Phylogenetic Relationships Among Members of Salvelinus Inferred from Mitochondrial DNA Divergence

1990 ◽  
Vol 47 (5) ◽  
pp. 984-991 ◽  
Author(s):  
Peter M. Grewe ◽  
Neil Billington ◽  
Paul D. N. Hebert
Keyword(s):  
Mitochondrial Dna ◽  
Salvelinus Alpinus ◽  
Restriction Analysis ◽  
Divergence Time ◽  
Sequence Divergence ◽  
Early Pleistocene ◽  
Related Taxon ◽  
Extant Species ◽  
Species Pairs ◽  
Restriction Sites

Mitochondrial DNA (mtDNA) was isolated from five species of the genus Salvelinus (alpinus, confluentus, fontinalis, malma, and namaycush) and from the closely related taxon, Hucho hucho. Restriction sites recognized by 14 endonucleases were mapped for each of the species and percent sequence divergence estimated between species pairs. A phylogeny of Savelinus based on restriction analysis of mtDNA, using Hucho as an outgroup, readily resolved the three subgenera: Baione, Cristivomer, and Salvelinus. Within Baione, no differences were detected between the mtDNA of brook (S. fontinalis fontinalis) and aurora (S. f. timagamiensis) trout. However, members of the subgenus Salvelinus were more variable such that two groups were resolved, one consisting of S. alpinus alpinus, S. a. oquassa, and S. malma, and the other of S. a. stagnalis and S. confluentus. A composite distance phenogram representing the phylogeny of the subfamily Salmoninae was constructed using the sequence divergence data obtained in the current study in conjunction with data from three other salmonid mtDNA studies. Estimates of divergence time between the major taxa of this group suggest that the salmonine genera originated in the late-Miocene to early-Pliocene, while extant species originated during the late-Pliocene to early-Pleistocene.

Restriction fragment analysis of mitochondrial DNA in Common Murres, Uria aalge, from four Norwegian seabird colonies

1991 ◽  
Vol 69 (6) ◽  
pp. 1577-1584 ◽  
Author(s):  
Truls Moum ◽  
Kjell Einar Erikstad ◽  
Eirik Bjørklid
Keyword(s):  
Mitochondrial Dna ◽  
Restriction Analysis ◽  
Sequence Divergence ◽  
Ancestral Population ◽  
Population Divergence ◽  
Uria Aalge ◽  
Population Bottlenecks ◽  
Geographic Population ◽  
Common Murres ◽  
Seabird Colonies

Alcid species (auks) breed in a restricted number of large seabird colonies and are considered highly philopatric. Mitochondrial DNA (mtDNA) of Common Murres, Uria aalge, from four Norwegian colonies was investigated by restriction analysis to assess the amount of geographic population structure and genetic variability in a colonial breeder. Eleven restriction endonucleases revealed 13 mtDNA genotypes among 51 individuals. Genetic diversity was low, with an average of 0.11% (range 0.0–0.55%) sequence divergence between all individuals. Population divergence within the surveyed region seems to be minimal, demonstrated by the low levels of sequence divergence between colonies and lack of spatial structuring of genotypes. Such results can be expected if birds originated from a smaller ancestral population during glaciation, and may have been reinforced by repeated population bottlenecks and considerable gene flow between colonies.

scholarly journals THE USE OF RESTRICTION ENDONUCLEASES TO MEASURE MITOCHONDRIAL DNA SEQUENCE RELATEDNESS IN NATURAL POPULATIONS. I. POPULATION STRUCTURE AND EVOLUTION IN THE GENUS PEROMYSCUS

Genetics ◽  
1979 ◽  
Vol 92 (1) ◽  
pp. 279-295
Author(s):  
John C Avise ◽  
Robert A Lansman ◽  
Rosemary O Shade
Keyword(s):  
Mitochondrial Dna ◽  
Restriction Analysis ◽  
Population Analysis ◽  
Natural Populations ◽  
Sequence Divergence ◽  
Female Parent ◽  
Restriction Endonucleases ◽  
Laboratory Animals ◽  
Molecular Technique ◽  
Mtdna Sequences

