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About me

Hi! My name is Katarina Piponi and I am a a fourth-year MSci Zoology student at the University of Nottingham. So far, my degree has taken me across continents from studying fireflies in Portugal and voles in Wales, to cheetah conservation in Namibia. My love for Zoology now brings me here, where I hope to provide informative and valuable posts about the scientific world behind the field of Zoology and hopefully supply contagious passion.

I am excited to begin this blogging journey where I will post ideas, opinions, commentary and updates on fields including: evolutionary developmental biology, evolutionary ecology, conservation, and animal behaviour. I believe blogs can be a phenomenal vehicle for accessible scientific communications and wonderfully complement scientific updates.

Welcome to Kats World of Zoology!

Check out some of my recent work on a bright novel derivative of crystal jelly’s (Aequorea victoria) green fluorescent protein (GFP) here.

Or listen to my brief discussion with Rosemary Felix about CRISPR/Cas mediated genome engineering here.

Flamboyant molluscs: how varicoloured snails help us understand evolution

Currently, I am undertaking an evolutionary genetics research project that aims to understand the molecular reason behind the existence of the Grove snail’s vibrant morphologies. Read on to find out why variations of their psychedelic shells are biologically enthralling, and the story of my research so far.

Graphic summary of my project.
My ornate study subject: the Grove snail.

Also known as the Brown-lipped Snail or simply Cepaea nemoralis, this timid button-sized mollusc is the most colourful and variable snail in the UK. You may have noticed their pink, yellow or brown banded shells dawdling through your garden shrubs.

Image: AJ Cann, Jubilee Walk Leire.

Beyond just providing geometrical aesthetics to our woodlands, the Grove snail has also been at the forefront of evolutionary studies and helped establish ecological genetics. Put simply, the striking colour variants are an exemplary instance of polymorphism (the occurrence of multiple-defined morphologies in a species population). As a result, the Grove snail has been a historical model used to showcase natural selection and rapid evolution. In fact, I fondly remember beginning my zoological journey with the Grove’s shell variants in the context of Mendelian inheritance (biological laws of inheritance that follow the principles originally proposed by Gregor Mendel).

Diagram of the three Grove snail morphs (pink, yellow and brown) exhibiting laws of Mendelian inheritance that follow dominant and recessive genes.
A snail left behind

For other polymorphic organisms, e.g. Heliconius butterflies, or peppered moths, research has determined the actual gene where the numerous possibilities of a trait are found. Essentially, these findings reveal how evolution works at a molecular level, but also the ways in which the genetic makeup within and around us can impact the zoological communities in our world.

Alas, despite being a classic evolutionary model, investigations into the molecular foundations of polymorphism have neglected the Grove snail. Put simply, the actual genetic origin of their polymorphic shell colour pigmentation have not yet been identified, and equally, neither has the genetic pathway that maintains their polymorphism within the population.

The genetic framework so far: a ‘super’ gene and a perplexed Mendel

My research aims to uncover some of the Grove snail’s molecular mystery, and so I am focusing on a particular gene (who’s identity is confidential) within its genetic makeup. This gene is among a few candidates that potentially influence the shell’s pigmentation outcome. Of course, however, things are not so simple.

A major reason for the Grove’s limited genetic research is its maddening genome repetitiveness, which force simple sequencing attempts into laborious jobs. Within this repetitive genome, research has confirmed that a supergene (multiple neighbouring genes that are inherited together because of close genetic linkage) primarily determines the shell morphology. Which, what or where the supergene lies, unfortunately, remains a mystery. Not only that, recent scientific research has then identified the morphological impacts of this supergene presence, whereby Mendelian inheritance is made subordinate.

Diagram of the impact caused by the presence of a supergene. The linkage map (left) is a theorised map made for the purpose of demonstrating a supergene’s impact, and was drawn according to Heliconius’s genetic map. Unfortunately, such a map does not yet exist for the Grove snail.
Reading genetic material

My project utilises the recent genetic data collected by Saenko and her colleagues, which is comprised of nucleotide arrangements that generate a draft genome sequence. In spite of the supergene-repetitiveness-complexity, a number of contigs (sets of overlapping DNA segments that together represent an area of DNA) were identified as associated with the Grove’s shell pigmentation. One contig in particular contains an alluring number of specific gene repeats. The repeated gene is my gene of interest, and so far I have isolated the gene and begun my in-depth analysis.

Fortunately, a few close relatives to the Grove snail have been sequenced and their genetic material is available for me to exploit (any information is precious information!). These relatives include the sought-after false hadra (Euhadra quaesita), the Asian trampsnail (Bradybaena similaris), and the Ram’s horn snail (Biomphalaria glabrata). Through aligning with this assortment of relatives, I have been able to piece together the exons (parts of the gene sequence that are expressed in a protein) by manually removing introns (portions of a gene that do not code for any parts of a protein).

