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A critical revision of the churchill snoutfish, genus Petrocephalus Marcusen, 1854 (Actinopterygii: Teleostei: Mormyridae), from southern and eastern Africa, with the recognition of Petrocephalus tanensis, and the description of five new species

TL;DR: Sequence data from mitochondrial DNA confirm differentiation of two new western and two eastern species, forming mutual sister groups in the southern African electric fish Petrocephalus catostoma, or churchill.
Abstract: We morphologically and genetically studied the southern African electric fish Petrocephalus catostoma, or churchill, and its six nominal species, five of which by synonymization (three valid subspecies). We reinstate the synonymized species, and recognize Petrocephalus tanensis (Whitehead and Greenwood, 1959) from the Tana River in Kenya, also using electric organ discharges. The Okavango delta (Botswana) is inhabited by Petrocephalus okavangensis sp. nov. and Petrocephalus magnitrunci sp. nov., and the Namibian Cunene River by Petrocephalus magnoculis sp. nov. We recognize Petrocephalus petersi sp. nov. for the Lower Zambezi River (Mozambique), and Petrocephalus longicapitis sp. nov. for the Upper Zambezi River (Namibia). The Lufubu River in Northern Zambia is inhabited by Petrocephalus longianalis sp. nov. For the southern churchill, Petrocephalus wesselsi Kramer and Van der Bank, 2000, we confirm intraspecific and interspecific differentiation. Sequence data from mitochondrial DNA confirm differentiati...

Summary (3 min read)

Electrical and morphological studies

  • A total of 566 specimens was examined morphologically and at least 16 measurements and at least three meristic characters were recorded.
  • Measurements are illustrated in Figure 3 and were made using vernier calliper readings to 0.1 mm.
  • Abbreviations used to represent institutions and collections follow Leviton et al. (1985) and Fricke and Eschmeyer (2011).

LSo

  • Institute for Aquatic Biodiversity, Grahamstown, South Africa ; at the Zoologische Staatssammlung, München, Germany (ZSM); and at the Senckenberg Forschungsinstitut und Naturmuseum Frankfurt, Frankfurt am Main, Germany (SFM).
  • Conductivity (±1 µS/cm) and temperature (±0.1 ◦C) were monitored using an electronic meter (LF92 by Wissenschaftlich-Technische Werkstätten WTW, 82362 Weilheim, Germany).
  • Before analysis, EODs were temperature-corrected to 25◦C using a Q10 of 1.5 (Kramer and Westby 1985), and normalized in amplitude (by setting the peak amplitude of the P1 phase, measured from baseline, equal to 1).
  • Statistical analyses as indicated in the Results section; P values are twotailed unless otherwise stated.

DNA isolation

  • DNA was isolated from muscle or scale tissue, which was preserved in ethanol, using a standard phenol/chloroform protocol (Sambrook et al. 1989).
  • The mitochondrial cytochrome b (cyt b) gene was amplified using the published mitochondrial DNA primers (Kramer et al. 2007).
  • Sequencing was carried out on an ABI 3730 automated capillary sequencer (Applied Biosystems, 64293 Darmstadt, Germany) with the ABI Prism Big Dye Terminator Cycle Sequencing Ready Reaction Kit 3.1 by STARSEQ GmbH (Mainz, Germany).

Phylogenetic analyses

  • The tree reconstruction was performed using the maximum likelihood method with the substitution model Tamura–Nei and the Nearest-Neighbour-Interchange algorithm.
  • Bootstrap was carried out with 600 replications and the mean pairwise p-distances were calculated following Nei (1987).
  • All of these analyses were conducted with MEGA version 5.0 (Tamura et al. 2011).

Morphological comparisons

  • The authors first concern was to investigate whether or not their own sample from the type region represented P. catostoma.
  • PC1 therefore represented a gradient for “length and depth of anterior trunk and depth of caudal peduncle vs length of rear section, especially of anal fin”, signifying that a long PAL and PDL and high CPD were associated with a short anal fin, small number of rays and short pD (and vice versa).
  • In conclusion, the authors recognize morphological differentiation on the species level for the samples from (1) the Tana River, (2) the Lower Zambezi delta, (3) the Upper Zambezi River (including Kafue), (4) the Okavango (Guma), (5) the Lufubu River, and (6) the Cunene River, and confirm such differentiation for Sabie River samples (i.e. P. wesselsi).
  • The specimen from Lake Rukwa is well differentiated from P. catostoma (as well as from any other nominal species in a huge perimeter: P. steindachneri, P. stuhlmanni, the Tana sample, P. s. congicus, P. degeni) in all anatomical characters listed on Table 1 but BD, CPD and CPL.

