Corrigendum to "Nucleotide sequence and results of test of adaptive evolution in the α-globin gene of octodontoid rodents" [Data Brief 15 (2017) 517-521].

[This corrects the article DOI: 10.1016/j.dib.2017.09.017.].

Nucleotide sequence and results of test of adaptive evolution in the α-globin gene of octodontoid rodents.

The data presented in this article are related to the research article entitled "Molecular adaptive convergence in the α-globin gene in subterranean octodontid rodents" (Tomasco et al., 2017) [1]. This article shows the nucleotide sequences of α-globin subunit gene of hemoglobin of several South American caviomorph rodents, including subterranean and fossorial species. These sequences are deposited in Genbank, with accession numbers ranging from MF169881 to MF169898. Of a total of 429 nucleotides analyzed (143 codons), 100 variable sites and 43 amino acid replacements were reported. In this article we also show the results of TreeSaap (Woolley et al., 2003) [2] and MEME (Murrell et al., 2012) [3], that identified some replacement changes as interesting for future studies of adaptive evolution in this large rodent radiation.

Genetic relationships between Atlantic and Pacific populations of the notothenioid fish Eleginops maclovinus: the footprints of Quaternary glaciations in Patagonia.

The genetic relationships between the Pacific and the Atlantic populations of marine coastal biota in Southern South America have been analyzed in few studies, most of them relying on a single mitochondrial locus. We analyzed 10 polymorphic microsatellite loci, isolated from a dinucleotide-enriched Eleginops maclovinus genomic library, in a total of 240 individuals (48 from each of 5 sampled sites: 2 Atlantic, 2 Pacific and 1 in Beagle Channel). The results were contrasted against a previous work on the same species with mitochondrial DNA (mtDNA). Observed heterozygosity within localities ranged from 0.85 to 0.88 with the highest overall number of alleles observed at the northernmost locality on the Pacific side (Concepción), but no clear geographic pattern arose from the data. On the other hand, the number of private alleles was negatively correlated with latitude (Spearman's rs test, P=0.017). Among-population variance was low but significant (1.35%; P<0.0001, analysis of molecular variance (AMOVA)) and low genetic differentiation between populations was observed (pairwise FST values ranged from 0 to 0.021). A Mantel test revealed a significant correlation between geographic distances and FST (r=0.56, P=0.047). This could be partially accounted by the Atlantic versus Pacific population differentiation detected in three different analyses (STRUCTURE, SAMOVA (Spatial Analysis of MOlecular VAriance) and a population phylogeny). The observed pattern is compatible with a history of separation into two glacial refugia that was better captured by the multilocus microsatellite data than by the mtDNA analysis.

Contrasting patterns of morphological variation with dietary preferences in Micropogonias furnieri: insights from stable-isotope and digestive-trait analyses.

The dietary preferences of populations of whitemouth croaker Micropogonias furnieri, which commonly inhabit estuarine and oceanic environments of the south-western Atlantic Ocean, were investigated using stable-isotope analysis and digestive traits, and compared with previous genetic and morphometric surveys of this species. Isotopic and C:N-derived data suggested that individuals from coastal lagoons are the most differentiated from the remaining localities surveyed. In contrast, the analysis of the digestive traits did not show the same differentiation pattern. The overall correlation between isotopic, molecular and morphological variations suggests that genetic and phenotypic differences among populations are accompanied by differential resource use, supporting the idea that selective forces could be playing an important role in population differentiation.

Evaluation of polymorphism in ten microsatellite loci in Uruguayan sheep flocks

The allele frequencies of 10 microsatellite loci previously described for sheep as BM1314, BM6526, OarFCB128, OarHH64, OarCP20, OarHH47, OarFCB48, OarHH35, OarHH72 and BM2508 were estimated for the Uruguayan flocks. A representative sample of 101 individuals composed by the two predominant breeds (76 percent Corriedale and 24 percent Australian Merino) was used. The sample did not show a significant tendency towards substructuring, in spite of presenting some significantly different allele frequencies between races. The Corriedale sample presents three loci in which the presence of null alleles is possible. The markers were highly variable, showing between 7 and 15 alleles each. The Polymorphism Information Content Index ranged from 0.63 to 0.87 and the Exclusion Probability from 0.39 to 0.75 for a cumulative Exclusion Probability of 99.98 percent. These results suggest the effectiveness of this set of loci for testing genetic relatedness. This is the first report of microsatellite variation in Corriedale

Molecular evolution of Aldolase A pseudogenes in mice: multiple origins, subsequent duplications, and heterogeneity of evolutionary rates.

The Aldolase multigene family comprises three functional genes (A, B, and C) with tissue-specific expression regulated during ontogeny. DGGE analysis and nucleotide sequencing reveal a family of retropseudogenes of type A in species of MUS: Significant variation in rates of evolution of Aldolase A retropseudogenes is apparent. Our analyses demonstrate that (1) multiple events of retrotransposition are needed to account for the diversity of Aldolase A processed pseudogenes found in mice; (2) some of these sequences have undergone further duplication subsequent to the original retrotransposition event; (3) the patterns of nucleotide substitution are broadly comparable with previous estimates; and (4) estimates of rates of divergence for this array of sequences are up to four times higher than those reported in the literature.

