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OUP CORRECTED AUTOPAGE PROOFS – FINAL, 01/12/20, SPi Habitat Ecology and Analysis OUP CORRECTED AUTOPAGE PROOFS – FINAL, 01/12/20, SPi OUP CORRECTED AUTOPAGE PROOFS – FINAL, 01/12/20, SPi Habitat Ecology and Analysis Joseph A. Veech Department of Biology, Texas State University, USA 1 OUP CORRECTED AUTOPAGE PROOFS – FINAL, 01/12/20, SPi 1 Great Clarendon Street, Oxford, OX2 6DP, United Kingdom Oxford University Press is a department of the University of Oxford. It furthers the University’s objective of excellence in research, scholarship, and education by publishing worldwide. Oxford is a registered trade mark of Oxford University Press in the UK and in certain other countries © Joseph A. Veech 2021 The moral rights of the author have been asserted First Edition published in 2021 Impression: 1 All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, without the prior permission in writing of Oxford University Press, or as expressly permitted by law, by licence or under terms agreed with the appropriate reprographics rights organization. Enquiries concerning reproduction outside the scope of the above should be sent to the Rights Department, Oxford University Press, at the address above You must not circulate this work in any other form and you must impose this same condition on any acquirer Published in the United States of America by Oxford University Press 198 Madison Avenue, New York, NY 10016, United States of America British Library Cataloguing in Publication Data Data available Library of Congress Control Number: 2020945816 ISBN 978–0–19–882928–7 (hbk.) ISBN 978–0–19–882941–6 (pbk.) DOI: 10.1093/oso/9780198829287.001.0001 Printed and bound by CPI Group (UK) Ltd, Croydon, CR0 4YY OUP CORRECTED AUTOPAGE PROOFS – FINAL, 01/12/20, SPi Preface I have always been impressed that the best way to labelled as wildlife ecology, and this line of research go about finding an animal (and perhaps a plant) is continues today. I consider myself to be an ecologist to go look for it in its habitat. My childhood was as well as a wildlife ecologist, and there are distinc- filled with me doing this, typically trying to capture tions between the two. Thus, I have written this the local reptiles and amphibians more so than book from a combined perspective, and I hope that other types of species. I often consulted field guides it will be of interest and use to students and practi- to get guidance on where to look. As I eventually tioners in both disciplines. transitioned into a formal education in ecology and The book can be considered as two parts. In the being a working professional ecologist, I became first part (Chapters 1–4) I discuss the history of the even more interested in how animals associate with habitat concept and differences between ecology particular types of habitat. My dissertation and and wildlife ecology, present a conceptual/prob- research endeavors early in my career did not have abil is tic model of the overriding importance of habi- much to do with habitat, at least not explicitly. tat, and outline goals of studying and analyzing Broadly speaking, my research has always been habitat. In the second part (Chapters 5–11) I explain directed at examining the ecological factors that some relatively common methods for analyzing determine the distribution and abundance of spe- habitat and discuss some related statistical issues. cies in nature as well as those factors affecting pat- This part of the book is intended as a user’s manual terns of biodiversity. I have used many different or reference guide for readers confronted with the approaches to research and worked on species in particular task of figuring out the habitat as so ci- various taxonomic groups without having any par- ations of a species. In writing the statistical part of ticular study species or system. In this context, I the book, I strove to use common language and have conducted studies at various spatial scales explain the “mysterious” terminology that some- from local ecological communities to landscapes to times accompanies descriptions of some statistical biogeographic regions. I have also always been techniques. My intention is that the reader need interested in developing new statistical approaches only have an introductory-level comprehension of and examining their performance. Over the years, statistics in order to get a practical understanding my research has been both field-based and computer- out of the second part of the book. Indeed, some of based as in simulation modeling. A few years ago, it Part II may be “review” to readers who have a more finally occurred to me that the common theme sophisticated and experienced perspective on underlying my disparate research interests was the stat is tics. recognition that habitat and a species’ habitat Given that my native language is English, there is requirements are fundamentally important to a lot an unintended neglect of the literature written in of what we study as ecologists. other languages, particularly with regard to Most of my formal training and education is Chapter 1 where I trace the history of the study of within