EVOLUTIONARY BIOLOGY EBIO 3080
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This 7 page Study Guide was uploaded by Madisen Robel on Thursday October 29, 2015. The Study Guide belongs to EBIO 3080 at University of Colorado at Boulder taught by Richard Noyes in Fall. Since its upload, it has received 21 views. For similar materials see /class/231851/ebio-3080-university-of-colorado-at-boulder in Ecology, Evolution, and Marine Biology at University of Colorado at Boulder.
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Date Created: 10/29/15
EBIO 3080 Evolutionary Biology WRITING ASSIGNMENT 3 Study Guide Included below are the main points from both of the primary research articles I ve included all information that may be pertinent for the essay but please don t include all of the information covered here Your essays would be way too long if you did Only use that which is essential to your essay Marshall Graves JA 2002 The rise and fall of SRY Trends in Genetics 18 259 264 Class Ivs Class 11 genes Class I genes have homologues on the X chromosome suggesting that they were inherited from the ancestral autosomes sequence expression pattern and function have not diverged single copy Class 11 genes are unique to the Y chromosome two possible modes of inheritance see below sequence expression pattern and lnction are testisspecific multicopy 1 Class 11 genes are highly modified genes inherited from the ancestral autosomes but have diverged due to selection such that homology with X genes cannot be determined 2 Class 11 genes are acquired from other autosomes through transposition events following the divergence of X and Y There is evidence to support both modes of inheritance Differences among mammals in the classification of the same gene e g ZFY as Class I or 11 suggest that rather than representing discrete classes there is a continuum of divergence at least for those genes that share common ancestry from the autosomes In other words there is a spectrum of degradation and divergence among Ygenes from conservation to unique gene sequence and function Male specific function probably result of changes in tissue specific control many Y specific genes are transcription factors ie regulate expression of other genes SRY as human testisdetermining gene Related to SOX family of genes 20 genes SOX 3 is phylogenetically most closely related gene involved in brain and central nervous system development SRY sequence is not very similar to other genes in the family suggesting selection for divergence associated its role in sex determination Divergence times absent in birds and reptiles lt 310 myr old present in marsupials and eutherians placental mammals gt130 myr old absent in monotremes diverged 170 mya 2 hypotheses explain this pattern H1 present in common ancestor of all mammals and lost in monotremes SRY arose 170310 mya H2 evolved in common ancestor of therians marsupialseutherians SRY arose 130170 mya possibly 40 myr after origin on chromosome in common ancestor of all mammals Potential candidate genes that triggered Ydetermination and subsequent degradation l DAXl on human Xp pseudoautsomal region on short arm duplication causes sex reversal ie female XY could have determined femaleness in protomammal because it is absent in marsupials and occurs in Xtransposed region probably not on original protoY probably not the gene that triggered Ydetermination 2 ATRX found in Xdegenerate region required for testes formation Y homologue in marsupials none in humans and mice eutherians present in ancestral mammals lost in eutherians no evidence of Xtransposition in marsupials to indicate independent acquisition in marsupial lineage 3 SOX3 SRY descended from this gene original function in male determination through control of SOX9 SOX9 involved in testes determination SOX3 in uences expression pattern of SOX9 evolution of null SOX9 allele set up 21 dosage difference two doses inhibit expression of SOX9 no testes form female one dose does not inhibit expression of SOX9 as well testes form male alleles diverge null SOX9 allele truncated to form SRY SRY inhibits expression of SOX3 because truncated allele incipient SRY is a stronger sexdetermining factor selectively favored SOX3 and SRY have overlapping expression patterns SOX3 strongly expressed in central nervous system weakly expressed in genital ridge SRY strongly expressed in genital ridge weakly expressed in central nervous system current evidence favors the SOX3 progenitor hypothesis SRY evolves very rapidly large differences in expression structure sequence divergence translates into differences in primary secondary and tertiary structure of protein product and function some copies of gene in mice produce untranslatable circular RNA 7 nonworking mutant COPY typical of genes on the Y chromosome in the nonrecombining region 7 accumulate mutations rapidly often deleterious Loss of SRY and Y chromosome Two species of mole