Tetsumi Takahashi

Systematics of Tanganyikan cichlid fishes (Teleostei: Perciformes)

The relationships among 53 genera of Tanganyikan cichlid fishes were analyzed based on internal and external morphological features. Comparison of the morphological cladistic tree with a previously proposed classification showed 5 of 12 tribes to be nonmonophyletic. Sixteen tribes were recognized, the changes in classification being that Trematocarini was treated as a junior synonym of Bathybatini; 5 new tribes were established for each of the following genera, Benthochromis, Boulengerochromis, “Ctenochromis” benthicola, Cyphotilapia, and Greenwoodochromis; “Ctenochromis” horei was transferred from Haplochromini to Tropheini; and “Gnathochromis” pfefferi was transferred from Limnochromini to Tropheini. The revised classification was supported by previously proposed molecular trees.

Application of RAD-based phylogenetics to complex relationships among variously related taxa in a species flock

Restriction site-associated DNA (RAD) sequences from entire genomes can be used to resolve complex phylogenetic problems. However, the processed data matrix varies depending on the strategies used to determine orthologous loci and to filter loci according to the number of taxa with sequence data for the loci, and often contains plenty of missing data. To explore the utility of RAD sequences for elucidating the phylogenetics of variously related species, we conducted RAD sequencing for the Ohomopterus ground beetles and attempted maximum-likelihood phylogenetic analyses using 42 data matrices ranging from 1.6×10(4) to 8.1×10(6) base pairs, with 11-72% missing data. We demonstrate that robust phylogenetic trees, in terms of bootstrap values, do not necessarily result from larger data matrices, as previously suggested. Robust trees for distantly related and closely related taxa resulted from different data matrices, and topologically different robust trees for distantly related taxa resulted from various data matrices. For closely related taxa, moderately large data matrices strongly supported a topology that is incompatible with morphological evidence, possibly due to the effect of introgressive hybridization. Practically, exploring variously prepared data matrices is an effective way to propose important alternative phylogenetic hypotheses for this study group.

The Adaptive Radiation of Cichlid Fish in Lake Tanganyika: A Morphological Perspective

Lake Tanganyika is the oldest of the Great Ancient Lakes in the East Africa. This lake harbours about 250 species of cichlid fish, which are highly diverse in terms of morphology, behaviour, and ecology. Lake Tanganyikas cichlid diversity has evolved through explosive speciation and is treated as a textbook example of adaptive radiation, the rapid differentiation of a single ancestor into an array of species that differ in traits used to exploit their environments and resources. To elucidate the processes and mechanisms underlying the rapid speciation and adaptive radiation of Lake Tanganyikas cichlid species assemblage it is important to integrate evidence from several lines of research. Great efforts have been, are, and certainly will be taken to solve the mystery of how so many cichlid species evolved in so little time. In the present review, we summarize morphological studies that relate to the adaptive radiation of Lake Tanganyikas cichlids and highlight their importance for understanding the process of adaptive radiation.

Food habits of great cormorant Phalacrocorax carbo hanedae at Lake Biwa, Japan, with special reference to ayu Plecoglossus altivelis altivelis

The recent increase in numbers of individuals of a piscivorous bird, the great cormorant Phalacrocorax carbo hanedae, around Lake Biwa has affected the commercial catch of ayu Plecoglossus altivelis altivelis. The food habits of the bird were studied based on 66 stomachs in 1998 and 2001–2002, and a seasonal variation in food contents was observed. The proportion of ayu in stomachs increased after April, and became most dominant during July and August (0.62 in proportion of weight, 0.85 in frequency of occurrence). In contrast, ayu was not found in the stomachs after late October. The increase of ayu in individuals and density in the surface layer of the pelagic zone of the lake during spring was considered as a trigger for the change of the food habits of the birds. The feeding impact of great cormorant on ayu in Lake Biwa was estimated to be approximately 46 t during April to June, and 310 t in July and August. During the main period for the commercial ayu catch (November to the following June), the estimated mass consumed by the bird is much smaller in comparison with the commercial catch.

Genetic basis of male colour dimorphism in a Lake Tanganyika cichlid fish

Phenotypic polymorphisms can be applied to study the micro‐evolutionary forces that maintain genetic variation and can mediate speciation, but it can be difficult to determine the genetic basis of polymorphisms. Recently, restriction‐site‐associated DNA (RAD) sequencing has become popular, which can easily produce multiple single nucleotide polymorphisms from whole genomes. Here, we combined RAD sequencing, allele‐specific PCR and Sanger sequencing to determine the genetic basis underlying male colour dimorphism of a Lake Tanganyika cichlid fish, Cyprichromis leptosoma. Our analyses using both a cross‐family (two parents and 12 F2 males) and 64 wild individuals do not contradict a hypothesis that two alleles of one‐locus control male colour dimorphism. Also, the locus may be located on a genome region that experiences reduced levels of recombination. Although more analyses will be needed to conclude these findings, this study is the first to suggest the genetic basis of a colour polymorphism using RAD sequencing.

