| 1. |
- Bensch, Staffan, et al.
(författare)
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Amplified fragment length polymorphism analysis identifies hybrids between two subspecies of warblers.
- 2002
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 11:3, s. 473-481
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Tidskriftsartikel (refereegranskat)abstract
- In the western Pyrenees (Southwest France and Northwest Spain), a narrow hybrid zone exists between the common chiffchaff Phylloscopus (collybita) collybita and the Iberian chiffchaff Phylloscopus (c.) brehmii. In this zone, which is approximately 20 km wide, mixed matings and individuals singing the songs of both taxa occur at substantial frequencies (24 and 8.6%, respectively), suggesting frequent hybridization. Previous studies have shown very weak mitochondrial gene flow (Nm = 0.065), whereas four microsatellites suggested much higher nuclear gene flow (Nm = 4.9). In this study we used the amplified fragment length polymorphism (AFLP) method in order to identify hybrids and early backcrosses. We typed 91 birds from both allopatric and sympatric areas for 12 informative AFLP markers (of > 141 polymorphic fragments), obtained by screening 13 AFLP primer combinations. These individuals were previously typed for song (brehmii, collybita or mixed singers), mitochondrial DNA (mtDNA) haplotype and allelic genotypes at four microsatellite loci. Assignment tests demonstrated that in the zone of sympatry, a substantial number of intermediate genotypes existed among the birds previously believed to be pure collybita and brehmii, based on song and mtDNA haplotype. The majority of the mixed singers had intermediate genotypes. Our data suggest that the fraction of the adult population having a hybrid origin (hybrids or backcrosses) is in the order of 10%. With such a frequency of genetic hybrids, there would have been much more mtDNA introgression than observed, had female hybrids been perfectly fertile/viable. This result is consistent with male-biased gene flow and Haldane's rule.
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| 2. |
- Aaltonen, Kristina, et al.
(författare)
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Nuclear and chloroplast microsatellites reveal extreme population differentiation and limited gene flow in the Aegean endemic Brassica cretica (Brassicaceae)
- 2007
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Ingår i: Molecular Ecology. - 0962-1083. ; 16:23, s. 4972-4983
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Tidskriftsartikel (refereegranskat)abstract
- Nuclear and chloroplast microsatellite markers were used to study population structure and gene flow among seven Cretan populations of the Aegean endemic plant species Brassica cretica (Brassicaceae). Both nuclear and chloroplast markers revealed exceptionally high levels of population differentiation (overall FST = 0.628 and 1.000, respectively) and relatively little within-population diversity (overall HS = 0.211 and 0.000, respectively). Maximum-likelihood estimates of directional migration rates were low among all pairs of populations (average Nm = 0.286). There was no evidence that differences in flower colour between populations had any influence on historical levels of gene flow. In addition, a haplotype network showed that all five chloroplast haplotypes found in the sample were closely related. Together, these results suggest that current patterns of diversification in B. cretica are mainly a result of genetic drift during the last half million years. The main conclusions from the present study are consistent with the prevailing hypothesis that plant diversification in the Aegean region is driven by random rather than adaptive differentiation among isolated populations.
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| 3. |
- Abbott, J. K., et al.
(författare)
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Patterns of differentiation in a colour polymorphism and in neutral markers reveal rapid genetic changes in natural damselfly populations
- 2008
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Ingår i: Molecular Ecology. - : Wiley-Blackwell. - 0962-1083 .- 1365-294X. ; 17:6, s. 1597-1604
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Tidskriftsartikel (refereegranskat)abstract
- The existence and mode of selection operating on heritable adaptive traits can be inferred by comparing population differentiation in neutral genetic variation between populations (often using F-ST values) with the corresponding estimates for adaptive traits. Such comparisons indicate if selection acts in a diversifying way between populations, in which case differentiation in selected traits is expected to exceed differentiation in neutral markers [F-ST (selected) > F-ST (neutralfl, or if negative frequency-dependent selection maintains genetic polymorphisms and pulls populations towards a common stable equilibrium [FST (selected) < F-ST (neutral)]. Here, we compared F-ST values for putatively neutral data (obtained using amplified fragment length polymorphism) with estimates of differentiation in morph frequencies in the colour-polymorphic damselfly Ischnura elegans. We found that in the first year (2000), population differentiation in morph frequencies was significantly greater than differentiation in neutral loci, while in 2002 (only 2 years and 2 generations later), population differentiation in morph frequencies had decreased to a level significantly lower than differentiation in neutral loci. Genetic drift as an explanation for population differentiation in morph frequencies could thus be rejected in both years. These results indicate that the type and/or strength of selection on morph frequencies in this system can change substantially between years. We suggest that an approach to a common equilibrium morph frequency across all populations, driven by negative frequency-dependent selection, is the cause of these temporal changes. We conclude that inferences about selection obtained by comparing F-ST values from neutral and adaptive genetic variation are most useful when spatial and temporal data are available from several populations and time points and when such information is combined with other ecological sources of data.
