VL9 Reconstructiong the past Flashcards
What is phylogeny?
Phylogeny is the evolutionary history and relationships among species, often represented as a phylogenetic tree, which can also depict the relationships of genes or loci.
Who introduced the hierarchical system of species classification and what did it lack?
Carolus Linnaeus introduced the hierarchical system based on shared morphological characteristics, but it lacked the concept of common ancestry and evolutionary relationships.
How did Charles Darwin’s classification differ from Linnaeus’s?
Darwin’s classification was based on common ancestry, grouping species by characters shared through descent and considering the historical process of species evolution.
What are the key components of a phylogenetic tree?
Nodes, sister species, monophyletic groups, branches, branch lengths, lineages, root, and tree topology.
What is the importance of rooted phylogenies?
Rooted phylogenies provide a time axis and direction of evolution, identifying the common ancestor of all taxa in the tree and the deepest evolutionary split.
What is the significance of homologous traits in phylogenetic inference?
Homologous traits, resulting from common ancestry, are the basis for inferring evolutionary relationships and distinguishing between derived and ancestral states.
What are the challenges in molecular phylogenetics?
Challenges include
* selecting homologous sequences,
* computing optimal sequence alignments,
* choosing the right phylogenetic inference method,
* dealing with mutational saturation,
* and distinguishing species trees from gene trees.
What is the role of models in molecular phylogenetics?
Models estimate genetic distances by determining the frequency of different mutations, accounting for multiple substitutions in distant sequences.
What are distance methods in phylogenetic inference?
Distance methods like Neighbor Joining and UPGMA use genetic distance matrices to construct trees quickly, though more accurate methods are preferred.
What are character-based methods in phylogenetic inference?
Character-based methods include
1) parsimony, which seeks the tree with the fewest changes, and
2) statistical methods like maximum likelihood and Bayesian inference, which use probabilistic models to find the best tree.
What is bootstrapping in phylogenetics?
Bootstrapping is a statistical method to estimate the variance and confidence intervals of clades in a phylogeny by resampling alignment columns with replacement and computing phylogenies multiple times.
Aus dem Buch:
Resampling of a dataset with replacemnet in order to get a measurment of sample error. For phlogenic trees, this means repeatedly resampling informative loci and estimating trees in orer to get an idea of the support for branching patterns in the tree.
What is the difference between gene trees and species trees?
Gene trees depict the evolutionary history of individual genes or loci, which may not always align with species trees due to factors like incomplete lineage sorting and gene flow.
What is incomplete lineage sorting (ILS)?
ILS occurs when alleles coalesce before or after lineage splits, leading to gene trees that may not reflect the true species relationships, often due to large ancestral population sizes or short divergence times.
What is phylogenomics?
Phylogenomics involves large-scale phylogenetic analysis of multiple genes or loci from many samples to study organismal evolution and gene function, tries overcoming stochastic errors and lack of sufficient signal in individual loci.
What are haplotype networks?
Haplotype networks visualize intraspecific variation in haplotypes, showing the frequency of each haplotype and the number of nucleotide substitutions between them.
* node diameter: haplotype frequency
* links: number of nt substitutions between haplotypes
* Each color represents a different population while each circle represents a specific haplotype.
What is the ABBA-BABA test (D-statistics) for detecting gene flow?
The ABBA-BABA test compares the counts of specific allele patterns (ABBA and BABA) to detect introgression between populations, with a D value of zero indicating no gene flow and a non-zero D value indicating introgression.
