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Mitochondrial DNA Sequences (mitochondrial + dna_sequence)
Terms modified by Mitochondrial DNA Sequences Selected AbstractsGenetically solving a zoological mystery: was the kouprey (Bos sauveli) a feral hybrid?JOURNAL OF ZOOLOGY, Issue 4 2006G. J. Galbreath Abstract A famous zoological discovery of the 20th century was that of the kouprey Bos sauveli, a medium-sized ox inhabiting Cambodian forests. The kouprey was suspiciously intermediate between banteng oxen and domestic zebu cattle in its structure. Mitochondrial DNA sequences of mainland banteng are compared here with a published kouprey sequence, and the comparison demonstrates a close relationship. Either the kouprey derives partly from banteng or (less likely) these particular banteng acquired kouprey DNA via recent genetic introgression. The kouprey may have been a feral hybrid form, a descendant of domestic oxen, rather than a natural species. [source] Camouflaged invasion of Lake Malawi by an Oriental gastropodMOLECULAR ECOLOGY, Issue 8 2004MARTIN J. GENNER Abstract In this study we report the first animal invasion, to our knowledge, into Lake Malawi. The colonizer is a non-native morph of the gastropod Melanoides tuberculata that differs substantially in external shell characters from co-occurring indigenous forms. However, because the species possesses extensive within-Africa geographical variation in shell morphology, it was unclear whether the invasion was range expansion of a native African morph, or a colonization from elsewhere. Mitochondrial DNA sequences indicate a southeast Asian origin for the invader, suggesting that shell variation found among indigenous allopatric populations camouflaged an intercontinental invasion. [source] Phylogeography of colonially nesting seabirds, with special reference to global matrilineal patterns in the sooty tern (Sterna fuscata)MOLECULAR ECOLOGY, Issue 11 2000John C. Avise Abstract Sooty tern (Sterna fuscata) rookeries are scattered throughout the tropical oceans. When not nesting, individuals wander great distances across open seas, but, like many other seabirds, they tend to be site-faithful to nesting locales in successive years. Here we examine the matrilineal history of sooty terns on a global scale. Assayed colonies within an ocean are poorly differentiated in mitochondrial DNA sequence, a result indicating tight historical ties. However, a shallow genealogical partition distinguishes Atlantic from Indo-Pacific rookeries. Phylogeographic patterns in the sooty tern are compared to those in other colonially nesting seabirds, as well as in the green turtle (Chelonia mydas), an analogue of tropical seabirds in some salient aspects of natural history. Phylogeographic structure within an ocean is normally weak in seabirds, unlike the pronounced matrilineal structure in green turtles. However, the phylogeographic partition between Atlantic and Indo-Pacific rookeries in sooty terns mirrors, albeit in shallower evolutionary time, the major matrilineal subdivision in green turtles. Thus, global geology has apparently influenced historical gene movements in these two circumtropical species. [source] Integration of DNA barcoding into an ongoing inventory of complex tropical biodiversityMOLECULAR ECOLOGY RESOURCES, Issue 2009DANIEL H. JANZEN Abstract Inventory of the caterpillars, their food plants and parasitoids began in 1978 for today's Area de Conservacion Guanacaste (ACG), in northwestern Costa Rica. This complex mosaic of 120 000 ha of conserved and regenerating dry, cloud and rain forest over 0,2000 m elevation contains at least 10 000 species of non-leaf-mining caterpillars used by more than 5000 species of parasitoids. Several hundred thousand specimens of ACG-reared adult Lepidoptera and parasitoids have been intensively and extensively studied morphologically by many taxonomists, including most of the co-authors. DNA barcoding , the use of a standardized short mitochondrial DNA sequence to identify specimens and flush out undisclosed species , was added to the taxonomic identification process in 2003. Barcoding has been found to be extremely accurate during the identification of about 100 000 specimens of about 3500 morphologically defined species of adult moths, butterflies, tachinid flies, and parasitoid wasps. Less than 1% of the species have such similar barcodes that a molecularly based taxonomic identification is impossible. No specimen with a full barcode was misidentified when its barcode was compared with the barcode library. Also as expected from early trials, barcoding a series from all morphologically defined species, and correlating the morphological, ecological and barcode traits, has revealed many hundreds of overlooked presumptive species. Many but not all of these cryptic species can now be distinguished by subtle morphological and/or ecological traits previously ascribed to ,variation' or thought to be insignificant for species-level recognition. Adding DNA barcoding to the inventory has substantially improved the quality and depth of the inventory, and greatly multiplied the number of situations requiring further taxonomic work for resolution. [source] High mitochondrial differentiation levels between wild and domestic Bactrian camels: a basis for rapid detection of maternal hybridizationANIMAL GENETICS, Issue 3 2010K. Silbermayr Summary Hybridization between wild species and their domestic congeners often threatens the gene pool of the wild species. The last wild Bactrian camel (Camelus ferus) populations in Mongolia and China