1,721,132 research outputs found
Progressive colonization and restricted gene flow shape island-dependent population structure in Galapagos marine iguanas (Amblyrhynchus cristatus)
Full text linkSteinfartz S, Glaberman S, Lanterbecq D, et al. Progressive colonization and restricted gene flow shape island-dependent population structure in Galapagos marine iguanas (Amblyrhynchus cristatus). BMC Evolutionary biology. 2009;9(1):297.Background: Marine iguanas (Amblyrhynchus cristatus) inhabit the coastlines of large and small islands throughout the Galapagos archipelago, providing a rich system to study the spatial and temporal factors influencing the phylogeographic distribution and population structure of a species. Here, we analyze the microevolution of marine iguanas using the complete mitochondrial control region (CR) as well as 13 microsatellite loci representing more than 1200 individuals from 13 islands. Results: CR data show that marine iguanas occupy three general clades: one that is widely distributed across the northern archipelago, and likely spread from east to west by way of the South Equatorial current, a second that is found mostly on the older eastern and central islands, and a third that is limited to the younger northern and western islands. Generally, the CR haplotype distribution pattern supports the colonization of the archipelago from the older, eastern islands to the younger, western islands. However, there are also signatures of recurrent, historical gene flow between islands after population establishment. Bayesian cluster analysis of microsatellite genotypes indicates the existence of twenty distinct genetic clusters generally following a one-cluster-per-island pattern. However, two well-differentiated clusters were found on the easternmost island of San Cristobal, while nine distinct and highly intermixed clusters were found on youngest, westernmost islands of Isabela and Fernandina. High mtDNA and microsatellite genetic diversity were observed for populations on Isabela and Fernandina that may be the result of a recent population expansion and founder events from multiple sources. Conclusions: While a past genetic study based on pure FST analysis suggested that marine iguana populations display high levels of nuclear ( but not mitochondrial) gene flow due to male-biased dispersal, the results of our sex-biased dispersal tests and the finding of strong genetic differentiation between islands do not support this view. Therefore, our study is a nice example of how recently developed analytical tools such as Bayesian clustering analysis and DNA sequence-based demographic analyses can overcome potential biases introduced by simply relying on FST estimates from markers with different inheritance patterns
Phylogeography and molecular rates of subterranean aquatic Stenasellid Isopod within a peri-Tyrrhenian distribution.
No full textThe subterranean Isopods belonging to the genus Stenasellus have an interesting disjunct distribution in the peri-Tyrrhenian area with morphologically closely related taxa occurring in Sardinia, Corsica, Tuscany and in the Pyrenees phreatic and interstitial waters. Because the dispersal capacities of these organisms are limited, their distribution has been associated traditionally with the tectonic events leading to the separation of the Sardinia-Corsica microplate from the Pyrenees and its subsequent movement towards the Italian peninsula. We sequenced a fragment of the mtDNA cytochrome oxidase I gene (COI) for multiple populations of the S. racovitzai species-group (Corsica, Sardinia, Tuscany) and S. virei (Pyrenees). We found that multiple phylogenetic analyses always gave the same topology, which is consistent with the genetic relations found using allozyme data, and with the palaeogeography of the area. The molecular data suggest that a combination of vicariance and dispersal events explain most effectively the present distribution pattern of these organisms. We also calculated COI rates and calibrated them against absolute time, taking advantage of the availability of two geologically based time estimates. Rates on all substitutions are similar to those published for other crustaceans for the same COI fragment, including taxonomically and ecologically distant groups. Rates on third codon positions or on transversions are generally lower than those found in other crustaceans
Short report: A new polymerase chain reaction-restriction fragment length polymorphism method to identify Anopheles arabiensis from An. gambiae and its two molecular forms from degraded DNA templates or museum samples.
No full textGenetic differentiation in the African malaria vector, Anopheles gambiae s.s., and the problem of taxonomic status
No full textOf the seven recognized species of the Anopheles gambiae complex, A. gambiae s.s. is the most widespread and most important vector of malaria. It is becoming clear that, in parts of West Africa, this nominal species is not a single panmictic unit. We found that the internal transcribed spacer (ITS) of the X-linked rDNA has two distinct sequences with three fixed nucleotide differences; we detected no heterozygotes at these three sites, even in areas of sympatry of the two ITS types. The intergenic spacer (IGS) of this region also displays two distinct sequences that are in almost complete linkage disequilibrium with the distinct ITS alleles. We have designated these two types as S/type I and M/type II. These rDNA types correspond at least partly to the previously recognized chromosomal forms. Here we expand the geographic range of sampling to 251 individuals from 38 populations. Outside of West Africa, a single rDNA type, S/type 1, corresponds to the Savanna chromosomal form. In West Africa, both types are often found in a single local sample. To understand if these findings might be due to unusual behavior of the rDNA region, we sequenced the same region for 46 A. arabiensis, a sympatric sibling species. No such distinct discontinuity was observed for this species. Autosomal inversions in one chromosome arm (2R), an insecticide resistance gene on 2L, and this single X-linked region indicate at least two genetically differentiated subpopulations of A. gambiae. Yet, rather extensive studies of other regions of the genome have failed to reveal genetic discontinuity. Evidently, incomplete genetic isolation exists within this single nominal species
Sequence analysis of Intron I of the voltage gated Sodium channel gene in the Anopheles gambiae complex.