the large and encompassing academic field habitat. I know I have missed including the early of ecology. However, early in my career, I also con- writings of ecologists from countries such as ducted studies that most accurately could be Germany, France, Japan, Italy, Spain, various Latin v OUP CORRECTED AUTOPAGE PROOFS – FINAL, 01/12/20, SPi vi PREFACE American countries, and perhaps others. An early I was writing this book over a 2-year period, I was ecology textbook (Adams 1913, cited in Chapter 1) not as diligent to the needs of my graduate students provides an excellent list of references by German as I would have been otherwise; however, they all naturalists and ecologists. Otherwise, in writing remained patient with me and I thank them for that. this book, I have attempted to draw on a wide var- It was a pleasure working with Ian Sherman and iety of studies conducted by researchers from Charlie Bath (OUP) in putting together this book. around the world studying all sorts of animals. Lastly, my wife and daughter allowed me a nice I very much appreciate colleagues and students quiet room at home to work on the book, particularly who either reviewed parts of the book, provided me in spring 2020 when those fortunate enough to work with important materials, or engaged in email con- from home were doing so, for obvious reasons. versation. They are Ivan Castro-Arellano, Jared Joseph A. Veech Haney, Steve Jenkins, John Majoris, Curt Meine, San Marcos, Texas, USA Randy Simpson, Stan Temple, Jeff Troy, and graduate June 2020 students in my habitat ecology course in fall 2019. As OUP CORRECTED AUTOPAGE PROOFS – FINAL, 01/12/20, SPi CHAPTER 1 Introduction Habitat is where an organism lives—that’s the sim- “inhabit,” “habitant”) that have a greater realm of plest definition. However, as a concept integral to usage than just in biology or ecology. Carl Linnaeus many areas of ecological investigation and know- used the term in 1745 in Flora Svecica as did his stu- ledge, habitat is a bit more complicated and com- dent, Johan Gustaf Hallman, in his dissertation in prehensive than simply where an organism lives. the same year, titled Dissertatio Botanica de Passiflora. I accessed the immense ISI Web of Science literature By the 1766 edition of Systema Naturae, Linnaeus database and did a keyword search on “habitat” was routinely using “habitat” to denote the general and several other terms often used by ecologists. Of area where a species was from, such as “Mari medi- course in return I received many results—more terraneo” (Mediterranean Sea) for “Testudo coriacea,” papers than I could read in several lifetimes and a now known as the leatherback sea turtle (Dermochelys list of titles that would take several days or longer coriacea). This particular usage con tinued for well to go through, never mind reading the abstracts. over 120 years and was relatively common in My point: for ecologists, “habitat” is a very familiar broad taxonomic treatises wherein each species was term, concept, and real-world entity and has been described in a consistent format of categories such for a very long time. Perhaps it could even be con- as “appearance,” “diet,” “habits,” and “habitat.” sidered a level of ecological (if not biological) The latter would typically be followed by only a organization. As a term of common usage, it ranks few words indicating the geographical region right up there with several others (Fig. 1.1). Thus (sometimes as a geopolitical label, e.g., “Mexico”) “habitat ecology,” broadly defined as the study of the or even a single locality where the species existed habitat requirements of species and effects of habitat on and was collected. This was hardly a description of individual survival, population persistence, and spatial habitat in the modern sense of the word. Incidentally, distribution, has had a prominent place in the devel- the word “habits” probably dates back even further opment of ecology as an academic field and as a and today is somewhat archaic with regard to usage knowledge base for conserving and managing the in ecological literature; it generally meant the planet’s living natural resources. behavior of the species. A slightly more modern usage of “habitat” appeared by 1791. The very first volume of Transac- 1.1 History of the habitat concept tions of the Linnean Society of London (a journal that is In the scientific literature, use of “habitat” predates no longer in print) included accounts of some lichen “ecology” as the latter was not coined until 1866 by “species” collected from southern Europe. For each the famous German biologist and philosopher, species account, there was a habi tat category filled Ernst Haeckel (Stauffer 1957). The habitat concept with a very short descriptor in Latin such as rupibus developed over a period of at least 200 years (Fig. 1.2). calcareis (limestone rock), rupibus alpinis (alpine To my knowledge, no one has ever tracked down rock), ericetis alpinis (alpine moor), truncis arborum the first use of the word “habitat.” This would be a (tree trunk), and corticibus olearum (bark of olive difficult task anyway given that the word has trees) (Smith 1791). In the same