biodiversity informatics and related developments · 2015-11-07 · global biodiversity information...

Biodiversity Informatics and

Related Developments

Keping MA

kpma@ibcas.ac.cn

Institute of Botany, Chinese Academy of Sciences 2015-11-05

What is Biodiversity Informatics

History of the term "Biodiversity Informatics

According to correspondence reproduced by Walter

Berendsohn, the term "Biodiversity Informatics" was coined

by John Whiting in 1992 to cover the activities of an entity

known as the Canadian Biodiversity Informatics Consortium,

a group involved with fusing basic biodiversity information

with environmental economics and geospatial information in

the form of GPS and GIS. Subsequently it appears to have

lost any obligate connection with the GPS/GIS world and be

associated with the computerized management of any

aspects of biodiversity information.

Development of BiodivInform

Science,2000, Special feature: 5 papers

Philosophical Transactions of Royal

Society of London, Series B, Biological

Sciences, 2004. Taxonomy for the twenty-

first century:19 papers;

BMC：Bioinformatics，2009，

Biodiversity Informatics: the emergence of

a field:10 papers.

Key issues of BiodivInform

Global species names(CoL, GNA, IPNI, Ubio, GNI)

Digitization of baseline data(species, specimens, images,

literatures)

Standards/Protocols (Darwin Core, Dublin Core, ABCD, SDD,

TNC, SPM, TAPIR)

Data mining（GARP, MaxEnt, Random forest等）

Global Biodiversity Information Facility : GBIF

Catalogue of Life-Species2000: CoL

Biodiversity Heritage Library: BHL

EDIT: European Distributed Institute of Taxonomy

Tree of Life: TOL

Barcode of Life Data Systems :BOLD

Encyclopedia of Life: EOL

TROPICOS

Fishbase

ILDIS

GPI

The Plant list

DataONE

More than 600 projects on BI recorded by TDWG

Projects and organizations

11,106,374 NameBank Records

全球生物物种名录（CoL）

Catalogue of Life--China

Catalogue of

Life China

(2015)

includes

73,255

species and

10,035

infraspecific

taxa.

Species 2000 China Node (http://www.sp2000.cn/)

Species Catalogue of China

全球植物名录(TPL)

The International Plant Names

Index(IPNI)

Global Names

Key Issues of Multi hub Network

The contents of the system expanded from a

single taxonomic tree to multiple taxonomic trees.

Difference of concepts

and status of a name on

trees (if any), and

difference of tree’s

structures.

全球生物多样性信息网络(GBIF)

Basis of Record Record

s

Availabilit

y

Time

Cost

Examples GBIF(m)

Human

Observation

records

Millions

+

Easy if

online

Middle CFH, PPBC, Flickr,

interest groups,

iNaturalist, weibo

320 / 73.8

Specimen

records

Millions

+

Middle Long NSII, Herbarium

database

115 / 54.8

Observation

records

Millions

+

Middle Long Observatories, GEO BON,

CForBio, Protect area

97 / 30

Unknown

evidence records

34 / 8.5

Fossil records 4.8 / 0.7

Machine

Observation

records

Millions

+

Easy if

online

Short Automatic camera,

sensors,

1.4 / 0.34

Living Specimen

records

Millions

+

Easy if

online

Long Botanical Gardens, BGCI, 0.8 / 0.6

Literature Millions Easy Short or Web(BHL, IPNI, TPL), 0.46 /

GBIF Status(2015-7-31):

Animal：380.7million(66.3%), Plant：168.7million(29.4%)

Global Biodiversity Information Facility

GBIF-China

网络生命大百科

荷兰国家标本馆（Leiden）标本数字化流程示意图

荷兰国家标本馆（Leiden）标本数字化进展统计（3000万欧元）

2014-042010-2015

法国国家

自然历史

博物馆

600多万

份植物腊

叶标本全

部数字化

iDigBio--USA

ALA--Australia

All-in-one Design:

NSII(National Specimen Information Infrastructure)

Plant Rock

Protected Area

PolarAnimal

Education

Global

Regional

National

Thematic

Local

NSII

>12 million specimens, 100+ institutes & universities

Supporting

Database

DNA Barcode

Literature

Distribution

Ecology (Habitat)

User & Communities

国家标本资源共享平台(NSII)

Chinese Virtual Herbarium

(CVH)

生物多样性历史文献图书馆Biodiversity Heritage Library

生物多样性历史文献图书馆

Biodiversity Heritage Library

Flora of China

Botanical

Map of Life

MOL Status

http://mol.org/

1. Only 45 of 194 (23%) datasets are about plant data (2,565,659 records, about 0.7% of the total MOL)2. Only 5% dataset are point observation, and more are inventory, checklist, map and survey.

