Salinity appears to be the main factor shaping spatial COI diversity of Corbicula lineages within the Chinese Yangtze River Basin

Aim

To date, few studies have examined the phylogenetics of Corbicula clams in their native range and the environmental parameters influencing their distribution, although this could provide great insights into the biological adaptation and invasion dynamics of Corbicula clams. We sought to identify the genetic lineages of native Corbicula clams and elucidate the environmental factors shaping the distributions of identified lineages.

Location

China, mainly the Yangtze River Basin.

Methods

The alignment comprised 558 COI sequences including samples from China and 222 COI sequences from published studies. This dataset was used to generate phylogenetic trees and compare population diversity. We used dbRDA method to assess the relationship between these COI data and environmental factors measured to identify the important factors affecting Corbicula's distribution.

Results

The COI phylogenetic tree delineated the monophyly of 3 major COI clades and 77 distinct COI haplotypes in the Yangtze River Basin. The invasive lineage C/S (FW17) was not identified in our sampling in China, while invasive lineages A/R (FW5 = Hap6), B (FW1 = Hap17) and Rlc (FW4 = Hap43) were identified, abundant and widely distributed in the middle and lower reaches of Yangtze River. Focusing on populations from Yangtze River Basin, both the COI haplotype and nucleotide diversity in the lakes along the Yangtze River increased with longitude, except for the river mouth population. The AMOVA tests showed significant differentiation between the middle and lower reaches of the Yangtze River and among populations. The dbRDA results suggested that the parameter chloride explained most of the spatial COI haplotype distribution variation in the Yangtze River Basin, with the three invasive lineages tolerating broad fluctuations of salinity (chloride levels ranging from 4 to 60 mg/L).

Conclusions

The Corbicula COI haplotypes found within the Yangtze River Basin had distinct distribution preferences, with the invasive androgenetic lineages being the most abundant and widely distributed. Genetic diversity was higher in this native region than in invaded areas in Europe and America, while it decreased with increasing distance from the river mouth. Salinity appeared to be the main environmental factor shaping the COI haplotype distribution of Corbicula lineages within their native range.     

Historical sampling reveals dramatic demographic changes in western gorilla populations

Background  

Today many large mammals live in small, fragmented populations, but it is often unclear whether this subdivision is the result of long-term or recent events. Demographic modeling using genetic data can estimate changes in long-term population sizes while temporal sampling provides a way to compare genetic variation present today with that sampled in the past. In order to better understand the dynamics associated with the divergences of great ape populations, these analytical approaches were applied to western gorillas (Gorilla gorilla) and in particular to the isolated and Critically Endangered Cross River gorilla subspecies (G. g. diehli).     

Right Place,Wrong Species: A 20-Year Review of Rabies Virus Cross Species Transmission among Terrestrial Mammals in the United States

Introduction

In the continental US, four terrestrial mammalian species are reservoirs for seven antigenic rabies virus variants. Cross species transmission (CST) occurs when a rabies virus variant causes disease in non-reservoir species.

Methods

This study analyzed national surveillance data for rabies in terrestrial mammals. The CST rate was defined as: number of rabid non-reservoir animals/number of rabid reservoir animals. CST rates were analyzed for trend. Clusters of high CST rate counties were evaluated using space-time scanning statistics.

Results

The number of counties reporting a raccoon variant CST rate >1.0 increased from 75 in 1992 to 187 in 2011; counties with skunk variant CST rates >1.0 remained unchanged during the same period. As of 2011, for every rabid raccoon reported within the raccoon variant region, there were 0.73 cases of this variant reported in non-reservoir animals. Skunks were the most common non-reservoir animal reported with the raccoon rabies variant. Domestic animals were the most common non-reservoir animal diagnosed with a skunk rabies virus variant (n = 1,601). Cross species transmission rates increased fastest among domestic animals.

