Chelonia mydas), an analogue of tropical seabirds in some salient aspects of natural history. Phylogeographic structure within an ocean is normally weak in seabirds, unlike the pronounced matrilineal structure in green turtles. However, the phylogeographic partition between Atlantic and Indo‐Pacific rookeries in sooty terns mirrors, albeit in shallower evolutionary time, the major matrilineal subdivision in green turtles. Thus, global geology has apparently influenced historical gene movements in these two circumtropical species.
A molecular analysis of ground sloth diet through the last glaciation
Authors: Hofreiter M. , Poinar H. N. , Spaulding W. G. , Bauer K. , Martin P. S. , Possnert G. , Pääbo S.
Published: March 2003

DNA was extracted from five coprolites, excavated in Gypsum Cave, Nevada and radiocarbon dated to approximately 11 000, 20 000 and 28 500 years bp. All coprolites contained mitochondrial DNA sequences identical to a DNA sequence determined from a bone of the extinct ground sloth Nothrotheriops shastensis. A 157‐bp fragment of the chloroplast gene for the large subunit of the ribulosebisphosphate carboxylase (rbcL) was amplified from the boluses and several hundred clones were sequenced. In addition, the same DNA fragment was sequenced from 99 plant species that occur in the vicinity of Gypsum Cave today. When these were compared to the DNA sequences in GenBank, 69 were correctly (two incorrectly) assigned to taxonomic orders. The plant sequences from the five coprolites as well as from one previously studied coprolite were compared to rbcL sequences in GenBank and the contemporary plant species. Thirteen families or orders of plants that formed part of the diet of the Shasta ground sloth could be identified, showing that the ground sloth was feeding on trees as well as herbs and grasses. The plants in the boluses further indicate that the climate 11 000 years bp was dryer than 20 000 and 28 500 years bp. However, the sloths seem to have visited water sources more frequently at 11 000 bp than at earlier times.
Nested clade analysis of the freshwater shrimp, Caridina zebra (Decapoda: Atyidae), from north‐eastern Australia
Authors: Hurwood David A. , Hughes Jane M.
Published: March 2003

The freshwater shrimp, Caridina zebra, is endemic to montane rainforest streams of the Atherton Tableland, north‐eastern Australia. As the confluences of many of the headwater streams are in unsuitable habitat, dispersal is expected to be highly restricted. Results from a previous allozyme survey for this species suggested that historical dispersal between separate river drainages had occurred due to rearrangements of the drainage lines at some stage in the recent past. The aim of this study was to use temporal information from the mitochondrial cytochrome oxidase subunit I (CO‐I) gene to determine whether the observed genetic structure was a result of historical processes, or alternatively, due to low levels of terrestrial dispersal. The mitochondrial DNA (mtDNA) data were analysed using nested clade analysis, which can differentiate between historical fragmentation and range expansion vs. contemporary restricted gene flow. The results displayed three divergent clades that were likely to have arisen in allopatry. One widespread clade, with individuals in more than one river drainage, reflected a pattern of restricted gene flow. This suggests that this species is capable of terrestrial dispersal.
Small genets of Lactarius xanthogalactus, Russula cremoricolor and Amanita francheti in late‐stage ectomycorrhizal successions
Authors: Redecker Dirk , Szaro Timothy M. , Bowman Ryan J. , Bruns Thomas D.
Published: March 2003

We determined the size of genets of late‐stage ectomycorrhizal fungi in field sites in coastal Northern California. Basidiocarps were collected, mapped and subjected to genetic fingerprinting using amplified fragment length polymorphisms (AFLPs). The minimum size estimates for the largest genets of Amanita francheti, Lactarius xanthogalactus and Russula cremoricolor were 1.5, 9.3 and 1.1 m2, respectively. The molecular markers also showed that R. cremoricolor is dimorphic, with red‐ and white‐capped morphotypes of this species forming a continuous population. Our results suggest that spore propagation plays a much more important role in the life history of the Russulaceae in undisturbed forest settings than previously recognized. Fungi appearing late in the succession sequence and systems without obvious disturbance therefore do not necessarily colonize primarily by mycelium.
Microsatellite analysis of the inbreeding grass weed Barren Brome (Anisantha sterilis) reveals genetic diversity at the within‐ and between‐farm scales
Authors: Green J. M. , Barker J. H. A. , Marshall E. J. P. , Froud‐Williams R. J. , Peters N. C. B. , Arnold G. M. , Dawson K. , Karp A.
Published: March 2003

