Research: Research

Research Projects

Altitude shapes gut microbiome composition accounting for diet, thyroid hormone levels, and host genetics in a subterranean blind mole rat

2021 - 2024

The gut microbiome of animals acts as a crucial link between the host and its environment, playing a vital role in various aspects such as diet consumption, metabolism, physiology, and fitness. Employing 16S and 18S rRNA metabarcoding techniques to analyze microbiome and diet compositions, along with microsatellite markers for host genetics, we investigated the effect of altitude on the microbiome composition of Anatolian Blind Mole Rats (ABMR, Nannospalax xanthodon) across six locations at three altitudinal groups in the Central Taurus Mountains, considering diet and host genetics. The findings underscore the significant influence of altitude on microbiome variation, with notable differences in the relative abundance of specific bacterial taxa across altitudes. Interestingly, the previously reported altitude-linked bacterial genus Prevotella was absent in our dataset. In contrast to prior research, no substantial difference was observed in the abundance of strictly anaerobic bacteria among altitudinal groups, while facultatively anaerobic bacteria were still more prevalent in high-altitude animals. Microbiome (alpha) diversity displayed an increase at middle altitude, entirely composed of elements found at low or high elevations. Conversely, beta diversity exhibited significant changes with altitude. Although the alpha diversity of the ABMR diet did not significantly differ by altitude, altitude strongly influenced diet composition, likely reflecting the local plant communities. Surprisingly, no distinct altitude-related genetic structure was evident among host populations, and no significant correlations were identified between host genetic similarity and microbiome composition or between host microbiome and diet.

Research Team: Halil Mert Solak, Jakub Kreisinger, Dagmar Čížková, Efe Sezgin, Lucie Schmiedová , Marine Murtskhvaladze, Yoshiyuki Henning , Faruk Çolak, Ferhat Matur, Alexey Yanchukov

Supported by TUBITAK 1002 (220Z032), Czech Science Foundation (19-19307S), German Research Foundation (Deutsche Forschungsgemeinschaft, grant number HE 7661/1-1 to Y.H.) and the IFORES program of the Faculty of Medicine, University of Duisburg-Essen, EMBO Exchange Grant (#9427) and WAME Research Exchange Scheme (funded by the European Society for Evolutionary Biology)

The complete, genome-wide phylogenetic history of speciation and adaptive radiation in Blind Mole Rats (Spalax and Nannospalax) in their entire distribution range.

2020 - 2024

The Blind Mole Rats (BMR), sub-family Spalacinae, with two genera Nannospalax and Spalax, are known for their complex evolutionary history. These rodents are uniquely adapted to obligate subterranean lifestyle, can tolerate extreme hypoxic stress and are resistant to cancer. The BMR has most likely originated in the Near East ~16 million years ago, but their subsequent history of divergence and speciation in Anatolia, Balkans, Levant and the Black Sea region is still unclear. The presence of exceptionally high number of chromosomal forms in the genus Nannospalax (but not in Spalax) is particularly puzzling, since their current diversity and distribution are difficult to explain by the contemporary variation in the habitat or in climate. Comparative analysis of DNA sequences is a reliable method to infer phylogenetic history, which can be applied to the BMR. However, all previous research aimed at the phylogeny reconstruction used partial mitochondrial DNA sequences, a method that can produce biased results and generally provides limited resolution. No study covered an entire geographic distribution range of the BMR nor anyone looked at the nuclear DNA sequences. Based on the current knowledge of BMR biogeography as well as on our preliminary results, we propose a hypothesis that multiple narrowly distributed cytogenetically (Nannospalax) or morphologically (Spalax) distinct forms could be the surviving relics of populations with much larger distribution in the past. To test our hypothesis, we aim to reveal, for the first time, the evolutionary relationships between all major forms of BMR using DNA samples collected in Turkey, Romania, Moldova, Ukraine, Russia, Kazakhstan, Georgia, Bulgaria, Greece and Egypt. We will use Genotyping-by-Sequencing approach to sequence hundreds of individuals at hundreds of ddRAD (double digest Restriction site Associated DNA) markers to construct a robust, time-calibrated phylogeny of all species and all major cytogenetic forms of Spalax and Nannospalax, and will complement these results with phylogeny based on partial mtDNA sequences. Using combined nuclear and mtDNA data, we will be able to infer the timing of the major divergence events in the evolutionary history of BMR, and will reveal whether there is ongoing hybridization between different populations. The results of the project will a have a significant impact on the international scientific community working on the evolutionary and biogeographic history of the Middle East, Black Sea region and Europe.

Research Team: Alexey Yanchukov (PI), Raşit Bilgin, Faruk Çolak, Ferhat Matur, Mustafa Sözen, Mikhail Rusin, Ortaç Çetintaş, Halil Mert Solak.

Supported by TUBITAK 1001 (119Z400).

Adaptation to living in high altitude mountain environment in a subterranean rodent, the blind mole rat Nannospalax xanthodon.

2017 - 2020

The Anatolian Blind Mole Rat (Nannospalax xanthodon) is an obligate subterranean rodent found from the sea level to up to 3000 m. a.s.l. (Sözen 2004). Despite getting some protection from the elements underground, it is still affected by the short vegetation season and colder temperatures in the mountains. At 3000 m a.s.l., it must also cope with low atmospheric concentration of oxygen, additionally exaggerated by decreased O2 and elevated CO2 levels in the closed underground burrows (Shams, Avivi, and Nevo 2005). This combined effect would make BMR one of the most hypoxia-tolerant animals known. Common genetic adaptations to hypoxia in mammals involve fixation of certain nucleotide sequence or structural mutations that increase the O2 affinity of hemoglobin (Storz 2007). To test if this is the case in BMR, we are currently looking at the primary DNA structure of the alpha- and beta- globin gene clusters in animals collected from two populations at different altitudes in Central Taurus mountains. Adaptation to high altitudes can also be caused by biotic factors, such as different abundance/composition or parasites and the energy costs and/or benefits of maintaining a strong immune system in the mountains. In collaboration with Jamie Winternitz at the University of Bielefeld, Germany, we are comparing the strengths of the immune defense between the same two populations (high and low altitude) using experimental immunochemistry assays. The first results suggest that the mole rats from the high altitude have a stronger standing immune system. Our working hypothesis is that it might help them to avoid the risk of getting serious infections in a demanding mountain environment, but further investigation of other immune system components, such as adaptive immunity and MHC gene variation will be performed to make more robust conclusions.

Research Team: Alexey Yanchukov (PI), Faruk Çolak, Ferhat Matur, Mustafa Sözen, Halil Mert Solak, Cihan Ayanoğlu, Jamie Winternitz.

Partly supported by TUBITAK 3001 (117Z596).