<i>trnL</i> outperforms <i>rbcL</i> as a DNA metabarcoding marker when compared with the observed plant component of the diet of wild white-faced capuchins (<i>Cebus capucinus</i>, Primates)

<div><p>DNA metabarcoding is a powerful tool for assessing the diets of wild animals, but there is no clear consensus on which proposed plant barcoding marker is most suitable for dietary analysis. This study compares two DNA plant barcoding markers that are commonly used for dietary analyses from degraded DNA, <i>rbcL</i> and <i>trnL</i>, to detailed dietary observations of wild white-faced capuchins (<i>Cebus capucinus</i>). Observational dietary data and fecal samples (n = 170) were collected for one year from a group of individually recognizable monkeys at La Suerte Biological Field Station, Costa Rica. DNA was extracted and portions of the <i>rbcL</i> and <i>trnL</i> chloroplast were amplified and sequenced on the Illumina MiSeq platform. Sequences were analyzed using <i>obitools</i>. Of the two barcoding markers tested, <i>trnL</i> yielded greater numbers of sequences with equal sequencing effort, higher resolution taxonomic identifications (albeit with a larger reference database), and identified a greater number of families also found in the observed diet. There was no relationship between observed capuchin feeding behavior and dietary composition based on either sequence occurrence or relative abundance of sequences using <i>rbcL</i> as a marker. However, dietary composition based on the relative abundance of <i>trnL</i> sequences was significantly positively associated with the observed percentage of feeding and foraging time capuchins’ spent on each plant species. Additionally, in 35% of cases, the relative abundance of <i>trnL</i> sequences assigned to particular plant families in fecal samples was highly positively correlated with time spent consuming plants from those same families. Our results indicate that <i>trnL</i> is a more robust DNA metabarcoding marker for plant dietary analysis and may potentially be used to quantitatively assess differences in diet within or between species.</p></div

Observed fruit diet based on the percentage of feeding and foraging time spent on each fruit species.

<p>Observed fruit diet based on the percentage of feeding and foraging time spent on each fruit species.</p

Relationship between feeding and foraging time and frequency of occurrence of <i>rbcL</i> and <i>trnL</i> sequences.

<p>Correlations between observed percentage of group feeding and foraging time spent on each plant family in a given month and the frequency of occurrence of <i>rbcL</i> or <i>trnL</i> sequences in the same month.</p

Relationship between feeding and foraging time and relative abundance of <i>trnL</i> sequences.

<p>Correlations between observed percentage of group feeding and foraging time spent on each plant family in a given month and the average relative abundance of <i>trnL</i> sequences for the same month.</p

Comparison of <i>rbcL</i> and <i>trnL</i> sequencing performance, resolution, and accuracy.

<p>Comparison of <i>rbcL</i> and <i>trnL</i> sequencing performance, resolution, and accuracy.</p

Percentage of observed feeding and foraging records assigned to each family of fruit and frequency of occurrence and relative abundance of <i>rbcL</i> and <i>trnL</i> sequences over the course of the entire study period.

<p>Percentage of observed feeding and foraging records assigned to each family of fruit and frequency of occurrence and relative abundance of <i>rbcL</i> and <i>trnL</i> sequences over the course of the entire study period.</p

TMRCA estimates for the putative common ancestors of haplogroup C1d and subhaplogroup C1d3.

<p>BSP: Bayesian skyline plot. See Tables A and B in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0141808#pone.0141808.s004" target="_blank">S2 Text</a> for further details.</p><p>TMRCA estimates for the putative common ancestors of haplogroup C1d and subhaplogroup C1d3.</p

A South American Prehistoric Mitogenome: Context, Continuity, and the Origin of Haplogroup C1d

<div><p>Based on mitochondrial DNA (mtDNA), it has been estimated that at least 15 founder haplogroups peopled the Americas. Subhaplogroup C1d3 was defined based on the mitogenome of a living individual from Uruguay that carried a lineage previously identified in hypervariable region I sequences from ancient and modern Uruguayan individuals. When complete mitogenomes were studied, additional substitutions were found in the coding region of the mitochondrial genome. Using a complete ancient mitogenome and three modern mitogenomes, we aim to clarify the ancestral state of subhaplogroup C1d3 and to better understand the peopling of the region of the Río de la Plata basin, as well as of the builders of the mounds from which the ancient individuals were recovered. The ancient mitogenome, belonging to a female dated to 1,610±46 years before present, was identical to the mitogenome of one of the modern individuals. All individuals share the mutations defining subhaplogroup C1d3. We estimated an age of 8,974 (5,748–12,261) years for the most recent common ancestor of C1d3, in agreement with the initial peopling of the geographic region. No individuals belonging to the defined lineage were found outside of Uruguay, which raises questions regarding the mobility of the prehistoric inhabitants of the country. Moreover, the present study shows the continuity of Native lineages over at least 6,000 years.</p></div

Map showing the location of the Uruguayan samples belonging to subhaplogroup C1d3 with the five complete mitogenomes used in this study.

<p>The locations of the living individuals (circles) correspond to their mothers’ birthplace. The archaeological site where the prehistoric sample was recovered is marked with a square.</p

Dloop_Hap_Seq

Haplotype sequence