Parametric and non-parametric masking of randomness in sequence alignments can be improved and leads to better resolved trees

<p>Abstract</p> <p>Background</p> <p>Methods 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 <it>a priori </it>rating of parameter space and therefore more objective.</p> <p>Results</p> <p>ALISCORE 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.</p> <p>Conclusions</p> <p>Alignment 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.</p

Effects of Late-Cenozoic glaciation on habitat availability in Antarctic benthic shrimps (Crustacea: Decapoda: Caridea)

Marine invertebrates inhabiting the high Antarctic continental shelves are challenged by disturbance of the seafloor by grounded ice, low but stable water temperatures and variable food availability in response to seasonal sea-ice cover. Though a high diversity of life has successfully adapted to such conditions, it is generally agreed that during the Last Glacial Maximum (LGM) the large-scale cover of the Southern Ocean by multi-annual sea ice and the advance of the continental ice sheets across the shelf faced life with conditions, exceeding those seen today by an order of magnitude. Conditions prevailing at the LGM may have therefore acted as a bottleneck event to both the ecology as well as genetic diversity of today’s fauna. Here, we use for the first time specific Species Distribution Models (SDMs) for marine arthropods of the Southern Ocean to assess effects of habitat contraction during the LGM on the three most common benthic caridean shrimp species that exhibit a strong depth zonation on the Antarctic continental shelf. While the shallow-water species Chorismus antarcticus and Notocrangon antarcticus were limited to drastically reduced habitat during the LGM, the deep-water shrimp Nematocarcinus lanceopes found refuge in the Southern Ocean deep sea. The modeling results are in accordance with genetic diversity patterns available for C. antarcticus and N. lanceopes and support the hypothesis that habitat contraction at the LGM resulted in a loss of genetic diversity in shallow water benthos

Genetic homogeneity and circum-Antarctic distribution of two benthic shrimp species in the Southern Ocean, Chorismus antarcticus and Nematocarcinus lanceopes

During the last years, molecular studies revealed significant population differentiation and cryptic species within various benthic and pelagic marine Antarctic taxa. This is unexpected due to the lack of obvious barriers to gene flow 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 differentiation. For both species, the 16S and the 28S fragment were invariant. However, for COI we found 24 different haplotypes for Chorismus antarcticus and 54 for Nematocarcinus lanceopes. No significant differentiation 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 shallow-water shrimp Chorismus antarcticus, supporting a (re)colonization and demographic expansion of this shrimp species in response to climate oscillation.Electronic supplementary material: The online version of this article (doi:10.1007/s00227-010-1451-3) contains supplementary material, which is available to authorized users

Nightly Biting Cycles of Anopheles Species in Rural Northwestern Burkina Faso

The biting behavior of anophelines is an important determinant of malaria transmission. Understanding the local vector host-seeking behavior, its outdoor/indoor biting preference, and nocturnal biting periods is essential for effectively applying and improving vector control methods, such as Long Lasting Insecticidal Nets (LLINs) and personal protective measures. To better understand the biting and host-seeking patterns of Anopheles mosquitoes in Northwestern Burkina Faso, we performed biweekly Human Landing Catches (HLC) in six villages during the period of highest mosquito abundance and malaria transmission. We applied a negative binomial regression framework to statistically analyze the host-seeking activities of Anopheles species and test for differences across hours, months, and villages, as well as for differences between indoor and outdoor capture points. Anopheles gambiae s.l. was identified as the main malaria vector in this region, representing about 90% of the total anopheline population. Biting activity was significantly different across hours and showed a peaked plateau between 2000 and 0200 hours. Differences in the pattern of biting cycles were observed between the early and late rainy season. This study shows that anopheline biting activity in Northwest Burkina Faso is high throughout the night, at indoor and outdoor posts alike. Consequently, bed nets alone may not provide sufficient protection against early biting anophelines and should be complemented with additional strategies such as indoor residual spraying (IRS) and larval source management (LSM) to meet the WHO's ambitious goals that are reflected in the global technical malaria strategy for 2030

Correction: Effects of Late-Cenozoic Glaciation on Habitat Availability in Antarctic Benthic Shrimps (Crustacea: Decapoda: Caridea).

[This corrects the article DOI: 10.1371/journal.pone.0046283.]

Data from: Isolation and characterization of nine polymorphic microsatellite markers for the deep-sea shrimp Nematocarcinus lanceopes (Crustacea: Decapoda: Caridea)

BACKGROUND: The shrimp Nematocarcinus lanceopes Bate, 1888 is found in the deep sea around Antarctica and sub-Antarctic islands. Previous studies on mitochondrial data and species distribution models provided evidence for a homogenous circum-Antarctic population of N. lanceopes. However, to analyze the fine-scale population genetic structure and to examine influences of abiotic environmental conditions on population composition and genetic diversity, a set of fast evolving nuclear microsatellite markers is required. FINDINGS: We report the isolation and characterization of nine polymorphic microsatellite markers from the Antarctic deep-sea shrimp species Nematocarcinus lanceopes (Crustacea: Decapoda: Caridea). Microsatellite markers were screened in 55 individuals from different locations around the Antarctic continent. All markers were polymorphic with 9 to 25 alleles per locus. The observed heterozygosity ranged from 0.545 to 0.927 and the expected heterozygosity from 0.549 to 0.934. CONCLUSIONS: The reported markers provide a novel tool to study genetic structure and diversity in Nematocarcinus lanceopes populations in the Southern Ocean and monitor effects of ongoing climate change in the region on the populations inhabiting these

Isolation and characterization of nine polymorphic microsatellite markers for the deep-sea shrimp Nematocarcinus lanceopes (Crustacea: Decapoda: Caridea)

Background: The shrimp Nematocarcinus lanceopes Bate, 1888 is found in the deep sea around Antarctica and sub-Antarctic islands. Previous studies on mitochondrial data and species distribution models provided evidence for a homogenous circum-Antarctic population of N. lanceopes. However, to analyze the fine-scale population genetic structure and to examine influences of abiotic environmental conditions on population composition and genetic diversity, a set of fast evolving nuclear microsatellite markers is required. Findings: We report the isolation and characterization of nine polymorphic microsatellite markers from the Antarctic deep-sea shrimp species Nematocarcinus lanceopes (Crustacea: Decapoda: Caridea). Microsatellite markers were screened in 55 individuals from different locations around the Antarctic continent. All markers were polymorphic with 9 to 25 alleles per locus. The observed heterozygosity ranged from 0.545 to 0.927 and the expected heterozygosity from 0.549 to 0.934. Conclusions: The reported markers provide a novel tool to study genetic structure and diversity in Nematocarcinus lanceopes populations in the Southern Ocean and monitor effects of ongoing climate change in the region on the populations inhabiting these

msat_sequences

This file contains the nucleotide sequence information for the described microsatellite markers. Primer sites are indicated in the sequences

Present potential distribution maps.

<p>The potential distribution of <i>N. lanceopes</i>, <i>N. antarcticus</i> and <i>C. antarcticus</i> (A–C) computed with Maxent 3.3.3e derived from current conditions. Display window for the area Weddell Sea and Antarctic Peninsula. Indicated the early summer near-surface currents <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046283#pone.0046283-Lumpkin1" target="_blank">[78]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046283#pone.0046283-Lumpkin2" target="_blank">[79]</a>, which are likely to affect the drift of larval stages. Shaded areas (MESS) indicate climate conditions out of the species range.</p