Allopatric churchill species

  • For the four female EOD characters without significant interaction term (see below) the overall MANCOVA P value of <10–4 showed that also female EODs depended on origin, a result that was confirmed by univariate ANCOVAs for all four characters (Table 7).
  • Between P. longicapitis sp. nov. and P. wesselsi males both EOD characters differed significantly.

Genetic studies

  • DNA sequencing of southern African electric fishes does not involve all the species mentioned, because it was not possible to recover intact DNA from some species.
  • For four species the phylogenetic relationships could be reconstructed.
  • Neighbour joining, maximum parsimony and maximum likelihood produced identical trees, of which the maximum likelihood tree is shown in Figure 13.
  • Two sister clades of Petrocephalus are apparent: P. catostoma forms a sister species to P. wesselsi (Mokolo form) and P. longicapitis sp. nov. to P. magnoculis sp. nov.
  • The genetic distances between clades ranged between 0.8% and 4.2% (p-distance; Table 9), supporting the findings from morphology and electrophysiology, that these taxa are distinct species.

Systematics

  • For Material examined, see Material and methods section.
  • Petrocephalus congicus (David and Poll, 1937), also known as Current status.
  • Presently known only from the lower and the upper reaches of the Upper Zambezi River: East Caprivi, Namibia, and Lumwana River, Zambia.

Discussion

  • Following a multitude of new species descriptions by the early explorers of Africa’s freshwater ichthyofauna, there has been a strong tendency to synonymize younger names.
  • Even when only including southern African forms, the hypothesis of a Petrocephalus catostoma species complex, that is, closely related sibling species or subspecies, cannot be maintained in the present form.
  • The authors conclude that the first three principal components readily account for consistent morphological gradients in churchill fish.
  • As hypothesized by Bratton and Kramer (1988) for the West African Pollimyrus adspersus with a similar, triphasic EOD waveform (and a similar, statistically significant sex difference with wide overlap), a stronger P2 phase in male EODs may be a result of a higher testosterone titre.
  • Petrocephalus longicapitis sp. nov. was chosen because the Limpopo valley was once the Zambezi’s outlet to the Indian Ocean, hence the Upper Zambezi may have seeded South Africa with churchills .

Acknowledgments

  • The authors thank the editor, Dr Louise Allcock, an anonymous referee, and Dr J. P. Sullivan for their constructive comments that have greatly improved the manuscript.
  • For taking anatomical measurements, the authors are grateful to Ellen Fröhlich, Kathrin Kahler, Peter Machnik, Birgit Blaul, Sabine Hartl, Henriette Seichert, Lena Dietz, Andreas Lechner.
  • R. Bills was supported by the Sociedade para a Gestão e Desenvolvimento da Reserva do Niassa, Moçambique (S.R.N.), Conservation International in Botswana and the All Catfish Species Inventory (NSF programme) in Zambia.
  • The authors thank Hedi Sauer-Gürth (IPMB, Heidelberg) for technical assistance in DNA analysis.
  • This work was supported by Deutsche Forschungsgemeinschaft (DFG) Kr 446/10-12.

