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GENE CLADOGRAMS: HIGHER APES

DOES MOLECULAR EVIDENCE SUGGEST THAT ORGANISMS ARE RELATED?

     What organisms are related to each other?  Are humans related to chimpanzees?  Are amphibians more related to sarcopterygian fish than actinopterygian fish?  Are birds closely related to reptiles?  The word “clade” is used to describe a group of organisms which are more closely related to each other than to any organism outside the clade.  Are Apes a clade?  Are primates a clade?  Are Mammals a clade? 

     Biologists hope to identify groups which are real, not arbitrary lumpings of unrelated organisms.  Genetics can help.  Organisms which are closely related are expected to be more similar genetically.  This relationship can be studied in the genes they possess, their chromosome number, and the chromosomal locations of their genes.  Now that proteins and DNA can be sequenced, more powerful comparisons are possible with the amino acid sequences of proteins and the nucleotide sequences of genes, noncoding DNA, introns, and mitochondrial DNA.   Some DNA regions are more suited for this type of comparison than others.  If natural selection pressures differ in one lineage to the next, genetic changes may accumulate at different rates. 

      An incredible number of DNA and protein sequences have been determined.  What relationships do they depict among the organisms on earth?  There are a number of clades which have been strongly supported by the genetic evidence, grouping organisms which are more closely related to each other than to any others.   The more genetic evidence is studied, the greater our appreciation for the common ancestry of life on earth.

 GENETIC TREES

     There is no one molecule upon which a tree of life can be based.  Comparing molecular sequences to establish phylogeny requires that the various groups being compared have all experienced equivalent selection with regards to the molecule being sequenced.  The best trees will undoubtedly come from the comparisons of many sequences to limit the distortions of selection which was experienced by only one of the groups of organisms being compared.  That being said, the rRNA genes have proved extremely useful in clarifying relationships between organisms.  Not all of the rRNA genes have evolved at the same rate: the small subunit rRNA is one of the slowest evolving genes known (virtually no changes are known in placental mammals) and it is very useful in analyze the oldest branching points in the history of life.  The sequences of the large subunit are more useful for the clarifying the relationships of organisms which arose in the Paleozoic and Mesozoic.  Mitochondrial rRNA genes have accumulated changes at a faster rate and are best used for phylogenetic branching which occurred in the Cenozoic.  5 S and 5.8 S sequences are less useful because of their small size; most of the groups which have evolved since the Paleozoic have very similar 5.8 S sequences, for example.

     Such trees support an evolutionary unfolding of life.  Since ribosomes have equivalent functions in all organisms, no patterns are expected to be evident in their sequences.  If patterns exist, they could be the result of adaptations to temperature, chemicals found in the environment 9e.g. antimicrobials), habitat, etc.  The nested hierarchy of relationship suggested by the rRNA sequences supports the same general relationships as anatomical, embryological, and paleontological data, as well as the data obtained from sequencing unrelated genes.  Such sequences identify both similarities and dissimilarities—a new phylum of Archebacteria was identified on the basis of its rRNA sequences (Nanoarchaeum, the smallest known archebacterium with a .5 megabase genome and a diameter of .4 microns).

     An overwhelming amount of comparative genetic evidence suggests that modern living organisms are descended from common ancestors and can be divided into a hierarchy of related groups, reflecting the gradual branching of separate lineages over time.  The clades supported by the genetic evidence are the same clades supported by anatomical evidence, embryological evidence, and the analysis of the fossil record.

