Biodiversity Conservation and Phylogenetic Systematics

Biodiversity Conservation and Phylogenetic Systematics

Biodiversity Conservation and Phylogenetic Systematics

395 Pages ·2016·11.83 MB ·English

Biodiversity Conservation and Phylogenetic Systematics

Topics in Biodiversity and Conservation


Roselix00Pellens


Philippex00Grandcolas E ditors


Biodiversity


Conservation


and Phylogenetic


Systematics


Preserving our evolutionary heritage


in an extinction crisis Topics in Biodiversity and Conservation


Volume 14 More information about this series at h ttp://www.springer.com/series/7488 Roseli Pellens (cid:129) Philippe Grandcolas



Editors


Biodiversity Conservation


and Phylogenetic Systematics


Preserving our evolutionary heritage in an


extinction crisis



With the support of Labex BCDIV and ANR BIONEOCAL Editors


Roseli Pellens Philippe Grandcolas


Institut de Systématique, Evolution, Institut de Systématique, Evolution,


Biodiversité, ISYEB – UMR 7205 Biodiversité, ISYEB – UMR 7205


CNRS MNHN UPMC EPHE, CNRS MNHN UPMC EPHE,


Muséum National d’Histoire Naturelle Muséum National d’Histoire Naturelle


Sorbonne Universités Sorbonne Universités


Paris , France Paris , France


ISSN 1875-1288 ISSN 1875-1296 (electronic)


Topics in Biodiversity and Conservation


ISBN 978-3-319-22460-2 ISBN 978-3-319-22461-9 (eBook)


DOI 10.1007/978-3-319-22461-9


Library of Congress Control Number: 2015960738


Springer Cham Heidelberg New York Dordrecht London


© The Editor(s) (if applicable) and The Author(s) 2016 . The book is published with open access at


SpringerLink.com.


Chapter 15 was created within the capacity of an US governmental employment. US copyright protection


does not apply.


Open Access This book is distributed under the terms of the Creative Commons Attribution


Noncommercial License, which permits any noncommercial use, distribution, and reproduction in any


medium, provided the original author(s) and source are credited.


All commercial rights are reserved by the Publisher, whether the whole or part of the material is


concerned, specifi cally the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting,


reproduction on microfi lms or in any other physical way, and transmission or information storage and


retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known


or hereafter developed.


The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication


does not imply, even in the absence of a specifi c statement, that such names are exempt from the relevant


protective laws and regulations and therefore free for general use.


The publisher, the authors and the editors are safe to assume that the advice and information in this book


are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the


editors give a warranty, express or implied, with respect to the material contained herein or for any errors


or omissions that may have been made.


Printed on acid-free paper


Springer International Publishing AG Switzerland is part of Springer Science+Business Media


(www.springer.com) Foreword


The desperate, and seemingly inexorably worsening, state of biodiversity on Earth


is arguably not a consequence of conscious choices. That is much of the problem.


There are undoubtedly cases, and many of them, in which people made explicit


decisions to forgo the variety of life naturally present in a given area in favour of


some alternative benefi t (e.g. agricultural activity, energy production, housing).


However, by and large, the global losses of species, and the reductions in the abun-


dances and distributions of increasingly the majority of others, are the outcome of


outright ignorance of the impacts of anthropogenic activities, of underestimation or


misunderstanding of the impacts of those activities, and, perhaps most signifi cantly,


a host of individual decisions which whilst independently perhaps quite rational


have led to a combined pressure on biodiversity that is far from what it can sustain.


The fi eld of conservation biology has done much to highlight the status and


trends in biodiversity, but especially the need for active and explicit choices as to its


future. Frustrating as is their failure to date to be realized, the establishment of base-


lines and targets for biodiversity at regional, national and global scales is the logical


framework within which decisions can properly be made as to what environmental


changes and management actions are and are not carried forward, and with what


consequences. The ‘agony of choice’ needs to be a real choice, albeit the agony may


not always be avoided.


