Extensive homoplasy, nonstepwise mutations, and shared ancestral polymorphism at a complex microsatellite locus in Lake Malawi cichlids

Recent studies have suggested that size homoplasy is a prevalent feature of microsatellites and is expected to increase with time of divergence among populations and taxa. In this study, we performed sequence analysis of alleles from a complex microsatellite locus (Pzeb4, initially isolated from Pseudotropheus (Maylandia) zebra) from 1 midwater-feeding and 10 rock-dwelling cichlid fish species from Lake Malawi, East Africa, to investigate how widespread size homoplasy is among closely related taxa at this locus. All cichlid fishes endemic to this lake are believed to have originated within the last 700,000 years, and some species may be less than 200 years old. The number of eletromorphs found per species varied from 3 to 13. Sequence analysis of 95 cloned Pzeb4 PCR products (representing 18 electromorphs) revealed 13 new alleles. Ten of the 13 electromorphs (77%) were found to show size homoplasy due to either single nucleotide substitutions/indels or large indels. To investigate how well this locus fits the single-step mutation model (SMM), the minimum number of mutations required to explain the length differences between pairs of alleles was plotted against their size differences. Of the 300 comparisons, 166 (55.3%) corresponded to SMM expectations and 86 (28.7%) required a smaller number of mutations, and for 48 (16.0%) pairwise comparisons, a larger number of mutations were required to explain the length differences as compared with SMM expectations. Finally, a large deletion in the microsatellite sequence observed in the three rock-dwelling species Pseudotropheus lucerna, Pseudotropheus (Tropheops) 'band,' and Pseudotropheus (Tropheops) 'rust' and the midwater-feeding species Copadichromis sp. is believed to represent a shared ancestral polymorphism.     

Morphometric analysis on ecomorphologically equivalent cichlid species from Lakes Malawi and Tanganyika

Landmark-based geometric morphometric techniques were used to test the hypothesis that Petrochromis spp. from Lake Tanganyika are ecomorphologically equivalent to Petrotilapia spp. from Lake Malawi. Both genera are epilithic algal feeders and inhabit the rocky shores of their respective lakes. We investigated the morphological component of the ecomorphology hypothesis by investigating body shape, using landmark-based morphometric techniques. A MANOVA revealed significant differences among species and an ordination of all species along the first two CV axes showed clear separation of the two genera in the morphospace with Petrochromis fasciolatus as an intermediate. A thin-plate spline analysis revealed that Petrochromis spp. had a deeper, broader anterior body, larger gape, shorter anal fin base and narrower caudal peduncle than Petrotilapia spp. Basically, differences between lakes were found, but there were no similarities or clusters of presumptive ecomorphs. Based on such results, we reject the hypothesis of morphological equivalence between these two genera. However, considering the non-significant difference in body shape revealed between P. fasciolatus , Petrotilapia genalutea and Petrotilapia 'mumbo blue', we conclude that these three species represent morphological equivalence and hence display a best example of convergent evolution.     

Assortative mating among rock-dwelling cichlid fishes supports high estimates of species richness from Lake Malawi

It has been estimated that Lake Malawi, Africa, contains 500–650 endemic species of cichlid fishes, the largest number of vertebrate species endemic to any comparable sized area on the planet. As many of these putative species cannot be distinguished anatomically, these estimates of species richness depend to a great extent on the assumption that sympatrically occurring male colour morphs represent biological species. We have tested this assumption using a combination of behavioural observations of courtship and microsatellite DNA analysis for six putative species of the Pseudotropheus ( Tropheops ) complex and three of the Pseudotropheus ( Maylandia ) complex occurring sympatrically at Nkhata Bay. We were unable to demonstrate assortative courtship for the species pairs Pseudotropheus ( Maylandia ) zebra / P . 'gold zebra' or P. ( Tropheops ) 'band'/ P. ( T .) 'rust' because we were unable to distinguish between the females of these taxa. All other taxa showed clear assortative courtship, except for P. ( T .) 'deep', a deep-water species which was rarely observed. Fixation indices (θ_ST for the infinite allele model, and R _ST for the stepwise mutation model) calculated from six microsatellite DNA loci demonstrated significant deviations from panmixia in all pairwise comparisons of putative species, indicating little or no gene flow between populations. All taxa showed high levels of allelic diversity providing evidence that genetic bottlenecking may have been of limited importance in the speciation process. Assortative mating among taxa differing only in male colouration is supportive of theories that speciation in these fishes has been driven by sexual selection by female choice.     

