Population genetic structuring in pacu (Piaractus mesopotamicus) across the Paraná-Paraguay basin: evidence from microsatellites

The Paraná-Paraguay basin encompasses central western Brazil, northeastern Paraguay, eastern Bolivia and northern Argentina. The Pantanal is a flooded plain with marked dry and rainy seasons that, due to its soil characteristics and low declivity, has a great water holding capacity supporting abundant fish fauna. Piaractus mesopotamicus, or pacu, endemic of the Paraná-Paraguay basin, is a migratory species economically important in fisheries and ecologically as a potential seed disperser. In this paper we employ eight microsatellite loci to assess the population structure of 120 pacu sampled inside and outside the Pantanal of Mato Grosso. Our main objective was to test the null hypothesis of panmixia and to verify if there was a different structuring pattern between the Pantanal were there were no physical barriers to fish movement and the heavily impounded Paraná and Paranapanema rivers. All loci had moderate to high levels of polymorphism, the number of alleles varied from three to 18. The average observed heterozygosity varied from 0.068 to 0.911. After the Bonferroni correction three loci remained significant for deviations from Hardy-Weinberg, and for those the frequency of null alleles was estimated. F ST and R ST pairwise comparisons detected low divergence among sampling sites, and differentiation was significant only between Paranapanema and Cuiabá and Paranapanema and Taquari. No correlation between genetic distance and the natural logarithm of the geographic distance was detected. Results indicate that for conservation purposes and for restoration programs small genetic differences detected in the Cuiabá and Paranapanema rivers should be taken in consideration.A bacia Paraná-Paraguai compreende o oeste do Brasil, nordeste do Paraguai, leste da Bolívia e o norte da Argentina. O Pantanal do Mato Grosso é uma planície inundada com estações de chuva e seca bem definidas, as características do solo e baixa declividade favorecem a retenção de água proporcionando abrigo para uma abundante ictiofauna. O Piaractus mesopotamicus, ou pacu, endêmico da bacia do Paraná-Paraguai, é uma espécie migratória com importância econômica na pesca e ecológica como potencial dispersor de sementes. Neste estudo utilizamos oito loci de microssatélites para verificar a estrutura populacional de 120 pacus coletados dentro e fora do Pantanal do Mato Grosso. Nosso principal objetivo foi testar a hipótese de panmixia e verificar se haviam diferentes padrões de estruturação entre o Pantanal onde não existem barreiras físicas ao movimento migratório desses peixes em relação aos rios Paraná e Paranapanema com suas inúmeras barragens. Todos os loci apresentaram níveis de polimorfismo de moderado a alto e o número de alelos variou de três a 18. A heterozigosidade média observada variou de 0,068 a 0,911. Depois da correção usando o método de Bonferroni três loci permaneceram estatisticamente significantes para desvios de Hardy-Weinberg, para estes a frequência de alelos nulos foi calculada. Comparações par a par de F ST e R ST detectaram baixa divergência genética entre os locais de coleta e as diferenças foram significantes apenas entre amostras do Paranapanema e Cuiabá e Paranapanema e Taquari. Não foi detectada correlação entre a diversidade genética e o logaritmo natural da distância geográfica. Os resultados indicam que as pequenas diferenças genéticas encontradas nos rios Cuiabá e Paranapanema devem ser levadas em consideração quando se tratar de programas de conservação desta espécie.FAPES

Should Networks Supplant Tree Building?

Recent studies suggested that network methods should supplant tree building as the basis of genealogical analysis. This proposition is based upon two arguments. First is the observation that bacterial and archaeal lineages experience processes oppositional to bifurcation and hence the representation of the evolutionary process in a tree like structure is illogical. Second is the argument tree building approaches are circular—you ask for a tree and you get one, which pins a verificationist label on tree building that, if correct, should be the end of phylogenetic analysis as we currently know it. In this review, we examine these questions and suggest that rumors of the death of the bacterial tree of life are exaggerated at best

An Investigation of How Environmental Science Textbooks Link Human Environmental Impact to Ecology and Daily Life

Making direct connections between humanity and the environment is of ever-increasing importance in the context of today’s environmental crisis. We used qualitative content analysis of precollege- and college-level introductory environmental science textbook case studies to study how they portray humanity’s link to the environment. We assessed case studies for how specific and data rich they are and for how they link together daily life, human impact, and ecological interactions. We found that, for many textbooks, case study stories were vaguely drawn and included few data. We also found that, for all textbooks, case studies almost always described human impacts without linking to their ecological underpinnings and daily life connections were frequently missing from human impact discussion. We use comparisons of case studies to make the argument that data and specific details tell more fleshed-out relatable stories, that connecting to daily life will more likely challenge student perceptions of people as separate from the environment, and that explicit inclusion of ecological interactions into environmental stories better explains how people connect to and impact the rest of the living world

