Mitochondrial DNA patterns among endemic stickleback from the Queen Charlotte Islands: a preliminary survey

1989 ◽  
Vol 67 (5) ◽  
pp. 1324-1328 ◽  
Author(s):  
M. H. Gach ◽  
T. E. Reimchen
Keyword(s):  
Mitochondrial Dna ◽  
Gasterosteus Aculeatus ◽  
Size Variation ◽  
Sequence Divergence ◽  
Isolated Populations ◽  
Base Pairs ◽  
Queen Charlotte Islands ◽  
Freshwater Habitats ◽  
Unique Restriction ◽  
High Degree

Mitochondrial DNA (mtDNA) restriction fragments were analyzed in 30 individuals from four populations of Gasterosteus aculeatus from the Queen Charlotte Islands, British Columbia. Two morphologically divergent endemic freshwater populations (Boulton Lake, Drizzle Lake), a typical stream form, and a brackish form were sampled. mtDNA size variation of 70 to 180 base pairs was noted among individuals from all populations, and 1.1 and 5.0 kilobase duplications were observed in mtDNAs from two individuals. Analysis of 75 mtDNA fragments produced by five restriction endonucleases revealed seven clones differing by less than 1.0% sequence divergence. While the high degree of genetic similarity is consistent with a postglacial origin of these populations, the presence of a unique restriction site among geographically isolated populations suggests that these endemics may have had a common freshwater ancestor that inhabited periglacial freshwater habitats rather than being independently derived from marine forms.

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.

Audiological Features and Mitochondrial DNA Sequence in a Large Family Carrying Mitochondrial A1555G Mutation without Use of Aminoglycoside

2005 ◽  
Vol 114 (2) ◽  
pp. 153-160 ◽  
Author(s):  
Tatsuo Matsunaga ◽  
Hiroshi Kumanomido ◽  
Yu-ichi Goto ◽  
Masae Shiroma ◽  
Shin-ichi Usami
Keyword(s):  
Hearing Loss ◽  
Mitochondrial Dna ◽  
Dna Sequences ◽  
Large Family ◽  
Outer Hair Cells ◽  
Japanese Family ◽  
A1555g Mutation ◽  
Genetic Mechanisms ◽  
High Degree ◽  
Sibling Group

To elucidate the pathophysiological and genetic mechanisms of hearing loss associated with the homoplasmic mitochondrial A1555G mutation in the absence of aminoglycoside exposure, we conducted audiological and genetic analyses on 67 maternally related members of a large Japanese family carrying this mutation. A consistent pattern was evident in the audiograms, with features of sensory presbycusis, cochlear origin at all levels of hearing loss, and a high degree of vulnerability of outer hair cells. That the degree of hearing loss was similar in affected subjects within the same sibling group but differed between sibling groups suggests the involvement of nuclear modifier genes. Total mitochondrial DNA sequences were completely identical among subjects with various levels of hearing loss, and lacked additional pathogenic mutations. For the diagnosis of sensorineural hearing loss, the mitochondrial A1555G mutation should be considered when these features are present even in the absence of aminoglycoside exposure.

scholarly journals Comparative analysis reveals within-population genome size variation in a rotifer is driven by large genomic elements with highly abundant satellite DNA repeat elements

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
C. P. Stelzer ◽  
J. Blommaert ◽  
A. M. Waldvogel ◽  
M. Pichler ◽  
B. Hecox-Lea ◽  
...  
Keyword(s):  
Genome Size ◽  
Satellite Dna ◽  
Gc Content ◽  
Size Variation ◽  
Isolated Populations ◽  
Genome Size Variation ◽  
Variable Regions ◽  
Geographic Population ◽  
Genome Size Evolution ◽  
Size Evolution

