The genome of Mekong tiger perch (Datnioides undecimradiatus) provides insights into the phylogenetic position of Lobotiformes and biological conservation

Mekong tiger perch (Datnioides undecimradiatus) is an ornamental and vulnerable freshwater fish native to the Mekong basin in Indochina, belonging to the order Lobotiformes. Here, we generated 121X stLFR co-barcode clean reads and 18X Oxford Nanopore MinION reads and obtained a 595 Mb Mekong tiger perch genome, which is the first whole genome sequence in the order Lobotiformes. Based on this genome, the phylogenetic tree analysis suggested that Lobotiformes is more closely related to Sciaenidae than to Tetraodontiformes, resolving a long-time dispute. We depicted the genes involved in pigment development in Mekong tiger perch and results confirmed that the four rate-limiting genes of pigment synthesis had been retained after fish-specific genome duplication. We also estimated the demographic history of Mekong tiger perch, which showed that the effective population size suffered a continuous reduction possibly related to the contraction of immune-related genes. Our study provided a reference genome resource for the Lobotiformes, as well as insights into the phylogenetic position of Lobotiformes and biological conservation.

Characterization of a Y-specific duplication/insertion of the anti-Mullerian hormone type II receptor gene based on a chromosome-scale genome assembly of yellow perch, Perca flavescens

Yellow perch, Perca flavescens, is an ecologically and economically important species native to a large portion of the northern United States and southern Canada and is also a promising candidate species for aquaculture. However, no yellow perch reference genome has been available to facilitate improvements in both fisheries and aquaculture management practices. By combining Oxford Nanopore Technologies long-reads, 10X Genomics Illumina short linked reads and a chromosome contact map produced with Hi-C, we generated a high-continuity chromosome-scale yellow perch genome assembly of 877.4 Mb. It contains, in agreement with the known diploid chromosome yellow perch count, 24 chromosome-size scaffolds covering 98.8% of the complete assembly (N50 = 37.4 Mb, L50 = 11). We also provide a first characterization of the yellow perch sex determination locus that contains a male-specific duplicate of the anti-Mullerian hormone type II receptor gene (amhr2by) inserted at the proximal end of the Y chromosome (chromosome 9). Using this sex-specific information, we developed a simple PCR genotyping assay which accurately differentiates XY genetic males (amhr2by+ ) from XX genetic females (amhr2by- ). Our high-quality genome assembly is an important genomic resource for future studies on yellow perch ecology, toxicology, fisheries and aquaculture research. In addition, characterization of the amhr2by gene as a candidate sex-determining gene in yellow perch provides a new example of the recurrent implication of the transforming growth factor beta pathway in fish sex determination, and highlights gene duplication as an important genomic mechanism for the emergence of new master sex determination genes.

The First Highly Contiguous Genome Assembly of Pikeperch (Sander lucioperca), an Emerging Aquaculture Species in Europe

The pikeperch (Sander lucioperca) is a fresh and brackish water Percid fish natively inhabiting the northern hemisphere. This species is emerging as a promising candidate for intensive aquaculture production in Europe. Specific traits like cannibalism, growth rate and meat quality require genomics based understanding, for an optimal husbandry and domestication process. Still, the aquaculture community is lacking an annotated genome sequence to facilitate genome-wide studies on pikeperch. Here, we report the first highly contiguous draft genome assembly of Sander lucioperca. In total, 413 and 66 giga base pairs of DNA sequencing raw data were generated with the Illumina platform and PacBio Sequel System, respectively. The PacBio data were assembled into a final assembly size of ~900 Mb covering 89% of the 1,014 Mb estimated genome size. The draft genome consisted of 1966 contigs ordered into 1,313 scaffolds. The contig and scaffold N50 lengths are 3.0 Mb and 4.9 Mb, respectively. The identified repetitive structures accounted for 39% of the genome. We utilized homologies to other ray-finned fishes, and ab initio gene prediction methods to predict 21,249 protein-coding genes in the Sander lucioperca genome, of which 88% were functionally annotated by either sequence homology or protein domains and signatures search. The assembled genome spans 97.6% and 96.3% of Vertebrate and Actinopterygii single-copy orthologs, respectively. The outstanding mapping rate (99.9%) of genomic PE-reads on the assembly suggests an accurate and nearly complete genome reconstruction. This draft genome sequence is the first genomic resource for this promising aquaculture species. It will provide an impetus for genomic-based breeding studies targeting phenotypic and performance traits of captive pikeperch.