are examples of populations facing such a hybridization threat. To address this key issue in the conservation of wild camels, we analysed wild, hybrid and domestic Bactrian camels (Camelus bactrianus) originating from Mongolia, China and Austria. Through screening of an 804-base-pair mitochondrial fragment, we identified eight mitochondrial haplotypes and found high sequence divergence (1.9%) between C. ferus and C. bactrianus. On the basis of a mitochondrial DNA sequence fixed difference, we developed a diagnostic PCR restriction fragment length polymorphism (PCR-RFLP) assay to differentiate between wild and domestic camel samples. We applied the assay to 81 individuals and confirmed the origin of all samples including five hybrids with known maternal ancestry. The PCR-RFLP system was effective for both traditional (blood, skin) and non-invasive samples (faeces, hair), as well as for museum specimens. Our results demonstrate high levels of mitochondrial differentiation between wild and domestic Bactrian camels and that maternal hybridization can be detected by a rapid and reliable PCR-RFLP system. [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 2009P. 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] Genetic differentiation in pointing dog breeds inferred from microsatellites and mitochondrial DNA sequenceANIMAL GENETICS, Issue 1 2008D. Parra Summary Recent studies presenting genetic analysis of dog breeds do not focus specifically on genetic relationships among pointing dog breeds, although hunting was among the first traits of interest when dogs were domesticated. This report compares histories with genetic relationships among five modern breeds of pointing dogs (English Setter, English Pointer, Epagneul Breton, Deutsch Drahthaar and German Shorthaired Pointer) collected in Spain using mitochondrial, autosomal and Y-chromosome information. We identified 236 alleles in autosomal microsatellites, four Y-chromosome haplotypes and 18 mitochondrial haplotypes. Average FST values were 11.2, 14.4 and 13.1 for autosomal, Y-chromosome microsatellite markers and mtDNA sequence respectively, reflecting relatively high genetic differentiation among breeds. The high gene diversity observed in the pointing breeds (61.7,68.2) suggests contributions from genetically different individuals, but that these individuals originated from the same ancestors. The modern English Setter, thought to have arisen from the Old Spanish Pointer, was the first breed to cluster independently when using autosomal markers and seems to share a common maternal origin with the English Pointer and German Shorthaired Pointer, either via common domestic breed females in the British Isles or through the Old Spanish Pointer females taken to the British Isles in the 14th and 16th centuries. Analysis of mitochondrial DNA sequence indicates the isolation of the Epagneul Breton, which has been formally documented, and shows Deutsch Drahthaar as the result of crossing the German Shorthaired Pointer with other breeds. Our molecular data are consistent with historical documents. [source] LINKING COEVOLUTIONARY HISTORY TO ECOLOGICAL PROCESS: DOVES AND LICEEVOLUTION, Issue 10 2003Dale H. Clayton Abstract Many host-specific parasites are restricted to a limited range of host species by ecological barriers that impede dispersal and successful establishment. In some cases, microevolutionary differentiation is apparent on top of host specificity, as evidenced by significant parasite population genetic structure among host populations. Ecological barriers responsible for specificity and genetic structure can, in principle, reinforce macroevolutionary processes that generate congruent host-parasite phylogenies. However, few studies have explored both the micro- and macroevolutionary ramifications of close association in a single host-parasite system. Here we compare the macroevolutionary histories of two genera of feather lice (Phthiraptera: Ischnocera) that both parasitize New World pigeons and doves (Aves: Columbiformes). Earlier work has shown that dove body lice (genus Physconelloides) are more host specific and have greater population genetic structure than dove wing lice (Columbicola). We reconstructed phylogenies for representatives of the two genera of lice and their hosts, using nuclear and mitochondrial DNA sequences. The phylogenies were well resolved and generally well supported. We compared the phylogenies of body lice and wing lice to the host phylogeny using reconciliation analyses. We found that dove body lice show strong evidence of cospeciation whereas dove wing lice do not. Although the ecology of body and wing lice is very similar, differences in their dispersal ability may underlie these joint differences in host specificity, population genetic structure, and coevolutionary history. [source] THE HISTORICAL BIOGEOGRAPHY OF TWO CARIBBEAN BUTTERFLIES (LEPIDOPTERA: HELICONIIDAE) AS INFERRED FROM GENETIC VARIATION AT MULTIPLE LOCIEVOLUTION, Issue 3 2002Neil 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] Neritid and thiarid gastropods from French Polynesian streams: how reproduction (sexual, parthenogenetic) and dispersal (active, passive) affect population structureFRESHWATER BIOLOGY, Issue 3 2000Marilyn J. Myers Summary 1The streams of French Polynesia contain several species of Neritidae and Thiaridae (Mollusca: Gastropoda). The neritids are dioecious and amphidromous with a freshwater adult stage and a poorly known, marine larval stage. The thiarids are parthenogenetic and viviparous, and rely on passive dispersal for colonisation of new habitats. 