Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

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Modern Applied Statistics With S

The evidentiary basis of the currently accepted classification of living amphibians is discussed and shown not to warrant the degree of authority conferred on it by use and tradition. A new taxonomy of living amphibians is proposed to correct the deficiencies of the old one. This new taxonomy is based on the largest phylogenetic analysis of living Amphibia so far accomplished. We combined the comparative anatomical character evidence of Haas (2003) with DNA sequences from the mitochondrial transcription unit H1 (12S and 16S ribosomal RNA and tRNAValine genes, ≈ 2,400 bp of mitochondrial sequences) and the nuclear genes histone H3, rhodopsin, tyrosinase, and seven in absentia, and the large ribosomal subunit 28S (≈ 2,300 bp of nuclear sequences; ca. 1.8 million base pairs; x = 3.7 kb/terminal). The dataset includes 532 terminals sampled from 522 species representative of the global diversity of amphibians as well as seven of the closest living relatives of amphibians for outgroup comparisons. The...

https://bioone.org/journals/Bulletin-of-the-American-Museum-of-Natural-History/volume-2006/issue-297/0003-0090(2006)297[0001:TATOL]2.0.CO;2/THE-AMPHIBIAN-TREE-OF-LIFE/10.1206/0003-0090(2006)297[0001:TATOL]2.0.CO;2.pdf

The amphibian tree of life

LEARNING The objectives of BIOS 781 are to present: OBJECTIVES: 1. basic population and quantitative genetic principles, including classical genetics, chromosomal theory of inheritance, and meiotic recombination 2. an exposure to QTL mapping methods of complex quantitative traits and linkage methods to detect co-segregation with disease 3. methods for assessing marker-disease linkage disequilibrium, including case-control approaches 4. methods for genome-wide association and stratification control.

Genetic Data Analysis

The accuracy of gene flow estimates is unknown in most natural populations because direct estimates of dispersal are often not possible. These estimates can be highly imprecise or even biased because population genetic structure reflects more than a simple balance between genetic drift and gene flow. Most of the models used to estimate gene flow also assume very simple patterns of movement. As a result, multiple interpretations of population structure involving contemporary gene flow, departures from equilibrium, and other factors are almost always possible. One way to isolate the relative contribution of gene flow to population genetic differentiation is to utilize comparative methods. Population genetic statistics such as FST, heterozygosity and Nei's D can be compared between species with differing dispersal abilities if these species are otherwise phylogenetically, geographically and demographically comparable. Accordingly, the available literature was searched for all groups that meet these criteria ...

Dispersal, gene flow, and population structure

Sequence divergence for segments of three mitochondrial DNA (mtDNA) genes encoding the 12S and 16S ribosomal RNA and cytochrome b was examined in newts belonging to the genus Euproctus (E. asper, E. montanus, E. platycephalus) and in three other species belonging to the same family (Salamandridae), Triturus carnifex, T. vulgaris, and Pleurodeles waltl. The three Euproctus species occur (one species each) in Corsica, Sardinia, and the Pyrenees. This vicariant distribution is believed to have been determined by the disjunction and rotation of the Sardinia-Corsica microplate from the Pyreneean region. Because time estimates are available for the tectonic events that led to the separation of the three landmasses, we used sequence data to estimate rates of evolution for the three gene fragments and investigated whether they conform to the rate-constancy hypothesis. By the Tajima (1993, Genetics 135:599-607) test, we could not detect rate heterogeneities for the ribosomal genes and for transversions in the cytochrome b gene. Assuming that these sites are evolving linearly over time and that cessation of gene flow occurred simultaneously with vicariant events, we compared the time of divergence estimated by molecular distances with the divergence times based on the geological estimates. Because we have two estimates of divergence time from the geological record, the split of Corsica/Sardinia from the Pyrenees and the split of Corsica from Sardinia, we could compare ratios of molecular divergence with the ratio of geological time divergence. The ratios are very similar, indicating that the molecular clock hypothesis cannot be rejected. These geological events also allowed us to calculate absolute rates of evolution for ribosomal and cytochrome b genes and compare them to rates for the same regions in other salamandrids and other vertebrates. Ribosomal mtDNA rates are comparable to those reported for other vertebrates, but cytochrome b rates are 3-7 times lower in salamanders than in other ectotherms. From a phylogenetic perspective, our data suggest that the cladogenic events leading to species formation in Euproctus and Triturus occurred very closely in time, indicating that the two genera may not be monophyletic. A duplication of the cytochrome b gene in T. carnifex was found, and the implications of this finding for mtDNA phylogenetic studies are discussed.

