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Why taxonomists have a tough life

1. identifying species2. arbitrariness of taxa and ranks3. stability of taxonomy4. general lack of credit

How do we discover and identify 'bits of biodiversity'worthy of a name?How do we slice up the Tree of Life to species?

Things to recall:

1. Speciation takes time, and evolution is relentless2. Some alleles may coalesce deeper in time than species form.3. Many alleles may coalesce much shallower in time.

Note: species are usually discovered with genetic data, but are expected to be diagnosed with other data (due to a correlation between genetic and phenotypic divergence)

Mitochondrial gene phylogeny

Corresponds to the'true' tree. Why?

mtDNA is inherited through the maternal line.If a woman only has sons, or no kids at all,

her mtDNA lineage goes extinct.Sooner or later this happens to all lineages

but one: form of genetic drift

‘coalescence theory’ in action ->

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Due to drift, samples of mitochondrial DNA are related as a tree, and if we can reconstruct that tree, we should be able to infer many things about the populations

Species A Species B

Coalescent time is generally 4Ne generations, but mtDNA is haploid -- so 2Ne generationsand only matrilineal --- so Ne generations! (4 x faster)

J. Visser

Microcebus murinus (Miller 1777) (Primate Info Net)

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Mouse lemur (Microcebus) mtDNA tree (Yoder et al. 2000)

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c cc

cc c

Species 1 Species 2 Species 3

13Sp. 1 Sp. 2 Sp. 3 Sp. 1 Sp. 2 Sp. 3

Actual history a,b,c alleles

Deeper coalescence than speciation?

Mouse lemur (Microcebus) intron tree(Heckman et al. MPE 43:353, 2007)

All three are in IUCN as good species, though rufus split basedon genetic data

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Ebersberger et al., 2007

So, if you can find such a locus with such alleles, you can designate a "Phylogenetic Species"

3. Many alleles may coalesce much shallower in time(than species 'form').

8 'traditional' species

3 'new' species basedgenetic distance, but no typelocation, 'variable' pelage

11 'new' species basedon mtDNA and allopatryalone!

Lepilemur (sportive lemurs)

Neighbor-joining tree, mtDNA

Two new species describedbase on mtDNADescription is entirely'diagnostic base pairs'

Craul et al. BMC Evolutionary Biology 2007, 7:83 doi:10.1186/1471-2148-7-83

Description of two new species Lepilemur otto sp. nov

HolotypeIndividual 02y04bibo, adult male captured in Ambodimahabibo

DescriptionThe dorsal pelage, including shoulders and the upper and lower arms, is predominantly grey-brown. A dark diffuse line runs from the middle of the upper skull down the spine, ending in the middle or at the lower part of the back, but is never present on the tail. The ventral pelage is generally grey to creamy. The coloration of the tail is grey-brown to deep brown, sometimes with a white tail tip. The face and forehead are essentially grey.

DiagnosisThe sequenced mtDNA of Lepilemur otto has eleven diagnostic sites, eight in the ND4 (positions 42 = G, 57 = T, 123 = G, 255 = A, 306 = C, 630 = A, 631 = T, 632 = :C; see additional file 2: Diagnostic sites of the ND4 region for each terminal clade.), and three in the D-loop (positions 20 = C, 22 = A, 23 = T; see additional file 3: Diagnostic sites of the D-loop region for each terminal clade.). L. otto differs from its closest relative,L. edwardsi, in 2.92–2.99% and from its sister taxon L. manasamody in 3.50–3.57% in the sequenced mtDNA, respectively. The few morphometric data, which are available at the moment indicate that L. otto has a significant longer snout than the neighbouring species south of the Mahajamba River, L. edwardsi. The tail is significant short compared to the neighbouring species north of the Sofia River, L. manasamody and to L. edwardsi. L. otto shows a tendency to have a wider head than L. edwardsi and a bigger tail circumference than L. manasamody.

DistributionThe known distribution range of Lepilemur otto is so far limited to the sample site of Ambodimahabibo. This site is situated in the IRS II, which is limited by the Mahajamba River in the west and the Sofia River in the north. Intensive surveys are now required in this vastly deforested area to obtain additional information about the location and viability of other remaining populations, so that conservation measures can be proposed.

MaterialTissue and hair samples, morphometric measurements as well as photographs of 02y04bibo are stored at the Institute of Zoology of the University of Veterinary Medicine Hannover, Hannover, Germany.

Type locality

Madagascar: Province de Mahajanga, Ambodimahabibo (15°29'54,2"S, 47°28'47,2"E).

ParatypeIndividuals 01y04bibo, 03y04bibo and 04y04bibo were captured in Ambodimahabibo by M. Craul in 2004. Tissue and hair samples, morphometric measurements as well as photographs of each paratype are stored at the Institute of Zoology of the University of Veterinary Medicine Hannover, Hannover, Germany.