2Populations of the neritid Clithon spinosus and the thiarids Melanoides tuberculata and Thiara granifera were analysed using mitochondrial DNA sequences from COI to compare the population structure of the snails at three different scales: between streams (N = 9), between islands (N = 4), and between age and distance of paired islands. 3The amphidromous C. spinosus showed no evidence of genetic isolation at any of the scales tested (Fst values 0.02). Parsimony analyses resulted in two haplotype clusters separated by a three-step segment, which were not linked to geographic isolation. The larval phase of C. spinosus is most likely a long-lived planktotroph and a very effective disperser. 4Two haplotypes of M. tuberculata, separated by 16 base pairs, were found. Both haplotypes were found in snails on all islands, and individuals representing both were often collected in the same habitat. One haplotype of T. granifera was found. M. tuberculata has the characteristics of the ,general-purpose genotype' of clonal population structure and although it relies on passive dispersal, it has colonised nearly all freshwater habitats on the islands. [source] Phylogeny and biogeography of Yellow-headed and Blue-fronted Parrots (Amazona ochrocephala and Amazona aestiva) with special reference to the South American taxaIBIS, Issue 3 2007CAMILA C. RIBAS The Yellow-headed Parrot (Amazona ochrocephala) has a broad Neotropical distribution, ranging from Mexico to the Amazon Basin, and a history of complex taxonomy and controversial species limits. Recent molecular analyses have started to clarify the taxonomic arrangement of the complex, but have not included a representative geographical sampling from South America. These studies have shown that the Yellow-headed complex can be divided into three main lineages, and seems to be paraphyletic, due to the inclusion of the Blue-fronted Parrot (Amazona aestiva) that occurs in central South America. Here we present a phylogenetic analysis based on mitochondrial DNA sequences of 45 representatives of the Yellow-headed complex from South and Central America, plus 13 Blue-fronted individuals from different localities in South America. Our analyses recover the three primary lineages found previously in the Yellow-headed complex, show that there is genetic structure in the South American lineage, which can be divided into two well-supported, closely related clades, and demonstrate that Blue-fronted samples are distributed in both clades. Differentiation of South American Blue-fronted and Yellow-headed Parrot populations does not correspond to the plumage differences used to distinguish the Blue-fronted Parrot from the Yellow-headed Parrot, nor to plumage differences used to distinguish among South American Yellow-headed subspecies. This suggests that traditional taxonomy based on plumage characters needs revision, and that this may be an interesting example of ongoing divergence-with-gene-flow related to the forest/open area ecotone in southern Amazonia. [source] Relationship among five populations of Bactrocera dorsalis based on mitochondrial DNA sequences in western Yunnan, ChinaJOURNAL OF APPLIED ENTOMOLOGY, Issue 7 2008P. Chen Abstract Genetic variation in the Oriental fruit fly, Bactrocera dorsalis (Hendel), was analysed using five populations from western Yunnan, China, to elucidate the distribution and likely dispersal patterns of this fly. A 503-bp portion of the mitochondrial cytochrome oxidase gene was sequenced from a minimum of seven individuals from each of five fly populations; 25 haplotypes were observed among 57 individuals in these populations. High genetic diversity within populations was detected. Genetic distances between haplotypes reached 1.2%. Mantel tests did not indicate any isolation because of geographic distance. The Ruili (RL) population was significantly isolated from the others (pairwise Fst ranging from 0.10 to 0.21, and average genetic distances being higher than for all other four population comparisons). RL is geographically separated from the other sites by the Gaoligong Mountains. The Liuku (LK) population had a close genetic relationship with the Lujiangba (LJB) population, suggesting that the LK population probably originated from LJB that is located in the same valley to the south. The Baoshan (BS) and Dali (DL) populations were also geographically isolated from the others, not originating from LJB and RL, where the fly is present year-round. The north-south orientation of mountains and valleys in western Yunnan appears to prevent latitudinal gene exchange by dispersing flies and thus divides the five populations into four relatively independent zones, namely BS, DL, LK-LJB and RL. In addition, air currents that generally flow south to north appear to assist dispersing flies, especially in valleys between the mountain chains. [source] Population structure in the South American tern Sterna hirundinacea in the South Atlantic: two populations with distinct breeding phenologiesJOURNAL OF AVIAN BIOLOGY, Issue 4 2010Patrícia J. Faria The South American tern Sterna hirundinacea is a migratory species for which dispersal, site fidelity and migratory routes are largely unknown. Here, we used five microsatellite loci and 799,bp partial mitochondrial DNA sequences (Cytochrome b and ND2) to investigate the genetic structure of South American terns from the South Atlantic Ocean (Brazilian and Patagonian colonies). Brazilian and Patagonian colonies have two distinct breeding phenologies (austral winter and austral summer, respectively) and