Schema of the nucleotide sequence origins. Each snail’s nucleotide sequence acts as their genetic fingerprint and when aligned, allows us to compare the genetic differences that might be causing their morphological differences.
Repeat mania for the sake of dating

Remember I mentioned my gene in question has an alluring number of repeats? Although the actual number is confidential, I can share my bioinformatic endeavours.

So, now that I’ve removed the introns, the nucleotide sequence can be turned into a dependable arrangement of amino acids (the organic compounds that make up proteins). I am currently in the process of manually aligning the nucleotide and amino acid sequences of all the repeats to as many available land snail genomes as possible. The hope is that, together, they will allow me to loosely date when each repeat evolved depending on the repeat’s similarity to the relative’s sequences.

A small snippet of the Euhadra quaesita transcriptome. The full document contains over 59,000 rows, and provides a gratifying challenge for my dyslexic self.
Laboratory ventures

Along side the bioinformatic analysis mentioned above, my supervisor (Dr Angus Davison) and I have also decided to tackle the genetic whereabouts of the bewildering supergene. To do this we are using genetic crosses (snails bred from two individuals to produce an individual with a combination of genetic material) from Gonzalez’s research to analyse Grove snails that have obtained any recombination. Put simply, those that were born without recombinant morphology are demonstrating the strength of the supergene’s tight linkage. Therefore, we have decided to work backwards and apply polymerase chain reactions (PCR), a reaction that rapidly makes millions of DNA copies, to those that show recombination. The hope is that once sequenced they may reveal where the supergene is NOT, allowing us to narrow down the hunt for the supergene whereabouts.

Schema of the PCR process I am undertaking in the lab. *The negative control (N) contains the same buffers and enzymes as the other samples, but excludes a DNA sample.
I hope to report my findings on the blog – make sure to keep posted! In the mean time, enjoy some photos of Grove snails I found along the Trent river in Nottingham:

On another note, don’t miss Nat Geo’s short but wonderfully sentimental story about a snails life:

Breaking mammoth boundaries with million-year-old DNA

Sequencing ancient DNA breaks down mammoth-sized boundaries in studying speciation. Alluringly, it allows the opportunity to study the process of speciation in real time, opening a new era of research.

Tom van der Valk, Patricia Chrzanova Pecnerova, and their international research team achieved the somewhat impossible and sequenced DNA from three mammoth specimens that are up to 1.2 million years old. Put simply, their genetic analysis concluded that the Columbian mammoth (Mammuthus columbi), who inhabited North America during the last ice age, is in fact a hybrid between the woolly mammoth (Mammuthus primigenius) and previously unknown genetic lineages of mammoth.

For perspective, the senior author Love Dalén, a Professor of evolutionary genetics at the Centre for Palaeogenetics, explains that:

“The [DNA] samples are a thousand times older than Viking remains, and even pre-date the existence of humans and Neanderthals”.

The unforeseen evolutionary origin

One million years ago, neither the woolly mammoth nor the Columbian mammoths had evolved yet. Instead, their predecessors roamed North America where they eventually laid to rest in the Siberian permafrost. Before sequencing this ancient DNA, previous studies stipulated that only one species of mammoth existed in Siberia a million years ago – the steppe mammoth (Mammuthus trogontherii).

Now, after relying on minute amounts of degraded DNA remains, the researchers have gained new insights into mammoth evolution and migration. Through comparing the DNA with mammoths that lived more recently (the last known mammoths disappeared about 4,000 years ago), the team deduced that there were in fact two different genetic lineages: the Adycha mammoth and the Krestovka mammoth.

Illustration: Van der Valk et al. 2021. The updated evolutionary history of mammoths, based on the new knowledge gained.

According to their genetic analysis, the Adycha lineage gave rise to the woolly mammoth and the Krestovka lineage represents the previously unrecognized lineage that was ancestral to the first mammoths to colonize North America. Through extracting the DNA and mapping the sequences against living relatives (the African savannah elephant (Loxodonta africana) genome and an Asian elephant (Elephas maximus) mitochondrial genome), it became clear that the iconic Columbian mammoth that occupied North America was a hybrid of the two genetic lineages. Curiously, it appears to be a hybrid with roughly equal proportions. 

