Bayesian Technique and New Analysis Reveals Genomic Information of Philippine Geckos Throughout the Ice Age

Does the astounding biodiversity of the Philippines have anything to do with the ice ages' increasing and declining sea levels?

Scientists have long theorized that the Philippines' unusual geology, shifting ocean levels, and the separation and reunification of species groups periodically on islands formed a "species pump" that promoted remarkable variety. 

The concept of diversification is known as the Pleistocene Aggregate Island Complex (PAIC) model.

But up until now, there hasn't been any concrete evidence linking speciation booms to the particular dates that sea levels increased and decreased throughout the world.

Bayesian method and new statistical analysis of genomic data from geckos

(Photo : Leon Pauleikhoff/Unsplash)

According to co-author Rafe Brown, curator-in-charge of the herpetology division of the Biodiversity Institute and Natural History Museum at KU, the Philippines is a remote archipelago with more than 7,100 islands today, but this number may have been as low as six or seven giant islands during the Pleistocene.

Many of the smaller islands present today made up the combined landmasses; when the sea level dropped, dry ground joined them, and the excess water was trapped in glaciers.

This type of land fragmentation and fusion, which occurred over the course of the previous 4 million years while sea levels varied regularly, is thought to have set the setting for a unique evolutionary process that may have sparked concurrent clusters or bursts of speciation in unrelated species.

The scientists examined DNA samples of Philippine geckos as well as other species in the Philippines, where biologists at KU's Biodiversity Institute have been conducting fieldwork for decades.

Even with today's technology and the ability of scientists to characterize variation across the genome, however, the development of strong statistical approaches capable of handling genome-scale data is still catching up.

This is especially true in difficult cases, like the task of estimating the past times that species formed using genetic data collected from populations that are still alive today.

The model's precise predictions have been evaluated much more thoroughly, objectively, and statistically during the past 25 years using actual data from wild populations, which has been a significant advancement in Philippine biogeography.

For certain animals and plants, the predictions held true.

However, in other cases, the same predictions were repeatedly disproven when checked against actual data using sophisticated statistical techniques.

"When we looked at corollaries of the PAIC model in particular genera or clusters of closely related species in many of our own research at KU, we were astonished to see that the ice ages time frame wasn't even connected to much of the species diversity we observe today," said co-author Rafe Brown, curator-in-charge of the herpetology division of the Biodiversity Institute and Natural History Museum at KU, as per ScienceDaily.

Cameron Siler, a co-author from the University of Oklahoma, and Jamie Oaks, the lead author from Auburn University, were both graduate students at KU that Brown supervised.

They were joined by co-author Perry Wood Jr., now at the University of Michigan, who had previously worked as a postdoctoral researcher with Oaks and Brown at KU and Auburn.

In the past, researchers focusing on specific animals or plants have endorsed the general idea, but others have expressed skepticism because it didn't seem to hold true in other species they studied.

For two centuries, naturalists who studied species distributions in the Philippines have discussed, debated, and written numerous about the ideas underneath modern species pump theory or, in the Philippines, prognostications now making up the "PAIC Paradigm."

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Evolution of geckos

Scientists from Oregon State University and the National History Museum of London have dated the oldest fossilized gecko to be 100 million years old, as per Pets on Mom.

The oldest reptiles emerged during the Carboniferous Period, which is 300-350 million years ago.

Reptiles have a common ancestry.

Hylonomus, which the Journal of Geological Society dates to be 315 million years old, is the oldest reptile fossil known to science.

When geckos first developed their characteristic climbing feet is unclear. The gecko's feet and tail were partially visible in the 100 million-year-old fossil stated above, and the setae, or microscopic hairlike structures on the foot, were still visible.

Defense mechanisms like chameleon skills and the leaf-tailed gecko, which is well known for its tail that resembles a dried leaf, are other adaptations that may be observed in present species that suggest a divergence from their early progenitor.

The Global Gecko Association estimates that there are about 2,000 species of geckos now recognized, divided into five subfamilies.

One of the biggest differences among geckos is their color, with certain species being able to blend in with their environment.

One noteworthy difference is that certain females, like mourning geckos, are capable of reproducing on their own.

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