Examining Ancient Inter-domain Horizontal Gene Transfer

Details of the genomic changes that occurred in the ancestors of Eukarya, Archaea and Bacteria are elusive. Ancient interdomain horizontal gene transfer (IDHGT) amongst the ancestors of these three domains has been difficult to detect and analyze because of the extreme degree of divergence of genes in these three domains and because most evidence for such events are poorly supported. In addition, many researchers have suggested that the prevalence of IDHGT events early in the evolution of life would most likely obscure the patterns of divergence of major groups of organisms let alone allow the tracking of horizontal transfer at this level. In order to approach this problem, we mined the E. coli genome for genes with distinct paralogs. Using the 1,268 E. coli K-12 genes with 40% or higher similarity level to a paralog elsewhere in the E. coli genome we detected 95 genes found exclusively in Bacteria and Archaea and 86 genes found in Bacteria and Eukarya. These genes form the basis for our analysis of IDHGT. We also applied a newly developed statistical test (the node height test), to examine the robustness of these inferences and to corroborate the phylogenetically identified cases of ancient IDHGT. Our results suggest that ancient inter domain HGT is restricted to special cases, mostly involving symbiosis in eukaryotes and specific adaptations in prokaryotes. Only three genes in the Bacteria + Eukarya class (Deoxyxylulose-5-phosphate synthase (DXPS), fructose 1,6-phosphate aldolase class II protein and glucosamine-6-phosphate deaminase) and three genes–in the Bacteria + Archaea class (ABC-type FE3+-siderophore transport system, ferrous iron transport protein B, and dipeptide transport protein) showed evidence of ancient IDHGT. However, we conclude that robust estimates of IDHGT will be very difficult to obtain due to the methodological limitations and the extreme sequence saturation of the genes suspected of being involved in IDHGT

Character-based DNA barcoding allows discrimination of genera, species and populations in Odonata

© 2007 The Author et al. This is an open-access article distributed under the terms of the Creative Commons 2.5 Attribution License. The definitive version was published in Proceedings of The Royal Society B 275 (2008): 237-247, doi:10.1098/rspb.2007.1290.DNA barcoding has become a promising means for identifying organisms of all life stages. Currently, phenetic approaches and tree-building methods have been used to define species boundaries and discover 'cryptic species'. However, a universal threshold of genetic distance values to distinguish taxonomic groups cannot be determined. As an alternative, DNA barcoding approaches can be 'character based', whereby species are identified through the presence or absence of discrete nucleotide substitutions (character states) within a DNA sequence. We demonstrate the potential of character-based DNA barcodes by analysing 833 odonate specimens from 103 localities belonging to 64 species. A total of 54 species and 22 genera could be discriminated reliably through unique combinations of character states within only one mitochondrial gene region (NADH dehydrogenase 1). Character-based DNA barcodes were further successfully established at a population level discriminating seven population-specific entities out of a total of 19 populations belonging to three species. Thus, for the first time, DNA barcodes have been found to identify entities below the species level that may constitute separate conservation units or even species units. Our findings suggest that character-based DNA barcoding can be a rapid and reliable means for (i) the assignment of unknown specimens to a taxonomic group, (ii) the exploration of diagnosability of conservation units, and (iii) complementing taxonomic identification systems.The work was supported by the Federal Government Research Program (BMBF) BIOTA South Africa (S08) and the German Science Foundation (DFG) Special Priority Program 'Deep Metazoan Phylogeny' SP1174 (DFG HA 1947/5-1 and 5-2); grants given to the last author

Let’s end taxonomic blank slates with molecular morphology

Many known evolutionary lineages have yet to be described formally due to a lack of traditional morphological characters. This is true for genetically distinctive groups within the amoeboid Placozoa animals, the protists in ponds, and the bacteria that cover nearly everything. These taxonomic tabula rasae, or blank slates, are problematic; without names, communication is hampered and other scientific progress is slowed. We suggest that the morphology of molecules be used to help alleviate this issue. Molecules, such as proteins, have structure. Proteins are even visualizable with X-ray crystallography, albeit more easily detected by and easier to work with using genomic sequencing. Given their structured nature, we believe they should not be considered as anything less than traditional morphology. Protein-coding gene content (presence/absence) can also be used easily with genomic sequences, and is a convenient binary character set. With molecular morphology, we believe that each taxonomic tabula rasa can be solved

Determination of enriched histone modifications in non-genic portions of the human genome

Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) has recently been used to identify the modification patterns for the methylation and acetylation of many different histone tails in genes and enhancers.RESULTS:We have extended the analysis of histone modifications to gene deserts, pericentromeres and subtelomeres. Using data from human CD4+ T cells, we have found that each of these non-genic regions has a particular profile of histone modifications that distinguish it from the other non-coding regions. Different methylation states of H4K20, H3K9 and H3K27 were found to be enriched in each region relative to the other regions. These findings indicate that non-genic regions of the genome are variable with respect to histone modification patterns, rather than being monolithic. We furthermore used consensus sequences for unassembled centromeres and telomeres to identify the significant histone modifications in these regions. Finally, we compared the modification patterns in non-genic regions to those at silent genes and genes with higher levels of expression. For all tested methylations with the exception of H3K27me3, the enrichment level of each modification state for silent genes is between that of non-genic regions and expressed genes. For H3K27me3, the highest levels are found in silent genes.CONCLUSION:In addition to the histone modification pattern difference between euchromatin and heterochromatin regions, as is illustrated by the enrichment of H3K9me2/3 in non-genic regions while H3K9me1 is enriched at active genes; the chromatin modifications within non-genic (heterochromatin-like) regions (e.g. subtelomeres, pericentromeres and gene deserts) are also quite different

A Novel Analytical Framework for Dissecting the Genetic Architecture of Behavioral Symptoms in Neuropsychiatric Disorders

Background: For diagnosis of neuropsychiatric disorders, a categorical classification system is often utilized as a simple way for conceptualizing an often complex clinical picture. This approach provides an unsatisfactory model of mental illness, since in practice patients do not conform to these prototypical diagnostic categories. Family studies show notable familial co-aggregation between schizophrenia and bipolar illness and between schizoaffective disorders and both bipolar disorder and schizophrenia, revealing that mental illness does not conform to such categorical models and is likely to follow a continuum encompassing a spectrum of behavioral symptoms. Results and Methodology: We introduce an analytic framework to dissect the phenotypic heterogeneity present in complex psychiatric disorders based on the conceptual paradigm of a continuum of psychosis. The approach identifies subgroups of behavioral symptoms that are likely to be phenotypically and genetically homogenous. We have evaluated this approach through analysis of simulated data with simulated behavioral traits and predisposing genetic factors. We also apply this approach to a psychiatric dataset of a genome scan for schizophrenia for which extensive behavioral information was collected for each individual patient and their families. With this approach, we identified significant evidence for linkage among depressed individuals with two distinct symptom profiles, that is individuals with sleep disturbance symptoms with linkage on chromosome 2q13 and also a mutually exclusive group of individuals with symptoms of concentration problems with linkage on chromosome 2q35. In addition we identified a subset of individuals with schizophrenia defined by language disturbances with linkage to chromosome 2p25.1 and a group of patients with a phenotype intermediate between those of schizophrenia and schizoaffective disorder with linkage to chromosome 2p21. Conclusions: The findings presented are novel and demonstrate the efficacy of this approach in detection of genes underlying such complex human disorders as schizophrenia and depression

Spermatogenesis drives rapid gene creation and masculinization of the X chromosome in stalk-eyed flies (Diopsidae)

Throughout their evolutionary history, genomes acquire new genetic material that facilitates phenotypic innovation and diversification. Developmental processes associated with reproduction are particularly likely to involve novel genes. Abundant gene creation impacts the evolution of chromosomal gene content and general regulatory mechanisms such as dosage compensation. Numerous studies in model organisms have found complex and, at times contradictory, relationships among these genomic attributes highlighting the need to examine these patterns in other systems characterized by abundant sexual selection. Therefore, we examined the association among novel gene creation, tissue-specific gene expression, and chromosomal gene content within stalk-eyed flies. Flies in this family are characterized by strong sexual selection and the presence of a newly evolved X chromosome. We generated RNA-seq transcriptome data from the testes for three species within the family and from seven additional tissues in the highly dimorphic species, Teleopsis dalmanni. Analysis of dipteran gene orthology reveals dramatic testes-specific gene creation in stalk-eyed flies, involving numerous gene families that are highly conserved in other insect groups. Identification of X-linked genes for the three species indicates that the X chromosome arose prior to the diversification of the family. The most striking feature of this X chromosome is that it is highly masculinized, containing nearly twice as many testes-specific genes as expected based on its size. All the major processes that may drive differential sex chromosome gene content—creation of genes with male-specific expression, development of male-specific expression from pre-existing genes, and movement of genes with male-specific expression—are elevated on the X chromosome of T. dalmanni. This masculinization occurs despite evidence that testes expressed genes do not achieve the same levels of gene expression on the X chromosome as they do on the autosomes. © The Author 2016

Crossroads, Milestones, amd Landmarks in Insect Development and Evolution: Implications for Systematics

Our understanding of insect development and evolution has increased greatly due to recent advances in the comparative developmental approach. Modem developmental biology techniques such as in situ hybridization and molecular analysis of developmentally important genes and gene families have greatly facilitated these advances. The role of the comparative developmental approach in insect systematics is explored in this paper and we suggest two important applications of the approach to insect systematics--character dissection and morphologicallandmarking. Exi~ng morphological characters can be dissected into their genetic and molecular components in some cases and this will lead to more and richer character information in systematic studies. Character landmarking will be essential - to systematic studies for clarifying structures such as shapes or convergences, which are previously hard to analyze anatomical regions. Both approaches will aid greatly in expanding our understanding of homology in particular, and insect development in general