The roles of possible geographic barriers and geological events on the phylogeographic structure of the Eastern broad toothed field mouse (Apodemus mystacinus)

Mammalia ◽  
2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Gül Olgun Karacan ◽  
Reyhan Çolak ◽  
Ercüment Çolak
Keyword(s):  
Dna Sequences ◽  
Nuclear Dna ◽  
Phylogeographic Structure ◽  
Field Mouse ◽  
Interphotoreceptor Retinoid Binding Protein ◽  
Aegean Islands ◽  
Mitochondrial Data ◽  
D Loop ◽  
Physical Barriers ◽  
First Time

Abstract The Eastern broad toothed field mouse, Apodemus mystacinus, is a rodent species distributed in Turkey, the Middle East, and a few Aegean Islands. The aim of this study is to analyse the phylogeographic structure of A. mystacinus and possible causes of its differentiation, on the basis of mitochondrial and nuclear DNA sequences using a large number of new samples from Turkey. In this context, partial mitochondrial sequences of cytochrome b (Cytb), control region (D-loop) and a nuclear interphotoreceptor retinoid-binding protein (IRBP) gene were used to reveal the geographical differentiation among A. mystacinus populations and the validity of its subspecies. The estimated divergence times revealed that the first separation of A. mystacinus into three distinct groups (subspecies of A. mystacinus: A. m. mystacinus, A. m. smyrnensis, and A. m. euxinus) begun 0.641 Mya. The possible physical barriers in Anatolia such as high mountains and rivers could interrupt the gene flow between A. mystacinus populations. The results of the present study indicated that A. mystacinus might have used the high rocky areas along the Anatolian Diagonal as a dispersal way. Moreover, mitochondrial data in this study suggested for the first time that A. m. rhodius is synonymous with the nominative subspecies A. m. mystacinus.

scholarly journals Is Phylogeographic Congruence Predicted by Historical Habitat Stability, or Ecological Co-associations?

2021 ◽  
Vol 5 (5) ◽  
Author(s):  
Ryan C Garrick ◽  
Chaz Hyseni ◽  
Ísis C Arantes ◽  
Louis G Zachos ◽  
Peter C Zee ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Species Interactions ◽  
Ecological Niche Modeling ◽  
Nuclear Dna ◽  
Abiotic Factors ◽  
Genetic Data ◽  
Phylogeographic Structure ◽  
Biotic Factors ◽  
Effective Population ◽  
Species Responses

Abstract Comparative phylogeographic studies can distinguish between idiosyncratic and community-wide responses to past environmental change. However, to date, the impacts of species interactions have been largely overlooked. Here we used non-genetic data to characterize two competing scenarios about expected levels of congruence among five deadwood-associated (saproxylic) invertebrate species (i.e., a wood-feeding cockroach, termite, and beetle; a predatory centipede, and a detritivorous millipede) from the southern Appalachian Mountains—a globally recognized center of endemism. Under one scenario, abiotic factors primarily drove species’ responses, with predicted congruence based on the spatial overlap of climatically stable habitat areas estimated for each species via ecological niche modeling. The second scenario considered biotic factors to be most influential, with proxies for species interactions used to predict congruence. Analyses of mitochondrial and nuclear DNA sequences focused on four axes of comparison: the number and geographic distribution of distinct spatial-genetic clusters, phylogeographic structure, changes in effective population size, and historical gene flow dynamics. Overall, we found stronger support for the ecological co-associations scenario, suggesting an important influence of biotic factors in constraining or facilitating species’ responses to Pleistocene climatic cycles. However, there was an imperfect fit between predictions and outcomes of genetic data analyses. Thus, while thought-provoking, conclusions remain tentative until additional data on species interactions becomes available. Ultimately, the approaches presented here advance comparative phylogeography by expanding the scope of inferences beyond solely considering abiotic drivers, which we believe is too simplistic. This work also provides conservation-relevant insights into the evolutionary history of a functionally important ecological community.

scholarly journals Measwring and Testing Genetic Differentiation With Ordered Versus Unordered Alleles

Genetics ◽  
1996 ◽  
Vol 144 (3) ◽  
pp. 1237-1245 ◽  
Author(s):  
O Pons ◽  
R J Petit
Keyword(s):  
Dna Sequences ◽  
Nuclear Dna ◽  
Mutation Rates ◽  
Phylogeographic Structure ◽  
Published Data ◽  
Data Set ◽  
Subdivided Populations ◽  
Two Measures ◽  
The Difference ◽  
Single Data

