Technical terms

(< 2 Ma): geohistorical records

used to

(a) define baselines to compare conditions before and after disturbance,

(b) examine the response of species and ecosystems to recent natural and anthropogenic perturbations,

(c) develop a narrative of the historical range of variability,

(d) set realistic targets for restoration,

(e) differentiate between anthropogenic and nonanthropogenic change,

(f) recognize ecological legacies that can be explained only by events or conditions that are not present in the system today

The ‘BAM diagram’ (= simplified framework for understanding where species will and will not be distributed). Distributions of species !responding to 3 sets of factors: the abiotic niche (A) and the biotic niche (B) (~ fundamental ecological niche) !realized ecological niche (A – B = potential distribution). Further modification to distributional potential = access (= M for ‘movement’)

Paradoxically, despite the growth in marine and terrestrial protected areas globally, many species remain threatened and continue to decline. Attempts to conserve species in suboptimal habitats may in part explain this Protected Areas Paradox. Species confined to suboptimal habitats are recognized as refugee species. They may be identified as (a) having suffered historical range contractions, such that (b) they now occur in limited, less diverse habitats (compared to previous ranges) at (c) low densities, and with (d) anomalous resource (diet, habitat) use compared to historical records and that of close relatives. Conservation efforts of refugee species yield poor outcomes as long as the species is confined to suboptimal habitats where they suffer lower densities and fitness. One possible explanation for the Protected Area Paradox lies in the bias of the location of protected areas to less productive habitats that are less attractive to humans. The global bias of conservation areas to “high and steep” habitats (Joppa & Pfaff, 2009) suggests this phenomenon is widespread. Mmany of the species in such protected areas are refugee species.

In paleoecology and ecological forecasting, a no-analog community or climate is one that is compositionally different from a (typically modern) baseline for measurement. Alternative naming conventions to describe no-analog communities and climates may include novel, emerging, mosaic, disharmonious and intermingled

suhlen

global wear of tooth, valley in tooth, sharp/blunt

• Gras will wear down tooth

- Identification of taxa: DNA can help differentiate between (extinct) species that were originally thought to be the same (pseudo extinctions: or the other way around)

- Helps understand species dispersal over time

- If de-extinction/rebreeding is done: check, whether necessary adaptions are existing

o   Only possible if original DNA is known

- Sometimes DNA is found but no bones etc.

o   Maybe carcasses are defrosting and leak DNA

- DNA shows genetic diversity within a taxon (different likelihoods: extinction, repopulation with low genetic diversity)

- Shows hybridization (a lot of hybridization)

-          Macrofossils: Bones/shells, leaves, seeds, wood, macro charcoal

-          Microfossils: Animal remnants (small teeth (types of food), small shells, hair), Leave remnants (trichoms, seeds, epidermis etc.), phytoliths, wood fragments (environmental conditions), pollen, spores

-          Molecular fossils: Isotopic signature biomarkers

-          Sedimentary

-          Geochemical

o   some descendants and their common ancestor

§  Reptiles without birds

§  Lizards without snakes

Eine Kryptospezies oder auch kryptische Art ist in der Biologie eine morphologisch nicht unterscheidbare Gruppe von Lebewesen, bei der eine geschlechtliche Fortpflanzung mit anderen zur gleichen Art gerechneten Individuen jedoch nicht möglich ist oder nur nicht fortpflanzungsfähige Nachkommen erzeugt

one ancestor and its descendants (only natural structure)

parsimony is defined as the principle that, out of all possible explanations for a phenomenon, the simplest of the set is most likely to be correct. Parsimony is an important idea in the discipline of phylogeny, the study of the evolutionary history and relationships among organisms.

In phylogenetics, an autapomorphy is a distinctive feature, known as a derived trait, that is unique to a given taxon. That is, it is found only in one taxon, but not found in any others or outgroup taxa, not even those most closely related to the focal taxon (which may be a species, family or in general any clade).[2] It can therefore be considered an apomorphy in relation to a single taxon.

