| 1. |
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| 2. |
- Onuţ-Brännström, Ioana, et al.
(författare)
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Sharing of photobionts in sympatric populations of Thamnolia and Cetraria lichens : evidence from high-throughput sequencing
- 2018
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- In this study, we explored the diversity of green algal symbionts (photobionts) in sympatric populations of the cosmopolitan lichen-forming fungi Thamnolia and Cetraria. We sequenced with both Sanger and Ion Torrent High-Throughput Sequencing technologies the photobiont ITS-region of 30 lichen thalli from two islands: Iceland and Öland. While Sanger recovered just one photobiont genotype from each thallus, the Ion Torrent data recovered 10–18 OTUs for each pool of 5 lichen thalli, suggesting that individual lichens can contain heterogeneous photobiont populations. Both methods showed evidence for photobiont sharing between Thamnolia and Cetraria on Iceland. In contrast, our data suggest that on Öland the two mycobionts associate with distinct photobiont communities, with few shared OTUs revealed by Ion Torrent sequencing. Furthermore, by comparing our sequences with public data, we identified closely related photobionts from geographically distant localities. Taken together, we suggest that the photobiont composition in Thamnolia and Cetraria results from both photobiont-mycobiont codispersal and local acquisition during mycobiont establishment and/or lichen growth. We hypothesize that this is a successful strategy for lichens to be flexible in the use of the most adapted photobiont for the environment.
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| 3. |
- Arnqvist, Göran, Professor, 1961-, et al.
(författare)
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A chromosome-level assembly of the seed beetle Callosobruchus maculatus genome with annotation of its repetitive elements
- 2024
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Ingår i: G3. - : Oxford University Press. - 2160-1836. ; 14:2
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Tidskriftsartikel (refereegranskat)abstract
- Callosobruchus maculatus is a major agricultural pest of legume crops worldwide and an established model system in ecology and evolution. Yet, current molecular biological resources for this species are limited. Here, we employ Hi-C sequencing to generate a greatly improved genome assembly and we annotate its repetitive elements in a dedicated in-depth effort where we manually curate and classify the most abundant unclassified repeat subfamilies. We present a scaffolded chromosome-level assembly, which is 1.01 Gb in total length with 86% being contained within the 9 autosomes and the X chromosome. Repetitive sequences accounted for 70% of the total assembly. DNA transposons covered 18% of the genome, with the most abundant superfamily being Tc1-Mariner (9.75% of the genome). This new chromosome-level genome assembly of C. maculatus will enable future genetic and evolutionary studies not only of this important species but of beetles more generally.
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| 4. |
- Arnqvist, Göran, et al.
(författare)
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A chromosome-level assembly of the seed beetle Callosobruchus maculatus genome with annotation of its repetitive elements
- 2024
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Ingår i: G3. - 2160-1836. ; 14:2
-
Tidskriftsartikel (refereegranskat)abstract
- Callosobruchus maculatus is a major agricultural pest of legume crops worldwide and an established model system in ecology and evolution. Yet, current molecular biological resources for this species are limited. Here, we employ Hi-C sequencing to generate a greatly improved genome assembly and we annotate its repetitive elements in a dedicated in-depth effort where we manually curate and classify the most abundant unclassified repeat subfamilies. We present a scaffolded chromosome-level assembly, which is 1.01 Gb in total length with 86% being contained within the 9 autosomes and the X chromosome. Repetitive sequences accounted for 70% of the total assembly. DNA transposons covered 18% of the genome, with the most abundant superfamily being Tc1-Mariner (9.75% of the genome). This new chromosome-level genome assembly of C. maculatus will enable future genetic and evolutionary studies not only of this important species but of beetles more generally.
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| 5. |
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| 6. |
- Cossu, Rosa Maria, et al.
