No evidence for parallel sympatric speciation in cichlid species of the genus Pseudotropheus from north-western Lake Malawi

To test the hypothesis of parallel speciation by sexual selection, we examined length variation at six microsatellite loci of samples from four sites of four to six putative species belonging to two subgenera of rocky shore mbuna cichlids from Lake Malawi. Almost all fixation indices were significantly different from zero, suggesting that there is presently little or no gene flow among allopatric populations or sympatric species. Analysis of variance indicated that genetic distances among allopatric populations of putative conspecifics were significantly lower than among sympatric populations of heterospecifics. The topology of trees based on distance matrices was also largely consistent with the hypothesis that the putative species are monophyletic and have thus not evolved in parallel in their present locations. If parallel speciation does occur in Malawi cichlids, it may be on a larger spatial scale than investigated in our study.     

Extreme microallopatric divergence in a cichlid species from Lake Malawi

We demonstrate significant population structuring on an extremely small spatial scale between adjacent demes of a Lake Malawi haplochromine cichlid species of the mbuna group, Pseudotropheus callainos, separated by only 35 m of habitat discontinuity. This substantiates further the notion that intralacustrine allopatric divergence may help to explain the high level of species richness of the mbuna in comparison to other Malawian cichlids, as well as of the Malawian haplochromines as a whole.     

Speciation in rapidly diverging systems: lessons from Lake Malawi

Rapid evolutionary radiations provide insight into the fundamental processes involved in species formation. Here we examine the diversification of one such group, the cichlid fishes of Lake Malawi, which have radiated from a single ancestor into more than 400 species over the past 700 000 years. The phylogenetic history of this group suggests: (i) that their divergence has proceeded in three major bursts of cladogenesis; and (ii) that different selective forces have dominated each cladogenic event. The first episode resulted in the divergence of two major lineages, the sand- and rock-dwellers, each adapted to a major benthic macrohabitat. Among the rock-dwellers, competition for trophic resources then drove a second burst of cladogenesis, which resulted in the differentiation of trophic morphology. The third episode of cladogenesis is associated with differentiation of male nuptial colouration, most likely in response to divergent sexual selection. We discuss models of speciation in relation to this observed pattern. We advocate a model, divergence with gene flow, which reconciles the disparate selective forces responsible for the diversification of this group and suggest that the nonadaptive nature of the tertiary episode has significantly contributed to the extraordinary species richness of this group.     

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.     

Separated by sand, fused by dropping water: habitat barriers and fluctuating water levels steer the evolution of rock-dwelling cichlid populations in Lake Tanganyika

The conditions of phenotypic and genetic population differentiation allow inferences about the evolution, preservation and loss of biological diversity. In Lake Tanganyika, water level fluctuations are assumed to have had a major impact on the evolution of stenotopic littoral species, though this hypothesis has not been specifically examined so far. The present study investigates whether subtly differentiated colour patterns of adjacent Tropheus moorii populations are maintained in isolation or in the face of continuous gene flow, and whether the presumed influence of water level fluctuations on lacustrine cichlids can be demonstrated in the small-scale population structure of the strictly stenotopic, littoral Tropheus. Distinct population differentiation was found even across short geographic distances and minor habitat barriers. Population splitting chronology and demographic histories comply with our expectation of old and rather stable populations on steeper sloping shore, and more recently established populations in a shallower region. Moreover, population expansions seem to coincide with lake level rises in the wake of Late Pleistocene megadroughts ~100 KYA. The imprint of hydrologic events on current population structure in the absence of ongoing gene flow suggests that phenotypic differentiation among proximate Tropheus populations evolves and persists in genetic isolation. Sporadic gene flow is effected by lake level fluctuations following climate changes and controlled by the persistence of habitat barriers during lake level changes. Since similar demographic patterns were previously reported for Lake Malawi cichlids, our data furthermore strengthen the hypothesis that major climatic events synchronized facets of cichlid evolution across the East African Great Lakes.     