Key to determining baselines and targets, and what choices to make, is deciding


which metric to use to discriminate between different outcomes, and particularly to


compare those of current actions with alternatives. This book provides a cogent


argument for the use of phylogenetic diversity as a key metric – that is, measures of


biodiversity that capture evolutionary history – and phylogenetic systematics as a


core organizing principle. It highlights the benefi ts and constraints of such an


approach, explores the ways in which it can be implemented, and describes a rich


diversity of applications. This is the most comprehensive compilation of cutting-


edge contributions on this topic to date, provides many valuable insights, and a ‘go


to’ source of understanding. The intention to help improve the global condition of


biodiversity is apparent throughout.


v vi Foreword


Biological conservation has oft been hampered by those who have maintained


that priorities for action should only be established using approaches that are easily


understood by the general public. The same demand has not been made in many


other arenas of human endeavor (e.g. medicine, nuclear power), and neither should


it constrain biological conservation. That said, there does remain a substantial chal-


lenge of encouraging an informed citizenry around the justifi cation and goals of


using a phylogenetic diversity approach, and gaining their support. Only by so


doing will there be a genuine chance of aligning the multitude of biodiversity-criti-


cal decisions being made each and every day across the continents and oceans.


Environment and Sustainability Institute Kevin J. Gaston


University of Exeter , Exeter , UK Acknowledgements


This book could not exist without the participation of 38 research scientists who


took part in the elaboration of these chapters. We thank each of them for their


generosity in sharing their experience to make this common work. We are particularly


indebted to Dan Faith, for his always prompt and insightful suggestions. Without his


help this book would have been quite different. Every chapter was peer reviewed,


and reviewers’ suggestions and critical thinking helped to improve all manuscripts


and greatly contributed to our present understanding of phylogenetic diversity and


its importance for biodiversity conservation. So, we thank Anni Arponen, Lisa


Ballance, Sven Buerki, Maram Caesar, Marcel Cardillo, Pedro Cardoso, Ben Collen,


Rob Cowie, Jorge Crisci, Mike Crisp, Jonathan Davies, Dan Faith, Jon Fjeldså,


Felix Forest, Carlos Gonzalez-Orozco, Shan Huang, Jussi Laitila, Romain Julliard,


James Justus, Matjaz Kuntner, Frédéric Legendre, Rafael Loyola, Laura J. May-


Collado, Daniel Rafael Miranda-Esquivel, Claudia Moreno, Annemarie Ohler,


Fabio Pardi, Stéphane Prigent, Carlo Ricotta, Samuel Scheiner, Mike Steel, Andreas


Spiller, Géraldine Veron, and Kristen Williams, who kindly acted as referees (often


anonymously) for the chapters. The idea of making this book was born during the


preparation of a symposium entitled “Phylogenetic Tools for Conservation” that


Roseli Pellens organized for the 30th meeting of the Willi Hennig Society at São


José do Rio Preto, State of São Paulo, Brazil. We thank Fernando Barbosa Noll and


Dalton de Souza Amorim, the meeting organizers, for including this subject in their


agenda. We thank the Labex “Diversités biologiques et culturelles: origines,


évolution, interactions, devenir” (BCDIV, Jean-Denis Vigne) and the ANR


BIONEOCAL (PG) for the fi nancial support that permitted to make this publication


open access. We are also very grateful to David Hawksworth, the series editor, and


the people at Springer, for their kind help along the preparation of this volume.


vii Contents


Phylogenetics and Conservation Biology:


Drawing a Path into the Diversity of Life ..................................................... 1


Roseli Pellens and Philippe Grandcolas


Part I Questions


The Value of Phylogenetic Diversity .............................................................. 19


Christopher Lean and James Maclaurin


The PD Phylogenetic Diversity Framework: Linking


Evolutionary History to Feature Diversity


for Biodiversity Conservation ........................................................................ 39


Daniel P. Faith


Reconsidering the Loss of Evolutionary History: How Does


Non-random Extinction Prune the Tree-of-Life? ......................................... 57


Kowiyou Yessoufou and T. Jonathan Davies


Phylogenetics and Conservation in New Zealand:


The Long and the Short of It ......................................................................... 81


Steven A. Trewick and Mary Morgan-Richards


What Is the Meaning of Extreme Phylogenetic


Diversity? The Case of Phylogenetic Relict Species ..................................... 99


Philippe Grandcolas and Steven A. Trewick


Part II Methods


Using Phylogenetic Dissimilarities Among Sites for Biodiversity


Assessments and Conservation ...................................................................... 119


