Biodivers Conserv (2017) 26:2993–2998

DOI 10.1007/s10531-017-1401-1

COMMENTARY

Measuring biodiversity in the Anthropocene: a simple

guide to helpful methods

Claudia E. Moreno1 • Jaime M. Calderón-Patrón1 •

Vı́ctor Arroyo-Rodrı́guez2 • Felipe Barragán3 • Federico Escobar4 •

Yuriana Gómez-Ortiz5 • Natalia Martı́n-Regalado1 •

Ana P. Martı́nez-Falcón1 • Miguel Ángel Martı́nez-Morales6 •
Eduardo Mendoza7 • Ilse J. Ortega-Martı́nez1 •
Cisteil X. Pérez-Hernández8 • Eduardo Pineda9 •
Rubén Pineda-López10 • C. Lucero Rios-Dı́az1 • Pilar Rodrı́guez11 •

Fernando Rosas1 • Jorge E. Schondube2 • Iriana Zuria1

Received: 1 June 2017 / Accepted: 1 July 2017 / Published online: 12 July 2017
Ó Springer Science+Business Media B.V. 2017

Abstract Quantifying biodiversity patterns in the context of human-caused environmental

degradation is a fundamental task to improve conservation strategies; yet, it can be difficult
given the rapid increase of available analytical methods. To guide studies on the topic, in
this brief essay we present four approaches, accompanied by empirical examples, that can
be used to accurately assess the impact of human activities on different facets of biological

Communicated by Dirk Sven Schmeller.

& Claudia E. Moreno

cmoreno@uaeh.edu.mx
1
Centro de Investigaciones Biológicas, Instituto de Ciencias Básicas e Ingenierı́a, Universidad
Autónoma del Estado de Hidalgo, Pachuca, Mexico
2
Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de
México, Morelia, Mexico
3
División de Ciencias Ambientales, CONACYT-Instituto Potosino de Investigación Cientı́fica y
Tecnológica A.C., San Luis Potosı́, Mexico
4
Red de Ecoetologı́a, Instituto de Ecologı́a A.C., Xalapa, Mexico
5
División de Desarrollo Sustentable, Universidad Intercultural del Estado de México,
San Felipe del Progreso, Estado de México, Mexico
6
Departamento de Conservación de la Biodiversidad, El Colegio de la Frontera Sur,
San Cristóbal de las Casas, Mexico
7
Instituto de Investigaciones sobre los Recursos Naturales, Universidad Michoacana de San Nicolás
de Hidalgo, Morelia, Mexico
8
Instituto de Biologı́a, Universidad Nacional Autónoma de México, Mexico City, Mexico
9
Red de Biologı́a y Conservación de Vertebrados, Instituto de Ecologı́a, A.C., Xalapa, Mexico
10
Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Querétaro, Mexico
11
Comisión Nacional para el Conocimiento y Uso de la Biodiversidad, Mexico City, Mexico

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2994 Biodivers Conserv (2017) 26:2993–2998

diversity. Such approaches include: (1) measurement of alpha diversity by incorporating

interpolation-extrapolation techniques, Hill numbers and rank-abundance graphs; (2) beta
diversity and its components of turnover and richness differences due to nestedness; (3)
functional diversity, and (4) phylogenetic diversity. We highlight that a critical assessment,
understanding and appropriate application of these and other emerging concepts and
methods to assess biodiversity is needed to support both theoretical and applied studies,
especially in biological conservation.

