The Effects of Paleoclimatic Events on Mediterranean Trout: Preliminary Evidences from Ancient DNA

Abstract

In this pilot study for the first time, ancient DNA has been extracted from bone remains of Salmo trutta. These samples were from a stratigraphic succession located in a coastal cave of Calabria (southern Italy) inhabited by humans from upper Palaeolithic to historical times. Seven pairs of primers were used to PCR-amplify and sequence from 128 to 410 bp of the mtDNA control region of eleven samples. Three haplotypes were observed: two (ADcs-1 and MEcs-1) already described in rivers from the Italian peninsula; one (ATcs-33) belonging to the southern Atlantic clade of the AT Salmo trutta mtDNA lineage (sensu Bernatchez). The prehistoric occurrence of this latter haplotype in the water courses of the Italian peninsula has been detected for the first time in this study. Finally, we observed a correspondence between frequency of trout remains and variation in haplotype diversity that we related with ecological and demographic changes resulting from a period of rapid cooling known as the Younger Dryas.

Museum samples could help to reconstruct the original distribution of Salmo trutta complex in Italy

“…Several precautions to avoid sample contamination were used as reported in Splendiani et al . (). Genomic DNA was extracted following an ad hoc protocol for formalin‐fixed tissues (Campos & Gilbert, ).…”

“…Six pairs of primers designed by Splendiani et al . () were used to amplify overlapping fragments, ranging in size from 108 to 151 bp (primers included). This region of the mtDNA was chosen as it contains several single nucleotide polymorphism (SNP) diagnostics for the main S. trutta mtDNA lineages initially described by Bernatchez () and successively confirmed by various studies (Cortey et al ., ; Snoj et al ., ; Meraner et al ., ).…”

“…PCRs and sequencing were carried out as described previously by Splendiani et al . (). In all, 378 bp (primer sequences excluded) were sequenced from the 5′ end of the mtDNA control region of 17 museum samples.…”

“…() that proposed a sudden demographic expansion for both lineages. This hypothesis has recently been confirmed by a paleogenetic study carried out on S. trutta bone remains dating back to the Pleistocene–Holocene transition (Splendiani et al ., ).…”

The preservation of ancient DNA in archaeological fish bone

“…Interestingly, multiple studies have reported the successful retrieval of aDNA from archaeological fish bone for a variety of species, locations and age (Oosting et al, 2019). aDNA has been consistently amplified from herring (Speller et al, 2012), Pacific salmon (Grier et al, 2013; Johnson et al, 2018; Royle et al, 2018; Speller et al, 2005; Yang et al, 2004), Atlantic cod (Hutchinson et al, 2015; Ólafsdóttir et al, 2014), sturgeon (Ludwig et al, 2009; Nikulina & Schmölcke, 2016; Pagès et al, 2009), Mediterranean trout (Splendiani et al, 2016), Northern pike (Wooller et al, 2015), and other fish taxa (Arndt et al, 2003; Ciesielski & Makowiecki, 2005; Živaljević et al, 2017), in some cases from bones up to 6,000 yBP or older (Johnson et al, 2018; Nikulina & Schmölcke, 2016; Speller et al, 2012; Splendiani et al, 2016; Wooller et al, 2015; Yang et al, 2004). Fish aDNA has also been successfully amplified in metagenomic analyses using bulk bone approaches, even from warm tropical climates (Grealy et al, 2016).…”