First report on the herpetofauna of Pulau Aur, Johor, West Malaysia

With the exception ofTweedie's (1983) account ofCalamaria lovii, published accounts on the herpetofauna of Pulau Aur, located 63 km off the south-east coast of peninsular Malaysia in the South China Sea did not exist prior to this report. The only species known from the island were based on the museum records ofLimnonectes blythii, Mabuya multi/asciata, Bronchocela cristatella, Gehyra mutilata, Varanus nebulosus and Ahaetulla prasina deposited in the Raffles Museum of Biodiversity Research. A short expedition to the island on 15-16 July 2001 yielded an additional 12 species, comprising 10 lizards and two snakes: Limnonectes blythii; Bronchocela cristatella; Cnemaspis cf. Nigridia; Cosymbotus platyurus; Cyrtodactylus consobrinus; Gehyra mutilata; Gekko monarchus; Hemidactylus frenatus; Dasia o/ivacea; Emoia atrocostata; Lygosoma bowring;;; Mabuya multi/asciata; Sphenomorphus scotophi/us; Varanus nebulosus; Varanus salvator; Ramphotyphlops cf. braminus; Calamaria lovii and Macropisthodon flaviceps

Data from: Barcoding snakeheads (Teleostei, Channidae) revisited: discovering greater species diversity and resolving perpetuated taxonomic confusions

Snakehead fishes of the family Channidae are predatory freshwater teleosts from Africa and Asia comprising 38 valid species. Snakeheads are important food fishes (aquaculture, live food trade) and have been introduced widely with several species becoming highly invasive. A channid barcode library was recently assembled by Serrao and co-workers to better detect and identify potential and established invasive snakehead species outside their native range. Comparing our own recent phylogenetic results of this taxonomically confusing group with those previously reported revealed several inconsistencies that prompted us to expand and improve on previous studies. By generating 343 novel snakehead coxI sequences and combining them with an additional 434 coxI sequences from GenBank we highlight several problems with previous efforts towards the assembly of a snakehead reference barcode library. We found that 16.3% of the channid coxI sequences deposited in GenBank are based on misidentifications. With the inclusion of our own data we were, however, able to solve these cases of perpetuated taxonomic confusion. Different species delimitation approaches we employed (BIN, GMYC, and PTP) were congruent in suggesting a potentially much higher species diversity within snakeheads than currently recognized. In total, 90 BINs were recovered and within a total of 15 currently recognized species multiple BINs were identified. This higher species diversity is mostly due to either the incorporation of undescribed, narrow range, endemics from the Eastern Himalaya biodiversity hotspot or the incorporation of several widespread species characterized by deep genetic splits between geographically well-defined lineages. In the latter case, over-lumping in the past has deflated the actual species numbers. Further integrative approaches are clearly needed for providing a better taxonomic understanding of snakehead diversity, new species descriptions and taxonomic revisions of the group

Channid_coxI_778

Final coxI alignment of 777 chained individuals plus one outgrou

Barcoding snakeheads (Teleostei, Channidae) revisited: Discovering greater species diversity and resolving perpetuated taxonomic confusions

<div><p>Snakehead fishes of the family Channidae are predatory freshwater teleosts from Africa and Asia comprising 38 valid species. Snakeheads are important food fishes (aquaculture, live food trade) and have been introduced widely with several species becoming highly invasive. A channid barcode library was recently assembled by Serrao and co-workers to better detect and identify potential and established invasive snakehead species outside their native range. Comparing our own recent phylogenetic results of this taxonomically confusing group with those previously reported revealed several inconsistencies that prompted us to expand and improve on previous studies. By generating 343 novel snakehead coxI sequences and combining them with an additional 434 coxI sequences from GenBank we highlight several problems with previous efforts towards the assembly of a snakehead reference barcode library. We found that 16.3% of the channid coxI sequences deposited in GenBank are based on misidentifications. With the inclusion of our own data we were, however, able to solve these cases of perpetuated taxonomic confusion. Different species delimitation approaches we employed (BIN, GMYC, and PTP) were congruent in suggesting a potentially much higher species diversity within snakeheads than currently recognized. In total, 90 BINs were recovered and within a total of 15 currently recognized species multiple BINs were identified. This higher species diversity is mostly due to either the incorporation of undescribed, narrow range, endemics from the Eastern Himalaya biodiversity hotspot or the incorporation of several widespread species characterized by deep genetic splits between geographically well-defined lineages. In the latter case, over-lumping in the past has deflated the actual species numbers. Further integrative approaches are clearly needed for providing a better taxonomic understanding of snakehead diversity, new species descriptions and taxonomic revisions of the group.</p></div

Channid misidentifications.

