Assessing evolutionary processes over time in a conservation breeding program: a combined approach using molecular data, simulations and pedigree analysis

2021 ◽  
Author(s):  
Belinda R. Wright ◽  
Carolyn J. Hogg ◽  
Elspeth A. McLennan ◽  
Katherine Belov ◽  
Catherine E. Grueber
Keyword(s):  
Molecular Data ◽  
Pedigree Analysis ◽  
Breeding Program ◽  
Combined Approach ◽  
Evolutionary Processes ◽  
Conservation Breeding ◽  
Over Time

scholarly journals The importance of offshore origination revealed through ophiuroid phylogenomics

2017 ◽  
Vol 284 (1858) ◽  
pp. 20170160 ◽  
Author(s):  
Guadalupe Bribiesca-Contreras ◽  
Heroen Verbruggen ◽  
Andrew F. Hugall ◽  
Timothy D. O'Hara
Keyword(s):  
Deep Sea ◽  
Marine Invertebrates ◽  
Range Shift ◽  
Evolutionary Adaptation ◽  
Evolutionary Processes ◽  
Opposite Pattern ◽  
Bathymetric Range ◽  
Evolutionary Pattern ◽  
Transitional State ◽  
Over Time

Our knowledge of macro-evolutionary processes in the deep sea is poor, leading to much speculation about whether the deep sea is a source or sink of evolutionary adaptation. Here, we use a phylogenetic approach, on large molecular (688 species, 275 kbp) and distributional datasets (104 513 records) across an entire class of marine invertebrates (Ophiuroidea), to infer rates of bathymetric range shift over time between shallow and deep water biomes. Biome conservation is evident through the phylogeny, with the majority of species in most clades distributed within the same bathome. Despite this, bathymetric shifts have occurred. We inferred from ancestral reconstructions that eurybathic or intermediate distributions across both biomes were a transitional state and direct changes between shallow and deep sea did not occur. The macro-evolutionary pattern of bathome shift appeared to reflect micro-evolutionary processes of bathymetric speciation. Results suggest that most of the oldest clades have a deep-sea origin, but multiple colonization events indicate that the evolution of this group conforms neither to a simple onshore–offshore hypothesis, nor the opposite pattern. Both shallow and deep bathomes have played an important role in generating the current diversity of this major benthic class.

scholarly journals The Iberian lynx Lynx pardinus Conservation Breeding Program

2008 ◽  
Vol 42 (1) ◽  
pp. 190-198 ◽  
Author(s):  
A. VARGAS ◽  
I. SÁNCHEZ ◽  
F. MARTÍNEZ ◽  
A. RIVAS ◽  
J. A. GODOY ◽  
...  
Keyword(s):  
Breeding Program ◽  
Lynx Lynx ◽  
Iberian Lynx ◽  
Lynx Pardinus ◽  
Conservation Breeding

scholarly journals Interpretation of biological experiments changes with evolution of Gene Ontology and its annotations

2017 ◽  
Author(s):  
Aurelie Tomczak ◽  
Jonathan M. Mortensen ◽  
Rainer Winnenburg ◽  
Charles Liu ◽  
Dominique T. Alessi ◽  
...  
Keyword(s):  
Gene Ontology ◽  
High Throughput ◽  
Enrichment Analysis ◽  
Building Blocks ◽  
Molecular Data ◽  
Biological Phenomena ◽  
Go Enrichment ◽  
Human Genes ◽  
Go Enrichment Analysis ◽  
Over Time

ABSTRACTGene Ontology (GO) enrichment analysis is ubiquitously used for interpreting high throughput molecular data and generating hypotheses about underlying biological phenomena of experiments. However, the two building blocks of this analysis — the ontology and the annotations — evolve rapidly. We used gene signatures derived from 104 disease analyses to systematically evaluate how enrichment analysis results were affected by evolution of the GO over a decade. We found low consistency between enrichment analyses results obtained with early and more recent GO versions. Furthermore, there continues to be strong annotation bias in the GO annotations where 58% of the annotations are for 16% of the human genes. Our analysis suggests that GO evolution may have affected the interpretation and possibly reproducibility of experiments over time. Hence, researchers must exercise caution when interpreting GO enrichment analyses and should reexamine previous analyses with the most recent GO version.

scholarly journals Effects of Different Nursing Methods on the Behavioral Response of Adult Captive Giant Pandas (Ailuropoda Melanoleuca)

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 626
Author(s):  
Ming-Yue Zhang ◽  
Xiao-Hui Zhang ◽  
James Ayala ◽  
Rong Hou
Keyword(s):  
Genetic Diversity ◽  
Behavioral Response ◽  
Ex Situ Conservation ◽  
Breeding Program ◽  
Ex Situ ◽  
Ailuropoda Melanoleuca ◽  
Giant Pandas ◽  
Conservation Breeding

Although the ex situ conservation breeding program has basically created self-sustaining populations and genetic diversity in captive giant pandas (Ailuropoda melanoleuca) [...]