ABSTRACT In this study we introduce to natural population analysis a molecular technique that involves the use of restriction endonucleases to compare mitochondrial DNA (mtDNA) sequences. We have examined the fragment patterns produced by six restriction endonucleases acting upon mtDNA isolated from 23 samples of three species of the rodent Peromyscus. Our observations confirm the following conclusions derived from previous experiments with laboratory animals: (1) mtDNA within an individual appears homogeneous; (2) at least the majority of mtDNA present in an individual is inherited from the female parent. Our experiments demonstrate for the first time that there is detectable heterogeneity in mtDNA sequences within and among natural geographic populations of a species and that this heterogeneity can readily be used to estimate relatedness between individuals and populations. Individuals collected within a single locale show less than 0.5% sequence divergence, while those collected from conspecific populations separated by 50 to 500 miles differ by approximately 1.5%. The mtDNAs of the closely related sibling species P. polionotus and P. mniculutus differ from each other by 13 to 17%; nonsibling species differ by more than 20%. Qualitative and quantitative approaches to analysis of digestion patterns are suggested. The results indicate that restriction analysis of mtDNA may become the most sensitive and powerful technique yet available for reconstructing evolutionary relationships among conspecific organisms.

Restriction Analysis of Mitochondrial DNA from the Yellow-footed Rock-wallaby, Petrogale xanthopus: Implications for Management

1997 ◽  
Vol 24 (3) ◽  
pp. 289 ◽  
Author(s):  
M. D. B. Eldridge
Keyword(s):  
Mitochondrial Dna ◽  
New South ◽  
Restriction Analysis ◽  
Sequence Divergence ◽  
South Australia ◽  
Unique Haplotype ◽  
South Wales ◽  
In Captivity ◽  
Average Sequence Divergence ◽  
Average Sequence

The extent of mitochondrial DNA divergence between populations of the vulnerable yellow-footed rock- wallaby, Petrogale xanthopus, was assessed by restriction analysis. Of the 15 restriction endonucleases, five were informative, with a single unique haplotype identified in P. x. celeris from Queensland (Qld) (n = 8) and a further two unique haplotypes in three sampled populations of P. x. xanthopus from New South Wales (NSW) (n = 1) and South Australia (SA) (n = 9). The two subspecies of P. xanthopus were found to be genetically distinct (average sequence divergence = 0·72%). As this divergence is greater than that found between some Petrogale species, it is recommended that populations of P. x. xanthopus and P. x. celeris be managed independently both in captivity and the wild. The NSW population of P. x. xanthopus appears genetically similar to those in SA, although these data are limited.

scholarly journals Morphological, Ecological, and Molecular Divergence of Conogethes pinicolalis from C. punctiferalis (Lepidoptera: Crambidae)

Insects ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 455
Author(s):  
Na Ra Jeong ◽  
Min Jee Kim ◽  
Sung-Soo Kim ◽  
Sei-Woong Choi ◽  
Iksoo Kim
Keyword(s):  
Phylogenetic Analysis ◽  
First Generation ◽  
Incomplete Lineage Sorting ◽  
Divergence Time ◽  
Sequence Divergence ◽  
Lineage Sorting ◽  
Mitochondrial Coi ◽  
Feeding Type ◽  
Pine Trees ◽  
Yellow Peach Moth

Conogethes pinicolalis has long been considered as a Pinaceae-feeding type of the yellow peach moth, C. punctiferalis, in Korea. In this study, the divergence of C. pinicolalis from the fruit-feeding moth C. punctiferalis was analyzed in terms of morphology, ecology, and genetics. C. pinicolalis differs from C. punctiferalis in several morphological features. Through field observation, we confirmed that pine trees are the host plants for the first generation of C. pinicolalis larvae, in contrast to fruit-feeding C. punctiferalis larvae. We successfully reared C. pinicolalis larvae to adults by providing them pine needles as a diet. From a genetic perspective, the sequences of mitochondrial COI of these two species substantially diverged by an average of 5.46%; moreover, phylogenetic analysis clearly assigned each species to an independent clade. On the other hand, nuclear EF1α showed a lower sequence divergence (2.10%) than COI. Overall, EF1α-based phylogenetic analysis confirmed each species as an independent clade, but a few haplotypes of EF1α indicated incomplete lineage sorting between these two species. In conclusion, our results demonstrate that C. pinicolalis is an independent species according to general taxonomic criteria; however, analysis of the EF1α sequence revealed a short divergence time.