Mesowear is a widely applied tooth wear technique that can be used to infer a herbivore’s diet by scoring the height and sharpness of molar tooth cusps with the naked eye. Established as a fast and efficient tool for paleodiet reconstruction, the technique has seen multiple adaptations, simplifications, and extensions since its establishment, which have become complex to follow. The present study reviews all successive changes and adaptations to the mesowear technique in detail, providing a template for the application of each technique to the research question at hand. In addition, the array of species to which mesowear has been applied, along with the equivalent recorded diets have been compiled here in a large dataset. This review provides an insight into the metrics related to mesowear publication since its establishment. The large dataset overviews whether the species to which the various techniques of mesowear are applied are extant or extinct, their phylogenetic classification, their assigned diets and diet stability between studies, as a resource for future research on the topic.

Estimating divergence time of clades by looking at amino acid differences: neutral mutations crop up at random intervals, but if they are observed over a long time period the rate of change will appear to be approximately constant. Neutral drift will drive evolution at a fairly constant rate.

o   Alluvial sediments of the Ammer valley contain information about ecosystem dynamics

o   Pollen abundance over time (good indicator for climate conditions)

o   Barely ever decomposed

o   How to extract organic material from soil: mixing with high viscose fluid (or acid) lighter particles rise

§  Centrifuge

o   Classifying pollen: 1. size, 2. Shape, 3. Aperture (amount shape, size, arrangement), 4. surface structure

§  Spores usually bigger and thicker membranes

§  Polyades, vesiculate

In phylogenetics, a plesiomorphy ("near form") and symplesiomorphy are synonyms for an ancestral character shared by all members of a clade, which does not distinguish the clade from other clades.

Plesiomorphy, symplesiomorphy, apomorphy, and synapomorphy, all mean a trait shared between species because they share an ancestral species.

In phylogenetics, an apomorphy (or derived trait) is a novel character or character state that has evolved from its ancestral form (or plesiomorphy). A synapomorphy is an apomorphy shared by two or more taxa and is therefore hypothesized to have evolved in their most recent common ancestor. In cladistics, synapomorphy implies homology.

o   A Representative Concentration Pathway (RCP) is a greenhouse gas concentration (not emissions) trajectory adopted by the IPCC. Four pathways were used for climate modeling and research for the IPCC Fifth Assessment Report (AR5) in 2014. The pathways describe different climate change scenarios, all of which are considered possible depending on the amount of greenhouse gases (GHG) emitted in the years to come. The RCPs – originally RCP2.6, RCP4.5, RCP6, and RCP8.5 – are labelled after a possible range of radiative forcing values in the year 2100 (2.6, 4.5, 6, and 8.5 W/m2, respectively)

o   Low (RCP2.5) intermediate (RCP4.5 and RCP 6.0) and high (RCP8.5) emissions scenarios

not more existing individuals of the species

• a statistical calculation determining probable past conditions (as of marine wave characteristics at a given place and time

• to test (a mathematical model) by observing whether it would have correctly predicted a historical event

A living fossil is an extant taxon that phenotypically resembles related species known only from the fossil record. To be considered a living fossil, the fossil species must be old relative to the time of origin of the extant clade. Living fossils commonly are of species-poor lineages, but they need not be. While the body plan of a living fossil remains superficially similar, it is never the same species as the remote relatives it resembles, because genetic drift would inevitably change its chromosomal structure.

Living fossils exhibit stasis (also called "bradytely") over geologically long time scales. Popular literature may wrongly claim that a "living fossil" has undergone no significant evolution since fossil times, with practically no molecular evolution or morphological changes. Scientific investigations have repeatedly discredited such claims

• Mechanistic: Models created using data of species physiology to develop of a model of the environmental conditions under which the species can exist: model of the fundamental niche

• modelling climate scenarios to understand change dispersal

evolutionary development of species

o   Fossil data are scarce

o   Fossil record often poorly dated

o   Paleontological databases are incomplete and inefficient

o   Niche shift/stability over time remains difficult due to test or data missing

o   Do fossil data include aspects of the niche that have been lost during the past OR being currently unoccupied?