are under the influence of different oceanographic features (e.g. Brazil and Falklands/Malvinas ocean currents, respectively), that may promote genetic isolation between populations. Results show that the Atlantic populations are not completely panmictic, nevertheless, contrary to our expectations, low levels of genetic structure were detected between Brazilian and Patagonian colonies. Such low differentiation (despite temporal isolation of the colonies) could be explained by demographic history of these populations coupled with ongoing levels of gene flow. Interestingly, estimations of gene flow through Maximum likelihood and Bayesian approaches has indicated asymmetrical long term and contemporary gene flow from Brazilian to Patagonian colonies, approaching a source,sink metapopulation dynamic. Genetic analysis of other South American tern populations (especially those from the Pacific coast and Falklands,Malvinas Islands) and other seabird species showing similar geographical distribution (e.g. royal tern Thalasseus maximus), are fundamental in gaining a better understanding of the main processes involved in the diversification of seabirds in the southern hemisphere. [source] Surviving glacial ages within the Biotic Gap: phylogeography of the New Zealand cicada Maoricicada campbelliJOURNAL OF BIOGEOGRAPHY, Issue 4 2009Kathy B. R. Hill Abstract Aim, New Zealand is an ideal location in which to investigate the roles of landscape and climate change on speciation and biogeography. An earlier study of the widespread endemic cicada Maoricicada campbelli (Myers) found two phylogeographically distinguishable major clades , northern South Island plus North Island (northern-SI + NI) and Otago. These two clades appeared to have diverged on either side of an area of the South Island known as the Biotic Gap. We sampled more intensively to test competing theories for this divergence. We aimed to discover if M. campbelli had survived within the Biotic Gap during recent glacial maxima, and if predicted areas of secondary contact between the two major clades existed. Location, New Zealand. Methods, We analysed mitochondrial DNA sequences (1520 bp; 212 individuals; 91 populations) using phylogenetic (maximum likelihood, Bayesian), population genetic (analysis of molecular variance) and molecular dating methods (Bayesian relaxed clock with improved priors). Results, We found strong geographical structuring of genetic variation. Our dating analyses suggest that M. campbelli originated 1.83,2.58 Ma, and split into the two major clades 1.45,2.09 Ma. The main subclades in the northern-SI + NI clade arose almost simultaneously at 0.69,1.03 Ma. Most subclades are supported by long internal branches and began to diversify 0.40,0.78 Ma. We found four narrow areas of secondary contact between the two major clades. We also found a difference between calling songs of the Otago vs. northern-SI + NI clades. Main conclusions, Phylogeographical patterns within M. campbelli indicate an early Pleistocene split into two major clades, followed by late Pleistocene range expansion and in situ population differentiation of subclades. The northern-SI + NI clade diversified so rapidly that the main subclade relationships cannot be resolved, and we now have little evidence for a disjunction across the Biotic Gap. Structure within the main subclades indicates rapid divergence after a common bottlenecking event, perhaps attributable to an extremely cold glacial maximum at c. 0.43 Ma. Clade structure and dating analyses indicate that M. campbelli survived in many refugia during recent glacial maxima, including within the Biotic Gap. The narrow overlap between the two major clades is attributed to recent contact during the current interglacial and slow gene diffusion. The two major clades appear to be in the early stages of speciation based on genetic and behavioural differences. [source] ORIGINAL ARTICLE: Freshwater paths across the ocean: molecular phylogeny of the frog Ptychadena newtoni gives insights into amphibian colonization of oceanic islandsJOURNAL OF BIOGEOGRAPHY, Issue 1 2007G. 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] Combining mitochondrial DNA sequences and morphological data to infer species boundaries: phylogeography of lanceheaded pitvipers in the Brazilian Atlantic forest, and the status of Bothrops pradoi (Squamata: Serpentes: Viperidae)JOURNAL OF EVOLUTIONARY BIOLOGY, Issue 4 2001G. Puorto Phylogeographic studies using mitochondrial DNA sequence information are frequently used as the principal source of evidence to infer species boundaries. However, a critical analysis of further evidence is essential to test whether different haplotype clades identify different species. We demonstrate a hypothesis-testing approach, using a combination of phylogeographic methods, multivariate morphometrics and matrix association tests, to investigate species boundaries in eastern Brazilian pitvipers conventionally assigned to the species Bothrops leucurus and B. pradoi. Two basal haplotype clades with partly overlapping geographical distributions are identified, which could either represent two partly sympatric species, or multiple haplotypes within one organismal lineage. We use partial Mantel matrix association tests to verify whether generalized morphology, or any of four supposedly diagnostic characters for the two species, show any association with mtDNA variation. Negative results lead to the conclusion that the haplotype clades do not denote independently evolving organismal lineages, and do not constitute separate species