The specimens who shook the mammoth family tree

To report these findings, the researchers used genome data recovered from three Early-to-Middle Pleistocene mammoth molars. The samples were recovered from the fossil-packed Olyorian Suite of north-eastern Siberia in the 1970s, but have only now been sequenced. The specimen referred to as ‘Krestovka‘ is morphologically similar to the steppe mammoth and was recovered from deposits that were dated 1.2-1.1 millions years old. Likewise, the specimen referred to as ‘Adycha‘ also has steppe-like morphology but structurally suggests that it dates to the Early Olyorian (between 1.2 and 1.0 million years ago). Finally, the specimen referred to as ‘Chukochya‘ is morphologically consistent with being an early form of the woolly mammoth, and recovered from sediment dating 0.8-0.5 million years old.

Image: : Van der Valk et al. 2021. The three mammoth specimens – upper third molars in lateral and cross-sectional views.
Studying evolution in real time

The abundance of different-aged specimens allows the researchers to investigate how mammoths adapted to life in extreme environments and to what extent the adaptations evolved during the process of speciation. This opportunity is made valuable by its ability to expand our understanding of speciation, long-term adaptive evolution, and simply the origin of organisms.

Through comparing protein-coding changes, it became clear that cold adaptations in woolly mammoths were already present one million years ago. These adaptations include those associated with life in the arctic: cold tolerance, white and brown fat deposits, hair growth, thermoregulation and circadian rhythms. Their million-year-old presence is indicated by the genes related to these features being resident in 87% of the Adycha genome and 89% of the Chukochya genome. Hence, most adaptations within the mammoth lineage appear to have evolved slowly and gradually over time, rather than through single bursts of adaptive evolution.

Image: Carl Buell. An illustration of the woolly mammoth (left) and Columbian mammoth (right).
A perspective to consider

My four years studying Zoology has made me appreciate that biology struggles with formalizing terms due to the unique properties of living entities. For instance, evolution provides a simple, powerful framework to understand the living world, but is built on concepts with deep flaws – species, natural selection, intelligence, the self, and the power of nature versus nurture. Put simply, biological fields of science are unique in their holistic and metaphysical dependency. Present all-around, there is a human necessity to demarcate non-physical subjects, and appreciating this helps evaluate biological concepts and question the nature of knowledge.

When studying fossil records, our reality is that the bulk of the evidence available to us only represents a small fraction of the organisms that existed. Most organisms decompose rapidly after they die, especially those that are soft-bodied like worms or cartilaginous fish. For fossilisation to occur, the remains need to undergo a very specific process where they are covered by sediment soon after death. Over time, minerals present in the sediment then seep into the remains and they become fossilised.

This palaeogenetic study carried out by Tom van der Valk and his colleagues does not necessarily state the new ‘truth’, but instead the most likely scenario given the data available. Importantly, although contrasting previous Steppe-origin-verdicts, it is in fact consistent with previous work. There is supporting evidence that the major shifts in the habitat and morphology of mammoths happened very early in their evolution, and this is harmonious with the mammoth lineages evolving slowly over time. Equally, the morphology of the Krestovka specimen validates previously proposed models – that the earliest North American mammoth derived from Eurasian ancestors.

Video: Stockholm University. Listen to the senior author Love Dalén discuss their findings.

You can also read Patricia Chrzanova Pecnerova‘s personal account of how they broke the genetic boundaries and extracted the DNA samples here, or simply read more about the research at the Centre for Palaeogenetics here.

The despairing struggles of charisma-challenged species

Social media has catalysed global connectivity and innovative methods of collaboration, and this is distinctly evident in our unprecedented Covid-19 climate. But one controversy remains – charisma-challenged species get left behind.

Meet the Rando Drawf Galago (Paragalago rondoensis). Despite her adorable 0.1 kg in weight, huge fox-like ears and moon-eyed inquisitiveness she is critically endangered. Unfortunately, unlike her primate relatives such as Apes, Gorillas or Lemurs, the name ‘galago’ is not as evocative and tarnishes her ability to gain media attention. She and thousands of other species that are identified as critically endangered are not receiving any direct conservation or funding.

Image
Image: David Haring. The Rando Drawf Galago (Paragalago rondoensis).

Shamefully, conservational attention gets refocused on large organisms that we are accustomed to hearing about and resonate with. Included within this category are the famed mammals like Tigers, Lions and Elephants. According to professor Celine Albert their ‘attractiveness’, ‘appeal’ and ‘beauty’, or put simply their ‘charisma’, is what draws public attention. While the International Union for Conservation of Nature (IUCN) has evaluated nearly 100% of the world’s birds and 90% of mammals, it has evaluated only 70% of the world’s reptiles, 10% of flowering plants, and less than 1% of its insects. Regrettably, this unbalanced attention does not correspond to the animals’ importance in relation to conservation. In short, though charming and enthralling, these charismatic organisms are not the most important spotlight for conservational action.