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Journal of Natural History
Vol. 46, Nos. 35–36, September 2012, 2179–2258
A critical revision of the churchill snoutfish, genus Petrocephalus
Marcusen, 1854 (Actinopterygii: Teleostei: Mormyridae), from southern
and eastern Africa, with the recognition of Petrocephalus tanensis, and
the description of five new species
Bernd Kramer
a
*
, Roger Bills
b
,PaulSkelton
b
and Michael Wink
c
a
Zoological Institute, University of Regensburg, D-93040 Regensburg, Germany;
b
South African
Institute for Aquatic Biodiversity, Private Bag 1015, Grahamstown 6140, South Africa;
c
Institut
für Pharmazie und Molekulare Biotechnologie, Universität Heidelberg, D-69120 Heidelberg,
Germany
(Received 13 September 2011; final version received 28 June 2012)
We morphologically and genetically studied the southern African electric fish
Petrocephalus catostoma, or churchill, and its six nominal species, five of which
by synonymization (three valid subspecies). We reinstate the synonymized species,
and recognize Petrocephalus tanensis (Whitehead and Greenwood, 1959) from the
Tana River in Kenya, also using electric organ discharges. The Okavango delta
(Botswana) is inhabited by Petrocephalus okavangensis sp. nov. and Petrocephalus
magnitrunci sp. nov., and the Namibian Cunene River by Petrocephalus magnoculis
sp. nov. We recognize Petrocephalus petersi sp. nov. fortheLowerZambeziRiver
(Mozambique), and Petrocephalus longicapitis sp. nov. for the Upper Zambezi River
(Namibia). The Lufubu River in Northern Zambia is inhabited by Petrocephalus
longianalis sp. nov. For the southern churchill, Petrocephalus wesselsi Kramer
and Van der Bank, 2000, we confirm intraspecific and interspecific differentia-
tion. Sequence data from mitochondrial DNA confirm differentiation of two new
western and two eastern species, forming mutual sister groups.
Keywords: systematics; morphometrics; electric organ discharges; molecular
genetics; allopatric speciation
Introduction
The African snoutfish genus Petrocephalus Marcusen, 1854 is defined on characteris-
tic skeletal features (Taverne 1969), certain characters of external morphology, such
as a pair of narrowly spaced nostrils the posterior one of which is closely apposed
to the eye (Bigorne and Paugy 1991), and molecular DNA studies (Lavoué et al.
2000; Sullivan et al. 2000). About 25 species are distributed throughout the more
tropical regions of Africa, two in southern Africa. The type locality for the widely
distributed Petrocephalus catostoma (Günther, 1866), or churchill, is the Rovuma
River that arises in the highlands east of Lake Malawi (Livingstone Mountains),
whence it flows eastward into the Indian Ocean (Figure 1, no. 1). The Rovuma (also
Ruvuma) forms the border between Tanzania and Mozambique for about 600 km
at 11
S. Whitehead and Greenwood (1959) reviewed the status of “three closely
related species of Petrocephalus ...recorded from East Africa; these are P. degeni
*Corresponding author. Email: bernd.kramer@biologie.uni-regensburg.de
ISSN 0022-2933 print/ISSN 1464-5262 online
© 2012 Taylor & Francis
http://dx.doi.org/10.1080/00222933.2012.708452
http://www.tandfonline.com

2180 B. Kramer et al.
10° E
20° 30°
40°
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30°
20°
10° E
10°
S
20°
30°
30°
20°
10° S
1000 km
1
2
3
4
5
6
22
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Figure 1. Map of southern Africa indicating the origin of samples of the Petrocephalus species
studied. (1) Rovuma (Ruvuma) River, type locality for P. catostoma (Günther 1866) [BMNH
1863.10.12.4]; (2) Ruvu (Kingani) River, type locality for P. stuhlmanni Boulenger 1909 [BMNH
1907.12.3.1]; (3) Sabie River, type locality for P. wesselsi Kramer and Van der Bank 2000 [ZSM
28554 to ZSM 28566, SAIAB 054449]; (4) Groot Letaba River, Limpopo System [SAIAB
85920]; (5) Blyde River, Limpopo System [SAIAB 85923]; (6) Pongola River [SAIAB 85919]
(7) Upper Zambezi River near Katima Mulilo, type locality for P. longicapitis sp. nov. [SAIAB
85916]; (8) Kwando River [ZSM 38658]; (9) Okavango Delta, Nguma Lagoon, type locality for
P. okavangensis sp. nov. [SAIAB 030046]; (10) Tana River, type locality for P. catostoma tanensis
Whitehead and Greenwood, 1959, here recognized as P. tanensis (Whitehead and Greenwood,
1959) [SAIAB 85907]; (11) Lake Rukwa [SAIAB 059515]; (12) Lufubu River, Luapula River sys-
tem, P. longianalis sp. nov. [SAIAB 76758]; (13) East Lungu River, Kafue/Zambezi River system
[SAIAB 040074]; (14) East Lumwana River, Zambezi system [SAIAB 041208]; (15) Mwekera
Stream, Kafue/Zambezi River system [SAIAB 042559]; (16) Kapesha River, Lake Malawi
[SAIAB 039328]; (17) Dwangwa River, Lake Malawi [specimen SAIAB 050065]; (18) Kaombe
River, Lake Malawi [SAIAB 050155]; (19) Lake Chiuta [SAIAB 039264]; (20) Mulela River
[SAIAB 055875]; (21) Zambezi River Delta, type locality for P. p e t e r s i sp. nov. [SAIAB 060846];
(22) Mbuluzi River, Swaziland [SAIAB 067228]; (23) Cunene River, type locality for P. mag-
noculis sp. nov. [SAIAB 78788]; (24) Lukula River, type locality for P. haullevillii Boulenger
1912 [BMNH 1912.4.1.186-188]; (25) Rufiji basin, type locality for P. steindachneri Fowler
1958 [NMW 551181]; (26) Mukishi on Lomami River (Congo River basin), type locality for

