main.bbl

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\entry{Anderson2011}{article}{}
  \name{author}{14}{}{%
    {{}%
     {Anderson}{A.}%
     {Marti~J}{M.~J.}%
     {}{}%
     {}{}}%
    {{}%
     {Crist}{C.}%
     {Thomas~O}{T.~O.}%
     {}{}%
     {}{}}%
    {{}%
     {Chase}{C.}%
     {Jonathan~M}{J.~M.}%
     {}{}%
     {}{}}%
    {{}%
     {Vellend}{V.}%
     {Mark}{M.}%
     {}{}%
     {}{}}%
    {{}%
     {Inouye}{I.}%
     {Brian~D}{B.~D.}%
     {}{}%
     {}{}}%
    {{}%
     {Freestone}{F.}%
     {Amy~L}{A.~L.}%
     {}{}%
     {}{}}%
    {{}%
     {Sanders}{S.}%
     {Nathan~J}{N.~J.}%
     {}{}%
     {}{}}%
    {{}%
     {Cornell}{C.}%
     {Howard~V}{H.~V.}%
     {}{}%
     {}{}}%
    {{}%
     {Comita}{C.}%
     {Liza~S}{L.~S.}%
     {}{}%
     {}{}}%
    {{}%
     {Davies}{D.}%
     {Kendi~F}{K.~F.}%
     {}{}%
     {}{}}%
    {{}%
     {Harrison}{H.}%
     {Susan~P}{S.~P.}%
     {}{}%
     {}{}}%
    {{}%
     {Kraft}{K.}%
     {Nathan J~B}{N.~J.~B.}%
     {}{}%
     {}{}}%
    {{}%
     {Stegen}{S.}%
     {James~C}{J.~C.}%
     {}{}%
     {}{}}%
    {{}%
     {Swenson}{S.}%
     {Nathan~G}{N.~G.}%
     {}{}%
     {}{}}%
  }
  \list{publisher}{1}{%
    {Wiley Online Library}%
  }
  \keyw{Biodiversity,Biological,Coral Reefs,Ecology,El Nino-Southern
  Oscillation,Indonesia,Models,Multivariate Analysis}
  \strng{namehash}{AMJ+1}
  \strng{fullhash}{AMJCTOCJMVMIBDFALSNJCHVCLSDKFHSPKNJBSJCSNG1}
  \field{labelyear}{2011}
  \field{sortinit}{A}
  \field{abstract}{%
  A recent increase in studies of $\beta$ diversity has yielded a confusing
  array of concepts, measures and methods. Here, we provide a roadmap of the
  most widely used and ecologically relevant approaches for analysis through a
  series of mission statements. We distinguish two types of $\beta$ diversity:
  directional turnover along a gradient vs. non-directional variation.
  Different measures emphasize different properties of ecological data. Such
  properties include the degree of emphasis on presence/absence vs. relative
  abundance information and the inclusion vs. exclusion of joint absences.
  Judicious use of multiple measures in concert can uncover the underlying
  nature of patterns in $\beta$ diversity for a given dataset. A case study of
  Indonesian coral assemblages shows the utility of a multi-faceted approach.
  We advocate careful consideration of relevant questions, matched by
  appropriate analyses. The rigorous application of null models will also help
  to reveal potential processes driving observed patterns in $\beta$
  diversity.%
  }
  \verb{doi}
  \verb 10.1111/j.1461-0248.2010.01552.x
  \endverb
  \field{issn}{1461-0248}
  \field{number}{1}
  \field{pages}{19\bibrangedash 28}
  \field{title}{{Navigating the multiple meanings of beta diversity: a roadmap
  for the practicing ecologist.}}
  \verb{url}
  \verb http://onlinelibrary.wiley.com/doi/10.1111/j.1461-0248.2010.01552.x/ful
  \verb l http://www.ncbi.nlm.nih.gov/pubmed/21070562
  \endverb
  \field{volume}{14}
  \verb{file}
  \verb :home/tpoisot/Documents/Papers/Ecology Letters/Anderson et al. - 2011 -
  \verb  Navigating the multiple meanings of beta diversity a roadmap for the p
  \verb racticing ecologist.pdf:pdf
  \endverb
  \field{journaltitle}{Ecology Letters}
  \field{month}{01}
  \field{year}{2011}
\endentry

\entry{Darwin1859}{book}{}
  \name{author}{1}{}{%
    {{}%
     {Darwin}{D.}%
     {Charles}{C.}%
     {}{}%
     {}{}}%
  }
  \list{publisher}{1}{%
    {D. Appleton}%
  }
  \strng{namehash}{DC1}
  \strng{fullhash}{DC1}
  \field{labelyear}{1859}
  \field{sortinit}{D}
  \field{title}{{On the origin of species by means of natural selection, or the
  preservation of favoured races in the struggle for life}}
  \list{location}{1}{%
    {New York}%
  }
  \field{year}{1859}
\endentry

