1. Interpreting molecular phylogenetic trees Aidan Budd Structural and Computational Biology Unit EMBL Heidelberg, Germany EMBO Practical Course on Computational Molecular Evolution IMBG-HCMR, Heraklion, Greece Monday 3rd - Tuesday 4th May 2010

2. Part 2

3. Sequence Alignments

4. Sequence Alignment Sequence Alignment: Arrangement of two or more sequences in matrix/grid

5. Biological Sequence Alignment - Rows Residues in the same row are from the same biological macromolecule (protein or nucleic acid) Residues are arranged in the order they occur in the macromolecule N to C terminal in proteins 5' to 3' in nucleotides

6. Biological Sequence Alignment - Columns Elements/cells in the matrix only ever contain a single character (either a residue or a "blank"/"gap" character) Residues in the same column share a special 1:1 relationship that they don't share with residues in any other column

7. Biological Sequence Alignment - Gaps Gaps specify pairs of residues in the same sequence i.e. the residues flanking the gap within the same sequence Between the flanking residues, other sequences in the alignment have residues for which there is no 1:1 relationship in the gapped sequence

8. Biological Sequence Alignment - Gaps Gap-only column provide no information about relationships between residues in the alignment

9. Biological Sequence Alignment - Gaps Gap-only column provide no information about relationships between residues in the alignment Removing sequences sometimes leaves all-gap columns We usually remove these "Empty" columns does not effect (as this doesn't change the 1:1 relationships described by the rest of the alignment)

10. Structurally equivalent/similar Evolutionary equivalent/related/homologous Residues in the same column either: Different applications assume different types of equivalence Different types of similarity not necessarily equivalent! “Equivalence”/similarity of residues

11. Structural equivalence Demonstration: http://www.embl- heidelberg.de/~seqanal/courses/commonCourseC ontent/commonMsaExercises.html#Demonstrating StructuralEquivalence Bacterial toxins 1ji6 and 1i5p1ji6

12. 1i5p: 1 YVAPVVGTVSSFLLKKVGSLIGKR 111111111111111111111111 1ji6: 1 DAVGTGISVVGQILGVVGVPFAGA Structural equivalence Residues in the same alignment column are "structurally equivalent" i.e. they should be the residues in the two structures whose location with respect to the rest of the structure are most similar in the two structure Such residues will have similar structural/functional "roles" in the two proteins e.g. form similar side-chain interactions

13. Structural equivalence Some regions of the structures do not have structurally equivalent residues in the other structure 1i5p: DNFLNPTQN----PVPLSITSSVN 111111 111111111111ji6: NSWKKTPLSLRSKRSQDRIRELFS Alignment gaps are a sure sign of such residues Placing such residues in the same column as residues from other sequences is a misalignment - to be avoided!

14. “Evolutionary Equivalence” AGWYTI AGWWTI AGWYTI AGWWTI AAWYTI AGWWTI AAQQQWYTI Mutation / Substitution Y-W Substitution G-A QQQ Insertion AGWYTI Two copies of gene generated AGWYTI AGWWTI AGWYTI AGWWTI AAWYTI AG---WWTI AAQQQWYTI Residues in the same alignment column should trace their history back to the same residue in the ancestral sequence with any changes due only to point substitutions

15. Quiz - Evolutionary Interpretation of Alignments Which alignment of the final sequences (X, Y or Z) only places residues in the same column if they are related by substitution events? KGE--------PGIGL------PG KGIPG-----------DPAFGDPG RGIPGEVLGAQ-----------PG Z KGEPG------IGL------PG KGIPG---------DPAFGDPG RGIPGEVLGAQ---------PG Y KGEPG---IGLPG KGIPGDPAFGDPG RGIPGEVLGAQPG X

16. Quiz - Evolutionary Interpretation of Alignments RGIPGEVLGAQPG KGIPGDPAFGDP G ---KGEPGIGLPG PRANK KGEPG---IGLPG KGIPGDPAFGDPG RGIPGEVLGAQPG MAFFT K---GEPGIGLPG KGIPGDPAFGDPG RGIPGEVLGAQPG CLUSTALX Different automatic MSA software gives different results They're all "wrong".... Because their model of evolutionary process is very divergent from the (very strange...) one under which I told you they evolved KGE--------PGIGL------PG KGIPG-----------DPAFGDPG RGIPGEVLGAQ-----------PG Z KGEPG------IGL------PG KGIPG---------DPAFGDPG RGIPGEVLGAQ---------PG Y KGEPG---IGLPG KGIPGDPAFGDPG RGIPGEVLGAQPG X

