Molecular bio Lecture Week 11

Canary archipelago

The difficulty with the Canarian islands is the fact that the age decreases with the distance from Africa. This results in the older islands have a mix of old and young species.

Canary archipelago

Canary archipelago

However, the Canaries also provide examples where phylogeographical analysis has shown a pa>ern of colonisa?on not predictable by distance to the nearest con?nent and in opposi?on to the progression rule.

Canary archipelago

Canary archipelago

Fringella coelebs

Canary archipelago

Canary archipelago

Fringella coelebs

maderensis canariensis

palmae

Canary archipelago

The finches colonised the Canaries via the Azores and Madeira

Azores

Mainland

Madeira

Canaries

Back-‐dispersal refers to lineages that generally may follow the progression-‐rule, but in which one or more cases of dispersal from a younger to an older island occur, with subsequent specia?on occurring from the back-‐dispersed colonist.

Canary archipelago

Pimelia beetle

Madagascar

How many colonisa?on events did occur on Madagascar?

The mammals are represented by five orders only, nearly all of them endemic: • carnivores (the Malagasy civets, mongooses and fossa species)

Madagascar

Galidia elegans

• rodents

Malagasy giant rat

Madagascar

• primates

Madagascar

Lemurs

• insec?vores

Madagascar

Tenrecs

Lowland Streaked Tenrec (Hemicentetes semispinosus).

Madagascar

Madagascar sucker-‐footed bat (Myzopoda aurita)

• Bats

Malagasy mongooses

Fossa

Malagasy civet

Madagascar

Madagascar

The phylogene?c tree, constructed using various mt genes, and 2 nuclear genes, shows that the Malagasy clade is monophyle3c.

Mungo9c9s decemlineata: Two subspecies are described: M. d. decemlineata, in the northern range of the species, and M. d. lineata, formerly known only from the holotype at the southern limit of the range, but since recorded in the Manombo River valley (Hawkins et al. 2000, Goodman et al. 2005).

Madagascar

Madagascar

Did the mongooses arrive together with the lemurs?

NO

Madagascar

The phylogene?c evidence indicates that there was only a single colonisa?on event for the carnivores, and that the arrival of the carnivores on Madagascar about 18-‐24 mya came much later than that of the lemurs, who got there about 62-‐66 mya. This suggests that: •  Oceanic dispersal over such distances is rare The order, rather intriguingly matches the order of events in the breaking of Gondwanaland, but not the ?mings.

The Extraordinary Evolu3onary History of the Re3culoendotheliosis Viruses Anna Maria Niewiadomska, Robert J. Gifford

PLoS Biol 11(8): e1001642. doi:10.1371/journal.pbio.1001642

Retroviruses (family Retroviridae) inserted into germline cells and subsequently inherited as host alleles are called endogenous retroviruses (ERVs)(ver?cal transmission).

Thus, it is possible to inves?gate the evolu?on of the interac?on between host and virus by means of phylogene?c analyses

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The three major proteins encoded within the retroviral genome: Gag, Pol, and Env.

The re3culoendotheliosis viruses (REVs) comprise several closely related amphotropic (i.e. non-‐specialist) retroviruses isolated from birds

Previous Work: REV groups robustly within the Gammaretrovirus genus and is hypothesised to have originated in mammals

Amniotes

Horizontal transfer between species

Authors speculate it is a recent infec?on of birds

Spleen necrosis virus (SNV) and DIAV (Duck infectious anemia virus). Both these viruses were isolated from ducks that were experimentally infected with Plasmodium lophurae (SNV in 1959 and DIAV in 1972).

h>p://saturn.adarc.org/paleo/site/html/fossil-‐record/DIAV.html

Anas platyrhynchos

1999 paper concludes that Echidna’s were the unlikely source for the REV lineage

Figure 1. Evolu3onary rela3onships among the RT genes of exogenous Gammaretroviruses and related ERVs.

Shaded boxes indicate taxa that are known to occur as exogenous retroviruses.

The phylogeny shown was constructed using NJ and a multiple sequence alignment spanning 140 amino acid residues in the reverse transcriptase protein (RT)

All mammalian ERVs exhibiting a high degree of sequence similarity to REV in the gag-pol domain exhibited no such similarity in env, and vice versa. This can be assumed to reflect the recombinant genome structure of REV

Echidna-ERV, Galidia-ERV, and Mungotictis-ERV grouped robustly with REV isolates in phylogenies constructed using both the pol and env coding domains establishing that they share a common, recombinant ancestor with these viruses.

