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Next-generation sequencing technologies generate large amounts of data, and analysis of fungal marker-gene data is an active area of research.<ref name="one" /><ref name="fifteen">Lindahl, B. D., R. H. Nilsson, L. Tedersoo, K. Abarenkov, T. Carlsen, R. Kjoller, et al. (2013). Fungul community analysis by high-throughput sequencing of amplified markers – a user’s guide. New Phytologist doi: 10.1111/nph.12243</ref> Two primary areas of concern are methods for clustering sequences into operational taxonomic units by sequence similarity, and quality control of sequence data.<ref name="one" /><ref name="fifteen" /> Currently there is no consensus on preferred methods for clustering,<ref name="fifteen" /> and clustering and sequence processing methods can have a significant impact on results, especially for the variable-length ITS region.<ref name="one" /><ref name="fifteen" /> In addition, fungal species vary in intra-specific sequence similarity of the ITS region.<ref name="sixteen">Nilsson RH, Kristiansson E, Ryberg M, Hallenberg N. (2008). Intraspecific ITS variability in the kingdom Fungi as expressed in the international sequence databases and its implications for molecular species identification. Evol Bioinf Online 4: 193–201</ref> Recent research has been devoted to development of flexible clustering protocols that allow sequence similarity thresholds to vary by taxonomic groups, which are supported by well-annotated sequences in public sequence databases.<ref name="fourteen" />
Next-generation sequencing technologies generate large amounts of data, and analysis of fungal marker-gene data is an active area of research.<ref name="one" /><ref name="fifteen">Lindahl, B. D., R. H. Nilsson, L. Tedersoo, K. Abarenkov, T. Carlsen, R. Kjoller, et al. (2013). Fungul community analysis by high-throughput sequencing of amplified markers – a user’s guide. New Phytologist doi: 10.1111/nph.12243</ref> Two primary areas of concern are methods for clustering sequences into operational taxonomic units by sequence similarity, and quality control of sequence data.<ref name="one" /><ref name="fifteen" /> Currently there is no consensus on preferred methods for clustering,<ref name="fifteen" /> and clustering and sequence processing methods can have a significant impact on results, especially for the variable-length ITS region.<ref name="one" /><ref name="fifteen" /> In addition, fungal species vary in intra-specific sequence similarity of the ITS region.<ref name="sixteen">Nilsson RH, Kristiansson E, Ryberg M, Hallenberg N. (2008). Intraspecific ITS variability in the kingdom Fungi as expressed in the international sequence databases and its implications for molecular species identification. Evol Bioinf Online 4: 193–201</ref> Recent research has been devoted to development of flexible clustering protocols that allow sequence similarity thresholds to vary by taxonomic groups, which are supported by well-annotated sequences in public sequence databases.<ref name="fourteen" />

== Extra-pair fertilizations (EPFs) ==
In recent years, molecular data and analyses have been able to supplement traditional approaches of [[behavioral ecology]], the study of animal behavior in relation to its ecology and evolutionary history. One behavior that molecular data has helped scientists better understand is extra-pair fertilizations (EPFs), also know as [[Extra-pair copulation|extra-pair copulations (EPCs)]]. These are mating events that occur outside of a social bond, like monogamy and are hard to observe. Molecular data has been key to understanding the prevalence of and the individuals participating in EPFs.