Keywords Species accumulation curves
Hill numbers
Rank-abundance

graphs
Beta diversity
Functional diversity
Phylogenetic diversity

Measuring biodiversity is an extremely complex task, especially when it is defined with the
broad concept described by the Convention on Biological Diversity and global agendas
such as the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem
Services (Dı́az et al. 2015). Even when limiting the definition to changes in the abundance
and distribution of species and their attributes in time or space (not including genetic and
ecosystem diversity), the mission remains very complex. However, to understand biodi-
versity it is essential to have accurate quantitative metrics of the study systems, and thus
generate adequate conceptual and theoretical models that can be used to inform man-
agement and conservation practices (Maclaurin and Sterelny 2008). In fact, given the
reduced level of biodiversity conservation, mainly as a result of land use changes related to
anthropization (Newbold et al. 2016), adequately measuring biological diversity has never
been so urgent.
Under this scenario of complexity and urgency, methods for measuring biodiversity
have rapidly evolved, from the simple number of observed species, the traditional indices
of alpha diversity derived from information theory (e.g., Shannon–Weaver index) and
compositional similarity indices (e.g., Jaccard index) proposed at the beginning and middle
past century, to more sophisticated methods developed in the last decades to evaluate
different facets and dimensions of biological diversity. Paradoxically, such evolution of
methods, rather than encourage its use, may result overwhelming, especially for those that
are introducing themselves in this issue and that do not have a clear guide on how to
achieve a proper biodiversity assessment. Conceptual debates (e.g., Gorelick 2011;
Legendre 2014), controversies on commonly used methods (e.g., Chiarucci et al. 2008),
revivals of proposals that remained less used (Jost 2006), as well as proliferation of novel
methodological approaches (e.g., Villéger et al. 2008; Tucker et al. 2017) may discourage
or even intimidate those interested in measuring species diversity, or lead them to use
traditional methods without a proper methodological or conceptual basis. Moreover,
methods are dispersed in specialized scientific articles, and syntheses helping us to select
proper measures for each case are scarce (but see Magurran and McGill 2011). As an
attempt to guide future research on biodiversity patterns in human-modified environments,
in this brief essay we synthetically present four recent analytical approaches accompanied
by empirical examples that, in our opinion, are strongly valuable to assess spatial and
temporal patterns of biodiversity in different contexts, and understand the processes and
mechanisms that regulate such patterns.
First, for alpha diversity—diversity within ecological communities (sensu Whittaker
1960)—we highlight advances in methods used to compare among communities

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Biodivers Conserv (2017) 26:2993–2998 2995

standardizing sampling effort with interpolation (rarefaction) and extrapolation techniques

(Colwell et al. 2004; Chao et al. 2014), and comparing communities to the same sample
coverage (Chao and Jost 2012). In addition, Hill numbers (Hill 1973) and the analysis of
their properties and scope done by Jost (2006) have become widely used and applied. This
measure of diversity (qD, named true diversity sensu Jost 2006) can have different orders
(so-called order q) according to the importance given to species abundances. Its units are
effective number of species, which are the numbers of species with the same abundance
that theoretically can coexist in a community with the maximum evenness. Thus, this
measure has biological sense and their results are widely comparable among communities
(Jost 2006). These measures have been applied, for example, to assess the impact of
landscape composition and configuration on the diversity of dung beetles (Sánchez-de-
Jesús et al. 2016) and bats (Arroyo-Rodrı́guez et al. 2016) in the Lacandona rainforest,
southeastern Mexico. Conclusions from these two studies would be inaccurate if based on
traditional entropy measures, such as Shannon entropy, the Gini–Simpson index, and Renyi
entropies (see Jost 2009; Moreno et al. 2011). The use of Hill numbers combined with
rank-abundance graphs also allows us to describe the structure of communities and identity
of rare and dominant species (e.g., Arroyo-Rodrı́guez et al. 2013). The slope of rank-
abundance graphs may be helpful to assess and compare the effects of human disturbances
on species dominance, as well as to identify response thresholds of communities to
environmental gradients (MacGregor-Fors et al. 2012). Thus, species diversity and the
structure of communities allow us to uncover changes derived from human disturbances
that would not be apparent using only species richness.
Second, for beta diversity—the extent of change in species composition (sensu Whit-
taker 1960)—a contribution that has become extremely useful in the last years is the
partitioning of total dissimilarity into two components: dissimilarity due to species turn-
over and dissimilarity due to differences in species richness as a result of nestedness
(Baselga 2010). This approach has been helpful to disentangle diversity patterns of
amphibians worldwide (Baselga et al. 2012), mammals in Europe (Svenning et al. 2011),
metacommunities in boreal lakes (Angeler 2013) and vertebrates in heterogeneous regions
of Mexico (Calderón-Patrón et al. 2013, 2016). Partitioning beta diversity has allowed the
detection of zones with high species turnover where traditional beta diversity indices
masked the effects of simple richness differences among sites (Carvalho et al. 2012, 2013;
Cardoso et al. 2015). The results of this partitioning may have direct impacts on the design
of conservation strategies; for example, identifying the number and location of the areas
required to protect most of the regional diversity. Recently, beta partitioning has incor-
porated species relative abundance (Baselga 2017), thus total dissimilarity can be divided
into two components measuring: (1) the balanced variation in abundance, which occurs
when individuals of some species are substituted by the same number of individuals of
other species in another site, and (2) abundance gradients that occur when the number of
individuals decreases from one site to another. These analyses may be especially useful at
fine scales to assess, for example, local gradients of human disturbance or habitat frag-
mentation processes.
Third, as the classical methods of taxonomic diversity do not always reflect human
disturbance gradients, novel approaches proposed in recent years assess other facets or
dimensions of biodiversity, such as functional and phylogenetic diversities. Functional
diversity indices measure the variation in roles performed by species or sets of species in
ecosystems, and can be very useful to understand the relationship between biodiversity and
ecosystem functioning (Cadotte et al. 2011). The most common measures are multi-trait
indices based on dendrograms and indices based on the location of species within a