\entry{Dunne2006}{incollection}{}
  \name{author}{1}{}{%
    {{}%
     {Dunne}{D.}%
     {Jennifer~A}{J.~A.}%
     {}{}%
     {}{}}%
  }
  \name{editor}{2}{}{%
    {{}%
     {Pascual}{P.}%
     {Mercedes}{M.}%
     {}{}%
     {}{}}%
    {{}%
     {Dunne}{D.}%
     {Jennifer~A}{J.~A.}%
     {}{}%
     {}{}}%
  }
  \list{publisher}{1}{%
    {Oxford University Press}%
  }
  \strng{namehash}{DJA1}
  \strng{fullhash}{DJA1}
  \field{labelyear}{2006}
  \field{sortinit}{D}
  \field{booktitle}{Ecological Networks: Linking Structure to Dynamics in Food
  Webs}
  \field{pages}{27\bibrangedash 86}
  \field{title}{{The network structure of food webs}}
  \list{location}{1}{%
    {Oxford}%
  }
  \verb{file}
  \verb :home/tpoisot/Documents/Papers/Ecological Networks Linking Structure to
  \verb  Dynamics in Food Webs/Dunne - 2006 - The network structure of food web
  \verb s.pdf:pdf
  \endverb
  \field{year}{2006}
\endentry

\entry{Elton1927}{book}{}
  \name{author}{1}{}{%
    {{}%
     {Elton}{E.}%
     {Charles~S}{C.~S.}%
     {}{}%
     {}{}}%
  }
  \list{publisher}{1}{%
    {University of Chicago Press}%
  }
  \strng{namehash}{ECS1}
  \strng{fullhash}{ECS1}
  \field{labelyear}{1927}
  \field{sortinit}{E}
  \field{booktitle}{Animal ecology}
  \field{title}{{Animal ecology}}
  \field{year}{1927}
\endentry

\entry{Frank1993}{article}{}
  \name{author}{1}{}{%
    {{}%
     {Frank}{F.}%
     {Steven~A}{S.~A.}%
     {}{}%
     {}{}}%
  }
  \list{publisher}{1}{%
    {Springer}%
  }
  \strng{namehash}{FSA1}
  \strng{fullhash}{FSA1}
  \field{labelyear}{1993}
  \field{extrayear}{1}
  \field{sortinit}{F}
  \field{number}{1}
  \field{pages}{45\bibrangedash 75}
  \field{title}{{Coevolutionary genetics of plants and pathogens}}
  \field{volume}{7}
  \verb{file}
  \verb :home/tpoisot/Documents/Papers/Evolutionary Ecology/Frank - 1993 - Coev
  \verb olutionary genetics of plants and pathogens.pdf:pdf
  \endverb
  \field{journaltitle}{Evolutionary Ecology}
  \field{year}{1993}
\endentry

\entry{Frank1993b}{article}{}
  \name{author}{1}{}{%
    {{}%
     {Frank}{F.}%
     {Steven~A}{S.~A.}%
     {}{}%
     {}{}}%
  }
  \strng{namehash}{FSA1}
  \strng{fullhash}{FSA1}
  \field{labelyear}{1993}
  \field{extrayear}{2}
  \field{sortinit}{F}
  \field{number}{6}
  \field{pages}{1721\bibrangedash 1732}
  \field{title}{{Evolution of host-parasite diversity}}
  \verb{url}
  \verb http://www.csa.com/partners/viewrecord.php?requester=gs\&collection=ENV
  \verb \&recid=3713621
  \endverb
  \field{volume}{47}
  \verb{file}
  \verb :home/tpoisot/Documents/Papers/Evolution/Frank - 1993 - Evolution of ho
  \verb st-parasite diversity.pdf:pdf
  \endverb
  \field{journaltitle}{Evolution}
  \field{year}{1993}
\endentry

\entry{Frank1993a}{article}{}
  \name{author}{1}{}{%
    {{}%
     {Frank}{F.}%
     {Steven~A}{S.~A.}%
     {}{}%
     {}{}}%
  }
  \list{publisher}{1}{%
    {The Royal Society}%
  }
  \strng{namehash}{FSA1}
  \strng{fullhash}{FSA1}
  \field{labelyear}{1993}
  \field{extrayear}{3}
  \field{sortinit}{F}
  \field{number}{1341}
  \field{pages}{191\bibrangedash 197}
  \field{title}{{Specificity versus detectable polymorphism in host-parasite
  genetics}}
  \field{volume}{254}
  \verb{file}
  \verb :home/tpoisot/Documents/Papers/Proceedings of the Royal Society B Biolo
  \verb gical Sciences/Frank - 1993 - Specificity versus detectable polymorphis
  \verb m in host-parasite genetics.pdf:pdf
  \endverb
  \field{journaltitle}{Proceedings of the Royal Society B: Biological Sciences}
  \field{year}{1993}
\endentry