Mitochondrial dna rates and biogeography in european newts (genus euproctus)

This study focuses on phylogenetic relationships in two distinct species assemblages of cave-dwelling beetles with similar disjunct distributions in the Pyrenees and Sardinia. One assemblage contains six species in the genera Ovobathysciola (four species) and Patriziella (two species) on Sardinia and one species of Anillochlamys in the Pyrenees. Species within the two Sardinian genera co-occur in the same karst area. Although, they are believed to be each others closest relative, they have very different body types (globular body with short appendages in Ovobathysciola; elongated body with long appendages in Patriziella), which are believed to reflect different degrees of adaptation to cave life. The other assemblage of Bathysciine beetles includes three species in the genus Speonomus in the Pyrenees and one on Sardinia. All the species are rare and many are endangered. One issue of particular interest was whether Ovobathysciola and Patriziella are reciprocally monophyletic or whether each of the Patriziella species evolved independently from the co-occurring Ovobathysciola species, as the similar morphology of the Patriziella species might be due to convergence rather than common descent. Based on DNA sequences of the cytochrome oxidase I (COI) region of the mtDNA, neither scenario was supported. Rather, the two Patriziella species are sister taxa embedded within the Ovobathysciola radiation. In addition, the well-dated geological history of this region allowed us to calibrate absolute rates of COI evolution, the first such estimates for any insect. Finally this study suggests that the evolutionary acquisition of typical cave adaptations (e.g., elongated body and appendages) may occur at about the same rate as loss of traits (e.g., eyes and pigmentation) associated with cave life.

Molecular biogeography of cave life: a study using mitochondrial dna from bathysciine beetles

Bottleneck effects and the depression of genetic variability in hatchery stocks of Penaeus japonicus (Crustacea, Decapoda)

The chironomid midges Belgica antarctica, Eretmoptera murphyi (subfamily Orthocladiinae) and Parochlus steinenii (subfamily Podonominae), are the only Diptera species currently found in Antarctica. The relationships between these species and a range of further taxa of Chironomidae were examined by sequencing domains 1 and 3–5 of 28S ribosomal RNA. The resulting molecular relationships between B. antarctica and E. murphyi, within Orthocladiinae, were highly supported by validation analyses, confirming their position within Chironomidae, as generated by classical taxonomy. Within Podonominae, P. steinenii from the Maritime Antarctic was more closely related to material from sub-Antarctic South Georgia than to material from Patagonia. Taking advantage of the availability of a molecular substitution rate calculated for this gene in Diptera, a dating of divergence between our study taxa was tentatively established. The divergence dates obtained were 49 million years (Myr), between B. antarctica and E. murphyi, and 68.5 Myr between these species and the closest Orthocladiinae taxon tested from Patagonia, suggesting that B. antarctica and E. murphyi were representatives of an ancient lineage. As both are endemic to their respective tectonic microplates, their contemporary distribution is, therefore, likely to have been shaped by vicariance rather than dispersal.

A molecular phylogeny of antarctic chironomidae and its implications for biogeographical history

Genetic data are currently providing a large amount of new information on past distribution of species and are contributing to a new vision of Pleistocene ice ages. Nonetheless, an increasing number of studies on the 'time dependency' of mutation rates suggest that date assessments for evolutionary events of the Pleistocene might be overestimated. We analysed mitochondrial (mt) DNA (COI) sequence variation in 225 Parnassius mnemosyne individuals sampled across central and eastern Europe in order to assess (i) the existence of genetic signatures of Pleistocene climate shifts; and (ii) the timescale of demographic and evolutionary events. Our analyses reveal a phylogeographical pattern markedly influenced by the Pleistocene/Holocene climate shifts. Eastern Alpine and Balkan populations display comparatively high mtDNA diversity, suggesting multiple glacial refugia. On the other hand, three widely distributed and spatially segregated lineages occupy most of northern and eastern Europe, indicating postglacial recolonization from different refugial areas. We show that a conventional 'phylogenetic' substitution rate cannot account for the present distribution of genetic variation in this species, and we combine phylogeographical pattern and palaeoecological information in order to determine a suitable intraspecific rate through a Bayesian coalescent approach. We argue that our calibrated 'time-dependent' rate (0.096 substitutions/ million years), offers the most convincing time frame for the evolutionary events inferred from sequence data. When scaled by the new rate, estimates of divergence between Balkan and Alpine lineages point to c. 19 000 years before present (last glacial maximum), and parameters of demographic expansion for northern lineages are consistent with postglacial warming (5-11 000 years before present).

/pdf/pleistocene-evolutionary-history-of-the-clouded-apollo-1bz60p6icy.pdf

Pleistocene evolutionary history of the Clouded Apollo (Parnassius mnemosyne): genetic signatures of climate cycles and a ‘time-dependent’ mitochondrial substitution rate

Valerio Sbordoni

Papers

Mitochondrial dna rates and biogeography in european newts (genus euproctus)

Molecular biogeography of cave life: a study using mitochondrial dna from bathysciine beetles

Bottleneck effects and the depression of genetic variability in hatchery stocks of Penaeus japonicus (Crustacea, Decapoda)

A molecular phylogeny of antarctic chironomidae and its implications for biogeographical history

Pleistocene evolutionary history of the Clouded Apollo (Parnassius mnemosyne): genetic signatures of climate cycles and a ‘time-dependent’ mitochondrial substitution rate