EVOLUTION, Issue 5 2004
M. Alice Pinto
Abstract The invasion of Africanized honeybees (Apis mellifera L.) in the Americas provides a window of opportunity to study the dynamics of secondary contact of subspecies of bees that evolved in allopatry in ecologically distinctive habitats of the Old World. We report here the results of an 11-year mitochondrial DNA survey of a feral honeybee population from southern United States (Texas). The mitochondrial haplotype (mitotype) frequencies changed radically during the 11-year study period. Prior to immigration of Africanized honeybees, the resident population was essentially of eastern and western European maternal ancestry. Three years after detection of the first Africanized swarm there was a mitotype turnover in the population from predominantly eastern European to predominantly A. m. scutellata (ancestor of Africanized honeybees). This remarkable change in the mitotype composition coincided with arrival of the parasitic mite Varroa destructor, which was likely responsible for severe losses experienced by colonies of European ancestry. From 1997 onward the population stabilized with most colonies of A. m. scutellata maternal origin. [source]

HISTORIC CYCLES OF FRAGMENTATION AND EXPANSION IN PARNASSIUS SMINTHEUS (PAPILIONIDAE) INFERRED USING MITOCHONDRIAL DNA

EVOLUTION, Issue 1 2004
Eric G. DeChaine
Abstract Climate oscillations of the Quaternary drove the repeated expansion and contraction of ecosystems. Alpine organisms were probably isolated in sky island refugia during warm interglacials, such as now, and expanded their range by migrating down-slope during glacial periods. We used population genetic and phylogenetic approaches to infer how paleoclimatic events influenced the distribution of genetic variation in the predominantly alpine butterfly Parnassius smintheus. We sequenced a 789 bp region of cytochrome oxidase I for 385 individuals from 20 locations throughout the Rocky Mountains, ranging from southern Colorado to northern Montana. Analyses revealed at lease two centers of diversity in the northern and southern Rocky Mountains and strong population structure. Nested clade analysis suggested that the species experienced repeated cycles of population expansion and fragmentation. The estimated ages of these events, assuming a molecular clock, corresponded with paleoclimatic data on habitat expansion and contraction over the past 400,000 years. We propose that alpine butterflies persisted in an archipelago of isolated sky islands during interglacials and that populations expanded and became more connected during cold glacial periods. An archipelago model implies that the effects of genetic drift and selection varied among populations, depending on their latitude, area, and local environment. Alpine organisms are sensitive indicators of climate change and their history can be used to predict how high-elevation ecosystems might respond to further climate warming. [source]

DISAPPEARANCE OF MALE MITOCHONDRIAL DNA AFTER THE FOUR-CELL STAGE IN SPOROPHYTES OF THE ISOGAMOUS BROWN ALGA SCYTOSIPHON LOMENTARIA (SCYTOSIPHONACEAE, PHAEOPHYCEAE),

JOURNAL OF PHYCOLOGY, Issue 1 2010
Kei Kimura
Mitochondrial DNA (mtDNA) of the isogamous brown alga Scytosiphon lomentaria (Lyngb.) Link is inherited maternally. We used molecular biological and morphological analyses to investigate the fate of male mitochondria. Ultrastructural observations showed that the number of 25 mitochondria in a zygote coincided with the number of mitochondria derived from male and female gametes. This number remained almost constant during the first cell division. Strain-specific PCR in single germlings suggested that mtDNA derived from the female gamete remained in the germling during development, while the male mtDNA gradually and selectively disappeared after the four-cell stage. One week after fertilization, male mtDNA had disappeared in sporophytic cells. Using bisulfite DNA modification and methylation mapping assays, we found that the degree of methylation on three analyzed sites of mtDNA was not different between male and female gametes, suggesting that maternal inheritance of mtDNA is not defined by its methylation. This study indicates that the mechanism of selective elimination of male mtDNA is present in each cell of a four-celled sporophyte and that it does not depend on different degrees of DNA methylation between male and female mtDNA. [source]

PATERNAL LEAKAGE OF MITOCHONDRIAL DNA IN A FUCUS (PHAEOPHYCEAE) HYBRID ZONE,

JOURNAL OF PHYCOLOGY, Issue 3 2009
Galice Hoarau
Eukaryotic mitochondria are mostly uniparentally (maternally) inherited, although mtDNA heteroplasmy has been reported in all major lineages. Heteroplasmy, the presence of more than one mitochondrial genome in an individual, can arise from recombination, point mutations, or by occasional transmission of the paternal mtDNA (=paternal leakage). Here, we report the first evidence of mtDNA paternal leakage in brown algae. In Denmark, where Fucus serratus L. and Fucus evanescens C. Agardh have hybridized for years, we found eight introgressed individuals that possessed the very distinct haplotypes of each parental species. The finding of heteroplasmy in individuals resulting from several generations of backcrosses suggests that paternal leakage occurred in earlier generations and has persisted through several meiotic bottlenecks. [source]

Amplifying Nuclear and Mitochondrial DNA from African Elephant Ivory: a Tool for Monitoring the Ivory Trade

