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What is “phyloinformatics”?

Phyloinformatics: Introduction

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Page 1: Phyloinformatics: Introduction

What is “phyloinformatics”?

Page 2: Phyloinformatics: Introduction
Page 3: Phyloinformatics: Introduction
Page 4: Phyloinformatics: Introduction

Linking biodiversity data together

Page 5: Phyloinformatics: Introduction

Apomys datae

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Apomys specimen

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How do we integrate these data?

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Why integrate?

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Learn stuff we don’t know

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• There are known knowns, things we know that we know

• There are known unknowns, things we now know we don’t know

• But there are also unknown unknowns, things we do not know we don't know

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Unknown knowns

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Things we know …without knowing that we know

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Melissotarsus insularis

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Melissotarsus insularis no hit

CASENT0107663-D01 DQ176312

Melissotarsus sp. BLF m1DQ176312

CASENT0107663-D01Melissotarsus insularis

1

Melissotarsus insularisMelissotarsus sp. BLF m1 =

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No one source has all the answers

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19

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Single source

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Many sources

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Combine sources

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ispecies.org

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Linking

• Finding information about organisms

• Linking together in “mashups”

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Geography

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@rdmpage

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@andrewxhill

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Geography

• Species distributions

• Geophylogenies

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Taxonomy

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36

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Names can change…Leptodactylus fuscus (Schneider)

1799 Rana fusca Schneider1802 Rana typhonia Sonnini & Latreille1803 Rana typhonia Daudin1824 Rana sibilatrix Wied1826 Leptodactylus typhonius Fitzinger1841 Cystignathus typhonius Dumeril & Bibron1843 Leptodactylus typhonius Fitzinger1858 Cystignathus fuscus Günther1882 Leptodactylus typhonius Boulenger1927 Leptodactylus sibilatrix Müller1935 Leptodactylus sibilatrix Parker1968 Leptodactylus fuscus Heyer

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Taxonomy as a source of data

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“Dark taxa”

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Classification

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http://synthesis.eol.org/media/treemap/

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@kzelnio Think how great of a tool that could be at museumson a large flat screen at 4 year old height.

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Taxonomy

• Names

• Synonyms

• Classifications

• Visualisation

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Phylogeny

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0

1000

2000

3000

4000

5000

6000

7000

1975 1980 1985 1990 1995 2000 2005

Year

Cumulative number

Rate of growth of phylogenetic knowledge

Number of papers with “molecular” and “phylogeny” in Web of Science

Number of studies in TreeBASE

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@dr_pi

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Phylogeny

• Finding a phylogeny for a group of organisms

• Displaying on the web (visualisation)

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Data mining

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Text mining

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Morphological and molecular description of Haematoloechus meridionalis n. sp. (Digenea: Plagiorchioidea: Haematoloechidae) from Rana vaillanti brocchi of Guanacaste, Costa Rica

Halipegus eschi n. sp. (Digenea: Hemiuridae) in Rana vaillanti from Guanacaste Province, Costa Rica

Haematoloechus danbrooksi n. sp. (Digenea: Plagiorchioidea) from Rana vaillanti from Los Tuxtlas, Veracruz, Mexico

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What do crustaceans live on?

Greenplants

Bacteria

FungiVertebrates

Arthropods

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What do insects live on?

Greenplants

Bacteria

FungiVertebrates

Arthropods

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Data mining

• Extracting information from the literature

• Extracting information from databases

Page 64: Phyloinformatics: Introduction

The End


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