scholarly journals Integrating natural history-derived phenomics with comparative genomics to study the genetic architecture of convergent evolution

2019 ◽  
Author(s):  
Sangeet Lamichhaney ◽  
Daren C. Card ◽  
Phil Grayson ◽  
João F.R. Tonini ◽  
Gustavo A. Bravo ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Natural History ◽  
Convergent Evolution ◽  
Phenotypic Diversity ◽  
Taxonomic Diversity ◽  
Gold Rush ◽  
Phenotypic Data ◽  
Natural History Collection ◽  
Genomic Studies ◽  
Genetic Mechanisms

AbstractEvolutionary convergence has been long considered primary evidence of adaptation driven by natural selection and provides opportunities to explore evolutionary repeatability and predictability. In recent years, there has been increased interest in exploring the genetic mechanisms underlying convergent evolution, in part due to the advent of genomic techniques. However, the current ‘genomics gold rush’ in studies of convergence has overshadowed the reality that most trait classifications are quite broadly defined, resulting in incomplete or potentially biased interpretations of results. Genomic studies of convergence would be greatly improved by integrating deep ‘vertical’, natural history knowledge with ‘horizontal’ knowledge focusing on the breadth of taxonomic diversity. Natural history collections have and continue to be best positioned for increasing our comprehensive understanding of phenotypic diversity, with modern practices of digitization and databasing of morphological traits providing exciting improvements in our ability to evaluate the degree of morphological convergence. Combining more detailed phenotypic data with the well-established field of genomics will enable scientists to make progress on an important goal in biology: to understand the degree to which genetic or molecular convergence is associated with phenotypic convergence. Although the fields of comparative biology or comparative genomics alone can separately reveal important insights into convergent evolution, here we suggest that the synergistic and complementary roles of natural history collection-derived phenomic data and comparative genomics methods can be particularly powerful in together elucidating the genomic basis of convergent evolution among higher taxa.

scholarly journals Integrating natural history collections and comparative genomics to study the genetic architecture of convergent evolution

2019 ◽  
Vol 374 (1777) ◽  
pp. 20180248 ◽  
Author(s):  
Sangeet Lamichhaney ◽  
Daren C. Card ◽  
Phil Grayson ◽  
João F. R. Tonini ◽  
Gustavo A. Bravo ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Natural History ◽  
Convergent Evolution ◽  
Phenotypic Diversity ◽  
Taxonomic Diversity ◽  
Gold Rush ◽  
Phenotypic Data ◽  
Natural History Collections ◽  
Natural History Collection ◽  
Genomic Studies

Evolutionary convergence has been long considered primary evidence of adaptation driven by natural selection and provides opportunities to explore evolutionary repeatability and predictability. In recent years, there has been increased interest in exploring the genetic mechanisms underlying convergent evolution, in part, owing to the advent of genomic techniques. However, the current ‘genomics gold rush’ in studies of convergence has overshadowed the reality that most trait classifications are quite broadly defined, resulting in incomplete or potentially biased interpretations of results. Genomic studies of convergence would be greatly improved by integrating deep ‘vertical’, natural history knowledge with ‘horizontal’ knowledge focusing on the breadth of taxonomic diversity. Natural history collections have and continue to be best positioned for increasing our comprehensive understanding of phenotypic diversity, with modern practices of digitization and databasing of morphological traits providing exciting improvements in our ability to evaluate the degree of morphological convergence. Combining more detailed phenotypic data with the well-established field of genomics will enable scientists to make progress on an important goal in biology: to understand the degree to which genetic or molecular convergence is associated with phenotypic convergence. Although the fields of comparative biology or comparative genomics alone can separately reveal important insights into convergent evolution, here we suggest that the synergistic and complementary roles of natural history collection-derived phenomic data and comparative genomics methods can be particularly powerful in together elucidating the genomic basis of convergent evolution among higher taxa. This article is part of the theme issue ‘Convergent evolution in the genomics era: new insights and directions’.

scholarly journals Comparison of Automated Georeferencing Tools Using Insect Collection Data

2019 ◽  
Vol 3 ◽  
Author(s):  
Leonor Venceslau ◽  
Luis Lopes
Keyword(s):  
Natural History ◽  
Average Distance ◽  
Sampling Location ◽  
Reference Dataset ◽  
Global Biodiversity Information Facility ◽  
Google Maps ◽  
Reference Location ◽  
Natural History Collection ◽  
Collection Data ◽  
Insect Collection

