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PubMed1997

Genetic relationships among populations of wild resident, and wild and hatchery anadromous brook charr

To determine the genetic relationship of anadromous and resident life-history types within and among drainages, and compare several hatchery strains to their progenitor populations, brook charr Salvelinus fontinalis were examined for allozyme and mitochondrial DNA variation. Greater genetic similarity of sympatric anadromous and resident charr was found compared to similar life-history forms allopatrically, suggesting the two life-history types are not reproductively isolated. Low divergence among the mtDNA haplotypes suggests that the two life-history types are members of the same evolutionary lineage. Population differentiation from mtDNA data exceeded that from estimates based on allozymes. Genetic deviations from expectations suggest that the hatchery strains were derived from few individuals. 1997 The Fisheries Society of the British Isles

Journal Article↗
PubMed1996

Comparison of protein markers and microsatellites in differentiation of cattle populations.

Five cattle populations, representing four breeds, were analysed for 14 protein markers and five microsatellite loci. The breeds studied were Brown Swiss and three autochthonous Spanish cattle: Avileña-Negra Ibérica (A-NI), two populations (A-NI 1 and A-NI 2) from different, reproductively isolated, locations; Sayaguesa; and Morucha. A total of 752 animals were examined for biochemical polymorphisms, of which 488 were also DNA typed. Genetic parameters and phylogenetic trees were obtained separately for each group of markers and results were compared. Estimates of heterozygosity and genetic distances from microsatellites were greater than those obtained using protein markers. The overall topology of the two dendrograms was similar. A-NI 1 and A-NI 2 populations were grouped together, related to Morucha, and the three of them related to Sayaguesa. Brown Swiss appeared in a separate branch from Spanish cattle. These results support the usefulness of microsatellites in the study of genetic relationships among closely related populations and breeds.

Animals↗
PubMed1992

Phylogeny of cytoplasmic incompatibility micro-organisms in the parasitoid wasp genus Nasonia (Hymenoptera: Pteromalidae) based on 16S ribosomal DNA sequences.

Cytoplasmic incompatibility results in embryo mortality in diploids, or all male offspring in haplodiploids, when individuals carrying different cytoplasmic factors are crossed. Cytoplasmic factors have been identified as intracellular micro-organisms. Microbe-induced cytoplasmic incompatibility is found in many insect taxa and may play a role in reproductive isolation between populations. Such micro-organisms cause bidirectional incompatibility between species of the parasitoid wasp genus Nasonia. The phylogenetic relationship of cytoplasmic incompatibility microorganisms (CIM) of different Nasonia species was analysed using their 16S ribosomal DNA (rDNA) sequence. Two 16S rDNA operons were detected in the CIM of each Nasonia species. Sequence analysis indicates that the Nasonia CIM are closely related and belong to the alpha group of the Proteobacteria.

Animals↗
PubMed2005

Analysis of the sex pheromone extract of individual male Lutzomyia longipalpis sandflies from six regions in Brazil.

Although the phlebotomine sandfly Lutzomyia longipalpis (Lutz & Neiva, 1912) (Diptera: Psychodidae) is generally accepted to be a species complex, it is unclear how many members there are, how they are related and which are the main vectors of leishmaniasis. The vectorial capacity of each sibling species is likely to differ, thus a means of identifying the most important vector species is of critical importance to the epidemiology and control of this debilitating disease in South and Central America. In Brazil four chemotypes have been distinguished by sex pheromone analysis. In this study the sex pheromone extracts of L. longipalpis from six regions of Brazil were analysed in detail. Samples included the sympatric 1-spot, 2-spot and intermediate spot morphotypes from Sobral, Ceará State. The results strongly suggest that members of the complex that produce different sex pheromones are reproductively isolated, thus strengthening the argument that the different chemotypes represent true sibling species. The study also found significant differences in morphology and the amounts of sex pheromone produced by members of each chemotype from different parts of Brazil, which suggests population substructuring that has not previously been recognized. Evidence of a fifth chemotype in Brazil is also presented.