Abstract Background Eukaryotic genomes are known to display an enormous variation in size, but the evolutionary causes of this phenomenon are still poorly understood. To obtain mechanistic insights into such variation, previous studies have often employed comparative genomics approaches involving closely related species or geographically isolated populations within a species. Genome comparisons among individuals of the same population remained so far understudied—despite their great potential in providing a microevolutionary perspective to genome size evolution. The rotifer Brachionus asplanchnoidis represents one of the most extreme cases of within-population genome size variation among eukaryotes, displaying almost twofold variation within a geographic population. Results Here, we used a whole-genome sequencing approach to identify the underlying DNA sequence differences by assembling a high-quality reference genome draft for one individual of the population and aligning short reads of 15 individuals from the same geographic population including the reference individual. We identified several large, contiguous copy number variable regions (CNVs), up to megabases in size, which exhibited striking coverage differences among individuals, and whose coverage overall scaled with genome size. CNVs were of remarkably low complexity, being mainly composed of tandemly repeated satellite DNA with only a few interspersed genes or other sequences, and were characterized by a significantly elevated GC-content. CNV patterns in offspring of two parents with divergent genome size and CNV patterns in several individuals from an inbred line differing in genome size demonstrated inheritance and accumulation of CNVs across generations. Conclusions By identifying the exact genomic elements that cause within-population genome size variation, our study paves the way for studying genome size evolution in contemporary populations rather than inferring patterns and processes a posteriori from species comparisons.

scholarly journals A new species of Amphisbaena (Squamata: Amphisbaenidae) from the Orinoquian region of Colombia

2021 ◽  
Vol 71 ◽  
pp. 55-74
Author(s):  
Juan José Torres-Ramírez ◽  
Teddy Angarita-Sierra ◽  
Mario Vargas-Ramírez
Keyword(s):  
Mitochondrial Dna ◽  
New Species ◽  
Phylogenetic Analyses ◽  
Similar Species ◽  
General Knowledge ◽  
Southern Brazil ◽  
Base Pairs ◽  
Northern South America ◽  
Great Genetic Distance ◽  
A New Species

In northern South America, amphisbaenians are rarely seen among the herpetofauna.Thus, general knowledge about them is very poor. During a herpetological survey in 2012 at Casanare, Colombia, we found two specimens of an unusual Amphisbaena. A third specimen sharing the same morphotype labeled Amphisbaena sp. from Vichada department was found deposided in an Colombian reptile collection. Based on morphological analyses together with phylogenetic analyses of 1029 base pairs of the mitochondrial DNA (mtDNA), we describe a new species of Amphisbaena that inhabits in the Orinoquian region of Colombia. The new species is part of a phylogenetic clade together with A. mertensii and A. cunhai (central-southern Brazil), exhibiting a great genetic distance (26.1–28.9%) between the newly identified lineage versus those taxa, and versus the sympatric taxa A. alba and A. fuliginosa. Morphologically, this new Amphisbaena can be distinguished from their congeners by characters combination of number of preocloacal pores, absence of malar scale, postgenial scales and body and caudal annuli counts. Amphisbaena gracilis is on morphology grounds the most similar species. However, the new species can be distinguished from it by having higher body annuli counts, angulus ories aliegned with the edges of the ocular scales and center of frontal scales, less number of large middorsal segments of the first and second body annulus, and rostral scale visible from above. The description of this new Amphisbaena species points out the urgent need to increase the knowledge of worm lizards in Colombia

scholarly journals A new cryptic arboreal species of the Cyrtodactylus brevipalmatus group (Squamata: Gekkonidae) from the uplands of western Thailand

2021 ◽  
Vol 71 ◽  
pp. 723-746
Author(s):  
L. Lee Grismer ◽  
Chatmongkon Suwannapoom ◽  
Parinya Pawangkhanant ◽  
Roman A. Nazarov ◽  
Platon V. Yushchenko ◽  
...  
Keyword(s):  
New Species ◽  
Mitochondrial Gene ◽  
Sequence Divergence ◽  
Field Work ◽  
Morphological Characters ◽  
Sister Species ◽  
Base Pairs ◽  
Meristic Characters ◽  
Nadh Dehydrogenase Subunit 2 ◽  
A New Species

