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Integrated dataset of anatomical, morphological, and architectural traits for plant species in Madagascar

September 2017
Data in Brief 15

DOI:10.1016/j.dib.2017.09.004

License
CC BY 4.0

Authors:

Amira Azizan

Université de Montpellier

Patrick Langbour

Cirad - La recherche agronomique pour le développement

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In this work, we present a dataset, which provides information on the structural diversity of some endemic tropical species in Madagascar. The data were from CIRAD xylotheque (since 1937), and were also collected during various fieldworks (since 1964). The field notes and photographs were provided by French botanists; particularly by Francis Hallé. The dataset covers 250 plant species with anatomical, morphological, and architectural traits indexed from digitized wood slides and fieldwork documents. The digitized wood slides were constituted by the transverse, tangential, and radial sections with three optical magnifications. The main specific anatomical traits can be found within the digitized area. Information on morphological and architectural traits were indexed from digitized field drawings including notes and photographs. The data are hosted in the website ArchiWood (http://archiwood.cirad.fr).

Available via license: CC BY 4.0

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Data Article

Integrated dataset of anatomical, morphological,

and architectural traits for plant species

in Madagascar

Amira Azizan

, Emma Guillon

, Yves Caraglio

Patrick Langbour

, Sébastien Paradis

, Pierre Bonnet

Yannick Brohard

, Christine Heinz

, Nabila Boutahar

Loïc Brancheriau

University of Montpellier, Dept. of Biodiversity, Ecology and Evolution, Montpellier, France

CIRAD, UR BioWooEB, 34398, Montpellier, France

CIRAD, UMR AMAP, 34398, Montpellier, France

article info

Article history:

Received 7 July 2017

Accepted 5 September 2017

Available online 12 September 2017

Keywords:

Morpho-architectural traits

Plant architecture

Wood anatomy

Madagascar

abstract

In this work, we present a dataset, which provides information on

the structural diversity of some endemic tropical species in

Madagascar. The data were from CIRAD xylotheque (since 1937),

and were also collected during various ﬁeldworks (since 1964).

The ﬁeld notes and photographs were provided by French bota-

nists; particularly by Francis Hallé. The dataset covers 250 plant

species with anatomical, morphological, and architectural traits

indexed from digitized wood slides and ﬁeldwork documents. The

digitized wood slides were constituted by the transverse, tangen-

tial, and radial sections with three optical magniﬁcations. The main

speciﬁc anatomical traits can be found within the digitized area.

Information on morphological and architectural traits were

indexed from digitized ﬁeld drawings including notes and photo-

graphs. The data are hosted in the website ArchiWood (http://

archiwood.cirad.fr).

&2017 The Authors. Published by Elsevier Inc. This is an open

access article under the CC BY license

(http://creativecommons.org/licenses/by/4.0/).

Contents lists available at ScienceDirect

journal homepage: www.elsevier.com/locate/dib

Data in Brief

http://dx.doi.org/10.1016/j.dib.2017.09.004

2352-3409/&2017 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY license

(http://creativecommons.org/licenses/by/4.0/).

Corresponding author.

E-mail address: loic.brancheriau@cirad.fr (L. Brancheriau).

Data in Brief 15 (2017) 92–96

Speciﬁcations Table

Subject area Botany

More speciﬁc

subject area

Anatomy, morphology and architecture of plant species

Type of data Tables of anatomical traits and morpho-architectural traits

Images of microscope slides for wood anatomy

Field drawings with notes

Photographs

How data was

acquired

Microscope

Field observations

Data format Tables in MSExcel format *.xlsx

Images of microscope slides in 24-bit RGB TIFF (1600×1200 pixels)

Digitized ﬁeld drawings and notes in 24-bit RGB JPG (300 dpi)

Scanned photographs of 24×36 mm format in 24-bit RGB JPG (600 dpi)

Experimental

factors

–

Experimental

features

–

Data source

location

Madagascar

Data accessibility Data package title: ArchiWood dataset

Resource link: http://archiwood.cirad.fr

Identiﬁer: doi:10.18167/archiwood/1

Usage rights: Creative Commons Attribution –NonCommercial –ShareAlike

4.0 International (CC BY-SA-NC 4.0)

Value of the data



The dataset consolidates anatomical, morphological, and architectural traits of plant species from

different sources (xylotheque, ﬁeld notes, and photographs).



The described traits of tropical plant species can be useful to understand the biogeographical

variation within species and genera in plant anatomy regarding the ontogeny and structure of

sampled plants.



To understand the diversity of wood characteristics and technological behaviors that directly

governed the choice of tropical timber use.



To understand the relationship between tropical wood structure and certain physical, mechanical,

chemical, and biological properties of the material.