Evolution of the premaxillary fraenum and substratum in snubnose darters and allies (Percidae: Etheostoma)

Darters (Percidae: Etheostomatinae), a species-rich group of North American freshwater fishes, vary in the presence of a premaxillary fraenum, a strip of skin that connects the premaxillary bones to the snout, and it is hypothesized that this trait is a trophic adaptation to particular substrata. Ancestral state reconstructions and analyses of phylogenetic associations between presence of the premaxillary fraenum and preferred stream substratum were conducted in a clade of closely related darters (snubnose darters and allies) that vary in morphology and habitat preferences. The most recent common ancestor of this clade was inferred to possess a fraenum and to inhabit rocky substrata, consistent with previous hypotheses, but a significant correlation between fraenum presence and substratum type across the phylogeny was not found.

Of paleo-genes and Perch: what if an "alien" is actually a native?

Documenting whether a biotic taxon is native or alien to an ecosystem has theoretical value for ecological and evolutionary studies, and has practical value because it can potentially identify a taxon as a desirable component of an ecosystem or target it for removal. In some cases, however, such background information is inadequate or unavailable. Here we use paleo-DNA to re-evaluate the historical status of yellow perch in the 6 million acre Adirondack State Park of northern New York. Yellow perch DNA in a 2200-year sediment record reveals a long-term native status for these supposedly alien fish and challenges assumptions that they necessarily exclude native trout from upland lakes. Similar approaches could be applied to other species with uncertain historical distributions and could help to identify unrecognized pockets of biodiversity.

Comparative susceptibility among three stocks of yellow perch, Perca flavescens (Mitchill), to viral haemorrhagic septicaemia virus strain IVb from the Great Lakes

The Great Lakes strain of viral haemorrhagic septicaemia virus IVb (VHSV-IVb) is capable of infecting a wide number of naive species and has been associated with large fish kills in the Midwestern United States since its discovery in 2005. The yellow perch, Perca flavescens (Mitchill), a freshwater species commonly found throughout inland waters of the United States and prized for its high value in sport and commercial fisheries, is a species documented in several fish kills affiliated with VHS. In the present study, differences in survival after infection with VHSV IVb were observed among juvenile fish from three yellow perch broodstocks that were originally derived from distinct wild populations, suggesting innate differences in susceptibility due to genetic variance. While all three stocks were susceptible upon waterborne exposure to VHS virus infection, fish derived from the Midwest (Lake Winnebago, WI) showed significantly lower cumulative % survival compared with two perch stocks derived from the East Coast (Perquimans River, NC and Choptank River, MD) of the United States. However, despite differences in apparent susceptibility, clinical signs did not vary between stocks and included moderate-to-severe haemorrhages at the pelvic and pectoral fin bases and exophthalmia. After the 28-day challenge was complete, VHS virus was analysed in subsets of whole fish that had either survived or succumbed to the infection using both plaque assay and quantitative PCR methodologies. A direct correlation was identified between the two methods, suggesting the potential for both methods to be used to detect virus in a research setting.

Genetic and morphometric differences demonstrate fine-scale population substructure of the yellow perch Perca flavescens: need for redefined management units

Whole-body morphometrics and 15 nuclear DNA microsatellite loci were analysed for 158 Perca flavescens collected during the spawning season from four spawning locations in central Lake Erie, two along the northern shore and two along the southern shore, to evaluate fine-scale variation (spanning 17-94 km). Results showed significant morphological and genetic differences among P. flavescens from the four locations. The magnitudes of differences were unrelated to geographic distance, demonstrating spatially heterogeneous levels of genetic divergence. These results linked morphometric and genetic variation, showing a discontinuity of scale between currently defined management units and population structure of P. flavescens in Lake Erie, and support that P. flavescens might exist as one or more metapopulations. Findings demonstrate the value of using complementary techniques for evaluating population structure.

Characterization and expression of a myosin heavy-chain isoform in juvenile walleye Sander vitreus

In this study, myosin, the major component of myofibrillar protein in the skeletal muscle, was characterized and its expression was monitored during growth in juvenile walleye Sander vitreus. First, the coding region of myosin heavy chain (MyHC) from the fast skeletal muscle of walleye was amplified by long-distance PCR using a full-length cDNA. Phylogenetic analysis was used to determine the evolutionary relationship of this S. vitreus myosin sequence to other vertebrate myosin sequences. Next, it was established that the myosin isoform was most prevalent in the white muscle, compared with the red and cardiac muscle. Myosin expression was monitored over a series of experiments designed to influence growth. Specifically, change in MyHC mRNA was monitored after acute changes in feeding. Fish exposed to a one-week fasting period showed significant decreases in MyHC mRNA levels by the end of the fast. The effect of feeding was also examined more closely over a 24 h period after feeding, but results showed no significant change in myosin expression levels through this time period. Finally, fish with higher growth rates had higher MyHC mRNA and protein expression levels. This study indicates that MyHC mRNA expression is sensitive to the factors that may influence growth in juvenile S. vitreus.