The first integrative taxonomic analysis of the Cyrtodactylus brevipalmatus group of Southeast Asia recovered two newly discovered populations from the Tenasserim Mountains in Suan Phueng District, Ratchaburi Province, Thailand as a new species described here as C. rukhadeva sp. nov. Based on 1397 base pairs of the mitochondrial gene NADH dehydrogenase subunit 2 (ND2), C. rukhadeva sp. nov. is the well-supported sister species to a clade containing three undescribed species, C. ngati, and C. cf. interdigitalis with a large uncorrected pairwise sequence divergence from other species in the brevipalmatus group ranging from 15.4–22.1%. Cyrtodactylus elok and C. brevipalmatus are recovered as poorly supported sister species and the well-supported sister lineage to the remainder of the brevipalmatus group. Cyrtodactylus rukhadeva sp. nov. is putatively diagnosable on the basis of a number of meristic characters and easily separated from the remaining species of the brevipalmatus group by a number of discrete morphological characters as well as its statistically significant wide separation in multivariate morphospace. The discovery of C. rukhadeva sp. nov. continues to underscore the unrealized herpetological diversity in the upland forests of the Tenasserim Mountains and that additional field work will undoubtedly result in the discovery of additional new species.

scholarly journals Genetic divergence in mitochondrial DNA of Anopheles nuneztovari (Diptera: Culicidae) from Brazil and Colombia

2000 ◽  
Vol 23 (1) ◽  
pp. 71-78 ◽  
Author(s):  
Vera Margarete Scarpassa ◽  
Silvia Geurgas ◽  
Ana Maria L. Azeredo-Espin ◽  
Wanderli Pedro Tadei
Keyword(s):  
Mitochondrial Dna ◽  
Genetic Divergence ◽  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Sequence Divergence ◽  
Brazilian Amazon ◽  
Restriction Endonucleases ◽  
Separate Species ◽  
Geographic Populations

In the present study, we have examined the variability in Anopheles nuneztovari mitochondrial DNA of three populations from the Brazilian Amazon and one from western Colombia (Sitronela), using four restriction endonucleases (BclI, ClaI, HindIII, SstI). The haplotype diversity (h) was slightly elevated in all populations (0.5000 to 0.6765), whereas the nucleotide diversity (pi) was lower in the Sitronela population (0.0029) and higher in populations from the Brazilian Amazon (0.0056 to 0.0098). The degree of sequence divergence (delta) estimated within the Brazilian Amazon and that in Sitronela (0.0329 to 0.0371) suggests that these geographic populations of A. nuneztovari may eventually constitute separate species. The low sequence divergence values among the three Brazilian Amazon populations (0.0012 to 0.0031) indicate that these populations are genetically similar. These results are consistent with those recently reported for allozymes of these same populations.

Strong genetic subdivision in Leptobrachium hendricksoni (Anura: Megophryidae) in Southeast Asia

2018 ◽  
Vol 39 (1) ◽  
pp. 99-111
Author(s):  
Gordon Draškić ◽  
Sansareeya Wangkulangkul ◽  
Iñigo Martínez-Solano ◽  
Judit Vörös
Keyword(s):  
Southeast Asia ◽  
Sequence Divergence ◽  
Population Divergence ◽  
Geological History ◽  
Base Pairs ◽  
Sea Levels ◽  
Phylogenetic Studies ◽  
High Sequence Divergence ◽  
Southern Thailand ◽  
Rising Sea Levels

Many biodiversity hotspots are located in areas with a complex geological history, like Southeast Asia, where species diversity may still be far underestimated, especially in morphologically conservative groups like amphibians. Recent phylogenetic studies on the frog genusLeptobrachiumfrom Southeast Asia revealed the presence of deeply divergent mitochondrial clades inLeptobrachium hendricksonifrom Malaysia and Sumatra but populations from Thailand have not been studied so far. In this study, we re-evaluate patterns of intraspecific genetic diversity inL. hendricksonibased on the analysis of combined sequences of mitochondrial 12S and 16S genes (1310 base pairs) including for the first time samples from southern Thailand. Thai populations ofL. hendricksoniformed a distinct clade with respect to populations from central and southern Malaysia and Sumatra. High sequence divergence between lineages from Thailand, Malaysia and Sumatra suggests the possible presence of cryptic species inL. hendricksoni. Divergence withinL. hendricksonidates back to the late Miocene, around 6 Mya, when lineages from Thailand, north Malaysia and Sumatra split from a lineage in south Malaysia, at about the same time as rising sea levels isolated the Thai-Malay peninsula. Subsequent splits took place later in the Pliocene, around 4.5 and 2.6 Mya. Our results highlight the role of geological history in promoting population divergence and speciation.

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