Nine microsatellites were used to screen 131 samples of Barren Brome (Anisantha sterilis: synonym Bromus sterilis) collected from within the fields of three English farms [from Oxfordshire (Oxon), Leicestershire (Leics) and Wiltshire (Wilts)] and eight seeds taken from samples of each of 10 farms across England, UK. Most individuals (~97%) were homozygous. Polymorphism occurred at all nine loci in all three farms sampled at the field scale, and at most loci for nine of the other 10 farm samples. Between three and 11 alleles were found per locus. Gene diversity (D = 1 − ∑pi2) ranged from 0.088 to 0.760. Polymorphism occurred among individuals within and among fields, and farms. Some alleles were found in only one farm. On the basis of the alleles at all nine loci in the 211 sampled plants, a total of 92 (44%) different genotypes was identified. Clustering analysis using the unweighted pair group method with arithmetic averages (upgma) for the combined Oxon, Wilts and Leics samples did not cluster them into their respective farms. Similarly, a phenogram of samples from all 10 farms showed considerable mixing of individuals with respect to farm origins. Identification of genotypes on field plans showed evidence of both spatial localization and mixing. Previous reports have suggested that A. sterilis is strictly inbreeding with little intrapopulation variation at the genetic level. Our data reveal that A. sterilis exists as numerous separate and genetically different lines, which are maintained by inbreeding but which very occasionally outcross. Possible explanations for this pattern of high genetic diversity are discussed.
Haplotype (mtDNA) diversity of brown trout Salmo trutta in tributaries of the Austrian Danube: massive introgression of Atlantic basin fish — by man or nature?
Authors: Weiss S. , Schlötterer C. , Waidbacher H. , Jungwirth M.
Published: March 2003

Mitochondrial haplotype diversity in 27 populations of brown trout, Salmo trutta L., in Austria was investigated by sequencing the 5′ end of the mitochondrial DNA (mtDNA) control region. Although all populations are within the Danube drainage, 44% of all individuals carried Atlantic basin haplotypes. It is argued that the presence of these haplotypes in Austria primarily reflects introgression stemming from the stocking of hatchery‐reared fish. However, several lines of evidence suggest that some natural colonization from Atlantic lineages may have contributed to the present haplotype diversity. Nonetheless, the more diverse Danubian clade is represented by regionally distinct haplotype diversity that should be protected from the continued introduction of domesticated strains of exogenous fish.
Mitochondrial phylogeography and population history of pine martens Martes martes compared with polecats Mustela putorius
Authors: Davison Angus , Birks Johnny D. S. , Brookes Rachael C. , Messenger John E. , Griffiths Huw I.
Published: March 2003

The flora and fauna of Europe are linked by a common biogeographic history, most recently the Pleistocene glaciations that restricted the range of most species to southern refugial populations. Changes in population size and migration, as well as selection, have all left a signature on the genetic differentiation. Thus, three paradigms of postglacial recolonization have been described, inferred from the patterns of DNA differentiation. Yet some species, especially wide‐ranging carnivores, exhibit little population structuring between the proposed refugia, although relatively few have been studied due to the difficulty of obtaining samples. Therefore, we investigated mitochondrial variation in pine martens, Martes martes, in order to understand the extent to which they were affected by glacial cycles, and compared the results with an analysis of sequences from polecats, Mustela putorius. A general lack of ancient lineages, and a mismatch distribution that is consistent with an expanding population, is evidence that the present‐day M. martes and Mu. putorius in central and northern Europe colonized from a single European refugium following a recent glaciation. There has also been interspecific mitochondrial introgression between M. martes and the sable M. zibellina in Fennoscandia.
Comparative analysis of population structure across environments and geographical scales at major histocompatibility complex and microsatellite loci in Atlantic salmon (Salmo salar)
Authors: Landry Christian , Bernatchez Louis
Published: March 2003