While most bird species are socially monogamous, molecular data has revealed that less than 25% of these species are genetically monogamous<ref>{{Cite journal|last=Griffith|first=Simon C.|last2=Owens|first2=Ian P. F.|last3=Thuman|first3=Katherine A.|date=2002-11-01|title=Extra pair paternity in birds: a review of interspecific variation and adaptive function|url=http://onlinelibrary.wiley.com/doi/10.1046/j.1365-294X.2002.01613.x/abstract|journal=Molecular Ecology|language=en|volume=11|issue=11|pages=2195–2212|doi=10.1046/j.1365-294X.2002.01613.x|issn=1365-294X}}</ref>. EPFs complicate matters, especially for male individuals, because it does not make sense for an individual to care for offspring that are not their own. Studies have found that males will adjust their parental care in response to changes in their paternity<ref>{{Cite journal|last=Hunt|first=J.|last2=Simmons|first2=L. W.|date=2002-09-01|title=Confidence of paternity and paternal care: covariation revealed through the experimental manipulation of the mating system in the beetle Onthophagus taurus|url=http://onlinelibrary.wiley.com/doi/10.1046/j.1420-9101.2002.00442.x/abstract|journal=Journal of Evolutionary Biology|language=en|volume=15|issue=5|pages=784–795|doi=10.1046/j.1420-9101.2002.00442.x|issn=1420-9101}}</ref><ref>{{Cite journal|last=Neff|first=Bryan D.|title=Decisions about parental care in response to perceived paternity|url=http://www.nature.com/doifinder/10.1038/nature01528|journal=Nature|volume=422|issue=6933|pages=716–719|doi=10.1038/nature01528}}</ref>. Other studies have shown that in socially monogamous species, some individuals will employ an alternative strategy to be reproductively successful since a social bond does not always equal reproductive success<ref>{{Cite journal|last=Conrad|first=K. F.|last2=Johnston|first2=P. V.|last3=Crossman|first3=C.|last4=Kempenaers|first4=B.|last5=Robertson|first5=R. J.|last6=Wheelwright|first6=N. T.|last7=Boag|first7=P. T.|date=2001-05-01|title=High levels of extra-pair paternity in an isolated, low-density, island population of tree swallows (Tachycineta bicolor)|url=http://onlinelibrary.wiley.com/doi/10.1046/j.1365-294X.2001.01263.x/abstract|journal=Molecular Ecology|language=en|volume=10|issue=5|pages=1301–1308|doi=10.1046/j.1365-294X.2001.01263.x|issn=1365-294X}}</ref><ref>{{Cite journal|last=Kempenaers|first=Bart|last2=Everding|first2=Susie|last3=Bishop|first3=Cheryl|last4=Boag|first4=Peter|last5=Robertson|first5=Raleigh J.|date=2001-01-18|title=Extra-pair paternity and the reproductive role of male floaters in the tree swallow (Tachycineta bicolor)|url=http://link.springer.com/article/10.1007/s002650000305|journal=Behavioral Ecology and Sociobiology|language=en|volume=49|issue=4|pages=251–259|doi=10.1007/s002650000305|issn=0340-5443}}</ref>.

It appears that EPFs in some species is driven by the good genes hypothesis<ref>{{Cite book|title=Molecular Ecology|last=Freeland|first=Joanna|last2=Kirk|first2=Heather|last3=Petersen|first3=Stephen|publisher=John Wiley & Sons, Ltd.|year=2011|isbn=978-1-119-99308-7|location=West Sussex, UK|pages=295}}</ref> (295). In red-back shrikes (''Lanius collurio'') extra-pair males had significantly longer tarsi than within-pair males, and all of the extra-pair offspring were males, supporting the prediction that females will bias their clutch towards males when they mate with an "attractive" male<ref>{{Cite journal|last=Schwarzová|first=Lucie|last2=Šimek|first2=Jaroslav|last3=Coppack|first3=Timothy|last4=Tryjanowski|first4=Piotr|date=2008-06-01|title=Male-Biased Sex of Extra Pair Young in the Socially Monogamous Red-Backed Shrike Lanius collurio|url=http://www.bioone.org/doi/abs/10.3161/000164508X395379|journal=Acta Ornithologica|volume=43|issue=2|pages=235–239|doi=10.3161/000164508X395379|issn=0001-6454}}</ref>. In house wrens (''Troglodytes aedon)'', extra-pair offspring were also found to be male-biased compared to within-offspring<ref>{{Cite journal|last=Johnson|first=L. Scott|last2=Thompson|first2=Charles F.|last3=Sakaluk|first3=Scott K.|last4=Neuhäuser|first4=Markus|last5=Johnson|first5=Bonnie G. P.|last6=Soukup|first6=Sheryl Swartz|last7=Forsythe|first7=Shannon Janota|last8=Masters|first8=Brian S.|date=2009-06-22|title=Extra-pair young in house wren broods are more likely to be male than female|url=http://rspb.royalsocietypublishing.org/content/276/1665/2285|journal=Proceedings of the Royal Society of London B: Biological Sciences|language=en|volume=276|issue=1665|pages=2285–2289|doi=10.1098/rspb.2009.0283|issn=0962-8452|pmc=2677618|pmid=19324727}}</ref>.