Conclusions

Cross species transmission of rabies virus variants into non-reservoir animals increases the risk of human exposures and threatens current advances toward rabies control. Cross species transmission in raccoon rabies enzootic regions increased dramatically during the study period. Pet owners should vaccinate their dogs and cats to ensure against CST, particularly in regions with active foci of rabies circulation. Clusters of high CST activity represent areas for further study to better understand interspecies disease transmission dynamics. Each CST event has the potential to result in a rabies virus adapted for sustained transmission in a new species; therefore further understanding of the dynamics of CST may help in early detection or prevention of the emergence of new terrestrial rabies virus variants.     

Evolutionary history of the alpha2,8-sialyltransferase (ST8Sia) gene family: Tandem duplications in early deuterostomes explain most of the diversity found in the vertebrate ST8Sia genes

Background

The Salangid icefish Neosalanx taihuensis (Salangidae) is an economically important fish, which is endemic to China, restricted to large freshwater systems (e.g. lakes, large rivers and estuaries) and typically exhibit low vagility. The continuous distribution ranges from the temperate region of the Huai and Yellow River basins to the subtropical region of the Pearl River basin. This wide ranging distribution makes the species an ideal model for the study of palaeoclimatic effects on population genetic structure and phylogeography. Here, we aim to analyze population genetic differentiation within and between river basins and demographic history in order to understand how this species responded to severe climatic oscillations, decline of the sea levels during the Pleistocene ice ages and tectonic activity.

Results

We obtained the complete mtDNA cytochrome b sequences (1141 bp) of 354 individuals from 13 populations in the Pearl River, the Yangze River and the Huai River basin. Thirty-six haplotypes were detected. Haplotype frequency distributions were strongly skewed, with most haplotypes (n = 24) represented only in single samples each and thus restricted to a single population. The most common haplotype (H36) was found in 49.15% of all individuals. Analysis of molecular variance (AMOVA) revealed a random pattern in the distribution of genetic diversity, which is inconsistent with contemporary hydrological structure. Significant levels of genetic subdivision were detected among populations within basins rather than between the three basins. Demographic analysis revealed that the population size in the Pearl River basin has remained relatively constant whereas the populations in the Yangze River and the Huai River basins expanded about 221 and 190 kyr ago, respectively, with the majority of mutations occurring after the last glacial maximum (LGM).

Conclusion

The observed complex genetic pattern of N. taihuensis is coherent with a scenario of multiple unrelated founding events by long-distance colonization and dispersal combined with contiguous population expansion and locally restricted gene flow. We also found that this species was likely severely impacted by past glaciations. More favourable climate and the formation of large suitable habitations together facilitated population expansion after the late Quaternary (especially the LGM). We proposed that all populations should be managed and conserved separately, especially for habitat protection.     

Genetic affinities of the central Indian tribal populations

Background

The central Indian state Madhya Pradesh is often called as ‘heart of India’ and has always been an important region functioning as a trinexus belt for three major language families (Indo-European, Dravidian and Austroasiatic). There are less detailed genetic studies on the populations inhabited in this region. Therefore, this study is an attempt for extensive characterization of genetic ancestries of three tribal populations, namely; Bharia, Bhil and Sahariya, inhabiting this region using haploid and diploid DNA markers.

Methodology/Principal Findings

Mitochondrial DNA analysis showed high diversity, including some of the older sublineages of M haplogroup and prominent R lineages in all the three tribes. Y-chromosomal biallelic markers revealed high frequency of Austroasiatic-specific M95-O2a haplogroup in Bharia and Sahariya, M82-H1a in Bhil and M17-R1a in Bhil and Sahariya. The results obtained by haploid as well as diploid genetic markers revealed strong genetic affinity of Bharia (a Dravidian speaking tribe) with the Austroasiatic (Munda) group. The gene flow from Austroasiatic group is further confirmed by their Y-STRs haplotype sharing analysis, where we determined their founder haplotype from the North Munda speaking tribe, while, autosomal analysis was largely in concordant with the haploid DNA results.