voles have lost Y chromosome and SRY gene sexdetermination controlled by another gene was probably involved in sex determining pathway before being coopted as sexdetermining gene Y probably lost in incremental stages further research into sexdetermination in mole voles may provide insight into how sexdetermination genes evolve Rate ofloss on genes 36 lost per myr assumes clocklike rate of loss estimate Y chromosome will lose all genes and disappear in 10 myr Consequences of lost Y fertility genes will be lost first function replaced by autosomal genes SRY lost replaced by another gene in sexdetermining pathway located on autsomes new sexdetermining loci on autosomes will reset sex chromosome determination 7 new sex chromosome will evolve males will be maintained buy via different genetic pathways if different human populations evolve different sexdetermining genes may result in divergence of hominids into two separate species Skaletsky H 2003 The male specific region of the human Y chromosome is a mosaic of descrete sequence classes Nature 423 825 837 Renamed the nonrecombining portion of the Y chromosome NRY the malespecific region MSY due to evidence of YY recombination gene conversion J both the 39 in and hetei 39 quot regions of the Y but only report results from the euchromatic region Don t worry about the details of how they sequenced it Gene identification 156 transcription units 78 proteincoding units genes 60 belong to 9 MSYspecific gene families members ofthe same family share 98 sequence identity 18 are present in only one copy no other copies from the same gene family l8927 distinct proteinsprotein families 12 expressed throughout body 11 expressed predominantly in the testes Three major classes of sequences 1 Xtransposed 99 sequence identity with a portion of the X chromosome present on MSY because of a transposition event that occurred 34 mya following humanchimp divergence ie unique to humans region is split by an inversion event following transposition do not recombine with X chromosome despite identity because located in the MSY region only 2 genes identified analogous to Class I genes 2 Xdegenerate 27 homologues of Xlinked genes 6096 sequence identity with Xlinked homologues l3 pseudogenes not transcribed 14 transcribed functional singlecopy genes that transcribe protein isoforms similar but not identical between X and Y chromosomes account for 16 of the 27 unique proteinsprotein families encoded on the MSY all 12 genes expressed throughout body are in Xdegenerate regions SRY is the only malespecifrc gene found in Xdegenerate region analogous to Class 11 genes 3 Amplicons characterized by high levels of intrachromsomal sequence identity 60 share more than 999 sequence identity with other regions of MSY located in 7 segments on both the long and short arms of the Y highest density of genes of the 3 classes 9 unique protein families represented by multiple copies of the genes 235 number of copies probably varies among individuals 60 coding transcription units 75 noncoding transcription units no evidence that they code for proteins expression mostly or entirely restricted to testes 8 palindromic sequences sequence inverted and repeated eg ATGCCGTA 9997 nucleotide sequence identity between arms excluding insertions and deletions account for 25 of MSY euchromatin 6 of 8 palindromes contain proteincoding genes 7 genes on opposite arms are identical or nearly so 8 of the 9 multicopy gene families are represented in the palindromes 7 families of noncoding transcription units the authors provide no explanation for what these units may do so don Evolution of MSY compared age and position on X chromosome of 27 pairs of Xdegenerate genes 2 X transposed genes 2 ampliconic gene families oldest Xdegenerate pairs and 2 ampliconic pairs found on distal end of Y long arm decrease in age moving toward the centromere youngest found on distal end of short arm supports the hypothesis that there were 4 stages of Y chromosome evolution in which inversions preceded suppression of recombination between the X and Y all Xdegenerate genes and at least 2 of ampliconic gene families are products of same molecular evolutionary process regionbyregion suppression of recombination followed by divergence between the X and Y copies young age of Xtransposed regions in older Xdegenerate region supports hypothesis of recent transposition event the authors suggest that the boundaries between the 4 stages are blurred but don t worry about the details of this section Evolution of Xdegenerate and ampliconic sequences Similarities interspersed on the Y chromosome respectively represent 38 and 45 of MSY s euchromatic sequences comparable diversity of malespecific ages 10100 millions of years evolved in parallel under similar circumstances in which they were inherited only in the male germline and suppressed recombination with the X homologue Differences ampliconic sequences contain palindromes