Geometric morphometrics applied to viscerocranial bones in three populations of the Lake Tanganyika cichlid fish Tropheus moorii

Lake Tanganyika comprises the oldest and most diverse species flock of cichlid fishes. Many species are subdivided into numerous populations, often classified as geographical races, colour morphs or sister species. Unlike younger species flocks, in which speciation is accompanied by eco-morphological diversification that of Lake Tanganyika is at a mature stage with little further morphological change, most probably caused by stabilizing selection. This study addresses body shape differences among three genetically distinct but morphologically similar populations of Tropheus  moorii , by focusing on bony structures of the cichlid head. We test by means of geometric morphological methods whether shape changes in the cichlid head are based on particular osteological differences. Specimens were disarticulated enzymatically, and standardized digital images of the disarticulated bony elements were taken. A landmark system was established for the dentary, articular, premaxilla, quadrate and the preopercle. Only the dentary shows significant differentiation among the three populations. Since all three populations live in similar cobble habitats and occupy the same trophic niche, the observed difference in the shape of the dentary can either be explained by different directional selection due to subtle habitat differences, or by neutral drift constrained by borders enforced through stabilizing selection. Lack of difference might indicate stabilizing selection on bone shape.     

Morphological convergence of shell shape in distantly related scallop species (Mollusca: Pectinidae)

Morphological convergence is a central concept in evolutionary biology, but convergent patterns remain under‐studied in nonvertebrate organisms. Some scallop species exhibit long‐distance swimming, a behaviour whose biomechanical requirements probably generate similar selective regimes. We tested the hypothesis that shell shape similarity in long‐distance swimming species is a result of convergent evolution. Using landmark‐based geometric morphometrics, we quantified shell shape in seven species representing major behavioural habits. All species displayed distinct shell shapes, with the exception of the two long‐distance swimmers, whose shells were indistinguishable. These species also displayed reduced morphological variance relative to other taxa. Finally, a phylogenetic simulation revealed that these species were more similar in their shell shape than was expected under Brownian motion, the model of character evolution that best described changes in shell shape. Together, these findings reveal that convergent evolution of shell shape occurs in scallops, and suggest that selection for shell shape and behaviour may be important in the diversification of the group. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 163 , 571–584.     

Karyological evolution in Rhaponticum Vaill. (Asteraceae, Cardueae) and related genera

Chromosome counts are reported in 29 populations representing 20 species and one subspecies of the genera Callicephalus (one sp.), Klasea (seven spp.), Myopordon (two spp.), Oligochaeta (one sp.), and Rhaponticum (nine spp., one ssp.). Eleven reports are new, the others supplement limited previous data. New and published cytological data are summarized and evaluated critically in light of current taxonomic treatments and evolutionary hypotheses. Basic chromosome numbers are a valuable source of taxonomic information and relate well to the phylogeny. They are quite conserved in Klasea (only x  = 15), the sister group of the remaining genera, and in the early branching genera of the Rhaponticum group ( x  = 14 for Centaurothamnus and Callicephalus ). However, a more complex pattern of genome evolution is present among the more derived clades, Oligochaeta plus Myopordon ( x  = 12, 14) and the genus Rhaponticum ( x  = 12, 13). The occurrence of x  = 12 in Oligochaeta divaricata and Rhaponticum carthamoides seems to be the result of a recent event of chromosome fusion, as suggested by the fragility of particularly long pairs of chromosomes. The use of chromomycin staining, including an enzymatic digestion step that facilitates spreading and permits a reduction of potential fragmentation, only partially resolves this problem.  © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society , 2007, 153 , 193–201.     

Species differences in courtship acoustic signals among five Lake Malawi cichlid species (Pseudotropheus spp.)

Male courtship acoustic signals from five Lake Malawi cichlid fish species of the Pseudotropheus zebra complex were recorded and compared. Sounds made by males of P. zebra , Pseudotropheus callainos and the undescribed species known as Pseudotropheus 'zebra gold' from Nkhata Bay, and Pseudotropheus emmiltos and Pseudotropheus faizilberi from Mphanga Rocks, differed significantly in the number of pulses and in pulse period. The largest differences in acoustic variables were found among the sympatric Mphanga Rocks species that, in contrast to the other three species, show relatively minor differences in male colour and pattern. These findings suggest that interspecific mate recognition is mediated by multimodal signals and that the mass of different sensory channels varies among sympatric species groups. This study also showed that sound peak frequency was significantly negatively correlated with male size and that sound production rate increased significantly with courtship rate.     