Shallow genetic and morphological divergence among seaperches in the South Pacific (family Scorpaenidae; genus Helicolenus)

The phylogenetic relationships among populations of seaperch, Helicolenus spp., in the south-west Pacific were examined with mtDNA markers. Parts of the cytochrome b gene [459 base pair (bp)] and the control region (448 bp) were sequenced in 58 specimens from the south-west Pacific and four specimens of Helicolenus lengerichi from Chile. Only one clade was recognized in New Zealand coastal waters, despite a wide range of colour morphs. This clade also occurred in the mid Tasman Sea on the Norfolk Ridge and around Tasmania and Victoria. A second sympatric clade was identified around Tasmania and Victoria and to the west of New Zealand. A third allopatric clade was identified to the north of New Zealand and in deep water on the Chatham Rise and a fourth clade on the Foundation Seamounts and the Louisville Ridge. Helicolenus lengerichi from Chile formed a fifth clade. Assuming a molecular clock, the clades were estimated to have diverged c. 0.7-2.6 million years ago. Only two clades, around Tasmania and Victoria, were separated using morphology, colour (in live) and dorsal-fin soft ray counts and were confirmed as Helicolenus percoides and Helicolenus barathri. Two characters, orbit diameter and colour variation, previously used to identify two species in New Zealand waters were unreliable characters for species discrimination. Principle component analyses of 11 morphological measures from 67 individuals did not delineate the clades. A canonical discriminant analysis was able to separate four of the five clades, but mean discriminate probabilities were low (77.6%), except for the five Chilean specimens of H. lengerichi (100%).

Systematics of the subgenus Oligocephalus (Teleostei: Percidae: Etheostoma) with complete subgeneric sampling of the genus Etheostoma

The genus Etheostoma is the most diverse clade of freshwater fishes in North America. While studies have been performed with complete sampling of a single subgenus, none have included representatives of all remaining subgenera. The subgenus Oligocephalus is the largest, consisting of 25-27 species in four species groups, and its monophyly has never been clearly demonstrated. The monophyly of this subgenus and its constituent groups was tested using parsimony and Bayesian analyses of ND2 (mtDNA) and the first intron of S7 (nDNA) with complete species sampling from Oligocephalus and complete subgeneric sampling from Etheostoma. Although the subgenus Oligocephalus was not recovered as a monophyletic group in any analyses, monophyletic E. whipplei, Southwestern Darter, and E. spectabile (in part) species groups were recovered in all analyses. All analyses agree that E. okaloosae and both subspecies of E. hopkinsi are not closely related to other members of the subgenus Oligocephalus. E. exile is, however, presenting the strongest evidence yet that recognition of the subgenus Boleichthys is unwarranted.

AFLPs resolve cytonuclear discordance and increase resolution among barcheek darters (Percidae: Etheostoma: Catonotus)

The use of mitochondrial DNA (mtDNA) sequences in phylogenetic analysis has been the subject of increasing scrutiny. A recent phylogenetic study of barcheek darters (Percidae: Etheostoma: Catonotus) revealed cytonuclear discordance, discordance among mtDNA loci, and discordance between mtDNA and morphometric hypotheses. In particular, mtDNA analyses hypothesized a paraphyletic barcheek darter clade, and a combined mtDNA and nuclear sequence topology was not well resolved. Here, we used amplified fragment length polymorphisms to test the monophyly of barcheek darters and to resolve relationships within the group. By including multiple populations of each species, we were able to generate a highly resolved tree that supports both the monophyly of barcheek darters as well as recently elevated species within the group. Analysis of three mtDNA loci indicates that saturation of highly variable sites best explains the discordant topologies among mtDNA partitions.