volume, the habitat shared etymology with other similar words (e.g., of the buff ermine moth (Phalaena bombyx, now Habitat Ecology and Analysis. Joseph A. Veech, Oxford University Press (2021). © Joseph A. Veech. DOI: 10.1093/oso/9780198829287.003.0001 OUP CORRECTED AUTOPAGE PROOFS – FINAL, 01/12/20, SPi 4 HABITAT ECOLOGY AND ANALYSIS Figure 1.1 Word cloud depicting usage of “habitat” and select other terms in the ecological literature from 1864–2018. Each word was searched in ISI Web of Science along with “ecolog*” so as to eliminate papers that were not ecological. Each term appeared in the title or abstract of the following number of papers (×1,000): species—1,657, population—1,576, behavior—750, soil—749, community—728, resource—726, habitat—695, environment—592, reproduction—536, organism—415, wildlife—392, climate—352, ecosystem—333, individual—322, biodiversity—223, adaptation—210, gene—210, foraging—145, landscape—117, competition—107, dispersal—106, predation—105, photosynthesis—77, trophic—67, parasitism—52, niche—52, succession—52, primary production—51, food web—38, decomposition—38, pollination—27, and mutualism—24. Spilarctia luteum) was listed as arboribus pomiferis and Owen had a specific goal for doing his habitat ana- quercu (fruit-bearing trees and oaks) (Marsham lysis—he wanted to test a hypothesis. He proposed 1791). These examples represent a transition to a that the suborbital, maxillary, and inguinal glands modern concept of habitat in that the habitat of each found in some species, but absent or underdevel- species was viewed as the type of vegetation or sub- oped in others, had the purpose of facilitating the strate where the species exists rather than as the geo- aggregation of individuals of a species. That is, graphical location where the specimen was collected. individual antelopes would secrete onto vegetation Another notable advancement occurred in 1836. or large rocks and these secretions “might serve to Early in his career, the well-known naturalist and direct individuals of the same species to each other.” biologist, Richard Owen, prepared and presented a Owen was looking to see whether species inhabiting table of the habitats of antelope species in India and open plains lacked the glands (due to the absence of Africa during the Proceedings of the Zoological shrubs and rocks to secrete on) whereas those of for- Society of London (Owen 1836). For each of 60 spe- est areas had the glands, and further whether cies, the table gave a short descriptor of the habitat, gregarious species had the glands whereas solitary such as hilly forests, open plains, stony plains and species did not. According to Owen, his table valleys, desert borders, rocky hills, thickets, reedy showed that some of the plains-inhabiting species banks, and Acacia groves. Of particular importance, lacked the glands and some had the glands irre- OUP CORRECTED AUTOPAGE PROOFS – FINAL, 01/12/20, SPi INTRODUCTION 5 Figure 1.2 Historical timeline for the development of the habitat concept. spective of whether the species was gregarious or ample opportunity to do so. Instead he used “sta- solitary. A similar lack of pattern was evident in the tion” and “habitation” in contexts where “habitat” forest-dwelling species. Hence, Owen rejected his could have fit, although both the former were also own hypothesis. In addition to testing a hypothesis, used in Voyage to denote a location of human settle- his study is notable in several other respects. He ment or occupation. In the 574 pages of The Geo- had at least a dozen or so habitat types represented graphical Distribution of Animals (1876), Alfred Russel among the 60 species indicating a fairly detailed Wallace used “habitat,” “habitation,” and “station” classification of habitat. Owen had a specific bio- each a few times. However, he did attempt to define logic al and ecological reason for identifying the and distinguish “habitat” and “station” (p. 4). He habitat of each species. Presumably, he compiled defined “station” as a locality wherein two or more the table from previously published literature— stations are separated by some distance but tend perhaps an early forerunner of studies that use a nonetheless to have the same habitat. In comparison macroecological approach or the comparative with stations, habitats were recognized as having method, both of which involve species as the units distinct vegetation or terrain. Wallace defined both of analysis. Lastly, Owen implicitly recognized the terms in the context of changes in the species inh abit- possibility that a physical structure on an organism ing each. In his words, “The whole area over which might relate to the habitat where it occurs and have a particular animal is found may consist of any a specific function related to behavior. Of course, in number of stations, but rarely of more than one 1836 he did not use the word “adaptation”—the habit at” (p. 4). With neither Darwin nor Wallace do development of that concept would be left to some- we find a specific and detailed concept of habitat, one a couple decades later. nonetheless, Wallace’s writings began to at least hint Interestingly, Charles Darwin