o   Models not accounting for biotic interactions

o   Past climate inference: reliable?

o   Cryptic species:

• Almost unable to differ cryptic species as fossils

• May differ ecologically

• by comparing created models with dispersal of fossil find by overlapping

• Niche overlap analysis

-         ENM predictions + land use >plan large-scale corridors between fragmented suitable habitats

-         Hard to compare current climate change because it is faster than ever

-         Isolated protected areas prevent movement of species: need of corridors

o   Restriction of models

fossilized feces

• Pollen and genetic material can be found within the poo

• Lot of pollen might indicate a pollination function

• Online databases Global Biodiversity Information Facility-GBIF

• Fossil records: Paleobiology Database

• Mapped on grid cells (e.g., 0.5 resolution ~55 × 55 km at the equator)

• Climate data: simulations from combined atmosphere ocean general circulation models AOGCMs

o   ecoclimate database:

§  pre-processed climate layers w/ 19 bioclimatic variables at 0.5° resolution

§  for important periods of past (Last Glacial Maximum—LGM and mid-Holocene), present (pre-industrial) and future

§  RCPs

theoretical construct of a number of vectors defining a niche in which a species is able to survive

“area presenting appropriate conditions of abiotic and biotic conditions (=potential distribution)”

o   Using DNA to estimate time difference between species and clades

o   Helps to figure out divergence dates

Maintnance of particular ecosystem states, species or population sizes (taxon-based, historical)

(= artifact of time averaging, postmortem mixture of species with different ecological requirements)

·         Sometimes hard to distinguish different times of fossils

a part of the fundamental niche where the species is actually distributed (abiotic and biotic conditions are fulfilled and accessible for dispersal)

(> 2 Ma): archive or repeated

natural experiments

(a) Analysis of biotic responses to system perturbations of diverse kinds and magnitudes, some of which approximate present-day disturbances of those predicted for the near future (e.g. climate warming, ocean acidification)

(b) Also permits testing of biotic responses under a broader array of conditions than is available in the modern world or its recent past.

(c) In particular, observation of consistent patterns involving now-extinct species at remote periods in the past can strengthen the ecological theory underlying conservation practice

refugee species are defined as those that can no longer access optimal habitat, but are confined to suboptimal habitats, with consequences of decreased fitness and density, and attendant conservation risks.

replacement species, similar/same niche but other species

o   Risk of invasive species

species is extinct in the wild (not ex situ)

Keystone species play a critical role in maintaining the structure of an ecological community, affecting many other organisms in an ecosystem and helping to determine the types and numbers of various other species in the community. Without keystone species, the ecosystem would be dramatically different or cease to exist altogether. Some keystone species, such as the wolf, are also apex predators.

Examples:

o   Animals as seed disperser

o   Plants change albedo by reflecting/absorbing sunlight

o   Methane changes climate

o   BBAAAAM everything is effected

Conservation Paleoecology is a rapidly developing socially relevant field that uses information from geohistorical records to adress current problems in the conservation and restoration of biodiversity and ecosystem services.

eine morphologisch nicht unterscheidbare Gruppe (Population) von Lebewesen, bei der eine geschlechtliche Fortpflanzung mit anderen (bisher) zur gleichen Art gerechneten Individuen jedoch nicht möglich ist oder nur nicht fortpflanzungsfähige Nachkommen

Maintnance of progress, functions, and resilience (taxon-free, novel)

Climate envelope models describe the climate where a species currently lives (its climate "envelope"), and then map the geographic shift of that envelope under climate change. Because we can't know for certain how climate will change in the future, multiple climate change scenarios are used in these models.

• Comparison of the variety of DNA sequences available from sediment and coprolites versus bone

• allowes distinction of species distribution

• detecting pseudo extinctions

• tracking evolutionary processes (divergence of populations)

• detection of hybridization

->short-term:

• change of geographic distribution

• Extinctions

• Shift of biomes

• Formation of no-analog biomes (“novel ecosystems”)

-> long-term:

• Evolutionary change, new species (if sufficient genetic diversity)

• a) nucleus (nuclear DNA or nDNA)

• b) mitochondrion (mitochondrial DNA or mtDNA, inherited from the mother)

• (c) in chloroplast (in plants)

• CO2-Levels

• warming

• invasive species

• hybridization

• extinction

• human control of food webs

The maximum possible distribution of a species in the environment.