Evidence of selection acting on major histocompatibility complex (MHC) genes has been illustrated with the analysis of their nucleotide sequences and allele frequency distribution. Comparing the patterns of population differentiation at neutral markers and MHC genes in the wild may provide further insights about the relative role of selection and neutrality in shaping their diversity. In this study, we combine both methods to assess the role of selection on a MHC gene in Atlantic salmon. We compare variation at a MHC class II B locus and microsatellites among 14 samples from seven different rivers and seven subpopulations within a single river system covering a variety of habitats and different geographical scales. We show that diversifying selection is acting on the sites involved in antigen presentation and that balancing selection maintains a high level of polymorphism within populations. Despite important differences in habitat type, the comparison of the population structure at MHC and microsatellites on large geographical scales reveals a correlation between patterns of differentiation, indicating that drift and migration have been more important than selection in shaping population differentiation at the MHC locus. In contrast, strong discrepancies between patterns of population differentiation at the two types of markers provides support for the role of selection in shaping population structure within rivers. Together, these results confirm that natural selection is influencing MHC gene diversity in wild Atlantic salmon although neutral forces may also be important in their evolution.
Population structure of an endangered species living in contrasted habitats: Parnassia palustris (Saxifragaceae)
Authors: Bonnin Isabelle , Colas Bruno , Bacles Cécile , Holl Anne‐Catherine , Hendoux Frédéric , Destiné Benoit , Viard Frédérique
Published: March 2003

In endangered species, it is critical to analyse the level at which populations interact (i.e. dispersal) as well as the levels of inbreeding and local adaptation to set up conservation policies. These parameters were investigated in the endangered species Parnassia palustris living in contrasted habitats. We analysed population structure in 14 populations of northern France for isozymes, cpDNA markers and phenotypic traits related to fitness. Within population genetic diversity and inbreeding coefficients were not correlated to population size. Populations seem not to have undergone severe recent bottleneck. Conversely to pollen migration, seed migration seems limited at a regional scale, which could prevent colonization of new sites even if suitable habitats appear. Finally, the habitat type affects neither within‐population genetic diversity nor genetic and phenotypic differentiation among populations. Thus, even if unnoticed local adaptation to habitats exists, it does not influence gene flow between populations.
Evaluating the effect of stage‐specific survivorship on the Ne/N ratio
Authors: Waples Robin S.
Published: March 2003

Evaluating effective population size (Ne) and the effective size to census size ratio (Ne/N) in species with Type III survivorship curves is complicated when key demographic parameters [mean (k̄) and variance (Vk) of family size] are measured during early life stages. The method of Crow & Morton (1955) for scaling demographic data collected at a juvenile stage to expected values at adulthood is extended to consider sequential episodes of random and family correlated survival. Results show the following: (i) The order in which the episodes of random and family‐correlated survival occur does not affect Ne or Ne/N; (ii) If a population experiences an episode of family‐correlated survival, Ne/N scaled to its expected value in a population of constant size (k̄ = 2) is simply the survival rate during the family‐correlated stage. If multiple such stages occur, scaled Ne/N is the product of the survivals during all family‐correlated life stages; (iii) Under the assumption of random post‐enumeration survival, adjusting the variance effective size to its expected value at k̄ = 2 is equivalent to computing the inbreeding effective size at the earlier life stage. Application to experimental data for hatchery populations of Pacific salmon (Oncorhynchus spp.) indicates that nonrandom survival during the marine phase led to estimated reductions in effective size of 0–62% (mean 19%) in 12 different cohorts. This approach can provide insights into Ne/N in highly fecund species, including some marine species in which Ne has been estimated to be several orders of magnitude less than N.
Evolution on oceanic islands: molecular phylogenetic approaches to understanding pattern and process
Authors: Emerson B. C.
Published: March 2003

By their very nature oceanic island ecosystems offer great opportunities for the study of evolution and have for a long time been recognized as natural laboratories for studying evolution owing to their discrete geographical nature and diversity of species and habitats. The development of molecular genetic methods for phylogenetic reconstruction has been a significant advance for evolutionary biologists, providing a tool for answering questions about the diversity among the flora and fauna on such islands. These questions relate to both the origin and causes of species diversity both within an archipelago and on individual islands. Within a phylogenetic framework one can answer fundamental questions such as whether ecologically and/or morphologically similar species on different islands are the result of island colonization or convergent evolution. Testing hypotheses about ages of the individual species groups or entire community assemblages is also possible within a phylogenetic framework. Evolutionary biologists and ecologists are increasingly turning to molecular phylogenetics for studying oceanic island plant and animal communities and it is important to review what has been attempted and achieved so far, with some cautionary notes about interpreting phylogeographical pattern on oceanic islands.
The highly cross‐fertile coral species,Acropora hyacinthusandAcropora cytherea, constitute statistically distinguishable lineages
Authors: Márquez L. M. , Van Oppen M. J. H. , Willis B. L. , Reyes A. , Miller D. J.
Published: March 2003