did not use “habi- toward the modern concept of habitat. tat” in Voyage of the Beagle (1839) or On the Origin of In the early to mid-nineteenth century, published Species (1859) although there would have been journals devoted to natural history began to emerge. OUP CORRECTED AUTOPAGE PROOFS – FINAL, 01/12/20, SPi 6 HABITAT ECOLOGY AND ANALYSIS Prior to this, there had been scientific journals for at or even captive individuals. But there was either no least 150 years, dating back to the Philosophical mention of “habitat,” or habitat was denoted as a Transactions of the Royal Society established in 1665 region or locality where the species or individual by the Royal Society, which itself had been organ- originated, as though following the precedent set ized in England only 5 years earlier. Perhaps the by Linnaeus more than 100 years earl ier. Many of earliest exclusively biological journals were Transac- these natural history accounts appeared in the tions of the Linnean Society of London (1791) and Pro- American Naturalist between 1867 and 1880 by ceedings of the Zoological Society of London (1830), and authors such as Elliott Coues, Augustus Fowler, both of these often contained natural history contri- Samuel Lockwood, Alpheus Packard, and Charles butions and species accounts. During the early Abbott (see Abbott 1860, 1870a, b, c, 1873; Packard years, scientific studies were read to members of the 1867, 1871, 1876; Fowler 1868a, b; Lockwood 1875, societies at regular meetings—this practice con- 1876). Another form of natural history writing, tinued well into the nineteenth century as repre- which might now be thought of as early taxonomy, sented by the famous readings of Darwin and involved a systematic treatise of a group of species Wallace’s theories about natural selection to mem- in which specific characteristics of each species, bers of the Linnean Society of London on July 1, sometimes including “habitat,” were presented in 1858. Even relatively mundane papers were read at an orderly way. Again, habitat was conceived by meetings, such as the previously described study these authors only in the Linnaean fashion of iden- by Owen presented at the meeting of the Zoological tifying the collecting location or geographic region Society of London on March 22, 1836. Owen pre- where the species existed. Naturalists engaged in sented his hypothesis and assessment of antelope this type of writing typically had formal scientific habitat as a follow-up to a paper read by Edward training and advanced degrees and to a modern Bennett in which he described the facial glands of audience their papers sound more scientific than Indian antelopes. Eventually the “reading to the the narratives of the other type of natural history society members” route to publishing a scientific writing. These papers appeared in all the previ- study became outdated. Henceforth, scientific jour- ously mentioned journals; particularly prolific nals could organize (perhaps under the auspices of writers included Edward Cope, David Jordan, a professional society or organization although not Charles Abbott, Albert Günther, and Charles Cory a necessity) without being tied to the physical pro- (see Abbott 1860, 1870a, b, c, 1873; Cope 1869, 1896; cess of a paper first being read at a meeting. The fol- Günther 1871, 1875; Jordan 1874, 1877; Jordan and lowing journals emerged with a definite focus on Copeland 1877; Cory 1891, 1886). The authors of natural history and in particular reporting on the both types of paper often presented very compre- discovery of new species: Annals and Magazine of hensive measurements and information on the mor- Natural History (1838), Ibis (1859), American Natural- phological traits of the species with no description ist (1867), Bulletin of the American Museum of Natural of habitat—again this reflects an early em phasis on History (1881), and The Auk (1884). taxonomy and classifying species (often by authors The time period from about 1850–1900 may have with close associations with museums) rather than been the golden age of natural history writing. Prior on studying the species’ ecological role in nature. to this, much of the scientific biological literature This inattention to habitat (as we conceive it from was written in Latin or in a very obtuse and long- our modern perspective) was prevalent and perva- winded way. Into the nineteenth century there were sive in the period 1850–1900. Naturalists of various still many species to be discovered and many regions nationalities writing about all types of organisms in to be explored and inventoried. Professional and all regions of the world generally neglected to even amateur naturalists came along and began writing mention the habitat of their subjects or defined the in a very easy-to-read conversational type of prose. habitat in a very broad and often geographic con- Their writings often consisted of presenting behav- text; that is, the Linnaean way (Table 1.1). There ioral and basic ecological information on a given were occasional exceptions. Abbott (1870a) wrote species often obtained by direct observation of wild about “mud-loving fishes” and even used that term