Animals↗
PubMed2005

On the verge of extinction: genetics of the critically endangered Iberian plant species, Borderea chouardii (Dioscoreaceae) and implications for conservation management.

Borderea chouardii is a relictual and dioecious, strictly sexually reproducing, long-living geophyte of the Dioscoreaceae family. Previous biological and demographic studies have indicated the existence of a uniformly distributed panmictic population of this taxon at the southernmost Spanish pre-Pyrenean mountain ranges where it occurs in rather inaccessible crevices of a single limestone cliff. However, individuals of B. chouardii are spatially subdivided into two subpopulations located, respectively, on the upper and lower parts of the cliff, and vertically separated 150 m. Because of its extreme rarity, B. chouardii was the first Iberian taxon to have a specific conservation plan and has been included in several red lists under the category of critically endangered (CR). However, no previous attempts have been conducted to analyse the fine scale evolutionary mechanisms involved in its present microspatial distribution. Genetic diversity and population structure have been investigated through the analysis of neutral hypervariable markers such as simple sequence repeats (SSRs) and randomly amplified polymorphic DNAs (RAPDs) to unravel the impact of life history traits in the differentiation of the two subpopulations. Both types of molecular markers were unequivocal in distinguishing two genetically distinct groups of individuals corresponding to their spatial separation. However, SSRs detected a higher level of subpopulation differentiation (F(ST) = 0.35, R(ST) = 0.32) than RAPDs (F(ST) = 0.21). SSR data indicated significant deviation from random dispersal of genes and genotypes between the two groups, suggesting that mating occurs mainly among individuals within subpopulations, thus, favouring the divergence between the two groups. This microevolutionary differentiation scenario might have been caused by a coupled effect of past genetic drift and reproductive isolation, as a result of strong glacial age bottlenecks and inefficient dispersal system of pollen and seeds, respectively. The identification of such genetic structure in this narrow endemic prompts a modification of the management strategies of its single extant population.

Conservation of Natural Resources↗
PubMed2005

Northwestern song sparrow populations show genetic effects of sequential colonization.

Two genetic consequences are often considered evidence of a founder effect: substantial loss in genetic diversity and rapid divergence between source and founder populations. Single-step founder events have been studied for these effects, but with mixed results, causing continued controversy over the role of founder events in divergence. Experiments of serial bottlenecks have shown losses of diversity, increased divergence, and rapid behavioural changes possibly leading to reproductive isolation between source and final populations. The few studies conducted on natural, sequentially founded systems show some evidence of these effects. We examined a natural vertebrate system of sequential colonization among northwestern song sparrows (Melospiza melodia). This system has an effectively linear distribution, it was probably colonized within the last 10,000 years, there are morphological and behavioural differences among populations, and the westernmost populations occur in atypical habitats for the species. Eight microsatellite loci from eight populations in Alaska and British Columbia (n = 205) showed stepwise loss of genetic diversity, genetic evidence for strong population bottlenecks, and increased population divergence. The endpoint population on Attu Island has extremely low diversity (H(E) = 0.18). Our study shows that sequential bottlenecks or founder events can have powerful genetic effects in reducing diversity, possibly leading to rapid evolutionary divergence.

Alaska↗
PubMed2005

Analysis of sex-linked sequences supports a new mammal species in Europe.

European mammals have been the focus of particularly detailed taxonomic studies by traditional morphological methods. However, DNA analyses have the potential to reveal additional, cryptic species. We describe two highly divergent evolutionary lineages within a small Eurasian mammal, the field vole (Microtus agrestis). We show that the two lineages can be detected not only with maternally (mitochondrial DNA), but also with paternally (Y chromosome) and biparentally (X chromosome) inherited DNA sequences. Reciprocal monophyly of all genealogies and their congruent geographical distributions is consistent with reproductive isolation. Our results suggest that the field vole should be reclassified as two separate species.

Animals↗
PubMed2005

The panmixia paradigm of eastern Pacific olive ridley turtles revised: consequences for their conservation and evolutionary biology.