Recurrent amplifications and deletions of satellite DNA accompanied chromosomal diversification in South American tuco-tucos (genus Ctenomys, Rodentia: Octodontidae): a phylogenetic approach.

We investigated the relationship between satellite copy number and chromosomal evolution in tuco-tucos (genus Ctenomys), a karyotypically diverse clade of rodents. To explore phylogenetic relationships among 23 species and 5 undescribed forms, we sequenced the complete mitochondrial cytochrome b genes of 27 specimens and incorporated 27 previously published sequences. We then used quantitative dot-blot techniques to assess changes in the copy number of the major Ctenomys satellite DNA (satDNA), named RPCS. Our analysis of the relationship between variation in copy number of RPCS and chromosomal changes employed a maximum-likelihood approach to infer the copy number of the satellite RPCS in the ancestors of each clade. We found that amplifications and deletions of RPCS were associated with extensive chromosomal rearrangements even among closely related species. In contrast, RPCS copy number stability was observed within clades characterized by chromosomal stability. This example reinforces the suspected role of amplification, deletion, and intragenomic movement of satDNA in promoting extensive chromosomal evolution.

The molecular phylogenetics of tuco-tucos (genus Ctenomys, Rodentia: Octodontidae) suggests an early burst of speciation.

Variation in the nucleotide sequence of the entire mitochondrial cytochrome b gene (1140 bp) was examined for 27 individuals representing 13 species of South American rodents of the genera Ctenomys, Octodontomys, Tympanoctomys, and Spalacopus. Representatives of the family Echimyidae, Euryzygomatomys and Mesomys, were used as outgroups to test the monophyly of the Octodontinae and Ctenomyinae. Relationships among species of tuco-tucos (genus Ctenomys) were also examined including representatives of the three described subgenera and the two sperm morphs. Reciprocal monophyly of the Octodontinae and Ctenomyinae is strongly supported. Several basal relationships among species of the genus Ctenomys are poorly resolved, suggesting the possibility of a hard polytomy due to a rapid and potentially simultaneous radiation early in the history of the genus. In other cases, clades within the Ctenomyinae previously identified on the basis of allozymes, chromosomes, parasites, or skull morphology were supported. Calibrations based on the fossil record suggest that the mitochondrial cytochrome b of these caviomorphs has evolved at a rapid rate, comparable to those proposed for Mus-Rattus, and three to four times higher than ungulate rates.

Screening techniques for detecting allelic variation in DNA sequences.

This article reviews four 'DNA screening techniques', namely heteroduplex analysis, single-strand conformational polymorphism (SSCP), denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) as tools for the study of allelic variation in natural populations. The resolving power, advantages, and limitations of each technique are discussed and compared. We also provide some criteria for choosing among techniques and illustrate some practical issues with examples taken primarily from our own laboratory experience.

Rapid surveying of DNA sequence variation in natural populations.

DNA sequencing can be costly and time consuming for population studies because of the relative rarity of variation along exons. These problems can be substantially reduced by the use of the polymerase chain reaction on introns using primers from the exon region. These problems can be further reduced by the use of denaturing gradient gel electrophoresis to identify those alleles in need of sequencing.

Morphological evolution of subterranean mammals: integrating structural, functional, and ecological perspectives.

The widely recognized convergence of subterranean mammals offers unique opportunities for the study of patterns, causes and consequences of morphological integration. For example, behavioral and biomechanical observations have revealed a diversity of digging modes among subterranean mammals. In rodents, scratch-digging and chisel-tooth digging, alone or combined, are widespread. This dual nature of the digging apparatus must be understood to avoid erroneous assessments of specializations based on forelimb modifications only. Additionally, bulldozing and disposal of loose soil is performed by head-lifting, by means of the forelimbs, or with the hindlimbs. Insectivores are known to resort to scratch-digging, sand-swimming, or to a unique system known as humeral rotation. Semi-fossorial species among rodents and insectivores are scratch-diggers. In contrast, fully subterranean taxa show further specializations for scratch-digging and/or resort to some of the other digging modes. The ecological correlates of these morphological trends are still poorly known; work in geomyids suggests that scratch-digging specializations are efficient in friable soils, whereas tooth-digging allows the utilization of a much broader spectrum of soil types. This indicates that alternative pathways of morphological specialization are not equivalent in their ecological potentialities. Important morphological features, such as incisor procumbency among tooth-diggers, are shown to be constrained by structural, allometric, and mechanical factors. In geomyids, the same procumbent morphologies may be acquired as a byproduct of size increases, by means of adaptive shifts independent from size, or by a combination of both. Thus, geometric similarity may not be indicative of functional similarity. Further constraints result from the integration of different functions. For instance, it is suggested that mastication imposes limitations upon potential modifications of jaw morphology for tooth-digging. Scratch-digging appears to be less constrained by locomotion, but the effects of integration of various functions in fore- and hind-limbs are largely unexplored. Multiple approaches, combining behavioral, functional, ecological, structural, and phylogenetic data, are necessary for the study of morphological evolution among subterranean mammals.