Madagascar

Madagascar

Mongooses did not arrive together with the lemurs

Germline invasion occurred between 18 and 8 Ma

Origin of the Avian REVs

ML phylogenies constructed using (a) an alignment spanning residues 183–481 of the Pol polyprotein (DIAV coordinates) and containing REV and mammalian gammaretroviruses sequences

In conclusion, historical, phylogene?c, and paleovirological evidence supports a scenario wherein REVs originated as mammalian retroviruses that were iatrogenically introduced into avian hosts, and subsequently integrated into the FWPV and GHV-‐2 genomes, genera?ng recombinant DNA viruses that now circulate in wild birds and poultry

Thus, rather than mere ver3cal transmission, there is human-‐assisted horizontal transmission. Zoos and domes3cated animals

What about the echidna? It is from the Philadelphia Zoo.

Species iden3fica3on and discovery

Scott Baker (http://mmi.oregonstate.edu/c-scott-baker)

Using DNA species identification to trace illegal whale meat

From which whale species is the meat really and is the meat from whales shot for scientific research in the places Japanese officials say?


Vireo gilvus Tringa solitaria Sturnella magna

Cistothorus palustris

Sturnella magna

Vireo gilvus

Tringa solitaria


Will depend on the DNA barcoding gap

recently diverged species might not be dis?nguishable on the basis of their COI sequences

Mitochondrial DNA

DNA barcoding GAP


MOTU is an acronym coined in the late 1990's by Blaxter et al to describe the clusters of specimens based on sequence iden?ty. (h>p://www.nematodes.org/research/barcoding/motu_defined.shtml)

Debate whether that is the case -‐ not always – different taxa may either show few or large amounts of varia?on One needs to decide what level of molecular difference defines a biologically relevant taxon

•  species delimita?on based upon varia?on within the cytochrome c oxidase subunit I gene

•  assumes gene?c varia?on between species > within species

•  clustering of sequences into groups (MOTUs) that differ by a pre-‐defined number of base pairs

DNA barcoding GAP


Correct species iden?fica?on is of course important in a variety of research contexts (e.g. ecological – see talk Dr Gibbs, CEH) If North American birds reveal cryp?c species and specia?on events, what about these:

As few as 1% of global parasitoid species have so far been described


Ideally, DNA barcoding should be used alongside tradi?onal taxonomic tools and using other genes than COI, so that problem cases can be iden?fied and errors detected. It is a great first step though to detect errors in species iden?fica?on and detect cryp?c species.

Oceanic metagenomics


Ver?cal gene transfer


horizontal gene transfer



En?re biochemical pathways may be passed from one bacterial species to another in a single DNA transfer


Classically, microbiologists studied prokaryotes by growing them in culture, isola?ng pure strains to study their morphology, biochemistry, metabolism and in general how they adapt to environmental condi?ons. Problem: Majority (99%) of bacterial species/strains are difficult to grow in culture, and they quickly “adapt” to lab condi?ons


From natural samples containing complex mixtures, it is possible to amplify and determine sequences directly without culturing individual strains. 1.  Clarify evolu?onary rela?onships 2.  appreciate the rela?onships and interac?ons among

different species that share an ecosystem 3.  Thus open up research into bacteria/organisms we could

otherwise not study


16s rRNA

Pros: 1.  Tradi?onal role as a

molecule that varies at an appropriate rate to dis?nguish ancient phylogene?c branching pa>erns

2.  It is not prone to horizontal gene transfer


Cons: rRNA does not reveal any details of the metabolism or other adapta?ons of the species


Genomes as “parts” lists – in some ways as we are trying to do in the field of evo-‐devo. Easier to do in bacteria as they are unicellular Evo-‐devo deals with mul?cellular organisms which poses challenges


h>p://www.sorcerer2expedi?on.org/version1/HTML/main.htm


1 billion base pairs were sequenced A millimetre of ocean water may contain 100 to 200 species A total of 1800 different microbial species were found in the samples 148 previously unknown species (labelled as phylotypes – MOTUs) 1.2 million unknown genes Many photosynthe?c bacteria do not use chlorophyl

Molecular bio Lecture Week 11

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