Palaeoecology

Palaeoecology.

Palaeoecology is a diverse field. Some of it relies on clever analogies with living creatures, whilst some uses hardcore quantitative/computational techniques. There's a fair bit in between those two as well. I've done my best to create a narrative for you that ties this all together! I hope you enjoy it.

Introduction

We're going to cover:

The ecology of fossils (palaeoautoecology) – Section 1.
An introduction to ecology and palaeosynecology:

Ecological niches – Section 2 & 3.
Environmental gradients – Section 4.

Fossils as indicators of an environment – Section 5.
Large scale trends – Section 6.

Palaeoecology a really important field – it allows us to understand ecosystems in the past, and thus what was going on in the biosphere at the time. This, coupled with our knowledge of past climates, lets us better understand how life responds to a climate change. The field also incorporates skills which help geologists work out the environment a rock was deposited in. All in all, it's useful stuff. Let's jump right in.

1 – Palaeoautoecology

Let's start by defining terms, and then looking examples of the ecology of individual (fossil) species: how they lived their lives, and what role they played in their ecosystem. This is the world of palaeoautoecology.

Summary

We can split palaeoecology into two subfields – palaeoautoecology, described above, and palaeosynecology (the study of ecosystems in the past).
Palaeoautoecology will often focus broadly on mode of life and life traits, through drawing inferences from the morphology of organisms (=functional morphology).
The inferences of functional morphology build on adaptations of organisms to the environment in which they live.
We can do this with fossil species by using organisms that are alive today as an analogy, or by using quantitative techniques.

2 – Ecological niches

We deal with different aspects of palaeosynecology over the next five videos. Let's start with niches. These are an important concept that explains why we find particular animals in particular environments. We'll also touch on some basics of ecology!

Summary

We can split the biosphere into a series of hierarchical categories, and there are ecospaces associated with these.
Communities occupy ecosystems; the breadth of interactions in these make them really complex.
Species occupy a niche, which we can split into their prospective and realised niche – the latter is the portion of ecospace in which a species actually lives.
The principle of competitive exclusion states that two species cannot coexist within a niche.

3 – Niche partitioning

The thing about niches – well, a thing about niches – is that organisms can help define their niche through their behaviour. This means that there are lots of ways in which niches can be differentiated. This is called niche partitioning – let's learn about it!

Summary

There are many ways in which niches can be differentiated.
We've met four examples:

Resource partitioning: species specialise in the resources they require (e.g. space, food) allowing them to avoid direct competition.
Predator partitioning: this relies on the differential impact of predators/pathogens that are prey/host specific.
Conditional differentiation: occurs when competing species differ in their ability to consume/employ a resource through varying environmental conditions.
Temporal partitioning: niches are partitioned based on timings of their activity.
(of course, if time leads to conditions changing, this could be a form of conditional differentiation, but if you consider time a resource, it is a form of resource partitioning!)

4 – Environmental gradients

In the real world, conditions vary in space. When they do so, this often occurs along gradients – gradual transitions across an environment. Here we meet these and see how they interact with ecological niches.

Summary

The spatial distribution of organisms and their associations are controlled by physical, chemical and biological factors which often change along gradients.
Along a gradient, within a niche, we expect organisms to have optimal conditions under a species is most successful.
This allows us to use species as, for example, bioindicators. These allow us to assess the quality of the environment.
The interaction of gradients and niches defines community distributions, but the nature of this interaction isn't clear cut.

5 – An example from the fossil record

Let's have a look at the impact that this interaction of niches and gradients has on the distribution of fossil groups in rocks. The exact nature of this impact is defined by the environment and time period in which fossils were deposited: palaeontologists spend significant amounts of time building up expertise that allows them to make nuanced interpretations of fossil assemblages, that take into account (palaeo)biogeography, environmental conditions, and fossil preservation (taphonomy). Our next video provides a quick overview of how this all works, and can help us understand the water depth in which a sediment was deposited on ancient clastic shelves: common sequences of environments from beaches into the deep sea.

