Integrating multi-taxon palaeogenomes and sedimentary ancient DNA to study past ecosystem dynamics.

Ancient DNA (aDNA) has played a major role in our understanding of the past. Important advances in the sequencing and analysis of aDNA from a range of organisms have enabled a detailed understanding of processes such as past demography, introgression, domestication, adaptation and speciation. However, to date and with the notable exception of microbiomes and sediments, most aDNA studies have focused on single taxa or taxonomic groups, making the study of changes at the community level challenging. This is rather surprising because current sequencing and analytical approaches allow us to obtain and analyse aDNA from multiple source materials. When combined, these data can enable the simultaneous study of multiple taxa through space and time, and could thus provide a more comprehensive understanding of ecosystem-wide changes. It is therefore timely to develop an integrative approach to aDNA studies by combining data from multiple taxa and substrates. In this review, we discuss the various applications, associated challenges and future prospects of such an approach.

Author Correction: Heavy reliance on plants for Romanian cave bears evidenced by amino acid nitrogen isotope analysis.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Heavy reliance on plants for Romanian cave bears evidenced by amino acid nitrogen isotope analysis.

Heavy reliance on plants is rare in Carnivora and mostly limited to relatively small species in subtropical settings. The feeding behaviors of extinct cave bears living during Pleistocene cold periods at middle latitudes have been intensely studied using various approaches including isotopic analyses of fossil collagen. In contrast to cave bears from all other regions in Europe, some individuals from Romania show exceptionally high δ15N values that might be indicative of meat consumption. Herbivory on plants with high δ15N values cannot be ruled out based on this method, however. Here we apply an approach using the δ15N values of individual amino acids from collagen that offsets the baseline δ15N variation among environments. The analysis yielded strong signals of reliance on plants for Romanian cave bears based on the δ15N values of glutamate and phenylalanine. These results could suggest that the high variability in bulk collagen δ15N values observed among cave bears in Romania reflects niche partitioning but in a general trophic context of herbivory.

Ancient DNA reveals differences in behaviour and sociality between brown bears and extinct cave bears.

Ancient DNA studies have revolutionized the study of extinct species and populations, providing insights on phylogeny, phylogeography, admixture and demographic history. However, inferences on behaviour and sociality have been far less frequent. Here, we investigate the complete mitochondrial genomes of extinct Late Pleistocene cave bears and middle Holocene brown bears that each inhabited multiple geographically proximate caves in northern Spain. In cave bears, we find that, although most caves were occupied simultaneously, each cave almost exclusively contains a unique lineage of closely related haplotypes. This remarkable pattern suggests extreme fidelity to their birth site in cave bears, best described as homing behaviour, and that cave bears formed stable maternal social groups at least for hibernation. In contrast, brown bears do not show any strong association of mitochondrial lineage and cave, suggesting that these two closely related species differed in aspects of their behaviour and sociality. This difference is likely to have contributed to cave bear extinction, which occurred at a time in which competition for caves between bears and humans was likely intense and the ability to rapidly colonize new hibernation sites would have been crucial for the survival of a species so dependent on caves for hibernation as cave bears. Our study demonstrates the potential of ancient DNA to uncover patterns of behaviour and sociality in ancient species and populations, even those that went extinct many tens of thousands of years ago.

Oribatid mite fossils from pre-Quaternary sediments in Slovenian caves II. Amiracarus pliocennatus n.gen., n.sp. (Microzetidae) from Pliocene, with comments on the other species of the genus.

Amiracarus pliocennatus n. gen., n. sp. is described based on fossils found in Pliocene and Pleistocene clastic sediments in caves of the Slovenian Classical Karst (Kras). Diagnosis and relationships of the new genus are given and relationships within the extant species of the genus are discussed as well as variability and reliability of some characters, used for species differentiation. Amiracarus senensis (Bernini 1975) n. comb. is proposed as a type species of the new genus, and other four extant species are newly placed in Amiracarus n. gen.: A. abeloosi (Lions 1978) n. comb., A. discrepans (Mahunka 1966) n. comb., A. grootaerti (Wauthy &Ducarme 2011) n. comb. and A. similis (Subìas & Iturrondobeitia 1978) n. comb. Finding of a fossil individual of M. senensis Bernini 1975 in Ponicova Cave of South-West Carpathians in Romania is reported and a description of this individual is given. Relationships with the genus Miracarus Kunst 1959 are discussed and a new diagnosis of this genus is also given, along with the redescription of its type species, M. hurkai Kunst 1959.