CONSERVATION BIOLOGY, Issue 6 2003
KENINE E. COMSTOCK
cacería furtiva; elefante africano; Loxodonta africana; marfil; microsatélites Abstract: The ability to extract DNA from ivory provides the basis for genetically tracking the origin of poached ivory and thus has important implications for elephant conservation and management. We describe a method to isolate and amplify both genomic and mitochondrial DNA from African elephant ivory that requires very small amounts of ivory taken from any location on the tusk. We pulverized ivory and isolated DNA with a modified QIAamp kit. Ivory as old as 10 to 20 years, stored at ambient conditions, was amenable to DNA isolation with this method. The isolated DNA was robustly amplified at 16 elephant microsatellite loci and two mitochondrial DNA loci. This method has important applications for the forensic analysis of poached African elephant ivory. It enables determination of where stronger antipoaching efforts are needed and provides the basis for monitoring the extent of the trade as well as the consequences of future international trade decisions. Resumen: La habilidad para extraer ADN del marfil proporciona la base para rastrear genéticamente el origen de marfil furtivo y por tanto tiene implicaciones importantes para la conservación y el manejo de elefantes. Describimos un método para aislar y amplificar ADN genómico y mitocondrial de marfil de elefante africano que requiere de cantidades muy pequeñas de marfil tomadas de cualquier parte del colmillo. Pulverizamos el marfil y aislamos el ADN con un equipo QIAamp modificado. Con este método, fue posible aislar el ADN de marfil de 10 a 20 años, conservado en condiciones ambientales. El ADN aislado fue amplificado robustamente en 16 loci microsatélite y dos loci de ADN mitocondrial. Este método tiene aplicaciones importantes para el análisis forense de marfil de elefantes africanos cazados furtivamente. Permite la identificación de sitios donde se requieren mayores esfuerzos para combatir la cacería furtiva y proporciona la base para monitorear la extensión del comercio así como las consecuencias de decisiones futuras de comercio internacional. [source]

RIVER CAPTURE, RANGE EXPANSION, AND CLADOGENESIS: THE GENETIC SIGNATURE OF FRESHWATER VICARIANCE

EVOLUTION, Issue 5 2006
C. P. Burridge
Abstract River capture is potentially a key geomorphological driver of range expansion and cladogenesis in freshwater-limited taxa. While previous studies of freshwater fish, in particular, have indicated strong relationships between historical river connections and phylogeographic pattern, their analyses have been restricted to single taxa and geological hypotheses were typically constructed a posteriori. Here we assess the broader significance of river capture among taxa by testing multiple species for the genetic signature of a recent river capture event in New Zealand. During the Quaternary an upper tributary of the Clarence River system was diverted into the headwaters of the Wairau River catchment. Mitochondrial DNA (control region and cytochrome b) sequencing of two native galaxiid fishes (Galaxias vulgaris and Galaxias divergens) supports headwater exchange: populations from the Clarence and Wairau Rivers are closely related sister-groups, whereas samples from the geographically intermediate Awatere River are genetically divergent. The upland bully Gobiomorphus breviceps (Eleotridae), in contrast, lacks a genetic signature of the capture event. We hypothesize that there is an increased likelihood of observing genetic signatures from river capture events when they facilitate range expansion, as is inferred for the two galaxiid taxa studied here. When river capture merely translocates genetic lineages among established populations, by contrast, we suggest that the genetic signature of capture is less likely to be retained, as might be inferred for G. breviceps. Rates of molecular evolution calibrated against this recent event were elevated relative to traditional estimates, consistent with the contribution of polymorphisms to branch lengths at shallow phylogenetic levels prior to fixation by purifying selection and drift. [source]

THE HISTORICAL BIOGEOGRAPHY OF TWO CARIBBEAN BUTTERFLIES (LEPIDOPTERA: HELICONIIDAE) AS INFERRED FROM GENETIC VARIATION AT MULTIPLE LOCI

EVOLUTION, Issue 3 2002
Neil Davies
Abstract Mitochondrial DNA and allozyme variation was examined in populations of two Neotropical butterflies, Heliconius charithonia and Dryas iulia. On the mainland, both species showed evidence of considerable gene flow over huge distances. The island populations, however, revealed significant genetic divergence across some, but not all, ocean passages. Despite the phylogenetic relatedness and broadly similar ecologies of these two butterflies, their intraspecific biogeography clearly differed. Phylogenetic analyses of mitochondrial DNA sequences revealed that populations of D. iulia north of St. Vincent are monophyletic and were probably derived from South America. By contrast, the Jamaican subspecies of H. charithonia rendered West Indian H. charithonia polyphyletic with respect to the mainland populations; thus, H. charithonia seems to have colonized the Greater Antilles on at least two separate occasions from Central America. Colonization velocity does not correlate with subsequent levels of gene flow in either species. Even where range expansion seems to have been instantaneous on a geological timescale, significant allele frequency differences at allozyme loci demonstrate that gene flow is severely curtailed across narrow ocean passages. Stochastic extinction, rapid (re)colonization, but low gene flow probably explain why, in the same species, some islands support genetically distinct and nonexpanding populations, while nearby a single lineage is distributed across several islands. Despite the differences, some common biogeographic patterns were evident between these butterflies and other West Indian taxa; such congruence suggests that intraspecific evolution in the West Indies has been somewhat constrained by earth history events, such as changes in sea level. [source]

Association between mitochondrial DNA 10398A>G polymorphism and the volume of amygdala