Summary

There are many roles fossils can play that are really useful to geologists. An important one is differentiating depositional environments.
But we do need to be aware of the biases introduced by the processes of fossilisation.
We can identify water depth in marine environments based on fossil assemblages that vary with depth, and through time.
This is true of both body, and trace fossils: but we always have to consider potential confounding factors.

Benthic assemblages

In this video and the lecture, I introduced biofacies and the associated benthic assemblages. The table below provides an overview of each of these benthic assemblages! It was published in the following textbook:

Brenchley, P.J., Brenchley, P. and Harper, D., 1998. Palaeoecology: Ecosystems, environments and evolution. CRC Press.

You don't need to learn this, but it might be useful to you to give them a read to get a better idea of the differences between these assemblages.

Brackish Lagoonal Environments

Context	Commonly associated with terrestrial, barrier bar, estuarine, marsh or shallow marine shoreface facies.
Lithology	Typically shales though siltstone, sandstones and less commonly coarser grained sediments may be introduced by tidal or storm processes in flood-tidal deltas and washover fans.
Taphonomy	Dispersed in situ or disturbed neighbourhood assemblages, typically as thin shell concentrations. Tidal and storm processes may introduce allochthonous assemblages from shoreface and inner shelf environments.
Taxonomy/Diversity	In situ faunas typically of low diversity; usually ostracodes, bivalves and gastropods.
Abundance	Variable, commonly low in thin shell accumulations, but high in thick, typically monospecific, shell beds.
Ichnology	Imperfectly described; low diversity assemblages of the Psilonichnus, Glossifungites, Cruziana and Zoophycos ichnofacies may each occur depending on energy and salinity levels, grain size, substrate consistency and specific depositional environment within a lagoon.

Shoreface Environments (BA1)

Context	Nearshore and associated beach facies, distinguished from inner shelf deposits by generally having only rare mudstones interbedded with sandstones. Shoreface facies commonly cap upward-coarsening shallow marine cycles.
Lithology	Typically sandstones with locally developed mudstones. Sandstones exhibit planar- or cross-stratification formed by wave, tidal or wind-forced currents, or hummocky cross-stratification formed by oscillatory or combined flow.
Taphonomy	Allochthonous shell concentrations that may occur as coquinas, on bedding planes or cross-stratified foresets.
Taxonomy/Diversity	Palaeozoic assemblages characterized mainly by brachiopods with more rarely bivalves and gastropods. Mesozoic/Cenozoic assemblages characterized by varied bivalves (including deep burrowers and attached forms) and gastropods. Taxa affected by substrate mobility (e.g. Corals) are rare. In situ faunas rare. Diversity, though still generally low, can be elevated by introduction of allochthonous faunas by storm, tidal and wave activity.
Abundance	Generally low in Palaeozoic rocks, but Cenozoic strata typically possess more abundant remains. In more subdued shoreface environments shells may be relatively common in coquinas.
Ichnology	Typically Skolithos, more rarely Psilonichnus and Cruziana ichnofacies depending on substrate mobility and subtle gradients in hydrological sedimentological and ecological parameters. Diversity typically low.

Inner (shallow) Shelf Environments (BA2)