17. Interpreting Alignments Special 1:1 relationship between residues in the same column Structural: Very similar structural environment Evolutionary: Related by point mutations/no mutations from the same residue in the ancestral sequence Structural and Evolutionary equivalence need not necessarily be the same Not all residues have 1:1 equivalents in other structures

18. Non-Equivalence of Evolutionary and Structural Alignments Demonstration 1: Structural equivalence without evolutionary equivalence Structural alignment of SH3-interaction motifs from nef and ncf1 nef/fyn1 PDB:1efn ncf1 PDB:1w70 aligned ncf1/nef1 SH3 interaction motifs

19. Non-Equivalence of Evolutionary and Structural Alignments Demonstration 2: Evolutionary equivalence without structural equivalence Human Lymphotactin adopts different folds depending on the conditions PDB:2jp1 PDB:1j8i

20. Mis-alignment “Gold-standard” structural alignment “Gold-standard” structural alignment (with CLUSTALX default colouring) Mis-alignment of same region - residues that are known to be functionally equivalent are NOT in the same coloumns

21. Quiz - Numbers of Insertions (a) 2(b) 1(c) 0(d) 3 The minimum number of insertion events required to account for the section of haemoglobin alignment shown above is?

22. Quiz - Numbers of Insertions If all sequences are the same length, we can explain their diversity without inferring ANY insertions or deletions If and alignment contains sequences that are all either length x or y, then we can explain their diversity by inferring just one insertion or deletion The minimum number of insertion events required to account for the section of haemoglobin alignment shown above is?

23. Quiz - Numbers of Insertions The minimum number of insertion events required to account for the section of haemoglobin alignment shown above is? We can ALWAYS explain observed sequence length diversity with: 0 insertions (all length variation due to deletion) 0 deletions (all length variation due to insertion) a combination of insertions and deletions Perhaps we should instead focus on inferring the most likely scenario? (Although if this is not particularly relevant for our analysis, perhaps we should focus instead on something completely different!)

24. Manipulating Alignments "Manually" Demonstration and Exercise Examining and manipulating alignments using JalView

25. Branch Lengths

26. Unscaled Trees Branch lengths provide no information Branch lengths usually chosen to align OTU labels Re-rooting the tree typically changes the choice of branch lengths Same unscaled unrooted tree

27. Scaled Trees Branch length usually represents some measure of the difference/distance between TUs at ends of the branch Tree should be presented together with a scale bar Same unscaled unrooted tree Same scaled unrooted tree For rectangular trees, “node lines” are NOT branches! Their length provides no indication of intertaxa difference/distance! i.e. distance between taxa C and G is the sum of the green and cyan lines (it does NOT include the length of the red line!) CG

28. Usually an ESTIMATE of the EXPECTED/AVERAGE number of substitutions per site between two sequences Branch Lengths SeqA SeqB 0.2 SeqA IKTILKWWSP... SeqB IKTIVKWDSP... If we assume: All identical residues between two sequences have not experienced substitutions All different residues have experienced one substitution Mean/Average No. Substitutions = 2/10 = 0.2

29. Usually an ESTIMATE of the EXPECTED/AVERAGE number of substitutions per site between two sequences Branch Lengths SeqA SeqB 0.2 SeqA IKTILKWWSP... SeqB IKTIVKWDSP... Branch-length estimate depends on SUBSTITUTION MODEL Further assumptions of this model All alignment positions/residues evolve (are substituted at) the same rate All residues substitute to all other residues at the same rate i.e. A->G at same frequency as A->W

30. Branch Lengths and Visualising Trees Demonstration and Exercise Working with scaled trees in Dendroscope Formatting trees for figures Working with large trees

31. B C E D G F H I J A Clades Clade: A set of OTUs that includes all descendants of a given internal ancestral/internal branch Branch xy specifies the clade ABCDEF z y x w v u Clades: ABCDEFG - no branch has ALL and ONLY these taxa as descendants IJ is a clade as there is a branch vu which has only IJ as its descendants Clades:

32. Clans Of clades and clans: terms for phylogenetic relationships in unrooted trees. Wilkinson M, McInerney JO, Hirt RP, Foster PG, Embley TM. Trends Ecol Evol. 2007 Mar;22(3):114-5. PMID: 17239486 Group of OTUs are a clan if there is at least one rooted phylogeny where they form a clade. clades therefore EFG form a clan However! Under some rootings EFG does not form a clade