GENES, BRAIN AND BEHAVIOR, Issue 6 2008
H. Yamasue
Mitochondrial calcium regulation plays a number of important roles in neurons. Mitochondrial DNA (mtDNA) is highly polymorphic, and its interindividual variation is associated with various neuropsychiatric diseases and mental functions. An mtDNA polymorphism, 10398A>G, was reported to affect mitochondrial calcium regulation. Volume of hippocampus and amygdala is reportedly associated with various mental disorders and mental functions and is regarded as an endophenotype of mental disorders. The present study investigated the relationship between the mtDNA 10398A>G polymorphism and the volume of hippocampus and amygdala in 118 right-handed healthy subjects. The brain morphometry using magnetic resonance images employed both manual tracing volumetry in the native space and voxel-based morphometry (VBM) in the spatially normalized space. Amygdala volume was found to be significantly larger in healthy subjects with 10398A than in those with 10398G by manual tracing, which was confirmed by the VBM. Brain volumes in the other gray matter regions and all white matter regions showed no significant differences associated with the polymorphism. These provocative findings might provide a clue to the complex relationship between mtDNA, brain structure and mental disorders. [source]

Phylogeography of the introduced species Rattus rattus in the western Indian Ocean, with special emphasis on the colonization history of Madagascar

JOURNAL OF BIOGEOGRAPHY, Issue 3 2010
Charlotte Tollenaere
Abstract Aim, To describe the phylogeographic patterns of the black rat, Rattus rattus, from islands in the western Indian Ocean where the species has been introduced (Madagascar and the neighbouring islands of Réunion, Mayotte and Grande Comore), in comparison with the postulated source area (India). Location, Western Indian Ocean: India, Arabian Peninsula, East Africa and the islands of Madagascar, Réunion, Grande Comore and Mayotte. Methods, Mitochondrial DNA (cytochrome b, tRNA and D-loop, 1762 bp) was sequenced for 71 individuals from 11 countries in the western Indian Ocean. A partial D-loop (419 bp) was also sequenced for eight populations from Madagascar (97 individuals), which were analysed in addition to six previously published populations from southern Madagascar. Results, Haplotypes from India and the Arabian Peninsula occupied a basal position in the phylogenetic tree, whereas those from islands were distributed in different monophyletic clusters: Madagascar grouped with Mayotte, while Réunion and Grand Comore were present in two other separate groups. The only exception was one individual from Madagascar (out of 190) carrying a haplotype that clustered with those from Réunion and South Africa. ,Isolation with migration' simulations favoured a model with no recurrent migration between Oman and Madagascar. Mismatch distribution analyses dated the expansion of Malagasy populations on a time-scale compatible with human colonization history. Higher haplotype diversity and older expansion times were found on the east coast of Madagascar compared with the central highlands. Main conclusions, Phylogeographic patterns supported the hypothesis of human-mediated colonization of R. rattus from source populations in either the native area (India) or anciently colonized regions (the Arabian Peninsula) to islands of the western Indian Ocean. Despite their proximity, each island has a distinct colonization history. Independent colonization events may have occurred simultaneously in Madagascar and Grande Comore, whereas Mayotte would have been colonized from Madagascar. Réunion was colonized independently, presumably from Europe. Malagasy populations may have originated from a single successful colonization event, followed by rapid expansion, first in coastal zones and then in the central highlands. The congruence of the observed phylogeographic pattern with human colonization events and pathways supports the potential relevance of the black rat in tracing human history. [source]

ORIGINAL ARTICLE: Freshwater paths across the ocean: molecular phylogeny of the frog Ptychadena newtoni gives insights into amphibian colonization of oceanic islands

JOURNAL OF BIOGEOGRAPHY, Issue 1 2007
G. John Measey
Abstract Aim, Amphibians are a model group for studies of the biogeographical origins of salt-intolerant taxa on oceanic islands. We used the Gulf of Guinea islands to explore the biogeographical origins of island endemism of one species of frog, and used this to gain insights into potential colonization mechanisms. Location, São Tomé and Príncipe, two of the four major islands in the Gulf of Guinea, West Africa, are truly oceanic and have an exceptionally high biodiversity. Methods, Mitochondrial DNA is used to test the endemic status of a frog from São Tomé and compare it with congeneric taxa from tropical Africa. Existing data on surface currents, surface salinity, atmospheric circulation and bird migration in the Gulf of Guinea are summarized to address hypotheses concerning colonization mechanisms. Results, The endemic status of Ptychadena newtoni (Bocage) is supported here by mitochondrial DNA sequences, and analysis of this and other molecular data indicates that an East African species close to Ptychadena mascareniensis (Duméril and Bibron) is its nearest relative. We refute the possibility that this population was anthropogenically introduced, in favour of a natural dispersal mechanism. Main conclusions, With six endemic frogs and one caecilian, the Gulf of Guinea islands harbour a diverse amphibian fauna. Five of these species appear to have their closest relatives in East Africa. Insufficient evidence exists for transportation by storms, birds or rafts alone. However, we propose a synergy of rafting, favourable surface currents and a reduction in salinity of surface waters. Catastrophic events, or wet periods in climatic history, could allow freshwater paths to open far enough to enable continental flora and fauna to reach these and other isolated oceanic islands. [source]

Age-associated mitochondrial DNA mutations lead to small but significant changes in cell proliferation and apoptosis in human colonic crypts

