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• The ﬁeld of conserva)on paleobiology studies geological and biological history to understand ecology and evolu;on of current species and their responses to changing environments A recently published review of the ﬁeld analyzes recent paleobiological perspec;ves on current conserva;on problems of par;cular general interest are eﬀorts to document recent and ancient ex;nc;ons to understand how ex;nc;ons took place and to assess current ex;nc;on risks understand how and where species survived periods of clima;c change obtain ancient DNA ‐ for example showing that the arc;c fox (Alopex lagopus) became ex;nct in Europe likely because it could not migrate in response to past climate changes (it is s;ll present in northeastern Siberia) nega;ve eﬀects of ancient human coloniza;ons on biodiversity fossil history of insect damage to plant leaves ‐ a global warming episode 55.8 million years ago was associated with increased insect herbivory on plants hLp://www.nsf.gov/news/news_summ.jsp?
k reviewing some terms • homozygote – an individual with two iden;cal alleles at a locus (adjec;ve: homozygous) – e.g. AA (also wriLen as A/A) • heterozygote – an individual with two diﬀerent alleles at a locus (adjec;ve: heterozygous) – e.g. Aa (also wriLen as A/a) – in the 9 bp sequence below (one DNA strand shown for each allele) this individual is heterozygous at 3 of the 9 posi;ons (underlined) • the average two humans diﬀer at 1 in every thousand base pairs – =>base pair level heterozygosity is common at 1 in every thousand posi;ons in humans • adjec;ve: hemizygous – describes genotypes on the X and Y chromosomes in males Genes and genomes • What is a gene? – A transcrip;on unit • Encodes an RNA • Most encode mRNAs that are translated by ribosomes into proteins • Others encode func;onal RNAs – Ribosomal RNA – RNA enzymes – Small regulatory RNAs (e.g. micro‐RNAs) Gene anatomy Transcrip;on start 5’ EYE WING LEG exon BRAIN intron 3’ exon transcrip;on pre‐mature messenger RNA (mRNA) splicing ATG Transla;on start REGULATORY REGIONS Muta;ons in ENHANCERS can aﬀect speciﬁc ;ssues and not others. CODING REGION Muta;ons in coding region usually aﬀect all ;ssues in which protein is expressed. mature mRNA Muta;on in a coding region “normal” gene (…ACTGGT…) messenger RNA mRNA (…ACUGGU…) protein (…Thr Gly…) func;on/phenotype “mutant” gene (…GCTGGT…) messenger RNA mRNA (…GCUGGU…) altered protein (…Ala Gly…) “NON‐synonymous subs;tu;on” altered func;on/phenotype Some muta;ons alter the amino acid sequence, others do not The gene;c code is degenerate; mul;ple codon sequences can encode the same amino acid. “synonymous subs;tu;on” [aka muta;on at a “silent site”] “normal” gene (…ACTGGT…) messenger RNA mRNA (…ACUGGU…) protein (…Thr Gly…) func;on/phenotype “mutant” gene (…ACCGGT…) messenger RNA mRNA (…ACCGGU…) same protein (…Thr Gly…) same func;on/phenotype What is a genome? • The set of all genes plus all noncoding DNA • Noncoding DNA – Introns (in eukaryotes) – Sequences between genes – Repe;;ve DNA • Some noncoding DNA may be “junk” but many func;ons of noncoding DNA are becoming known – e.g. Enhancers (see above) func;on in regula;on of gene expression Return to homology • Traits that two species share due to inheritance from a common ancestor • Homology of DNA and protein sequences is determined by aligning the sequences of diﬀerent species Various events can contribute to divergence of two species from their common ancestor Subs;tu;ons do not all occur at equal frequencies ‐various mathema;cal models are used to reconstruct evolu;onary history of DNA sequences A protein alignment (cytochrome C) Molecular evolu)on in nature is inferred from sequences • But we can witness it in the lab • Aoer the experiment, bacterial strains can be completely sequenced • Morphologies evolved mul;ple ;mes • Diﬀerent nucleo;de subs;tu;ons led to same morphologies • These muta;ons also occurred in the shaken cultures but did not persist Synonymous vs. nonsynonymous subs;tu;ons • Syn >> Nonsyn • A pseudogene is a nonfunc;onal copy of a func;onal gene – Neutral: Neither advantageous nor disadvantageous varia;on at the protein and DNA sequence level • in the 1960s‐1980s it became apparent that molecular varia;on within popula;ons and species was very, very common • The idea that natural selec;on might have liLle or no eﬀect on this varia;on came from the above observa;on – this varia;on could mostly be “adap;vely neutral” • many amino acid subs;tu;ons might be func;onally equivalent – don’t change the charge or shape of a protein domain • very many DNA nucleo;de subs;tu;ons might be selec;vely neutral – noncoding regions – synonymous subs;tu;ons in coding regions ...
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- Spring '08
- Ecology, ons, Messenger RNA mRNA