Major efforts are being made to digitize natural history collections to make these data available online for retrieval and analysis (Beaman and Cellinese 2012). Georeferencing, an important part of the digitization process, consists of obtaining geographic coordinates from a locality description. In many natural history collection specimens, the coordinates of the sampling location are not recorded, rather they contain a description of the site. Inaccurate georeferencing of sampling locations negatively impacts data quality and the accuracy of any geographic analysis on those data. In addition to latitude and longitude, it is important to define a degree of uncertainty of the coordinates, since in most cases it is impossible to pinpoint the exact location retrospectively. This is usually done by defining an uncertainty value represented as a radius around the center of the locality where the sampling took place. Georeferencing is a time-consuming process requiring manual validation; as such, a significant part of all natural history collection data available online are not georeferenced. Of the 161 million records of preserved specimens currently available in the Global Biodiversity Information Facility (GBIF), only 86 million (53.4%) include coordinates. It is therefore important to develop and optimize automatic tools that allow a fast and accurate georeferencing. The objective of this work was to test existing automatic georeferencing services and evaluate their potential to accelerate georeferencing of large collection datasets. For this end, several open-source georeferencing services are currently available, which provide an application programming interface (API) for batch georeferencing. We evaluated five programs: Google Maps, MapQuest, GeoNames, OpenStreetMap, and GEOLocate. A test dataset of 100 records (reference dataset), which had been previously individually georreferenced following Chapman and Wieczorek 2006, was randomly selected from the Museu Nacional de História Natural e da Ciência, Universidade de Lisboa insect collection catalogue (Lopes et al. 2016). An R (R Core Team 2018) script was used to georeference these records using the five services. In cases where multiple results were returned, only the first one was considered and compared with the manually obtained coordinates of the reference dataset. Two factors were considered in evaluating accuracy: Total number of results obtained and Distance to the original location in the reference dataset. Total number of results obtained and Distance to the original location in the reference dataset. Of the five programs tested, Google Maps yielded the most results (99) and was the most accurate with 57 results < 1000 m from the reference location and 79 within the uncertainty radius. GEOLocate provided results for 87 locations, of which 47 were within 1000 m of the correct location, and 57 were within the uncertainty radius. The other 3 services tested all had less than 35 results within 1000 m from the reference location, and less than 50 results within the uncertainty radius. Google Maps and Open Street Map had the lowest average distance from the reference location, both around 5500 m. Google Maps has a usage limit of around 40000 free georeferencing requests per month, beyond which the service is paid, while GEOLocate is free with no usage limit. For large collections, this may be a factor to take into account. In the future, we hope to optimize these methods and test them with larger datasets.

scholarly journals Phenotypic diversity and marker-trait association studies under heat stress in tomato (Solanum lycopersicum L.)

2019 ◽  
Vol 13 ((04) 2019) ◽  
pp. 578-587 ◽  
Author(s):  
Muhammed Alsamir ◽  
Nabil Ahmad ◽  
Vivi Arief ◽  
Tariq Mahmood ◽  
Richard Trethowan
Keyword(s):  
Heat Stress ◽  
High Temperature ◽  
Temperature Stress ◽  
Phenotypic Diversity ◽  
Association Studies ◽  
High Temperature Stress ◽  
Control Treatment ◽  
Genome Wide Association Studies ◽  
Phenotypic Data ◽  
Tomato Genotypes

Tomato is a mild season crop and high temperature stress impacts productivity negatively. However, the development of cultivars with improved heat tolerance is possible as genetic variability has been consistently reported. This study aimed to identify candidate genes that impact various traits under heat stress. Genome-wide association studies (GWAS) were conducted on a diverse set of 144 tomato genotypes collected from various germplasm centers and breeding programs. The genotypes were grown under control and heat stress in poly tunnels having mean temperatures of 30°C and 45°C for two seasons and phenotypic data were collected on seven agro-physiological traits. All individuals were genotyped withthe80K DArTseq platform using 31237 SNP markers. Data were analysed using a mixed model based on restricted maximum likelihood (REML). Pattern analysis of the phenotypic data showed five primary clusters each with genotypes from multiple origins. Based on the genotypic data, three wild tomato genotypes showed a degree of un-relatedness with the other materials as they were distantly located from the rest of the genotypes in the scatter plot. Control treatment data were used to ascertain markers that are exclusively important under high temperature stress. A large number of markers were significantly associated with various traits under heat stress. These included strong marker associations for number of inflorescence/plant (IPP), number of flowers/inflorescence (FPI), fresh fruit weight (FFrW), and electrolyte leakage (EL). High association with EL was found due to two SNPs 7858523|F|0-25:G>A-25:G>A and 4705224|F|0-60:C>G-60:C>G located on Chr 6. Other less pronounced marker-trait associations were observed for plant dry weight (PDW), and number of fruit/plant (FrPP).