Secondary contact during adaptive radiation: a community matrix for Lake Malawi cichlids

We used a community of Lake Malawi rock‐dwelling cichlids to study secondary contact during adaptive radiation. Using abundance data from survey plots we constructed a matrix of pair‐wise interaction coefficients for males of 21 native and eight transplanted species. After controlling for the effects of habitat variation, correlations among residual male abundances suggest that coevolved species compete less than those brought into artificial secondary contact 30 years ago and that species with the same body colour compete more than those with different body colours. The latter result provides evidence that a trait related to reproductive isolation affects competitive interactions and the distribution of individuals throughout an entire community. Our results further suggest lake level fluctuations that divide and reconnect communities act to increase local (alpha), as well as total (gamma) diversity, in this adaptive radiation. The communities are not, however, unsaturated in the simplest sense; new species can enter a community, but they disproportionately reduce the abundance of original community members.     

Variation in habitat preference and population structure among three species of the Lake Malawi cichlid genus Protomelas

Several studies have demonstrated strong population structuring over small distances in the rocky-shore mbuna cichlid fishes from Lake Malawi, suggesting the potential for allopatric speciation. However, many endemic Lake Malawi cichlids are neither mbuna, nor confined to rocky shores. Using microsatellites, we investigated the population structure in three species of the non-mbuna genus Protomelas. The rocky-shore P. taeniolatus showed high levels of population structure even over distances of less than 1 km, while the sandy-shore species P. similis showed no significant structure over distances up to 21 km. Protomelas fenestratus, which is generally found at the interface between rocks and sand, also showed low levels of population structure. Our results suggest that the model of allopatric speciation based on habitat fragmentation within the current lake basin may be equally applicable to rocky-shore non-mbuna as to mbuna, but that an alternative model is required to explain speciation among sandy-shore species as well as the deep-water and pelagic species.     

Microsatellite data reveals weak population substructuring in Copadichromis sp.'virginalis kajose', a demersal cichlid from Lake Malawi, Africa

Small but significant differences were found in allele frequencies among five populations (overall F _ST estimate (θ)=0·004, P=0·006; overall R _ST estimate (RHO)=0·019, P <0·00001) of the demersal cichlid Copadichromis sp.'virginalis kajose', collected from five locations in Lake Malawi. Pairwise F _ST estimates revealed significant differences between the most southerly population (Cape Maclear), and the three most northerly populations (Mbamba Bay, Metangula and Chilola). Pairwise R _ST estimates also revealed significant differences between some populations, but no geographical pattern was discernible. There was no evidence of isolation by distance using either the shortest straight-line distance between samples, or the distance around the shoreline following a 50 m depth contour. F _ST estimates were considerably lower than found in previous studies on the mbuna (rock-dwelling species), but higher than those found in a study of three pelagic cichlid species from Lake Malawi. Substructuring in C. sp.'virginalis kajose' appears to be on a similar scale to the Atlantic cod.     

Genetic variability and gene flow in the globally, critically-endangered Taita thrush

Analysis of 155 individuals with seven polymorphicmicrosatellite DNA markers showed significant genetic differentiationbetween the only three remaining subpopulations of the globally,critically-endangered Taita thrush. Small, recently-disturbedsubpopulations such as studied here may violate the assumptions ofmutation-drift and gene flow-drift equilibrium inherent to mostpopulation genetic tools that estimate gene flow. We thereforeidentified putative dispersers using two recently-developed assignmenttests based on individual genotypes. Previous-generation and currentmigration rates between any two subpopulations were estimated at one andzero individuals per generation, respectively. Strong congruence withnon-genetic estimates of between-fragment dispersal provided indirectevidence for the accuracy of the assignment test. From a conservationperspective, the available demographic and genetic data suggest asubstantial threat to the long-term survival of at least the smallestsubpopulation.     