Previous studies of the olive ridley Lepidochelys olivacea population structure in the tropical eastern Pacific have indicated the existence of a single panmictic population ranging from Costa Rica to Mexico. This information has been used to design specific management measures to conserve primary nesting beaches in Mexico. However, little is known about olive ridleys in the Baja California Peninsula, their northernmost reproductive limit, where recent observations have shown differences in nesting female behaviour and size of hatchlings relative to other continental rookeries. We used mtDNA control region sequences from 137 turtles from five continental and four peninsular nesting sites to determine whether such differences correspond to a genetic distinction of Baja California olive ridleys or to phenotypic plasticity associated with the extreme environmental nesting conditions of this region. We found that genetic diversity in peninsular turtles was significantly lower than in continental nesting colonies. Analysis of molecular variance revealed a significant population structure (Phi ST = 0.048, P = 0.006) with the inclusion of peninsular samples. Our results: (i) suggest that the observed phenotypic variation may be associated with genetic differentiation and reproductive isolation; (ii) support the recent colonization of the eastern Pacific by Lepidochelys; (iii) reveal genetic signatures of historical expansion and colonization events; and (iv) significantly challenge the notion of a single genetic and conservation unit of olive ridleys in the eastern Pacific. We conclude that conservation measures for olive ridleys in Mexico should be revised to grant peninsular beaches special attention.

Animals↗
PubMed2005

Phylogeography of pollinator-specific sexually deceptive Chiloglottis taxa (Orchidaceae): evidence for sympatric divergence?

Divergence in sexually deceptive orchids is thought to occur through shifts in the attraction of specific pollinators, a process that is mediated by changes in the floral odours that lure sexually excited male insects. We investigated the origin of reproductive isolation in a sexually deceptive species complex of Chiloglottis R.Br. (Orchidaceae: Diurideae). Two geographically separated montane regions in eastern Australia were sampled, each containing sympatric pairs of orchid taxa presently found under the name, Chiloglottis pluricallata. Behavioural tests confirmed at least three distinct orchid taxa that specifically attract different pollinators. An artificial crossing experiment among two taxa from one region demonstrated their interfertility, and confirmed isolation to be a function of pollinator attraction. A phylogeographic analysis using amplified fragment length polymorphisms (AFLPs) indicated that samples from each geographical region are most closely related, a pattern consistent with in situ or sympatric divergence. However, an extensive population genetic study on two taxa from one region failed to entirely reject the possibility of intertaxon gene flow. Although clear genetic differentiation of the taxa is evident in two out of three sites where both grow in direct sympatry, overall, the two taxa are not strongly distinguished by AFLP markers. The reconstruction of a simple bifurcating pattern of divergence may be confounded by a combination of contemporary population-level processes operating within each taxon, the retention of ancestral polymorphism or intertaxon gene flow.

Alleles↗
PubMed2005

Genetic structure of the whitefly Bemisia tabaci in the Asia-Pacific region revealed using microsatellite markers.

Bemisia tabaci (Hemiptera: Aleyrodidae) is a haplo-diploid species of sap-feeding insect belonging to the group of insects commonly known as whiteflies. From earlier analyses of mitochondrial and ribosomal markers it has been concluded that in the Asia-Pacific region there were three major indigenous races as well as a large collection of genotypes with no clear association with any race. This new study uses 15 microsatellite loci and demonstrates that the indigenous Asia-Pacific genotypes can be split into six genetic populations with little or no gene flow between them. These bare only superficial similarity to the mitochondrial and ribosomal defined races. Moreover, four of the six can be further split into two subpopulations that again show little evidence gene flow between them. While the patterns reflect a strong geographical structure, physical barriers alone cannot explain all the observed structure. Differential host-plant utilization explained some of the substructure, but could not explain the overall structure. The roles of mating interference and Wolbachia in developing the genetic structure are considered. The lack of gene flow between genetic populations and some subpopulations further suggests that the barriers were either sufficiently impermeable to immigration or that reproductive isolation and competitive interactions were sufficiently strong to prevent gene flow. If the latter is the case, it suggests that there may be as many as 10 morphologically indistinguishable species indigenous to the Asia-Pacific region.