Geometric morphometrics as a tool for understanding Dactylorhiza (Orchidaceae) diversity in European Russia

Geometric morphometric techniques were employed to assess the diversity of lip shapes (305 samples from 83 populations) in flowers of European Russian Dactylorhiza (Orchidaceae: Orchidinae). We found significant agreement between the results from geometric morphometrics, classic morphometrics and the distribution of certain nuclear DNA markers. The lip shapes from Arctic Dactylorhiza samples occupied an intermediate position between D. maculata and D. fuchsii samples from Central Russia, supporting a hybrid origin of 'northern tetraploids'. Lip shapes of the taxonomically controversial allotetraploid D. baltica were found to form a distinct group, with members having definite relationships with diploid D. incarnata samples from the same localities, indicating either their local origin or introgression with D. incarnata . In addition to demonstrating the value of geometric morphometric methods in studies of plant taxonomy and hybridization, we suggest future applications designed to explore pollinator-driven directional selection, developmental constraints and fluctuating asymmetry.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 85 , 1–12.     

Weak link between dispersal and parasite community differentiation or immunogenetic divergence in two sympatric cichlid fishes

Geographical isolation, habitat variation and trophic specialization have contributed to a large extent to the astonishing diversity of cichlid fishes in the Great East African lakes. Because parasite communities often vary across space and environments, parasites can accompany and potentially enhance cichlid species diversification. However, host dispersal may reduce opportunities for parasite‐driven evolution by homogenizing parasite communities and allele frequencies of immunity genes. To test for the relationships between parasite community variation, host dispersal and parasite‐induced host evolution, we studied two sympatric cichlid species with contrasting dispersal capacities along the shores of southern Lake Tanganyika. Whereas the philopatric Tropheus moorii evolved into several genetically differentiated colour morphs, Simochromis diagramma is phenotypically rather uniform across its distribution range and shows only weak population structure. Populations of both species were infected with divergent parasite communities and harbour differentiated variant pools of an important set of immune genes, the major histocompatibility complex (MHC). The overall extent of geographical variation of parasites and MHC genes was similar between host species. This indicates that immunogenetic divergence among populations of Lake Tanganyika cichlids can occur even in species that are strongly dispersing. However, because this also includes species that are phenotypically uniform, parasite‐induced evolution may not represent a key factor underlying species diversification in this system.     

Geographic variation in the long-nosed snake, Rhinocheilus lecontei (Colubridae): beyond the subspecies debate

Scalation, colour pattern, linear and geometric morphometrics were used to quantify geographical differentiation in the long-nosed snake, Rhinocheilus lecontei, and to test the hypothesis that all four subspecies are morphologically distinct. Also investigated were potential associations between morphological (scalation, colour pattern, linear measurements) and environmental variables (climate, vegetation, soil). Sexual dimorphism was weakest for geometric and strongest for linear morphometric variables. Morphological variables differed widely in their ability to differentiate subspecies. Linear morphometric variables achieved the most statistically significant pairwise Mahalanobis distances between subspecies, while geometric morphometrics largely failed to differentiate them. Colour pattern showed the strongest and linear morphometrics the weakest correlation with environment. Several characters varied continuously along latitudinal or longitudinal gradients, such that, in some cases, the clines for closely related traits were discordant. No one subspecies was consistently divergent in all analyses, leading to the conclusion that the three mainland subspecies are not sufficiently distinct to warrant separate subspecies status. The island subspecies, though not always statistically distinct, is geographically separate from other populations and differs in characters related to size. Given the small number of specimens available, a decision regarding its taxonomic status (i.e. elevation to species level) is best deferred until additional specimens can be examined and data on molecular variation can be analysed.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 83 , 65–85.     

Grazing rates of crustacean zooplankton communities on intact phytoplankton communities in Canadian Subarctic lakes and ponds

Quantitative genetic studies in natural populations are of growing interest to speciation research since divergence is often believed to arise through micro-evolutionary change, caused by natural selection on functional morphological traits. The species flock of cichlid fishes in Africa’s oldest lake, Lake Tanganyika, offers a rare opportunity to study this process. Using the cichlid species Tropheus moorii, we assessed the potential for microevolution in a set of morphological traits by estimating their quantitative genetic basis of variation. Two approaches were employed: (1) estimation of trait heritabilities (h ²) in situ from a sample of wild caught fish, and (2) estimation of h ² from first generation offspring produced in a semi-natural breeding experiment. In both cases, microsatellite data were used to infer pedigree structure among the sampled individuals and estimates of h ² were made using an animal model approach. Although power was limited by the pedigree structures estimated (particularly in the wild caught sample), we nonetheless demonstrate the presence of significant additive genetic variance for aspects of morphology that, in the cichlid species Tropheus moorii, are expected to be functionally and ecologically important, and therefore likely targets of natural selection. We hypothesize that traits showing significant additive genetic variance, such as the mouth position have most likely played a key role in the adaptive evolution of the cichlid fish Tropheus moorii.     