(författare)
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LTR Retrotransposons Show Low Levels of Unequal Recombination and High Rates of Intraelement Gene Conversion in Large Plant Genomes
- 2017
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Ingår i: Genome Biology and Evolution. - : Oxford University Press. - 1759-6653. ; 9:12, s. 3449-3462
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Tidskriftsartikel (refereegranskat)abstract
- The accumulat on and removal of transposable elements (TEs) is a major driver of genome size evolution in eukaryotes. In plants, long terminal repeat (LTR) retrotransposons (LTR-RTs) represent the majority of TEs and form most of the nuclear DNA in large genomes. Unequal recombination (UR) between LTRs leads to removal of intervening sequence and formation of solo-LTRs. UR is a major mechanism of LTR-RT removal in many angiosperms, but our understanding of LTR-RT-associated recombination within the large, LTR-RT-rich genomes of conifers is quite limited. We employ a novel read based methodology to estimate the relative rates of LTR-RT-associated UR within the genomes of four conifer and seven angiosperm species. We found the lowest rates of UR in the largest genomes studied, conifers and the angiosperm maize. Recombination may also resolve as gene conversion, which does not remove sequence, so we analyzed LTR-RT-associated gene conversion events (GCEs) in Norway spruce and six angiosperms. Opposite the trend for UR, we found the highest rates of GCEs in Norway spruce and maize. Unlike previous work in angiosperms, we found no evidence that rates of UR correlate with retroelement structural features in the conifers, suggesting that another process is suppressing UR in these species. Recent results from diverse eukaryotes indicate that heterochromatin affects the resolution of recombination, by favoring gene conversion over crossing-over, similar to our observation of opposed rates of UR and GCEs. Control of LTR-RT proliferation via formation of heterochromatin would be a likely step toward large genomes in eukaryotes carrying high LTR-RT content.
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| 7. |
- Horvath, Robert, 1988-
(författare)
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Population genomic analyses of regulatory variation and selection in Brassicaceae species
- 2020
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The impact of selection on regulatory variation and the contribution of regulatory changes to phenotypic variation has long been debated in evolutionary genetics. Because cis-regulatory elements such as promoters and enhancers can be difficult to identify, it has been more challenging to quantify the impact of selection on variation in cis-regulatory regions than in protein-coding regions. In this thesis, I use genomic tools to investigate gene expression variation and selection in Brassicaceae species. First, I investigated the genomic impact of selection on putative cis-regulatory regions in the genome of the crucifer species Capsella grandiflora (Brassicaceae) (Paper I). I used an assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) to empirically identify putative cis-regulatory regions as those located in accessible chromatin regions (ACRs) in the genome of the crucifer species Capsella grandiflora. Based on whole-genome resequencing data from a natural population, I then showed that ACRs are under stronger purifying selection than other intergenic regions and that they are depleted for transposable element (TE) insertions and enriched for expression quantitative trait loci (eQTL), as would be expected if ACRs are enriched for functional elements affecting gene expression. Second, I explored how the location and silencing of transposable elements (TEs) affects selection against TEs (Paper II). Specifically, I tested a trade-off model on epigenetic TE silencing, according to which the positive effects of TE silencing on preventing TE movement conflict with negative effects of TE silencing on nearby gene expression. I found that TE silencing through the RNA-directed DNA methylation (RdDM) pathway affects selection against TEs close to genes in C. grandiflora, which is consistent with the trade-off model. Third, I used Arabidopsis thaliana single-cell expression data to investigate the relationship between gene body methylation (gbM) and transcriptional regulation (Paper III). I found that there was an indirect correlation between gbM and gene expression noise as well as a direct correlation between gbM and gene expression consistency and potentially intron retention in Arabidopsis thaliana. Fourth, I investigated the impact of demographic history on genomic signatures of selection at linked sites (linked selection) (Paper IV). This study revealed that neutral genetic diversity in C. grandiflora with a stable effective population size is influenced by linked selection whereas in Arabidopsis lyrata, which underwent a recent and strong bottleneck, neutral diversity is mainly affected by population size change. In summary, this thesis offers new insights into determinants of gene expression variation, selection on genomic features linked to gene expression alteration, as well as on the effect of demographic history on linked selection patterns in Brassicaceae.
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| 8. |
- Kaiser, Kristine, et al.