33. Clans... Group of OTUs are a clan if there is at least one rooted phylogeny where they form a clade. NO rooted trees place EG in a clade Therefore EG is not a clan Of clades and clans: terms for phylogenetic relationships in unrooted trees. Wilkinson M, McInerney JO, Hirt RP, Foster PG, Embley TM. Trends Ecol Evol. 2007 Mar;22(3):114-5. PMID: 17239486 F

34. Unrooted Trees are Sometimes Sufficient Under all rootings, poisonous members of the order are non-monophyletic Polyphyletic origin of toxic Pitohui birds suggests widespread occurrence of toxicity in corvoid birds. Jønsson KA, Bowie RC, Norman JA, Christidis L, Fjeldså J. Biol Lett. 2008 Feb 23;4(1):71-4. PMID: 18055416 Adaptive evolution in the SRZ chemoreceptor families of Caenorhabditis elegans and Caenorhabditis briggsae. Thomas JH, Kelley JL, Robertson HM, Ly K, Swanson WJ. Proc Natl Acad Sci U S A. 2005 Mar 22;102(12):4476-81 PMID: 15761060 Sites of positive selection identified using reversible models of codon substitution

35. NEWICK/PHYLIP Tree Files/Format

36. Why bother reviewing the NEWICK format... 1. Sometimes we need to read it ourselves e.g. if software doesn’t accept our tree as input 2. Provides a different perspective on the structure of phylogenies helps reinforce our understanding of phylogeny structure When it’s not designed to be easy to read by humans?

37. NEWICK Format Tree Strings - Basics AB C NEWICK string includes the terminal node OTU labels ((A,B),C); Paired parentheses represent internal nodes Parentheses are paired if they contain/enclose the same number of open as close parentheses (i.e. the same number of '(' and ')' characters (a,((b,c),(d,e)))

38. Newick string is terminated by a semicolon ; NEWICK Format Tree Strings - Basics Comma-separated elements within paired parentheses... AB C ((A,B),C);... are nodes (HTU or OTU) that are direct descendants of the 'enclosing parenthesis pair' node

39. NEWICK Format - Polytomies More than two comma-separated nodes in a set of parentheses indicates a polytomy/multifurcation ((A,B,C),D); A B C D

40. NEWICK Format - Indicating Rooted Trees Does the outermost parentheses enclose ONLY TWO NODES? This indicates a rooted tree A B C D ((A,B,C),D);

41. NEWICK Format - Indicating Un-Rooted Trees Do the outermost parentheses enclose THREE NODES? Convention assumes this is an unrooted tree (although it could be a rooted tree with a polytomy at the root...) ((A,B),C,D); A B D C

42. NEWICK Format - Branch Lengths Branch lengths are assigned to nodes using a number preceded by a “:” AB C ((A:1,B:1):2,C:3) These described the lengths of the edges... from the (descendant) node attached to the branch length... to the enclosing/parental node 1.0

43. NEWICK Format: Compatibility Trouble-Shooting If tree string not accepted as input then check/try the following points: string should contain the same number of open and close parentheses i.e. the same number of '(' and ')' characters substitute 'special' characters in the node labels for any of A-Z a-z 0-9 _ remove gaps/whitespace from taxon names remove all whitespace from the string include the entire string on a single line of the input file remove branch length from the root node remove internal node labels change hard polytomies to soft - i.e. insert zero-length or very short internal branches to yield a bifurcating tree

44. Visualising Trees Demonstration/Exercis es Tree (NEWICK/PHYLIP format) Data Editing Trees Using MESQUITE

45. Which of the trees has the same TOPOLOGY and ROOT as tree A? B D Quiz: recognise identical topologies II A ((D,(E,((G,(K,L)),F))),(H,(J,((A,I),(B,C))))); C

46. Where does the root go? A B and C are all from the same unrooted tree Which rooted tree has the root in the most plausible position? A B C

47. Overview of Phylogeny Estimation Workflow

48. Help show how different components/stages of an analysis fit together/relate to each other Providing a guide for planning your own analyses Help placing different sessions/concepts/ideas presented in this course in context with each other Introduce some commonly-used tools Highlight some common problems Acquire Sequence s MSA "Reduced " MSA Initial Phylogeny Estimates Formulate Question Final Phylogeny Estimates

