Merge pull request #130 from VilmaPerez/patch-4

Update introduction-to-edna.qmd

Author: jfy133

introduction-to-edna.qmd

@@ -123,7 +123,7 @@ These methods encompass the following approaches:
 2. DNA metabarcoding methods that involve PCR amplification of marker loci, often referred to as "barcodes," coupled with high-throughput sequencing.
 3. Metagenomic strategies centred on untargeted shotgun sequencing of the entire pool of DNA retrieved from sediment.
 4. Hybridization-based target enrichment methods for the recovery of DNA fragments of interest from the sediment metagenome.
-    Hybridization capture involves the use of short RNA probes, often referred to as "baits," which are designed to complement specific DNA sequences of interest, such as taxonomic marker genes.
+    Hybridization capture involves the use of short DNA or RNA probes, often referred to as "baits," which are designed to complement specific DNA sequences of interest, such as taxonomic marker genes.
     These baits can then be employed to selectively extract the target DNA fragments from the DNA extract for subsequent sequencing.
 
 Recovered DNA sequences are then taxonomically and/or functionally annotated using a suite of bioinformatic tools to answer palaeoecological questions.
@@ -208,10 +208,18 @@ Once lake sediments are compacted, vertical pore water movement is minimal, lead
 The use of ancient environmental DNA has enabled the reconstruction of palaeoenvironments, facilitating the detection of hominins and the study of biotic turnovers in ecosystems.
 This has also provided insights into ecosystem restoration targets.
 
-### Palaeoenvironmental reconstruction
+Classical paleoecology has explored biotic responses to environmental change but often fails to capture the full diversity of organisms, their co-occurrences, and interactions.
+Sedimentary ancient DNA provides an opportunity to address this gap by potentially reconstructing ecosystem diversity examining all domains of life at a certain point in time.
+However, integrating traditional proxies into the studies, such as pollen and fossil analyses and archaeological evidence, remains essential, as each proxy provides complementary information, often with minimal overlap.
+Each method is influenced differently by factors such as differences in biomass production, distance from source to deposition, and preservation conditions.
+A combination of DNA and traditional proxies leads to a more robust interpretation of the results.
+
+For example, in a study by [@Parducci2019-bf], past vegetational communities were reconstructed from lake sediments in southern Sweden over the last 15,000 years using shotgun metagenomic analysis of sedimentary DNA alongside pollen and plant macrofossil analyses.
+Each proxy provided unique insights: pollen revealed information about both local and regional vegetation, plant macrofossils reflected local vegetational communities, and eDNA provided strong signals about local plant communities.
+By comparing these proxies, the researchers were able to distinguish plants growing within or close to the lake from those present in the broader region.
+Notably, sedaDNA offered a more robust indication of changes in plant communities compared to the other traditional proxies.
 
-Classical palaeoecology has explored the responses of biota to environmental change, but it has not fully captured the diversity of organisms, their co-occurrences, and interactions.
-SedaDNA offers an opportunity to achieve this, as _theoretically_ allows the reconstruction of an ecosystem diversity across all domains of life.
+### Palaeoenvironmental reconstruction
 
 A good example of this type of this application is the study published by [@Kjaer2022-bf].
 The Late Pliocene and Early Pleistocene epochs (3.6 to 0.8 million years ago) exhibited climates resembling future warming predictions.