(författare)
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When sounds collide : the effect of anthropogenic noise on a breeding assemblage of frogs in Belize, Central America
- 2011
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Ingår i: Behaviour. - 0005-7959 .- 1568-539X. ; 148:2, s. 215-232
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Tidskriftsartikel (refereegranskat)abstract
- Many organisms depend on acoustic communication for myriad functions, and have evolved behaviours to minimize effects of naturally occurring acoustic interference. However, as habitats are subject to increased alteration, anthropogenic noise becomes unavoidable, and how animals overcome such interference is not well understood. In most ecosystems, only a subset of frog species is associated with disturbed habitats; the ability of these species to overcome exogenous noise suggests that habitat associations may be related to species' response to noise. We tested the hypothesis that frogs associated with largely undisturbed forest habitat would be less likely to increase call output in response to exogenous noise than would those associated with disturbed or open habitat. While this relationship was not significant, we found a slight trend supporting the hypothesis. We then asked whether anthropogenic noise affects chorus tenure at individual- or at chorus-levels. Male frogs exposed to anthropogenic noise decreased both the number of days present at the chorus and the nightly chorus duration relative to controls. Because females generally join choruses late at night to breed, the effects of noise shown here are likely to substantially decrease frog reproductive success; thus, the acoustic environment may play an important role in shaping population dynamics and in amphibian declines.
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| 9. |
- Lin, Yao-Cheng, et al.
(författare)
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Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen
- 2018
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : NATL ACAD SCIENCES. - 0027-8424 .- 1091-6490. ; 115:46, s. E10970-E10978
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Tidskriftsartikel (refereegranskat)abstract
- The Populus genus is one of the major plant model systems, but genomic resources have thus far primarily been available for poplar species, and primarily Populus trichocarpa (Torr. & Gray), which was the first tree with a whole-genome assembly. To further advance evolutionary and functional genomic analyses in Populus, we produced genome assemblies and population genetics resources of two aspen species, Populus tremula L. and Populus tremuloides Michx. The two aspen species have distributions spanning the Northern Hemisphere, where they are keystone species supporting a wide variety of dependent communities and produce a diverse array of secondary metabolites. Our analyses show that the two aspens share a similar genome structure and a highly conserved gene content with P. trichocarpa but display substantially higher levels of heterozygosity. Based on population resequencing data, we observed widespread positive and negative selection acting on both coding and noncoding regions. Furthermore, patterns of genetic diversity and molecular evolution in aspen are influenced by a number of features, such as expression level, coexpression network connectivity, and regulatory variation. To maximize the community utility of these resources, we have integrated all presented data within the PopGenIE web resource (PopGenIE.org).
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| 10. |
- Lynch, Michael, et al.
(författare)
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NMD and the evolution of eukaryotic gene structure
- 2006
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Ingår i: Nonsense-Mediated mRNA Decay. - : Landes Bioscience/Eurekah.com. ; , s. 197-211
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Bokkapitel (refereegranskat)abstract
- All cells are confronted with undesirable transcripts derived from mutant alleles, but the production of aberrant transcripts from otherwise normal DNA may be an even greater challenge. The substantial fraction of problematical transcripts containing premature termination codons (PTCs) are subject to elimination by the nonsense-mediated mRNA decay (NMD) pathway. Phylogenetic analysis suggests that NMD and the exon junction complex (EJC) upon which it depends in mammals (see chapter by Maquat) are ancient, raising the possibility of an early association of NMD with introns. This may help explain why introns were able to proliferate to an apparently considerable degree in the stem eukaryote, despite the mutational burden that introns impose upon their host genes. A long-term evolutionary asso- ciation between NMD and introns also provides a possible explanation for the nonrandom spatial distribution of introns in the genes of multicellular species and for an apparent slow- down (and possible stabilization) of intron colonization in modern species. Several lineages, all of which are nearly devoid of ancestral introns, appear to have lost NMD and the EJC, and these taxa have exceptionally simple genomic features that minimize the chances of producing erroneous transcripts. Validation of these ideas will require empirical work on the degree of coordination between NMD, the EJC, and the locations of introns in a wide array of genes distributed across diverse phylogenetic lineages.
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| 11. |
- Mortellaro, Steve, et al.