higher density of transcription units lower density of intersperse repeats than Xdegenerate sequences most Xdegenerate genes expressed throughout body probably housekeeping genes involved in functions essential to cell viability most ampliconic genes expressed predominantly or exclusively in testes probably involved in spermatogenesis Decay of Xdegenerate sequences support the prevailing model of sex chromosome evolution X and Y chromosome evolved from autosomal pair most ancestral genes on X chromosome maintained because of recombination most ancestral genes on Y chromosome lost in absence of recombination accumulation of deleterious mutations leads to loss of function evidence of decayed intronbearing pseudogenes in Xdegenerate sequences lends further support to this model homologues of 13 Xlinked genes other genes were deleted leaving no evidence in the MSY sequence Origin and maintenance of ampliconic sequences model of X decay cannot explain evolution of MSY s ampliconic sequences testes specific expression palindromes similar to autosomal and Xchromosome sequences 3 possible origins of ampliconic sequences 1 ancestral genes derived from autosomes that gave rise to X and Y eg VCY and RBMY 2 transposition from autosome and subsequent amplification e g DAZ genes homologous with DAZL found on human chromosome 3 3 retrotransposition from a processed mRNA derived from autosomal genes and subsequent amplification eg CDY genes revised date of retrotransposition event to have occurred prior to divergence of marsupials and eutherians previously thought to have occurred along primate lineage despite diverse origins ampliconic sequences very similar occur as multiple nearly identical copies uniform patterns of tissue expression in spermatogenesis cells of testes selection favored evolution of malespecific domain MSY once isolated from recombination with X chromosome selection could operate on MSY exclusively to enhance malespecific germline development selection also favored amplification of ampliconic genes might have enhanced sperm production through high levels of expression may have allowed for a different kind of homologous recombination gene conversion to maintain gene function in the absence of crossing over Gene conversion nonreciprocal transfer of sequence information from one DNA strand to another for a more detailed discussion of gene conversion see the websites below httpwwwwebboolltscomMoBioFreeCh8D4htm httpusersrcncomjkimballmaultranetBiologyPagesDDNArepairhtml frequency of gene conversion on Y same as crossing over on homologous chromosomes occurs in 30 of MSY euchromatin evidence not presented in the paper that gene conversion has occurred in both human and chimp lineages and continues to occur in humans although not mentioned in the paper it probably continues to occur in chimps as well 30 of MSY euchromatin has intrachromosal identities of 999100 includes the 8 palindromes and the 1R2 and 1R3 inverted repeats almost all of the sequences with 2999 identity exist as inverted pairs conclude almost all of the 2999 identity sequences undergo gene conversion routinely confers levels of identity similar to that of alleles on homologous chromosomes types of recombination on the Y productive and common 1 crossing over with X in the pseudoautosomal region 2 YY gene conversion in the 2999 identity regions maintain functional genes purge deleterious mutations selectively favored deleterious and rare 3 YY or XY recombination events that perturb sex differentiation and fertility reduce reproductive fitness of affected individuals not selectively favored relative rates of recombination one XY recombination event per generation multiple YY gene conversion events per generation most homologous recombination events occur in MSY thus the renaming of the NRY noncombining region of the Y as the MSY male specific region of the Y testes gene families 8 of the 9 testes gene families have members with palindromic or inverted repeats typical of the 2999 identity sequences TSPY gene family is the exception 7 members found in a tandem array repeated sequences 2 types of genes in gene families 1 intact functional copies 2 pseudogenes with disrupted splice sites or reading frames pseudogenes found both inside and outside the 2999 identity sequences all 25 functional copies are found inside the 2999 identity sequences biological significance of correlation between functional copies and 2999 identity sequences that undergo gene conversion quot quot of J 39 to the spa 39 cells germ cells ofthe testes may be regulated by formation of cruciforms or unusual chromatin configurations caused by the nearly identical sequence pairs 2 gene conversion between MSY gene pairs as a mechanism for maintenance of gene function in the absence of crossing over The Implications for future studies section is pretty easy to read so I won t cover it here
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