Nuclear gene variation and molecular dating of the cichlid species flock of Lake Malawi

The cichlid fishes of Lake Malawi are famously diverse. However, evolutionary studies have been difficult because of their recent and uncertain phylogenetic history. Portions of 12 nuclear loci were sequenced in nine rock-dwelling species (mbuna) and three representatives of pelagic nonmbuna species. In contrast to the pattern of variation at mitochondrial genes, which do provide phylogenetic resolution at the level of mbuna versus nonmbuna, and among some genera, the nuclear loci were virtually devoid of phylogenetic signal. Only a small minority of variable positions were phylogenetically informative, and no phylogenetic branches are supported by more than one site. From the nuclear gene perspective the Malawian radiation appears to be a star phylogeny, as if the founding of the lake was accompanied by a partial bottleneck. The pattern is different from that found in Lake Victoria, in which nuclear loci share large amounts of ancestral variation. In the case of nuclear genes of Lake Malawi, the absence of phylogenetically informative variation suggests a relative absence of ancestral variation. Nuclear genes also differed from the mitochondria in having nearly twice the amount of divergence from Oreochromis (tilapia). An approximate splitting time between mbuna and nonmbuna lineages was estimated as 0.7 Myr. Oreochromis is estimated to have diverged from the cichlids in Lake Malawi and Lake Tanganyika about 18 MYA.     

Ultraviolet reflectivity in three species of Lake Malaŵi rock-dwelling cichlids

The body colouration extending into ultraviolet wavelengths in three species of Lake Malaŵi rock‐dwelling cichlids, Metriaclima zebra , Metriaclima benetos and Metriaclima barlowi was quantified. All three species were ultraviolet reflective with interspecific differences in reflectivity. In addition, individuals were able to behaviourally mediate their reflectivity.     

Lake flies and the deep-water demersal fish community of Lake Malawi

Larvae and pupae of Chaoborus edulis may be the most important food resource of some deep-water demersal fish species in southern Lake Malawi. C. edulis feed on crustacean zooplankton, which in turn feed on phytoplankton. Hence, demersal fish production is supported directly by planktonic primary production, rather than through a detrital food chain.     

Stark sexual display divergence among jumping spider populations in the face of gene flow

Gene flow can inhibit evolutionary divergence by eroding genetic differences between populations. A current aim in speciation research is to identify conditions in which selection overcomes this process. We focused on a state of limited differentiation, asking whether selection enables divergence with gene flow in a set of Habronattus americanus jumping spider populations that exhibit three distinct male sexual display morphs. We found that each population is at high frequency or fixed for a single morph. These strong phenotypic differences contrast with low divergence at 210 AFLP markers, suggesting selection has driven or maintains morph divergence. Coinciding patterns of isolation by distance and ‘isolation by phenotype’ (i.e. increased genetic divergence among phenotypically contrasting populations) across the study area support several alternative demographic hypotheses for display divergence, each of which entails gene flow. Display‐associated structure appears broadly distributed across the genome and the markers producing this pattern do not stand out from background levels of differentiation. Overall, the results suggest selection can promote stark sexual display divergence in the face of gene flow among closely related populations.     

Dams and canyons disrupt gene flow among populations of a threatened riparian plant

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Speciation with gene flow and the genetics of habitat transitions

Whether speciation can advance to completion in the face of initially high levels of gene flow is a very controversial topic in evolutionary biology. Extensive gene exchange is generally considered to homogenize populations and counteract divergence. Moreover, the role of introgressive hybridization in evolution remains largely unexplored in animals, particularly in freshwater zooplankton in which allopatric speciation is considered to be the norm. Our work investigates the genetic structure of two young ecological species: the pond species, Daphnia pulex and the lake species, Daphnia pulicaria. Phylogenetic and population genetics analyses were conducted on mitochondrial NADH dehydrogenase 5 (ND5) gene, the nuclear Lactate dehydrogenase (Ldh) gene and 21 nuclear microsatellite markers in 416 individuals from habitats with various degrees of permanence. The strong and consistent phylogenetic discordance between nuclear and mitochondrial markers suggests a complex evolutionary history of multiple independent habitat transition events that involved hybridization and introgression between lake and pond Daphnia. On the other hand, the low level of contemporary gene flow between adjacent populations indicates the presence of effective habitat isolating barriers. The Daphnia system provides strong evidence for a divergence-with-gene flow speciation model that involves multiple habitat transition events.     