AGING CELL, Issue 1 2010
Marco Nooteboom
Summary Mitochondrial DNA (mtDNA) mutations are a cause of human disease and are proposed to have a role in human aging. Clonally expanded mtDNA point mutations have been detected in replicating tissues and have been shown to cause respiratory chain (RC) defects. The effect of these mutations on other cellular functions has not been established. Here, we investigate the consequences of RC deficiency on human colonic epithelial stem cells and their progeny in elderly individuals. We show for the first time in aging human tissue that RC deficiency attenuates cell proliferation and increases apoptosis in the progeny of RC deficient stem cells, leading to decreased crypt cell population. [source]

Quantification of mitochondrial DNA mutation load

AGING CELL, Issue 5 2009
Laura C. Greaves
Summary Mitochondrial DNA (mtDNA) mutations are an important cause of genetic disease and have been proposed to play a role in the ageing process. Quantification of total mtDNA mutation load in ageing tissues is difficult as mutational events are rare in a background of wild-type molecules, and detection of individual mutated molecules is beyond the sensitivity of most sequencing based techniques. The methods currently most commonly used to document the incidence of mtDNA point mutations in ageing include post-PCR cloning, single-molecule PCR and the random mutation capture assay. The mtDNA mutation load obtained by these different techniques varies by orders of magnitude, but direct comparison of the three techniques on the same ageing human tissue has not been performed. We assess the procedures and practicalities involved in each of these three assays and discuss the results obtained by investigation of mutation loads in colonic mucosal biopsies from ten human subjects. [source]

Mitochondrial DNA in Atherina (Teleostei, Atheriniformes): differential distribution of an intergenic spacer in lagoon and marine forms of Atherina boyeri

JOURNAL OF FISH BIOLOGY, Issue 5 2008
V. MILANA
The big-scale sand smelt Atherina boyeri lives in fresh water, brackish water and sea water of the western Atlantic Ocean and Mediterranean Sea. Previous studies concerning distribution, biometric characters and genetic molecular markers have suggested the possible existence of two or even three different groups or species of sand smelt, one ,lagoon' type and one (or two , punctuated and non-punctuated on the flanks) ,marine' type. In this study, the presence and the localization of an insertion was described, c. 200 bp in length, in the mtDNA of the lagoon and marine punctuated specimens of A. boyeri and its absence in the marine non-punctuated specimens, as well as in other two congeneric species, Atherina hepsetus and Atherina presbyter, and in the atheriniform Menidia menidia. The intergenic spacer is located between the tRNAGlu and cytochrome b (cyt b) genes and shares a c. 50% sequence similarity with cyt b. The distribution and the features of the intergenic spacer suggest that it might have originated from an event of gene duplication, which involved the cyt b gene (or, more likely, a part of it) and which took place in the common ancestor of the lagoon and the marine punctuated specimens. The data obtained therefore support the hypothesis of the existence of three cryptic and, or sibling species within the A. boyeri taxon and provide a genetic molecular marker to distinguish them. [source]

Heteroplasmy in Hair: Study of Mitochondrial DNA Third Hypervariable Region in Hair and Blood Samples,

JOURNAL OF FORENSIC SCIENCES, Issue 3 2010
Greiciane G. Paneto M.Sc.
Abstract:, Mitochondrial DNA (mtDNA) analysis has proved useful for forensic identification especially in cases where nuclear DNA is not available, such as with hair evidence. Heteroplasmy, the presence of more than one type of mtDNA in one individual, is a common situation often reported in the first and second mtDNA hypervariable regions (HV1/HV2), particularly in hair samples. However, there is no data about heteroplasmy frequency in the third mtDNA hypervariable region (HV3). To investigate possible heteroplasmy hotspots, HV3 from hair and blood samples of 100 individuals were sequenced and compared. No point heteroplasmy was observed, but length heteroplasmy was, both in C-stretch and CA repeat. To observe which CA "alleles" were present in each tissue, PCR products were cloned and re-sequenced. However, no variation among CA alleles was observed. Regarding forensic practice, we conclude that point heteroplasmy in HV3 is not as frequent as in the HV1/HV2. [source]

The Effects of Chemical and Heat Maceration Techniques on the Recovery of Nuclear and Mitochondrial DNA from Bone,

JOURNAL OF FORENSIC SCIENCES, Issue 1 2006
Dawnie Wolfe Steadman Ph.D.
ABSTRACT: Forensic anthropologists use a number of maceration techniques to facilitate skeletal analysis of personal identity and trauma, but they may unwittingly eliminate valuable DNA evidence in the process. This study evaluated the effect of 10 maceration methods on gross bone structure and the preservation of DNA in ribs of 12 pigs (Sus scrofa). A scoring system was applied to evaluate the ease of maceration and resulting bone quality while DNA purity was quantified by optical densitometry analysis, followed by polymerase chain reaction (PCR) amplification of three mitochondrial and three nuclear loci. The results demonstrated that while mitochondrial DNA could be amplified for all experiments, cleaning treatments using bleach, hydrogen peroxide, ethylenediaminetetraacetic acid/papain, room temperature water and detergent/sodium carbonate followed by degreasing had low DNA concentrations and failed to generate nuclear PCR products. In general, treatments performed at high temperatures (90°C or above) for short durations performed best. This study shows that traditionally "conservative" maceration techniques are not necessarily the best methods to yield DNA from skeletal tissue. [source]