\entry{Holt1996}{article}{}
  \name{author}{1}{}{%
    {{}%
     {Holt}{H.}%
     {R~D}{R.~D.}%
     {}{}%
     {}{}}%
  }
  \list{publisher}{1}{%
    {Springer}%
  }
  \strng{namehash}{HRD1}
  \strng{fullhash}{HRD1}
  \field{labelyear}{1996}
  \field{sortinit}{H}
  \field{number}{1}
  \field{pages}{1\bibrangedash 11}
  \field{title}{{Demographic constraints in evolution: towards unifying the
  evolutionary theories of senescence and niche conservatism}}
  \field{volume}{10}
  \field{journaltitle}{Evolutionary Ecology}
  \field{year}{1996}
\endentry

\entry{PoisotBJLS2010}{article}{}
  \name{author}{2}{}{%
    {{}%
     {Poisot}{P.}%
     {Timoth\'{e}e}{T.}%
     {}{}%
     {}{}}%
    {{}%
     {Desdevises}{D.}%
     {Yves}{Y.}%
     {}{}%
     {}{}}%
  }
  \list{publisher}{1}{%
    {John Wiley \& Sons}%
  }
  \keyw{lamellodiscus,morphometry,speciation}
  \strng{namehash}{PTDY1}
  \strng{fullhash}{PTDY1}
  \field{labelyear}{2010}
  \field{sortinit}{P}
  \field{abstract}{%
  In the present study, we used morphometry as a proxy to study the
  microevolution of generalist Lamellodiscus (Monogenea, Diplectanidae)
  species, comprising gill parasites of sparid fish. We investigated 147
  individuals, belonging to nine described species, regrouped in four
  morphotypes. Morphometric measurements were taken on sclerotized parts of the
  attachment organ. The formation of groups on the basis of the global
  morphometry within a host species, or between several host species, was
  assessed using both exploratory analyses (principal component analysis and
  clustering analysis) and statistical tests. We showed that: (1) for three out
  of four morphotypes, the global morphometry was significantly different
  according to host species used, and (2) the coexistence of two populations of
  Lamellodiscus elegans on Diplodus sargus could reflect an ongoing intra-host
  speciation event. We suggest that generalist Lamellodiscus are undergoing
  specialization on their different hosts, which may lead to speciation.%
  }
  \verb{doi}
  \verb 10.1111/j.1095-8312.2009.01381.x
  \endverb
  \field{issn}{00244066}
  \field{number}{3}
  \field{pages}{559\bibrangedash 569}
  \field{title}{{Putative speciation events in Lamellodiscus (Monogenea:
  Diplectanidae) assessed by a morphometric approach}}
  \verb{url}
  \verb http://doi.wiley.com/10.1111/j.1095-8312.2009.01381.x
  \endverb
  \field{volume}{99}
  \verb{file}
  \verb :home/tpoisot/Documents/Papers/Biological Journal of the Linnean Societ
  \verb y/Poisot, Desdevises - 2010 - Putative speciation events in Lamellodisc
  \verb us (Monogenea Diplectanidae) assessed by a morphometric approach.pdf:pd
  \verb f
  \endverb
  \field{journaltitle}{Biological Journal of the Linnean Society}
  \field{month}{02}
  \field{year}{2010}
\endentry

\entry{R-Development-Core-Team2008}{manual}{}
  \name{author}{1}{}{%
    {{}%
     {{R Development Core Team}}{R.}%
     {}{}%
     {}{}%
     {}{}}%
  }
  \list{organization}{1}{%
    {R Foundation for Statistical Computing}%
  }
  \strng{namehash}{R1}
  \strng{fullhash}{R1}
  \field{labelyear}{2008}
  \field{sortinit}{R}
  \field{title}{{R: A Language and Environment for Statistical Computing}}
  \verb{url}
  \verb http://www.r-project.org
  \endverb
  \list{location}{1}{%
    {Vienna, Austria}%
  }
  \field{annotation}{%
  \{ISBN\} 3-900051-07-0%
  }
  \field{year}{2008}
\endentry