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| 4. |
- Abrego, Nerea, et al.
(författare)
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Accounting for environmental variation in co-occurrence modelling reveals the importance of positive interactions in root-associated fungal communities
- 2020
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 29:14, s. 2736-2746
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Tidskriftsartikel (refereegranskat)abstract
- Understanding the role of interspecific interactions in shaping ecological communities is one of the central goals in community ecology. In fungal communities, measuring interspecific interactions directly is challenging because these communities are composed of large numbers of species, many of which are unculturable. An indirect way of assessing the role of interspecific interactions in determining community structure is to identify the species co-occurrences that are not constrained by environmental conditions. In this study, we investigated co-occurrences among root-associated fungi, asking whether fungi co-occur more or less strongly than expected based on the environmental conditions and the host plant species examined. We generated molecular data on root-associated fungi of five plant species evenly sampled along an elevational gradient at a high arctic site. We analysed the data using a joint species distribution modelling approach that allowed us to identify those co-occurrences that could be explained by the environmental conditions and the host plant species, as well as those co-occurrences that remained unexplained and thus more probably reflect interactive associations. Our results indicate that not only negative but also positive interactions play an important role in shaping microbial communities in arctic plant roots. In particular, we found that mycorrhizal fungi are especially prone to positively co-occur with other fungal species. Our results bring new understanding to the structure of arctic interaction networks by suggesting that interactions among root-associated fungi are predominantly positive.
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| 5. |
- Ahlstrom, Christina A., et al.
(författare)
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Satellite tracking of gulls and genomic characterization of faecal bacteria reveals environmentally mediated acquisition and dispersal of antimicrobial-resistant Escherichia coli on the Kenai Peninsula, Alaska
- 2019
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Ingår i: Molecular Ecology. - : WILEY. - 0962-1083 .- 1365-294X. ; 28:10, s. 2531-2545
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Tidskriftsartikel (refereegranskat)abstract
- Gulls (Larus spp.) have frequently been reported to carry Escherichia coli exhibiting antimicrobial resistance (AMR E. coli); however, the pathways governing the acquisition and dispersal of such bacteria are not well described. We equipped 17 landfill-foraging gulls with satellite transmitters and collected gull faecal samples longitudinally from four locations on the Kenai Peninsula, Alaska to assess: (a) gull attendance and transitions between sites, (b) spatiotemporal prevalence of faecally shed AMR E. coli, and (c) genomic relatedness of AMR E. coli isolates among sites. We also sampled Pacific salmon (Oncorhynchus spp.) harvested as part of personal-use dipnet fisheries at two sites to assess potential contamination with AMR E. coli. Among our study sites, marked gulls most commonly occupied the lower Kenai River (61% of site locations) followed by the Soldotna landfill (11%), lower Kasilof River (5%) and upper Kenai River (<1%). Gulls primarily moved between the Soldotna landfill and the lower Kenai River (94% of transitions among sites), which were also the two locations with the highest prevalence of AMR E. coli. There was relatively high spatial and temporal variability in AMR E. coli prevalence in gull faeces and there was no evidence of contamination on salmon harvested in personal-use fisheries. We identified E. coli sequence types and AMR genes of clinical importance, with some isolates possessing genes associated with resistance to as many as eight antibiotic classes. Our findings suggest that gulls acquire AMR E. coli at habitats with anthropogenic inputs and subsequent movements may represent pathways through which AMR is dispersed.
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| 6. |
- Allendorf, Fred W., et al.
(författare)
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So long to genetic diversity, and thanks for all the fish
- 2014
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 23:1, s. 23-25
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- The world faces a global fishing crisis. Wild marine fisheries comprise nearly 15% of all animal protein in the human diet, but, according to the U.N. Food and Agriculture Organization, nearly 60% of all commercially important marine fish stocks are overexploited, recovering, or depleted (FAO 2012; Fig. 1). Some authors have suggested that the large population sizes of harvested marine fish make even collapsed populations resistant to the loss of genetic variation by genetic drift (e. g. Beverton 1990). In contrast, others have argued that the loss of alleles because of overfishing may actually be more dramatic in large populations than in small ones (Ryman et al. 1995). In this issue, Pinsky & Palumbi (2014) report that overfished populations have approximately 2% lower heterozygosity and 12% lower allelic richness than populations that are not overfished. They also performed simulations which suggest that their estimates likely underestimate the actual loss of rare alleles by a factor of three or four. This important paper shows that the harvesting of marine fish can have genetic effects that threaten the long-term sustainability of this valuable resource.