49. Formulating the Question Plays a key role in making decisions during the analysis Analysis is (usually) easier (i.e. takes less time/effort) for more specific questions For example - the following list of questions is sorted by increasing expected difficulty: Which human FGF is most closely related to chicken FGF4? Have there been any FGF gene duplications after the divergence of humans from mice? How are the FGF proteins related to each other? Acquire Sequence s MSA "Reduced " MSA Initial Phylogeny Estimates Formulate Question Final Phylogeny Estimates

50. Building an Initial MSA Unaligned Sequence s MSA build MSA automatically MUSCLE PRANK MAFFT PROBCONS etc. sequencing machine database searches keyword sequence similarity db cross-reference pre-calculated alignments assemble contigs Acquire Sequence s MSA "Reduced " MSA Initial Phylogeny Estimates Formulate Question Final Phylogeny Estimates

51. Building an Initial MSA Demonstration and Exercise Building an MSA from unaligned sequences

52. Refining Initial MSA: Sequences with (Possible) Sequence Errors MSA Identify sequences containing (potential) sequence errors ("wrong" sequences) unusually short sequences unusually evolving subsequences Acquire Sequence s MSA "Reduced " MSA Initial Phylogeny Estimates Formulate Question Final Phylogeny Estimates "Wrong" Sequence s No Yes Are "Wrong" Sequences Essential to Address Question?

53. Sequences with (Possible) Sequence Errors With CLUSTALX “”Quality”->”Show Low-Scorring Segments” switched on Short/fragmented sequences Unusually-evolving/wrong residues

54. Refining Initial MSA: Sequences with (Possible) Sequence Errors Demonstration and Exercise Choosing sequences to remove from an initial MSA

55. Refining Initial MSA: Sequences with (Possible) Sequence Errors Remove Sequences from MSA Acquire Sequence s MSA "Reduced " MSA Initial Phylogeny Estimates Formulate Question Final Phylogeny Estimates Check if Sequences Do Contain Errors MSA "Wrong" Sequence s No Yes Are "Wrong" Sequences Essential to Address Question? Exclude Problematic Regions/Columns from Analysis Yes Try to 'Fix' Errors No

56. Why Use "Reduced" Alignments? (Almost) all phylogeny estimation software ONLY models point substitutions Analysing data (alignment columns) related by any other process introduces systematic error in the phylogeny estimate AG C T α α α α α α Acquire Sequence s MSA "Reduced " MSA Initial Phylogeny Estimates Formulate Question Final Phylogeny Estimates

57. What is a "Reduced" MSA? Acquire Sequence s MSA "Reduced " MSA Initial Phylogeny Estimates Formulate Question Final Phylogeny Estimates

58. Preparing "Reduced" Alignments Choose which columns to remove: "by eye" (using an alignment editor e.g. JalView automatically (e.g. using GBLOCKS) Demonstration and Exercise

59. Initial Phylogeny Estimate Initial estimate using quick (relatively inaccurate) method Gives a quick overview of the diversity of your sequences and the "stability" of the phylogenetic signal If there are long (internal or external) branches, then if they are expected to exist sequences that could "break them up", then try and collect them and add them to the alignment, If "key" sequences are missing, go and collect them If support values are very low, look at ways of increasing the length of the alignment Initial Phylogeny Estimate Collect Additional Sequences Align New Sequences to Initial MSA "reduced" MSA MSA Quick, less accurate, tree estimation Examine Phylogeny Important Sequences Missing? Unnecessary Sequences? Remove Sequences Acquire Sequence s MSA "Reduced " MSA Initial Phylogeny Estimates Formulate Question Final Phylogeny Estimates

60. Include Additional Sequences in the MSA Demonstration and Exercise Aligning "new" sequences to a pre-calculated MSA

61. Final(ish) Phylogeny Estimate Acquire Sequence s MSA "Reduced " MSA Initial Phylogeny Estimates Formulate Question Final Phylogeny Estimates MSA "Reduced " MSA Initial Phylogeny Estimates Final Phylogeny Estimates Estimate phylogeny using a wide range of different approaches, software, molecules, models, support-values Ideally they will tend to all give the same answer to the initial question If not, either just acknowledge the diversity of possible answers, or try to understand why different analyses give different answers Explore different possible sources of model mis-specification

62. Final(ish) Phylogeny Estimate Acquire Sequence s MSA "Reduced " MSA Initial Phylogeny Estimates Formulate Question Final Phylogeny Estimates MSA "Reduced " MSA Initial Phylogeny Estimates Final Phylogeny Estimates Mis-alignment Recombination Heterotachy... Explore different possible sources of model mis-specification