Animals↗
PubMed2005

Hidden diversity and host specificity in cycliophorans: a phylogeographic analysis along the North Atlantic and Mediterranean Sea.

In order to elucidate the evolutionary history and the population structure of the members of the phylum Cycliophora, which live commensally on three species of lobsters, we studied sequence variation in the mitochondrial gene cyctochrome c oxidase subunit I. Overall 242 sequences from 16 locations on both coasts of the North Atlantic, including the North Sea and the Mediterranean, were analysed, revealing 28 haplotypes, with a maximum sequence divergence of 16.6%. Total genetic diversity was high (h = 0.8322, pi = 0.0898), as it was for the commensals on Homarus americanus (17 haplotypes, h = 0.7506, pi = 0.0504). However, it was low for commensals on Nephrops norvegicus (6 haplotypes, h = 0.3899, pi = 0.0035), and intermediate for cycliophorans on Homarus gammarus (5 haplotypes, h = 0.3020, pi = 0.0140). Although two of the host lobsters co-inhabit the coastal waters of Europe, a strong genetic structure (78.45% of the observed genetic variation) was detected among populations on all host species, indicating the existence of a reproductively isolated species on each lobster. In addition, genetic structure over long distances exists among populations on each host species. Such patterns can be explained by the limited dispersal ability of the cycliophoran chordoid larva. Demographic and phylogenetic analyses suggest old and possibly cryptic populations present on H. americanus and H. gammarus, while the latter may have experienced recent bottlenecks, perhaps during Pleistocene glaciations. Populations on N. norvegicus appear to be of recent origin.

Animals↗
PubMed2006

Speciation in reverse: morphological and genetic evidence of the collapse of a three-spined stickleback (Gasterosteus aculeatus) species pair.

Historically, six small lakes in southwestern British Columbia each contained a sympatric species pair of three-spined sticklebacks (Gasterosteus aculeatus). These pairs consisted of a 'benthic' and 'limnetic' species that had arisen postglacially and, in four of the lakes, independently. Sympatric sticklebacks are considered biological species because they are morphologically, ecologically and genetically distinct and because they are strongly reproductively isolated from one another. The restricted range of the species pairs places them at risk of extinction, and one of the pairs has gone extinct after the introduction of an exotic catfish. In another lake, Enos Lake, southeastern Vancouver Island, an earlier report suggested that its species pair is at risk from elevated levels of hybridization. We conducted a detailed morphological analysis, as well as genetic analysis of variation at five microsatellite loci for samples spanning a time frame of 1977 to 2002 to test the hypothesis that the pair in Enos Lake is collapsing into a hybrid swarm. Our morphological analysis showed a clear breakdown between benthics and limnetics. Bayesian model-based clustering indicated that two morphological clusters were evident in 1977 and 1988, which were replaced by 1997 by a single highly variable cluster. The most recent 2000 and 2002 samples confirm the breakdown. Microsatellite analysis corroborated the morphological results. Bayesian analyses of population structure in a sample collected in 1994 indicated two genetically distinct populations in Enos Lake, but only a single genetic population was evident in 1997, 2000, and 2002. In addition, genetic analyses of samples collected in 1997, 2000, and 2002 showed strong signals of 'hybrids'; they were genetically intermediate to parental genotypes. Our results support the idea that the Enos Lake species pair is collapsing into a hybrid swarm. Although the precise mechanism(s) responsible for elevated hybridization in the lake is unknown, the demise of the Enos Lake species pair follows the appearance of an exotic crayfish, Pascifasticus lenisculus, in the early 1990s.

Animals↗
PubMed2006

Parallelism in gene transcription among sympatric lake whitefish (Coregonus clupeaformis Mitchill) ecotypes.