(författare)
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Coefficients of Conservatism Values and the Floristic Quality Index for the vascular plants of south Florida
- 2012
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Ingår i: Southeastern naturalist (Steuben, Me.). - : Humboldt Field Research Institute. - 1528-7092 .- 1938-5412. ; 11:mo3, s. 1-62
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Tidskriftsartikel (refereegranskat)abstract
- Since pre-European settlement, major alterations to the native landscape have been made, due largely to urban and agricultural developments. In south Florida, these activities have caused extensive degradation to native plant communities leaving remnant native lands. Therefore, the floristic quality of these native lands is changing, and a tool to assess their quality is needed. Assignment of coefficient of conservatism (C) values (ranging from 0 to 10) to each native plant within south Florida allows for the use of the floristic quality index (FQI), a tool to assess the quality of natural or remnant native plant communities. The coefficient of conservatism concept is based on two factors: 1) plants have various degrees of fidelity to specific habitats and their quality, and 2) plants have varying tolerances to disturbances and respond in various degrees. The establishment of C values and the use of the FQI eliminate subjectivity and provide a standardized method to evaluate the floristic condition of a site, which allows for comparisons between different sites and monitoring of sites over time. Non-native plants are not assigned conservatism coefficients values because they did not evolve in the native landscape. In south Florida (Florida Keys excluded), there are approximately 2226 plants, of which 64% (1434) are considered native and 36% (792) are considered non-native. Of the 1434 plants examined, only 94 native plants remained unranked, because the team did not have enough experience with the plant to confidently assign a C value. Approximately 33% of plants ranked fell into the ruderal categories (0–4), whereas 67% fell into obligate to natural areas categories (5–10). Once a thorough inventory of a site has been completed, a mean C value and FQI can be calculated.
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| 12. |
- Nystedt, Björn, et al.
(författare)
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The Norway spruce genome sequence and conifer genome evolution
- 2013
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Ingår i: Nature. - : Nature Publishing Group. - 0028-0836 .- 1476-4687. ; 497:7451, s. 579-584
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Tidskriftsartikel (refereegranskat)abstract
- Conifers have dominated forests for more than 200 million years and are of huge ecological and economic importance. Here we present the draft assembly of the 20-gigabase genome of Norway spruce (Picea abies), the first available for any gymnosperm. The number of well-supported genes (28,354) is similar to the >100 times smaller genome of Arabidopsis thaliana, and there is no evidence of a recent whole-genome duplication in the gymnosperm lineage. Instead, the large genome size seems to result from the slow and steady accumulation of a diverse set of long-terminal repeat transposable elements, possibly owing to the lack of an efficient elimination mechanism. Comparative sequencing of Pinus sylvestris, Abies sibirica, Juniperus communis, Taxus baccata and Gnetum gnemon reveals that the transposable element diversity is shared among extant conifers. Expression of 24-nucleotide small RNAs, previously implicated in transposable element silencing, is tissue-specific and much lower than in other plants. We further identify numerous long (>10,000 base pairs) introns, gene-like fragments, uncharacterized long non-coding RNAs and short RNAs. This opens up new genomic avenues for conifer forestry and breeding.
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| 13. |
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| 14. |
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| 15. |
- Scofield, Douglas G., et al.