Conclusions/Significance

Bhil exhibited largely Indo-European specific ancestry, while Sahariya and Bharia showed admixed genetic package of Indo-European and Austroasiatic populations. Hence, in a landscape like India, linguistic label doesn''t unequivocally follow the genetic footprints.     

Effective ambiguity checking in biosequence analysis

Background  

Ambiguity is a problem in biosequence analysis that arises in various analysis tasks solved via dynamic programming, and in particular, in the modeling of families of RNA secondary structures with stochastic context free grammars. Several types of analysis are invalidated by the presence of ambiguity. As this problem inherits undecidability (as we show here) from the namely problem for context free languages, there is no complete algorithmic solution to the problem of ambiguity checking.     

Migration of Chadic speaking pastoralists within Africa based on population structure of Chad Basin and phylogeography of mitochondrial L3f haplogroup

Background  

Chad Basin, lying within the bidirectional corridor of African Sahel, is one of the most populated places in Sub-Saharan Africa today. The origin of its settlement appears connected with Holocene climatic ameliorations (aquatic resources) that started ~10,000 years before present (YBP). Although both Nilo-Saharan and Niger-Congo language families are encountered here, the most diversified group is the Chadic branch belonging to the Afro-Asiatic language phylum. In this article, we investigate the proposed ancient migration of Chadic pastoralists from Eastern Africa based on linguistic data and test for genetic traces of this migration in extant Chadic speaking populations.     

Various criteria in the evaluation of biomedical named entity recognition

Background  

Text mining in the biomedical domain is receiving increasing attention. A key component of this process is named entity recognition (NER). Generally speaking, two annotated corpora, GENIA and GENETAG, are most frequently used for training and testing biomedical named entity recognition (Bio-NER) systems. JNLPBA and BioCreAtIvE are two major Bio-NER tasks using these corpora. Both tasks take different approaches to corpus annotation and use different matching criteria to evaluate system performance. This paper details these differences and describes alternative criteria. We then examine the impact of different criteria and annotation schemes on system performance by retesting systems participated in the above two tasks.     

Nutrient loads to surface water from row crop production

Goals, Scope and Background  

Eutrophication and hypoxia, which are already serious environmental issues in the Midwestern region of the United States and the Gulf of Mexico, could worsen with an increase emphasis on the use of corn and soybeans for biofuels. Eutrophication impacts from agriculture are difficult to integrate into an LCA due to annual variability in the nutrient loads as a factor of climatic conditions. This variability has not been included in many relevant energy or row crop LCAs. The objective of this research was to develop a relatively simple method to accurately quantify nutrient loadings from row crop production to surface water that reflects annual variations due to weather. A set of watersheds that comprise most of eastern Iowa was studied. Ample data describing corn-soybean agriculture in this region and nutrient loadings to the Mississippi River enabled the development, calibration and validation of the model for this particular region.     

Seed dispersal by rivers in tropical dry forests: An overlooked process in tropical central Mexico

Aims

Rivers are important corridors for the movement, migration and dispersal of aquatic organisms, including seeds from riparian plants. Although tropical dry forests (TDF) are among the most extensive and floristically rich ecosystems of tropical habitats, and the most globally endangered ecosystem, less attention has been given to riparian corridors within this ecosystem. Although most TDFs manifest peak seed dispersal during dry seasons, we hypothesized that riparian corridors may show a dispersal peak during the rainy season, due to an anticipated ‘sweep or drag effect’, resulting from river overflow and bank erosion. Our main aims were to investigate whether there were any differences in the seed communities transported by the river to sites in rainy as opposed to dry seasons, and to evaluate any possible relationship between the riparian seed community and river flow.

Location

Amacuzac River, drainage of the Balsas basin, State of Morelos, Mexico.