Journal of Natural History 2181
B
LGR. 1906, P. stuhlmanni BLG R. 1909 and P. catostoma GÜNTHER, 1866”. These
authors concluded ...it became clear that size discrepancies and paucity of mate-
rial could explain why three ‘species’ had been recognised.” Therefore, they united all
three species as members of a single, widespread species, P. catostoma. To the list of
synonyms they added P. stuhlmanni congicus David and Poll, 1937 and P. haullevillii
Boulenger, 1912 from the distant and unconnected upper and lower Congo basins,
respectively, while recognizing that the “Congo form of this species clearly differs
from the eastern and southern subspecies ...”, and that “the two Congoan forms
may yet have to be united”. In consequence, P. steindachneri Fowler, 1958 of East
Africa became the sixth nominal species referred to P. catostoma (Seegers 1996).
Petrocephalus catostoma defined in this way ranged from the Katonga River, Lake
Victoria, in Uganda in the north to the Pongola River in South Africa (a distance of
3000 km); from the Atlantic Congo and Cunene Rivers in the west to the Indian Ocean
in the east (Whitehead and Greenwood 1959; Gosse 1984; Seegers 1996; Eschmeyer
2011) (Figure 2).
A critical comparison among a few allopatric samples from southern local-
ities revealed that South African churchills represented a different species from
P. catostoma (Kramer and Van der Bank 2000). The southern churchill, P. wesselsi
Kramer and Van der Bank, 2000, as it is now called, also differed genetically from
the Petrocephalus sampled from the Upper Zambezi (Van der Bank 1996). Additional
species diversity within Petrocephalus has similarly been discovered in other regions
of sub-Saharan Africa: in Gabon in Central Africa where a new (fourth) species of
Petrocephalus, P. sullivani Lavoué, Hopkins and Kamdem Toham, 2004, was recog-
nized on the basis of anatomical and electrical characters (Lavoué et al. 2004). Five
more species [supported by molecular genetics and electric organ discharge (EOD)
comparisons] have been found in a small region in the northwest of the Republic of
Congo (Lavoué et al. 2008, 2010; Lavoué 2011); one more species in the upper reaches
of the Congo basin in northern Zambia (Lavoué Forthcoming 2012). For a full revision
of only P. catostoma as traditionally understood (including all the nominal species), all
local populations need to be sampled and critically compared. Given the huge distri-
bution and the prevailing sparseness of museum specimens, especially type material,
this goal appeared difficult to achieve.
We took the opportunity to sample additional rivers, among them the Tana River,
type locality for P. c. tanensis Whitehead and Greenwood, 1959, for more material to
extend our comparisons of allopatric churchills (Figure 1). We compared anatomical
P. stuhlmanni congicus David and Poll 1937 [MRAC 30.807–30.808]; (27) Katonga River, Lake
Victoria (Uganda), type locality for P. degeni Boulenger 1906 [BMNH 1906.5.30]; (28) approx-
imate location for our type region material for P. catostoma (SAIAB 73802, 73808, 73887,
73894), (29) Luapula River [SAIAB 76582]; (30) Bangweulu Lake [SAIAB 76859 and SAIAB
76825]; (31) Okavango delta, Boro River, type locality for P. magnitrunci sp. nov. [SAIAB
67069]. (36) Lepalala River, tributary of Limpopo [SAIAB 96537]; (37) Mokolo River, tribu-
tary of Limpopo [SAIAB 95989]; (38) Nwanedzi River, tributary of Limpopo [SAIAB 58157],
(39) “Ruisseau affluent de la Lukinda”, close to Lake Moero, type locality of P. squalostoma
(Boulenger, 1915) [BMNH 1920.5.26.1]. Some rivers and lakes are too small to be shown at the
scale used.

