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There are two main tools for examining what went on in soil evolution over these millions of years. They are morphology (shape in fossils), and molecules (changes over time). To this, we can add:
1. AI Photography
2. 'Environment'
Morphology
Morphology
In my day' - up to 50 years ago, we would look down a microscope to identify dead creatures, by looking at their shape - morphology - as I did for half a million of them. It is not easy to work out what a dead creature does, other than making assumptions through the body shape - eg. feeding parts of mesostigmatid mite predators.
Putting the specimens together to see how they may relate is a bit like trying to work out what a tree is doing, only upside down. We cut it down, mash it up, recognise some of the creatures , then try to work out what was going on between the leaves and the insects, and then the birds. Yet, now down our soilscope, I could see this - a mesostigmatid mite making short work of springtails.
Information about evolutionary events hundreds of millions of years ago is mainly gleaned from fossils, like shells, exoskeletons, and bones, but also tracks and traces that organisms make while alive. similarly some soil has become fossilised. Fossil soil (or Paleosol) are not preserved soils but are soils that have been transformed by diagenesis (Selley, 2005) in the same way that a fossil is not always the original animal's shell, as many are are lithified. A former soil can be totally transformed and compacted and re-minerlised] by burial underneath either sediments (alluvium or loess and movement of marine sediments) or volcanic deposits (volcanic ash) They also include a soil which developed under a set of conditions that are no longer present, for example a soil which develops under tropical conditions in a country that later acquires becomes dry. The fossil record of soils starts about 570 million years ago.
For fascinating insights as to what paleosols can tell us about our world, read Soil grown tall (Retallack, 2002)
Molecular Clock
Molecular Clock
In the 1960s a new method of looking at the past was created called the ‘molecular clock’. We can now use genetic materials to track and trace events way in the past to help determine what may have happened. In general, ‘molecular clocks’ tend to estimate events earlier than fossil evidence, because it iis hard to determine the rates of molecular evolution (Smith and Peterson, 2002). This differential has recently reduced as molecular calculations improve and now take in environmental influences.
As molecular sequencing increases so too does progress on using molecules to predict the past. When molecuylar methods developed in the 1990s it was hoped they could fill in some fossil gaps and answer a few of the conundrums. They have in places, but they have also added to the confusion in othgers, as we will see throughout the soil story of evolution
Throughout our exploration of the evolution of soil, we will be using new molecular approach to soil. By accepting it as a living entity, it can be examined in a similar way to the rest of biology - through its DNA. Many papers are now being written on a new science - called metagenomics . This refers to function-based analysis of mixed microorganisms in the soil. Previously soil microorganisms were notoriously difficult to culture in labs. 'Shotgun' metagenomics goes further to analyse all genes in all microorganisms, so is even more accurate. As sequencing gets faster and cheaper, this is bound to lead to a better understanding of soil functions.
“Because the two groups of researchers are relying on different lines of evidence, the evolutionary stories told by the two groups are often in conflict. However, in recent years there has been a greater push to merge data from fossil organisms and modern organisms into more holistic studies, thus providing a more complete picture of the evolutionary histories of different groups of organisms" (Hunter 2020). Here we are working on that basis.
AI Photography
AI Photography
As well as morphological and molecular collection, we now also have AI & photography, for evidence. "CollembolAI, is a macrophotography and computer vision workflow to digitize and characterize samples of soil invertebrate communities" (Sys et al., 2022). This digitises samples at high resolution and scripts to support the researchers in creating an annotated dataset of soil animals, train the model, which learns to automatically detect and classify these animals. Of a mock community of 12 species of Collembola and Acari in ethanol, over 95% of specimens were correctly identified.
When there is no clear solution to various origins, despite all the existing evidence, as is often the case, we will also view the 'environment' at that time to try to work out what happened. This is what the famous Russian scientist Ghilarov recommended over 50 years ago. We will also use today's environment to try and understand what went on all those years ago.
LUCA
LUCA
According to modern evolutionary biology, all living beings are said to be descendants of a unique ancestor commonly referred to as the last universal common ancestor (LUCA) of all life on Earth.
Together these help our Phylogenetic analysis, more popularly called the 'Tree of Life') which supports the view that during the Cambrian radiation, Metazoa (multi-celled animals) evolved monophyletically from a single common ancestor:
"Over 600 million years ago (MYA), the multicellular progenitor of modern animals evolved from a unicellular flagellate. From such modest beginnings evolved the entire diversity of Metazoa: from deep-sea sponges to beetles, frogs, and humans.(King, 2004)
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LUCA - last universal common ancestor. Metazoans are all animals having a body composed of cells differentiated into tissues and organs and usually a digestive cavity lined with specialized cells. This all the animals we see today, with sponges at their base. Creatures with tissues were around at this period, in the place we are concentrating on in this early (Cambrian) period...
Phylogenetic Tree of 3 domains
Phylogeny
Phylogeny
The word ‘phylogeny’ was made by the German zoologist Haeckel in the mid 1800s, using the Greek ‘phyla’ for ‘tribe’ and ‘geny’for generation. The science of phylogeny helps us work out the relations of the various biological characters, which we will come across throughout soil space and time. Scientists who classiy the various organisms, are called taxonomists, and they use ‘phylogeny’ to see how various groups - or taxa, are related.We can say that phylogeny means the history of the evolution of a species or group, especially in reference to lines of descent and relationships among broad groups of organisms.Let’s call it the ‘family tree’.