(författare)
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Foraging patterns of acorn woodpeckers (Melanerpes formicivorus) on valley oak (Quercus lobata N,e) in two California oak savanna-woodlands
- 2011
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Ingår i: Oecologia. - : Springer Science and Business Media LLC. - 0029-8549 .- 1432-1939. ; 166:1, s. 187-196
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Tidskriftsartikel (refereegranskat)abstract
- Landscape characteristics and social behavior can affect the foraging patterns of seed-dependent animals. We examine the movement of acorns from valley oak (Quercus lobata) trees to granaries maintained by acorn woodpeckers (Melanerpes formicivorus) in two California oak savanna-woodlands differing in the distribution of Q. lobata within each site. In 2004, we sampled Q. lobata acorns from 16 granaries at Sedgwick Reserve in Santa Barbara County and 18 granaries at Hastings Reserve in Monterey County. Sedgwick has lower site-wide density of Q. lobata than Hastings as well as different frequencies of otherQuercus species common to both sites. We found acorn woodpeckers foraged from fewer Q. lobata seed source trees (K g = 4.1 ± 0.5) at Sedgwick than at Hastings (K g = 7.6 ± 0.6) and from fewer effective seed sources (N em* = 2.00 and 5.78, respectively). The differences between sites are due to a greater number of incidental seed sources used per granary at Hastings than at Sedgwick. We also found very low levels of seed source sharing between adjacent granaries, indicating that territoriality is strong at both sites and that each social group forages on its own subset of trees. We discovered an interesting spatial pattern in the location of granaries. At Sedgwick, acorn woodpeckers situated their granaries within areas of higher-than-average tree density, while at Hastings, they placed them within areas of lower-than-average tree density, with the outcome that granaries at the two sites were located in areas of similar valley oak density. Our results illustrate that landscape characteristics might influence the number of trees visited by acorn woodpeckers and the locations of territories, while woodpecker social behavior, such as territoriality, shapes which trees are visited and whether they are shared with other social groups.
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| 16. |
- Scofield, Douglas G., et al.
(författare)
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Influence of acorn woodpecker social behaviour on transport of coast live oak (Quercus agrifolia) acorns in a southern California oak savanna
- 2010
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Ingår i: Journal of Ecology. - : Wiley. - 0022-0477 .- 1365-2745. ; 98:3, s. 561-572
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Tidskriftsartikel (refereegranskat)abstract
- 1. Many plant species depend upon animals for seed dispersal, yet animals disperse seeds in pursuit of their own social and behavioural agendas. Animal social behaviour affects where and how they forage, so it must also shape patterns of seed dispersal.2. At Sedgwick Reserve, California, USA, we established a study population of Quercus agrifolia to determine patterns of acorn foraging by the acorn woodpecker (Melanerpes formicivorous). This cooperative breeder lives in social groups that defend territories surrounding arboreal seed caches (granaries), foraging communally within these territories.3. We genotyped pericarp tissue of 568 acorns, as well as 285 adult Q. agrifolia trees, including all adults within 150 m of 16 focal granaries. After quantifying genotyping error, we identified a genetically reliable subset of 524 acorns. We assigned a source tree to each acorn and estimated the number of seed sources per granary and seed source sharing among granaries.4. We found one to eight distinct seed-source genotypes per granary, and an effective source diversity ranging from 1.0 to 6.6 seed sources. Of all transport events, 96.5% involve source trees within 150 m of the granaries. For one granary, all sampled acorns were transported from five trees located more than 1.3 km away, with all source trees within 90 m of each other. No measure of seed-source diversity was associated with density of potential seed sources, and the pattern of acorn movement fits three traditional dispersal curves poorly.5. Woodpecker groups rarely collected acorns from overlapping sets of maternal sources. Some pairs of neighbouring granaries shared maternal sources, and we identify those that were probably maintained by the same woodpecker group.6.Synthesis. Territoriality of woodpecker groups restricts both the spatial area of foraging and the sharing of seed sources. This foraging behaviour limits distances and directions of acorn transport from oaks located within woodpecker territories. Dispersal agents with this type of social structure will create a high degree of local genetic structure. Extreme behavioural variations may result in anomalous long-distance dispersal events that increase genetic connectivity, but are likely to do so in an episodic and erratic fashion.
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| 17. |
- Smouse, Peter E., et al.
(författare)
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Using Seedling and Pericarp Tissues to Determine Maternal Parentage of Dispersed Valley Oak Recruits
- 2012
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Ingår i: Journal of Heredity. - : Oxford University Press (OUP). - 0022-1503 .- 1465-7333. ; 103:2, s. 250-259
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Tidskriftsartikel (refereegranskat)abstract
- The spatial pattern of established seedlings yields valuable information about variation in fecundity, dispersal, and spatial structure of distributed recruits, but separating maternal and paternal contributions in monoecious species has been hampered by the “2 parent” problem. It is now possible to determine the maternal parentage of established recruits with genetic assay of maternally derived tissues of the seed or fruit, but the DNA of weathered maternal tissues often yields unreliable genotypes, reducing the practical range of such assay. We develop a mixed assay of seedling and seed (pericarp) tissues and illustrate it with distributed recruits of California valley oak (Quercus lobata Née). Detailed analysis indicates correct maternal assignment rates of canopy patch recruits of 56% (seedling assay only) versus 94% (mixed assay). For open patch recruits, maternal assignment rates were less than 50% (seedling assay only) versus 91% (mixed assay). The strategy of choice is to use seedling genotypes to identify a small set of credible parental candidates and then deploy 3–4 well-chosen pericarp/endocarp loci to reduce that list to a single obvious maternal candidate. The increase in the number of recruits available for subsequent analysis is pronounced, increasing precision and statistical power for subsequent inference.