Broken Umbrellas

Researchers have long appreciated that saving charismatic species also conserves those that are less known. This circumstance is termed as the umbrella species theory. In other words, protecting big cats conserves their habitat, and, in theory, protects the survival of other species within that habitat, e.g. hares, impalas or wildebeest.

However, this is no longer reliable to assume. Olivia Couchman, manager for the EDGE of Existence program at the Zoological Society of London (ZSL), says that:

the habitat requirements for larger, more charismatic species do not always reflect the species needs of highly specialized micro-endemics”

The umbrella species theory undermines the fact that many organisms now require tailored action beyond generalised habitat protection. According to biologist Rebecca Stirnemann, the moa bird (Gymnomyza samoensis) urgently requires rat control within its breeding habitat in Somoa, while the toothbill pigeon (Didunculus strigirostris) needs feral cat control. Despite the fact that both the birds inhabit the same Samoan forests, they require different conservational strategies. With that in mind, what charismatic umbrella can protect the mao and toothbill pigeon?

Image: David Olson. The moa bird (Gymnomyza samoensis).
Effortless Charisma

It is not difficult to identify charismatic species. We all grew up with them in our bedtime stories and cherished childhood films, e.g. Free Willy (1993), The Lion King (1994), Madagascar (2005), and Happy Feet (2006). Public interest and funding have assisted a number of charismatic species not only from decline but from total extinction: think of the Europe’s largest living land animal – the European bison (Bison bonasus) that went extinct in 1919 but now harmlessly grazes Dutch forests.

From my own childhood I can recall ‘Big Cat Diary’, a docuseries following the lives of big cat families in Kenya’s Masai Mara. The series inspired my interest in wildlife and brought me here, studying zoology full time. However, species’ like the Rando Drawf Galago have not been given the same opportunity for us to fall in love.

Graph: Albert et al. 2018. Twenty most charismatic animals in ranking order.

Most alarmingly, the risk of extinction does not appear to influence how much financial support a species receives. For instance, the post-doctorate ecologist, Stefano Mammola, explains that the brown bear (Ursus arctos) and grey wolf (Canis lupus) have received the most funding (€47m and €33m) despite both being labelled “least concern” by IUCN. In contrast, the rate of extinction for invertebrates is eight times faster than that of birds, reptiles or mammals. In fact, known insect declines are described as the “tip of the iceberg” where there will be no return.

So, why bother focusing on a species if it is charisma-challenged?

Ecologically, charisma is fruitless when it comes to an organism’s contribution to its environment and its downstream effects. For instance, the purple sea star (Pisaster ochraceous), who has yet to be evaluated by the IUCN red list, is a keystone species. The United States Geological Survey (USGS) has released details of an ongoing purple sea star mortality event on the Western coast since June 2013. Yet, shamefully, the underlying cause of the die-off has yet to be identified. They feed primarily on mussels and subsequently control the mussel population. In their absence, mussel populations over-expand and cover the entire rocky intertidal shores. As a result, no other species can establish themselves amongst the mass of mussels. Hence, charisma does not correspond to conservational importance.

star fish - keystone example
Image: David Clode. The purple sea star (Pisaster ochraceous).
Beyond Ecology

The media coverage we are familiar with of animals is often tailored for western viewing, and organisms that do not fit western society’s concept of charisma are also disadvantaged. Yet, charisma-challenged species can be highly valuable for economical and commercial purposes. For instance, the tamaraw (Bubalus mindorensis) is an extremely vulnerable water buffalo which is endemic to the island of Mindoro in the Philippines.  The tamaraw is considered a national symbol of the Philippines and can be found on the 1980-1990 one-peso coins. In fact, the 2002 Presidential Proclamation 273 set October as a “Special Month for the Conservation and Protection of the Tamaraw in Mindoro.” However, tamaraw conservation has largely been unsuccessful due to rampant deforestation and international trade.

Image: Martin San Diego. The tamaraw (Bubalus mindorensis).

The evolution of technology and its accompanying media is exceptionally fast paced, so much so that its impact can be easily overlooked. Regarding conservation, social media platforms provide a venue for sharing biodiversity-related content and bringing awareness to many ecological issues. Telling a species’ story (particularly when including visual accompaniments) helps to inspire and encourage people to support conservational action. The media influence we are familiar with can offer insights into the Western public’s perception of charismatic species, and supply methods of harnessing it. Ultimately, understanding biases is a recurrent but important process in science and, as we scroll through our social media, we should pay more attention to the uncharismatic underdogs of the animal kingdom.

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