Methods

To evaluate the above assumption, we associated Amacuzac River flow with the number of species and seeds dispersed by water. We also characterized and evaluated differences between seed communities transported by the river during the rainy and dry seasons, and between four different sites located along the river. We used univariate and ordination NMDS techniques to evaluate patterns between seasons at the community level.

Results

Forty‐five plant species were identified from 909 seeds collected from the river. The composition of riparian seed communities was markedly different between seasons but not between sites. Seed abundances were significantly higher in the rainy than in the dry season and varied between sites. Seed species diversity in the river (H’ = 1.6–1.9) showed no significant differences between seasons or sites, but species assemblages and dominance varied according to season. Ordination techniques and subsequent fitting analyses showed that seed species composition was positively associated with river flow.

Conclusions

Seed dispersal patterns generated by rivers are significant mechanisms for structuring the composition and distribution of the riparian plant community in Mexican TDF. Varying species assemblages and seed abundance dispersed by the river throughout the year is a relevant and until now unknown consequence that may affect the dynamics and composition of riparian plant communities in this region. This study initiative will promote new avenues of research regarding plant establishment and succession.     

Genetic differentiation of European grayling (Thymallus thymallus) populations in Serbia,based on mitochondrial and nuclear DNA analyses

Background

The structure and diversity of grayling (Thymallus thymallus) populations have been well studied in most of its native habitat; however the southernmost populations of the Balkan Peninsula remain largely unexplored. The purpose of this study was to assess the genetic diversity of Serbian grayling populations, detect the impact of stocking and provide guidelines for conservation and management.

Methods

Eighty grayling individuals were collected from four rivers (Ibar, Lim, Drina and Rzav). The mitochondrial DNA control region (CR; 595 bp of the 3''end and 74 bp of flanking tRNA) and the ATP6 gene (630 bp fragment) were sequenced for 20 individuals (five from each locality). In addition, all individuals were genotyped with 12 microsatellite loci. The diversity and structure of the populations as well as the recent and ancient population declines were studied using specialized software.

Results

We detected three new haplotypes in the mtDNA CR and four haplotypes in the ATP6 gene of which three had not been described before. Previously, one CR haplotype and two ATP6 gene haplotypes had been identified as allochthonous, originating from Slovenia. Reconstruction of phylogenetic relations placed the remaining two CR haplotypes from the River Danube drainage of Serbia into a new clade, which is related to the previously described sister Slovenian clade. These two clades form a new Balkan clade. Microsatellite marker analysis showed that all four populations are genetically distinct from each other without any sign of intra-population structure, although stocking of the most diverse population (Drina River) was confirmed by mtDNA analysis. Recent and historical population declines of Serbian grayling do not differ from those of other European populations.

Conclusions

Our study shows that (1) the Ibar, Lim and Drina Rivers grayling populations are genetically distinct from populations outside of Serbia and thus should be managed as native populations in spite of some introgression in the Drina River population and (2) the Rzav River population is not appropriate for further stocking activities since it originates from stocked Slovenian grayling. However, the Rzav River population does not represent an immediate danger to other populations because it is physically isolated from these.     

Terrestrial invasion of pomatiopsid gastropods in the heavy-snow region of the Japanese Archipelago

Background  

Gastropod mollusks are one of the most successful animals that have diversified in the fully terrestrial habitat. They have evolved terrestrial taxa in more than nine lineages, most of which originated during the Paleozoic or Mesozoic. The rissooidean gastropod family Pomatiopsidae is one of the few groups that have evolved fully terrestrial taxa during the late Cenozoic. The pomatiopsine diversity is particularly high in the Japanese Archipelago and the terrestrial taxa occur only in this region. In this study, we conducted thorough samplings of Japanese pomatiopsid species and performed molecular phylogenetic analyses to explore the patterns of diversification and terrestrial invasion.     

