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First global map of genetic diver­sity shows impact of human activity

pub­lished 29 Octo­ber 2016 | mod­i­fied 07 Decem­ber 2018

By pulling together more than ninety thou­sands pub­licly avail­able data of genetic sequences from amphib­ians and ter­res­trial mam­mals, sci­en­tists from the Cen­tre for Macro­e­col­ogy, Evo­lu­tion and Cli­mate at the Uni­ver­sity of Copen­hagen devel­oped the first global dis­tri­b­u­tion map of intraspe­cific genetic diver­sity for ter­res­trial mam­mals and amphib­ians. The study, pub­lished on 30 Sep­tem­ber in the jour­nal Sci­ence, shows that genetic diver­sity is gen­er­ally higher in the trop­ics than in higher lat­i­tudes. It also shows that areas more impacted by humans, as urban areas and crop­lands, have reduced genetic diver­sity when com­pared to wilder regions.

Under­stand­ing what deter­mines bio­di­ver­sity is a major sci­en­tific chal­lenge for the 21st cen­tury, espe­cially in the light of global change. Bio­di­ver­sity encom­passes diver­sity at all lev­els of bio­log­i­cal orga­ni­za­tion, from genetic diver­sity within pop­u­la­tions, to species diver­sity within com­mu­ni­ties and the diver­sity of ecosys­tems in a land­scape. How­ever, most of the stud­ies to date on the global pat­terns of bio­di­ver­sity have been con­ducted at the species and ecosys­tem diver­sity lev­els. This is best illus­trated by the fact that, despite recent rapid advances in sequenc­ing tech­nol­ogy and the avail­abil­ity of an ever-​increasing amount of genetic sequence data in pub­lic repos­i­to­ries, we still lack cru­cial base­line infor­ma­tion on genetic diver­sity, such as a global map of its distribution.

The sci­en­tists from the Cen­tre for Macro­e­col­ogy, Evo­lu­tion and Cli­mate at the Uni­ver­sity of Copen­hagen address this gap by pro­vid­ing the first global dis­tri­b­u­tion map of intraspe­cific genetic diver­sity for ter­res­trial mam­mals and amphibians.

The study
To achieve this they took advan­tage of the immense wealth of pub­licly avail­able genetic sequences in Gen­Bank and
BOLD Sys­tems repos­i­to­ries. They then devel­oped bioin­for­matic tools to attach geo­graphic coor­di­nates to a total of 92,801 mito­chon­dr­ial sequences (31,029 for amphib­ians and 61,772 for ter­res­trial mam­mals) and adapted a widely-​used genetic diver­sity met­ric, nucleotide diver­sity, to explore how this diver­sity is dis­trib­uted across the globe.

We are now in a much stronger posi­tion to test which poten­tial mech­a­nisms have led to this spec­tac­u­lar bio­log­i­cal diver­sity in the trop­ics, and we are thus one step closer to unrav­el­ling the really big ques­tion of what deter­mines the global dis­tri­b­u­tion of biodiversity

Andreia Miraldo, lead author, post­doc­toral researcher, Cen­tre for Macro­e­col­ogy, Evo­lu­tion and Cli­mate, Uni­ver­sity of Copenhagen »

They were able to cal­cu­late genetic diver­sity in hun­dreds of local­i­ties through­out the world, allow­ing the team to map, for the first time, the dis­tri­b­u­tion of genetic diver­sity on Earth. This map and its func­tion­al­i­ties have been made pub­licly avail­able as a beta ver­sion via a web­page includ­ing instruc­tions to under­stand full func­tion­al­ity of the map­ping tool. One can use this tool to see the diver­sity of one or sev­eral species on a map of the world. It lets you explore the data under­ly­ing the paper in an inter­ac­tive man­ner. Addi­tion­ally, the site is based on google maps, so any func­tion­al­ity that google maps sup­ports (such as zoom­ing, ter­rain and national bound­aries) can be used in this map.

The results

Anthropocene map of genetic diversityGlobal dis­tri­b­u­tion of genetic diversity.(A to C) Aver­age num­ber of muta­tions per base pair for cytb across species of ter­res­trial mam­mals and amphib­ians together (A), ter­res­trial mam­mals alone (B), and amphib­ians alone ©. Dif­fer­ent col­ors rep­re­sent eight quan­tiles. The gray bar below each map rep­re­sents the total num­ber of cytb base pairs retrieved from Gen­Bank and BOLD; the green bar shows the num­ber of geo­ref­er­enced base pairs used to esti­mate the global dis­tri­b­u­tion of genetic diver­sity.
Image credit: Jour­nal Science/​AAAS An Anthro­pocene map of genetic diver­sity.

Trop­i­cal regions (i.e., trop­i­cal Andes, Ama­zo­nia and the trop­ics of East Asia) not only con­tain the high­est num­ber of species on Earth, they also turn out to hold the high­est amount of genetic diver­sity, the study shows. While the trop­ics con­sti­tute hotspots of genetic diver­sity, the study shows that it decreases when mov­ing towards the Polar Regions. Co-​author and Asso­ciate Pro­fes­sor David Nogués-​Bravo, elab­o­rates:
“Our results make it clear that the trop­ics really are the rich­est regions in terms of bio­di­ver­sity at all lev­els, rang­ing from tiny genes to major ecosys­tems. On the con­trary, we found very low lev­els of genetic diver­sity for amphib­ians in West­ern Europe. This sug­gests that the region’s long his­tory of human pres­ence and heavy alter­ation of nature, has taken its toll on genetic diver­sity. This leaves species in Europe and other areas altered by humans extra vul­ner­a­ble to envi­ron­men­tal change because low genetic diver­sity entails a higher risk of becom­ing extinct.”

Human activ­ity has already trans­formed the sur­face of the Earth. Now it also seems to reduce genetic diver­sity within ani­mals — putting them at higher risk of extinc­tion. Mam­mals and amphib­ians liv­ing in areas heav­ily altered by humans, as urban areas and crop­lands, have reduced genetic diver­sity when com­pared to wilder regions. There­fore they have less prospects of adapt­ing to changes in their envi­ron­ment. Lead author Andreia Miraldo explains:
“Hav­ing genetic vari­a­tion within a pop­u­la­tion means that whilst some indi­vid­u­als die from changed con­di­tions in their liv­ing envi­ron­ment, like an increase in tem­per­a­ture, oth­ers are able to sur­vive because they are dif­fer­ent at the genetic level and there­fore pos­sess dif­fer­ent traits. In this sense, genetic diver­sity within species deter­mines their abil­ity to sur­vive the increas­ing human impacts on the envi­ron­ment like cli­mate change.”

(Source: Cen­tre for Macro­e­col­ogy, Evo­lu­tion and Cli­mate press release, 29.09.2016)

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