Without molecular ecology, identifying individuals that participate in EPFs and the offspring that result from EPFs would be impossible.


== Notes and references ==
== Notes and references ==

Revision as of 13:57, 9 December 2016

For the scientific journal, see Molecular Ecology.

Molecular ecology is a field of evolutionary biology that is concerned with applying molecular population genetics, molecular phylogenetics, and more recently genomics to traditional ecological questions (e.g., species diagnosis, conservation and assessment of biodiversity, species-area relationships, and many questions in behavioral ecology). It is virtually synonymous with the field of "Ecological Genetics" as pioneered by Theodosius Dobzhansky, E. B. Ford, Godfrey M. Hewitt and others.[citation needed] These fields are united in their attempt to study genetic-based questions "out in the field" as opposed to the laboratory. Molecular ecology is related to the field of Conservation genetics.

Methods frequently include using microsatellites to determine gene flow and hybridization between populations. The development of molecular ecology is also closely related to the use of DNA microarrays, which allows for the simultaneous analysis of the expression of thousands of different genes. Quantitative PCR may also be used to analyze gene expression as a result of changes in environmental conditions or different response by differently adapted individuals.

Bacterial diversity

Molecular ecological techniques have recently been used to study in situ questions of bacterial diversity. This stems from the fact that many microorganisms are not easily obtainable as cultured strains in the laboratory, which would allow for identification and characterisation. It also stems from the development of PCR technique, which allows for rapid amplification of genetic material.

The amplification of DNA from environmental samples using general of group-specific primers leads to a mix of genetic material that has to be sorted out before sequencing and identification. The classic technique to achieve this is through cloning, which involves incorporating the amplified DNA fragments into bacterial plasmids. Techniques such as temperature gradient gel electrophoresis, allow for a faster result. More recently, the advent of relatively low-cost, next-generation DNA sequencing technologies, such as 454 and Illumina platforms, has allowed exploration of bacterial ecology in relation to continental-scale environmental gradients such as pH[1] that was not feasible with traditional technology.

Fungal diversity

Exploration of fungal diversity in situ has also benefited from next-generation DNA sequencing technologies. The use of high-throughput sequencing techniques has been widely adopted by the fungal ecology community since the first publication of their use in the field in 2009.[2] Similar to exploration of bacterial diversity, these techniques have allowed high-resolution studies of fundamental questions in fungal ecology such as phylogeography,[3] fungal diversity in forest soils,[4] stratification of fungal communities in soil horizons,[5] and fungal succession on decomposing plant litter.[6]

The majority of fungal ecology research leveraging next-generation sequencing approaches involves sequencing of PCR amplicons of conserved regions of DNA (i.e. marker genes) to identify and describe the distribution of taxonomic groups in the fungal community in question, though more recent research has focused on sequencing functional gene amplicons[2] (e.g. Baldrian et al. 2012[5]). The locus of choice for description of the taxonomic structure of fungal communities has traditionally been the internal transcribed spacer (ITS) region of ribosomal RNA genes [7] due to its utility in identifying fungi to genus or species taxonomic levels,[8] and its high representation in public sequence databases.[7] A second widely used locus (e.g. Amend et al. 2010,[3] Weber et al. 2013[9]), the D1-D3 region of 28S ribosomal RNA genes, may not allow the low taxonomic level classification of the ITS,[10][11] but demonstrates superior performance in sequence alignment and phylogenetics.[3][12] In addition, the D1-D3 region may be a better candidate for sequencing with Illumina sequencing technologies.[13] Porras-Alfaro et al.[11] showed that the accuracy of classification of either ITS or D1-D3 region sequences was largely based on the sequence composition and quality of databases used for comparison, and poor-quality sequences and sequence misidentification in public databases is a major concern.[14][15] The construction of sequence databases that have broad representation across fungi, and that are curated by taxonomic experts is a critical next step.[12][16]

Next-generation sequencing technologies generate large amounts of data, and analysis of fungal marker-gene data is an active area of research.[2][17] Two primary areas of concern are methods for clustering sequences into operational taxonomic units by sequence similarity, and quality control of sequence data.[2][17] Currently there is no consensus on preferred methods for clustering,[17] and clustering and sequence processing methods can have a significant impact on results, especially for the variable-length ITS region.[2][17] In addition, fungal species vary in intra-specific sequence similarity of the ITS region.[18] Recent research has been devoted to development of flexible clustering protocols that allow sequence similarity thresholds to vary by taxonomic groups, which are supported by well-annotated sequences in public sequence databases.[16]