under any criterion. [source] Phylogenetic relationships of the European lacertid genera Archaeolacerta and Iberolacerta and their relationships to some other ,Archaeolacertae' (sensu lato) from Near East, derived from mitochondrial DNA sequencesJOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, Issue 3 2003W. Mayer Abstract Parts of the mitochondrial genes coding for 12SrRNA and 16SrRNA (together about 960 bp) were sequenced for all Mediterranean species of ,Mountain lizards' of the genera Archaeolacerta (sensu lato) and Iberolacerta. All subspecies of the Iberian species Iberolacerta cyreni and I. monticola were included in this study. In addition, samples of Apathya cappadocica and Darevskia rudis were analysed to elucidate the relationships of the European ,Mountain lizards' to their possible relatives in the Near East. Maximum parsimony and neighbour joining analyses lead to the following major conclusions: (i) the monophyly of the genus Iberolacerta is very well supported; (ii) Archaeolacerta bedriagae (the type species of the genus) is most basal with respect to the ingroup taxa. If we accept Iberolacerta as a genus, Archaeolacerta becames paraphyletic. Therefore, we propose to restrict Archaeolacerta to the type species and to treat A. mosorensis and A. oxycephala provisionally as members of the collective genus Lacerta; (iii) within the genus Iberolacerta three groups were found: a Pyrenean group, an Iberian group and I. horvathi. The relationships among these groups remain unresolved; and (iv) the Peña de Francia lizards, described originally as a subspecies of I. cyreni, are in fact more closely related to I. monticola. Zusammenfassung Wir sequenzierten Teilabschnitte der Gene für 12SrRNA und 16SrRNA (zusammen ungefähr 960 Basenpaare) von allen europäischen ,Gebirgseidechsen' der Gattungen Archaeolacerta (sensu lato) und Iberolacerta. Alle Subspezies der iberischen Arten Iberolacerta cyreni und I. monticola wurden in die Studie aufgenommen. Zusätzlich wurden Proben von Apathya cappadocica und Darevskia rudis untersucht, um die phylogenetischen Beziehungen der europäischen ,Gebirgseidechsen' zu ihren möglichen Verwandten im Nahen Osten aufzuklären. Maximum Parsimony und Neighbor Joining Analysen führten zu folgenden wesentlichen Ergebnissen: i) Die Monophylie der Gattung Iberolacerta ist gut abgesichert. ii) Archaeolacerta bedriagae (die species typica der Gattung) hat eine basale Position innerhalb der Gruppe der ,Gebirgseidechsen'. Daher schlagen wir vor, Archaeolacerta auf die species typica zu restringieren und A. mosorensis und A. oxycephala provisorisch in der Sammelgattung Lacerta zu belassen. iii) Die Gattung Iberolacerta zerfällt in drei Gruppen: eine Pyrenäen-Gruppe, eine iberische Gruppe und I. horvathi. Die Beziehungen zwischen diesen Gruppen konnten nicht aufgeklärt werden. iv) Die Eidechsen von Peña de Francia, ursprünglich als Subspezies von I. cyreni beschrieben, sind tatsächlich näher mit I. monticola verwandt. [source] A new species of spitting cobra (Naja) from north-eastern Africa (Serpentes: Elapidae)JOURNAL OF ZOOLOGY, Issue 4 2003Wolfgang Wüster Abstract A new species of spitting cobra Naja nubiae sp. nov. is described from north-eastern Africa. The distinctiveness of the new species is confirmed by multivariate analysis of pattern and scalation data. Phylogenetic analysis of mitochondrial DNA sequences reveals the new species to be the sister taxon of N. pallida, but with considerable levels of sequence divergence relative to that species. The populations concerned had previously been assigned to N. pallida. The new species differs from N. pallida principally in having more than one dark band across the neck and under the throat, as well as a pair of spots under the throat. It occupies a disjunct range across Egypt, the Sudan, Chad, Niger and Eritrea, where it seems to occupy primarily relatively mesic habitats. Naja mossambica is more closely related to N. nigricollis than to N. pallida and the new species. A key to the African species of Naja is presented. [source] DNA detection rates of host mtDNA in bloodmeals of human body lice (Pediculus humanus L., 1758)MEDICAL AND VETERINARY ENTOMOLOGY, Issue 3 2007J. S. DAVEY Abstract Using polymerase chain reaction, we investigated the extent to which digestion affects the potential to amplify 12S mitochondrial DNA sequences from bloodmeals of individual human body lice (Pediculus humanus L.) (Phthiraptera, Pediculidae) up to 72 h after feeding on a surrogate rabbit host (Oryctolagus cuniculus L.) (Lagomorpha, Leporidae). Two rabbit-specific primer pairs were developed to produce amplicons of 199 bp and 283 bp, the smaller of which was found to have a significantly slower decay rate. Median detection periods (T50) for the amplicons were 20 h and 12 h, with maximum detection periods of 24 h and 12 h, respectively, suggesting an inversely proportional linear relationship between amplicon size and digestion time. The data provide an indication of timeframes essential for the design of forensic sampling protocols and a basis for investigating the feeding frequency of human lice. [source] Diversification within glacial refugia: tempo and mode of evolution of the polytypic fish Barbus sclateriMOLECULAR ECOLOGY, Issue 15 2009HUGO F. GANTE Abstract A diversity of evolutionary processes can be responsible for generating and maintaining biodiversity. Molecular markers were used to investigate the influence of Plio-Pleistocene climatic oscillations on the evolutionary history of taxa restricted to the freshwaters of a classical glacial