Genetic Pedigree Analysis of the Pilot Breeding Program for the Rediscovered Galapagos Giant Tortoise from Floreana Island

2018 ◽  
Vol 109 (6) ◽  
pp. 620-630 ◽  
Author(s):  
Joshua M Miller ◽  
Maud C Quinzin ◽  
Elizabeth H Scheibe ◽  
Claudio Ciofi ◽  
Fredy Villalva ◽  
...  
Keyword(s):  
Pedigree Analysis ◽  
Breeding Program

On the identity of Adelophryne pachydactyla Hoogmoed, Borges, and Cascon, 1994 (Brachycephaloidea: Eleutherodactylidae)

Zootaxa ◽  
2018 ◽  
Vol 4444 (5) ◽  
pp. 575 ◽  
Author(s):  
RAMON C. DOMINATO ◽  
CARLA S. CASSINI ◽  
JANISETE G. SILVA ◽  
VICTOR G. D. ORRICO
Keyword(s):  
Morphological Character ◽  
Molecular Data ◽  
Phylogenetic Position ◽  
Molecular Analyses ◽  
Fresh Material ◽  
Parsimonious Explanation ◽  
Southern Bahia ◽  
Collateral Effect ◽  
Specific Assignment ◽  
Over Time

The use of molecular data for documenting biodiversity has become more common over time as larger datasets can be generated faster. Nevertheless, studies addressing phenotypical data have not become as common. As a collateral effect, many samples used in molecular studies are assigned to a species without checking phenomic characters of the vouchers. Correct specific assignment is paramount for any biological hypothesis. A recent review of Phyzelaphryninae, while producing interesting results, has not specified how some vouchers used in molecular analyses were assigned to each species. Using new sequences from fresh material collected in Southern Bahia, we re-identify Adelophryne specimens based on molecular and morphological grounds. This new taxonomic understanding clarifies the phylogenetic position of A. pachydactyla and highlights a more parsimonious explanation for the evolution of a morphological character—the reduction of a phalange on Finger IV—within Adelophryne. 

Phylogenetic position of Coronastrum ellipsoideum and description of Parachlorella hussii sp. nov.

Biologia ◽  
2011 ◽  
Vol 66 (4) ◽  
Author(s):  
Christina Bock ◽  
Marie Pažoutová ◽  
Lothar Krienitz
Keyword(s):  
Molecular Data ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Combined Approach ◽  
Molecular Analyses ◽  
Phylogenetic Studies ◽  
The Family ◽  
Its Rrna Gene ◽  
Molecular Phylogenetic ◽  
First Time

AbstractFollowing traditional morphological concepts, the genus Coronastrum is considered to be a rare member of the Scenedesmaceae (Chorophyceae). This classification may be called into question when molecular data are taken into account as well. Recent molecular phylogenetic studies revealed the polyphyletic origin of the family Scenedesmaceae within the Chlorophyceae and Trebouxiophyceae. In a combined approach of morphological analyses, SSU/ITS rRNA gene phylogeny and comparison of the ITS secondary structure, we analysed the systematics of Coronastrum strains available in public strain collections. Our molecular analyses revealed a new subclade within the Chlorella clade of the Chlorellaceae consisting of Coronastrum ellipsoideum, two strains with Dictyosphaerium-like morphology and one strain which fits the description of the genus Parachlorella. Four additional strains formed together a new lineage within the genus Parachlorella in the Parachlorella clade of the Chlorellaceae. These strains differ from the already known Parachlorella species in complementary base changes within the ITS2 and are here described for the first time as Parachlorella hussii sp. nov.

scholarly journals Comparative genomics provides an operational classification system and reveals early emergence and biased spatio-temporal distribution of SARS-CoV-2

2020 ◽  
Author(s):  
Matteo Chiara ◽  
David S. Horner ◽  
Carmela Gissi ◽  
Graziano Pesole
Keyword(s):  
Classification System ◽  
Functional Characterization ◽  
Temporal Distribution ◽  
Genomic Analysis ◽  
Molecular Data ◽  
Comparative Genomic ◽  
Evolutionary Processes ◽  
Systematic Classification ◽  
Spatio Temporal

