Category: evolutionary biology

No endogenized phage gene in Helicobacter pylori genome

January 23, 2024

Bacteriophage attacks their corresponding host bacterial species in order to gain access to the host cell’s replication machinery and nutritional sources for building more phages, and thus, maintain the phage population in the environment. Hence, possibility exists that each bacterial species will have a corresponding phage that helps to control its population. Presence of the … More No endogenized phage gene in Helicobacter pylori genome

Genome scale phylogeny

January 15, 2024

Phylogenetic tree is the oft used tool for assessing the evolutionary relatedness between different species as well as probing the provenance of specific proteins. The approach typically requires the collection of relevant gene sequences, which will be put through multiple sequence alignments to yield a map of the differences between gene sequences that is the … More Genome scale phylogeny

Thoughts on Sisyphean evolution in Darwin’s finches

December 28, 2023

The number of species is 1, for the 6 sub-species of Darwin’s Finches under consideration. Firstly, there are observations that the 6 sub-species still interbreed and produce fertile hybrid offsprings. Thus, according to the Biological species concept, the 6 sub-species cannot be considered as separate species as there is no reproductive isolation. Next, contention that … More Thoughts on Sisyphean evolution in Darwin’s finches

Possible speciation of Cyanoderma erythropterum

December 28, 2023

At the present time, morphological characteristics may divide the Bornean and western Sundaic populations of Cyanoderma erythropterum as two species due to speciation events between the allopatric populations in Borneo and western Sumatra during the past 20 to 200 kya. Two ice ages between 20 to 200 kya likely exposed vast swathe of land bridge … More Possible speciation of Cyanoderma erythropterum

Dissecting the California Roach/Hitch species complex into constituent species

December 28, 2023

In many of the highly engineered watershed systems in California lives two endemic freshwater minnows (Cyprinidae), CA Roach (Hesperoleucus symmetricus) and Hitch (Lavinia exilicauda). Both exists as a species complex as they are known to hybridise. CA Roach, in particular, was previously considered a single species, but was recently spilt into 4 distinct species and … More Dissecting the California Roach/Hitch species complex into constituent species

Asgard bacteria moving us closer to the last common eukaryotic ancestor

December 27, 2023

We always want to know where do we come from? This age-old question has a new twist in light of recent research published in Nature. An international collaboration of microbiologists from Sweden, United States, Denmark, Belgium, New Zealand, and Japan discovered a missing link in our understanding of the last eukaryotic ancestors, and the origins … More Asgard bacteria moving us closer to the last common eukaryotic ancestor

Difficulty in finding suitable whole genome shotgun sequencing dataset to design a new genome assembly algorithm

December 10, 2023

Since the advent of genomics, there have been a plethora of genome sequencing projects aiming to obtain the whole genome sequence of various species of life on Earth. While there are a number of genome assembly software available for download on websites, I thought of learning the craft of genome assembly by designing a new … More Difficulty in finding suitable whole genome shotgun sequencing dataset to design a new genome assembly algorithm

Functional properties of proteins do not easily emanate from their structural model

November 20, 2023

Structure defines functions in biology, and this is the reason why obtaining a structural model of a protein is the first step in understanding its function. However, in some cases, functional properties of a protein are not easily discernible from its structural features without other ancillary assays or tests. To understand the problem, it is … More Functional properties of proteins do not easily emanate from their structural model

Multiple sequence alignment and phylogenetic trees are two major tools in evolutionary biology

November 13, 2023

Evolutionary biology concerns the study of relationships between organisms over time. Specifically, it attempts to map temporal phenotypic changes to genotypic changes with the goal of finding a particular mechanism. To this end, multiple sequence alignment and phylogenetic trees are two main tools for dissecting the evolutionary provenance of species. Multiple sequence alignments involve the … More Multiple sequence alignment and phylogenetic trees are two major tools in evolutionary biology

Exposed ancient proteins may not be well-preserved at archaeological sites

November 3, 2023

Ancient DNA is much sought after in ancient archaeological sites as they tell a chronological story of the human or animal in a specific environment and locale. But, what about ancient proteins? Compared to ancient DNA, ancient proteins are much more difficult to find in intact form as they can be hydrolyzed by water as … More Exposed ancient proteins may not be well-preserved at archaeological sites