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BIOLOGY Pu N -Sv D Fo* Th* Fiih«R*« Society of Tke British I$Ki Journal of BIOLOGY Pu N -sV d fo* tH* Fiih«r*« Society of tKe British i$ki Journal of Fish Biology (2013) 82, 165-188 doi:10.1111/jfb.12001, available online at wileyonlinelibrary.com Genetic and morphological studies of Nothobranchius (Cyprinodontiformes) from Malawi with description of Nothobranchius wattersi sp. nov. E. N o’oMA*f, S. V aldesalici|, K. Reichwald* and A. C ellerino*§ *Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstrafie 11, D-07745 Jena, Germany, %Via Ca Bertacchi 5, 42030 Viano (RE), Italy and §Neurobiology Laboratory, Scuola Normale Superiore, c/o Area di Ricerca del CNR, via Moruzzi 1, 56124 Pisa, Italy (Received 4 March 2012, Accepted 19 September 2012) Molecular and morphological data were used to explore evolutionary differentiation among popu­ lations of Nothobranchius in the Lake Malawi-upper Shire River and the Lakes Chilwa-Chiuta drainage systems in Malawi. The aim of the study was to test the hypothesis that Nothobranchius of the Malawi-Shire system constitute a separate evolutionary group from Nothobranchius kirki. Mitochondrial and nuclear sequence data show a strongly supported phylogenetic split into two monophyletic groups separating the Lake Malawi basin fish from N. kirki. Unlike N. kirki, Lake Malawi-Shire fish do not deviate from neutrality and express an excess of rare haplotypes and mutations in terminal branches, characteristic of recently expanded populations. Further, the two groups significantly differ in morphology. Two body characters (dorsal-fin base length and pre- pelvic-pre-anal distance) are significantly different between the two species in both sexes. Several other characters are significantly different in either male or female comparisons with respect to both standard and head lengths, and robust morphological differentiation is detected by multivariate analysis. The two groups are readily distinguished on the basis of male colouration, especially in scale centres and the caudal fin. On the basis of this differentiation at the molecular and morpholog­ ical levels, in addition to colouration, the Lake Malawi-Shire fish are hereby formally recognized as constituting a new species, Nothobranchius wattersi. This distinction is in agreement with the geomorphologic and recent climatic history in the region. © 2012 The Authors Journal of Fish Biology © 2012 The Fisheries Society of the British Isles Key words: divergence; male colouration; molecular divergence; new species. INTRODUCTION The killifish genus Nothobranchius Peters 1868 occurs in tropical and sub-tropical eastern Africa with a wide distribution from South Africa to southern Sudan, and from Chad to Zanzibar and the Mafia islands in Tanzania. All known species are annual fishes, living principally in temporary pools and swamps formed during the rainy season (Seegers, 1997; Wildekamp, 2004). fAuthor to whom correspondence should be addressed. Tel.: +49 176 627 80867; email: enoch@ fli-leibniz.de 165 © 2012 The Authors Journal of Fish Biology © 2012 The Fisheries Society of the British Isles 166 E . N G ’OMA E T A L . Detailed accounts of Nothobranchius in Malawi in the contexts of geology, distri­ bution of present Nothobranchius biotopes, documentation and collection for estab­ lishment in captivity, soil and climate are presented by Watters (1991a, b, c, 2009). Two species are presently known in Malawi including the spotted killifish Notho­ branchius orthonotus (Peters 1844) in the lower Shire River area in the southern part of the country, and Nothobranchius kirki Jubb 1969 in the depression of Lakes Chilwa and Chiuta c. 100 km south-east of Lake Malawi. A third species, the bluefin notho Nothobranchius rachovii Ahl 1926 long suspected in the Malawian section of the lower Shire based on its consistent sympatric occurrence with N. orthonotus throughout the distribution range of the latter (Watters, 1991c), was recently con­ firmed as present in the Mozambican lower Shire (Shidlovskiy et al., 2010). A further population cluster of Nothobranchius occupying the fluvial plains of the upper Shire River and the Lake Malawi basin as far north as Chia Lagoon in central Malawi has traditionally been assigned to N. kirki (Jubb, 1981). For example, specimens of Nothobranchius collected from Salima were referred to by Jubb (1975) as N. cf. kirki. Nothobranchius of the Lake Malawi basin have, however, later been argued to constitute a separate group based on colouration, morphology (Watters, 1991a, c) and karyotypic characteristics (Scheel, 1990; Watters, 1991c). This view is in fact supported by the geomorphological features of the region that suggest sepa­ ration of the Lake Malawi basin from the Chilwa-Chiuta depression by the early Pleistocene or before (Watters, 1991c; Delvaux, 1995). Lakes Chilwa and Chiuta, currently isolated from each other, are believed on the other hand to have constituted a single water body draining eastwards through the Lugenda-Ruvuma River system (Lancaster, 1981). These observations raise an important