AbstractEffective systems for the analysis of molecular data are of fundamental importance for real-time monitoring of the spread of infectious diseases and the study of pathogen evolution. While the Nextstrain and GISAID portals offer widely used systems for the classification of SARS-CoV-2 genomes, both present relevant limitations. Here we propose a highly reproducible method for the systematic classification of SARS-CoV-2 viral types. To demonstrate the validity of our approach, we conduct an extensive comparative genomic analysis of more than 20,000 SARS-CoV-2 genomes. Our classification system delineates 12 clusters and 4 super-clusters in SARS-CoV-2, with a highly biased spatio-temporal distribution worldwide, and provides important observations concerning the evolutionary processes associated with the emergence of novel viral types. Based on the estimates of SARS-CoV-2 evolutionary rate and genetic distances of genomes of the early pandemic phase, we infer that SARS-CoV-2 could have been circulating in humans since August-November 2019. The observed pattern of genomic variability is remarkably similar between all clusters and super-clusters, being UTRs and the s2m element, a highly conserved secondary structure element, the most variable genomic regions. While several polymorphic sites that are specific to one or more clusters were predicted to be under positive or negative selection, overall, our analyses also suggest that the emergence of novel genome types is unlikely to be driven by widespread convergent evolution and independent fixation of advantageous substitutions. While, in the absence of rigorous experimental validation, several questions concerning the evolutionary processes and the phenotypic characteristics (increased/decreased virulence) remain open, we believe that the approach outlined in this study can be of relevance for the tracking and functional characterization of different types of SARS-CoV-2 genomes.

scholarly journals Significant temporal shifts on clonal and plasmid backgrounds of Enterobacteriaceae producing acquired AmpC in Portuguese clinical settings

2019 ◽  
Author(s):  
T. G. Ribeiro ◽  
Â. Novais ◽  
C. Rodrigues ◽  
R. Nascimento ◽  
F. Freitas ◽  
...  
Keyword(s):  
Molecular Data ◽  
Clinical Settings ◽  
Bacterial Identification ◽  
Beta Lactams ◽  
E Coli ◽  
Epidemiological Changes ◽  
Differential Expansion ◽  
Third Generation Cephalosporins ◽  
Over Time ◽  
Selection Of

ABSTRACTOBJECTIVESTo provide detailed molecular data on clinical acquired AmpC (qAmpC)-producing Enterobacteriaceae from two different periods (2002-2008 and 2010-2013) in order to clarify the contribution of clonal and plasmid genetic platforms for the current epidemiological scenario concerning extended-spectrum beta-lactams resistance.METHODSWe analysed 1246 Enterobacteriaceae non-susceptible to third-generation cephalosporins from 2 hospitals and 1 community laboratory between 2010 and 2013. Bacterial identification, antibiotic susceptibility, identification of qAmpC and plasmid-mediated quinolone resistance genes, clonal (PFGE, MLST) and plasmid (S1-/I-CeuI-PFGE, replicon typing, hybridization) analysis were performed by standard methods. WGS was performed in two ST11-K. pneumoniae isolates harbouring DHA-1.RESULTSThe occurrence of qAmpC was lower (2.6%) than that observed in a previous survey (7.4%), and varied slightly over time. Isolates produced DHA-1 (53%), CMY-2 (44%) or DHA-6 (3%), but significant epidemiological changes were observed in the two surveys. While DHA-1 persisted in different institutions by selection of a worldwide epidemic IncR plasmid in a ST11 harbouring KL105, CMY-2 rates increased over time linked to IncI1 plasmids (instead of IncK or IncA/C2) in multiple E. coli clones.CONCLUSIONSThe higher frequency of DHA-1 qAmpC in these species contrasts with the scenario of most European countries. Furthermore, the different genetic backgrounds associated with either ESBL or qAmpC in our country might have contributed to their differential expansion.

scholarly journals Selecting the most appropriate time points to profile in high-throughput studies

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Michael Kleyman ◽  
Emre Sefer ◽  
Teodora Nicola ◽  
Celia Espinoza ◽  
Divya Chhabra ◽  
...  
Keyword(s):  
High Throughput ◽  
Combinatorial Problem ◽  
Molecular Data ◽  
High Rate ◽  
Mouse Lung ◽  
Point Selection ◽  
Time Points ◽  
Small Set ◽  
Changes Over Time ◽  
Over Time

Biological systems are increasingly being studied by high throughput profiling of molecular data over time. Determining the set of time points to sample in studies that profile several different types of molecular data is still challenging. Here we present the Time Point Selection (TPS) method that solves this combinatorial problem in a principled and practical way. TPS utilizes expression data from a small set of genes sampled at a high rate. As we show by applying TPS to study mouse lung development, the points selected by TPS can be used to reconstruct an accurate representation for the expression values of the non selected points. Further, even though the selection is only based on gene expression, these points are also appropriate for representing a much larger set of protein, miRNA and DNA methylation changes over time. TPS can thus serve as a key design strategy for high throughput time series experiments. Supporting Website: www.sb.cs.cmu.edu/TPS

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