1. DO THE VARIOUS GROUPS OF HUMANS FORM A CLADE RELATED BY COMMON DESCENT?

     When the sequences of genes taken from different human populations are studied, the sequence comparisons depict a pattern.  All individuals do not have the same gene sequences nor is each sequence so distinct that they suggest separate origins.  The pattern is not correlated with variable aspects of the individuals’ environment such as temperature, rainfall, food sources, etc.  The pattern depicts a branching family tree of gene sequences which have descended from common ancestral sequences.  This pattern suggests that all humans are related through descent from common ancestors. Examples of molecules whose study has supported a common ancestry include:

--b hemoglobin (Long, 1990)

--mitochondrial cytochrome oxidase II (Ruvulo, 1994)

--noncoding polymorphisms (Wainscoat, 1986)

chart

--mitochondrial DNA; Cann, 1987

chart

--nuclear DNA polymorphisms; Wainscoat, 1986.

chart

 


--b golbin haplotypes; Long, 1990.

 

2. DO THE VARIOUS SPECIES OF HIGHER APES FORM A CLADE RELATED BY COMMON DESCENT?

When the sequences of genes taken from different ape species are studied, the sequence comparisons depict a pattern.  All individuals do not have the same gene sequences nor is each sequence so distinct that they suggest separate origins.  The pattern is not correlated with variable aspects of the species’ environment such as temperature, rainfall, food sources, etc.  The pattern depicts a branching family tree of gene sequences which have descended from common ancestral sequences.  This pattern suggests that all higher apes are related through descent from common ancestors.  It is interesting that this pattern is even observed using noncoding DNA sequences which do not contribute to an individual’s phenotype.

     Because natural selection can act on the sequences of some species differently than the sequences of other species, these trees should give similar groupings but are not expected to always give the same groupings.  While every sequence comparison that I am aware of groups humans, chimps, and gorillas as a clade (a group whose members are more related to each other than they are to any species outside the clade), there are a few studies in this chapter and the following one which disagree on which of these three members are most closely related.  While most studies group humans and chimps together with gorillas as an outgroup, a few depict gorillas and chimps together with humans as an outgroup.  Once again, unless natural selection has acted on gene sequences in exactly the same way throughout time, different sequence comparisons can produce some differences in branching patterns, especially if short expanses of time separated the branching points.

 

HUMAN CHIMP GORILLA ORANGUTAN
chart

----yhglobin upstream and downstream flanking regions; Miyamoto, 1987

--noncoding DNA sequence data;Williams, Mol. Biol. Evol. 6: 325-330, 1989;

--28S rRNA gene and a transcribed spacer sequence data; Gonzalez, Mol. Biol. Evol. 7: 203-219; 1990.

--chromosome structure; Yunis, Science 215:1525-28

2A: Examples of molecules whose study has supported that humans and chimps form a clade include:

 --c-myc (Atchley, 1995)

--DNA hybridization (Caccone, 1989)

--red opsin (Deeb, 1994)

--MHC II genes (Edwards, 1997)

--DRB(Edwards, 1997)

--DNA hybridization (Felsenstein, 1987)

--Cu/Zn Superoxide dismutase (Fukuhara, 2002)

--a galactosyltransferase (Galili, 1991)

--sequences of 28S rRNA and ITS1 (Gonzalez, 1990)

--yh globin (Goodman, 1984)

--a globin (Goodman, 1984)

--h globin 3’ untranslated and flanking (Goodman, )

--h globin IVS 2 (Goodman, )

--h globin 5’ flanking through exon 2 (Goodman, )

--h globin IVS 1 (Goodman, )

--φη region (Goodman, 1994)

--γ globin region (Goodman, 1994)

--amino acid and nucleotide sequences (Goodman, 1985)

--serological analysis (Goodman, 1962)

--DNA sequences (Hoyer, )

--anterior cingulate cortex microarray probe (Uddin, 2004)

--Alu elements (Salem, 2003)

--albumin sequence (Isaac, )

--HERV-K18 (Johnson, 1999)

--RTVL-Ha (Johnson, 1999)

IFN alpha7 (Krause, 2005).

IFN alpha21 (Krause, 2005).

IFN alpha14 (Krause, 2005).

IFN alpha2 (Krause, 2005).

IFN alpha8 (Krause, 2005).

IL28 (Krause, 2005)

IFN-epsilon (Krause, 2005)

IFN –v (Krause, 2005).

