Mammalian Chromosomal Evolution: From Ancestral States to Evolutionary Regions

2010 ◽  
pp. 143-158 ◽  
Author(s):  
Terence J. Robinson ◽  
Aurora Ruiz-Herrera
Keyword(s):  
Chromosomal Evolution ◽  
Ancestral States

scholarly journals Microsatellite and Chromosome Evolution of Parthenogenetic Sitobion Aphids in Australia

Genetics ◽  
1996 ◽  
Vol 144 (2) ◽  
pp. 747-756 ◽  
Author(s):  
Paul Sunnucks ◽  
Phillip R England ◽  
Andrea C Taylor ◽  
Dinah F Hales
Keyword(s):  
Sexual Reproduction ◽  
Chromosome Evolution ◽  
Genetic Recombination ◽  
Allelic Variation ◽  
Repeat Unit ◽  
Chromosomal Evolution ◽  
Microsatellite Variation ◽  
Wide Range ◽  
Sexual Recombination ◽  
Minimum Numbers

Abstract Single-locus microsatellite variation correlated perfectly with chromosome number in Sitobion miscanthi aphids. The microsatellites were highly heterozygous, with up to 10 alleles per locus in this species. Despite this considerable allelic variation, only seven different S. miscanthi genotypes were discovered in 555 individuals collected from a wide range of locations, hosts and sampling periods. Relatedness between genotypes suggests only two successful colonizations of Australia. There was no evidence for genetic recombination in 555 S. miscanthi so the occurrence of recent sexual reproduction must be near zero. Thus diversification is by mutation and chromosomal rearrangement alone. Since the aphids showed no sexual recombination, microsatellites can mutate without meiosis. Five of seven microsatellite differences were a single repeat unit, and one larger jump is likely. The minimum numbers of changes between karyotypes corresponded roughly one-to-one with microsatellite allele changes, which suggests very rapid chromosomal evolution. A chromosomal fission occurred in a cultured line, and a previously unknown chromosomal race was detected. All 121 diverse S. near fragariae were heterozygous but revealed only one genotype. This species too must have a low rate of sexual reproduction and few colonizations of Australia.

scholarly journals Investigation of ancestral alleles in the Bovinae subfamily

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Maulana M. Naji ◽  
Yuri T. Utsunomiya ◽  
Johann Sölkner ◽  
Benjamin D. Rosen ◽  
Gábor Mészáros
Keyword(s):  
Extreme Points ◽  
Genetic Mutation ◽  
Zebu Cattle ◽  
Ancestral State ◽  
Initial State ◽  
High Count ◽  
Environmental Pressures ◽  
Ancestral States ◽  
Productive Traits ◽  
Species Specific

Abstract Background In evolutionary theory, divergence and speciation can arise from long periods of reproductive isolation, genetic mutation, selection and environmental adaptation. After divergence, alleles can either persist in their initial state (ancestral allele - AA), co-exist or be replaced by a mutated state (derived alleles -DA). In this study, we aligned whole genome sequences of individuals from the Bovinae subfamily to the cattle reference genome (ARS.UCD-1.2) for defining ancestral alleles necessary for selection signatures study. Results Accommodating independent divergent of each lineage from the initial ancestral state, AA were defined based on fixed alleles on at least two groups of yak, bison and gayal-gaur-banteng resulting in ~ 32.4 million variants. Using non-overlapping scanning windows of 10 Kb, we counted the AA observed within taurine and zebu cattle. We focused on the extreme points, regions with top 0. 1% (high count) and regions without any occurrence of AA (null count). High count regions preserved gene functions from ancestral states that are still beneficial in the current condition, while null counts regions were linked to mutated ones. For both cattle, high count regions were associated with basal lipid metabolism, essential for survival of various environmental pressures. Mutated regions were associated to productive traits in taurine, i.e. higher metabolism, cell development and behaviors and in immune response domain for zebu. Conclusions Our findings suggest that retaining and losing AA in some regions are varied and made it species-specific with possibility of overlapping as it depends on the selective pressure they had to experience.

scholarly journals Directional Selection and the Site-Frequency Spectrum

Genetics ◽  
2001 ◽  
Vol 159 (4) ◽  
pp. 1779-1788 ◽  
Author(s):  
Carlos D Bustamante ◽  
John Wakeley ◽  
Stanley Sawyer ◽  
Daniel L Hartl
Keyword(s):  
Maximum Likelihood ◽  
High Power ◽  
Negative Selection ◽  
Likelihood Estimation ◽  
Directional Selection ◽  
Likelihood Ratio Tests ◽  
Maximum Likelihood Estimates ◽  
Likelihood Methods ◽  
Ancestral States ◽  
Asymptotic Variances

Abstract In this article we explore statistical properties of the maximum-likelihood estimates (MLEs) of the selection and mutation parameters in a Poisson random field population genetics model of directional selection at DNA sites. We derive the asymptotic variances and covariance of the MLEs and explore the power of the likelihood ratio tests (LRT) of neutrality for varying levels of mutation and selection as well as the robustness of the LRT to deviations from the assumption of free recombination among sites. We also discuss the coverage of confidence intervals on the basis of two standard-likelihood methods. We find that the LRT has high power to detect deviations from neutrality and that the maximum-likelihood estimation performs very well when the ancestral states of all mutations in the sample are known. When the ancestral states are not known, the test has high power to detect deviations from neutrality for negative selection but not for positive selection. We also find that the LRT is not robust to deviations from the assumption of independence among sites.