DISAPPEARANCE OF MALE MITOCHONDRIAL DNA AFTER THE FOUR-CELL STAGE IN SPOROPHYTES OF THE ISOGAMOUS BROWN ALGA SCYTOSIPHON LOMENTARIA (SCYTOSIPHONACEAE, PHAEOPHYCEAE),

A7445G mtDNA mutation present in a Portuguese family exhibiting hereditary deafness and palmoplantar keratoderma

JOURNAL OF THE EUROPEAN ACADEMY OF DERMATOLOGY & VENEREOLOGY, Issue 4 2005
H Caria
ABSTRACT Mitochondrial DNA (mtDNA) A7445G point mutation has been shown to be responsible for familial nonepidermolytic palmoplantar keratoderma (NEPPK) associated with deafness without any additional features. To date, only a few cases have been described. We report a Portuguese pedigree presenting an inherited combination of NEPPK and sensorineural deafness compatible with maternal transmission. Clinical expression and age of onset of NEPPK and deafness were variable. Normal expression patterns of epidermal keratins and filaggrin, intercellular junction proteins including connexin 26, loricrin and cornified envelope proteins, were observed. Molecular analysis revealed that all the affected members, previously screened for Cx26 mutations with negative results, presented the mtDNA A7445G point mutation in the homoplasmic form. To our knowledge, this is the fifth family in whom inherited NEPPK and hearing loss are related to this mitochondrial mutation. [source]

Differences in molecular alterations of hepatocellular carcinoma between patients with a sustained virological response and those with hepatitis C virus infection

LIVER INTERNATIONAL, Issue 1 2009
Takehiro Hayashi
Abstract Background/Aims: The mechanism of hepatocarcinogenesis remains unclear in patients in whom hepatitis C virus (HCV) disappears after interferon (IFN) therapy. We compared molecular alterations in hepatocellular carcinoma (HCC) between patients with a sustained virological response (SVR) to IFN and patients with HCV. Methods: The study group comprised 44 patients with HCV and 13 patients with SVR. One patient in the SVR group had two tumour nodules, both of which were examined. Mitochondrial DNA (mtDNA) mutations in displacement-loop lesions were directly sequenced. Mutation of the TP53 gene was examined by direct sequencing. The methylation status of p16, p15, p14, RB and PTEN genes was evaluated by a methylation-specific polymerase chain reaction. Results: The average number of mtDNA mutations was 4.2 in 44 HCCs with HCV and 2.0 in 14 HCCs with SVR (P=0.0021). mtDNA mutation was less frequently detected in HCCs from patients with SVR than in patients with HCV. TP53 mutations were detected in 12 (27%) of 44 HCCs with HCV and 2 (14%) of 14 SVR-HCCs. Hypermethylation of the p16, p15, p14, RB and PTEN promoters was, respectively, detected in 34, 13, 8, 12 and 11 of 44 HCCs from patients with HCV and 14, 0, 0, 2 and 2 of 14 HCCs from patients with SVR (P=0.049, 0.021, 0.085, 0.322 and 0.402). Hypermethylation of p16 was one of the most important alterations in SVR-HCC. Conclusions: Molecular alterations in hepatocarcinogenesis of patients with SVR-HCC were different from those of patients with continuous HCV infection. [source]

Revealing the hidden complexities of mtDNA inheritance

MOLECULAR ECOLOGY, Issue 23 2008
DANIEL JAMES WHITE
Abstract Mitochondrial DNA (mtDNA) is a pivotal tool in molecular ecology, evolutionary and population genetics. The power of mtDNA analyses derives from a relatively high mutation rate and the apparent simplicity of mitochondrial inheritance (maternal, without recombination), which has simplified modelling population history compared to the analysis of nuclear DNA. However, in biology things are seldom simple, and advances in DNA sequencing and polymorphism detection technology have documented a growing list of exceptions to the central tenets of mitochondrial inheritance, with paternal leakage, heteroplasmy and recombination now all documented in multiple systems. The presence of paternal leakage, recombination and heteroplasmy can have substantial impact on analyses based on mtDNA, affecting phylogenetic and population genetic analyses, estimates of the coalescent and the myriad of other parameters that are dependent on such estimates. Here, we review our understanding of mtDNA inheritance, discuss how recent findings mean that established ideas may need to be re-evaluated, and we assess the implications of these new-found complications for molecular ecologists who have relied for decades on the assumption of a simpler mode of inheritance. We show how it is possible to account for recombination and heteroplasmy in evolutionary and population analyses, but that accurate estimates of the frequencies of biparental inheritance and recombination are needed. We also suggest how nonclonal inheritance of mtDNA could be exploited, to increase the ways in which mtDNA can be used in analyses. [source]

Differential admixture shapes morphological variation among invasive populations of the lizard Anolis sagrei