Evidence of disassortative mating in a Tanganyikan cichlid fish and its role in the maintenance of intrapopulation dimorphism

Morphological dimorphism in the mouth-opening direction (‘lefty’ versus ‘righty’) has been documented in several fish species. It has been suggested that this deflection is heritable in a Mendelian one-locus, two-allele fashion. Several population models have demonstrated that lateral dimorphism is maintained by negative frequency-dependent selection, resulting from interactions between predator and prey species. However, other mechanisms for the maintenance of lateral dimorphism have not yet been tested. Here, we found that the scale-eating cichlid fish Perissodus microlepis exhibited disassortative mating, in which reproductive pairings between lefties and righties occurred at higher than expected frequency (p<0.001). A previous study reported that a lefty–righty pairing produces a 1 : 1 ratio of lefty : righty young, suggesting that disassortative mating contributes to the maintenance of lateral dimorphism. A combination of disassortative mating and negative frequency-dependent selection may stabilize lateral dimorphism more than would a single mechanism.

Evidence for divergent natural selection of a Lake Tanganyika cichlid inferred from repeated radiations in body size

Divergent natural selection is thought to play a vital role in speciation, but clear, measurable examples from nature are still few. Among the many possible sources of divergent natural selection, predation pressure may be important because predators are ubiquitous in food webs. Here, we show evidence for divergent natural selection in a Lake Tanganyika cichlid, Telmatochromis temporalis, which uses burrows under stones or empty snail shells as shelters. This species contains normal and dwarf morphs at several localities. The normal morph inhabits rocky shorelines, whereas the dwarf morph invariably inhabits shell beds, where empty snail shells densely cover the lake bottom. Genetic evidence suggested that the dwarf morph evolved independently from the normal morph at two areas, and morphological analysis and evaluation of habitat structure revealed that the body sizes of morphs closely matched the available shelter sizes in their habitats. These findings suggest that the two morphs repeatedly evolved through divergent natural selection associated with the strategy for sheltering from predators.

Competition-driven speciation in cichlid fish.

Theoretically, competition can initiate divergence in habitat use between individuals of a species, leading to restricted gene flow and eventual speciation. Evidence that sister species differ in habitat use is commonplace and consistent with this mechanism, but empirical experimental support is surprisingly scarce. Here we provide evidence that competition has taken a key role in the evolution of genetically distinct ecomorphs of the Lake Tanganyika cichlid fish Telmatochromis temporalis. Experiments show that differences in substrate use between a large-bodied rock-living ecomorph and a neighbouring small-bodied shell-living ecomorph are mediated by size-dependent competition that drives assortative mate-pair formation. Specifically, adults of the larger ecomorph outcompete adults of the smaller ecomorph on favoured rock substrate, compelling the smaller adults to use shell habitat. These results support a role for competition in maintaining reproductive isolation, and highlight the need to identify ecological processes that impose selection to improve our understanding of speciation and adaptive radiation.

A robust phylogeny among major lineages of the East African cichlids.

The huge monophyletic group of the East African cichlid radiations (EAR) consists of thousands of species belonging to 12-14 tribes; the number of tribes differs among studies. Many studies have inferred phylogenies of EAR tribes using various genetic markers. However, these phylogenies partly contradict one another and can have weak statistic support. In this study, we conducted maximum-likelihood (ML) phylogenetic analyses using restriction site-associated DNA (RAD) sequences and propose a new robust phylogenetic hypothesis among Lake Tanganyika cichlid fishes, which cover most EAR tribes. Data matrices can vary in size and contents depending on the strategies used to process RAD sequences. Therefore, we prepared 23 data matrices with various processing strategies. The ML phylogenies inferred from 15 large matrices (2.0×10(6) to 1.1×10(7) base pairs) resolved every tribe as a monophyletic group with 100% bootstrap support and shared the same topology regarding relationships among the tribes. Most nodes among the tribes were supported by 100% bootstrap values, and the bootstrap support for the other node varied among the 15 ML trees from 70% to 100%. These robust ML trees differ partly in topology from those in earlier studies, and these phylogenetic relationships have important implications for the tribal classification of EAR.

A RAD-based phylogenetics for Orestias fishes from Lake Titicaca.

The fish genus Orestias is endemic to the Andes highlands, and Lake Titicaca is the centre of the species diversity of the genus. Previous phylogenetic studies based on a single locus of mitochondrial and nuclear DNA strongly support the monophyly of a group composed of many of species endemic to the Lake Titicaca basin (the Lake Titicaca radiation), but the relationships among the species in the radiation remain unclear. Recently, restriction site-associated DNA (RAD) sequencing, which can produce a vast number of short sequences from various loci of nuclear DNA, has emerged as a useful way to resolve complex phylogenetic problems. To propose a new phylogenetic hypothesis of Orestias fishes of the Lake Titicaca radiation, we conducted a cluster analysis based on morphological similarities among fish samples and a molecular phylogenetic analysis based on RAD sequencing. From a morphological cluster analysis, we recognised four species groups in the radiation, and three of the four groups were resolved as monophyletic groups in maximum-likelihood trees based on RAD sequencing data. The other morphology-based group was not resolved as a monophyletic group in molecular phylogenies, and some members of the group were diverged from its sister group close to the root of the Lake Titicaca radiation. The evolution of these fishes is discussed from the phylogenetic relationships.