A molecular phylogeny of the Percidae (Teleostei, Perciformes) based on mitochondrial DNA sequence

The family Percidae is among the most speciose families of northern hemisphere fishes with > 178 178 North American species and 14 Eurasian species. Previous phylogenetic studies have been hampered by a lack of informative characters, inadequate taxonomic sampling, and conflicting data. We estimated phylogenetic relationships among 54 percid species (9 of 10 genera and all but one subgenus of darters) and four outgroup taxa using mitochondrial DNA data from the 12S rRNA and cytochrome b genes. Four primary evolutionary lineages were consistently recovered: Etheostomatinae (Ammocrypta, Crystallaria, Etheostoma, and Percina), Perca, Luciopercinae (Romanichthys, Sander, and Zingel), and Gymnocephalus. Except Etheostoma and Zingel, all polytypic genera were monophyletic. The Etheostoma subgenus Nothonotus failed to resolve with other members of the genus resulting in a paraphyletic Etheostoma. The subfamily Percinae (Gymnocephalus and Perca) was not recovered in phylogenetic analyses with Gymnocephalus sister to Luciopercinae. Etheostomatinae and Romanichthyini were never resolved as sister groups supporting convergent evolution as the cause of small, benthic, stream-inhabiting percids in North American and Eurasian waters.

Molecular phylogeny of the snubnose darters, subgenus Ulocentra (genus Etheostoma, family Percidae)

Snubnose darters comprise one of the largest subgenera of the percid genus Etheostoma. Many species are described based on differences in male breeding coloration. Few morphological synapomorphies have been proposed for the subgenus and their relatives, making it difficult to delineate monophyletic clades. The phylogenetic relationships of the 20 snubnose darter species of the subgenus Ulocentra and 11 members of its proposed sister subgenus Etheostoma were investigated with partial mitochondrial DNA sequences including 1033 bp encompassing the entire mitochondrial control region, the tRNA-Phe gene, and part of the 12S rRNA gene. Two hypotheses on the relationship and monophyly of the two subgenera were evaluated. Both maximum-parsimony and neighbor-joining analyses supported monophyly of the subgenus Ulocentra and resolved some species-level relationships. The banded darter, E. zonale, and its sister taxon, E. lynceum, were not closely related to the snubnose darters and appear to be diverged from the other members of the subgenus Etheostoma, fitting their former distinction as the recognized subgenus Nanostoma. The sister group to Ulocentra appears to be a restricted species assemblage within the subgenus Etheostoma containing E. blennioides, E. rupestre, E. blennius, and the E. thalassinum species group. The placement of the harlequin darter, E. histrio, is problematic, and it may represent a basal member of Ulocentra or of the restricted subgenus Etheostoma. Despite recent estimates of divergence times between nominal Ulocentra taxa, each species exhibits its own unique set of mtDNA haplotypes, providing no direct evidence for current genetic exchange between species. The nominal taxa of snubnose darters thus appear to be evolving independently from each other and therefore constitute valid species under the Phylogenetic Species Concept.

Visual pigments and optical habitats of surfperch (Embiotocidae) in the California kelp forest

We studied the optical microhabitat use and visual pigment variation among a group of closely related teleosts (surfperch: Embiotocidae) living along the nearshore central California coast. We employed a diver-operated spectroradiometer to record the optical microhabitat use of eight surfperch species in Monterey Bay. and microspectrophotometry to measure visual pigment absorbance for nine surfperch species. Species were dichromatic with mixtures of A1- and A2-based visual pigments exhibiting extensive maximum absorbance (lambda(max)) variation across species: 455-482 nm for SWS cones and 527-546 nm for LWS cones. Interspecific variation in sidewelling irradiance measurements (mean lambdaFmaxs) significantly accounted for 63% of the variation in surfperch LWS visual pigments and 83% of the interspecific variation in SWS visual pigments using a phylogenetically-corrected regression technique. Optimality models for maximizing relative photon capture of background radiance demonstrate that the LWS cone lambda(max) values are tuned for maximizing photon capture of the species-specific horizontal visual field, while the SWS cone lambda(max), are well offset from the dominant background radiance. This study is one of the first to demonstrate species-specific differences in habitat usage at microhabitat scales accounting for differences in photoreceptor peak absorbance among closely related, sympatric species.

Intraspecific phylogeography of Percina evides (Percidae: Etheostomatinae): an additional test of the Central Highlands pre-Pleistocene vicariance hypothesis