Daniel P. Faith


ix


Topics in Biodiversity and Conservation


Roselix00Pellens


Philippex00Grandcolas E ditors


Biodiversity


Conservation


and Phylogenetic


Systematics


Preserving our evolutionary heritage


in an extinction crisis Topics in Biodiversity and Conservation


Volume 14 More information about this series at h ttp://www.springer.com/series/7488 Roseli Pellens (cid:129) Philippe Grandcolas



Editors


Biodiversity Conservation


and Phylogenetic Systematics


Preserving our evolutionary heritage in an


extinction crisis



With the support of Labex BCDIV and ANR BIONEOCAL Editors


Roseli Pellens Philippe Grandcolas


Institut de Systématique, Evolution, Institut de Systématique, Evolution,


Biodiversité, ISYEB – UMR 7205 Biodiversité, ISYEB – UMR 7205


CNRS MNHN UPMC EPHE, CNRS MNHN UPMC EPHE,


Muséum National d’Histoire Naturelle Muséum National d’Histoire Naturelle


Sorbonne Universités Sorbonne Universités


Paris , France Paris , France


ISSN 1875-1288 ISSN 1875-1296 (electronic)


Topics in Biodiversity and Conservation


ISBN 978-3-319-22460-2 ISBN 978-3-319-22461-9 (eBook)


DOI 10.1007/978-3-319-22461-9


Library of Congress Control Number: 2015960738


Springer Cham Heidelberg New York Dordrecht London


© The Editor(s) (if applicable) and The Author(s) 2016 . The book is published with open access at


SpringerLink.com.


Chapter 15 was created within the capacity of an US governmental employment. US copyright protection


does not apply.


Open Access This book is distributed under the terms of the Creative Commons Attribution


Noncommercial License, which permits any noncommercial use, distribution, and reproduction in any


medium, provided the original author(s) and source are credited.


All commercial rights are reserved by the Publisher, whether the whole or part of the material is


concerned, specifi cally the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting,


reproduction on microfi lms or in any other physical way, and transmission or information storage and


retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known


or hereafter developed.


The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication


does not imply, even in the absence of a specifi c statement, that such names are exempt from the relevant


protective laws and regulations and therefore free for general use.


The publisher, the authors and the editors are safe to assume that the advice and information in this book


are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the


editors give a warranty, express or implied, with respect to the material contained herein or for any errors


or omissions that may have been made.


Printed on acid-free paper


Springer International Publishing AG Switzerland is part of Springer Science+Business Media


(www.springer.com) Foreword


The desperate, and seemingly inexorably worsening, state of biodiversity on Earth


is arguably not a consequence of conscious choices. That is much of the problem.


There are undoubtedly cases, and many of them, in which people made explicit


decisions to forgo the variety of life naturally present in a given area in favour of


some alternative benefi t (e.g. agricultural activity, energy production, housing).


However, by and large, the global losses of species, and the reductions in the abun-


dances and distributions of increasingly the majority of others, are the outcome of


outright ignorance of the impacts of anthropogenic activities, of underestimation or


misunderstanding of the impacts of those activities, and, perhaps most signifi cantly,


a host of individual decisions which whilst independently perhaps quite rational


have led to a combined pressure on biodiversity that is far from what it can sustain.


The fi eld of conservation biology has done much to highlight the status and


trends in biodiversity, but especially the need for active and explicit choices as to its


future. Frustrating as is their failure to date to be realized, the establishment of base-


lines and targets for biodiversity at regional, national and global scales is the logical


framework within which decisions can properly be made as to what environmental


changes and management actions are and are not carried forward, and with what


consequences. The ‘agony of choice’ needs to be a real choice, albeit the agony may


not always be avoided.