2182 B. Kramer et al.
data and, where possible, also EODs and molecular genetics to test the hypothe-
sis of a P. catostoma species complex for the whole of southern and eastern Africa.
We attempted to reconstruct the systematics and phylogeography in what has tradi-
tionally been considered to represent a single species, the churchill (P. catostoma)of
subcontinental distribution, and to identify some of the local adaptations both for
morphology and the electric communication signal.
Material and methods
Electrical and morphological studies
A total of 566 specimens was examined morphologically and at least 16 measurements
and at least three meristic characters were recorded. Measurements are illustrated in
Figure 3 and were made using vernier calliper readings to 0.1 mm. The following abbre-
viations were used: PDL, predorsal length: distance tip of snout to dorsal fin origin;
PAL, preanal length: distance tip of snout to anal fin origin; LD, dorsal fin length; LA,
anal fin length; pD, distance dorsal fin origin to end of caudal peduncle; CPL, length
of caudal peduncle: end of anal fin base to midbase caudal fin; CPD, depth of caudal
peduncle: the least vertical distance across the caudal peduncle; LSo, length of snout:
distance tip of snout to posterior orbital rim of eye; LSc, length of snout: distance tip
of snout to centre of eye; HL, head length: distance tip of the snout to furthest bony
edge of the operculum; Na, distance between the pair of nares of one side (from cen-
tre to centre); OD, eye diameter: defined by orbital rims; LPF, length of pectoral fins:
from anterior base to tip; PPF, distance between anterior base of pectoral fin to ante-
rior base of pelvic fin; BD, body depth: the greatest vertical distance across the body;
SL, standard length: distance tip of snout to midbase caudal fin; nD, number of dorsal
fin rays; nA, number of anal fin rays; SPc, number of scales around caudal peduncle;
SLS, number of scales in linear series along the lateral line row, as detailed in Skelton
(2001: 67); SLS range of accuracy, ± 2 counts.
Abbreviations used to represent institutions and collections follow Leviton
et al. (1985) and Fricke and Eschmeyer (2011). Specimens collected during
the course of the present study are permanently stored at the South African
Figure 2(A–D). Photographs of members of southern and eastern African Petrocephalus species
studied (numbers refer to localities given in Figures 1, 6 and 9). (1) P. catostoma (Günther,
1866), Lectotype, BMNH 1863.10.12.4, right side, SL 4.7 cm. (2) P. stuhlmanni Boulenger, 1909,
holotype, BMNH 1907.12.3.1, SL 7.9 cm. (3) P. wesselsi Kramer and Van der Bank, 2000, right
side, SL 9.7 cm, SAIAB 85922 (R1). (7) P. longicapitis sp. nov., SMF 28265 (R1), SL 9 cm. (9) P.
okavangensis sp. nov., holotype, SAIAB 030046, right side, SL 6.1 cm. (10) P. catostoma tanensis
Whitehead and Greenwood, 1959, holotype, BMNH 1963.11.29.1, right side, SL 6.7 cm. (10a)
P. tanensis, field no. Ta05na, SL 8.7 cm, SAIAB 85907. (12) P. longianalis sp. nov., holotype, SL
8.2 cm, right side, SAIAB 76758. (21) P. p e t e r s i sp. nov., holotype, SAIAB 060846, right side, SL
6.4 cm. (23) P. magnoculis sp. nov., SL 8.9 cm, ZSM 38659. (24) P. haullevillii Boulenger, 1912,
BMNH 1912.4.1.186–188 (R1), right side, SL 5.7 cm. (25) P. steindachneri Fowler 1958, syntype,
NMW 55118:3, right side, SL 6.4 cm. (26) P. stuhlmanni congicus David and Poll, 1937, syntype,
MRAC 30807-30808, SL 7.8 cm. (27) P. degeni Boulenger, 1906, BMNH 1906.5.30.84, right side,
SL 8.12 cm. (28) P. catostoma, SAIAB 73894 (R1), right side, SL 6.4 cm. (31) P. magnitrunci sp.
nov., SL 8.5 cm, SAIAB 67069 (R5, right side), see map Figure 6. Scale bar, 1 cm.

Journal of Natural History 2183

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Cites background from "A critical revision of the churchil..."