MOLECULAR ECOLOGY, Issue 8 2007
JASON J. KOLBE
Abstract The biological invasion of the lizard Anolis sagrei provides an opportunity to study evolutionary mechanisms that produce morphological differentiation among non-native populations. Because the A. sagrei invasion represents multiple native-range source populations, differential admixture as well as random genetic drift and natural selection, could shape morphological evolution during the invasion. Mitochondrial DNA (mtDNA) analyses reveal seven distinct native-range source populations for 10 introduced A. sagrei populations from Florida, Louisiana and Texas (USA), and Grand Cayman, with 2,5 native-range sources contributing to each non-native population. These introduced populations differ significantly in frequencies of haplotypes from different native-range sources and in body size, toepad-lamella number, and body shape. Variation among introduced populations for both lamella number and body shape is explained by differential admixture of various source populations; mean morphological values of introduced populations are correlated with the relative genetic contributions from different native-range source populations. The number of source populations contributing to an introduced population correlates with body size, which appears independent of the relative contributions of particular source populations. Thus, differential admixture of various native-range source populations explains morphological differences among introduced A. sagrei populations. Morphological differentiation among populations is compatible with the hypothesis of selective neutrality, although we are unable to test the hypothesis of interdemic selection among introductions from different native-range source populations. [source]

Phylogeography, phylogeny and hybridization in trichechid sirenians: implications for manatee conservation

MOLECULAR ECOLOGY, Issue 2 2006
JULIANA A. VIANNA
Abstract The three living species of manatees, West Indian (Trichechus manatus), Amazonian (Trichechus inunguis) and West African (Trichechus senegalensis), are distributed across the shallow tropical and subtropical waters of America and the western coast of Africa. We have sequenced the mitochondrial DNA control region in 330 Trichechus to compare their phylogeographic patterns. In T. manatus we observed a marked population structure with the identification of three haplotype clusters showing a distinct spatial distribution. A geographic barrier represented by the continuity of the Lesser Antilles to Trinidad Island, near the mouth of the Orinoco River in Venezuela, appears to have restricted the gene flow historically in T. manatus. However, for T. inunguis we observed a single expanding population cluster, with a high diversity of very closely related haplotypes. A marked geographic population structure is likely present in T. senegalensis with at least two distinct clusters. Phylogenetic analyses with the mtDNA cytochrome b gene suggest a clade of the marine Trichechus species, with T. inunguis as the most basal trichechid. This is in agreement with previous morphological analyses. Mitochondrial DNA, autosomal microsatellites and cytogenetic analyses revealed the presence of hybrids between the T. manatus and T. inunguis species at the mouth of the Amazon River in Brazil, extending to the Guyanas and probably as far as the mouth of the Orinoco River. Future conservation strategies should consider the distinct population structure of manatee species, as well as the historical barriers to gene flow and the likely occurrence of interspecific hybridization. [source]

Rangewide population genetic structure of the African malaria vector Anopheles funestus

MOLECULAR ECOLOGY, Issue 14 2005
A. P. MICHEL
Abstract Anopheles funestus is a primary vector of malaria in Africa south of the Sahara. We assessed its rangewide population genetic structure based on samples from 11 countries, using 10 physically mapped microsatellite loci, two per autosome arm and the X (N = 548), and 834 bp of the mitochondrial ND5 gene (N = 470). On the basis of microsatellite allele frequencies, we found three subdivisions: eastern (coastal Tanzania, Malawi, Mozambique and Madagascar), western (Burkina Faso, Mali, Nigeria and western Kenya), and central (Gabon, coastal Angola). A. funestus from the southwest of Uganda had affinities to all three subdivisions. Mitochondrial DNA (mtDNA) corroborated this structure, although mtDNA gene trees showed less resolution. The eastern subdivision had significantly lower diversity, similar to the pattern found in the codistributed malaria vector Anopheles gambiae. This suggests that both species have responded to common geographic and/or climatic constraints. The western division showed signatures of population expansion encompassing Kenya west of the Rift Valley through Burkina Faso and Mali. This pattern also bears similarity to A. gambiae, and may reflect a common response to expanding human populations following the development of agriculture. Due to the presumed recent population expansion, the correlation between genetic and geographic distance was weak. Mitochondrial DNA revealed further cryptic subdivision in A. funestus, not detected in the nuclear genome. Mozambique and Madagascar samples contained two mtDNA lineages, designated clade I and clade II, that were separated by two fixed differences and an average of 2% divergence, which implies that they have evolved independently for ,1 million years. Clade I was found in all 11 locations, whereas clade II was sampled only on Madagascar and Mozambique. We suggest that the latter clade may represent mtDNA capture by A. funestus, resulting from historical gene flow either among previously isolated and divergent populations or with a related species. [source]

Mitochondrial DNA and microsatellite variation in the eider duck (Somateria mollissima) indicate stepwise postglacial colonization of Europe and limited current long-distance dispersal

MOLECULAR ECOLOGY, Issue 6 2004
R. Tiedemann
Abstract To unravel the postglacial colonization history and the current intercolony dispersal in the common eider, Somateria mollissima, we analysed genetic variation at a part of the mitochondrial control region and five unlinked autosomal microsatellite loci in 175 eiders from 11 breeding colonies, covering the entire European distribution range of this species. As a result of extreme female philopatry, mitochondrial DNA differentiation is substantial both among local colonies and among distant geographical regions. Our study further corroborates the previous hypothesis of a single Pleistocene refugium for European eiders. A nested clade analysis on mitochondrial haplotypes suggests that (i) the Baltic Sea eider population is genetically closest to a presumably ancestral population and that (ii) the postglacial recolonization progressed in a stepwise fashion via the North Sea region and the Faroe Islands to Iceland. Current long-distance dispersal is limited. Differentiation among colonies is much less pronounced at microsatellite loci. The geographical pattern of this nuclear genetic variation is to a large extent explained by isolation by distance. As female dispersal is very limited, the geographical pattern of nuclear variation is probably explained by male-mediated gene flow among breeding colonies. Our study provides genetic evidence for the assumed prominent postglacial colonization route shaping the present terrestrial fauna of the North Atlantic islands Iceland and the Faroes. It suggests that this colonization had been a stepwise process originating in continental Europe. It is the first molecular study on eider duck populations covering their entire European distribution range. [source]