1. Data

Madagascar is an important insular hotspot for biodiversity conservation [11]. More than 80% of

the currently known ﬂora species are endemic to the island [4]. Endemic tropical species in Mada-

gascar are well known for its important value in ecology and economy but are predicted to face mass

extinction in the near future because of global warming and deforestation [2,3]. Identiﬁcation of

Malagasy vascular plant species was documented and can be accessed via the website Tropicos

(Madagascar catalogue, http://www.tropicos.org/Project/Madagascar).

The architectural analysis on tropical species as described by [1,7,8] emphasize on the dynamics of

growth and structure of a plant species in the competitive nature of the forest, thereby conforming to

its architectural model. Recent studies of plant architecture may not only provide complimentary

information for species-level identiﬁcation purposes, but also for understanding plant structure

A. Azizan et al. / Data in Brief 15 (2017) 92–96 93

evolution within a clade [10] and their ecological strategies [5,6]. Together with stem anatomy, archi-

tectural variations involving the branching process, rhythmicity, and orientation can be comparatively

analyzed to study the evolution of growth in both temporal and spatial contexts [9].Thisapproachcan

also provide guidelines for tree selection and management in agroforestry practices [12].

The dataset gathers anatomical, morphological, and architectural traits of endemic plant species.

The aims is to promote and to make more accessible for scientiﬁc and public use a speciﬁc part of the

CIRAD wood collection and unpublished morpho-architectural data from Madagascar. More than

1000 microscopic anatomical wood slides, exclusively available in this open access dataset, were

sampled since the early 20th century and compiled with more than 500 digitized ﬁeld notes such as

botanical illustrations and photographs. Because diagrammatic representations of morpho-archi-

tectural traits are essential to assess plant structure and growth, digitized illustrations provided here

may serve as a reference for future architectural analysis and application. Metadata from approxi-

mately 250 indexed plant species also provide new insights to species identiﬁcation and scientiﬁc

research, such as in functional ecology or systematics as well as for forest conservation management.

2. Experimental design, materials and methods

2.1. Microscopic structure of wood

For each species, three microscope slides were prepared consisting of transverse, tangential, and

radial sections (Fig. 1). The slides were then digitized using a camera Olympus DP71 mounted onto a

microscope Olympus BX60. Each slide was digitized with three optical magniﬁcations: ×40, ×10 0,

and×200. The images (1600×1200 pixels) were then processed by Archimed Microvision® software

and stored in 24-bit RGB TIFF. Within each image, the main speciﬁc anatomical traits can be found,

and these traits were indexed following the List of Microscopic Features for Hardwood Identiﬁcation

from the IAWA (http://iawa-website.org/).

2.2. Morphology and architecture of plant structure

Information on morphological and architectural traits were indexed from illustrations of digitized

ﬁeld notes (300 dpi 24-bit RGB JPEG) (Fig. 2) and scanned photographs of 24×36 mm format (600 dpi,

24-bit RGB JPEG) from various researches in Madagascar, for extended visual information. The traits

were indexed following the modalities as reviewed in [1,7,8]. Both anatomical and morphological

traits may not apply to all of the species available in the dataset.

2.3. Temporal coverage

Concerning the wood collection, the anatomical slides were sampled since 1937. The ﬁeld notes

were reported since 1964 for the photographs, and since 1970 for the illustrations. Each document

Fig. 1. Digitized wood slides highlighting anatomical traits. From left to right: transverse (×40), tangential (×100) and radial

(×200) sections of Givotia madagascariensis Baill.

A. Azizan et al. / Data in Brief 15 (2017) 92–9694

was digitized and indexed between June 2015 and the end of 2016. This information were never

published.

2.4. Taxonomic coverage

The dataset gathered information on 102 families and 244 genera of angiosperm species (with the

addition of a bryophyte). For these species, the updated taxonomic names were provided and

retrieved from The Plant List (http://www.theplantlist.org/). Some traits were speciﬁed at the family

or genus level.

Funding

This work was supported by the French Digital Scientiﬁc Library (BSN5, 2014, ArchiWood project).

Acknowledgements

The authors would like to thank Laurence Dedieu (Cirad, Dist) for her valuable comments that

helped us to improve this article.

Transparency document. Supplementary material

Transparency data associated with this article can be found in the online version at http://dx.doi.

org/10.1016/j.dib.2017.09.004.

Fig. 2. Fieldwork illustrations of morpho-architectural traits. Diagrammatic representation of Givotia madagascariensis Baill for

whole plant (left) and branching system (right).