Diversity and Distributions, (Diversity Distrib.) (2012) 1–12

Imperilled phylogenetic endemism of Malagasy lemuriformes Renske M. Gudde1,2,†, Jeffrey B. Joy2,3,4 and Arne O. Mooers2,3,4*

>90 lemurs named on Madagascar in IUCN list>25 delineated solely through genetic distance, and IUCNcalls for their confirmation

mtDNA tree

This framework of the phylogenetic species concept is connected to 'DNA barcoding'

inside of cell

cytochrome oxidase 1

“Barcoding” species

Simple idea: Sequence 5’ end (658 bp fragment) of cytochrome c oxidase I genefrom each species, and make this sequence its ‘barcode’

Paul Hebert et al., Univ. Guelph. PRSLB,[ 2003] 270:313

-mitochondrial gene (no introns in most animal taxa)-stable, ‘universal’ primers-slower than Cytb, but still many 3rd base subs: seems to substitute at ~1% per million years (so about 12 differences after 1 my divergence between 2 spp)

http://www.barcodinglife.comHebert et al., 2003

known test

Two issues:

1. Getting the identification correct (ie, is it really a 'barcode'?)

2. using barcodes to DISCOVER species (PSC).

Identifying Canadian Freshwater Fishes through DNA Barcodes

Hubert et al. PLoS One 2008

194 of ~200 Canadian species barcoded (~8 ind./spp)

K2P distance(a 'corrected'proportion)

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15 named species did not separate properly (ie no true barcode dueto shared haplotypes among individuals)

two species showed 'deep splits' - each species actually 2?

brook stickleback Culaea inconstans

redfin pickerel, Esox americanus

Ok, what about higher taxa?

Taxonomy (naming and classifying organisms) serves two modern purposes:-facilitates identification and information retrieval-reflects phylogenetic relationships(NB: System Naturae of Linnaeus was not created to do thelatter, and many modern taxa- eg. genus Candida- still do not)

www.jmarcano.com/biografia/linneo.html

Logo by Rick Ree

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The named species are set into a nested set of ranks

Linnean ranks are nested and taxa are exclusive(e.g. no families inside families)

Pongo

Pongidae

Pongo pygmaeus

Pongo abelii

Pan

Pan troglodytes

Pan paniscus

Gorilla

Gorilla gorilla gorrila

Gorilla gorilla beringei

Kingdom Phylum Class Order Family - idae Subfamily - inae Tribe Genus species subspecies

‘Standard’ animal ranksPhasianidae (pheasants)

Type genus: Phasianus

Type species: Phasianus gallus (Linnaeus 1758)*

*in brackets, because he named this species Gallus gallus

Red Jungle Fowl

(A taxonomic Family also has a type genus, which has a type species, which should have a type specimen.)

31http://www.nhm.ac.uk/hosted-sites/iczn/code/index.jsp

Everyone agrees on the tree,but not on the taxonomy...

PanHomoGorillaPongo

arbitrariness

Hylobates

Hylobatidae

Hylobates

4 subgenera of gibbons

Pongidae

Pongo orangutan

Gorilla gorilla

Pan chimpanzee

Hominidae

Homo human

Original ‘Walker’s’ taxonomy (Nowak, 1991): 3 families

Family Hominidae Subfamily Homininae Tribe Hylobatini Subtribe Hylobatina Sympbalangus siamang Hylobates gibbons Tribe Hominini Subtribe Pongina Pongo orangutans Subtribe Hominina Gorilla gorillas Homo (Homo) humans Homo (Pan) chimpanzees, bonobo

Another taxonomy (Goodman et al., 1999): 1 family, with subfamilies, tribes and subtribes!

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Current taxonomy (Groves, 2005)

Hylobatidea (4 genera based on chromosome numbers)Pongo (2 species)Pan (2 species, 4 subspecies)Gorilla (2 species, each with 2 subspecies)Homo (1 species)

http://www.bucknell.edu/msw3/Wilson and Reeder's Mammal Species of the World

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Ranks also need not denote similar levels of differentiation:subspecies in one genus may = species in another (and likewise for families, etc.)

13 species of African Cichlid(bright, flashy)

3 orders of Primate(very attractive)

1 genus of Drosophila(they're flies)

Proposal for a standardized temporal scheme of biological classification for extant species Avise JC, Johns GC (1999) PNAS, 96: 7358-7363

arbitrary but at leastconsistent

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What about stability?

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3. Stability of the ranks

Death of an order: a comprehensive molecular phylogenetic study confirms that termites are eusocial cockroaches

The order Termites (Isoptera) has now become a family (Isopteridae) within the Order Blattodea (Cockroaches)!

1. Daegan Inward†, George Beccaloni and Paul Eggleton* Biology Letters 2007

40doi:10.1098/rsbl.2007.0102Biol. Lett. 22 June 2007 3: 331-335