Extra-pair fertilizations (EPFs)

In recent years, molecular data and analyses have been able to supplement traditional approaches of behavioral ecology, the study of animal behavior in relation to its ecology and evolutionary history. One behavior that molecular data has helped scientists better understand is extra-pair fertilizations (EPFs), also know as extra-pair copulations (EPCs). These are mating events that occur outside of a social bond, like monogamy and are hard to observe. Molecular data has been key to understanding the prevalence of and the individuals participating in EPFs.

While most bird species are socially monogamous, molecular data has revealed that less than 25% of these species are genetically monogamous[19]. EPFs complicate matters, especially for male individuals, because it does not make sense for an individual to care for offspring that are not their own. Studies have found that males will adjust their parental care in response to changes in their paternity[20][21]. Other studies have shown that in socially monogamous species, some individuals will employ an alternative strategy to be reproductively successful since a social bond does not always equal reproductive success[22][23].

It appears that EPFs in some species is driven by the good genes hypothesis[24] (295). In red-back shrikes (Lanius collurio) extra-pair males had significantly longer tarsi than within-pair males, and all of the extra-pair offspring were males, supporting the prediction that females will bias their clutch towards males when they mate with an "attractive" male[25]. In house wrens (Troglodytes aedon), extra-pair offspring were also found to be male-biased compared to within-offspring[26].

Without molecular ecology, identifying individuals that participate in EPFs and the offspring that result from EPFs would be impossible.