Abstract Estimates and variances of diversity and differentiation measures in subdivided populations are proposed that can be applied to haplotypes (ordered alleles such as DNA sequences, which may contain a record of their own histories). Hence, two measures of differentiation can be compared for a single data set: one (GST) that makes use only of the allelic frequencies and the other (NST) for which similarities between the haplotypes are taken into account in addition. Tests are proposed to compare NST and GST with zero and with each other. The difference between NST and GST can be caused by several factors, including sampling artefacts, unequal effect of mutation rates and phylogeographic structure. The method presented is applied to a published data set where a nuclear DNA sequence had been determined from individuals of a grasshopper distributed in 24 regions of Europe. Additional insights into the genetic subdivision of these populations are obtained by progressively combining related haplotypes and reanalyzing the data each time.

Karyological analysis and genome size in Milium (Gramineae) with special reference to polyploidy and chromosomal evolution

Genome ◽  
1991 ◽  
Vol 34 (6) ◽  
pp. 868-878 ◽  
Author(s):  
Simon T. Bennett ◽  
Sandra M. Thomas
Keyword(s):  
Genome Size ◽  
Geographical Distribution ◽  
Dna Sequences ◽  
Chromosome Evolution ◽  
Nuclear Dna ◽  
Chromosomal Evolution ◽  
System Support ◽  
Strong Resemblance ◽  
First Time ◽  
Dna Amounts

Karyotypes, nuclear DNA amounts, and meiotic behaviour are presented for Milium effusum L. (2n = 28), Milium montianum Parl. (2n = 22), and two cytotypes of Milium vernale Bieb. (2n = 8, 10). The bimodal karyotype of M. montianum (8 large and 14 small chromosomes) is described for the first time. Evidence from C-banding and geographical distribution suggests an ancient interracial allopolyploid origin for M. effusum (2n = 28). Although M. montianum is undoubtedly allopolyploid, its parentage is unconfirmed. A strong resemblance between the M. vernale (2n = 8) karyotype and the eight large chromosomes in M. montianum suggests a common ancestry. It is possible that a diploid form of M. effusum contributed the remaining 14 chromosomes. A selective loss of DNA sequences from the smaller chromosomes during the subsequent reorganization of the allopolyploid genome may have enhanced the bimodality of the karyotype. Geographical distribution and a change in the breeding system support the direction of the change x = 5 to x = 4 in M. vernale. Allopolyploidy appears to have played a central role in the chromosome evolution and speciation of Milium.Key words: Milium (Gramineae), karyotype analysis, genome size, polyploidy, chromosome evolution.

scholarly journals LENGTH MUTATIONS IN HUMAN MITOCHONDRIAL DNA

Genetics ◽  
1983 ◽  
Vol 104 (4) ◽  
pp. 699-711
Author(s):  
R L Cann ◽  
A C Wilson
Keyword(s):  
Nuclear Dna ◽  
Average Rate ◽  
Rapid Evolution ◽  
Human Species ◽  
Base Pairs ◽  
Human Mitochondrial Dna ◽  
Noncoding Sequences ◽  
Mitochondrial Dnas ◽  
D Loop ◽  
Length Mutations

ABSTRACT By high-resolution, restriction mapping of mitochondrial DNAs purified from 112 human individuals, we have identified 14 length variants caused by small additions and deletions (from about 6 to 14 base pairs in length). Three of the 14 length differences are due to mutations at two locations within the D loop, whereas the remaining 11 occur at seven sites that are probably within other noncoding sequences and at junctions between coding sequences. In five of the nine regions of length polymorphism, there is a sequence of five cytosines in a row, this sequence being comparatively rare in coding DNA. Phylogenetic analysis indicates that, in most of the polymorphic regions, a given length mutation has arisen several times independently in different human lineages. The average rate at which length mutations have been arising and surviving in the human species is estimated to be many times higher for noncoding mtDNA than for noncoding nuclear DNA. The mystery of why vertebrate mtDNA is more prone than nuclear DNA to evolve by point mutation is now compounded by the discovery of a similar bias toward rapid evolution by length mutation.

scholarly journals TERRA: A Novel Biomarker of Embryo Quality and Art Outcome

Genes ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 475
Author(s):  
Maria Santa Rocca ◽  
Ludovica Dusi ◽  
Andrea Di Nisio ◽  
Erminia Alviggi ◽  
Benedetta Iussig ◽  
...  
Keyword(s):  
Telomere Length ◽  
Dna Sequences ◽  
Male Fertility ◽  
Embryo Quality ◽  
Assisted Reproductive Technologies ◽  
Biological Clock ◽  
Reproductive Technologies ◽  
Age Related ◽  
Non Coding Rna ◽  
First Time