refugium. Population genetic, phylogenetic and phylogeographical methods allowed the inference of temporal dynamics of cladogenesis and processes shaping present-day genetic constitution of Barbus sclateri, a polytypic taxon found in several independent river drainages in southern Iberian Peninsula. Results from different analyses consistently indicate several range expansions, high levels of allopatric fragmentation, and admixture following secondary contacts throughout its evolutionary history. Using a Bayesian demographical coalescent model on mitochondrial DNA sequences calibrated with fossil evidence, all cladogenetic events within B. sclateri are inferred to have occurred during the Pleistocene and were probably driven by environmental factors. Our results suggest that glaciation cycles did not inhibit cladogenesis and probably interacted with regional geomorphology to promote diversification. We conclude that this polytypic taxon is a species complex that recently diversified in allopatry, and that Pleistocene glaciation,deglaciation cycles probably contributed to the generation of biological diversity in a classical glacial refugium with high endemicity. [source] Host-specificity and coevolution among pollinating and nonpollinating New World fig waspsMOLECULAR ECOLOGY, Issue 9 2007WENDY A. MARUSSICH Abstract Figs (Ficus spp., Moraceae) and their pollinating wasps (Hymenoptera, Agaonidae, Chalcidoidea) constitute a classic example of an obligate plant-pollinator mutualism, and have become an ideal system for addressing questions on coevolution, speciation, and the maintenance of mutualisms. In addition to pollinating wasps, figs host several types of nonpollinating, parasitic wasps from a diverse array of Chalcid subfamilies with varied natural histories and ecological strategies (e.g. competitors, gallers, and parasitoids). Although a few recent studies have addressed the question of codivergence between specific genera of pollinating and nonpollinating fig wasps, no study has addressed the history of divergence of a fig wasp community comprised of multiple genera of wasps associated with a large number of sympatric fig hosts. Here, we conduct phylogenetic analyses of mitochondrial DNA sequences (COI) using 411 individuals from 69 pollinating and nonpollinating fig wasp species to assess relationships within and between five genera of fig wasps (Pegoscapus, Idarnes, Heterandrium, Aepocerus, Physothorax) associated with 17 species of New World Urostigma figs from section Americana. We show that host-switching and multiple wasp species per host are ubiquitous across Neotropical nonpollinating wasp genera. In spite of these findings, cophylogenetic analyses (treemap 1.0, treemap 2.02,, and parafit) reveal evidence of codivergence among fig wasps from different ecological guilds. Our findings further challenge the classical notion of strict-sense coevolution between figs and their associated wasps, and mirror conclusions from detailed molecular studies of other mutualisms that have revealed common patterns of diffuse coevolution and asymmetric specialization among the participants. [source] Phylogeography and the geographic cline in the armament of a seed-predatory weevil: effects of historical events vs. natural selection from the host plantMOLECULAR ECOLOGY, Issue 13 2006HIROKAZU TOJU Abstract Japanese camellia (Camellia japonica) and its seed predator, the camellia weevil (Curculio camelliae), provide a notable example of a geographic mosaic of coevolution. In the species interaction, the offensive trait of the weevil (rostrum length) and the defensive trait of the plant (pericarp thickness) are involved in a geographically-structured arms race, and these traits and selective pressures acting on the plant defence vary greatly across a geographical landscape. To further explore the geographical structure of this interspecific interaction, we tested whether the geographical variation in the weevil rostrum over an 800-km range along latitude is attributed to local natural selection or constrained by historical (phylogeographical) events of local populations. Phylogeographical analyses of the mitochondrial DNA sequences of the camellia weevil revealed that this species has experienced differentiation into two regions, with a population bottleneck and subsequent range and/or population expansion within each region. Although these phylogeographical factors have affected the variation in rostrum length, analyses of competing factors for the geographical variation revealed that this pattern is primarily determined by the defensive trait of the host plant rather than by the effects of historical events of populations and a climatic factor (annual mean temperature). Thus, our study suggests the overwhelming strength of coevolutionary selection against the effect of historical events, which may have limited local adaptation. [source] The ruddy duck Oxyura jamaicensis in Europe: natural colonization or human introduction?MOLECULAR ECOLOGY, Issue 6 2006VIOLETA MUÑOZ-FUENTES Abstract Native to North America, ruddy ducks Oxyura jamaicensis now occur in 21 countries in the western Palaearctic (including Iceland) and their expanding population threatens the native white-headed duck, Oxyura leucocephala, through hybridization and possibly competition for food and nest sites. We used mitochondrial DNA sequences and nuclear microsatellites to test whether the European ruddy duck population is descended solely from the captive population in the UK, which traces to seven individuals imported from the USA in 