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| 18. |
- Sork, Victoria L., et al.
(författare)
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Impact of asymmetric male and female gamete dispersal on allelic diversity and spatial genetic structure in valley oak (Quercus lobata Nee)
- 2015
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Ingår i: Evolutionary Ecology. - : Springer Science and Business Media LLC. - 0269-7653 .- 1573-8477. ; 29:6, s. 927-945
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Tidskriftsartikel (refereegranskat)abstract
- The distribution and abundance of genetic diversity in plant populations is initiated by sexually asymmetric propagule dispersal through pollen and seeds. Because these processes occur serially, it is not transparent how each contributes to subsequent patterns of genetic diversity. Using combined seedling/seed coat assay for naturally distributed seedlings of Quercus lobata N,e, we extracted male and female gametic genotypes, and then assessed (wind-vectored) paternal and (gravity- and animal-vectored) maternal contributions to spatially distributed allelic diversity. We evaluated 200 naturally recruited seedlings from 4 open patches away from any adult canopies (denoted 'open'), and 174 seedlings from 14 patches immediately beneath adult canopies (denoted 'canopy'). The open patches included 19 % long distant dispersal events of > 1 km while the canopy patches contained seedlings from one tree overhead. For each patch type, we partitioned average allelic diversity for six microsatellite loci for the whole study site (gamma) into separate within-patch (alpha) and among-patch (beta) components, translated into among-patch divergence (delta). We found that alpha-diversity resulting from seed dispersal was much less than that from pollen dispersal in both patch types, while total gamma-diversity across the site was similar. Divergence (delta) among canopy patches was significantly greater than delta among open patches. We then evaluated spatial genetic autocorrelation (kinship) patterns for both open and canopy strata, separately for male and female gametes. Female gametes showed sharply declining kinship with increasing distance for canopy patches and modestly for open patches. In sharp contrast, male gametes from both patches showed only subtle decline of kinship, but seedlings still showed significant structure across patch types. On balance, sexual asymmetry in propagule dispersal shapes both the abundance and distribution of allelic diversity, with pollen dispersal promoting overall diversity but reducing spatial structure, but seed-dispersal reduces overall diversity and markedly increases spatial genetic structure.
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| 19. |
- Steige, Kim A., et al.
(författare)
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Cis-Regulatory Changes Associated with a Recent Mating System Shift and Floral Adaptation in Capsella
- 2015
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Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 32:10, s. 2501-2514
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Tidskriftsartikel (refereegranskat)abstract
- The selfing syndrome constitutes a suite of floral and reproductive trait changes that have evolved repeatedly across many evolutionary lineages in response to the shift to selfing. Convergent evolution of the selfing syndrome suggests that these changes are adaptive, yet our understanding of the detailed molecular genetic basis of the selfing syndrome remains limited. Here, we investigate the role of cis-regulatory changes during the recent evolution of the selfing syndrome in Capsella rubella, which split from the outcrosser Capsella grandiflora less than 200 ka. We assess allele-specific expression (ASE) in leaves and flower buds at a total of 18,452 genes in three interspecific F1 C. grandiflora x C. rubella hybrids. Using a hierarchical Bayesian approach that accounts for technical variation using genomic reads, we find evidence for extensive cis-regulatory changes. On average, 44% of the assayed genes show evidence of ASE; however, only 6% show strong allelic expression biases. Flower buds, but not leaves, show an enrichment of cis-regulatory changes in genomic regions responsible for floral and reproductive trait divergence between C. rubella and C. grandiflora. We further detected an excess of heterozygous transposable element (TE) insertions near genes with ASE, and TE insertions targeted by uniquely mapping 24-nt small RNAs were associated with reduced expression of nearby genes. Our results suggest that cis-regulatory changes have been important during the recent adaptive floral evolution in Capsella and that differences in TE dynamics between selfing and outcrossing species could be important for rapid regulatory divergence in association with mating system shifts.