A major challenge for understanding the evolutionary genetics of mass‐spawning corals is to explain the maintenance of discrete morphospecies in view of high rates of interspecific fertilizationin vitroand nonmonophyletic patterns in molecular phylogenies. In this study, we focused onAcropora cythereaandA. hyacinthus, which have one of the highest potentials for interspecific fertilization. Using sequences of a nuclear intron, we performed phylogenetic and nested clade analyses (NCA). Both species were polyphyletic in molecular phylogenies, but the NCA indicated that they constitute statistically distinguishable lineages. Phylogenetic analysis using an intergenic region of the mitochondrial DNA (mtDNA), was inconclusive because of low levels of variability in this marker. The position of these two species differed between the nuclear DNA (nDNA) and mtDNA phylogenies and was also at odds with a cladistic analysis based on morphology. We conclude that despite the potential for high levels of hybridization and introgression,A. cythereaandA. hyacinthusconstitute statistically distinguishable lineages and their taxonomic status is consistent with the cohesion species concept.
Gender and viability selection on morphology in fledgling pied flycatchers
Authors: Potti J. , Dávila J. A. , Tella J. L. , Frías Ó. , Villar S.
Published: March 2003

Until recently, analyses of gender‐dependent differences in viability selection and the ontogeny of sexual size dimorphism have been plagued by difficulties in determining the sex of nestling birds on the basis of morphology. Recently, this problem was overcome using molecular sex identification to report for the first time body‐size‐mediated antagonistic selection on the viability of male and female collared flycatchers. We used molecular sex identification to analyse natural selection on fledgling viability, sexual size dimorphism and effects of parasites in relation to gender in a Mediterranean population of the related pied flycatcherFicedula hypoleuca. There was directional positive selection on fledgling weight but no selection on tarsus length. Fledgling weight was the most important determinant of fledgling survival, with heavier fledglings having increased viability. Although selective trends were of the same sign for both sexes, only among female fledglings were selection differentials and gradients statistically significant. Therefore, similar trends in selection were revealed in analyses of a data set where sex was ignored and in separate analyses using same‐sex sibship trait means. Mite nest ectoparasites negatively affected fledgling weight, and the effects were stronger in female than male fledglings. There was no effect of parasitism on the tarsus length in males, as previously reported in retrospective analyses performed without knowledge of sex until recruitment. Overall, selection on fledgling viability on the basis of morphological traits and hatching date was not confounded by an individual's gender.
High levels of genetic monogamy in the group‐living Australian lizardEgernia stokesii
Authors: Gardner M. G. , Bull C. M. , Cooper S. J. B.
Published: March 2003

The Australian lizardEgernia stokesiilives in spatially and temporally stable groups of up to 17 individuals. We have recently shown that these groups are comprised of breeding partners, their offspring and, in some cases, highly related adults, providing the first genetic evidence of a family structure in any lizard species. Here we investigated the mating system ofE. stokesiiusing data from up to eight polymorphic microsatellite loci and tested the hypothesis that breeding partners are monogamous both within and between mating seasons. Among 16 laboratory‐born litters from field collected gravid females from two sites in South Australia, 75% had a single male parent and no male contributed to more than one litter, indicating a high level of genetic monogamy within a season. Additional analyses of field caught individuals, captured between 1994 and 1998, enabled assignment of parentage for 70 juveniles and subadults. These data showed that most young (88.6%) had both parents from within the same group and that high proportions of males (88.9%) and females (63.6%) have multiple cohorts of offspring only with the same partner. Our results suggest that monogamy both within and between seasons is a common mating strategy ofE. stokesiiand that breeding partners maintain stable associations together and with multiple cohorts of their offspring over periods of up to at least 5 years.
Likely multiple origins of a diploid hybrid sunflower species
Authors: Schwarzbach A. E. , Rieseberg L. H.
Published: March 2003