A. Azizan et al. / Data in Brief 15 (2017) 92–96 95

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Sep 2002
CONSERV BIOL

Nearly half the world's vascular plant species and one-third of terrestrial vertebrates are endemic to 25 “hotspots” of biodiversity, each of which has at least 1500 endemic plant species. None of these hotspots have more than one-third of their pristine habitat remaining. Historically, they covered 12% of the land's surface, but today their intact habitat covers only 1.4% of the land. As a result of this habitat loss, we expect many of the hotspot endemics to have either become extinct or—because much of the habitat loss is recent—to be threatened with extinction. We used World Conservation Union [ IUCN ] Red Lists to test this expectation. Overall, between one-half and two-thirds of all threatened plants and 57% of all threatened terrestrial vertebrates are hotspot endemics. For birds and mammals, in general, predictions of extinction in the hotspots based on habitat loss match numbers of species independently judged extinct or threatened. In two classes of hotspots the match is not as close. On oceanic islands, habitat loss underestimates extinction because introduced species have driven extinctions beyond those caused by habitat loss on these islands. In large hotspots, conversely, habitat loss overestimates extinction, suggesting scale dependence (this effect is also apparent for plants). For reptiles, amphibians, and plants, many fewer hotspot endemics are considered threatened or extinct than we would expect based on habitat loss. This mismatch is small in temperate hotspots, however, suggesting that many threatened endemic species in the poorly known tropical hotspots have yet to be included on the IUCN Red Lists. We then asked in which hotspots the consequences of further habitat loss (either absolute or given current rates of deforestation) would be most serious. Our results suggest that the Eastern Arc and Coastal Forests of Tanzania-Kenya, Philippines, and Polynesia-Micronesia can least afford to lose more habitat and that, if current deforestation rates continue, the Caribbean, Tropical Andes, Philippines, Mesoamerica, Sundaland, Indo-Burma, Madagascar, and Chocó–Darién–Western Ecuador will lose the most species in the near future. Without urgent conservation intervention, we face mass extinctions in the hotspots. Resumen: Casi la mitad del total de plantas vasculares del mundo y un tercio de los vertebrados terrestres son endémicos en 25 “áreas críticas” para la biodiversidad, cada una de las cuales tiene por lo menos 1500 especies de plantas endémicas. En ninguno de estos sitios permanece más de un tercio de su hábitat prístino. Históricamente, cubrían 12% de la superficie terrestre, pero en la actualidad su hábitat intacto cubre solo 1.4% del terreno. Como resultado de esta pérdida de hábitat esperamos que muchas de las especies endémicas a estos sitios estén extintas o – porque la pérdida de hábitat es reciente – se encuentren amenazadas de extinción. Utilizamos Listas Rojas de UICN para comprobar esta predicción. En general, entre la mitad y dos tercios de las plantas amenazadas y el 57% de los vertebrados terrestres amenazados son endémicos de áreas críticas para la biodiversidad. Para aves y mamíferos en general, las predicciones de extinción en las áreas críticas para la biodiversidad, basadas en la pérdida de hábitat, coinciden con el número de especies consideradas extintas o amenazadas independientemente. En dos clases de áreas críticas para la biodiversidad la coincidencia no es muy grande. En islas oceánicas, la pérdida de hábitat subestima la extinción porque las especies introducidas han causado más extinciones que las producidas por la reducción del hábitat. Por lo contrario, la pérdida de hábitat sobrestima la extinción en áreas críticas para la biodiversidad extensas, lo que sugiere una dependencia de escala (este efecto también es aparente para plantas). Para reptiles, anfibios y plantas mucho menos especies endémicas son consideradas amenazadas o extintas por pérdida de hábitat. Sin embargo, esta discordancia es pequeña en áreas críticas para la biodiversidad en zonas templadas templadas, lo que sugiere que muchas especies endémicas amenazadas en las poco conocidas áreas críticas para la biodiversidad en zonas tropicales aun están por incluirse en las Listas Rojas. Posteriormente nos preguntamos en que áreas críticas para la biodiversidad serían más serias las consecuencias de una mayor pérdida de hábitat (absoluta o con las tasas actuales de deforestación). Nuestros resultados sugieren que el Arco Oriental y los Bosques Costeros de Tanzania/Kenia, Filipinas, Polinesia/Micronesia no pueden soportar mayores pérdidas y que, si continúan las tasas de deforestación actuales, el Caribe, Andes Tropicales, Filipinas, Mesoamérica, Sundaland, Indo-Burma, Madagascar y Chocó/Darién/Ecuador Occidental perderán más especies en el futuro. Sin acciones urgentes de conservación, habrá extinciones masivas en las áreas críticas para la biodiversidad.

Recherches sur l'archictecture et la dynamique de croissance des arbres tropicaux

Article

Jan 1968

Francis Hallé

Biodiversity hotspot for conservation priorities

Article

Mar 2000

Conservationists are far from able to assist all species under threat, if only for lack of funding. This places a premium on priorities: how can we support the most species at the least cost? One way is to identify 'biodiversity hotspots' where exceptional concentrations of endemic species are undergoing exceptional loss of habitat. As many as 44% of all species of vascular plants and 35% of all species in four vertebrate groups are confined to 25 hotspots comprising only 1.4% of the land surface of the Earth. This opens the way for a 'silver bullet' strategy on the part of conservation planners, focusing on these hotspots in proportion to their share of the world's species at risk.