Diatom Phylogenies in OneZoom format

A web space to store published phylogenies of diatoms and other algae. The repository holds two general types of files:

1) methodologicaly explicit phylogenetic trees based on phenotypic or genetic data. These are trees derived from coded data via a tree building algorithm.

2) informal hypotheses about evolutionary relationships.These are diagrams reflecting author's interpretation or beleif. They are derived from data that in most cases is not formally coded or procesed through a tree building program. There wont be many of these to start with.

Each tree is represented by the following:

1) the phylogenetic tree displayed in the wonderful OneZoom Tree of Life Explorer format

2) doi or link of the publication where this tree comes from (if available)

3) TreeBase or Dryad study ID of the publication where nexus files of the tree and data can be found (if available)

4) If 2) and/or 3) are missing, a full reference where the tree comes from is provided.

Trees


Chronogram of the Thalassiosirales from Alverson (2014, Paleobiology).

Thalassiosirales

Dryad: doi 10.5061/dryad.85q50


Chronogram of Pinnularia and outgroup taxa from Souffreau et al (2011, Molecular Phylogenetics and Evolution).

Pinnularia

TreeBase: 11769


Tree of diatoms and a number of closely and distantly related eukaryotes from Theriot et al. (2009, European Journal of Phycology).

Diatoms and eukaryotes

TreeBase: 10114

Note: Branch lengths and node ages on this tree are meaningless. The TreeBase entry for this tree does not include branch lengths. To make the tree compatible with OneZoom, polytomies were first randomly resolved and branch lengths added by sampling from a normal distribution. This artificial "phylogram" was then smoothed to a relative time chronogram with root age 1 billion years. This is a larger tree with 1336 taxa and the diatoms are at the very tip.


Tree of diatoms and Bolidomonas as outgroup from Theriot et al. (2010, Plant Ecology and Evolution).

Diatoms and Bolidomonas

TreeBase: 10953

Note: Node ages on this tree are arbitrary as the published tree is not proportional to time. The phylogram reported in the paper was smoothed to a relative time chronogram with root age 500 million years.


Tree of diatoms and Bolidomonas as outgroup from Ashworth et al. (2013, Journal of Phycology).

Diatoms and Bolidomonas

Note: Node ages on this tree are arbitrary as the published tree is not proportional to time. The phylogram reported in the paper was smoothed to a relative time chronogram with root age 500 million years.


Tree of raphid diatoms from Ruck and Theriot (2011, Protist).

Raphid diatoms

Note: Node ages on this tree are arbitrary as the published tree is not proportional to time. The phylogram reported in the paper was smoothed to a relative time chronogram with root age 100 million years.

TreeBase: S11192


Tree of heterokonts and outgroups from Goertzen and Theriot (2003, Journal of Phycology).

Heterokonts and outgroups - SSU tree

Heterokonts and outgroups - rbcL tree

Heterokonts and outgroups - SSU + rbcL tree

Note: Branch lengths and node ages on these trees are meaningless. The TreeBase entry for these trees does not include branch lengths. To make the tree compatible with OneZoom, branch lengths added by sampling from an exponential distribution with rate=10. This artificial "phylogram" was then smoothed to a relative time chronogram with root age 500 million years.

TreeBase: S909


Trees of Amphora among other raphid taxa from Sato et al. (2013, Phycologia).

Amphora and relatives - Maximum likelihood tree

Amphora and relatives - Bayesian inference tree

Note: The trees were scaled to 100 million years root age. The node ages are arbitrary.

TreeBase: S13483


Tree of diatoms and Bolidomonas from Sato et al. (2008, Phycologia).

Diatoms and Bolidomonas - focus on Psammoneis

Note: Branch lengths and node ages on this tree are meaningless. The TreeBase entry did not include branch lengths. To make the tree compatible with OneZoom, branch lengths added by sampling from an exponential distribution with rate=10. This artificial "phylogram" was then smoothed to a relative time chronogram with root age 500 million years.

TreeBase: S2106


Tree of diatoms and Bolidomonas from Sato et al. (2008, Phycologia).

Diatoms and Bolidomonas - focus on Pseudostriatella

Note: Branch lengths and node ages on this tree are meaningless. The TreeBase entry did not include branch lengths. To make the tree compatible with OneZoom, branch lengths added by sampling from an exponential distribution with rate=10. This artificial "phylogram" was then smoothed to a relative time chronogram with root age 500 million years.

TreeBase: S2107


Tree of Skeletonema and outgroups from Sarno et al. (2007, Protist).

Skeletonema and ougroups

Note: Branch lengths and node ages on this tree are meaningless. The TreeBase entry did not include branch lengths. To make the tree compatible with OneZoom, branch lengths added by sampling from an exponential distribution with rate=10. This artificial "phylogram" was then smoothed to a relative time chronogram with root age 20 million years.

TreeBase: S1922


Tree of Thalassiosirales from Alverson (2007, Limnology & Oceanoraphy).

Thalassiosirales - tree from silicon transported genes (SIT)

Note: Branch lengths and node ages on this tree are meaningless. The TreeBase entry did not include branch lengths. To make the tree compatible with OneZoom, branch lengths added by sampling from an exponential distribution with rate=10. This artificial "phylogram" was then smoothed to a relative time chronogram with root age 100 million years.

TreeBase: S2047


Trees based on morphological data of Cyclotella nana (Thalassiosira pseudonana) and allies from Alverson et al. (2011, BMC Evolutionary Biology).

Cyclotella nana and allies - Parsimony 1

Cyclotella nana and allies - Parsimony 2

Cyclotella nana and allies - Parsimony 3

Cyclotella nana and allies - Parsimony 4

Cyclotella nana and allies - Parsimony 5

Cyclotella nana and allies - Parsimony 6

Cyclotella nana and allies - Parsimony 7

Cyclotella nana and allies - Parsimony 8

Note: Branch lengths and node ages on these trees are meaningless. The TreeBase entry did not include branch lengths. To make the trees compatible with OneZoom, branch lengths added by sampling from an exponential distribution with rate=10. Artificial "phylograms" were then smoothed to relative time chronograms with root age 100 million years.

TreeBase: S11009


Trees of Stephanodiscus based on morphological data from Julius et al. (2006, Phycological Research).

Stephanodiscus - without S. kasuensis - Parsimony

Stephanodiscus - with S. kasuensis - Parsimony. Polytomies randomly resolved.

Stephanodiscus - with S. kasuensis - Parsimony. Polytomies randomly resolved.

Stephanodiscus - with S. kasuensis - Parsimony. Polytomies randomly resolved.

Note: Branch lengths and node ages on these trees are meaningless. The TreeBase entry did not include branch lengths. To make the trees compatible with OneZoom, branch lengths added by sampling from an exponential distribution with rate=10. Artificial "phylograms" were then smoothed to relative time chronograms with root age 20 million years.

TreeBase: S11011