The linkage disequilibrium between chloroplast DNA and mitochondrial DNA haplotypes in Beta vulgaris ssp. maritima (L.): the usefulness of both genomes for population genetic studies

MOLECULAR ECOLOGY, Issue 2 2000
B. Desplanque
Abstract The structure and evolution of the plant mitochondrial genome may allow recurrent appearance of the same mitochondrial variants in different populations. Whether the same mitochondrial variant is distributed by migration or appears recurrently by mutation (creating homoplasy) in different populations is an important question with regard to the use of these markers for population genetic analyses. The genetic association observed between chloroplasts and mitochondria (i.e. two maternally inherited cytoplasmic genomes) may indicate whether or not homoplasy occurs in the mitochondrial genome. Four-hundred and fourteen individuals sampled in wild populations of beets from France and Spain were screened for their mitochondrial and chloroplast polymorphisms. Mitochondrial DNA (mtDNA) polymorphism was investigated with restriction fragment length polymorphism (RFLP) and chloroplast DNA (cpDNA) polymorphism was investigated with polymerase chain reaction PCR,RFLP, using universal primers for the amplification. Twenty and 13 variants for mtDNA and cpDNA were observed, respectively. Most exhibited a widespread geographical distribution. As a very strong linkage disequilibrium was estimated between mtDNA and cpDNA haplotypes, a high rate of recurrent mutation was excluded for the mitochondrial genome of beets. Identical mitochondrial variants found in populations of different regions probably occurred as a result of migration. We concluded from this study that mtDNA is a tool as valuable as cpDNA when a maternal marker is needed for population genetics analyses in beet on a large regional scale. [source]

A South African mixed ancestry family with Huntington disease-like 2: Clinical and genetic features

MOVEMENT DISORDERS, Issue 14 2007
Soraya Bardien PhD
Abstract Huntington disease-like 2 (HDL2) is a neurodegenerative disorder caused by an expansion of a CTG repeat in the junctophilin-3 gene (JPH3). A limited number of HDL2 families have been reported, all of apparently Black African ancestry. We report on a South African family that presented with progressive dementia and a movement disorder affecting numerous family members. Genotyping of the JPH3 CTG repeat revealed pathogenic expansions in three affected individuals. Whereas HDL2 is thought to be clinically indistinguishable from Huntington disease (HD), 2 of the patients in this study presented with clinical symptoms that differed substantially from HD; one had myoclonus and the other had Parkinsonism. Moreover, brain magnetic resonance imaging scans of these patients showed imaging features atypical for HD. Mitochondrial DNA and Y-chromosome DNA analysis on a family member showed that his maternal and paternal ancestries are typical of that found among the South African mixed ancestry or colored population. A difference in the distribution of CTG repeats between Caucasian and Black individuals was detected. We conclude that the phenotype of HDL2 is broad and can differ from that of typical HD. The diagnosis therefore should be considered in a wide spectrum of neuropsychiatric and abnormal movement presentations. © 2007 Movement Disorder Society [source]

Molecular neuropathology of MELAS: level of heteroplasmy in individual neurones and evidence of extensive vascular involvement

NEUROPATHOLOGY & APPLIED NEUROBIOLOGY, Issue 4 2006
J. Betts
Mitochondrial DNA (mtDNA) disease is an important genetic cause of neurological disability. A variety of different clinical features are observed and one of the most common phenotypes is MELAS (Mitochondrial Myopathy, Encephalopathy, Lactic Acidosis and Stroke-like episodes). The majority of patients with MELAS have the 3243A>G mtDNA mutation. The neuropathology is dominated by multifocal infarct-like lesions in the posterior cortex, thought to underlie the stroke-like episodes seen in patients. To investigate the relationship between mtDNA mutation load, mitochondrial dysfunction and neuropathological features in MELAS, we studied individual neurones from several brain regions of two individuals with the 3243A>G mutation using dual cytochrome c oxidase (COX) and succinate dehydrogenase (SDH) histochemistry, and Polymerase Chain Reaction Restriction Fragment Lenght Polymorphism (PCR-RFLP) analysis. We found a low number of COX-deficient neurones in all brain regions. There appeared to be no correlation between the threshold level for the 3243A>G mutation to cause COX deficiency within single neurones and the degree of pathology in affected brain regions. The most severe COX deficiency associated with the highest proportion of mutated mtDNA was present in the walls of the leptomeningeal and cortical blood vessels in all brain regions. We conclude that vascular mitochondrial dysfunction is important in the pathogenesis of the stroke-like episodes in MELAS patients. As migraine is a commonly encountered feature in MELAS, we propose that coupling of the vascular mitochondrial dysfunction with cortical spreading depression (CSD) might underlie the selective distribution of ischaemic lesions in the posterior cortex in these patients. [source]

Do mitochondrial DNA haplogroups play a role in susceptibility to tuberculosis?