<p>Summary of channid misidentifications and incompletely identified channid specimens with their BIN assignment, GenBank accession numbers and number of specimens found in GenBank, with how many specimens have been used and / or generated by [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0184017#pone.0184017.ref032" target="_blank">32</a>].</p

Barcode gap analysis.

<p>Dotplot illustrating the presence/absence of local barcode gaps. For each individual the maximum intraspecific distance is plotted against the minimum interspecific distance. The "species" groupings were A) current taxonomy with the exception of species with prominent intraspecific clades that were split into distinct units (<i>Channa bankanensis</i>, <i>C</i>. <i>gachua</i>, <i>C</i>. <i>marulius</i>, <i>C</i>. <i>striata</i>), B) according to the 90 BINs identified in this study. The slope 1:1 is indicated by a red line.</p

Summary of channid species and their BIN and clade assignment following the clade order in Fig 1.

<p>Species names according to [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0184017#pone.0184017.ref032" target="_blank">32</a>] if different from this study are given, BINs reported by [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0184017#pone.0184017.ref032" target="_blank">32</a>] are indicated and those species with multiple BINs in the [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0184017#pone.0184017.ref032" target="_blank">32</a>] study and in this study are indicated.</p

Distance tree of snakehead barcodes.

<p>Neighbour joining tree based on HKY distances of 777 channid coxI sequences. Individuals have been collapsed into 61 BINs and 29 potential new BINs (indicated as clades 1–29 and highlighted in dark grey); see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0184017#pone.0184017.t001" target="_blank">Table 1</a>. The <i>Parachanna africana</i> clade is highlighted in light grey. Numbers in brackets behind species names refer to number of individuals from this study / number of individuals from GenBank, followed by BIN or clade designation. BINs from BOLD not previously reported by [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0184017#pone.0184017.ref032" target="_blank">32</a>] are indicated in brackets with "new" (BOLD accessed March 31, 2016). Red dots indicate clades containing misidentified or incomplete identified specimens; see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0184017#pone.0184017.t002" target="_blank">Table 2</a> and the following comments: (a) <i>Protopterus annectens</i> BIN containing five lungfish specimens, (b) three <i>Pa</i>. <i>africana</i> and two <i>Pa</i>. <i>obscura</i> included, (c) one <i>Pa</i>. sp included, (d) two <i>Pa</i>. <i>insignis</i> included, (e) nine <i>Channa</i> sp. included, (f) one <i>C</i>. cf. <i>marulius</i> included, (g) ten <i>C</i>. <i>marulius</i> with accession numbers EU342199-EU342200, HM117192-HM117196, KJ937341, KJ937348, KJ937388 included. These might be <i>C</i>. <i>pseuomarulius</i>, but were not counted as misidentifications since this species was only recently revalidated by Britz <i>et al</i>. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0184017#pone.0184017.ref048" target="_blank">48</a>], (h) includes an exceptionally long branch for a single specimen (accession number JX983243 shown as a grey bar) probably due to sequencing errors, (i) one <i>C</i>. cf. <i>nox</i> included, (j) five <i>C</i>. <i>marulius</i> included, (k) one <i>C</i>. <i>orientalis</i> included, (l) BIN number is for unpublished <i>C</i>. <i>orientalis</i> in BOLD, (m) five <i>C</i>. <i>orientalis</i> included, (n) six <i>C</i>. <i>orientalis</i> included, (o) six <i>C</i>. <i>orientalis</i> included, (p) 17 <i>C</i>. <i>orientalis</i> included, (q) misidentification should be <i>C</i>. <i>bleheri</i> see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0184017#pone.0184017.t002" target="_blank">Table 2</a>, (r) one C. <i>stewartii</i> included, (s) one <i>C</i>. cf. <i>stewartii</i> included, (t) five <i>C</i>. <i>barca</i> included, (u) misidentification should be <i>C</i>. <i>andrao</i> see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0184017#pone.0184017.t002" target="_blank">Table 2</a>, (v) three <i>C</i>. <i>gachua</i> included, (w) BOLD ID showed 97.39% similarity with ACS3540, (x) five <i>C</i>. <i>stewartii</i> included, (y) BOLD ID showed 97.98% similarity with AAC3925, (z) one <i>C</i>. <i>gachua</i> included. For clades composed of misidentified specimens only, the original species designation was kept and these clades are underlined (ACB7513 and ACB8348).</p