A plan for phylogenetic studies of Southern African reptiles : proceedings of a workshop held at Kirstenbosch, February 2006

2006·3.8 MB·English

by  Branch, Bill (William R.)

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PKylogenetic
Studies
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§outherrf African
Branch
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.x.A. Tolley
M. Cunningham
AyM. Bauer
G. Alexander
J.A. Harrison
A.A. Turner
M.F. Bates
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SANBI
Biodiversi
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HyaauroofC'-
l^iV»rr^ University
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SANBI
Biodiversity Series
SANBI
Biodiversity Series 5
A
plan for phylogenetic studies
of southern African reptiles
Proceedings of a workshop held at Kirstenbosch,
February 2006
Editors:
W.R. Branch
K.A. Tolley
M. Cunningham
A.M. Bauer
G. Alexander
J.A. Harrison
A.A. Turner and M.R Bates
national
biodiversity
institute
SANBI
Pretoria
2006
SANBI
SANBI Biodiversity Series
The South African National Biodiversity Institute (SANBI) was established on 1 Sep-
tember 2004 through the signing into force of the National Environmental Manage-
ment: Biodiversity Act (NEMBA) No.10 of 2004 by President Thabo Mbeki. The Act
expands the mandate of the former National Botanical Institute to include respon-
sibilities relating to the full diversity of South Africa's fauna and flora, and builds on
the internationally respected programmes in conservation, research, education and
visitor services developed by the National Botanical Institute and its predecessors
over the past century.
The vision of SANBI is to be the leading institution in biodiversity science in Africa,
facilitating conservation, sustainable use of living resources, and human wellbeing.
SANBI's mission is to promote the sustainable use, conservation, appreciation and
enjoyment of the exceptionally rich biodiversity of South Africa, for the benefit of all
people.
SANBI Biodiversity Series will publish occasional reports on projects, technologies,
workshops, symposia and other activitiesl(u=wtiated by or executed in partnership with
SANBI. 3K
Technical editor: Gillian de Jager
Design & layout: Sandra Turck
Cover design: Sandra Turck. Photographs provided by Marius Burger.
Citation
Branch, W.R., Tolley, K.A., Cunningham, M., Bauer, A.M., Alexander, G.,
Harrison, J.A., Turner, A.A. & Bates, M.F. (eds) 2006. A plan for phylogenet-
ic studies of southern African reptiles: proceedings of a workshop held at Kirsten-
bosch, February 2006. Biodiversity Series 5. South African National Biodiversity
Institute, Pretoria.
Branch, W.R. 2006. Priorities for systematic studies on southern African reptiles.
Pp. 2-20 in: W.R. Branch, K.A. Tolley, M. Cunningham, A.M. Bauer, G. Alexan-
der, J.A. Harrison, A.A. Turner & M.F. Bates (eds). A plan for phylogenetic studies
of southern African reptiles: proceedings of a workshop held at Kirstenbosch,
February 2006. Biodiversity Series 5. South African National Biodiversity Institute,
Pretoria.
ISBN 1-919976-33-7
©
Published by: South African National Biodiversity Institute.
Obtainable from: SANBI Bookshop, Private Bag XI01, Pretoria, 0001 South Africa.
Tel.: [phone]. E-mail: [email protected]. Website: www.sanbi.org.
Printed by United Litho, 22 Eland Street, Koedoespoort, Pretoria, 0186 South Africa.
Contents
: Introduction
J.A. Harrison
CHAPTER 1 Priorities for systematic studies on southern African
/ reptiles
W.R. Branch
^r\&Q CHAPTER 2 Taxonomic units relevant to conservation planning
A.M. Bauer
nr* CHAPTER 3 Mismatches between morphology and genetics
5^
G. Alexander
CHAPTER 4 Methods, techniques and protocols for phylogenetic
34
studies on southern African reptiles
K.A. Tolley, M. Cunningham and A.A. Turner
CHAPTER 5 A sampling and implementation strategy for phylo-
40
genetic studies on southern African reptiles
M. Cunningham, J.A. Harrison and K.A. Tolley
48 List °f workshop participants