The recurrent origin of diploid hybrid species is theoretically improbable because of the enormous diversity of hybrid genotypes generated by recombination. Recent greenhouse experiments, however, indicate that the genomic composition of hybrid lineages is shaped in part by deterministic forces, and that recurrent diploid hybrid speciation may be more feasible than previously believed. Here we use patterns of variation from chloroplast DNA (cpDNA), nuclear microsatellite loci, cross‐viability and chromosome structure to assess whether a well‐characterized diploid hybrid sunflower species,Helianthus anomalus, was derived on multiple occasions from its parental species,H. annuusandH. petiolaris. Chloroplast DNA and crossability data were most consistent with a scenario in whichH. anomalusarose three times: three differentH. anomalusfertility groups were discovered, each with a unique cpDNA haplotype. In contrast, there was no clear signature of multiple, independent origins from the microsatellite loci. Given the age ofH. anomalus(> 100 000 years bp), it may be that microsatellite evidence for recurrent speciation has been eroded by mutation and gene flow through pollen.
Population genetic structure of the cyclic snowshoe hare (Lepus americanus) in southwestern Yukon, Canada
Authors: Burton Cole , Krebs Charles J. , Taylor Eric B.
Published: March 2003

Spatial population structure has important ecological and evolutionary consequences. Little is known about the population structure of snowshoe hares (Lepus americanus), despite their ecological importance in North American boreal forests. We used seven variable microsatellite DNA loci to determine the spatial genetic structure of snowshoe hares near Kluane Lake, Yukon during a cyclic population peak. We sampled 317 hares at 12 sites separated by distances ranging from 3 to 140 km, and used 46 additional samples from Alaska and Montana. The level of genetic variation was high (13.4 alleles/locus, 0.67 expected heterozygosity) and the distribution of alleles and genotypes was not homogeneous across the sites. The degree of differentiation was low among Yukon sites (FST = 0.015) and between Yukon and Alaska (FST = 0.012), but the Montana site was highly differentiated (FST = 0.20). A weak pattern of isolation by distance was found over the Yukon study area, with an indication that local genetic drift may be important in shaping the regional genetic structure. Landscape barriers expected to influence gene flow did not consistently affect genetic structure, although there was evidence for a partial barrier effect of Kluane Lake. The high level of inferred gene flow confirms that snowshoe hare dispersal is widespread, successful and equal between the sexes. A stepping‐stone model of gene flow, potentially influenced by the synchronous density cycle, appears to best explain the observed genetic structure. Our results suggest that despite their dramatic fluctuations in density, snowshoe hares in the northern boreal forest have a large evolutionary effective population size and are not strongly subdivided by either physical or social barriers to gene flow.
Mitochondrial and nuclear DNA phylogeography of Thymallus spp. (grayling) provides evidence of ice‐age mediated environmental perturbations in the world's oldest body of fresh water, Lake Baikal
Authors: Koskinen Mikko T. , Knizhin Igor , Primmer Craig R. , Schlötterer Christian , Weiss Steven
Published: March 2003

Theories on the hydrological history of Lake Baikal, the world's oldest and deepest body of freshwater, and its surrounding great rivers, are currently based solely on geological evidence and are conflicting. Baikal is inhabited by numerous zoogeographical enigmas but their high level of endemism has hindered phylogeographic inferences. We provide a biological perspective of the region's palaeo‐hydrological development based on the demographic and genealogical history of the widespread Thymallus spp. (grayling). Phylogenetic reconstruction reveals that old lineages of grayling (pre‐Pleistocene) currently inhabit the Enisey, Lena and Amur River basins. For Lake Baikal however, we conclude that a mid‐Pleistocene colonization (110 000–450 000 years ago) of an unoccupied niche has occurred. Population genetic inferences support an Enisey–Angara river route of colonization into Baikal, corresponding to the cataclysmic palaeo‐hydrological event that led to the formation of the lake's only contemporary outlet, and a subsequent range expansion several thousand kilometres into the uppermost reaches of the Selenga River basin. The evolutionary history of Lake Baikal grayling is congruent with the controversial hypothesis of repeated glaciation. However, considering the extraordinary levels of endemism and proposed Miocene or Oligocene coalescence of other faunal lineages, a less profound but equally consequential cycle of environmental perturbations may have taken place. Bi‐parentally inherited microsatellite DNA loci supported the phylogenetic relationships of Thymallus spp. and the geographical expansion of Baikal grayling strikingly well. A Markov Chain Monte Carlo modelling approach suggested severe contemporary population decline during the last century, possibly reflecting the influence of an uncontrolled fishery on this treasured ecosystem. These complementary pictures of the demographic history of grayling underscore the breadth of historical inquiry that can be entertained through the modelling of sufficient molecular data, and may significantly alter the zoogeographical and limnological perspectives of Baikal's history.