Morphological divergence patterns among populations of Poecilia vivipara (Teleostei Poeciliidae): test of an ecomorphological paradigm

The structure of body size and shape divergence among populations of Poecilia vivipara inhabiting quaternary lagoons in South-eastern Brazil was studied. This species is abundant throughout an environmental gradient formed by water salinity differences. The salinity gradient influences the habitat structure (presence of macrophytes) and the fish community (presence of large predators). Size and shape variation within and among populations was quantified by geometric morphometrics and analysed by indirect and direct gradient ordinations, using salinity and geography as a framework. Morphological divergence was associated with the salinity gradient. The evolutionary allometries observed were independent of within-group static allometries. Sexually dimorphic patterns were observed in size variation and within-population allometries. Specimens from freshwater (higher predation) sites presented smaller sizes, relatively longer caudal regions, lower anterior regions and a ventrally displaced eye. These features are consistent with an ecomorphological paradigm for aquatic organisms from populations subject to intense predation. A process of directional selection is postulated as the most likely force driving diversification among P. vivipara populations.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 93 , 799–812.     

Evolution of novel jaw joints promote trophic diversity in coral reef fishes

We investigated the functional morphology and ecology of biting among the squamipinnes, an assemblage of nine successful and distinctive reef fish families. We demonstrate that an intramandibular joint (IMJ) may have evolved at least three and possibly five times in this assemblage and discuss the impact of this recurring innovation in facilitating prey-capture by biting. Using character mapping on a supertree for the squamipinnes, we reveal up to seven gains or losses of intramandibular flexion, all associated with trophic transitions between free-living and attached prey utilization. IMJs are basal in six of the studied families whereas the origin of intramandibular flexion in the Chaetodontidae (butterflyfishes) coincides with a transition from ram-suction feeding to benthic coral feeding, with flexion magnitude reaching its peak (49 ± 2.7°) in the coral scraping subgenus Citharoedus . Although IMJs generally function to augment vertical gape expansion during biting behaviours to remove small invertebrates, algae or coral from the reef, the functional ecology of IMJs in the Pomacanthidae (angelfishes) stands in contrast. Pomacanthid IMJs exhibit over 35° of flexion, permitting gape closure when the jaws are fully protruded. We demonstrate the widespread IMJ occurrence among extant biters to result from a complex convergent evolutionary history, indicating that the IMJ is a major functional innovation that enhances biting strategies in several prominent reef fish groups.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 93 , 545–555.     

Molecular systematics of mantelline frogs from Madagascar and the evolution of their femoral glands

Several genera of frogs from Madagascar, classified in the family Mantellidae, subfamily Mantellinae, possess structures commonly called 'femoral glands' on the ventral side of their shanks. The question arises as to the origin and phylogenetic significance of these glands. A molecular phylogeny based on 3601 nucleotide DNA sequences of three mitochondrial and two nuclear genes of 30 mantellid species provided strong support for monophyly of the included mantellines, all characterized by enlarged femoral gland clusters, as well as for those with gland clusters of coordinated central arrangement of secretion ducts. However, the phylogeny also strongly supported the hypothesis of convergent evolution of structurally similar glands in unrelated frogs ( Indirana , Petropedetes ), and several trends of convergent evolution of gland structure within mantellines. We studied the light microscopic structure of the femoral glands in a representative array of 18 mantellid species. Males of all species of the subfamily Mantellinae were characterized by clusters of distinct single glands. Each was structurally similar to an enlarged granular gland and secreted independently, probably through a single duct. By contrast, the largely semi-aquatic frogs in the genus Mantidactylus had a specialized cluster of glands, in which the secretion ducts led into a macroscopically recognizable central depression. In Boophis opisthodon , a mantellid species of the subfamily Boophinae without externally recognizable femoral glands, we observed a large number of enlarged granular glands of various sizes in the ventral skin of the shank. This observation is consistent with the hypothesis that the large and more uniform organs of mantellines are derived granular glands.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 92 , 529–539.     