Abstract We tested the hypothesis that phenotypic parallelism between dwarf and normal whitefish ecotypes (Coregonus clupeaformis, Salmonidae) is accompanied by parallelism in gene transcription. The most striking phenotypic differences between these forms implied energetic metabolism and swimming activity. Therefore, we predicted that genes showing parallel expression should mainly belong to functional groups associated with these phenotypes. Transcriptome profiles were obtained from white muscle by using a 3557 cDNA gene microarray developed for the Atlantic salmon (Salmo salar). A total of 1181 genes expressed in both lake populations hybridized on the array. Significant differential expression between ecotypes was detected for 134 (11.3%) and 195 (16.5%) gene clones in Cliff Lake and Indian Pond, respectively. Fifty-one genes (4.3%) showed parallel differential expression between lakes, among which 35 were expressed in opposite directions. Sixteen genes (1.35%) showed true parallelism of transcription, which mainly belonged to energetic metabolism and regulation of muscle contraction functional groups. Variance in expression was significantly reduced for these genes compared to those not showing directionality in parallelism of expression. Candidate genes associated with parallelism in swimming activity and energetic metabolism based on their level and variance in expression were identified. These results add to the growing evidence that parallel phenotypic evolution also involves parallelism at both the genotypic and regulatory level, which may at least partly be associated with genetic constraints. It also provides further evidence for the determinant role of divergent natural selection in driving phenotypic divergence, and perhaps reproductive isolation, in the adaptive radiation of lake whitefish. This study adds to a nascent field employing microarrays as powerful tools for investigating the evolutionary processes of adaptive divergence among natural populations.

Animals↗
PubMed2006

Estimating population structure under nonequilibrium conditions in a conservation context: continent-wide population genetics of the giant Amazon river turtle, Podocnemis expansa (Chelonia; Podocnemididae).

Giant Amazon river turtles, Podocnemis expansa, are indigenous to the Amazon, Orinoco, and Essequibo River basins, and are distributed across nearly the entire width of the South American continent. Although once common, their large size, high fecundity, and gregarious nesting, made P. expansa especially vulnerable to over-harvesting for eggs and meat. Populations have been severely reduced or extirpated in many areas throughout its range, and the species is now regulated under Appendix II of the Convention on International Trade in Endangered Species. Here, we analyse data from mitochondrial DNA sequence and multiple nuclear microsatellite markers with an array of complementary analytical methods. Results show that concordance from multiple data sets and analyses can provide a strong signal of population genetic structure that can be used to guide management. The general lack of phylogeographic structure but large differences in allele and haplotype frequencies among river basins is consistent with fragmented populations and female natal-river homing. Overall, the DNA data show that P. expansa populations lack a long history of genetic differentiation, but that each major tributary currently forms a semi-isolated reproductive population and should be managed accordingly.

Animals↗
PubMed2006

Patterns of genetic variation in the adaptive radiation of New World crossbills (Aves: Loxia).

Incipient species groups or young adaptive radiations such as crossbills (Aves: Loxia) present the opportunity to investigate directly the processes occurring during speciation. New World crossbills include white-winged crossbills (Loxia leucoptera), Hispaniolan crossbills (Loxia megaplaga), and red crossbills (Loxia curvirostra complex), the last of which is comprised of at least nine morphologically and vocally differentiated forms ('call types') where divergent natural selection for specialization on different conifer resources has been strongly implicated as driving diversification. Here we use amplified fragment length polymorphism (AFLP) markers to investigate patterns of genetic variation across populations, call types, and species of New World crossbills. Tree-based analyses using 440 AFLP loci reveal strongly supported clustering of the formally recognized species, but did not separate individuals from the eight call types in the red crossbill complex, consistent with recent divergence and ongoing gene flow. Analyses of genetic differentiation based on inferred allele frequency variation however, reveal subtle but significant levels of genetic differentiation among the different call types of the complex and indicate that between call-type differentiation is greater than that found among different geographic locations within call types. Interpreted in light of evidence of divergent natural selection and strong premating reproductive isolation, the observed genetic differentiation suggests restricted gene flow among sympatric call types consistent with the early stages of ecological speciation.