North America exhibits the most diverse freshwater fish fauna among temperate regions of the world. Species diversity is concentrated in the Central Highlands, drained by the Mississippi, Gulf Slope and Atlantic Slope river systems. Previous investigations of Central Highlands biogeography have led to conflicting hypotheses involving dispersal and vicariance to explain the diversity and distribution of the freshwater fish fauna. In this investigation predictions of the Central Highlands pre-Pleistocene vicariance hypothesis are tested with a phylogeographic analysis of the percid species Percina evides, which is widely distributed in several disjunct areas of the Central Highlands. Phylogenetic analysis of complete gene sequences of mitochondrially encoded cytochrome b recover three phylogroups, with very low levels of sequence polymorphism within groups. The two western phylogroups are monophyletic with respect to the eastern phylogroup. The recovery of two monophyletic lineages with an eastern and western distribution in the disjunct highland areas is a pattern expected from vicariance, but is not predicted by the Central Highlands pre-Pleistocene vicariance hypothesis. The recovery of very limited mitochondrial DNA polymorphism and lack of phylogeographic structuring across the entire range of the eastern clade, very shallow polymorphism between the disjunct Missouri River and upper Mississippi River populations, and lack of sequence polymorphism in the upper Mississippi River populations, support a hypothesis of dispersal during or following the Pleistocene. The present distribution of P. evides is best explained by both vicariant and dispersal events.

Identification of Nile perch (Lates niloticus), grouper (Epinephelus guaza), and wreck fish (Polyprion americanus) fillets by PCR amplification of the 5S rDNA gene

Nile perch (Lates niloticus), grouper (Epinephelus guaza), and wreck fish (Polyprion americanus) were differentiated by polymerase chain reaction (PCR) amplification of the nuclear 5S rDNA gene. The design of 3 species-specific primers complementary to the nontranscribed intergenic spacer region from the 5S rDNA molecule allowed amplification of clearly distinguishable gene fragments in each fish species. This approach is rapid and reliable and offers the potential to detect fraudulent or unintentional mislabeling of these species in routine seafood authentication analysis.

Divergence with gene flow in the rock-dwelling cichlids of Lake Malawi

Within the past two million years, more than 450 species of haplochromine cichlids have diverged from a single common ancestor in Lake Malawi. Several factors have been implicated in the diversification of this monophyletic clade, including changes in lake level and low levels of gene flow across limited geographic scales. The objectives of this study were to determine the effect of recent lake-level fluctuations on patterns of allelic diversity in the genus Metriaclima, to describe the patterns of population structure within this genus, and to identify barriers to migration. This was accomplished through an analysis of allele frequencies at four microsatellite loci. Twelve populations spanning four species within Metriaclima were surveyed. The effect of lake-level fluctuations can be seen in the reduced genetic diversity of the most recently colonized sites; however, genetic diversity is not depressed at the species level. Low levels of population structure exist among populations, yet some gene flow persists across long stretches of inhospitable habitat. No general barrier to migration was identified. The results of this study are interpreted with respect to several speciation models. Divergence via population bottlenecks is unlikely due to the large allelic diversity observed within each species. Genetic drift and microallopatric divergence are also rejected because some gene flow does occur between adjacent populations. However, the reduced levels of gene flow between populations does suggest that minor changes in the selective environment could cause the divergence of populations.

Phylogenetic utility of the tyrosine kinase gene X-src for assessing relationships among representative cichlid fishes

The nuclear gene X-src is a member of the tyrosine-kinase class of proto-oncogenes whose normal product is localized within the cytoplasm of the cell. The X-src gene has been used in only a few phylogenetic studies, each focusing on systematics of killifishes (Cyprinodontiformes). The present study is an attempt to examine the phylogenetic utility of X-src for uncovering relationships of representative cichlid fishes, especially the cichlids of Middle America. The family Cichlidae is a species-rich group of tropical freshwater fish made up of more than 1000 species which show a Gondwanan pattern of distribution. Cichlid fish have been the focus of numerous studies ranging from behavioral to biogeographical to systematic in nature. Particular emphasis has focused on the cichlids of the African Great Lakes and the explosive adaptive radiation of this group. However, Neotropical cichlids have received considerably less attention than their African counterparts. Our findings regarding the utility of X-src concur with those of previous phylogenetic analyses showing the exons of X-src to be highly conserved and useful mostly for revealing deep relationships among taxa. Like previous X-src studies, we also found the intron sequences of the gene to be variable in length and difficult to align across distantly related taxa but they provided useful information for resolving relationships among more closely related taxa. The X-src phylogeny supports the monophyly of Neotropical cichlids and cichlasomines groups A (=heroines) + B (=cichlasomines). A highly resolved tree is obtained within the heroines but little support is evident for most nodes based on the low number of unambiguous substitutions. The X-src gene is likely to be quite useful for resolving deep phylogenetic relationships such as those among major groups of actinopterygian fishes.