Past vegetation dynamics in the Yellowstone region highlight the vulnerability of mountain systems to climate change

Aim

Reconstruct the long‐term ecosystem dynamics of the region across an elevational gradient as they relate to climate and local controls. In particular, we (1) describe the dominant conifers' history; (2) assess changes in vegetation composition and distribution; and (3) note periods of abrupt change versus stability as means of better understanding vegetation responses to environmental variability.

Location

Greater Yellowstone Ecosystem (GYE; USA).

Time period

16.5 ka bp ‐present.

Major taxa studied

Juniperus, Picea, Abies, Pinus, Pseudotsuga.

Methods

The vegetation reconstruction was developed from 15 pollen records. Results were interpreted based on modern pollen–vegetation relationships estimated from a suite of regression‐based approaches.

Results

Calibrated pollen data suggest that late‐glacial vegetation, dominated by shrubs and Juniperus, lacks a modern counterpart in the area. Picea, Abies and Pinus expanded at 16 ka bp in association with postglacial warming and co‐occurred in mixed‐conifer parkland/forest after 12 ka bp . This association along with Pinus contorta forest, which was present after 9 ka bp , has persisted with little change at middle and high elevations to the present day. This stability contrasts with the dynamic history of plant communities at low elevations, where shifts between parkland, steppe and forest over the last 8,000 years were likely driven by variations in effective moisture and fire.

Main conclusions

The postglacial vegetation history of the GYE highlights the dynamic nature of mountain ecosystems and informs on their vulnerability to future climate change: (1) most of the conifers have been present in the area for >12,000 years and survived climate change by adjusting their elevational ranges; (2) some plant associations have exhibited stability over millennia as a result of nonclimatic controls; and (3) present‐day forest cover is elevationally more compressed than at any time in history, probably due to the legacy of the Medieval Climate Anomaly and the Little Ice Age.     

Problems in Cross-Cultural Use of the Hospital Anxiety and Depression Scale: “No Butterflies in the Desert”

Objective

The Hospital Anxiety and Depression Scale (HADS) is widely used to screen for anxiety and depression. A large literature is citable in support of its validity, but difficulties are increasingly being identified, such as inexplicably discrepant optimal cutpoints and inconsistent factor-structures. This article examines whether these problems could be due to the construction of the HADS that poses difficulties for translation and cross-cultural use.

Methods

Authors’ awareness of difficulties translating the HADS were identified by examining 20% of studies using the HADS, obtained by a systematic literature search in Pubmed and PsycINFO in May 2012. Reports of use of translations and validation studies were recorded for papers from non-English speaking countries. Narrative and systematic reviews were examined for how authors dealt with different translations.

Results

Of 417 papers from non-English speaking countries, only 45% indicated whether a translation was used. Studies validating translations were cited in 54%. Seventeen reviews, incorporating data from diverse translated versions, were examined. Only seven mentioned issues of language and culture, and none indicated insurmountable problems in integrating results from different translations.

Conclusion

Initial decisions concerning item content and response options likely leave the HADS difficult to translate, but we failed to find an acknowledgment of problems in articles involving its translation and cross-cultural use. Investigators’ lack of awareness of these issues can lead to anomalous results and difficulties in interpretation and integration of these results. Reviews tend to overlook these issues and most reviews indiscriminately integrate results from studies performed in different countries. Cross-culturally valid, but literally translated versions of the HADS may not be attainable, and specific cutpoints may not be valid across cultures and language. Claims about rates of anxiety and depression based on integrating cross-cultural data or using the same cutpoint across languages and culture should be subject to critical scrutiny.     

Whole genome sequencing of an ethnic Pathan (Pakhtun) from the north-west of Pakistan

Background

Pakistan covers a key geographic area in human history, being both part of the Indus River region that acted as one of the cradles of civilization and as a link between Western Eurasia and Eastern Asia. This region is inhabited by a number of distinct ethnic groups, the largest being the Punjabi, Pathan (Pakhtuns), Sindhi, and Baloch.

