About 2800 mitochondrial genomes of Metazoa are present in NCBI RefSeq today, two thirds belonging to vertebrates. Metazoan phylogeny was recently challenged by large scale EST approaches (phylogenomics), stabilizing classical nodes while simultaneously supporting new sister group hypotheses. The use of mitochondrial data in deep phylogeny analyses was often criticized because of high substitution rates on nucleotides, large differences in amino acid substitution rate between taxa, and biases in nucleotide frequencies. Nevertheless, mitochondrial genome data might still be promising as it allows for a larger taxon sampling, while presenting a smaller amount of sequence information. We present the most comprehensive analysis of bilaterian relationships based on mitochondrial genome data. The analyzed data set comprises more than 650 mitochondrial genomes that have been chosen to represent a profound sample of the phylogenetic as well as sequence diversity. The results are based on high quality amino acid alignments obtained from a complete reannotation of the mitogenomic sequences from NCBI RefSeq database. However, the results failed to give support for many otherwise undisputed high-ranking taxa, like Mollusca, Hexapoda, Arthropoda, and suffer from extreme long branches of Nematoda, Platyhelminthes, and some other taxa. In order to identify the sources of misleading phylogenetic signals, we discuss several problems associated with mitochondrial genome data sets, e.g. the nucleotide and amino acid landscapes and a strong correlation of gene rearrangements with long branches.

BackgroundMethods of alignment masking, which refers to the technique of excluding alignment blocks prior to tree reconstructions, have been successful in improving the signal-to-noise ratio in sequence alignments. However, the lack of formally well defined methods to identify randomness in sequence alignments has prevented a routine application of alignment masking. In this study, we compared the effects on tree reconstructions of the most commonly used profiling method (GBLOCKS) which uses a predefined set of rules in combination with alignment masking, with a new profiling approach (ALISCORE) based on Monte Carlo resampling within a sliding window, using different data sets and alignment methods. While the GBLOCKS approach excludes variable sections above a certain threshold which choice is left arbitrary, the ALISCORE algorithm is free of a priori rating of parameter space and therefore more objective.ResultsALISCORE was successfully extended to amino acids using a proportional model and empirical substitution matrices to score randomness in multiple sequence alignments. A complex bootstrap resampling leads to an even distribution of scores of randomly similar sequences to assess randomness of the observed sequence similarity. Testing performance on real data, both masking methods, GBLOCKS and ALISCORE, helped to improve tree resolution. The sliding window approach was less sensitive to different alignments of identical data sets and performed equally well on all data sets. Concurrently, ALISCORE is capable of dealing with different substitution patterns and heterogeneous base composition. ALISCORE and the most relaxed GBLOCKS gap parameter setting performed best on all data sets. Correspondingly, Neighbor-Net analyses showed the most decrease in conflict.ConclusionsAlignment masking improves signal-to-noise ratio in multiple sequence alignments prior to phylogenetic reconstruction. Given the robust performance of alignment profiling, alignment masking should routinely be used to improve tree reconstructions. Parametric methods of alignment profiling can be easily extended to more complex likelihood based models of sequence evolution which opens the possibility of further improvements.

Anthropogenic global climate change has already led to alterations in biodiversity patterns by directly and indirectly affecting species distributions. It has been suggested that poikilothermic animals, including reptiles, will be particularly affected by global change and large-scale reptile declines have already been observed. Currently, half of the world's freshwater turtles and tortoises are considered threatened with extinction, and climate change may exacerbate these declines. In this study, we assess how global chelonian species richness will change in the near future. We use species distribution models developed under current climate conditions for 78% of all extant species and project them onto different Intergovernmental Panel on Climate Change (IPCC) scenarios for 2080. We detect a strong dependence of temperature shaping most species ranges, which coincide with their general temperature-related physiological traits (i.e., temperature-dependent sex determination). Furthermore, the extent and distribution of the current bioclimatic niches of most chelonians may change remarkably in the near future, likely leading to a substantial decrease of local species abundance and ultimately a reduction in species richness. Future climatic changes may cause the ranges of 86% of the species to contract, and of these ranges, nearly 12% are predicted to be situated completely outside their currently realized niches. Hence, the interplay of increasing habitat fragmentation and loss due to climatic stress may result in a serious threat for several chelonian species.

During the last years, molecular studies revealed signiWcant population diVerentiation and cryptic species within various benthic and pelagic marine Antarctic taxa. This is unexpected due to the lack of obvious barriers to gene Xow and strong current systems. Using mitochondrial (COI, 16S rDNA) and nuclear (28S rDNA: D2) gene fragments, we tested whether two circum-Antarctic benthic shrimps with planktotrophic larvae, Chorismus antarcticus and Nematocarcinus lanceopes, show patterns of regional diVerentiation. For both species, the 16S and the 28S fragment were invariant. However, for COI we found 24 diVerent haplotypes for Chorismus antarcticus and 54 for Nematocarcinus lanceopes. No signiWcant diVerentiation was observed among populations or regions. Furthermore, we found signatures of a population expansion in the late Pleistocene hinting at an impact of large-scale glaciations in particular on the shallowwater shrimp Chorismus antarcticus, supporting a (re)colonization and demographic expansion of this shrimp species in response to climate oscillation.

The climatic cycles of the Quaternary, during which global mean annual temperatures have regularly changed by 5–10°C, provide a special opportunity for studying the rate, magnitude, and effects of geographic responses to changing climates. During the Quaternary, high- and mid-latitude species were extirpated from regions that were covered by ice or otherwise became unsuitable, persisting in refugial retreats where the environment was compatible with their tolerances. In this study we combine modern geographic range data, phylogeny, Pleistocene paleoclimatic models, and isotopic records of changes in global mean annual temperature, to produce a temporally continuous model of geographic changes in potential habitat for 59 species of North American turtles over the past 320 Ka (three full glacial-interglacial cycles). These paleophylogeographic models indicate the areas where past climates were compatible with the modern ranges of the species and serve as hypotheses for how their geographic ranges would have changed in response to Quaternary climate cycles. We test these hypotheses against physiological, genetic, taxonomic and fossil evidence, and we then use them to measure the effects of Quaternary climate cycles on species distributions. Patterns of range expansion, contraction, and fragmentation in the models are strongly congruent with (i) phylogeographic differentiation; (ii) morphological variation; (iii) physiological tolerances; and (iv) intraspecific genetic variability. Modern species with significant interspecific differentiation have geographic ranges that strongly fluctuated and repeatedly fragmented throughout the Quaternary. Modern species with low genetic diversity have geographic distributions that were highly variable and at times exceedingly small in the past. Our results reveal the potential for paleophylogeographic models to (i) reconstruct past geographic range modifications, (ii) identify geographic processes that result in genetic bottlenecks; and (iii) predict threats due to anthropogenic climate change in the future.