Documenting whether a biotic taxon is native or alien to an ecosystem has theoretical value for ecological and evolutionary studies, and has practical value because it can potentially identify a taxon as a desirable component of an ecosystem or target it for removal.
It is not always clear if a species discovered in a new range is actually really alien or even invasive. We have to rely on observational records but these are not always available, often sketchy and by no means a source of accurate information on past biogeography. However, we need to be able to react swiftly to new invasions of non-native species but it is not always clear where they've originated or if they had been in the region long before but not encountered. A good example is the invasion of the Great Lakes by the sea lamprey (Petromyzon marinus) which is usually considered an invader introduced from the Atlantic Ocean. This species clearly threatens a lot of the other native species in the lakes and management programs are long underway. However, results from some studies indicate that the sea lampreys are either natives of Lake Ontario or what we call an invasion is actually part of a natural migration from the Saint Lawrence River.
A new study just published in PLoS ONE focuses on the case of the Yellow Perch (Perca flavescens) which is thought to be introduced to the Adirondack uplands during the last century or so. This region in the northeastern part of the state of New York in the U.S. comprises of about 3000 lakes and ponds and the assumed alien status influences fisheries management policy. Yellow perch are widely distributed in the northeastern U.S. and eastern Canada but historical records did not document any native occurrence in the Adirondack region which led to the believe that the species is invasive.
The colleagues from the Paul Smith's College in New York state tried to trace the history of yellow perch in the region by analyzing eDNA specific for yellow perch in sediment core samples. Such eDNA can remain suspended in lakes long after being shed or following decomposition, and has been shown to persist as "paleo-DNA" for centuries to millennia in aquatic sediments.
A 124 base pair portion of the mitochondrial (mt) DNA cytochrome oxidase subunit 1 (CO1) gene was chosen as a species-specific barcode marker for yellow perch . This traditional DNA barcode region is approximately 650 base pairs, but a smaller amplicon size was selected because DNA degradation may have interfered with detection of the full-length barcode region and because small amplicons within the CO1 gene have been shown to be effective in species identification of fishes.
Their findings clearly show that this species is not an invader but a fish with a rather long regional history:
Yellow perch DNA in a 2200-year sediment record reveals a long-term native status for these supposedly alien fish and challenges assumptions that they necessarily exclude native trout from upland lakes.
In light of the historical and paleo-DNA evidence which document the native status of yellow perch in the Adirondack uplands as well as the unique genetic composition of subpopulations of this species in the adjacent Champlain basin we suggest that a more nuanced approach to the management and conservation of this species may be advisable. Similar use of paleo-DNA holds great potential to address other unresolved questions in aquatic ecology as well, including the evolution and dispersal of taxa, the relative effects of "top-down" and "bottom-up" trophic cascades on lake productivity, and the contribution of acid deposition to the distribution of fishless lakes in acid-sensitive regions.