Various forms of all the characters bacteria, archea and eukaryotes in the family tree above would have been around half a billion years ago. But how did the rest of life emerge from them? We can say the base of the tree represents the ‘common ancestor’. Taxonomists are often found to be arguing over this ‘common ancestor’. The stem denotes those organisms which have the same attributes as any organism in the three main groups, bacteria, archea and eukarytoes, as they are called the ‘stem group’. We’ll find the next mention of a ‘stem group’ when we find the tardigrades. You can imagine there would be roots to this tree, representing those organisms that gave rise to the common ancestor.
Going up the stem, we come to ‘nodes’ . These are the common ancestor of the branch coming out at that point. The branch is a family of its own - with some common characters as the stem, but different traits too. These branches/families which are also subject of controversy, especially where that node, their ‘common ancestor, occurs. These branchs/ familes are called ‘clades’. Clade is a group of organisms that includes an ancestor and all descendants of that ancestor. By definition, these clades are said to be ‘monophlyletic’ ie have only one (common) ancestor. If they have two, then there are two different branches and two different clades.
Much discussion focusses around whether a particular bit of twig (new ‘taxon’) is a continuation of the branch or something sticking out, or part of another twig. Twigs adjacent along the branch are then considered ‘sisters’ (There do not seem to be ‘brother’ groups) The branch can continue and produce other twigs distinct from the sisters. There is a fabulous depiction of the tree of life , with my sponsored link to predatory soil mite (Pergamasus), which we will hear about later.
Cladists
Cladists
A group of scientists came along looking at genes, using various DNA techniques, to track relations. There was a new category of taxonomists, called ‘cladists’ who came to the fore in the second half of the end of the 20th century.
In the 1990s, the development of effective polymerase chain reaction techniques (making millions to billions of copies) allowed the application of cladistic methods to biochemical and molecular genetic traits of organisms, vastly expanding the amount of data available for phylogenetics (above).
We thought they would sort out several of the big phylogenetic dilemma, in terms of who is related with whom. the dilemmas. But instead of relations being sorted out, there seem to be even more arguments – often between the ‘morphologists’ looking at the body forms, and between the ‘moleculists’, looking at the genes. For instance, there is still much debate about the ancestry of joint-legged creatures (Arthropods). While there is agreement that they are from one ancestor (monophyly) there is no agreement about the relations of their subordinates.
Clades
Clades
The molecularists like to discuss more about ‘clades’ and it seems that their grail is to always find the monophyletic nature for a clade – and its common ancestor. Yet no attempt is made as to how and why the various ‘boxes’/groups or ‘clades’ actually evolve with other, as they must. If we beleive the soil evolved, did it do so monophyletically? Or were there several soources, that came together later?
These organisms are not static, in a filing cabinet, but move. There are often boxes and lines between relations but few explanations of how they got from one to the other. They move in ways that affect others movement. And it must have been going on in soils for 300 million years. It is not just an actual movement of the organisms, but also changes in the way they were structured. As Darwin postulated, these creatures would develop, such that some were better fitted to the environment. And increasingly that environment would include the soil environment. And as we are seeing that soil environment itself is continually evolving.
This is called ‘cladism’ – studying the relation between groups. And it is fascinating, but it doesn’t not talk about how one group may have evolved in relation to another. How did ‘b’ get from ‘a’? These are physical and biological processes over millions of years determined largely by existing conditions. So, will somebody challenge me and explain how these primitive insects actually appear – what and where did they come from? Sometimes I look at the lines being drawn between the groups and ask – how did that get to that? Just drawing a line, and arguing about it, does not do it. We must look at the environment
Family Tree
Family Tree
The family tree of life guides us with what and how all organisms may be related to each other. We usually concentrate on what we can see above ground. Here we concentrate on what's going on below, which may shed some light on the familiar tree of life.
Debate
You may think that is pretty straightforward where various creatures drop into their allotted slots, according to the science. Yet, it is anything other than straightforward. There is constant debate about what goes where. You hear: 'Is this a ‘sister’ group - or part of same branch or stem?'
The debate is often about whether a particular group (whether species or taxa) should be moved to some other group In the past this has been the history of fossil hunters who looked at the shape (morphology) of the organisms.
Nowadays we add molecules to the mix, and it doesn't always solve the dilemmas.
Molecular phylogeny of oribatids Maraun 2004
Springtails not insects now, but own 'Class'. (Bellini 2023)
More on soil fauna classifications Hedde 2022
When telling this story of soil evolution, we shall refer to the geological ages, but not follow them rigidly. This is because soil is a different separate entity, related to, but not determined by, rock formations. Soil develops differently in different places, yet somehow has the same basic functions and properties worldwide. We have to explain this. Now the groundwork has been done in this story, we need to study the relationship between geology and soil evolution a lot more - but that's for somebody else!
The real challenge is for people to start seeing soil, this massive mass of life, as a dynamic entity not a static lump of dirt. That applies to scientists too. While it now lives as a whole all working together, all the parts arrived somehow at some point. I will make suggestions as to how. They will all be possible, but I would also like them to be plausible too, but it will be a long time before they are provable. There is much debate to be had from this new perspective. And some suggestions - as there are so many - will be wrong. But in the future, hopefully, those debates will be in terms of the environmental changes occurring at the time. That way we should be able to make a lot more sense of the extensive findings we have already made.
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