Molecular phylogeny and speciation of the surfperches (Embiotocidae, Perciformes)

Labroid fishes include a variety of families, such as wrasses (Labridae), odacids (Odacidae), damselfishes (Pomacentridae), parrotfishes (Scaridae), cichlids (Cichlidae), and surfperches (Embiotocidae). With only 23 species, the small embiotocid family exhibits a remarkably low species diversity compared to the large species diversity of the Cichlidae. Using mitochondrial DNA sequences of all 14 extant embiotocid genera, we established a molecular phylogeny of the family and compared it with a previously proposed morphological phylogeny. Genetic differentiation among embiotocids was compared to that among cichlids. Although species numbers are extremely different between these two families, the degrees of genetic differentiation within each family was found to be very similar.

Replicated evolution of trophic specializations in an endemic cichlid fish lineage from Lake Tanganyika

The current phylogenetic hypothesis for the endemic Lake Tanganyika cichlid fishes of the tribe Eretmodini is based solely on morphology and suggests that more complex trophic morphologies derived only once from a less specialized ancestral condition. A molecular phylogeny of eretmodine cichlids based on partial mitochondrial DNA cytochrome b and control-region sequences was used to reconstruct the evolutionary sequence of trophic adaptations and to test alternative models of morphological divergence. The six mitochondrial lineages found disagree with the current taxonomy and the morphology-based phylogeny. Mitochondrial lineages with similar trophic morphologies are not grouped monophyletically but are typically more closely related to lineages with different trophic phenotypes currently assigned to other genera. Our results indicate multiple independent origins of similar trophic specializations in these cichlids. A pattern of repeated divergent morphological evolution becomes apparent when the phylogeography of the mitochondrial haplotypes is analyzed in the context of the geological and paleoclimatological history of Lake Tanganyika. In more than one instance within Lake Tanganyika, similar morphological divergence of dentitional traits occurred in sympatric species pairs. Possibly, resource-based divergent selective regimes led to resource partitioning and brought about similar trophic morphologies independently and repeatedly.

Genetic evidence for different migration routes of freshwater fish into Norway revealed by analysis of current perch (Perca fluviatilis) populations in Scandinavia

To elucidate the colonization of freshwater fish into Norway following the last deglaciation of Europe 10,000 years ago, we have performed a survey using mitochondrial DNA variation (20 populations) and multilocus DNA fingerprinting (14 populations) of the widely distributed perch (Perca fluviatilis) from the Scandinavian peninsula and the Baltic Sea. Sequence analysis of a 378 bp segment of the perch mitochondrial control region (D-loop) revealed 12 different haplotypes. A nested clade analysis was performed with the aim of separating population structure and population history. This analysis revealed strong geographical structuring of the Scandinavian perch populations. In addition, the level of genetic diversity was shown to differ considerably among the various populations as measured by the bandsharing values (S-values) obtained from multilocus DNA fingerprinting, with intrapopulation S-values ranging from 0.19 in Sweden to 0.84 in the central part of Norway. Analysis of the intrapopulation S-values, with S-value as a function of lake surface area and region, showed that these differences were significant. The mitochondrial and DNA fingerprinting data both suggest that the perch colonized Norway via two routes: one from the south following the retreating glacier, and the other through Swedish river systems from the Baltic Sea area. Perch utilizing the southern route colonized the area surrounding Oslofjord and the lakes which shortly after deglaciation were close to the sea. Fish migrating from the Baltic Sea seem to have reached no further than the east side of Oslofjord, where they presumably mixed with perch which had entered via the southern route. It seems likely that the migration events leading to the current distribution of perch also apply to other species of freshwater fish showing a similar distribution pattern.

Linkage relationships and haplotype polymorphism among cichlid Mhc class II B loci

The species flocks of cichlid fishes in the Great East African Lakes are paradigms of adaptive radiation and hence, of great interest to evolutionary biologists. Phylogenetic studies of these fishes have, however, been hampered by the lack of suitable polymorphic markers. The genes of the major histocompatibility complex hold the promise to provide, through their extensive polymorphism, a large number of such markers, but their use has been hampered by the complexity of the genetic system and the lack of definition of the individual loci. In this study we take the first substantial step to alleviate this problem. Using a combination of methods, including the typing of single sperm cells, gyno- or androgenetic individuals, and haploid embryos, as well as sequencing of class II B restriction fragments isolated from gels for Southern blots, we identify the previously characterized homology groups as distinct loci. At least 17 polymorphic class II B loci, all of which are presumably transcribed, have been found among the different species studied. Most of these loci are shared across the various cichlid species and genera. The number of loci per haplotype varies from individual to individual, ranging from 1 to 13. A total of 21 distinct haplotypes differing in the number of loci they carry has thus far been identified. All the polymorphic loci are part of the same cluster in which, however, distances between at least some of the loci (as indicated by recombination frequencies) are relatively large. Both the individual loci and the haplotypes can now be used to study phylogenetic relationships among the members of the species flocks and the mode in which speciation occurs during adaptive radiation.