  • ...…signal, referred to as the electric organ discharge (EOD) that is often species-specific and has been used as a taxonomic character in systematic studies of this group (Alves-Gomes & Hopkins 1997; Boden et al. 1997; Moritz et al. 2009, Kramer et al. 2012; Kramer 2013a; Kramer et al. in press)....

    [...]

  • ...%) and by Kramer et al. (2012) (0.8–4.2%)....

    [...]

Journal ArticleDOI
10 Apr 2014-ZooKeys
TL;DR: A comparative molecular analysis including 21 other Petrocephalus species shows Petrocephalu boboto sp.
Abstract: A specimen of the African weakly electric fish genus Petrocephalus (Osteoglossomorpha, Mormyridae) collected in the Congo River at Yangambi, Orientale Province, Democratic Republic of Congo, is described as a new species. Petrocephalus boboto sp. n. can be distinguished from other Central African species of Petrocephalus by a combination of the following characteristics: three distinct black spots on the body, one at the origin of the pectoral fin, one at the origin of the caudal fin and one below the anterior base of the dorsal fin; Nakenrosette and Khelrosette electroreceptor clusters distinct on head but Augenrosette cluster reduced in size; 23 branched dorsal rays, 34 branched anal rays, and electric organ discharge waveform triphasic. Petrocephalus boboto sp. n. most closely resembles the holotype of Petrocephalus binotatus but is easily distinguished from it by its smaller mouth. A comparative molecular analysis including 21 other Petrocephalus species shows Petrocephalus boboto sp. n. to be genetically distinctive and to represent a deep lineage in the genus. Two specimens of Petrocephalus collected at Yangambi are morphologically similar and genetically closely related to specimens previously assigned to Petrocephalus binotatus, collected in the northwestern Congo River basin within Odzala-Kokua National Park, Republic of the Congo. This prompts us to formally describe a new species from these collections, Petrocephalus arnegardi sp. n., that, although similar to the holotype of Petrocephalus binotatus, can be distinguished from it by its smaller mouth and shorter interorbital width.

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Cites background or methods from "A critical revision of the churchil..."

  • ...…of Petrocephalus, the sole petrocephalin genus, the pace of new species discovery and description has been rapid in recent years, with about one third of Petrocephalus diversity having been described in the 21th century (Lavoué et al. 2004, 2010, Lavoué 2011, 2012, Kramer et al. 2012)....

    [...]

  • ...Petrocephalus binotatus in Lavoué et al. (2010), Lavoué (2011, 2012), Carlson et al. (2011)....

    [...]

  • ...…synonymized with Petrocephalus catostoma, we assigned revised names to two specimens (and their corresponding cytochrome b sequences) treated in Lavoué (2012): one specimen of P. catostoma from the Rufiji River is renamed Petrocephalus steindachneri and one specimen of P. catostoma from the…...

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  • ...The three new partial cytochrome b sequences were added to the dataset published in Lavoué (2012) from which individuals uninformative for interspecific comparisons have been removed....

    [...]

  • ...Comparative material including type specimens from all valid species from the Congo River basin and the Lower Guinea province is listed in Lavoué et al. (2004, 2010) and Lavoué (2012)....

    [...]

References
More filters
Book
15 Jan 2001
TL;DR: Molecular Cloning has served as the foundation of technical expertise in labs worldwide for 30 years as mentioned in this paper and has been so popular, or so influential, that no other manual has been more widely used and influential.
Abstract: Molecular Cloning has served as the foundation of technical expertise in labs worldwide for 30 years. No other manual has been so popular, or so influential. Molecular Cloning, Fourth Edition, by the celebrated founding author Joe Sambrook and new co-author, the distinguished HHMI investigator Michael Green, preserves the highly praised detail and clarity of previous editions and includes specific chapters and protocols commissioned for the book from expert practitioners at Yale, U Mass, Rockefeller University, Texas Tech, Cold Spring Harbor Laboratory, Washington University, and other leading institutions. The theoretical and historical underpinnings of techniques are prominent features of the presentation throughout, information that does much to help trouble-shoot experimental problems. For the fourth edition of this classic work, the content has been entirely recast to include nucleic-acid based methods selected as the most widely used and valuable in molecular and cellular biology laboratories. Core chapters from the third edition have been revised to feature current strategies and approaches to the preparation and cloning of nucleic acids, gene transfer, and expression analysis. They are augmented by 12 new chapters which show how DNA, RNA, and proteins should be prepared, evaluated, and manipulated, and how data generation and analysis can be handled. The new content includes methods for studying interactions between cellular components, such as microarrays, next-generation sequencing technologies, RNA interference, and epigenetic analysis using DNA methylation techniques and chromatin immunoprecipitation. To make sense of the wealth of data produced by these techniques, a bioinformatics chapter describes the use of analytical tools for comparing sequences of genes and proteins and identifying common expression patterns among sets of genes. Building on thirty years of trust, reliability, and authority, the fourth edition of Mol