IFN beta (Krause, 2005).

IFN Kappa (Krause, 2005).

IFN amn (Krause, 2005).

human chimp (or before; somewhere between human chimp lineage and basal primates) a novel gene CE1 is inserted into a homeobox gene cluster (Wu, 2006)

167 genes (Kumar, 2005)

Cytochrome c (De Grassi, 2006)

MRG receptors (Yang, 2005)

--yh globin (Koop, 1986)

--ECP (Larson, 1996)

--intergenic DNA between y and d globin (Maeda, 1988)

--lysozyme amino acid sequences (Messier, 1997)

--flanking regions of yh globin (Miyamoto, 1987)

--Albumin intron (Page, 2001)

--Noncoding DNA in γ globin region (Page, 2001)

--Ig light chain λ and κ.  (Pilstrom, 2002)

--mitochondrial cytochrome oxidase II (Ruvulo, 1994)

--albumin cross reactions with sera (Sarich, 1967)

--DNA-DNA hybridization (Sibley, 1990)

--IgE (Vernersson, 2004).

--noncoding DNA sequences (Williams, 1989)

--chorionic somatomammatropin A (Ye, 2005)

--growth hormone (Ye, 2005)

--growth hormone variant (Ye, 2005)

--primate growth hormone (Ye, 2005)

--chromosome structure (Yunis, )

--eosinophil cationic protein (Zhang, 1998a)

--eosinophil-derived neurotoxin (Zhang, 1998a)

--KGF (Zimonjic, 1997)

TGIFLX (Wang, 2004)

 

 

2B: Examples of molecules whose study has supported that African apes (humans, chimps, and gorillas) form a clade include:

--immunological distance, plasma proteins, and DNA hybridization (Cronin, 1982)

--red opsin (Deeb, 1994)

--β2 microglobulin (Dijkstra, 2003)

--sequences of 28S rRNA and ITS1 (Gonzalez, 1990)

--yh globin (Goodman, 1984)

--g globin (Goodman, 1984)

--e globin sequences (Goodman, 1998)

--φη region (Goodman, 1994)

--γ globin region (Goodman, 1994)

--amino acid and nucleotide sequences (Goodman, 1985)

--mitochondrial DNA (Horai, 1992)

IFN γ(Krause, 2005).

MRG receptors (Yang, 2005)

--yh globin (Koop, 1986)

--BC200 mutations  (Kuryshev, 2001)

--ECP (Larson, 1996)

--EDN (Larson, 1996)

 --intergenic DNA between y and d globin (Maeda, 1988)

 --lysozyme amino acid sequences (Messier, 1997)

--flanking regions of yh globin (Miyamoto, 1987)

--SRY (Nagai, 2001)

--MHC B (Nei, 1997)

--MHC A (Nei, 1997)

--prolactin inducible protein (Osawa, 2004)

--seminal vesicle autoantigen (including primate pseudogene) (Osawa, 2004)

--Albumin intron (Page, 2001)

--Noncoding DNA in γ globin region (Page, 2001)

--mitochondrial cytochrome oxidase II (Ruvulo, 1994)

--chromosome banding (Stanyon, 1988)

--IgA (Vernersson, 2004).

--noncoding DNA sequences (Williams, 1989)

--chromosome structure (Yunis, )

--mitochondrial DNA (Ferris, )

--mitochondrial DNA (Brown, )

--DNA-DNA hybridization (Sibley, )

--transferrin sequence (Isaac, )

--albumin sequence (Isaac, )

--DNA sequences (Hoyer, )

--rRNA (Hixson, )

--SRY (Magararit, 1998)

--DNA hybridization (Marks, 1988)

--DNA hybridization (Felsenstein, 1987)

--DNA hybridization (Templeton, 1985)

--DNA hybridization (Sibley, 1990)

--DNA hybridization (Caccone, 1989)

--3 muts AF apes (Linman, 2003)

--h globin 3’ untranslated and flanking (Goodman, )