Results

We analyzed the first ethnic male Pathan genome by sequencing it to 29.7-fold coverage using the Illumina HiSeq2000 platform. A total of 3.8 million single nucleotide variations (SNVs) and 0.5 million small indels were identified by comparing with the human reference genome. Among the SNVs, 129,441 were novel, and 10,315 nonsynonymous SNVs were found in 5,344 genes. SNVs were annotated for health consequences and high risk diseases, as well as possible influences on drug efficacy. We confirmed that the Pathan genome presented here is representative of this ethnic group by comparing it to a panel of Central Asians from the HGDP-CEPH panels typed for ~650 k SNPs. The mtDNA (H2) and Y haplogroup (L1) of this individual were also typical of his geographic region of origin. Finally, we reconstruct the demographic history by PSMC, which highlights a recent increase in effective population size compatible with admixture between European and Asian lineages expected in this geographic region.

Conclusions

We present a whole-genome sequence and analyses of an ethnic Pathan from the north-west province of Pakistan. It is a useful resource to understand genetic variation and human migration across the whole Asian continent.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1290-1) contains supplementary material, which is available to authorized users.     

A Multi-Site Knowledge Attitude and Practice Survey of Ebola Virus Disease in Nigeria

Background

The 2014 Ebola Virus Disease (EVD) outbreak was characterised by fear, misconceptions and irrational behaviours. We conducted a knowledge attitude and practice survey of EVD in Nigeria to inform implementation of effective control measures.

Methods

Between July 30^th and September 30^th 2014, we undertook a cross sectional study on knowledge, attitude and practice (KAP) of Ebola Virus Disease (EVD) among adults of the general population and healthcare workers (HCW) in three states of Nigeria, namely Bayelsa, Cross River and Kano states. Demographic information and data on KAP were obtained using a self-administered standardized questionnaire. The percentage KAP scores were categorised as good and poor. Independent predictors of good knowledge of EVD were ascertained using a binary logistic regression model.

Results

Out of 1035 study participants with median age of 32 years, 648 (62.6%) were males, 846 (81.7%) had tertiary education and 441 (42.6%) were HCW. There were 218, 239 and 578 respondents from Bayelsa, Cross River and Kano states respectively. The overall median percentage KAP scores and interquartile ranges (IQR) were 79.46% (15.07%), 95.0% (33.33%) and 49.95% (37.50%) respectively. Out of the 1035 respondents, 470 (45.4%), 544(52.56%) and 252 (24.35%) had good KAP of EVD defined using 80%, 90% and 70% score cut-offs respectively. Independent predictors of good knowledge of EVD were being a HCW (Odds Ratio-OR-2.89, 95% Confidence interval-CI of 1.41–5.90), reporting ‘moderate to high fear of EVD’ (OR-2.15, 95% CI-(1.47–3.13) and ‘willingness to modify habit’ (OR-1.68, 95% CI-1.23–2.30).

Conclusion

Our results reveal suboptimal EVD-related knowledge, attitude and practice among adults in Nigeria. To effectively control future outbreaks of EVD in Nigeria, there is a need to implement public sensitization programmes that improve understanding of EVD and address EVD-related myths and misconceptions, especially among the general population.     

Patterns,biases and prospects in the distribution and diversity of Neotropical snakes

Motivation

We generated a novel database of Neotropical snakes (one of the world's richest herpetofauna) combining the most comprehensive, manually compiled distribution dataset with publicly available data. We assess, for the first time, the diversity patterns for all Neotropical snakes as well as sampling density and sampling biases.

Main types of variables contained

We compiled three databases of species occurrences: a dataset downloaded from the Global Biodiversity Information Facility (GBIF), a verified dataset built through taxonomic work and specialized literature, and a combined dataset comprising a cleaned version of the GBIF dataset merged with the verified dataset.

Spatial location and grain

Neotropics, Behrmann projection equivalent to 1° × 1°.