question whether there is genetic divergence among fishes from the Chilwa-Chiuta and those from Lake Malawi-upper Shire basins. In this study, the morphological and genetic differentiation of Nothobranchius from these regions was assessed. MATERIALS AND METHODS FISHES Fish materials used for sequence analysis were collected in April 2009 from four repre­ sentative locations in the plains of Lakes Chilwa and Malawi [Figs 1 and 2(a), (b)]. Chilwa fishes were sampled from the western side of Lake Chilwa at the Njala Rice Scheme, Kachulu (KCH) and from Ntaja (NTJ) on the northern fringes of the lake (Table I). At both Chilwa sites (c. 90 km apart), specimens were collected from rice paddies that form part of the con­ tinuous seasonal marginal swamps of the lake. On the Lake Malawi plain, specimens were collected some 40 km south of Salima (SAL) town, and from Golomoti (GOL) some 60 km further south of Salima. Fishes were collected with either a dip-net, a two-man seine, or a traditional fish trap [Fig. 2(c)] and euthanized with an overdose of clove oil. Specimens were preserved in formaldehyde after removal of pectoral fins for DNA analysis. All materials for DNA were preserved in 96% ethanol. Specimens for morphological description were collected between 1988 and 2009 from 18 locations (Nothobranchius wattersi) (Table I), representing the entire known distribution range of Nothobranchius in the Lake Malawi plains. Compar­ ative materials of N. kirki were collected from five locations in the Lake Chiuta and Lake Chilwa catchments. © 2012 The Authors Journal of Fish Biology © 2012 The Fisheries Society of the British Isles, Journal of Fish Biology 2013, 82, 165-188 EVOLUTIONARY DIVERGENCE IN MALAWI KILLIFISHES 167 33 ° 34 ° 35° Fig. 1. Map of parts of central and southern Malawi (Africa insert) with known distribution of Nothobranchius wattersi (•, ^, type locality) and Nothobranchiuskirki ^ ) . Sites for populations of each species analysed for molecular divergence , N. wattersi; @ , N. kirki) are indicated. MOLECULAR METHODS Genomic DNA was isolated from fin material of ethanol preserved samples by the phe- nol-chloroform method (Kingsley Lab Protocols, 2004) and used to examine parts of the mitochondrial gene cytochrome c oxidase subunit I (coxl) and of five nuclear genes. Degen­ erate primers for coxl were defined based on conserved areas of a coxl sequence alignment of Nothobranchius furzeri Jubb 1971, N. rachovi and Fundulusoma thierryi Ahl 1924 [this last species is retained in Fundulusoma based on Murphy & Collier (1998) whose analysis of mitochondrial DNA supports the paraphyly of Fundulusoma from Nothobranchius; molecular analyses (unpubl. data) support the results of Murphy & Collier (1998)]. For nuclear loci, Li et al. (2007) defined degenerate primers for 10 genes in ray-finned fishes. Five of these genes were selected for this study including myh6, glyt, zic1, sh3px3 and gpr85 based on robustness of polymerase chain reaction (PCR) amplification in most Nothobranchius species (unpubl. data). Two nesting sets of primers (Table II) were used for each nuclear locus. PCRs were performed in 25 |il final volumes, each with 2-5 |il x10 PCR buffer, 1-5 |il 25 mM MgCl2, 0-5 |il each of 10 mM deoxynucleotide triphosphate (dNTP) mix, 10 |iM for­ ward primer, 10 |iM reverse primer, 0-25 |il 5 U |il-1 Taq Polymerase (Qiagen; www.qiagen. com) and 100-150 ng of genomic DNA. PCR conditions were 94° C, 2 min initial denat- uration followed by 35 cycles of 94° C, 30 s denaturation; 55° C (57° C for nesting), 30 s annealing; 72° C, 30 s extension and a final extension step of 1 min at 72° C. Nested PCR was carried out with 1 |il of 1:1000 dilutions of respective PCR product as template. © 2012 The Authors Journal of Fish Biology © 2012 The Fisheries Society of the British Isles, Journal of Fish Biology 2013, 82, 165-188 168 E . N G ’OMA E T A L . Fig. 2. Representative localities where specimens were collected: (a) rice fields accessed by canoe in the Group Village Headman Mkhuzumba on the northern fringes of a marsh near Ntaja town on Lake Chilwa, (b) near rice fields in Ngwimbi village, Golomoti, some 2-5 km east of the M5 road and (c) the traditional fish trap (m ono) belonging to local fishermen among whose catches many specimens for this study were collected. All amplification reactions were performed with an Eppendorf thermocycler (Mastercycler ep gradients; www.eppendorf.com). The cox1 gene was sequenced in 69 specimens (Table III) representing two sub-populations of N. kirki (KCH and NTJ) and two sub-populations of the new species N. wattersi (GOL and SAL). Nuclear genes were sequenced in six individuals each of N. kirki and N. wattersi selected randomly. Direct sequencing of PCR products using PCR primers was performed using the BigDye Terminator v3.1 Cycle Sequencing Kit (ABI; www.appliedbiosystems.com), followed by separation on ABI 3730xl capillary sequencers. After quality clipping, sequences were assembled based on overlaps using the GAP4 module of the Staden Sequence Analysis Package (Staden, 1996).
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