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  • 1
    In: Molecular Ecology Resources, Wiley, Vol. 19, No. 1 ( 2019-01), p. 77-89
    Abstract: Long‐read sequencing technologies are transforming our ability to assemble highly complex genomes. Realizing their full potential is critically reliant on extracting high‐quality, high‐molecular‐weight (HMW) DNA from the organisms of interest. This is especially the case for the portable MinION sequencer which enables all laboratories to undertake their own genome sequencing projects, due to its low entry cost and minimal spatial footprint. One challenge of the MinION is that each group has to independently establish effective protocols for using the instrument, which can be time‐consuming and costly. Here, we present a workflow and protocols that enabled us to establish MinION sequencing in our own laboratories, based on optimizing DNA extraction from a challenging plant tissue as a case study. Following the workflow illustrated, we were able to reliably and repeatedly obtain 〉 6.5 Gb of long‐read sequencing data with a mean read length of 13 kb and an N50 of 26 kb. Our protocols are open source and can be performed in any laboratory without special equipment. We also illustrate some more elaborate workflows which can increase mean and average read lengths if this is desired. We envision that our workflow for establishing MinION sequencing, including the illustration of potential pitfalls and suggestions of how to adapt it to other tissue types, will be useful to others who plan to establish long‐read sequencing in their own laboratories.
    Type of Medium: Online Resource
    ISSN: 1755-098X , 1755-0998
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2019
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    SSG: 12
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  • 2
    In: Journal of Biogeography, Wiley, Vol. 41, No. 4 ( 2014-04), p. 659-672
    Abstract: Our aim was to test hypothesized biogeographical barriers using small‐bodied terrestrial U peroleia frogs, to identify P leistocene refugia and to define biogeographical units. Location The A ustralian M onsoonal T ropics, defined as the open woodlands and savanna north of the inland arid and eastern winter‐rainfall zones. Methods A multi‐locus molecular phylogeny of the U peroleia lithomoda , U . trachyderma and U . minima species complex, with supporting morphological and acoustic data, was generated to test species boundaries and clarify distributions. Ecological niche modelling with current climate and Last Glacial Maximum climate data was used to identify biogeographical units, barriers to dispersal, and regions of stability that may have served as P leistocene refugia. Results Our combined data supported five clades that comprise four allopatric species. Ecological niche models of the resolved species suggest that the K imberley P lateau represents a distinct bioregion, the Top End extends from the edge of the K imberley P lateau to the C arpentarian G ap, and the transition from sandstone escarpments to flat, sandy soils represents a major barrier to dispersal between the Top End and the N orthern D eserts. The N orthern D eserts were found to comprise two distinct subregions. Population‐ and species‐level divergences were evident in a north–south line in the N orthern T erritory, representing a newly identified biogeographical break. Putative P leistocene refugia were predicted in the north‐west K imberley P lateau, the western half of the Top End, the S elwyn R ange and western C ape Y ork. Main conclusions By combining detailed genetic, morphological and acoustic data with newly developed statistical methods, we have delineated species boundaries, identified cryptic species and provided a region‐wide assessment of the biogeography of northern A ustralia. We have identified previously unrecognized biogeographical barriers, better defined biogeographical regions, and proposed new hypotheses about the effects of P leistocene climate cycles on the present‐day diversity of northern A ustralia. Our work provides a solid foundation for the investigation of biogeographical patterns in other taxa.
    Type of Medium: Online Resource
    ISSN: 0305-0270 , 1365-2699
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2014
    detail.hit.zdb_id: 2020428-0
    detail.hit.zdb_id: 188963-1
    SSG: 12
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  • 3
    Online Resource
    Online Resource
    Wiley ; 2011
    In:  Evolution Vol. 65, No. 2 ( 2011-02), p. 606-611
    In: Evolution, Wiley, Vol. 65, No. 2 ( 2011-02), p. 606-611
    Type of Medium: Online Resource
    ISSN: 0014-3820
    URL: Issue
    RVK:
    Language: English
    Publisher: Wiley
    Publication Date: 2011
    detail.hit.zdb_id: 2036375-8
    SSG: 12
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  • 4
    Online Resource
    Online Resource
    Wiley ; 2016
    In:  Molecular Ecology Vol. 25, No. 18 ( 2016-09), p. 4438-4449
    In: Molecular Ecology, Wiley, Vol. 25, No. 18 ( 2016-09), p. 4438-4449
    Abstract: Mitochondrial DNA remains one of the most widely used molecular markers to reconstruct the phylogeny and phylogeography of closely related birds. It has been proposed that bird mitochondrial genomes evolve at a constant rate of ~0.01 substitution per site per million years, that is that they evolve according to a strict molecular clock. This molecular clock is often used in studies of bird mitochondrial phylogeny and molecular dating. However, rates of mitochondrial genome evolution vary among bird species and correlate with life history traits such as body mass and generation time. These correlations could cause systematic biases in molecular dating studies that assume a strict molecular clock. In this study, we overcome this issue by estimating corrected molecular rates for birds. Using complete or nearly complete mitochondrial genomes of 475 species, we show that there are strong relationships between body mass and substitution rates across birds. We use this information to build models that use bird species’ body mass to estimate their substitution rates across a wide range of common mitochondrial markers. We demonstrate the use of these corrected molecular rates on two recently published data sets. In one case, we obtained molecular dates that are twice as old as the estimates obtained using the strict molecular clock. We hope that this method to estimate molecular rates will increase the accuracy of future molecular dating studies in birds.
