Tag: phylogenetics

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Defining the Core: the Human Gut Pan-Microbiome

Background:

In 1996, Kenneth Wilson and Rhonda Blitchington pioneered the use of DNA sequencing to analyze the composition of microbes in human fecal samples (Wilson and Blitchington 1996). Since then, studies around the world have investigated the specific make-up of the human gut microbiome via sequencing technologies. The most common way to analyze the composition of the microbiome is Next Generation Sequencing (NGS). The use of NGS has   identified of a large number of microorganisms found in the human gut.

Analysis of sequence data can identify types, abundances, and shifts in the composition of the gut microbiome of people with medical conditions and health concerns. Finding potential links between diseased states and the makeup of the human gut microbiome begins with DNA analysis of the “condition” gut, and continues with comparison to the types and abundances of microbiota in the “healthy” human gut. Continue reading “Defining the Core: the Human Gut Pan-Microbiome”

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Lonely at the Top: isolated mountain tops served as ice age refugia

Nebria is a genus of flightless beetle found in montane alpine habitats, sometimes at altitudes over 3,000m. Nebria have special adaptations, such as anti-freeze enzymes, which allow them to thrive on snowy mountain tops where other insects could not. In fact, Nebria feed upon arthropod fallout, insects which are blown to high altitudes and become immobilized on the cold snow. These same cold-tolerant adaptations may prevent them from surviving at lower altitudes (Lohse et al. 2011). As a result, their mountain top homes act like isolated “sky islands.’ Dispersing between sky islands is challenging when you can’t fly. Continue reading “Lonely at the Top: isolated mountain tops served as ice age refugia”

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The Case of the Flying Kiwi

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At some point in elementary school– maybe third or fifth grade– your teacher likely pulled out a chart showing maps of the world throughout geological history, showing all the continents cozily squished together for a while as Pangea before they all started wandering off on their own. You probably traced the routes they took, noticed how South America and Africa seemed to fit together like puzzle pieces, and probably sat through an explanation involving dinosaur and fern fossils found throughout the Southern Hemisphere and an unlucky German weatherman who was unfortunate enough to be the first person to seriously suggest that the continents moved around throughout time. At some point, if your class was anything like my fifth grade science class, the teacher probably got into more detail about what all this continental rambling about meant for the plants and animals still around today- that all the fantastic and weird marsupials of Australia and the lemurs of Madagascar came to be because those two landmasses left the Gondwanan party early, before the more typical mammals took over, and that certain animals were found on all of the different continents of the Southern Hemisphere, distant cousins who all rode the bits and pieces of the former southern supercontinent to their current positions. At this point, in all likelihood, somebody brought up ratites. Continue reading “The Case of the Flying Kiwi”

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Going gaga for ferns!

Picture of Lady Gaga and heart-shaped fern gametophyte.
Fig. 1: One of the inspirations behind Li et al. naming an entire fern genus after Lady Gaga was the costume she wore for her performance at the 2010 Grammys, which resembles a gametophyte (image from Duke University).

Background

Hybridization has been shown to play a critical role in the evolution of plants (Rieseberg and Wendel 1993) and molecular studies have allowed scientists to re-evaluate taxonomy through multiple methods besides just morphological characteristics (Li et al. 2012). However, some ferns, such as the cheilanthoid ferns in the family Pteridaceae, had not been re-classified as of 2012 even though they were known to be non-monophyletic (that they didn’t all share a single common ancestor). Li et al. (2012) were particularly interested in a group of about twenty cheilanthoid ferns referred to as the “Cheilanthes marginata group,” which are found in arid habitats ranging from Arizona and Texas all the way to Bolivia. They hoped to distinguish this group from its most closely related fern relatives and revise the taxonomy based on the number of chromosomes (an organism’s condensed DNA) and genetic relatedness. Continue reading “Going gaga for ferns!”