Genetics & Phylogenetics - A Summary of Workshop Discussions

The liveliest sessions at these workshops revolved around the complexities of taxonomic harmonization and genetics,  topics which are strongly intertwined.  Here, the workshop discussions focused on future research initiatives and also challenges faced by geneticists studying ostracodes.

A.  Special challenges faced by geneticists when studying ostracodes:

1.  We need an established, standard protocol for studying the same individuals for genetics and morphometrics, especially if the community decides to pursue analyses of variation in paleo-indicator species.  For example, vouchers must be saved and curated.   It was pointed out that it is now possible for DNA and morphological characters to be measured from the same specimen.

2.  Some morphology is plastic, and is determined by environmental factors more than by inherited, genetic factors.  Differences need to be sorted out.  For example, is there a standard morphological feature that might act like a "barcode" (Todd Oakley raised this issue).  Are morphometric techniques a possible avenue here?

3.  Some taxa have no good morphological characters, yet characterizing morphology is critical because we cannot obtain molecular data from the fossil record.  Although soft tissue is theoretically a source of DNA in samples as old as 100,000 years, the actual recovery of fossil ostracodes is typically confined to the calcite shells.  We need to choose our taxa wisely for these kinds of analyses.

4.  Some research questions may best be answered by barcode analyses, which can identify differences present in single populations.  Other questions require full genetic and morphologic analyses, often with little prior genetic work available. 

 B. A basic question (raised by Todd Oakley) that is fundamental in developing relevant research initiatives is "How do morphological and molecular variation relate to spatial and ecological variation?"  This complex question has a rich potential research field.  An example of research focused on this question is that of the SexAsex project which devoted many person-years to trying to answer this for just one species, Eucypris virens.  What can we learn from this project and use to advance our knowledge of this variation in other taxa?  One answer to this question seems to be that morphological and molecular variation relate to spatial and ecological variation in ways that are complex and often related to historical contingency, i.e. how the components of a population got there and where they came from, over various timescales including the geological.   A core assumption of the scientific community in using tolerance ranges of living species as proxies for past conditions is that variation is negligible over Quaternary time, and that evolution does not have a great impact on the time scale in question.  Recent publications reporting on other groups (including humans) indicate that evolutionary drivers are indeed functioning on Quaternary and Holocene time scales.    What then, of the ostracodes? 

C.  Future Research Initiatives:

1.  Understanding temporal and spatial variability in populations:  The ostracodology community could create a database of DNA and "morphological barcodes" for key paleoindicator species, based on 10's to 100's of individuals.  The database could be equipped with search tools, such that any researcher could obtain the DNA or "morphological barcode" for a new individual, and find the closest match within the database.  The ecological atributes of the closest match in the database could be weighted more heavily in paleoclimate inferences. 

2.  A pilot study combining taxonomic harmonization and genetics: One species (or species complex) could be selected with variable morphology across the geographic range, and a second species selected with little variation across the geographical range.  Criteria for choosing these species would include its usefulness as a paleoindicator or other tool, its availability and reliability for sampling across a wide geographic range.  Examples included Candona candida and Cypria ophthalmica/turneri.

3.  Targeting ostracodes for full genome sequencing:  Careful selection of key species with value in two or more research areas (such as biogeography, paleoclimate, evolutionary ecology...) should be carried out for full genome sequencing.  Species considered as good candidates for full genome sequencing should be culturable and reproduce easily in the lab, with short generation times.  There should be extensive literature, including ecological and paleoecological studies on the species or related species.  Clear taxonomy would be advantageous, and a larger species would be easier to work with.  Small genome size would make the sequencing less expensive.  Valuable species mentioned include: Cypria, Eucypris virens (although few fossils), Candona candida, Macrocypris, Cytherissa lacustris (currently under study by Isa Schön and colleagues), Darwinula (but a long generation time) and Limnocythere inopinata.  A whole genus or clade could make a valuable target.  The genus Candona was mentioned as a good candidate, with useful, well known species such as candida, neglecta, levanderi, and acutula.   

4.  A DNA barcoding pilot study is needed to confirm whether standard DNA barcoding loci, such as mitochondrial CO1 regions, can identify within-species variation, which would be very useful in research questions regarding cosmopolitan vs endemic populations.  In Charlotte, North Carolina, Renate Matzke-Karasz gave a presentation on the results of a study using barcoding to identify different populations of particular species inhabiting a botanical water garden.  She was able to show how a single species present in the water garden was composed of members from different populations, probably originating from the plant specimen sources, by using CO1 barcoding.  Such studies could be very useful in understanding species migration and invasion. 

5.  Investigating the deep time perspective as it influences Quaternary species distributions- Questions concerning how and when groundwater systems, or freshwater surface water bodies were invaded during evolution, and what genetic and morphological changes were associated with these habitat shifts, may be answered by the deep time perspective.  Did past key events such as these correspond with important events in Earth history?  Todd Oakley suggested that an interesting approach would be to examine species that have transitioned from surface to groundwater habitats, and Claude Meisch then mentioned that Cypria ophthalmica and C. caverna are probably closely related species that would serve in such a study.  It was suggested (by Dave Horne) that the Limnocytheridae could be a valuable study group, with its rich fossil record, ecological diversity and global distribution, shells with useful morphological features to study, good documentation of modern diversity, and transitions to ground water (e.g. in the Timiriaseviinae).     

 

D. Recommendations

1.  We need to attract geneticists as collaborators in ostracode research!  There are many interesting problems with significant potential impact to the fields of evolutionary development, evolutionary ecology, phylogeography, and phylogenetics.

2.  Develop and agree upon a standard protocol for sampling DNA and studying the morphology of a single specimen.

3.  Begin with particular species with known trans-regional and hemispheric distributions, and develop in-tandem studies of DNA and morphology

4.  Upload genetic data to appropriate databases. The community needs to build a library of DNA data in order to extract important patterns with environmental and ecological processes.

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