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| 20. |
- Steige, Kim A., et al.
(författare)
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Genomic analysis reveals major determinants of cis-regulatory variation in Capsella grandiflora
- 2017
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 114:5, s. 1087-1092
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Tidskriftsartikel (refereegranskat)abstract
- Understanding the causes of cis-regulatory variation is a long-standing aim in evolutionary biology. Although cis-regulatory variation has long been considered important for adaptation, we still have a limited understanding of the selective importance and genomic determinants of standing cis-regulatory variation. To address these questions, we studied the prevalence, genomic determinants, and selective forces shaping cis-regulatory variation in the outcrossing plant Capsella grandiflora. We first identified a set of 1,010 genes with common cis-regulatory variation using analyses of allele-specific expression (ASE). Population genomic analyses of whole-genome sequences from 32 individuals showed that genes with common cis-regulatory variation (i) are underweaker purifying selection and (ii) undergo less frequent positive selection than other genes. We further identified genomic determinants of cis-regulatory variation. Gene body methylation (gbM) was a major factor constraining cis-regulatory variation, whereas presence of nearby transposable elements (TEs) and tissue specificity of expression increased the odds of ASE. Our results suggest that most common cis-regulatory variation in C. grandiflora is under weak purifying selection, and that gene-specific functional constraints are more important for the maintenance of cis-regulatory variation than genome-scale variation in the intensity of selection. Our results agree with previous findings that suggest TE silencing affects nearby gene expression, and provide evidence for a link between gbM and cis-regulatory constraint, possibly reflecting greater dosage sensitivity of body-methylated genes. Given the extensive conservation of gbM in flowering plants, this suggests that gbM could be an important predictor of cis-regulatory variation in a wide range of plant species.
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| 21. |
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| 22. |
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| 23. |
- Thompson, Pamela G., et al.
(författare)
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What seeds tell us about birds : A multi-year analysis of acorn woodpecker foraging movements
- 2014
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Ingår i: Movement Ecology. - : Springer Science and Business Media LLC. - 2051-3933. ; 2, s. 12-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Foraging movements of animals shape their efficiency in finding food and their exposure to the environment while doing so. Our goal was to test the optimal foraging theory prediction that territorial acorn woodpeckers (Melanerpes formicivorus) should forage closer to their ‘central place’ in years of high resource availability and further afield when resources are less available. We used genetic data on acorns stored in caching sites (granaries) and adult trees for two oak species (Quercus lobata and Quercus agrifolia) to track acorn movements across oak savanna habitat in central California. We also compared the patterns of trees these territorial bird groups foraged upon, examining the effective numbers of source trees represented within single granaries (α), the effective number of granaries (β), the diversity across all granaries (γ), and the overlap (ω) in source trees among different granaries, both within and across years.Results: In line with optimal foraging theory predictions, most bird groups foraged shorter distances in years with higher acorn abundance, although we found some exceptionally long distance foraging movements in high acorn crop years. The α-diversity values were significantly higher for Quercus lobata, but not for Quercus agrifolia, in years of high acorn production. We also found that different woodpecker family groups visited almost completely non-overlapping sets of source trees, and each particular group visited largely the same set of source trees from year to year, indicating strong territorial site fidelity.Conclusions: Acorn woodpeckers forage in a pattern consistent with optimal foraging theory, with a few fascinating exceptions of long distance movement. The number of trees they visit increases in years of high acorn availability, but the extra trees visited are mostly local. The territorial social behavior of the birds also restricts their movement patterns to a minimally overlapping subsets of trees, but the median movement distance appears to be shaped more by the availability of trees with acorns than by rigid territorial boundaries.