Using image analysis on the ventral colour pattern in Salamandrina perspicillata (Amphibia: Salamandridae) to discriminate among populations

The ventral colour pattern in Salamandrina perspicillata is characteristic of each individual and remains invariant throughout the salamanders' life. The present study aimed to determine, using statistical methods applied to quantitative image analysis, whether the coloration pattern is population-specific. The images of ventral colour pattern of 180 salamanders belonging to five populations were analysed. The images were previously warped by geometric morphometry. To our knowledge, this is the first study to use an approach based on geometric morphometrics to standardize ventral shapes. This technique is useful for eliminating form distortions. The results of an analysis of similarities recognized more coloration similarity among individuals of the same population than among individuals from different populations. Analysis by partial least squares correctly classified the 88.88% of individuals into the correct population. The similarities or differences among individuals of different populations are not related to the geographical distances. The results obtained showed that the coloration of the ventral side of the head of the salamanders can be used for discriminating among populations.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 96 , 35–43.     

Chromosome counts in Asian Artemisia L. (Asteraceae) species: from diploids to the first report of the highest polyploid in the genus

This work comprises 24 reports of chromosome numbers in 24 Artemisia L. species from Asia. Ten are included in the subgenus Dracunculus Besser and the rest belong to other subgenera. Seven counts are new reports, 14 are consistent with scarce previous ones, and three contribute new ploidy levels. That carried out in A. medioxima reports the highest ploidy level ever counted for the genus (16 x ). There is only one species with x  = 8 as the basic chromosome number. In the remaining x  = 9-based species, ploidy levels range from 2 x to 16 x , illustrating the great role played by polyploidy in the evolution of the genus.  © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society , 2007, 153 , 301–310.     

Establishment and expansion of Lake Malawi rock fish populations after a dramatic Late Pleistocene lake level rise

Major environmental events that fragment populations among multiple island habitats have potential to drive large-scale episodes of speciation and adaptive radiation. A recent palaeolimnological study of sediment cores indicated that Lake Malawi underwent major climate-driven desiccation events 75 000–135 000 years ago that lowered the water level to at least 580 m below the present state and severely reduced surface area. After this period, lake levels rose and stabilized, creating multiple discontinuous littoral rocky habitats. Here, we present evidence supporting the hypothesis that establishment and expansion of isolated philopatric rock cichlid populations occurred after this rise and stabilization of lake level. We studied the Pseudotropheus ( Maylandia ) species complex, a group with both allopatric and sympatric populations that differ in male nuptial colour traits and tend to mate assortatively. Using coalescent analyses based on mitochondrial DNA, we found evidence that populations throughout the lake started to expand and accumulate genetic diversity after the lake level rise. Moreover, most haplotypes were geographically restricted, and the greatest genetic similarities were typically among sympatric or neighbouring populations. This is indicative of limited dispersal and establishment of assortative mating among populations following the lake level rise. Together, this evidence is compatible with a single large-scale environmental event being central to evolution of spatial patterns of genetic and species diversity in P. ( Maylandia ) and perhaps other Lake Malawi rock cichlids. Equivalent climate-driven pulses of habitat formation and fragmentation may similarly have contributed to observed rapid and punctuated cladogenesis in other adaptive radiations.     

Resource control by territorial male cichlid fish in Lake Malawi

1. The rocky habitat communities of Lake Malawi contain a high diversity of ecologically similar, predominantly herbivorous, cichlid fish species. How so many species can coexist is still unknown.
2. Adult males of the majority of these species hold permanent territories which form dense multispecies mosaics across the shores.
3. The study examined six coexisting species of cichlids from the rocky habitat where males are known to control access to the algal food resources within their territorial space. These included four sibling species of the Pseudotropheus ( Tropheops ) species complex, which are specialized epilithic algal herbivores, and two sibling species of the trophically more generalist P . ( Maylandia ) species complex which feed upon both epilithic algae and plankton.
4. The hypotheses that both intraspecific and interspecific territoriality occur in these communities and that interspecific aggression initiated by territorial males is preferentially directed at species with the most similar diets to their own were tested.
5. It was found that males preferred to exclude conspecific intruders, while they tolerated intruders with different diets to their own. Also, male P . ( Tropheops ) preferentially excluded similar heterospecific dietary specialists, while male P. ( Maylandia ) tolerated similar heterospecific dietary generalists.
6. Based on this study, it is proposed that interspecific territoriality may be reducing competition between species with different diets and promoting their coexistence, while it may be enhancing competition between species with the same diet. Furthermore, it suggests that ecological generalism may be reducing the intensity of interspecific competition, while specializations for the same resources may be increasing competition.