No full textDivergenza evolutiva nelle tartarughe delle Galápagos
No full textLe tartarughe delle Galápagos rappresentano uno dei molteplici endemismi che hanno avuto origine nell'arcipelago delle Galapagos, il cui nome si origina dalla forma a sella del carapace di questi animali. Nonostante la loro notorietà, le origini evolutive di queste tartarughe, la storia della loro colonizzazione dell'arcipelago, ed i livelli di divergenza tra le varie popolazioni sono ancora incerti. Reperti fossili testimoniano che tartarughe giganti erano diffuse in passato in tutti i continenti (tranne Australia ed Antartide). In tempi storici questi giganti sono sopravvissuti solo in remote isole oceaniche (Mascarene, Seychelles, e Galápagos). La popolazione nelle Mascarene si è estinta nel 1804. Nelle Seychelles una popolazione sopravvive nell'atollo di Aldabra. Solo nelle Galápagos queste tartarughe persistono con popolazioni distinte in diverse località. Purtroppo anche nelle Galápagos la maggioranza delle sottospecie è a rischio di estinzione (tre delle quindici sottospecie descritte sono estinte nello scorso secolo). In collaborazione con Jeff Powell (Yale University), James Gibbs (SUNY University) e Michel Milinkovitch (University of Bruxelles) abbiamo intrapreso un progetto di studio a lungo termine sui livelli e la dinamica di variazione genetica esistenti in questa specie. In questa sede
presentiamo i dati di sequenza a livello del DNA mitocondriale e nucleare. Abbiamo sequenziato regioni multiple di DNA mitocondriale (mtDNA) e nucleare per produrre una filogenesi molecolare del gruppo, individuare la specie continentale a loro più vicina, analizzare il livello di differenziamento genetico tra le varie sottospecie e confrontarlo con il corrispondente differenziamento morfologico. Dai quattro ai venti individui di ciascuna sottospecie sono stati sequenziati per complessivamente 8Kb di frammenti di DNA sia nucleare che mitocondriale.
Come outgroups abbiamo utilizzato le tre specie sudamericane di Geochelone (G. carbonaria, G. denticulata, e G. chilensis) ed una specie congenerica africana, G. pardalis. I dati molecolari indicano chiaramente che la specie vivente più vicina alle tartarughe delle Galapagos è Geochelone chilensis. All'interno dell'arcipelago i dati sul DNA mitocondriale permettono di identificare gli individui di ciascuna isola e permettono di interpretare la dinamica di colonizzazione delle isole. Studi basati su analisi morfologiche e di allozimi non consentivano la discriminazione delle diverse sottospecie. Oltre allo studio della variazione genetica a livello mitocondriale sono state sequenziate sei regioni nucleari teoricamente ad alto tasso evolutivo (5 introni e la regione ITS del DNA ribosomale) per lo stesso gruppo di individui. Livelli e dinamiche di variabilità genetica in entrambe le regioni sono state confrontate e discusse, con particolare riferimento alla loro utilità per la discriminazione di taxa di origine recente. I siti diagnostici per ciascuna sottospecie sono stati inoltre utilizzati per identificare la linea paterna e materna di individui in cattività di origine incerta. Questo risultato è di notevole importanza pratica per la gestione sia di popolazioni naturali che in cattività di questa specie
Attempts to molecularly distinguish cryptic taxa in Anopheles gambiae s.s.
