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Global Map of Amphibian, Land Mammal Genetic Diversity Reveals Impact of Human Habitation

NEW YORK (GenomeWeb) – A University of Copenhagen-led team of researchers has mapped out the global genetic diversity of amphibians and land mammals.

Genetic diversity is a key component of biodiversity — the variation it confers on a species could enable some members of that species to tolerate environmental changes, such as human-driven climate change. As such, the researchers said that understanding its global distribution is important for conservation and other efforts.

Using publicly available, georeferenced mitochondrial DNA sequences, Copenhagen's David Nogués-Bravo and his colleagues examined the global distribution of genetic diversity for more than 4,500 species. The tropics, they found, are home to high levels of genetic diversity, but regions affected by human habitation and development appear to harbor lower levels of genetic diversity of amphibians and likely also of mammals, as the researchers reported in Science today.

"[T]he tropics really are the richest regions in terms of biodiversity at all levels… On the contrary, we found very low levels of genetic diversity for amphibians in Western Europe," Nogués-Bravo said in a statement. "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 similar areas also altered by humans extra vulnerable to environmental change because low genetic diversity entails a higher risk of becoming extinct."

Nogués-Bravo and his colleagues mined both the GenBank and BOLD repositories for sequences from amphibians and land mammals. While some 13 percent of these sequences already had explicit georeferenced coordinates, about another 30 percent had place names. For those, the researchers assigned spatial coordinates to those locality names. In this way, they gathered a dataset of 92,801 mitochondrial sequences, 31,029 from amphibians and 61,772 from land mammals.

Using cytochrome b sequences, the researchers performed species-specific alignments for 4,675 species and calculated the nucleotide diversity per site for each species through a pairwise comparison of the aligned sequences.

To map the average number of genetic mutations, Nogués-Bravo and his colleagues divvied the globe into grid cells of equal areas and then, for each, averaged the cytochrome b nucleotide diversity across all the species present there.

The resulting maps indicate that the tropics — which are a hotbed of species diversity — are also home to high levels of genetic diversity for both amphibian and terrestrial mammals, the researchers reported. Other areas of high genetic diversity include areas in the Sino-Japanese region for amphibians and parts of South Africa for mammals. They observed broadly similar results when they used the cytochrome oxidase subunit I gene for mammals for the same analysis.

Overall, Nogués-Bravo and his colleagues observed higher levels of genetic diversity in the tropics that then tapered off toward the poles, a pattern that is also reflected the gradient of species richness. Some scientists have suggested that the higher temperatures in the tropics boosted evolutionary rates by increasing mutation rates and generation times, leading to this pattern of species richness, and Nogués-Bravo and his colleagues said that their findings on genetic diversity are in line with this evolutionary speed hypothesis.

How close the sites are to human activity also appeared to influence genetic diversity among animals, the researchers reported. For amphibians, they found that as they moved from areas heavily affected by people, such as villages and farmland, toward those less affected by people, such as forests and rangelands, there was an increase in genetic diversity. They similarly observed such a pattern in mammals when they examined diversity of the cytochrome oxidase subunit I gene. However, when they looked at the cytochrome b gene in land mammals, the differences between such regions weren't statistically significant.

In a related commentary appearing in Science, Henrique Pereira from the German Center for Integrative Biodiversity Research wrote that the study has implications for conservation efforts. "Protected areas have arguably been one of the most important tools for conserving the world's biodiversity. It remains unclear whether areas prioritized for conservation based on species diversity or even phylogenetic diversity also capture intraspecific diversity," he added.