--h globin IVS 2 (Goodman, )

--h globin 5’ flanking through exon 2 (Goodman, )

--h globin IVS 1 (Goodman, )

--intergenic DNA in b globin cluster (Maeda, )

--h globin (Koop, 1986)

--a galactosyltransferase (Galili, 1991)

--MHC II genes (Edwards, 1997)

--serological analysis (Goodman, )

--serological analysis (Goodman, 1962)

--HERV-K HmL6.17 (Johnson, 1999)

--HERV-K18 (Johnson, 1999)

--RTL-Ia (Johnson, 1999)

--RTVL-Ha (Johnson, 1999)

--lysozyme (Messier, 1997)

--anterior cingulate cortex microarray probe (Uddin, 2004)

--Alu elements (Salem, 2003)

--IgA  (Wilson, 1997)

--eosinophil cationic protein (Zhang, 1998a)

--eosinophil-derived neurotoxin (Zhang, 1998a)

TGIFLX (Wang, 2004)

 

2C: Examples of molecules whose study has supported that higher apes (humans, chimps, gorillas, and orangutans) form a clade include:

--ZNF91 gene family (Bellefroid, 1995)

--Higher ape: SRY (Bowles, 2000)

--red opsin (Deeb, 1994)

--β2 microglobulin (Dijkstra, 2003)

--DRB(Edwards, 1997)

--sequences of 28S rRNA and ITS1 (Gonzalez, 1990)

--e globin sequences (Goodman, 1998)

--φη region (Goodman, 1994)

--γ globin region (Goodman, 1994)

--yh globin (Koop, 1986)

--BC200 mutations  (Kuryshev, 2001)

--ECP (Larson, 1996)

MRG receptors (Yang, 2005)

--intergenic DNA between y and d globin (Maeda, 1988)

--lysozyme amino acid sequences (Messier, 1997)

--flanking regions of yh globin (Miyamoto, 1987)

--Albumin intron (Page, 2001)

--Noncoding DNA in γ globin region (Page, 2001)

--e globin sequences (Porter, 1997)

--chromosome structure (Yunis, )

--noncoding DNA sequences (Williams, 1989)

--chromosome banding (Stanyon, 1988)

--mitochondrial cytochrome oxidase II (Ruvulo, 1994)

--immunological distance, plasma proteins, and DNA hybridization (Cronin, 1982)

--mitochondrial DNA (Horai, 1992)

--mitochondrial DNA (Ferris, )

--mitochondrial DNA (Brown, )

--DNA-DNA hybridization (Sibley, )

--transferrin sequence (Isaac, )

--albumin sequence (Isaac, )

--DNA sequences (Hoyer, )

--rRNA (Hixson, )

--DNA hybridization (Marks, 1988)

--DNA hybridization (Felsenstein, 1987)

--DNA hybridization (Templeton, 1985)

--DNA hybridization (Sibley, 1990)

--DNA hybridization (Caccone, 1989)

--h globin 3’ untranslated and flanking (Goodman, )

--h globin IVS 2 (Goodman, )

--h globin 5’ flanking through exon 2 (Goodman, )

--h globin IVS 1 (Goodman, )

--HERV-K HmL6.17 (Johnson, 1999)

--HERV-K(C4) (Johnson, 1999)

--RTL-Ia (Johnson, 1999)

--intergenic DNA in b globin cluster (Maeda, )

--h globin (Koop, 1986)

--a galactosyltransferase (Galili, 1991)--serological analysis (Goodman, )

--serological analysis (Goodman, 1962)

--lysozyme (Messier, 1997)

--MHC B (Nei, 1997)

--MHC A (Nei, 1997)

--Alu elements (Salem, 2003)

--Higher IgE (Vernersson, 2004).

--KGF (Zimonjic, 1997)

--eosinophil cationic protein (Zhang, 1998a)

--eosinophil-derived neurotoxin (Zhang, 1998a)

TGIFLX (Wang, 2004)