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| 24. |
- Urbina, Hector, et al.
(författare)
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DNA-metabarcoding uncovers the diversity of soil-inhabiting fungi in the tropical island of Puerto Rico
- 2016
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Ingår i: Mycoscience. - : The Mycological Society of Japan. - 1340-3540 .- 1618-2545. ; 57:3, s. 217-227
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Tidskriftsartikel (refereegranskat)abstract
- Soil fungal communities in tropical regions remain poorly understood. In order to increase the knowledge of diversity of soil-inhabiting fungi, we extracted total DNA from top-organic soil collected in seven localities dominated by four major ecosystems in the tropical island of Puerto Rico. In order to comprehensively characterize the fungal community, we PCR-amplified the internal transcribed spacer 2 (ITS2) fungal barcode using newly designed degenerated primers and varying annealing temperatures to minimize primer bias. Sequencing results, obtained using Ion Torrent technology, comprised a total of 566,613 sequences after quality filtering. These sequences were clustered into 4140 molecular operational taxonomic units (MOTUs) after removing low frequency sequences and rarefaction to account for differences in read depth between samples. Our results demonstrate that soil fungal communities in Puerto Rico are structured by ecosystem. Ascomycota, followed by Basidiomycota, dominates the diversity of fungi in soil. Amongst Ascomycota, the recently described soil-inhabiting class Archaeorhizomycetes was present in all localities, and taxa in Archaeorhizomycetes were among the most commonly observed MOTUs. The Basidiomycota community was dominated by soil decomposers and ectomycorrhizal fungi with a distribution strongly affected by local variation to a greater degree than Ascomycota.
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| 25. |
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| 26. |
- Wang, Mi, et al.
(författare)
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RPASE : Individual-based allele-specific expression detection without prior knowledge of haplotype phase
- 2018
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Ingår i: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 18:6, s. 1247-1262
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Tidskriftsartikel (refereegranskat)abstract
- Variation in gene expression is believed to make a significant contribution to phenotypic diversity and divergence. The analysis of allele-specific expression (ASE) can reveal important insights into gene expression regulation. We developed a novel method called RPASE (Read-backed Phasing-based ASE detection) to test for genes that show ASE. With mapped RNA-seq data from a single individual and a list of SNPs from the same individual as the only input, RPASE is capable of aggregating information across multiple dependent SNPs and producing individual-based gene-level tests for ASE. RPASE performs well in simulations and comparisons. We applied RPASE to multiple bird species and found a potentially rich landscape of ASE.
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| 27. |
- Zuccolo, Andrea, et al.
(författare)
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The Ty1-copia LTR retroelement family PARTC is highly conserved in conifers over 200 MY of evolution
- 2015
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Ingår i: Gene. - : Elsevier BV. - 0378-1119 .- 1879-0038. ; 568:1, s. 89-99
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Tidskriftsartikel (refereegranskat)abstract
- Long Terminal Repeat retroelements (LTR-RTs) are a major component of many plant genomes. Although well studied and described in angiosperms, their features and dynamics are poorly understood in gymnosperms. Representative complete copies of a Ty1-copia element isolate in Picea abies and named PARTC were identified in six other conifer species (Picea glauca, Pinus sylvestris, Pinus taeda, Abies sibirica, Taxus baccata and Juniperus communis) covering more than 200 million years of evolution. Here we characterized the structure of this element, assessed its abundance across conifers, studied the modes and timing of its amplification, and evaluated the degree of conservation of its extant copies at nucleotide level over distant species. We demonstrated that the element is ancient, abundant, widespread and its paralogous copies are present in the genera Picea, Pinus and Abies as an LTR-RT family. The amplification leading to the extant copies of PARTC occurred over long evolutionary times spanning 10 s of MY and mostly took place after the speciation of the conifers analyzed. The level of conservation of PARTC is striking and may be explained by low substitution rates and limited removal mechanisms for LTR-RTs. These PARTC features and dynamics are representative of a more general scenario for LTR-RTs in gymnosperms quite different from that characterizing the vast majority of LTR-RT elements in angiosperms. (C) 2015 Elsevier B.V. All rights reserved.
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