Key to determining baselines and targets, and what choices to make, is deciding


which metric to use to discriminate between different outcomes, and particularly to


compare those of current actions with alternatives. This book provides a cogent


argument for the use of phylogenetic diversity as a key metric – that is, measures of


biodiversity that capture evolutionary history – and phylogenetic systematics as a


core organizing principle. It highlights the benefi ts and constraints of such an


approach, explores the ways in which it can be implemented, and describes a rich


diversity of applications. This is the most comprehensive compilation of cutting-


edge contributions on this topic to date, provides many valuable insights, and a ‘go


to’ source of understanding. The intention to help improve the global condition of


biodiversity is apparent throughout.


v vi Foreword


Biological conservation has oft been hampered by those who have maintained


that priorities for action should only be established using approaches that are easily


understood by the general public. The same demand has not been made in many


other arenas of human endeavor (e.g. medicine, nuclear power), and neither should


it constrain biological conservation. That said, there does remain a substantial chal-


lenge of encouraging an informed citizenry around the justifi cation and goals of


using a phylogenetic diversity approach, and gaining their support. Only by so


doing will there be a genuine chance of aligning the multitude of biodiversity-criti-


cal decisions being made each and every day across the continents and oceans.


Environment and Sustainability Institute Kevin J. Gaston


University of Exeter , Exeter , UK Acknowledgements


This book could not exist without the participation of 38 research scientists who


took part in the elaboration of these chapters. We thank each of them for their


generosity in sharing their experience to make this common work. We are particularly


indebted to Dan Faith, for his always prompt and insightful suggestions. Without his


help this book would have been quite different. Every chapter was peer reviewed,


and reviewers’ suggestions and critical thinking helped to improve all manuscripts


and greatly contributed to our present understanding of phylogenetic diversity and


its importance for biodiversity conservation. So, we thank Anni Arponen, Lisa


Ballance, Sven Buerki, Maram Caesar, Marcel Cardillo, Pedro Cardoso, Ben Collen,


Rob Cowie, Jorge Crisci, Mike Crisp, Jonathan Davies, Dan Faith, Jon Fjeldså,


Felix Forest, Carlos Gonzalez-Orozco, Shan Huang, Jussi Laitila, Romain Julliard,


James Justus, Matjaz Kuntner, Frédéric Legendre, Rafael Loyola, Laura J. May-


Collado, Daniel Rafael Miranda-Esquivel, Claudia Moreno, Annemarie Ohler,


Fabio Pardi, Stéphane Prigent, Carlo Ricotta, Samuel Scheiner, Mike Steel, Andreas


Spiller, Géraldine Veron, and Kristen Williams, who kindly acted as referees (often


anonymously) for the chapters. The idea of making this book was born during the


preparation of a symposium entitled “Phylogenetic Tools for Conservation” that


Roseli Pellens organized for the 30th meeting of the Willi Hennig Society at São


José do Rio Preto, State of São Paulo, Brazil. We thank Fernando Barbosa Noll and


Dalton de Souza Amorim, the meeting organizers, for including this subject in their


agenda. We thank the Labex “Diversités biologiques et culturelles: origines,


évolution, interactions, devenir” (BCDIV, Jean-Denis Vigne) and the ANR


BIONEOCAL (PG) for the fi nancial support that permitted to make this publication


open access. We are also very grateful to David Hawksworth, the series editor, and


the people at Springer, for their kind help along the preparation of this volume.


vii Contents


Phylogenetics and Conservation Biology:


Drawing a Path into the Diversity of Life ..................................................... 1


Roseli Pellens and Philippe Grandcolas


Part I Questions


The Value of Phylogenetic Diversity .............................................................. 19


Christopher Lean and James Maclaurin


The PD Phylogenetic Diversity Framework: Linking


Evolutionary History to Feature Diversity


for Biodiversity Conservation ........................................................................ 39


Daniel P. Faith


Reconsidering the Loss of Evolutionary History: How Does


Non-random Extinction Prune the Tree-of-Life? ......................................... 57


Kowiyou Yessoufou and T. Jonathan Davies


Phylogenetics and Conservation in New Zealand:


The Long and the Short of It ......................................................................... 81


Steven A. Trewick and Mary Morgan-Richards


What Is the Meaning of Extreme Phylogenetic


Diversity? The Case of Phylogenetic Relict Species ..................................... 99


Philippe Grandcolas and Steven A. Trewick


Part II Methods


Using Phylogenetic Dissimilarities Among Sites for Biodiversity


Assessments and Conservation ...................................................................... 119


Daniel P. Faith


ix


Please note: To fully read this free PDF ebook completely for free you need .