215,169 citations

Book
01 Jan 1983
TL;DR: In this Section: 1. Multivariate Statistics: Why? and 2. A Guide to Statistical Techniques: Using the Book Research Questions and Associated Techniques.
Abstract: In this Section: 1. Brief Table of Contents 2. Full Table of Contents 1. BRIEF TABLE OF CONTENTS Chapter 1 Introduction Chapter 2 A Guide to Statistical Techniques: Using the Book Chapter 3 Review of Univariate and Bivariate Statistics Chapter 4 Cleaning Up Your Act: Screening Data Prior to Analysis Chapter 5 Multiple Regression Chapter 6 Analysis of Covariance Chapter 7 Multivariate Analysis of Variance and Covariance Chapter 8 Profile Analysis: The Multivariate Approach to Repeated Measures Chapter 9 Discriminant Analysis Chapter 10 Logistic Regression Chapter 11 Survival/Failure Analysis Chapter 12 Canonical Correlation Chapter 13 Principal Components and Factor Analysis Chapter 14 Structural Equation Modeling Chapter 15 Multilevel Linear Modeling Chapter 16 Multiway Frequency Analysis 2. FULL TABLE OF CONTENTS Chapter 1: Introduction Multivariate Statistics: Why? Some Useful Definitions Linear Combinations of Variables Number and Nature of Variables to Include Statistical Power Data Appropriate for Multivariate Statistics Organization of the Book Chapter 2: A Guide to Statistical Techniques: Using the Book Research Questions and Associated Techniques Some Further Comparisons A Decision Tree Technique Chapters Preliminary Check of the Data Chapter 3: Review of Univariate and Bivariate Statistics Hypothesis Testing Analysis of Variance Parameter Estimation Effect Size Bivariate Statistics: Correlation and Regression. Chi-Square Analysis Chapter 4: Cleaning Up Your Act: Screening Data Prior to Analysis Important Issues in Data Screening Complete Examples of Data Screening Chapter 5: Multiple Regression General Purpose and Description Kinds of Research Questions Limitations to Regression Analyses Fundamental Equations for Multiple Regression Major Types of Multiple Regression Some Important Issues. Complete Examples of Regression Analysis Comparison of Programs Chapter 6: Analysis of Covariance General Purpose and Description Kinds of Research Questions Limitations to Analysis of Covariance Fundamental Equations for Analysis of Covariance Some Important Issues Complete Example of Analysis of Covariance Comparison of Programs Chapter 7: Multivariate Analysis of Variance and Covariance General Purpose and Description Kinds of Research Questions Limitations to Multivariate Analysis of Variance and Covariance Fundamental Equations for Multivariate Analysis of Variance and Covariance Some Important Issues Complete Examples of Multivariate Analysis of Variance and Covariance Comparison of Programs Chapter 8: Profile Analysis: The Multivariate Approach to Repeated Measures General Purpose and Description Kinds of Research Questions Limitations to Profile Analysis Fundamental Equations for Profile Analysis Some Important Issues Complete Examples of Profile Analysis Comparison of Programs Chapter 9: Discriminant Analysis General Purpose and Description Kinds of Research Questions Limitations to Discriminant Analysis Fundamental Equations for Discriminant Analysis Types of Discriminant Analysis Some Important Issues Comparison of Programs Chapter 10: Logistic Regression General Purpose and Description Kinds of Research Questions Limitations to Logistic Regression Analysis Fundamental Equations for Logistic Regression Types of Logistic Regression Some Important Issues Complete Examples of Logistic Regression Comparison of Programs Chapter 11: Survival/Failure Analysis General Purpose and Description Kinds of Research Questions Limitations to Survival Analysis Fundamental Equations for Survival Analysis Types of Survival Analysis Some Important Issues Complete Example of Survival Analysis Comparison of Programs Chapter 12: Canonical Correlation General Purpose and Description Kinds of Research Questions Limitations Fundamental Equations for Canonical Correlation Some Important Issues Complete Example of Canonical Correlation Comparison of Programs Chapter 13: Principal Components and Factor Analysis General Purpose and Description Kinds of Research Questions Limitations Fundamental Equations for Factor Analysis Major Types of Factor Analysis Some Important Issues Complete Example of FA Comparison of Programs Chapter 14: Structural Equation Modeling General Purpose and Description Kinds of Research Questions Limitations to Structural Equation Modeling Fundamental Equations for Structural Equations Modeling Some Important Issues Complete Examples of Structural Equation Modeling Analysis. Comparison of Programs Chapter 15: Multilevel Linear Modeling General Purpose and Description Kinds of Research Questions Limitations to Multilevel Linear Modeling Fundamental Equations Types of MLM Some Important Issues Complete Example of MLM Comparison of Programs Chapter 16: Multiway Frequency Analysis General Purpose and Description Kinds of Research Questions Limitations to Multiway Frequency Analysis Fundamental Equations for Multiway Frequency Analysis Some Important Issues Complete Example of Multiway Frequency Analysis Comparison of Programs