RESPIROLOGY, Issue 6 2007
Massoud HOUSHMAND
Background and objectives: Mitochondrial DNA has a unique role in ATP production and subsequent mitochondrial reactive oxygen species (ROS) production in eukaryotic cells and there is a potential role for ROS and oxygen burst against Mycobacterium tuberculosis, an intracellular pathogen. This study aimed to determine whether the frequency of different mitochondrial haplogroups was significantly different in patients with tuberculosis (TB) compared with a normal population. Methods: Mitochondrial DNA haplogroups M, N, J and K were studied by PCR-restriction fragment length polymorphism and sequencing. Cases were 54 patients with confirmed smear positive pulmonary TB. Controls were 256 healthy persons. Results: There were no statistically significant differences between those with TB and the control group. Conclusions: There was no statistically significant association between mtDNA haplogroups and the presence of TB infection. [source]

Cytochrome b sequences of ancient cattle and wild ox support phylogenetic complexity in the ancient and modern bovine populations

ANIMAL GENETICS, Issue 5 2009
F. Stock
Summary Mitochondrial DNA has been the traditional marker for the study of animal domestication, as its high mutation rate allows for the accumulation of molecular diversity within the time frame of domestic history. Additionally, it is exclusively maternally inherited and haplotypes become part of the domestic gene pool via actual capture of a female animal rather than by interbreeding with wild populations. Initial studies of British aurochs identified a haplogroup, designated P, which was found to be highly divergent from all known domestic haplotypes over the most variable portion of the D-loop. Additional analysis of a large and geographically representative sample of aurochs from northern and central Europe found an additional, separate aurochs haplotype, E. Until recently, the European aurochs appeared to have no matrilinear descendants among the publicly available modern cattle control regions sequenced; if aurochs mtDNA was incorporated into the domestic population, aurochs either formed a very small proportion of modern diversity or had been subsequently lost. However, a haplogroup P sequence has recently been found in a modern sample, along with a new divergent haplogroup called Q. Here we confirm the outlying status of the novel Q and E haplogroups and the modern P haplogroup sequence as a descendent of European aurochs, by retrieval and analysis of cytochrome b sequence data from twenty ancient wild and domesticated cattle archaeological samples. [source]

Mitochondrial DNA-based analysis of genetic variation and relatedness among Sri Lankan indigenous chickens and the Ceylon junglefowl (Gallus lafayetti)

ANIMAL GENETICS, Issue 1 2009
P. Silva
Summary Indigenous chickens (IC) in developing countries provide a useful resource to detect novel genes in mitochondrial and nuclear genomes. Here, we investigated the level of genetic diversity in IC from five distinct regions of Sri Lanka using a PCR-based resequencing method. In addition, we investigated the relatedness of IC to different species of junglefowls including Ceylon (CJF; Gallus lafayetti), a subspecies that is endemic to Sri Lanka, green (Gallus varius), grey (Gallus sonneratii) and red (Gallus gallus) junglefowls. A total of 140 birds including eight CJF were used to screen the control region of the mitochondrial DNA sequence for single nucleotide polymorphisms (SNPs) and other variants. We detected and validated 44 SNPs, which formed 42 haplotypes and six haplogroups in IC. The SNPs observed in the CJF were distinct and the D-loop appeared to be missing a 62-bp segment found in IC and the red junglefowl. Among the six haplogroups of IC, only one was region-specific. Estimates of haplotype and nucleotide diversities ranged from 0.901 to 0.965 and from 0.011 to 0.013 respectively, and genetic divergence was generally low. Further, variation among individuals within regions accounted for 92% of the total molecular variation among birds. The Sri Lankan IC were more closely related to red and grey junglefowls than to CJF, indicating multiple origins. The molecular information on genetic diversity revealed in our study may be useful in developing genetic improvement and conservation strategies to better utilize indigenous Sri Lankan chicken resources. [source]

Inferring Continental Ancestry of Argentineans from Autosomal, Y-Chromosomal and Mitochondrial DNA

ANNALS OF HUMAN GENETICS, Issue 1 2010
Daniel Corach
Summary We investigated the bio-geographic ancestry of Argentineans, and quantified their genetic admixture, analyzing 246 unrelated male individuals from eight provinces of three Argentinean regions using ancestry-sensitive DNA markers (ASDM) from autosomal, Y and mitochondrial chromosomes. Our results demonstrate that European, Native American and African ancestry components were detectable in the contemporary Argentineans, the amounts depending on the genetic system applied, exhibiting large inter-individual heterogeneity. Argentineans carried a large fraction of European genetic heritage in their Y-chromosomal (94.1%) and autosomal (78.5%) DNA, but their mitochondrial gene pool is mostly of Native American ancestry (53.7%); instead, African heritage was small in all three genetic systems (<4%). Population substructure in Argentina considering the eight sampled provinces was very small based on autosomal (0.92% of total variation was between provincial groups, p = 0.005) and mtDNA (1.77%, p = 0.005) data (none with NRY data), and all three genetic systems revealed no substructure when clustering the provinces into the three geographic regions to which they belong. The complex genetic ancestry picture detected in Argentineans underscores the need to apply ASDM from all three genetic systems to infer geographic origins and genetic admixture. This applies to all worldwide areas where people with different continental ancestry live geographically close together. [source]