63. Final(ish) Phylogeny Estimate Acquire Sequence s MSA "Reduced " MSA Initial Phylogeny Estimates Formulate Question Final Phylogeny Estimates MSA "Reduced " MSA Initial Phylogeny Estimates Final Phylogeny Estimates Use several (more) accurate phylogeny estimation methods and implementations Bayesian - MrBayes ML - RAxML, PhyML Estimate using different parameter values within each implementation Models Specifics of tree search algorithm Support values

64. Final(ish) Phylogeny Estimate Acquire Sequence s MSA "Reduced " MSA Initial Phylogeny Estimates Formulate Question Final Phylogeny Estimates MSA "Reduced " MSA Initial Phylogeny Estimates Final Phylogeny Estimates Analyse phylogeny of datasets expected to have evolved under the same tree topology Paralogous groups of genes from the same family Different gene families from the same set of organisms Nucleotide dataset from the same gene

65. File Formats Software only accepts data in particular format(s) Format sometimes not very precisely specified Common problems: taxon labels contain any characters other than A-Z and 0-9 (e.g. white space '" "', slashes '\' or'/', pipes '|' etc.) are not unique (e.g. two sequences labeled HumanA) are the wrong length (often a maximum of 10, sometimes exactly 10 is required)

66. File Formats Software only accepts data in particular format(s)Format sometimes not very precisely specifiedCommon problems: sequence representationif gaps allowed - wrong character used to represent them (e.g. '.' instead of '-')if gaps not allowed - the presence of gaps in the alignmentsequence is of the wrong kind of molecule (DNA instead of protein etc.)sequence contains any characters other than the "alphabet" describing the sequences e.g. 'X' for protein alignments, 'N' for DNA alignmentsall sequences not the same length (check using JalView)

67. File Formats Demonstration and Exercise Re-formatting sequences for analysis by MrBayes

68. Summarising Sets of Phylogenies

69. Summarising Phylogenies: Example Use Case Estimate phylogenies from three different loci from the same 200 species, 50 on the island, 150 from the adjacent mainland The three analyses yield three different 'best' tree topologies Consensus trees/split networks are used to identify agreement/disagreement of this kind Is the history of a set of island species well explained by a single colonialization event - i.e. do all island species form a clan Specific Question: NOT If all three trees include the 50 island species in a clann A problem?! Often used to summarise the trees from: phylogenetic bootstrapping Bayesian phylogenetic estimation

70. Splits Each branch of a tree describes a split of OTUs into two sets These sets correspond to the two clans associated with the branch e.g. black branch of the tree specifies the split ABCD | EFG can also be written ADCB | GFE etc. i.e. the taxon lists in the two halves of the split are unordered

71. Splits Splits are either trivial example: F | ABCDEG associated with terminal branches provide no information about topology structure non-trivial example: ABCD | EFG associated with internal branches provide information about topology structure

72. Splits Complete list of splits described by a tree allows reconstruction of that tree’s topology D F DF | ABCEGH A E BCDFGH | AE ABEGH | CDF C BH | ACDEFG BH G Helps to consider the sets of clans described by the splits

73. Split Compatibility Sets (e.g. pairs) of splits are either: compatible a tree can be drawn that contains all splits in the set incompatible a tree cannot be drawn that contains all splits in the set Which of these sets of splits is incompatible? AB | CDEDE | ABC (i) BCDFGH | AEABEGH | CDF BG | ACDEFH (ii) AB | CDEAC | BDE (iii)

74. Strict Consensus Trees iiiiiiivvviviiviii AB | CDEF ******** 8 CD | ABEF ** 2 EF | ABCD ***** 5 ABC | DEF ** 2 DE | ABCF * 1 CF | ABED ** 2 ABD | ECF *** 3 ABF | CDE * 1 A B C D E F (i) A B C D E F (ii) A B D E C F (vi) A B E D C F (vii) (iii) A B C D E F (v) A B D C E F A B F E C D (iv) A B D C E F (viii) AB C D F E

75. 50%/Majority Rule Consensus Trees iiiiiiivvviviiviii AB | CDEF ******** 8 CD | ABEF ** 2 EF | ABCD ***** 5 ABC | DEF ** 2 DE | ABCF * 1 CF | ABED ** 2 ABD | ECF *** 3 ABF | CDE * 1 A B C D E F (i) A B C D E F (ii) A B D E C F (vi) A B E D C F (vii) (iii) A B C D E F (v) A B D C E F A B F E C D (iv) A B D C E F (viii) AB C D F E 5 8