Time period

Specimens housed in museums during the last 150 years.

Major taxa studied

Squamata: Serpentes.

Software format

Geographical information system (GIS).

Results

The combined dataset provides the most comprehensive distribution database for Neotropical snakes to date. It contains 147,515 records for 886 species across 12 families, representing 74% of all species of snakes, spanning 27 countries in the Americas. Species richness and phylogenetic diversity show overall similar patterns. Amazonia is the least sampled Neotropical region, whereas most well‐sampled sites are located near large universities and scientific collections. We provide a list and updated maps of geographical distribution of all snake species surveyed.

Main conclusions

The biodiversity metrics of Neotropical snakes reflect patterns previously documented for other vertebrates, suggesting that similar factors may determine the diversity of both ectothermic and endothermic animals. We suggest conservation strategies for high‐diversity areas and sampling efforts be directed towards Amazonia and poorly known species.     

Tracing the Tiger: Population Genetics Provides Valuable Insights into the Aedes (Stegomyia) albopictus Invasion of the Australasian Region

Background

The range of the Asian tiger mosquito Aedes albopictus is expanding globally, raising the threat of emerging and re-emerging arbovirus transmission risks including dengue and chikungunya. Its detection in Papua New Guinea''s (PNG) southern Fly River coastal region in 1988 and 1992 placed it 150 km from mainland Australia. However, it was not until 12 years later that it appeared on the Torres Strait Islands. We hypothesized that the extant PNG population expanded into the Torres Straits as an indirect effect of drought-proofing the southern Fly River coastal villages in response to El Nino-driven climate variability in the region (via the rollout of rainwater tanks and water storage containers).

Methodology/Principal Findings

Examination of the mosquito''s mitochondrial DNA cytochrome oxidase I (COI) sequences and 13 novel nuclear microsatellites revealed evidence of substantial intermixing between PNG''s southern Fly region and Torres Strait Island populations essentially compromising any island eradication attempts due to potential of reintroduction. However, two genetically distinct populations were identified in this region comprising the historically extant PNG populations and the exotic introduced population. Both COI sequence data and microsatellites showed the introduced population to have genetic affinities to populations from Timor Leste and Jakarta in the Indonesian region.

Conclusions/Significance

The Ae. albopictus invasion into the Australian region was not a range expansion out of PNG as suspected, but founded by other, genetically distinct population(s), with strong genetic affinities to populations sampled from the Indonesian region. We now suspect that the introduction of Ae. albopictus into the Australian region was driven by widespread illegal fishing activity originating from the Indonesian region during this period. Human sea traffic is apparently shuttling this mosquito between islands in the Torres Strait and the southern PNG mainland and this extensive movement may well compromise Ae. albopictus eradication attempts in this region.     

Site specific rates of mitochondrial genomes and the phylogeny of eutheria

Background  

Traditionally, most studies employing data from whole mitochondrial genomes to diagnose relationships among the major lineages of mammals have attempted to exclude regions that potentially complicate phylogenetic analysis. Components generally excluded are 3^rd codon positions of protein-encoding genes, the control region, rRNAs, tRNAs, and the ND6 gene (encoded on the opposite strand). We present an approach that includes all the data, with the exception of the control region. This approach is based on a site-specific rate model that accommodates excessive homoplasy and that utilizes secondary structure as a reference for proper alignment of rRNAs and tRNAs.     

ErmineJ: Tool for functional analysis of gene expression data sets

Background  

It is common for the results of a microarray study to be analyzed in the context of biologically-motivated groups of genes such as pathways or Gene Ontology categories. The most common method for such analysis uses the hypergeometric distribution (or a related technique) to look for "over-representation" of groups among genes selected as being differentially expressed or otherwise of interest based on a gene-by-gene analysis. However, this method suffers from some limitations, and biologist-friendly tools that implement alternatives have not been reported.