• oldest DNA from mammoths 1.2 Ma in permafrost

dramatic decrease in genetic diversity through the extinction of many genetic lineages as a result of a significant reduction in the size of a population

Re-breeding species to be genetically close to an extinct ancestor

- Mammoth-re-breeding-program

Cloning

o   Introduction of original DNA into reproductive cells

Genome editing

o   Trying to recreate original features by breeding

Why: restoration of ecological functions

model the observed distribution of a species as a function of environmental conditions. Model of the realized niche

• georeferenced primary occurrence data for species

• in combination with digital maps representing environmental parameters

• prediction of species distribution using modelled climate scenarios

• oral histories and other sources

• ecosystem baselines

• climate phenomena and information on natural cycles

• holistic ecosystem assessments and management information

• sensor readings and other info

• direct seasonal-to-daily measurements of ecological and climate variables

• written and image records

• Qualitative information on climate cycles

• often focused on economically relevant natural resources

Proxy data is data that paleoclimatologists gather from natural recorders of climate variability, e.g., tree rings, ice cores, fossil pollen, ocean sediments, coral and historical data. By analyzing records taken from these and other proxy sources, scientists can extend our understanding of climate far beyond the 140-year instrumental record. Proxies are natural records of past climate variations, such as tree rings, ice cores, sediment layers, and coral reefs, which can provide valuable insights into historical climate patterns and fluctuations. These proxy records are essential for understanding natural climate variability, identifying long-term trends, and contextualizing the current climate change.

• somatic cells are harvested from a living organism and cultured in vitro.

• Nuclei are removed from these cultured cells

• At the same time, egg cells are harvested from a closely related species and enucleated.

• The nucleus from the somatic cell is fused to the enucleated egg

• the cell begins to divide

• The embryo is implanted into a surrogate maternal host, which

• gives birth to a genetic copy of the somatic cell harvested in 1 individual

mitochondriale DNA

Während in der Genetik meist die Untersuchung und Wirkung einzelner Gene im Vordergrund steht, werden in der Genomik (engl. genomics) sämtliche DNA-Sequenzen des gesamten Genoms eines bestimmten Organismus analysiert. Dabei wird die DNA innerhalb einer Zelle, eines Gewebes oder eines Organismus vollständig erfasst und untersucht.

• can be sampled from biological archives, such as sediment cores within lake and marine sediments.

• providing continuous data on biodiversity patterns between the present day and the past

Als Haplotyp, eine Abkürzung von „haploider Genotyp“, wird eine Variante einer Nukleotidsequenz auf ein und demselben Chromosom im Genom eines Lebewesens bezeichnet. Ein bestimmter Haplotyp kann individuen-, populations- oder auch artspezifisch sein.

the higher the density, the cooler the climate (less amtosheric CO2)

De-extinction (also known as resurrection biology, or species revivalism) is the process of generating an organism that either resembles or is an extinct species. There are several ways to carry out the process of de-extinction.

How?

- Back breeding (only based on phenotype)

- Cloning (needs ancient DNA)

- Genome editing (needs ancient DNA)

Why?

- Restoration of ecological functions?

Example: Quagga, (Aurochs), Pinta Island Tortoise

• Occur in almost all sediments in high quantities

• Even small sample volumes contain microfossils in such an abundance that dating and paleoenvironmental studies are possible

• Microfossils often are adequate proxies and leading fossils ( Leitfossil

• Far reaching distribution > Parallelizing is possible

• Occurrence in high abundances

• High preservation potential

• Easy to identify

• Small stratigraphic range

Überdachung

• Pollen and spores have an exine out of sporopollenin, which makes them resistant against decomposition

• Preserved in many sediments since the Precambrian. Present in all plant groups!