Adaptation, Biological↗
PubMed2006

When invaders meet locally adapted types: rapid moulding of hybrid zones between sculpins (Cottus, Pisces) in the Rhine system.

Hybrid zones are commonly studied to dissect the processes that drive divergence among lineages, which have incomplete barriers of reproduction. Most hybrid zones have existed for an extended time making inferences on the initial mode of formation difficult. It is a priori unclear how fast a nascent hybrid zone would form as a response to endogenous and exogenous factors. We have studied several hybrid zones between two lineages of sculpins (Cottus spp.), which emerged due to a recent range expansion of one of the lineages along the river Rhine in the early 1990s. Applying a dense sampling across two contact areas and using a highly informative set of 45 microsatellite markers we found pronounced genetic structure. Steep genetic clines suggest that strong selective forces have shaped the respective hybrid zones from the beginning. We find that the zones are coupled to ecological transitions from small streams to larger rivers. The width of these zones is much smaller than estimates of annual individual dispersal distances, as estimated outside of the hybrid zones. The pattern is apparently not strongly affected by pre- or postzygotic reproductive isolation because numerous backcross hybrids occur within the zones. This suggests that strong natural selection acts against immigrant genotypes. The study exemplifies how local adaptation can play a key role in preventing admixture in dependence of the ecological context.

Adaptation, Physiological↗
PubMed2006

Tracking factors modulating cytoplasmic incompatibilities in the mosquito Culex pipiens.

Wolbachia are maternally inherited endosymbiotic bacteria that infect many arthropod species and may induce cytoplasmic incompatibility (CI), resulting in abortive embryonic development. One Wolbachia host, Culex pipiens complex mosquitoes, displays high levels of variability in both CI crossing types (cytotypes) and DNA markers. We report here an analysis of 14 mosquito strains, containing 13 Wolbachia variants, and with 13 different cytotypes. Cytotypes were Wolbachia-dependent, as antibiotic treatment rendered all strains tested compatible. Cytotype distributions were independent of geographical distance between sampling sites and host subspecies, suggesting that Wolbachia does not promote a reproductive isolation depending on these parameters. Backcross analysis demonstrated a mild restoring effect of the nuclear genome, indicating that CI is mostly cytoplasmically determined for some crosses. No correlation was found between the phenotypic and genotypic variability of 16 WO prophage and transposon markers, except for the WO prophage Gp15 gene, which encodes a protein similar to a bacterial virulence factor. However, Gp15 is partially correlated with CI expression, suggesting that it could be just linked to a CI gene.

Animals↗
PubMed2006

Cryptic biodiversity and phylogeographical patterns in a snapping shrimp species complex.

Recent investigations suggest that marine biodiversity may be much higher than earlier estimates, and an important hidden source of diversity in marine systems is the phenomenon of cryptic species complexes. Such complexes are informative models for research into the evolutionary processes that govern species compositions of marine fauna. The snapping shrimp genera Alpheus and Synalpheus are known to harbour large numbers of cryptic species; here, I characterize the genetic structure of the Alpheus armillatus species complex in the northern Caribbean, west Atlantic, and Gulf of Mexico using mitochondrial and nuclear sequence data. Over this geographical region, the complex harbours at least three lineages that are probable reproductively isolated species; all major lineages diverged subsequent to the close of the Isthmus of Panama. Only one lineage was present in the Gulf of Mexico, whereas outside the Gulf of Mexico there was no clear tendency for lineage dominance by geographical region, as most sites were populated by shrimp from at least two lineages. However, within each lineage, there was strong evidence of population genetic differentiation between geographical regions. All lineages showed strong signals of demographic expansion, and one lineage showed sharply reduced genetic diversity, suggestive of past population bottlenecks or recently founded populations with low gene flow from other sites. These results show that evolutionary processes leading to divergence and speciation have been common and recent in the snapping shrimp, and suggest that connectivity among shrimp populations may be limited.

Americas↗