Telomeres are considered to be an internal biological clock, and their progressive shortening has been associated with the risk of age-related diseases and reproductive alterations. Over recent years, an increasing number of studies have focused on the association between telomere length and fertility, identifying sperm telomere length (STL) as a novel biomarker of male fertility. Although typically considered to be repeated DNA sequences, telomeres have recently been shown to also include a long non-coding RNA (lncRNA) known as TERRA (telomeric repeat-containing RNAs). Interestingly, males with idiopathic infertility show reduced testicular TERRA expression, suggesting a link between TERRA and male fertility. The aim of this study was to investigate the role of seminal TERRA expression in embryo quality. To this end, STL and TERRA expression were quantified by Real Time qPCR in the semen of 35 men who underwent assisted reproductive technologies (ART) and 30 fertile men. We found that TERRA expression in semen and STL was reduced in patients that underwent ART (both p < 0.001). Interestingly, TERRA and STL expressions were positively correlated (p = 0.010), and TERRA expression was positively associated with embryo quality (p < 0.001). These preliminary findings suggest a role for TERRA in the maintenance of sperm telomere integrity during gametogenesis, and for the first time, TERRA expression was found as a predictive factor for embryo quality in the setting of assisted reproduction.

The Age of Nonsynonymous and Synonymous Mutations in Animal mtDNA and Implications for the Mildly Deleterious Theory

Genetics ◽  
1999 ◽  
Vol 153 (1) ◽  
pp. 497-506 ◽  
Author(s):  
Rasmus Nielsen ◽  
Daniel M Weinreich
Keyword(s):  
Dna Sequences ◽  
Purifying Selection ◽  
Data Sets ◽  
Deleterious Mutations ◽  
Synonymous Mutations ◽  
Weak Evidence ◽  
Mitochondrial Data ◽  
The Mean ◽  
Excess Number ◽  
Neutral Mutations

Abstract McDonald/Kreitman tests performed on animal mtDNA consistently reveal significant deviations from strict neutrality in the direction of an excess number of polymorphic nonsynonymous sites, which is consistent with purifying selection acting on nonsynonymous sites. We show that under models of recurrent neutral and deleterious mutations, the mean age of segregating neutral mutations is greater than the mean age of segregating selected mutations, even in the absence of recombination. We develop a test of the hypothesis that the mean age of segregating synonymous mutations equals the mean age of segregating nonsynonymous mutations in a sample of DNA sequences. The power of this age-of-mutation test and the power of the McDonald/Kreitman test are explored by computer simulations. We apply the new test to 25 previously published mitochondrial data sets and find weak evidence for selection against nonsynonymous mutations.

scholarly journals Mitochondrial DNA Methylation and Human Diseases

2021 ◽  
Vol 22 (9) ◽  
pp. 4594
Author(s):  
Andrea Stoccoro ◽  
Fabio Coppedè
Keyword(s):  
Dna Methylation ◽  
Mitochondrial Dna ◽  
Mitochondrial Genome ◽  
Nuclear Dna ◽  
Epigenetic Modification ◽  
Nuclear Genome ◽  
Epigenetic Modifications ◽  
Human Diseases ◽  
Loop Region ◽  
D Loop

Epigenetic modifications of the nuclear genome, including DNA methylation, histone modifications and non-coding RNA post-transcriptional regulation, are increasingly being involved in the pathogenesis of several human diseases. Recent evidence suggests that also epigenetic modifications of the mitochondrial genome could contribute to the etiology of human diseases. In particular, altered methylation and hydroxymethylation levels of mitochondrial DNA (mtDNA) have been found in animal models and in human tissues from patients affected by cancer, obesity, diabetes and cardiovascular and neurodegenerative diseases. Moreover, environmental factors, as well as nuclear DNA genetic variants, have been found to impair mtDNA methylation patterns. Some authors failed to find DNA methylation marks in the mitochondrial genome, suggesting that it is unlikely that this epigenetic modification plays any role in the control of the mitochondrial function. On the other hand, several other studies successfully identified the presence of mtDNA methylation, particularly in the mitochondrial displacement loop (D-loop) region, relating it to changes in both mtDNA gene transcription and mitochondrial replication. Overall, investigations performed until now suggest that methylation and hydroxymethylation marks are present in the mtDNA genome, albeit at lower levels compared to those detectable in nuclear DNA, potentially contributing to the mitochondria impairment underlying several human diseases.

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