\entry{Tuomisto2010}{article}{}
  \name{author}{1}{}{%
    {{}%
     {Tuomisto}{T.}%
     {Hanna}{H.}%
     {}{}%
     {}{}}%
  }
  \strng{namehash}{TH1}
  \strng{fullhash}{TH1}
  \field{labelyear}{2010}
  \field{sortinit}{T}
  \verb{doi}
  \verb 10.1111/j.1600-0587.2009.05880.x
  \endverb
  \field{issn}{09067590}
  \field{number}{1}
  \field{pages}{2\bibrangedash 22}
  \field{title}{{A diversity of beta diversities: straightening up a concept
  gone awry. Part 1. Defining beta diversity as a function of alpha and gamma
  diversity}}
  \verb{url}
  \verb http://doi.wiley.com/10.1111/j.1600-0587.2009.05880.x
  \endverb
  \field{volume}{33}
  \verb{file}
  \verb :home/tpoisot/Documents/Papers/Ecography/Tuomisto - 2010 - A diversity
  \verb of beta diversities straightening up a concept gone awry. Part 1. Defin
  \verb ing beta diversity as a function of alpha and gamma diversity.pdf:pdf
  \endverb
  \field{journaltitle}{Ecography}
  \field{month}{02}
  \field{year}{2010}
\endentry

\entry{Tuomisto2011}{article}{}
  \name{author}{1}{}{%
    {{}%
     {Tuomisto}{T.}%
     {Hanna}{H.}%
     {}{}%
     {}{}}%
  }
  \keyw{alpha diversity \'{a} beta,diversity \'{a},gamma diversity \'{a}
  diversity,information on,partitioning \'{a} species turnover,quantifying
  taxonomic diversity requires,terminology,the need for consistent}
  \strng{namehash}{TH1}
  \strng{fullhash}{TH1}
  \field{labelyear}{2011}
  \field{sortinit}{T}
  \field{abstract}{%
  Meaningful quantification of species diversity requires that both 'species'
  and 'diversity' are unambiguously defined. Rigorous rules of nomenclature
  exist to ensure that each species has a single unique name, but the naming of
  concepts is much more variable. As a consequence, 'diversity' has been
  defined in so many different ways that its ability to transfer accurate
  information has been compromised. This problem can be solved by defining
  'diversity' as the effective number of species (or other types of interest),
  and using the term 'true diversity' to specify that this narrow concept is
  being used (analogously to using the term 'true bugs' when adhering to a
  narrow circumscription of 'bugs'). Other measures related to diversity (such
  as entropies and probabilities) continue to be useful, but they represent
  different phenomena and should therefore be referred to by different names.
  Total species diversity in a dataset can be partitioned into two components
  in several different ways. The components of a specific multiplicative
  partitioning can be called true alpha diversity and true beta diversity. When
  the partitioning is done in some other way, the resulting components are
  different and should be called by other names. For example, the beta
  component of additive partitioning does not equal true beta diversity, but
  can logically be called species turnover. All the phenomena that have been
  called 'beta diversity' in the ecological literature have also been called by
  alternative unique names. Consequently, a consistent terminology is already
  available; only a general agreement to use it is lacking.%
  }
  \verb{doi}
  \verb 10.1007/s00442-011-2128-4
  \endverb
  \field{issn}{1432-1939}
  \field{pages}{903\bibrangedash 911}
  \field{title}{{Commentary: do we have a consistent terminology for species
  diversity? Yes, if we choose to use it.}}
  \verb{url}
  \verb http://www.ncbi.nlm.nih.gov/pubmed/21947563
  \endverb
  \field{volume}{167}
  \verb{file}
  \verb :home/tpoisot/Documents/Papers/Oecologia/Tuomisto - 2011 - Commentary d
  \verb o we have a consistent terminology for species diversity Yes, if we cho
  \verb ose to use it.pdf:pdf
  \endverb
  \field{journaltitle}{Oecologia}
  \field{month}{09}
  \field{year}{2011}
\endentry

\entry{Yang2012}{article}{}
  \name{author}{2}{}{%
    {{}%
     {Yang}{Y.}%
     {Ziheng}{Z.}%
     {}{}%
     {}{}}%
    {{}%
     {Rannala}{R.}%
     {Bruce}{B.}%
     {}{}%
     {}{}}%
  }
  \list{publisher}{1}{%
    {Nature Publishing Group}%
  }
  \strng{namehash}{YZRB1}
  \strng{fullhash}{YZRB1}
  \field{labelyear}{2012}
  \field{sortinit}{Y}
  \verb{doi}
  \verb 10.1038/nrg3186
  \endverb
  \field{issn}{1471-0056}
  \field{number}{May}
  \field{title}{{Molecular phylogenetics: principles and practice}}
  \verb{url}
  \verb http://www.nature.com/doifinder/10.1038/nrg3186
  \endverb
  \field{volume}{13}
  \verb{file}
  \verb :home/tpoisot/Documents/Papers/Nature Reviews Genetics/Yang, Rannala -
  \verb 2012 - Molecular phylogenetics principles and practice.pdf:pdf
  \endverb
  \field{journaltitle}{Nature Reviews Genetics}
  \field{month}{03}
  \field{year}{2012}
\endentry

\lossort
\endlossort

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