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2996 Biodivers Conserv (2017) 26:2993–2998

functional space (Weiher 2011; Gómez-Ortı́z and Moreno 2017). An important contribu-
tion relies on measures that separately assess functional richness, evenness and divergence
(Villéger et al. 2008), because they assess the degree of functional dominance in a com-
munity. These methods have been used, for example, to estimate the effect of land use
change due to cattle ranching in dung beetle communities (Barragán et al. 2014), the
impact of deforestation on bat communities (Garcı́a-Morales et al. 2016) and the success of
a forest restoration program for amphibian conservation (Dı́az-Garcı́a et al. 2017). In these
cases, the study of functional diversity has shown trends of change that differ from those
found when only neutral measures of diversity are used (i.e., those that do not take into
account differences among species), such as species richness or traditional alpha and beta
indices. Measures of functional diversity can also be very important to assess the loss of
ecological redundancy and its impact on ecosystem resilience due to anthropization. These
measures could be helpful to evaluate the impact of defaunation on biotic interactions such
as frugivory, and how this is related (through trophic cascading effects) to changes in
tropical tree sapling communities (Camargo-Sanabria et al. 2015; Camargo-Sanabria and
Mendoza 2016).
Finally, regarding the phylogenetic diversity, the methods proposed to quantify this
dimension of biodiversity have also emerged in the last few years, allowing the incorpo-
ration of evolutionary history from the structure of phylogenetic trees as a surrogate of
phenotypic, genetic, behavioral and/or phenological differences among lineages (Tucker
et al. 2017). The acceptance of these methods has been so high, that there are currently
more than 70 indices to measure phylogenetic diversity (Winter et al. 2013; Tucker et al.
2017; Miller et al. 2017). This approach has strengthened the way we uncover processes
driving biodiversity. For example, the effective numbers of lineages, mean phylogenetic
distance and phylogenetic dispersion indices have been used to demonstrate the importance
of facilitation on the phylogenetic diversity of plant communities (Valiente-Banuet and
Verdú 2007) and the phylogenetic impoverishment of remaining plant assemblages asso-
ciated with chronic human disturbances (Ribeiro et al. 2016).
These and other methods have been implemented in more creative and novel ways with
ample potential of use in biological conservation. For example, functional and phyloge-
netic beta diversity measures have been used to assess virus turnover in bat communities in
an anthropization gradient (Rico-Chávez et al. 2015). Doubtlessly, recent effervescence in
these methods will also be fundamental to the success in ecological restoration programs,
to assess the relationship between biodiversity and emergent diseases, the impact of cli-
mate change, among other research topics with applied implications. Therefore, we
encourage the study and proper application of the multiple concepts and current methods to
evaluate biodiversity, especially to students and teachers of disciplines related to biodi-
versity and conservation, as well as those involved in environmental issues in an ample
range of sectors (academia, governmental agencies, environmental consultancies, NGOs,
among others). We urge the formation of critical users that analyze the biological meaning
of information provided by each measure of diversity, and claim them to pay attention to
the multiple and constant proposals that will surely remain arising in this dynamic research
field.

Acknowledgements This contribution was inspired by the authors’ opinions during an update workshop on
concepts and methods to assess biodiversity, organized with the support of the Conacyt Basic Science
Project 222632 ‘‘Evaluación de la diversidad de especies mediante el análisis e integración de elementos
ecológicos, funcionales y evolutivos’’ and the Conacyt Red Temática 251272 ‘‘Biologı́a, Manejo y Con-
servación de la Fauna Nativa en Ambientes Antropizados’’.

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Biodivers Conserv (2017) 26:2993–2998 2997

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