• DNA is extracted from the remains of an extinct species and used to sequence and assemble a genome, which is used to identify sequence differences between a closely related living species.

• Cells are harvested from that close living relative

• cultured in vitro.

• Genome editing is used to change the genome sequence of that living cell so that it more closely resembles that of the extinct species. (v–xi) are the same as cloning

• fossil and archaeological information

• ecoevolutionary information from body trace, and chemical fossils

• climate proxy records

• extremly long term Earth system information

demographic changes, by adding up 'gains' (births and immigration) and 'losses' (deaths and emigration)

Chronocline, phylogenetische Reihe, bei der sich ein allmählicher Formenwandel nachweisen läßt.

little balloons on pollen

often found on Gymnosperm-pollen

multiple pollen packed together

No-analog communities are defined by the existence of extant species in groupings that are not currently seen in modern biomes, or populations that have history of species assemblages that are no longer seen in the modern world. Formation of no-analog communities can be due to multiple factors, including climate conditions, environmental changes, human action, disease or species interactions. Migrations of species causes displacement and colonization into areas that may have been outside of what was known to be their fundamental niche, such as northern species moving south and mountain fauna being removed entirely or isolated to the peaks

predicting the geographical distribution of species across space and time.

• pollen with one “hole” found on Poaceae

• pollen with rough, sharp/spiky surface

• for example Fagus

• pollen with three holes (pores)

• for example betula

made up of sand and earth left by rivers, floods

Pseudoextinction (or phyletic extinction) of a species occurs when all members of the species are extinct, but members of a daughter species remain alive. The term pseudoextinction refers to the evolution of a species into a new form, with the resultant disappearance of the ancestral form. Pseudoextinction results in the relationship between ancestor and descendant still existing even though the ancestor species no longer exists.

The classic example is that of the non-avian dinosaurs. While the non-avian dinosaurs of the Mesozoic died out, their descendants, birds, live on today. Many other families of bird-like dinosaurs also died out as the heirs of the dinosaurs continued to evolve, but because birds continue to thrive in the world today their ancestors are only pseudoextinct.

Pollen

• Apertures

• Thin walled

Spores

• fissures, no apertures

• thick walled

• pollen with three furrows

• for example Quercus

• pollen that look like those spiky massage-balls

• for example Asteraceae

• Positive: pollen with little strings on the surface (for example Fraxinus)

• negative: pollen with little holes on the surface (not pores)

• pollen with multiple (5+?) furrows/colpi

• for example Galium

• pollen with multiple holes (6+ i guess, pores)

• for example Alnus

• pollen with a rough, rock-like texture on the surface

• for example hedera helix

Taphonomy is now most widely defined as the study of what happens to objects after they leave the biosphere (living contexts), enter the lithosphere (buried contexts), and are subsequently recovered and studied.

• holes (pores) or furrows (colpi) in pollen

• DNA is the least stable biomarker :(

• Ancient DNA is heavily fragmented and massively contaminated :(

  • Paleogenetic analysis needs very strict protocols to remove ancient contamination and avoid modern contamination

  • The time depth of paleogenetic research is limited to < 1 Ma (no Jurassic Park)

• individuals are selected for breeding based on phenotype.

• After many generations of selective breeding, the extinct phenotype is resurrected.

Cellular units for reproduction and dispersion of land plants

• spores evolved before pollen

A polyphyletic group is an assemblage that includes organisms with mixed evolutionary origin but does not include their most recent common ancestor. The term is often applied to groups that share similar features known as homoplasies, which are explained as a result of convergent evolution.

In phylogenetics, a plesiomorphy ("near form") and symplesiomorphy are synonyms for an ancestral character shared by all members of a clade, which does not distinguish the clade from other clades. Plesiomorphy, symplesiomorphy, apomorphy, and synapomorphy, all mean a trait shared between species because they share an ancestral species

Monophyletic groups one ancestor and its descendants (only natural structure)

are rigid, microscopic structures made of silica, found in some plant tissues and persisting after the decay of the plant. These plants take up silica from the soil, whereupon it is deposited within different intracellular and extracellular structures of the plant.