Fine-scale spatial genetic structure and gene flow in a small, fragmented population of Sinojackia rehderiana (Styracaceae), an endangered tree species endemic to China

Populations of Sinojackia rehderiana are highly threatened and have small and scattered distribution due to habitat fragmentation and human activities. Understanding changes in genetic diversity, the fine-scale spatial genetic structure (SGS) at different life stages and gene flow of S. rehderiana is critical for developing successful conservation strategies for fragmented populations of this endangered species. In this study, 208 adults, 114 juveniles and 136 seedlings in a 50 × 100-m transect within an old-growth forest were mapped and genotyped using eight microsatellite makers to investigate the genetic diversity and SGS of this species. No significant differences in genetic diversity among different life-history stages were found. However, a significant heterozygote deficiency in adults and seedlings may result from substantial biparental inbreeding. Significant fine-scale spatial structure was found in different life-history stages within 19 m, suggesting that seed dispersal mainly occurred near a mother tree. Both historical and contemporary estimates of gene flow (13.06 and 16.77 m) indicated short-distance gene dispersal in isolated populations of S. rehderiana. The consistent spatial structure revealed in different life stages is most likely the result of limited gene flow. Our results have important implications for conservation of extant populations of S. rehderiana. Measures for promoting pollen flow should be taken for in situ conservation. The presence of a SGS in fragmented populations implies that seeds for ex situ conservation should be collected from trees at least 19-m apart to reduce genetic similarity between neighbouring individuals.     

黑麂(Muntiacus crinifrons)栖息地片断化对种群基因流的影响

栖息地片断化可能影响种群的基因流,进而导致近交,降低个体生活力,是生物多样性丧失和物种绝灭的主要因素.被列为国家I级保护动物的黑麂(Muntiacus crinifrons),由于自身目前的濒危状况和生物学特异性,使得栖息地片断化对其影响更甚.为了更好的保护该珍稀物种,研究运用地理信息系统划分了浙江遂昌的九龙山自然保护区和开化的古田山自然保护区黑麂栖息地的片断化斑块,并通过所得片断化斑块数据进行两个保护区在片断化程度的计算,同时从片断化斑块获取黑麂的组织、粪便样品,提取黑麂的线粒体DNA,估算其基因流大小.以此初步确定两个保护的黑麂栖息地片断化程度对种群基因流的影响.各项片断化指数均表明,九龙山自然保护区的黑麂栖息地片断化程度要小于古田山自然保护区.九龙山自然保护区黑麂片断化种群的平均基因流Nm达到了3.65,明显高于古田山自然保护区的1.12.结果表明,栖息地片断化可能对黑麂种群的基因流产生了一定的影响.应及时采取有效措施保护和恢复黑麂栖息地,否则将严重阻碍片断化种群间的个体迁移、扩散和基因交流.     

Homing and home-site fidelity in rock-dwelling cichlids (Pisces: Teleostei) of Lake Malawi,Africa

Synopsis Existence of home site fidelity and homing ability was established for Pseudotropheus aurora. Territorial males stayed up to 1 1/2 years within the same territories. Females showed long-term fidelity to certain places. Transplantation experiments revealed that P. aurora males home over distances of up to at least 2500 m but would not cross deep water. The territorial males of five other sympartic species returned from 1000 m to their territories. The mechanisms and functions of homing in cichlids are discussed.     

The influence of gene flow and drift on genetic and phenotypic divergence in two species of Zosterops in Vanuatu

Colonization of an archipelago sets the stage for adaptive radiation. However, some archipelagos are home to spectacular radiations, while others have much lower levels of diversification. The amount of gene flow among allopatric populations is one factor proposed to contribute to this variation. In island colonizing birds, selection for reduced dispersal ability is predicted to produce changing patterns of regional population genetic structure as gene flow-dominated systems give way to drift-mediated divergence. If this transition is important in facilitating phenotypic divergence, levels of genetic and phenotypic divergence should be associated. We consider population genetic structure and phenotypic divergence among two co-distributed, congeneric (Genus: Zosterops) bird species inhabiting the Vanuatu archipelago. The more recent colonist, Z. lateralis, exhibits genetic patterns consistent with a strong influence of distance-mediated gene flow. However, complex patterns of asymmetrical gene flow indicate variation in dispersal ability or inclination among populations. The endemic species, Z. flavifrons, shows only a partial transition towards a drift-mediated system, despite a long evolutionary history on the archipelago. We find no strong evidence that gene flow constrains phenotypic divergence in either species, suggesting that levels of inter-island gene flow do not explain the absence of a radiation across this archipelago.