1948, or, alternatively, has been augmented by natural dispersal of birds from North America. Limited genetic diversity in the European population is consistent with a founder population as small as seven birds. In addition, shifts in allele frequencies at several loci, presumably due to genetic drift in the founding population, result in significant differentiation between the European and North American populations. Despite the recent separation of these populations, almost all individuals could be unambiguously assigned based on their composite genotypes, to one of two distinct populations, one comprising all of the European ruddy ducks we sampled (including those from Iceland and captive birds in the UK) and the other comprising all North American samples. Our results confirm that the European ruddy duck population is likely to derive solely from the captive population in the UK and we find no evidence of recent arrivals from North America or of admixture between ruddy ducks from Europe and North America. [source] Y chromosome haplotyping in Scandinavian wolves (Canis lupus) based on microsatellite markersMOLECULAR ECOLOGY, Issue 8 2001A.-K. Sundqvist Abstract The analysis of mitochondrial DNA sequences has for a long time been the most extensively used genetic tool for phylogenetic, phylogeographic and population genetic studies. Since this approach only considers female lineages, it tends to give a biased picture of the population history. The use of protein polymorphisms and microsatellites has helped to obtain a more unbiased view, but complementing population genetic studies with Y chromosome markers could clarify the role of each sex in natural processes. In this study we analysed genetic variability at four microsatellite loci on the canid Y chromosome. With these four microsatellites we constructed haplotypes and used them to study the genetic status of the Scandinavian wolf population, a population that now contains 60,70 animals but was thought to have been extinct in the 1970s. In a sample of 100 male wolves from northern Europe we found 17 different Y chromosome haplotypes. Only two of these were found in the current Scandinavian population. This indicates that there should have been at least two males involved in the founding of the Scandinavian wolf population after the bottleneck in the 1970s. The two Scandinavian Y chromosome haplotypes were not found elsewhere in northern Europe, which indicates low male gene flow between Scandinavia and the neighbouring countries. [source] Evolutionary history of the land snail Helix aspersa in the Western Mediterranean: preliminary results inferred from mitochondrial DNA sequencesMOLECULAR ECOLOGY, Issue 1 2001A. Guiller Abstract Intraspecific phylogeographic methods provide a means of examining the history of genetic exchange among populations. As part of a study of the history of Helixaspersa in the Western Mediterranean, we performed a phylogenetic analysis based on partial sequences of the mitochondrial large ribosomal subunit (16S) gene. Our samples include 31 H. a. aspersa populations from North Africa previously investigated for anatomical and biochemical characters. To clarify subspecific relationships, three individuals of the subspecies H. a. maxima were also studied. The molecular phylogeny inferred agrees largely with previous results, in splitting H. a. aspersa haplotypes into an eastern and a western group. H. a. maxima haplotypes form a third lineage arising before the H. a.aspersa groups. Divergence times estimated between the lineages suggest that dispersal during Pleistocene glaciation and vicariance events due to Pliocene geological changes in the western Mediterranean may both have played a significant part in the establishment of the present range of H. aspersa. [source] DNA barcoding of stylommatophoran land snails: a test of existing sequencesMOLECULAR ECOLOGY RESOURCES, Issue 4 2009ANGUS DAVISON Abstract DNA barcoding has attracted attention because it is a potentially simple and universal method for taxonomic assignment. One anticipated problem in applying the method to stylommatophoran land snails is that they frequently exhibit extreme divergence of mitochondrial DNA sequences, sometimes reaching 30% within species. We therefore trialled the utility of barcodes in identifying land snails, by analysing the stylommatophoran cytochrome oxidase subunit I sequences from GenBank. Two alignments of 381 and 228 base pairs were used to determine potential error rates among a test data set of 97 or 127 species, respectively. Identification success rates using neighbour-joining phylogenies were 92% for the longer sequence and 82% for the shorter sequence, indicating that a high degree of mitochondrial variation may actually be an advantage when using phylogeny-based methods for barcoding. There was, however, a large overlap between intra- and interspecific variation, with assignment failure (per cent of samples not placed with correct species) particularly associated with a low degree of mitochondrial variation (Kimura 2-parameter distance < 0.05) and a small GenBank sample size (< 25 per species). Thus, while the optimum intra/interspecific threshold value was 4%, this was associated with an overall error of 32% for the longer sequences and 44% for the shorter sequences. The high error rate necessitates that barcoding of land snails is a potentially useful method to discriminate species of land snail, but only when a baseline has first been established using conventional taxonomy and sample DNA sequences. There is no evidence for a barcoding gap, ruling