Big data VS. Small sources,

80% datasets are less than

10,000 records.

ABCDNet重点推动的项目

亚洲生物物种名录(Asia Species Checklist)；

亚洲物种红色名录(Asia Species Red List)；

亚洲植物制图(Mapping Asia Plants, MAP);

亚洲100种最受威胁物种 (100 most threatened

species)；

东南亚生物多样性信息平台 (Southeast Asia

Biodiversity Information

Infrastructure, SEABio)

Existing Platforms in

Asia

Asia Biodiversity Information in

Global SyntheticSystems Asia

Biodiversity Information in

Global Thematic Database

亚洲生物多样性保护与信息网络

利用GBIF数据发表的论文

Maps of (a) collection density and (b) inventory incompleteness as indicators of

collecting effort for vascular plants in 2377 Chinese counties. (c) Relationship between

collection density and inventory incompleteness. (d) Map of absolute residuals from

ordinary least-squares regression in (c).

Mountainous areas are most

intensively collected in China, whereas

densely populated areas tend to be

neglected by plant collectors. This

sampling bias leads to woefully

incomplete inventories, particular in

urban and agricultural areas, and thus

to a pronounced ‘Wallacean shortfall’,

i.e. an incomplete documentation of

species ranges.

Distribution of Endemic Plants in China

Families: 193

Genera: 1513

Species: 15103

Maps of spatial turnover of Yunnan floristic assemblages in taxonomic

composition (a) and phylogenetic composition (b). Color scale depicts the

degree of taxonomic and phylogenetic turnover between the focal region

and all other regions. The maps were generated using DIVA-GIS 7.5.

A phylogenetically informed delineation of floristic

regions within a biodiversity hotspot in Yunnan, China

Rong Li, Nathan J. B. Kraft, Jie Yang & Yuhua Wang

Dendrogram (a) and map (b)

resulting from Ward

hierarchical clustering and

scatter plot (c) from non-metric

multidimensional scaling

(NMDS) two-dimensional

ordination for floristic

assemblages of Yunnan based

on phylogenetic beta diversity

distance matrices at the genus

level. The eight distinct floristic

regions are highlighted in the

dendrogram with large colored

rectangles and displayed in the

map in different colors. The

map was generated using

DIVA-GIS 7.5.

Spatiotemporal trends in crofton

weed ( Eupatorium adenophorum)

invasion in south-west China.

Geographical distribution of

training data was plotted on the

bottom x–y axis. Invasion history of

distribution points based on

recording dates was plotted on the

vertical axis. The black lines

represent the equal invasion time

and the grey arrows indicate the

direction of spread.

Geographic predictions for crofton weed (Eupatorium adenophorum) in China. Blue

triangles represent the 390 spots used to train the predicted models and where the

weed is known to occur, and white circles represent 51 extrinsic testing data used to

test the predicted geographic range.

Distribution of orchid

richness in China:

(a) all orchids,

(b) terrestrial orchids,

(c) epiphytic orchids,

(d) lithophytic orchids,

(e) orchids endemic to

China, and (f) orchids

non-endemic to China.

Regression between the

strength of phylogenetic

conservatism in flowering

phenology (Blomberg’s K) and

latitude, and the geographical

patterns of the K-values in

China estimated at the

province scale. Each point in

the regression represents a

province of China. The line is

the polynomial regression line

with a quadratic term.

Through analyses of 10,295 herbarium specimens of Himalayan

Rhododendron collected by plant hunters and botanists since 1884, we

were able to separate these responses into significant components.

However, over the full 125 y of collections, mean flowering time shows a

significant response to year-to-year changes in temperature, and this

response varies with season of warming. Mean flowering advances with

annual warming (2.27 d earlier per 1 °C warming), and also is delayed

with fall warming (2.54 d later per 1 °C warming). The lack of a directional

response suggests that contrasting phenological responses to temperature

changes may obscure temperature sensitivity in plants. By drawing on

large collections from multiple herbaria, made over more than a century, we

show how these data may inform studies even of remote localities, and we

highlight the increasing value of these and other natural history collections

in understanding long-term change.

The way forward

Biodiversity Mapping

LiteraturesSpecimens Plots & maps/RS Observations

Phylogenetic

dataTrait

data

Paleotological

data

On line

workflowsEcological

data

Thanks