53,113 citations

Journal ArticleDOI
TL;DR: The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models, inferring ancestral states and sequences, and estimating evolutionary rates site-by-site.
Abstract: Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version 5 (MEGA5), which is a user-friendly software for mining online databases, building sequence alignments and phylogenetic trees, and using methods of evolutionary bioinformatics in basic biology, biomedicine, and evolution. The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models (nucleotide or amino acid), inferring ancestral states and sequences (along with probabilities), and estimating evolutionary rates site-by-site. In computer simulation analyses, ML tree inference algorithms in MEGA5 compared favorably with other software packages in terms of computational efficiency and the accuracy of the estimates of phylogenetic trees, substitution parameters, and rate variation among sites. The MEGA user interface has now been enhanced to be activity driven to make it easier for the use of both beginners and experienced scientists. This version of MEGA is intended for the Windows platform, and it has been configured for effective use on Mac OS X and Linux desktops. It is available free of charge from http://www.megasoftware.net.

39,110 citations


"A critical revision of the churchil..." refers methods in this paper

  • ...All of these analyses were conducted with MEGA version 5.0 (Tamura et al. 2011)....

    [...]

  • ...Evolutionary analyses were conducted in MEGA5 (Tamura et al. 2011)....

    [...]

Book
01 Feb 1987
TL;DR: Recent developments of statistical methods in molecular phylogenetics are reviewed and it is shown that the mathematical foundations of these methods are not well established, but computer simulations and empirical data indicate that currently used methods produce reasonably good phylogenetic trees when a sufficiently large number of nucleotides or amino acids are used.
Abstract: Recent developments of statistical methods in molecular phylogenetics are reviewed. It is shown that the mathematical foundations of these methods are not well established, but computer simulations and empirical data indicate that currently used methods such as neighbor joining, minimum evolution, likelihood, and parsimony methods produce reasonably good phylogenetic trees when a sufficiently large number of nucleotides or amino acids are used. However, when the rate of evolution varies exlensively from branch to branch, many methods may fail to recover the true topology. Solid statistical tests for examining'the accuracy of trees obtained by neighborjoining, minimum evolution, and least-squares method are available, but the methods for likelihood and parsimony trees are yet to be refined. Parsimony, likelihood, and distance methods can all be used for inferring amino acid sequences of the proteins of ancestral organisms that have become extinct.

15,840 citations


"A critical revision of the churchil..." refers methods in this paper

  • ...Bootstrap was carried out with 600 replications and the mean pairwise p-distances were calculated following Nei (1987)....

    [...]

Book ChapterDOI
01 Jan 1969

10,262 citations

Frequently Asked Questions (1)
Q1. What are the contributions in "A critical revision of the churchill snoutfish, genus petrocephalus marcusen, 1854 (actinopterygii: teleostei: mormyridae), from southern and eastern africa, with the recognition of petrocephalus tanensis, and the description of five new species" ?

The authors morphologically and genetically studied the southern African electric fish Petrocephalus catostoma, or churchill, and its six nominal species, five of which by synonymization ( three valid subspecies ).