    Type of Medium: Online Resource
    ISSN: 0962-1083 , 1365-294X
    URL: Issue
    RVK:
    Language: English
    Publisher: Wiley
    Publication Date: 2016
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  • 5
    Online Resource
    Online Resource
    Wiley ; 2015
    In:  Journal of Experimental Zoology Part B: Molecular and Developmental Evolution Vol. 324, No. 6 ( 2015-09), p. 517-524
    In: Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, Wiley, Vol. 324, No. 6 ( 2015-09), p. 517-524
    Abstract: Ancestral state reconstruction (ASR) is a popular method for exploring the evolutionary history of traits that leave little or no trace in the fossil record. For example, it has been used to test hypotheses about the number of evolutionary origins of key life‐history traits such as oviparity, or key morphological structures such as wings. Many studies that use ASR have suggested that the number of evolutionary origins of such traits is higher than was previously thought. The scope of such inferences is increasing rapidly, facilitated by the construction of very large phylogenies and life‐history databases. In this paper, we use simulations to show that the number of evolutionary origins of a trait tends to be overestimated when the phylogeny is not perfect. In some cases, the estimated number of transitions can be several fold higher than the true value. Furthermore, we show that the bias is not always corrected by standard approaches to account for phylogenetic uncertainty, such as repeating the analysis on a large collection of possible trees. These findings have important implications for studies that seek to estimate the number of origins of a trait, particularly those that use large phylogenies that are associated with considerable uncertainty. We discuss the implications of this bias, and methods to ameliorate it. J. Exp. Zool. (Mol. Dev. Evol.) 324B: 517–524, 2015 . © 2015 Wiley Periodicals, Inc.
    Type of Medium: Online Resource
    ISSN: 1552-5007 , 1552-5015
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2015
    detail.hit.zdb_id: 2113204-5
    SSG: 12
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  • 6
    In: Molecular Ecology, Wiley, Vol. 20, No. 15 ( 2011-08), p. 3087-3101
    Type of Medium: Online Resource
    ISSN: 0962-1083
    RVK:
    Language: English
    Publisher: Wiley
    Publication Date: 2011
    detail.hit.zdb_id: 2020749-9
    detail.hit.zdb_id: 1126687-9
    SSG: 12
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  • 7
    Online Resource
    Online Resource
    Wiley ; 2018
    In:  Methods in Ecology and Evolution Vol. 9, No. 5 ( 2018-05), p. 1353-1362
    In: Methods in Ecology and Evolution, Wiley, Vol. 9, No. 5 ( 2018-05), p. 1353-1362
    Abstract: Non‐random species sampling is the rule rather than the exception in phylogenetics, but most phylogenetic methods to infer macroevolutionary and macroecological processes assume that the tips of the phylogenetic tree are either completely sampled or randomly sampled. In this study, we focus on extending the popular Bi SSE framework to better account for non‐random sampling of species. The existing Bi SSE correction (which we describe hereafter as the unresolved clade correction) cannot be used on trees with clades of more than about 200 species, or when lineages that originate near the root are not sampled. We propose new correction that does not have these two limitations. To assess the performance of our correction relative to the unresolved clade correction, we simulate trees using a common sampling strategy in which representative species of higher clades (e.g. genera) are sampled to include in a phylogeny. Compared to the unresolved clade correction, we show that our new correction gives less biased parameter estimates; has higher power but a slightly elevated false positive rate to detect state dependence in speciation and extinction rates; and is less sensitive to a failure to sample all extant groups of taxa. Over all simulation scenarios, our correction perform equally well under conditions where the unresolved clade correction is applicable and conditions where the unresolved clade correction is inapplicable. Given that both our correction and the unresolved clade correction have their own advantages and disadvantages, we suggest combining the two corrections. This can be done by applying our correction to groups that exceed the size limit of the unresolved clade correction or to account for the uncertainties in the placement of the lineages that originate near the root.
    Type of Medium: Online Resource
    ISSN: 2041-210X , 2041-210X
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2018
    detail.hit.zdb_id: 2528492-7
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