Notes and references

  1. ^ Lauber CL, Hamady M, Knight R, Fierer N. (2009). Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Apllied and Environmental Microbiology 75: 5111-5120
  2. ^ a b c d e Větrovský T, Baldrian P (2013). Analysis of soil fungal communities by amplicon pyrosequencing: current approaches to data analysis and the introduction of the pipeline SEED. Biol Fertil Soils 49: 1027-1037
  3. ^ a b c Amend AS, Seifert KA, Samson R, Bruns TD. (2010). Indoor fungal composition is geographically patterned and more diverse in temperate zones than in the tropics. Proc Natl Acad Sci U S A 107: 13748–13753.
  4. ^ Buéé M, Reich M, Murat C, Morin E, Nilsson RH, Uroz S, Martin F (2009) 454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity. New Phytol 184:449–456
  5. ^ a b Baldrian P, Kolarik M, Stursova M, Kopecky J, Valaskova V, Vetrovsky T, et al. (2012). Active and total microbial communities in forest soil are largely different and highly stratified during decomposition. ISME J 6: 248-258
  6. ^ Voříšková J, Baldrian P (2013). Fungal community on decomposing leaf litter undergoes rapid successional changes. ISME J 7:477– 486
  7. ^ a b Seifert KA. (2009). Progress towards DNA barcoding of fungi. Mol Ecol Resour 9: 83–89
  8. ^ Horton TR and TD Bruns. (2001). The molecular revolution in ectomycorrhizal ecology: peeking into the black-box. Molecular Ecology 10: 1855-1871
  9. ^ Weber, C. F., R. Vilgalys and C. R. Kuske. (2013). Changes in fungal community composition in response to elevated atmospheric CO2 and nitrogen fertilization varies with soil horizon. Frontiers in Terrestrial Microbiology 4: 78 doi: 10.3389/fmicb.2013.00078
  10. ^ Schoch, C. L. and K. A. Seifert. (2012). Reply to Kiss: internal transcribed spacer (ITS) remains best candidate as a universal DNA barcode marker for Fungi despite imperfections. PNAS 109(27): E1812.
  11. ^ a b Porras-Alfaro A, Liu KL, Kuske CR, Xie G. (2013). From Genus to Phylum: LSU and ITS rRNA operon regions showed similar classification accuracy influenced by database composition. Appl Environ Microbiol doi:10.1128/AEM.02894-13
  12. ^ a b Kõljalg U, Larsson K-H, Abarenkov K, Nilsson RH, Alexander IJ, Eberhardt U, et al. (2005). UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi. New Phytol 166: 1063–1068
  13. ^ Liu KL, Porras-Alfaro A, Kuske CR, Eichorst SA, Xie G. (2012). Accurate, rapid taxonomic classification of fungal large-subunit rRNA genes. Applied and Environmental Microbiology 78: 1523–1533
  14. ^ Vilgalys R. (2003). Taxonomic misidentification in public DNA databases. New Phytol 160: 4-5
  15. ^ Nilsson RH, Tedersoo L, Abarenkov K, Ryberg M, Kristiansson E, Hartmann M, et al. (2012). Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences MycoKeys 4: 37-63
  16. ^ a b Kõljalg U, Nilsson H, Abarenkov K, Tedersoo L, Taylor AFS, Bahram M, et al. (2013). Towards a unified paradigm for sequence-based identification of fungi. Molecular Ecology 22: 5271-5277
  17. ^ a b c d Lindahl, B. D., R. H. Nilsson, L. Tedersoo, K. Abarenkov, T. Carlsen, R. Kjoller, et al. (2013). Fungul community analysis by high-throughput sequencing of amplified markers – a user’s guide. New Phytologist doi: 10.1111/nph.12243
  18. ^ Nilsson RH, Kristiansson E, Ryberg M, Hallenberg N. (2008). Intraspecific ITS variability in the kingdom Fungi as expressed in the international sequence databases and its implications for molecular species identification. Evol Bioinf Online 4: 193–201
  19. ^ Griffith, Simon C.; Owens, Ian P. F.; Thuman, Katherine A. (2002-11-01). "Extra pair paternity in birds: a review of interspecific variation and adaptive function". Molecular Ecology. 11 (11): 2195–2212. doi:10.1046/j.1365-294X.2002.01613.x. ISSN 1365-294X.
  20. ^ Hunt, J.; Simmons, L. W. (2002-09-01). "Confidence of paternity and paternal care: covariation revealed through the experimental manipulation of the mating system in the beetle Onthophagus taurus". Journal of Evolutionary Biology. 15 (5): 784–795. doi:10.1046/j.1420-9101.2002.00442.x. ISSN 1420-9101.
  21. ^ Neff, Bryan D. "Decisions about parental care in response to perceived paternity". Nature. 422 (6933): 716–719. doi:10.1038/nature01528.
  22. ^ Conrad, K. F.; Johnston, P. V.; Crossman, C.; Kempenaers, B.; Robertson, R. J.; Wheelwright, N. T.; Boag, P. T. (2001-05-01). "High levels of extra-pair paternity in an isolated, low-density, island population of tree swallows (Tachycineta bicolor)". Molecular Ecology. 10 (5): 1301–1308. doi:10.1046/j.1365-294X.2001.01263.x. ISSN 1365-294X.
  23. ^ Kempenaers, Bart; Everding, Susie; Bishop, Cheryl; Boag, Peter; Robertson, Raleigh J. (2001-01-18). "Extra-pair paternity and the reproductive role of male floaters in the tree swallow (Tachycineta bicolor)". Behavioral Ecology and Sociobiology. 49 (4): 251–259. doi:10.1007/s002650000305. ISSN 0340-5443.
  24. ^ Freeland, Joanna; Kirk, Heather; Petersen, Stephen (2011). Molecular Ecology. West Sussex, UK: John Wiley & Sons, Ltd. p. 295. ISBN 978-1-119-99308-7.
  25. ^ Schwarzová, Lucie; Šimek, Jaroslav; Coppack, Timothy; Tryjanowski, Piotr (2008-06-01). "Male-Biased Sex of Extra Pair Young in the Socially Monogamous Red-Backed Shrike Lanius collurio". Acta Ornithologica. 43 (2): 235–239. doi:10.3161/000164508X395379. ISSN 0001-6454.
  26. ^ Johnson, L. Scott; Thompson, Charles F.; Sakaluk, Scott K.; Neuhäuser, Markus; Johnson, Bonnie G. P.; Soukup, Sheryl Swartz; Forsythe, Shannon Janota; Masters, Brian S. (2009-06-22). "Extra-pair young in house wren broods are more likely to be male than female". Proceedings of the Royal Society of London B: Biological Sciences. 276 (1665): 2285–2289. doi:10.1098/rspb.2009.0283. ISSN 0962-8452. PMC 2677618. PMID 19324727.

See also

External links

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