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| 7. |
- Ament-Velasquez, Sandra Lorena, et al.
(författare)
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Population genomics of sexual and asexual lineages in fissiparous ribbon worms (Lineus, Nemertea) : hybridization, polyploidy and the Meselson effect
- 2016
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 25:14, s. 3356-3369
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Tidskriftsartikel (refereegranskat)abstract
- Comparative population genetics in asexual vs. sexual species offers the opportunity to investigate the impact of asexuality on genome evolution. Here, we analyse coding sequence polymorphism and divergence patterns in the fascinating Lineus ribbon worms, a group of marine, carnivorous nemerteans with unusual regeneration abilities, and in which asexual reproduction by fissiparity is documented. The population genomics of the fissiparous L. pseudolacteus is characterized by an extremely high level of heterozygosity and unexpectedly elevated pi(N)/pi(S) ratio, in apparent agreement with theoretical expectations under clonal evolution. Analysis of among-species allele sharing and read-count distribution, however, reveals that L. pseudolacteus is a triploid hybrid between Atlantic populations of L. sanguineus and L. lacteus. We model and quantify the relative impact of hybridity, polyploidy and asexuality on molecular variation patterns in L. pseudolacteus and conclude that (i) the peculiarities of L. pseudolacteus population genomics result in the first place from hybridization and (ii) the accumulation of new mutations through the Meselson effect is more than compensated by processes of heterozygosity erosion, such as gene conversion or gene copy loss. This study illustrates the complexity of the evolutionary processes associated with asexuality and identifies L. pseudolacteus as a promising model to study the first steps of polyploid genome evolution in an asexual context.
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| 8. |
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| 9. |
- Andersson, Anna-Carin, et al.
(författare)
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No apparent reduction of gene flow in a hybrid zone between the West and North European karyotypic groups of the common shrew, Sorex araneus.
- 2004
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Ingår i: Mol Ecol. - 0962-1083. ; 13:5, s. 1205-15
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Tidskriftsartikel (refereegranskat)abstract
- The common shrew, Sorex araneus, exhibits an unusually high level of karyotypic variation. Populations with identical or similar karyotypes are defined as chromosome races, which are, in turn, grouped into larger evolutionary units, karyotypic groups. Using six microsatellite markers, we investigated the genetic structure of a hybrid zone between the Sidensjo and Abisko chromosome races, representatives of two distinct karyotypic groups believed to have been separated during the last glacial maximum, the West European karyotypic group (western group) and the North European karyotypic group (northern group), respectively. Significant FST values among populations suggest some weak genetic structure. All hierarchical levels show similar levels of genetic differentiation, equivalent to levels of genetic structure in several intraracial studies of common shrew populations from central Europe. Notably, genetic differentiation was of the same order of magnitude between and within karyotypic groups. Although the genetic differentiation was weak, the correlation between genetic and geographical distance was positive and significant, suggesting that the genetic variation observed between populations is a function of geographical distance rather than racial origin. Hence, considerable chromosomal differences do not seem to prevent extensive gene flow.
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| 10. |
- Andersson, Anastasia, 1987-, et al.
(författare)
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Monitoring genetic diversity with new indicators applied to an alpine freshwater top predator
- 2022
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 31:24, s. 6422-6439
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Tidskriftsartikel (refereegranskat)abstract
- Genetic diversity is the basis for population adaptation and long-term survival, yet rarely considered in biodiversity monitoring. One key issue is the need for useful and straightforward indicators of genetic diversity. We monitored genetic diversity over 40 years (1970–2010) in metapopulations of brown trout (Salmo trutta) inhabiting 27 small mountain lakes representing 10 lake systems in central Sweden using >1200 fish per time point. We tested six newly proposed indicators; three were designed for broad, international use in the UN Convention on Biological Diversity (CBD) and are currently applied in several countries. The other three were recently elaborated for national use by a Swedish science-management effort and applied for the first time here. The Swedish indicators use molecular genetic data to monitor genetic diversity within and between populations (indicators ΔH and ΔFST, respectively) and assess the effective population size (Ne-indicator). We identified 29 genetically distinct populations, all retained over time. Twelve of the 27 lakes harboured more than one population indicating that brown trout biodiversity hidden as cryptic, sympatric populations are more common than recognized. The Ne indicator showed values below the threshold (Ne ≤ 500) in 20 populations with five showing Ne < 100. Statistically significant genetic diversity reductions occurred in several populations. Metapopulation structure appears to buffer against diversity loss; applying the indicators to metapopulations suggest mostly acceptable rates of change in all but one system. The CBD indicators agreed with the Swedish ones but provided less detail. All these indicators are appropriate for managers to initiate monitoring of genetic biodiversity.
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