Evolutionary Lineages

Question 1

Reconstructing Phylogenies

Answer 1

Important to remember:

1) different methods with different flaws and strengths
2) phylogenies are hypotheses - we can only generate the most probably tree given the data
3) The field of Phylogenetic Systematics was developed by Willi Hennig and revolutionized the outlook on phylogenies
4) Robust phylogenetic reconstruction is a key step in modern analytical biogeography

Question 2

Phylogenetic Systematics

Answer 2

A philosophy and methodology for the reconstruction of ancestor-descendant relationships among a set of taxa

Question 3

Tenets of phylogenetic systematics

Answer 3

1) Characters used to reconstruct a phylogeny are modifications of existing characters. DNA sequence variation and morphological traits are the most commonly employed characters.
2) History of changes in character states reflects the ancestor-descendant relationships of organisms bearing the same characters
3) The distribution of characters among a set of taxa is used to identify monophyletic groups. Monophyletic groups are also known as clades and phylogenetic trees as cladograms
4) Monophyletic groups are identified by shared derived traits (aka synapomorphies). All other taxa outside the monophyletic groups possess the ancestral or plesiomorphic traits.

Question 4

Cladistics

Answer 4

a common criterion for interring phylogenies is a maximum parsimony

Question 5

Caveats of a Cladogram

Answer 5

cladogram is a represation of a phylogenetic hypothesis but not necessarily true

Reversals of character states could confound pylogenetic reconstruction - and we often have to esimate rates of reversals (in DNA sequence data)

Parallel or convergent evolution (i.e homoplasy) can be confounding

Question 6

Phylogenetic reconstructions

Answer 6

Lars Brundin was the first to conduct a phylogenetic reconstruction of the biogeographic history of a taxon (southern hemisphere midges)

Question 7

Consensus area cladogram

Answer 7

Summary of the shared biogeographic history of multiple taxa inferred from congruent cladograms
Ex. consensus area cladogram for southern beech trees and midges vs for hylid frogs, ratite, and galliform birds

Question 8

Cladogenesis on the hawaiian islands

Answer 8

The different islands are different ages therefore the endemic species on each island is related to the placement on the cladogram

Question 9

Microevolutionary and Macroevolutionary processes

Answer 9

Micro can extrapolate and explain macro differences among species and higher taxa.

Question 10

Phylogeography

Answer 10

The phylogenetic analysis of organismal data in the context of the geographical distribution of the organism. The phylogenetic analysis of geographically contextualized genetic data for testing hypotheses regarding the causal relationship among geographic events, demographic events, species distributions and speciation.

An approach in historical biogeography that studies the geographic distribution of genealogical lineages within species and among similar species and attempts to differentiate between historical and ongoing processes leading to the development of observed patterns.

Question 11

Use of mtDNA

Answer 11

Why is it used so often? 
Lack of recombination 
Haploid 
Selectively neutral variation (maybe) 
Small effective population size 
rapid evolution in animals 
many copies per cell

Ex. used to figure out haplotype network and evolutionary relationships among bowfin fish
Used to look at the distribution of mtDNA haplotypes in pocket gophers
Compared the distributions between bowfins and pocket gophers and see congruent discontinuities in all distributions corresponding to river drainages

Ex. green turtles that nest in different areas has different sequence divergence percentages which can indicate time of divergence and etc

Question 12

Statistical Phylogeography

Answer 12

The framing of phylogeographic investigations within a rigorous statistical framework through development of alternative hypotheses

Question 13

Coalescence

Answer 13

In a gene tree the point in time at which two allelic lineages diverged from an ancestral lineage.
Node of a tree

At any point in time a population has many genes competing for success - some will go extinct by drift
after enough time only one will remain (i.e. fixation)
This is called lineage sorting

Question 14

Time till coalescence

Answer 14

Diplod populations size N
4N generations
Haploid population size N:
2N generations

Question 15

Processes that affect pattern of coalescence

Answer 15

1) Population growth: coalescence is most likely to occur at the point when population size expanded
2) Vicariance: coalescence of gene copies present in each region may occur near the time of vicariance

Question 16

Species tree : history of related species

Answer 16

Species arise when groups of individuals stop exchanging genes

Question 17

Some genes don’t reflect species history

Answer 17

This is called incomplete lineage sorting

This occurs when time between species divergences is short compared to the population size (short wide branches)