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Genome of the tar­sier, the car­niv­o­rous pri­mate, reveals ties to humans

pub­lished 16 Octo­ber 2016 | mod­i­fied 16 Octo­ber 2016

TarsierSmall enough to fit into the palm of your hand, with enor­mous eyes and an appetite for meat, tar­siers are an anom­aly of nature. They are also our dis­tant cousins, accord­ing to sci­en­tists at Wash­ing­ton Uni­ver­sity School of Med­i­cine in St. Louis, who recently sequenced and analysed the tar­sier genome.

The find­ings, pub­lished online on 6 Octo­ber in Nature Com­mu­ni­ca­tions, place tar­siers on an impor­tant branch of the pri­mate evo­lu­tion­ary tree — along the same branch that leads to mon­keys, great apes and humans.

We sequenced the tar­sier not only to deter­mine where they fit in pri­mate evo­lu­tion, but because their phys­i­ol­ogy, anatomy and feed­ing behav­iour are very unique,” said Wes­ley War­ren, PhD, an asso­ciate pro­fes­sor of genet­ics and the study’s senior author.

Tar­siers are the only exclu­sively car­niv­o­rous pri­mate. They eat insects, small birds, rodents and lizards. With eyes twice as big as their brains, a head that can rotate 180 degrees in each direc­tion and the abil­ity to track prey using ultra­sound, the tiny ani­mals are for­mi­da­ble noc­tur­nal hunters. Their legs and feet are adapted for sud­den, pow­er­ful leaps, with an elon­gated ankle bone, the tar­sus, for which they are named.

Under­stand­ing pri­mate evo­lu­tion
The posi­tion of tar­siers among pri­mates has been con­sid­ered con­tro­ver­sial. Their teeth and jaws are more sim­i­lar to ‘wet-​nosed’ pri­mates such as lemurs, but their eyes and noses are more sim­i­lar to ‘dry-​nosed’ pri­mates such as mon­keys and humans. By sequenc­ing the com­plete genome of a tar­sier, Wes­ley War­ren, Jür­gen Schmitz of the Uni­ver­sity of Mun­ster in Ger­many, and col­leagues defin­i­tively placed tar­siers in the dry-​nosed category.

Jump­ing genes help us under­stand how species diverged from one another over mil­lions of years ago. The tar­sier genome is a mod­ern archive of evo­lu­tion­ary changes that led to humans.
Jür­gen Schmitz, co-​author, Uni­ver­sity of Mun­ster, Germany »

The researchers analysed DNA sequences known as trans­posons, or ‘jump­ing genes,’ which can jump from one part of the genome to another, often dupli­cat­ing them­selves in the process. Over time, trans­posons lose the abil­ity to jump. Newer trans­posons can jump into older trans­posons, but not vice versa. By analysing which trans­posons were embed­ded inside oth­ers, the researchers were able to deter­mine when par­tic­u­lar fam­i­lies of trans­posons lost the abil­ity to jump and thereby date the dif­fer­ent fam­i­lies of transposons.

The researchers com­pared the trans­po­son fam­i­lies of tar­siers, humans, bush­ba­bies (a wet-​nosed pri­mate) and squir­rel mon­keys (a dry-​nosed pri­mate). Tar­siers shared more recent trans­po­son fam­i­lies with squir­rel mon­keys and humans, and only the old­est ones with bush­ba­bies, indi­cat­ing that tar­siers belong with the dry-​nosed primates.

Primate evolution tree including tarsierThe key posi­tion of the tar­sier between Strep­sir­rhini and Simi­iformes (Anthro­poidea) is depicted. DNA trans­posons (DNA; black line) and fos­sil left Alu monomers (FLAMs; orange line) were active at the ori­gin of pri­mates but became inac­tive some­time after tar­siers diverged from the anthro­poid lin­eage, pos­si­bly dur­ing an inten­sive anthro­poid pop­u­la­tion bot­tle­neck. Alu ele­ments were active in all pri­mate lin­eages (red line). Young tar­sier AluJ ele­ments (with per­fect tar­get site dupli­ca­tions — TSDs) show a pref­er­ence for more AT-​rich tar­get sequences com­pared with older AluJ ele­ments (with diverged TSDs), which accu­mu­lated in more GC-​rich regions. TINE ele­ments evolved on the tar­sier lin­eage (blue line). FLAMs (7,301) were detected on the tar­sier branch and 6,324 FLAMs inserted in the com­mon ances­tor of anthro­poids. After­wards, the activ­ity of FLAMs within anthro­poid lin­eages was sig­nif­i­cantly reduced. Only 367 ele­ments were detected in the mar­moset (Platyrrhini) and 595 ele­ments were esti­mated for the lin­eages lead­ing to human. Draw­ings of ani­mals are pro­vided by Jon Bal­dur Hlioberg. Draw­ings for Tar­si­iformes and Homi­noidea have been repro­duced from Har­tig et al. with per­mis­sion.
Credit: Schmitz, J. et al. Genome sequence of the basal hap­l­or­rhine pri­mate Tar­sius syrichta reveals unusual inser­tions. Nat. Com­mun. 7, 12997 doi: 10.1038/ncomms12997 (2016).

Under­stand­ing tar­siers unique­ness and per­haps … human dis­eases
Hav­ing the com­plete tar­sier genome also allowed the researchers to com­pre­hen­sively study the genes that make tar­siers unique. Since, for exam­ple, the tar­siers’ eyes and ankle bones dif­fer so much from those of other pri­mates, the genes asso­ci­ated with eye or bone growth and devel­op­ment are likely to dif­fer as well.

By com­par­ing gene sequences from tar­siers with those from other pri­mates, the researchers iden­ti­fied 192 genes that are chang­ing faster or slower than what is hap­pen­ing in other pri­mates. These genes likely are linked to the tar­siers’ unusual traits. They then scanned the sci­en­tific lit­er­a­ture to iden­tify human dis­eases asso­ci­ated with those genes and found 47 dis­eases. About a quar­ter were related to vision and another quar­ter to mus­cu­loskele­tal problems.

The tar­sier genes that dis­play unique alter­ations can give us a clue into human dis­eases involv­ing the same genes,” War­ren said. “If an amino acid has been uniquely changed and it is puta­tively asso­ci­ated with the tarsier’s novel mus­cu­la­ture, maybe it’s an impor­tant part of the pro­tein and wor­thy of a closer look when linked to human disease.”

What about tar­sier species pop­u­la­tion health?
Analy­sis of the tar­sier genome also showed that these fas­ci­nat­ing ani­mals are dis­play­ing signs of pop­u­la­tion decline.

We think the pop­u­la­tion size is declin­ing and not rebound­ing,” War­ren said. “Most of the decline is due to loss of habi­tat, but the pet trade also is con­tribut­ing. Once cap­tured, sadly, the result is often death due to phys­i­cal and dietary needs not being met. It’s pos­si­ble that some tar­sier species will go extinct if we don’t change these trajectories.”

The researchers are hop­ing to obtain DNA from other tar­sier species and pop­u­la­tions, which they plan to use to assess the health of the tar­sier pop­u­la­tion, among other studies.

If we can sequence the genome of other tar­siers, we can mea­sure the pop­u­la­tion diver­sity. A pop­u­la­tion with a greater amount of diver­sity should be more capa­ble of sur­viv­ing changes in its envi­ron­ment,” War­ren said. “It will help us deter­mine how endan­gered they really are so we can imple­ment mea­sures to bet­ter pro­tect them.”

(Source: Wash­ing­ton Uni­ver­sity School of Med­i­cine in St. Louis news release, 06.10.2016)

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