No full textAnalyses of inversions in polytene chromosomes indicate that, in West Africa, Anopheles gambiae (sensu stricto) may be a complex of more than a single taxonomic unit, and these units have been called chromosomal forms. In order to determine whether this genetic discontinuity extends to the rest of the genome, as would be expected if reproductive isolation exists, we have sequenced several regions of both the nuclear and mitochondrial genomes. With one exception, we were unable to identify any nucleotide sites that differentiate the chromosomal forms. The exception was the internal transcribed spacer (ITS) of the ribosomal DNA (rDNA). Three sites in this region distinguish Mopti chromosomal form from Savanna and Bamako in Mall and Burkina Faso. However, outside these two countries, the association between chromosomal form and rDNA type does not always hold. Together with the variants in the rDNA intergenic spacer (IGS) described in the accompanying papers (della Torre et al., 2001; Favia et al., 2001), we can recognize two major types of rDNA, Type I and Type II (corresponding to molecular forms S and M in della Torre et al,, 2001). Type I is widespread in West Africa and is the only type found outside of West Africa (i.e. Tanzania and Madagascar). Type II is confined to West Africa,We were unable to detect any heterozygosity for the ITS types even in five collections containing both types. A sample from the island of Sao Tome could not be classified into either Type I or Type II as the rDNA had characteristics of both. In general, our results confirm that An. gambiae is not a single pan-mictic unit, but exactly how to define any new taxa remains problematic. Finally, we have found minor variants of the major rDNA types fixed in local populations; contrary to most previous studies, this suggests restricted gene flow among populations of this species
Acclimation of the European sea bass to freshwater: Monitoring genetic changes by RAPD polymerase chain reaction to detect DNA polymorphisms
No full textWe investigated the use of the polymerase chain reaction (PCR) and the associated random amplification of polymorphic DNA (RAPD) technique to study variation in samples of the sea bass, Dicentrarchus labrax, before and after acclimation to freshwater. Acclimation trials were repeated twice, in 1989 and 1990, for two samples originating from the same broodstock (individuals from different localities along the Italian coasts), with overall mortality rates averaging 94 and 75% in the 2 yr, respectively. Analyses are based on 126 polymorphic RAPD markers, scored in at least 39 individuals for each of the starting and acclimated samples in both years. Analysis of RAPD patterns revealed high levels of DNA polymorphism in both 1989 and 1990 starting samples. The acclimated samples maintained similar polymorphism levels. Shifts in marker frequencies between starting and acclimated samples occurred in both years. A correspondence analysis carried out on multimarker individual profiles suggests that the two starting samples resulted from uneven sampling of the same heterogenous broodstock. This analysis clearly separates RAPD phenotypes from starting and acclimated samples in both years and identifies the RAPD markers responsible for such displacement. Patterns of RAPD varia tion are compared with previous allozymic studies carried out on the same samples. A major difference between the two studies was the number of markers available. Fewer allozyme loci were studied than were RAPD markers. The cause of repeated shifts for allozyme alleles in replicate experiments were almost certainly due to selection, while statistical chance could explain the repeated shift of only one out of more than 100 RAPD markers. We have shown that RAPD analysis, if carried out carefully, is quite reproducible and sensitive enough to reveal high levels of variation among individuals from the same broodstock. A major drawback of this approach is the still unclear inheritance patterns of RAPD polymorphisms. The use of multivariate analyses is suggested as a possible alternative to traditional population genetics techniques to analyze patterns of variation in the absence of a precise genetic interpretation
Cytochrome b sequence divergence in the European sea bass (Dicentrarchus labrax) and phylogenetic relationships among some Perciformes species
No full textThe entire cytochrome b (cyt b) gene has been sequenced in eight Mediterranean populations of the European sea bass, Dicentrarchus labrax and in one of D. punctatus. Our data indicate that both eastern (Greece and Egypt) and northwestern (French coast) populations of D. labrax were genetically differentiated from the Tyrrhenian ones, which were nearly indistinguishable from each other at the cyt b level. The D. labrax population from the Atlantic coast (Portugal) was genetically quite distinct from all the Mediterranean ones. These results strongly confirm the conclusions from previous studies where the same populations were screened for allozymes, random amplified polymorphic DNA (RAPD) and mitochondrial DNA (mtDNA) D-loop variation. Seven other species of Perciformes belonging to five different families (Sparidae, Serranidae, Carangidae, Pomatomidae, Sciaenidae) were sequenced to explore the usefulness of the cyt b gene for inferring evolutionary relationships at different hierarchical levels. The data were analysed together with other published cyt b sequences from Perciformes fishes. Our data suggest thar the superfamily Percoidea is not monophyletic. At the family level, the Sparidae and Moronidae seem to be monophyletic. The evolutionary relationships among families were not resolved. Possible causes for this lack of resolution are discussed
Origin and evolutionary relationships of giant Galapagos tortoises
Full text linkPerhaps the most enduring debate in reptile systematics has involved the giant Galapagos tortoises (Geochelone nigra), whose origins and systematic relationships captivated Charles Darwin and remain unresolved to this day. Here we report a phylogenetic reconstruction based on mitochondrial DNA sequences from Galapagos tortoises and Geochelone from mainland South America and Africa. The closest living relative to the Galapagos tortoise is not among the larger-bodied tortoises of South America but is the relatively small-bodied Geochelone chilensis, or Chaco tortoise. The split between G. chilensis and the Galapagos lineage probably occurred 6 to 12 million years ago, before the origin of the oldest extant Galapagos island. Our data suggest that the four named southern subspecies on the largest island, Isabela, are not distinct genetic units, whereas a genetically distinct northernmost Isabela subspecies is probably the result of a separate colonization. Most unexpectedly, the lone survivor of the abingdoni subspecies from Pinta Island ("Lonesome George") is very closely related to tortoises from San Cristobal and Espanola, the islands farthest from the island of Pinta, To rule out a possible recent transplant of Lonesome George, we sequenced DNA from three tortoises collected on Pinta in 1906, They have sequences identical to Lonesome George, consistent with his being the last survivor of his subspecies. This finding may provide guidance in finding a mate for Lonesome George, who so far has failed to reproduce
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