A novel family of short interspersed repetitive elements (SINEs) from cichlids: the patterns of insertion of SINEs at orthologous loci support the proposed monophyly of four major groups of cichlid fishes in Lake Tanganyika

Short interspersed repetitive elements (SINEs) have been shown to be excellent markers of molecular phylogeny, since the integration of a SINE at a particular position in a genome can be considered an unambiguous derived homologous character. In the present study, we isolated a new family of SINEs from cichlids in Lake Tanganyika, whose speciation and diversification have been regarded as prime examples of explosive adaptive radiation. Members of this new SINE family, which we named the AFC family, are about 320 bp in length, and each has a tRNA-related region in its 5' region, as do most of the members of SINE families reported to date. A dot blot hybridization experiment showed that this family is distributed extensively in the genomes of cichlids in Africa, with estimated copy numbers of 2 x 10(3)-2 x 10(4) per haploid genome. Our investigations of the patterns of insertion of members of this family at six orthologous loci demonstrated clearly that four previously identified tribes, namely, the Lamprologini, Ectodini, Tropheini, and Perissodini, each form a monophyletic group. These results provide a basis for the elucidation of the phylogenetic framework of the cichlid fishes in Lake Tanganyika.

Systematics and evolution of lower Central American cichlids inferred from analysis of cytochrome b gene sequences

Central American cichlids allied to the genus "Cichlasoma" are thought to be of South American ancestry. The group has apparently undergone extensive morphological, ecological, and behavioral differentiation in Central America following colonization. Uncertainties regarding the systematics of the group and the timing of colonization complicate interpretation of the biological history of cichlids in Central America. We determined complete cytochrome b gene sequences for 54 individual cichlids representing 21 species to test hypotheses regarding the time of origin and pattern of diversification of lower Central American cichlids. The data also bear on issues relating to the systematics and taxonomy of heroine cichlids. Our results suggest that cichlids have been in Central America since the middle to late Miocene. Moreover, the data provide evidence of a rapid radiation early in the history of the group. Similar ecomorphological types have evolved multiple times. Inferences of convergent morphological evolution may, in part, explain a lack of concordance between the mitochondrial gene tree and previous inferences of phylogenetic relationships based on observable characteristics. Phylogenetic inferences based on the molecular data provide support for the recognition of "sections" [erected by Regan (1905) and others] as distinct genera and suggest that thorough revision of Central American cichlids is necessary before the extent of biological diversity within the group can be fully appreciated.

Molecular systematics of Middle American cichlid fishes and the evolution of trophic-types in 'Cichlasoma (Amphilophus)' and 'C. (Thorichthys)'

The majority of Middle American cichlids are placed in the informal assemblage 'Cichlasoma.' The group is divided into eight sections which appear to be based primarily on trophic morphology. Although several members of 'Cichlasoma' have been used in ecomorphological, behavioral, and biogeographic studies, no phylogenetic hypotheses for the group exist. In an attempt to develop a better understanding of the phylogenetic relationships of 'cichlasomine' cichlids, we examined the evolution of the trophic specialization, substratum-sifting, in two sections, 'Cichlasoma (Thorichthys)' and 'C. (Amphilophus),' to determine whether the trait reflects common ancestry. We sequenced the complete mitochondrial cytochrome b gene for 19 cichlids representing six sections of 'Cichlasoma,' and representatives of other Neotropical Cichlidae. Additional cichlid, and noncichlid outgroup sequences were included for a total of 22 taxa. The molecular phylogeny supports the recognition of the section 'C. (Thoricthys)' as a natural group, and we place those cichlids in the genus Thorichthys. The phylogeny also depicts 'C. (Amphilophus)' as paraphyletic, with substratum-sifters and generalized predators forming separate nonsister clades. We recommend that the substratum-sifting clade of the section 'C. (Amphilophus)' be placed in the resurrected genus Astatheros. The generalized predator clade of 'C. (Amphilophus)' contains only two species, 'C. (A.) citrinellum' and 'C. (A.) labiatum,' which we place in the genus Amphilophus. The phylogenetic hypotheses generated indicate that the substratum-sifting genera Thorichthys and Amphilophus do not share a common ancestor. Reconstruction of the evolution of substratum-sifting is equivocal, requiring either the independent evolution of the trait on two separate occasions or its presence in a more inclusive clade and subsequent loss in nonsubstratum sifting species.