scholarly journals Genetic Diversities and Historical Dynamics of Native Ethiopian Horse Populations (Equus caballus) Inferred from Mitochondrial DNA Polymorphisms

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 155
Author(s):  
Kefena Effa ◽  
Sonia Rosenbom ◽  
Jianlin Han ◽  
Tadelle Dessie ◽  
Albano Beja-Pereira
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Genetic Differentiation ◽  
Sequence Divergence ◽  
Dna Polymorphisms ◽  
Base Pairs ◽  
Feral Horses ◽  
Domestic Horses ◽  
D Loop ◽  
Diversity Estimates

Matrilineal genetic diversity and relationship were investigated among eight morphologically identified native Ethiopian horse populations using polymorphisms in 46 mtDNA D-loop sequences (454 base pairs). The horse populations identified were Abyssinian, Bale, Borana, Horro, Kafa, Kundido feral horses, Ogaden and Selale. Mitochondrial DNA D-loop sequences were characterized by 15 variable sites that defined five different haplotypes. All genetic diversity estimates, including Reynolds’ linearized genetic distance, genetic differentiation (FST) and nucleotide sequence divergence (DA), revealed a low genetic differentiation in native Ethiopian horse populations. However, Kundido feral and Borana domestic horses were slightly diverged from the rest of the Ethiopian horse populations. We also tried to shed some light on the matrilineal genetic root of native Ethiopian horses from a network constructed by combining newly generated haplotypes and reference haplotypes deposited in the GenBank for Eurasian type Turkish Anatolian horses that were used as a genetic conduit between Eurasian and African horse populations. Ninety-two haplotypes were generated from the combined Ethio-Eurasian mtDNA D-loop sequences. A network reconstructed from the combined haplotypes using Median-Joining algorithm showed that haplotypes generated from native Ethiopian horses formed separate clusters. The present result encourages further investigation of the genetic origin of native African horses by retrieving additional mtDNA sequences deposited in the GenBank for African and Eurasian type horses.

scholarly journals Using a GTR+Γ substitution model for dating sequence divergence when stationarity and time-reversibility assumptions are violated

2020 ◽  
Vol 36 (Supplement_2) ◽  
pp. i884-i894
Author(s):  
Jose Barba-Montoya ◽  
Qiqing Tao ◽  
Sudhir Kumar
Keyword(s):  
Divergence Time ◽  
Sequence Divergence ◽  
Molecular Dating ◽  
Divergence Times ◽  
Time Reversibility ◽  
Sequence Alignments ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Substitution Process ◽  
The Impact

Abstract Motivation As the number and diversity of species and genes grow in contemporary datasets, two common assumptions made in all molecular dating methods, namely the time-reversibility and stationarity of the substitution process, become untenable. No software tools for molecular dating allow researchers to relax these two assumptions in their data analyses. Frequently the same General Time Reversible (GTR) model across lineages along with a gamma (+Γ) distributed rates across sites is used in relaxed clock analyses, which assumes time-reversibility and stationarity of the substitution process. Many reports have quantified the impact of violations of these underlying assumptions on molecular phylogeny, but none have systematically analyzed their impact on divergence time estimates. Results We quantified the bias on time estimates that resulted from using the GTR + Γ model for the analysis of computer-simulated nucleotide sequence alignments that were evolved with non-stationary (NS) and non-reversible (NR) substitution models. We tested Bayesian and RelTime approaches that do not require a molecular clock for estimating divergence times. Divergence times obtained using a GTR + Γ model differed only slightly (∼3% on average) from the expected times for NR datasets, but the difference was larger for NS datasets (∼10% on average). The use of only a few calibrations reduced these biases considerably (∼5%). Confidence and credibility intervals from GTR + Γ analysis usually contained correct times. Therefore, the bias introduced by the use of the GTR + Γ model to analyze datasets, in which the time-reversibility and stationarity assumptions are violated, is likely not large and can be reduced by applying multiple calibrations. Availability and implementation All datasets are deposited in Figshare: https://doi.org/10.6084/m9.figshare.12594638.