scholarly journals Chromosomal painting of the sandpiper (Actitis macularius) detects several fissions for the Scolopacidae family (Charadriiformes)

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Melquizedec Luiz Silva Pinheiro ◽  
Cleusa Yoshiko Nagamachi ◽  
Talita Fernanda Augusto Ribas ◽  
Cristovam Guerreiro Diniz ◽  
Patricia Caroline Mary O´Brien ◽  
...  
Keyword(s):  
Chromosome Painting ◽  
Diploid Number ◽  
Chromosomal Evolution ◽  
Long Distance ◽  
Chromosomal Painting ◽  
Cytogenetic Studies ◽  
Burhinus Oedicnemus ◽  
Clear Idea ◽  
First Time

Abstract Background The Scolopacidae family (Suborder Scolopaci, Charadriiformes) is composed of sandpipers and snipes; these birds are long-distance migrants that show great diversity in their behavior and habitat use. Cytogenetic studies in the Scolopacidae family show the highest diploid numbers for order Charadriiformes. This work analyzes for the first time the karyotype of Actitis macularius by classic cytogenetics and chromosome painting. Results The species has a diploid number of 92, composed mostly of telocentric pairs. This high 2n is greater than the proposed 80 for the avian ancestral putative karyotype (a common feature among Scolopaci), suggesting that fission rearrangements have formed smaller macrochromosomes and microchromosomes. Fluorescence in situ hybridization using Burhinus oedicnemus whole chromosome probes confirmed the fissions in pairs 1, 2, 3, 4 and 6 of macrochromosomes. Conclusion Comparative analysis with other species of Charadriiformes studied by chromosome painting together with the molecular phylogenies for the order allowed us to raise hypotheses about the chromosomal evolution in suborder Scolopaci. From this, we can establish a clear idea of how chromosomal evolution occurred in this suborder.

scholarly journals Xenopus Cytogenetics and Chromosomal Evolution

2015 ◽  
Vol 145 (3-4) ◽  
pp. 192-200 ◽  
Author(s):  
Vladimir Krylov ◽  
Tereza Tlapakova
Keyword(s):  
Developmental Biology ◽  
Genetic Linkage ◽  
Chromosome Banding ◽  
Chromosomal Evolution ◽  
Model Organisms ◽  
Gene Localization ◽  
Physical Maps ◽  
Gene Position ◽  
Tightly Coupled

The genus Xenopus represents important model organisms in the field of developmental biology and chromosomal evolution. Developmental processes are tightly coupled with the analysis of gene function via genetic linkage and mapping. Cytogenetic techniques such as chromosome banding or FISH are essential tools for the determination of gene position and subsequently for the construction of linkage and physical maps. Here, we present a summary of key achievements in X. tropicalis and X. laevis cytogenetics with emphasis on the gene localization to chromosomes. The second part of this review is focused on the chromosomal evolution regarding both above-mentioned species. With respect to methodology, hybridization techniques such as FISH and chromosome-specific painting FISH are highlighted.

Diversity and Karyotypic Evolution in the Genus Neacomys (Rodentia, Sigmodontinae)

2015 ◽  
Vol 146 (4) ◽  
pp. 296-305 ◽  
Author(s):  
Willam O. da Silva ◽  
Julio C. Pieczarka ◽  
Rogério V. Rossi ◽  
Horacio Schneider ◽  
Iracilda Sampaio ◽  
...  
Keyword(s):  
Molecular Phylogeny ◽  
Diploid Number ◽  
Constitutive Heterochromatin ◽  
Chromosomal Evolution ◽  
The Other ◽  
Karyotypic Evolution ◽  
Drastic Reduction ◽  
Ancestral Species ◽  
Pericentric Inversions ◽  
Amazonian Region

Neacomys (Sigmodontinae) comprises 8 species mainly found in the Amazonian region. We describe 5 new karyotypes from Brazilian Amazonia: 2 cytotypes for N. paracou (2n = 56/FNa = 62-66), 1 for N. dubosti (2n = 64/FNa = 68), and 2 for Neacomys sp. (2n = 58/FNa = 64-70), with differences in the 18S rDNA. Telomeric probes did not show ITS. We provide a phylogeny using Cytb, and the analysis suggests that 2n = 56 with a high FNa is ancestral for the genus, as found in N. paracou, being retained by the ancestral forms of the other species, with an increase in 2n occurring independently in N. spinosus and N. dubosti. Alternatively, an increase in 2n may have occurred in the ancestral taxon of the other species, followed by independent 2n-reduction events in Neacomys sp. and in the ancestral species of N. tenuipes, N. guianae, N. musseri, and N. minutus. Finally, a drastic reduction event in the diploid number occurred in the ancestral species of N. musseri and N. minutus which exhibit the lowest 2n of the genus. The karyotypic variations found in both intra- and interspecific samples, associated with the molecular phylogeny, suggest a chromosomal evolution with amplification/deletion of constitutive heterochromatin and rearrangements including fusions, fissions, and pericentric inversions.

scholarly journals Rates and Patterns of Chromosomal Evolution inDrosophila pseudoobscuraandD. miranda

Genetics ◽  
2006 ◽  
Vol 173 (2) ◽  
pp. 779-791 ◽  
Author(s):  
Carolina Bartolomé ◽  
Brian Charlesworth
Keyword(s):  
Chromosomal Evolution
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