scholarly journals Alteration of RH gene structure and expression in human dCCee and DCW- red blood cells: phenotypic homozygosity versus genotypic heterozygosity

Blood ◽  
1996 ◽  
Vol 88 (6) ◽  
pp. 2326-2333 ◽  
Author(s):  
CH Huang
Keyword(s):  
Red Blood Cells ◽  
Blood Cells ◽  
Phenotypic Diversity ◽  
Genomic Structure ◽  
Gene Organization ◽  
Exon 1 ◽  
Genetic Mechanisms ◽  
Gene Structure And Expression ◽  
Hybrid Genes ◽  
Exon 10

This report describes a comparative study on the dCCee and DCW-red blood cells devoid of RhD and CcEe antigens, respectively. Southern blots showed that the two variants carried opposite deletions in the D and non-D (CcEe) genes. Rh haplotyping and exon polymerase chain reaction (PCR) assay indicated that the deletions did not extend beyond the 5′ region upstream from exon 1 or the 3′ region downstream from exon 10 of the respective genes. This was confirmed by finding intact promoters and 3′ untranslated regions in both D and non-D genes in each variant. Reverse transcriptase-PCR and cDNA sequencing showed the expression of two transcripts in each cell type. In dCCee cells, one transcript was the regular Ce form and the other occurred as a D-Ce-D hybrid whose Ce sequence spanned exons 2 through 9. In DCW-cells, the two transcripts were derived from reversely arranged hybrid genes, ie, the CW-D gene was formed by fusion of CW exon 1 with D exons 2 through 10, whereas the reverse product was formed by fusion of D exons 1 through 9 with non-D exon 10. These results indicated that DNA deletion and recombination had occurred in either cis or trans configuration and involved both RH loci in the dCCee or DCW-genome. Identification of such compound alterations correlates the genotypes with phenotypes and explains the lost Rh antigenic expression. A reinvestigation of gene organization also led to the reassignment of several 5′ and 3′ splice sites. Together, this study not only shows the complexity of Rh phenotypic diversity, but also points to the importance of concurrent analysis of genomic structure and transcript expression in deciphering the underlying genetic mechanisms.

Marble Busts and Fish Fossils

Nuncius ◽  
2016 ◽  
Vol 31 (2) ◽  
pp. 439-483
Author(s):  
Elena Canadelli
Keyword(s):  
Eighteenth Century ◽  
Natural History ◽  
18Th Century ◽  
Museum Collections ◽  
The Public ◽  
Additional Information ◽  
Natural History Collection ◽  
Late 18Th Century ◽  
University Of Padua ◽  
The University

The historical catalogs of the museum collections contain a wealth of information for historians seeking to reconstruct their contents, how they were displayed and the ways in which they were used. This paper will present the complete transcription of a draft catalog that was prepared in 1797 for the Museum of Natural History and Antiquities of the University of Padua. Conserved in the university’s Museum of Geology and Paleontology, the catalog was the first to be compiled of the museum, which was established in 1733 thanks to the donation by Antonio Vallisneri Jr. of his father Antonio Vallisneri Sr.’s collection of antiquities and natural history. The catalog was compiled by the custodian of the museum, the herbalist and amateur naturalist Bartolomeo Fabris. It is of great interest because it provides a record of the number and nature of the pieces conserved in the museum at a time when natural history and archeology collections were still undivided. It also provides indications as to how such collections were arranged for display in the public halls of a university at the end of the eighteenth century. Based on this catalog, with additional information drawn from other manuscript and published sources and museum catalogs from the 1830s conserved in various institutes at the University of Padua, it is possible to reconstruct the contents and layout of a significant late 18th-century natural history collection.

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