Geographic population structure and sequence divergence in the mitochondrial DNA control region of the Japanese wild boar (Sus scrofa leucomystax), with reference to those of domestic pigs

1996 ◽  
Vol 34 (5-6) ◽  
pp. 179-189 ◽  
Author(s):  
Naohiko Okumura ◽  
Naotaka Ishiguro ◽  
Masuo Nakano ◽  
Katsuya Hirai ◽  
Akira Matsui ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Population Structure ◽  
Wild Boar ◽  
Control Region ◽  
Sus Scrofa ◽  
Sequence Divergence ◽  
Geographic Population ◽  
Mitochondrial Dna Control Region ◽  
Domestic Pigs ◽  
Japanese Wild Boar

Mitochondrial DNA polymorphism in a black fly, Simulium vittatum (Diptera: Simuliidae)

1998 ◽  
Vol 76 (3) ◽  
pp. 440-447 ◽  
Author(s):  
X Zhu ◽  
K P Pruess ◽  
T O Powers
Keyword(s):  
New York ◽  
Mitochondrial Dna ◽  
Rflp Analysis ◽  
Mitochondrial Haplotype ◽  
Black Flies ◽  
Mitochondrial Dna Polymorphism ◽  
Simulium Vittatum ◽  
Hybridization Probes ◽  
Restriction Sites ◽  
Mitochondrial Heterogeneity

Mitochondrial DNA (mtDNA) was extracted from pooled field-collected samples representing six species of black flies (Cnephia dacotensis, Simulium bivittaum, S. johansenni, S. luggeri, S. piperi, S. vittatum) and compared by restriction fragment length polymorphism (RFLP) analysis. Morphospecies were molecularly distinct, with few shared restriction fragments. Eleven populations of S. vittatum were found that appeared to be homogeneous for a single mitochondrial haplotype. Ten other populations of S. vittatum showed extensive mitochondrial heterogeneity. In part, these samples contained mixtures of two cytologically recognized siblings: IIIL-1 and IS-7. About 70% of the mitochondrial genome of a population pure for sibling IIIL-1 was cloned as five HindIII fragments, which were used as hybridization probes to examine individual black flies. Thirteen mtDNA haplotypes involving permutations of 10 HindIII restriction sites were identified in individual black flies examined from 26 populations. DNA from 168 larvae cut with both EcoR1 and HindIII revealed five additional haplotypes. One HindIII haplotype was present in 84% of 390 larvae examined and predominated in every population examined from New York to California and in both the IIIL-1 and IS-7 siblings. Nebraska populations had individuals with nearly all known haplotypes. The most common haplotype was usually the only form present in warm, silty streams with organic enrichment. Rarer haplotypes were found in cool, spring-fed streams but without clear geographic or phylogenetic components.

scholarly journals Intraspecific divergences and phylogeography of Panzerina lanata (Lamiaceae) in Northwest China

2018 ◽  
Author(s):  
Yanfen Zhao ◽  
Hongxiang Zhang ◽  
Borong Pan ◽  
Mingli Zhang
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Population Genetic ◽  
Divergence Time ◽  
Northwest China ◽  
Northwestern China ◽  
Intraspecific Diversity ◽  
Early Pleistocene ◽  
Helan Mountains ◽  
The Impact

Climactic fluctuations during the Quaternary played a crucial role in genetic diversity and population genetic structure of many plant species in northwestern China. In order to understand the impact of climate change on herbaceous plants, we studied Panzerina lanata (Lamiaceae), a widely distributed species. Two chloroplast DNA intergenic spacers (trnH-psbA and rpoB-trnC) were used to sequence 269 individuals from 27 populations and seven haplotypes were identified. Genetic structure and demographic characteristics were estimated using AMOVA, neutrality tests, and mismatch distribution analyses. The divergence times between the seven haplotypes were estimated using Beast. Our results revealed high levels of total genetic diversity (HT = 0.673±0.0869) and low levels of average within-population genetic diversity (HS = 0.033±0.0214). The analysis of molecular variance indicated major genetic differentiation among the three groups: northern, central, and eastern group. The species distribution modeling and demographic analysis indicated that P. lanata has not experience a recent range expansion. The divergence time within P. lanata occurred between the early Pleistocene and the late Pleistocene, which coincides with aridification and the expansion of the deserts in northwestern China that resulted in species diversification and habitat fragmentation. In addition, we speculate that the deserts and the Helan Mountains acted as effective geographic barriers that led to intraspecific diversity.

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