Introduction
The Southern African Reptile Conservation Assessment (SARCA) was launched in
May 2005. Its primaryaim isto produce a conservation assessmentforthe reptiles
ofSouth Africa, Lesotho and Swaziland within a four-year period (2005-2009). It has
the distinction of beingthe firstfaunal project ofthe newly constituted South African
National Biodiversity Institute (SANBI) which, in itsformer incarnation asthe National
Botanical Institute (NBI), was concerned onlywith plants.
SARCA was motivated principally by a clear need for an update ofthe South African Red
Listfor reptiles which was last updated in 1988. However, projects ofthis kind aimed
at beingcomprehensive in geographical and taxonomic scope, are confronted with
a discipline's knowledge gaps. These gaps are particularly acute in southern Africa,
wheretaxonomic studies in the last 20 years have revealed thatthe subcontinent is a
global hotspot of reptile diversity. Inadequacies in the geographical samplingof reptiles
are being addressed by a series ofSARCAsurveys in previously undersampled areas.
However, this effortalone cannotspecificallyaddressthe incomplete and sometimes
problematic nature ofthe region's reptile alpha taxonomy (the description and naming
ofspecies). As conservation assessmentand planningdepend fundamentallyon alpha
taxonomy, itwas soon apparentthat SARCA would have to help initiate a programme to
resolvethe pressingtaxonomic problems.
To this end, a workshop was organised to identify, listand prioritise all known taxonom-
ic problems. In addition, the workshop participants would discuss, resolve and describe
the methodological questions and the practicalities of methods and resources. This
workshop was held from 22-24 February 2006, atSANBI's Biodiversity Research
Building, Kirstenbosch, Cape Town. The eventwasfunded bythe South African National
Research Foundation (NRF), facilitated by Renee le Roux and hosted by SANBI, with the
particular assistance of Krystal Tolley.
The participants included Prof. Graham Alexander (Universityofthe Witwatersrand),
Mike Bates (National Museum, Bloemfontein), Prof. Aaron Bauer (University ofVil-
lanova, Pennsylvania), Dr Bill Branch (PE Museum), Marius Burger (ADU), Dr Michael
Cunningham (University ofthe Free State), DrSavel Daniels (UniversityofStellenbosch),
James Harrison (ADU), Prof. Margaretha Hofmeyr (University ofthe Western Cape),
Johan Marais (University ofthe Witwatersrand), Prof. Le Fras Mouton (University of
Stellenbosch), Dr Krystal Tolley (SANBI), AndrewTurner(CapeNature) and rapporteurs
Daniel Goedbloed (University ofthe Free State) and Lerina Kaars (University ofthe Free
State, SANBI intern). Additional inputwas given duringone session by DrJohn Donald-
son (SANBI) and Prof. Les Underhill (ADU). So, with few exceptions, the main research-
ers involved in thetaxonomy ofthe region's reptiles were present, and contributed
substantivelytothe proceedings ofthe workshop and to this report.
This report brings together, in a single document, a comprehensive set ofguidelinesfor
a whole section ofsouthern Africa's biodiversity research, and should remain relevant
forat least a decade. The herpetologists ofthe region congratulatethe institutions,
especiallySANBI and NRF, that have had the vision and commitmentto supportthis
endeavour.
J.A. Harrison
Avian Demography Unit, University of Cape Town, Rondebosch 7701
O

SANBI Biodiversity Series 5 (2006)
^CHAPTER
1 Priorities for systematic studies on
^\^^^
southern African reptiles
i&K$
and optimisethe taxonomic usefulness of
W.R. Branch these surveys, and the subsequentanalysis of
Bayworld (formerly Port Elizabeth Museum), voucher material, it is necessaryto reviewthe
P.O. Box 13147, Humewood 6013, taxonomic knowledge ofthe regional reptile
Port Elizabeth fauna and to identify and highlight problematic
taxa.
Southern Africa hasthe richest reptile diver-
sity in Africa (Bauer 1993; Branch 1999a), Approach
with a fauna that currently exceeds 520
A provisional list ofgenera in which cryptic
species (Branch 1998; subsequent updates).
taxa were known orsuspected to be present,
Lizardsform the dominant component ofthis
was prepared bythe author. Problematic taxa
rich fauna due, in part, to an exceptional radia-
included the following:
tion ofgeckos in the western arid region. Over •
100 species ofgecko are now known from the • species with subspecies (races) that have
subcontinent, while the families Scincidae and not been recently reviewed (seethe chap-
Cordylidae are also well represented and the ter by Bauer in this volumefor a discussion
amphisbaenid diversity isthe richest in Africa. ofspecies definitions and the subspecies
Only one introduced reptile {Rhamphotyphlops concept in herpetology);
braminus) has become established. • species with disjunct ranges and geo-
graphically isolated populations, which may
The current rate ofspecies description shows include cryptictaxa; and r
<
little indication of reachinga plateau (Branch • species with contiguous ranges, butwith
1999a), even after 250 years ofalmost con-
confusing morphological (includingcoloura-
tinuous study. This is evident in the increase tion) and/or habitatvariation.
in species numbers in recent decades (397 in
Branch 1988; 480 in Branch 1998; 520+ in These were discussed at a workshop at-
Branch unpubl. checklist). In addition to its di- tended by invited researchers (see Introduc-
versity, the southern African reptilefauna also tion for list). Following discussion, the listwas
displays high endemicity, particularly in lizards amended for oversights and new insights,
(mean 65.3%; Cordylidae 85.5%; Chamaeleo- and expanded to include details of proposed
nidae 95%). This endemicity exceeds that of and ongoing research projects. Discussion
frogs and freshwaterfish (50-60%) and is then prioritised the identified problem taxa
much greaterthan that of birds and mammals for attention (1-5, low-high) and the research Mi
(<25%). funding required to resolve these problems
(1-5). Problem taxa scored high iftheywere
A directed programme of reptile surveys is a known to contain numerous newtaxa, or had
componentofthe Southern African Reptile the potential to do so, based on the biological
Conservation Assessment (SARCA). The survey and distribution characteristics associated
localities were selected by usinga gap analy- with high species richness. High scoresfor
sis of known reptile distributions, based on research fundingwere based on a lack of
museum records in the majorSouth African existingfundingand a reasonable chance
museums. The gap analysis identified areas
ofobtainingessential study material. For
with known reptile diversities, which were the latter, the resolution ofsometaxonomic
significantly lowerthan those predicted byan
problems requires extralimital material that
analysis ofthe distribution maps published
is currently not readily available (e.g. from
in Branch (1998). In addition to collecting Angola). Duetothe interrelatedness ofthe
distribution data, the surveys mayserve a
reptile fauna ofsouthern Africa, the analysis of
useful ancillaryfunction by collecting material
problematictaxa was not limited tothe SARCA
fortaxonomic revisions, as well astissue for
region (South Africa, Lesotho and Swaziland).
use in molecularstudies. Moreover, theycan
be expected to uncover additional taxonomic
Results
novelties, as well as populations which do not
fit easily into current hypotheses ofspecies' Genera containing problematic taxa are sum-
distributions and diagnoses. To both direct marised in Appendix 1. The scores forthese
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