Context	Facies subject to frequent storm waves and tidal processes, commonly occurring below shoreface sandstones and above mid-shelf sequences in coarsening-upward cycles.
Lithology	Sandstones dominate, but may occur in equal abundance with interbedded shales. Storm-influenced facies exhibit hummocky cross-stratification; tidal facies may exhibit herringbone cross-stratification, sigmoidal cross-stratification or mud drapes.
Taphonomy	Allochthonous or disturbed neighbourhood assemblages at the base of storm sandstones, typically as coquinas. Tidally influenced sandstones commonly exhibit transported assemblages or shell lags distributed along foresets. Shales possess disarticulated and dispersed shells and bedding plane assemblages. In situ faunas rare or absent.
Taxonomy/Diversity	Palaeozoic strata dominated by moderately but variably diverse assemblages of brachiopods, particularly orthoids and strophomenoids: Mesozoic/Cenozoic strata typically possess variable infaunal and epifaunal bivalves. Representatives of other benthic macroinvertebrates may occur, sometimes in abundance.
Abundance	Generally moderate, but high in coquinas. Faunas can, however, be generally sparse where a freshwater influence is established, as, for example, in inner shelf environments in front of deltas.
Ichnology	Typically moderate to high diversity assemblages of the Cruziana and/or Skolithos ichnofacies. Mudstones commonly intensely bioturbated and possess trace fossils typical of the Cruziana ichnofacies: associated sandstones contain representatives of the Skolithos ichnofacies providing substrate mobility does not result in their destruction.

Middle Shelf Environments (BA3 and BA4)

Context	Commonly form portions of upward-coarsening sequences, but may also form part of a predominantly mudstone sequence. Below fair weather wave base, above storm wave base.
Lithology	Mudstones, typically intensely bioturbated, and interbedded sandstone tempestites with hummocky cross-stratification are common.
Taphonomy	Mudstones may contain in situ clumped or dispersed shells that are still commonly articulated, or as thin stringers or locally reworked disturbed neighbourhood assemblages. Sandstones commonly contain allochthonous lag assemblages or coquinas that are taxonomically similar or dissimilar to those assemblages within the associated mudstones.
Taxonomy/Diversity	Palaeozoic strata possess moderate to high diversity assemblages dominated by brachiopods represented by several orders. Crinoids, bryozoans, corals, trilobites and gastropods also common. Mesozoic/Cenozoic strata dominated by varied infaunal and epifaunal bivalve assemblages with gastropods, echinoderms, bryozoans and less commonly brachiopods also present.
Abundance	Generally high, decreasing with depth.
Ichnology	Similar to inner shelf environments with high diversity assemblages typical of the Arenicolites ichnofacies in sandstones, typically as opportunists following storm activity, and intense bioturbation by members of the Cruziana ichnofacies in associated mudstones.

Outer (deep) shelf environments (BA5)

Context	Mudrock-dominated sequences in association with shelf or slope/basin environments. Mainly below effective storm wave base, though extreme storms have disturbed shells.
Lithology	Bioturbated mudstones with uncommon, and where present typically thin, distal siltstone or sandstone tempestites.
Taphonomy	In situ dispersed, articulated faunas predominate. Thin stringers and bedding plane assemblages also common: disturbed neighbourhood assemblages may occur. Distal tempestites may contain allochthonous shells. though not commonly.
Taxonomy/Diversity	Palaeozoic strata dominated by brachiopods and trilobites: Mesozoic/Cenozoic strata by bivalves, particularly infaunal species - nuculoids are very common. Other groups also occur but in lower numbers. Pelagic forms eg. graptolites (Palaeozoic), ammonites, belemnites (Mesozoic) also commonly present. Diversity variable depending on parameters such as nutrients, oxygen levels, etc., but can be high, then typically markedly decreases at the shelf edge.
Abundance	Typically low.
Ichnology	Discrete ichnotaxa commonly difficult to recognise as a result of intense bioturbation. Representatives of Cruziana, Zoophycos or rarely Nereites ichnofacies may predominate depending on specific environmental conditions. Bioturbation intense though diversity commonly low to moderate.