76. ? C ? C Majority Rule (Extended) Consensus Tree iiiiiiivvviviiviii AB | CDEF ******** 8 CD | ABEF ** 2 EF | ABCD ***** 5 ABC | DEF ** 2 DE | ABCF * 1 CF | ABED ** 2 ABD | ECF *** 3 ABF | CDE * 1 A B C D E F (i) A B C D E F (ii) A B D E C F (vi) A B E D C F (vii) (iii) A B C D E F (v) A B D C E F A B F E C D (iv) A B D C E F (viii) AB F E D C 5 8 3

77. Splits Demonstration and Exercise Analysing splits 'by hand' Building consensus trees 'by hand' Building consensus trees using CONSENSE

78. 2 2 3 5 8 Split Networks - Visualising Split Incompatibility A B C D E F (i) A B C D E F (ii) A B D E C F (vi) A B E D C F (vii) (iii) A B C D E F (v) A B D C E F A B F E C D (iv) A B D C E F (viii) 2 iiiiiiivvviviiviii AB | CDEF ******** 8 CD | ABEF ** 2 EF | ABCD ***** 5 ABC | DEF ** 2 DE | ABCF * 1 CF | ABED ** 2 ABD | ECF *** 3 ABF | CDE * 1

79. Split Networks

80. Split Networks - Example Applications Molecular epidemiology of Campylobacter jejuni isolates from wild-bird fecal material in children's playgrounds.French NP, Midwinter A, Holland B, Collins- Emerson J, Pattison R, Colles F, Carter P.Appl Environ Microbiol. 2009 Feb;75(3):779-83.PMID: 19047378 Homologous recombination as an evolutionary force in the avian influenza A virus.He CQ, Xie ZX, Han GZ, Dong JB, Wang D, Liu JB, Ma LY, Tang XF, Liu XP, Pang YS, Li GR.Mol Biol Evol. 2009 Jan;26(1):177-87.PMID: 18931384 Interpreting non-tree-like region of the split network as evidence for reticulate evolution (here recombination in influenza virus) Identifying clans with unambiguous phylogenetic signal in a set of trees sampled from a Bayesian analysis of phylogeny

81. “Reticulate” Networks The net of life: reconstructing the microbial phylogenetic network. Kunin V, Goldovsky L, Darzentas N, Ouzounis CA. Genome Res. 2005 Jul;15(7):954-9. PMID: 15965028 Reconstructing the evolutionary history of polyploids from multilabeled trees. Huber KT, Oxelman B, Lott M, Moulton V. Mol Biol Evol. 2006 Sep;23(9):1784-91. PMID: 16798795 Genetic exchange among natural isolates of bacteria: recombination within the phoA gene of Escherichia coli.DuBose RF, Dykhuizen DE, Hartl DL.Proc Natl Acad Sci U S A. 1988 Sep;85(18):7036-40.PMID: 3045828 Describing evolutionary scenarios where some OTUs are believed to share multiple parental lineages HGT Hybridisation Recombination

82. Label the Branches! Resolving an ancient, rapid radiation in Saxifragales. Jian S, Soltis PS, Gitzendanner MA, Moore MJ, Li R, Hendry TA, Qiu YL, Dhingra A, Bell CD, Soltis DE. Syst Biol. 2008 Feb;57(1):38-57. PMID: 18275001 Branches of consensus tree labeled to indicate proportion of trees containing that branch/split

83. Label the Branches! Multilocus phylogenetics of a rapid radiation in the genus Thomomys (Rodentia: Geomyidae). Belfiore NM, Liu L, Moritz C. Syst Biol. 2008 Apr;57(2):294-310. Erratum in: Syst Biol. 2008 Jun;57(3):518. PMID: 18432550 Nodes with greater than 90% posterior probability support from analysis of seven individual loci (TBOXX) in MrBayes are marked with a box (□).

84. Label the Branches! Insights into early extracellular matrix evolution: spongin short chain collagen- related proteins are homologous to basement membrane type IV collagens and form a novel family widely distributed in invertebrates. Aouacheria A, Geourjon C, Aghajari N, Navratil V, Deléage G, Lethias C, Exposito JY. Mol Biol Evol. 2006 Dec;23(12):2288-302. PMID: 16945979