Widespread geographical distribution of mitochondrial haplotypes in rock-dwelling cichlid fishes from Lake Tanganyika

The spectacularly diverse cichlid fish species flocks of the East African Rift Lakes have elicited much debate on the potential evolutionary mechanisms responsible for the origin of these adaptive radiations. An historical perspective on population structure may offer insights into the processes driving population differentiation and possibly speciation. Here, we examine mitochondrial DNA (mtDNA) sequence variation in two endemic species of rock-dwelling cichlids, Simochromis babaulti and S. diagramma, from Lake Tanganyika. Phylogeographic analyses were used to infer what factors might have been important in the genetic structuring of Simochromis populations. Patterns of mtDNA differentiation in Simochromis were compared to those of other rock-dwelling cichlids to distinguish between competing hypotheses concerning the processes underlying their evolution. In striking contrast to previous findings, populations of Simochromis, even those separated by up to 300 km, were found to share mitochondrial DNA haplotypes. There is no correspondence between mtDNA genealogies and the geographical distribution of populations. Only S. babaulti, but not S. diagramma was found to have a significant association between genetic and geographic distance. These phylogeographic patterns suggest that the evolutionary effects of abiotic and biotic factors shaping population genetic structure may differ substantially even among closely related species of rock-dwelling cichlids. Physical events and barriers to gene flow that are believed to have had a major impact on the geographical distribution and intralacustrine speciation of Tropheus do not seem to have equally strongly affected its close relative Simochromis. These findings emphasize that no single mechanism can be responsible for the formation of population structure, speciation, and the adaptive radiation of all cichlid fishes.

Evolution of NADH dehydrogenase subunit 2 in east African cichlid fish

The complete sequence (1047 bp) of the mitochondrially encoded ND2 gene was obtained from 31 species of cichlid fishes to investigate the evolutionary history of the species flocks of the East African lakes. The observed pattern of nucleotide substitution in this sequence is typical of mitochondrial genes, showing a high transition bias and rapid mutational saturation, especially at codon positions where base frequencies are unequal. The base composition of the third position of codons is heterogeneous among species, suggesting frequent shifts in the pattern of substitution. Phylogenetic analysis of the sequences shows that the mtDNA variation in Lake Malawi cichlids is nested monophyletically within the range of variation shown by Tanganyikan cichlids. The closest Tanganyikan relatives of the Malawi flock are members of the tribe Tropheini. Classifications based on morphology are generally supported by the mtDNA data, with some significant exceptions in the Tropheini and Lamprologini. Because of an apparently rapid radiation of the Tanganyikan lineages, it is difficult to assess the basal topology of the Tanganyikan radiation at this time. Divergences among tribes are consistent with an intralacustrine radiation within the past 10 million years.

Biochemical attempt to characterize thirteen cichlid species by their muscular parvalbumins

This paper shows the usefulness of polyacrylamide gel electrophoresis (PAGE) separation of a few well-characterized muscle proteins, the parvalbumins, in the systematic study of 13 cichlid species. The separation of the isoforms of these abundant, quite species-specific fish parvalbumins is fast, easy, and requires but small quantities of muscle material. Used alone, this technique suggests hypotheses for species classification. In conjunction with morphological analysis, it makes it possible to confirm or invalidate doubts about the determination.

Conservation of a satellite DNA sequence (SATB) in the tilapiine and haplochromine genome (Pisces: Cichlidae)

We have cloned and sequenced a 1900-bp EcoRI fragment (SATB) from the tilapiine fish Oreochromis niloticus. The SATB sequence is highly reiterated in the tilapiine genome and organized in long tandem arrays. A 760-bp HindIII fragment, an internal component of SATB, has also been cloned and sequenced from the related tilapiine species Oreochromis hornorum. Hybridization of the radiolabelled 760-bp HindIII repeat detected the presence of the SATB repeat in the genomes of several tilapiine species as well as the haplochromine species Haplochromis (Protomelas) similis. The 760-bp HindIII fragment did not hybridize to genomic DNA of Etroplus maculatus (an Asian cichlid) or to that of Cichlasoma meeki (a South American cichlid). The SATB repeat sequence is 56% AT and constitutes 0.2-5% of the tilapiine genome depending on the species examined. Four imperfect 21-bp direct repeat sequences are present within the cloned 1900-bp EcoRI repeat. Alignment of the four direct repeats from the O. niloticus cloned 1900-bp DNA and the two homologous direct repeats from the O. hornorum 760-bp HindIII repeat revealed a core motif of 11 bp that exhibits 100% sequence identity between all of the direct repeats. The conservation of this motif in the SATB repeat suggests that this sequence may be under selective constraint.