out species discovery based on a threshold value alone. [source] Brief communication: Identification of the authentic ancient DNA sequence in a human bone contaminated with modern DNAAMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 3 2006Abigail S. Bouwman Abstract We present a method to distinguish authentic ancient DNA from contaminating DNA in a human bone. This is achieved by taking account of the spatial distribution of the various sequence families within the bone and the extent of degradation of the template DNAs, as revealed by the error content of the sequences. To demonstrate the veracity of the method, we handled two ancient human tibiae in order to contaminate them with modern DNA, and then subjected segments of the bones to various decontaminating treatments, including removal of the outer 1,2 mm, before extracting DNA, cloning, and obtaining a total of 107 mitochondrial DNA sequences. Sequences resulting from the deliberate contamination were located exclusively in the outer 1,2 mm of the bones, and only one of these 27 sequences contained an error that could be ascribed to DNA degradation. A second, much smaller set of relatively error-free sequences, which we ascribe to contamination during excavation or curation, was also located exclusively in the outer 1,2 mm. In contrast, a family of 72 sequences, displaying extensive degradation products but identifiable as haplogroup U5a1a, was distributed throughout one of the bones and represents the authentic ancient DNA content of this specimen. Am J Phys Anthropol, 2006. © 2006 Wiley-Liss, Inc. [source] Evidence for biogeographic patterning of mitochondrial DNA sequences in Eastern horse populationsANIMAL GENETICS, Issue 5 2006A. McGahern Summary Equine mitochondrial DNA (mtDNA) phylogeny reconstruction reveals a complex pattern of variation unlike that seen in other large domesticates. It is likely that this pattern reflects a process of multiple and repeated, although not necessarily independent, domestication events. Until now, no clear geographic affiliation of clades has been apparent. In this study, amova analyses have revealed a significant non-random distribution of the diversity among equine populations when seven newly sequenced Eurasian populations were examined in the context of previously published sequences. The association of Eastern mtDNA types in haplogroup F was highly significant using Fisher's exact test of independence (P = 0.00000). For the first time, clear biogeographic partitioning has been detected in equine mtDNA sequence. [source] Analysis of mitochondrial DNA protein-coding region in the Yeso Sika deer (Cervus nippon yesoensis)ANIMAL SCIENCE JOURNAL, Issue 4 2004Kenta WADA ABSTRACT In the present study, mitochondrial DNA sequences of the Yeso Sika deer (Cervus nippon yesoensis) were studied. Specifically, protein-coding genes as mitochondrial NADH dehydrogenase subunits (ND1, ND2, ND3, ND4L, ND4, ND5 and ND6), cytochrome c oxidase subunits (CO I and CO III), ATP synthase subunits (ATPase8 and ATPase6) and cytochrome b. Also, phylogenetic analyses on eight mammalian species were performed, including the Muntjac deer (Muntiacus reevesi). The rate of amino-acid substitution was lowest (3.74%) between Yeso Sika deer and Muntjac deer, and the values between Yeso Sika deer and other species (sheep, cattle, horse, pig, mouse, human and chimpanzee) were 6.63%, 7.30%, 12.55%, 13.03%, 23.59%, 24.82% and 25.04%, respectively. Among them, the highest value of divergence was recognized in ATPase8, and the second structure of ATPase8 showed a difference between the Yeso Sika deer and Muntjac deer as a result of the substitution of 34His,Tyr and 49Thr,Ile. In addition, we identified a substitution of an amino-acid sequence (19Thr,Ala) between the Yeso Sika deer and Yakushima Sika deer (C. n. yakushimae). From these results, ATPase8 was also a variable region in Cervidae. [source] Phylogeny, biogeography, and recurrent evolution of divergent bill types in the nectar-stealing flowerpiercers (Thraupini: Diglossa and Diglossopis)BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 1 2009WILLIAM M. MAUCK III Neotropical tanagers known as flowerpiercers (Diglossa and Diglossopis) have a novel feeding adaptation, comprising a downward curved hook on the maxilla that allows these species to obtain floral nectar without pollination. Using mitochondrial DNA sequences, the phylogenetic relationships of all 18 species of flowerpiercers were studied for the first time. Strong support was found for the monophyly of flowerpiercers and for the monophyly of four superspecies within flowerpiercers. However, previously described species-groups, as well as the genus Diglossopis, are not monophyletic. The biogeographic origin of flowerpiercers was identified as Andean, with a single dispersal event from the northern Andes to Central America and a single dispersal event from the northern Andes to the tepuis. The first principal component, representing a contrast between hook size and bill size, was mapped onto the phylogeny to examine the evolution of relative hook size in the group. Across the phylogeny, a relatively large hook and a relatively small hook evolved multiple times in unrelated lineages, indicating lability in bill morphology. Differences in hook size among sympatric species, together with habitat partitioning and behavioural differences, can explain the coexistence of multiple species of flowerpiercers at the same locality. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 98, 14,28. [source] | ||||||||||||||||||||||||||||