Slope and Basin (BA6 and below)

Context	Mudrock-dominated sequences with associated sediment gravity flows particularly, but not exclusively, turbidites. Submarine canyons and associated fans commonly occur in association with slope and continental rise sequences. Contourites also common on slope and continental rise environments.
Lithology	Pelagic and hemipelagic mudstones, turbiditic sandstones, and siltstones. Canyons and fans typically possess coarser grained lithofacies.
Taphonomy	Autochthonous faunas, typically dispersed and articulated, in pelagic/hemipelagic mudstones. Allochthonous faunas introduced particularly by turbidity currents.
Taxonomy/Diversity	Dominated by pelagic macroinvertebrates (eg. Palaeozoic - trilobites, graptolites, nautiloids; Mesozoic - ammonites, belemnites). In situ forms include Palaeozoic trilobites, hyolithids, etc. and Mesozoic/Cenozoic bivalves, gastropods and crinoids. Other groups may occur but are uncommon. Diversity is low.
Abundance	Very low, but can be higher in sediment gravity flow deposits.
Ichnology	Variable, with representatives of the Skolithos, Arenicolites and/or Glossifungites ichnofacies commonly occurring in association with well-oxygenated submarine canyons and fans; Zoophycos ichnofacies with slopes with restricted circulation and low oxygen levels and the Nereites ichnofacies in more stable, classical flysch-like settings in generally quiet, but oxygenated waters.

6 – Large scale trends

Let's finish by digging a tiny bit further into some cutting edge studies that use a quantitative approach to try and remove biases from the fossil record, and look at biodiversity and ecology in deep time.

Summary

There are a number of biases that we need to be aware of: we shouldn't just assume that number of fossils species is strongly related to the true biodiversity at the time those fossils were deposited.
Using large databases, we can correct for biases.
As an example, doing so for marine environments suggests that biodiversity does not continually increase to the present (it may rather reflect the prevalence of reef ecosystems).
We can also use these approaches to understand how species respond to changes in climate.
In the latest Carboniferous, aridification reduced diversity, but increased cosmopolitanism (i.e. species became more widespread).
These insights help us understand the impact that current environmental changes might have.

Bonus stuff!

As I said in the last video, I think palaeoecology, especially the computational analyses in section 6, is a fast developing and super exciting field. Here are some bonus bits if you want to read more about the latest in palaeoecology!

Those super cool papers

Let's start with links to the two papers that I used as examples. The marine biodiversity study – from a team of super talented palaeoecologists – can be found here:.

Close, R.A., Benson, R.B., Saupe, E.E., Clapham, M.E. and Butler, R.J., 2020. The spatial structure of Phanerozoic marine animal diversity. Science, 368(6489), pp.420-424.

And here is the second, crazy cool, study. Also from a gifted bunch of palaeo people!

Dunne, E.M., Close, R.A., Button, D.J., Brocklehurst, N., Cashmore, D.D., Lloyd, G.T. and Butler, R.J., 2018. Diversity change during the rise of tetrapods and the impact of the 'Carboniferous rainforest collapse'. Proceedings of the Royal Society B: Biological Sciences, 285(1872), p.20172730.

Want to do some analysis yourself?

Computational palaeoecology is developing fast. And there's nothing like actually doing an analysis to get a feel for a field. If, like me, you like fiddling with code, you may want to give an analysis a shot.

If you do, then look no further. Below I link to a workshop for the Progressive Palaeontology 2020 student conference that was developed and then kindly released to the public by three colleagues, Bethany Allen, Alex Dunhill and Graeme Lloyd from the University of Leeds:

Sampling Bias in the Fossil Record: A workshop developed for Progressive Palaeontology 2020.

The above link includes all the code you need (you'll need to install R). I've put the introductory video below, so you can watch this first if this is all of interest to you. It covers the sources of sampling bias in the fossil record.

And this, second video, provides an overview of what sampling bias means for palaeontologists.

As a general note, I am not just very grateful for my colleagues who made this workshop and released it for free, but am very jealous of... you! Back when I was training as a palaeontologist, resources like this were rather harder to come by. I think it's fair to say that fewer palaeontologists, even a decade ago, used computer-based approaches. That you can do this sort of analysis on your own PC from anywhere in the world is... just super cool!