Ancient Faunal History Revealed by Interdisciplinary Biomolecular Approaches

Starting four decades ago, studies have examined the ecology and evolutionary dynamics of populations and species using short mitochondrial DNA fragments and stable isotopes. Through technological and analytical advances, the methods and biomolecules at our disposal have increased significantly to now include lipids, whole genomes, proteomes, and even epigenomes. At an unprecedented resolution, the study of ancient biomolecules has made it possible for us to disentangle the complex processes that shaped the ancient faunal diversity across millennia, with the potential to aid in implicating probable causes of species extinction and how humans impacted the genetics and ecology of wild and domestic species. However, even now, few studies explore interdisciplinary biomolecular approaches to reveal ancient faunal diversity dynamics in relation to environmental and anthropogenic impact. This review will approach how biomolecules have been implemented in a broad variety of topics and species, from the extinct Pleistocene megafauna to ancient wild and domestic stocks, as well as how their future use has the potential to offer an enhanced understanding of drivers of past faunal diversity on Earth

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

Assessing copepod (Crustacea: Copepoda) species richness at different spatial scales in northwestern Romanian caves

The aim of the present study was to assess copepod species richness in groundwater habitats from the Pădurea Craiului Mountains, Transylvania (northwestern Romania). Five species richness estimators (one asymptotic, based on species accumulation curves, and four non-parametric) were compared by testing their performances in estimating copepod species richness at three hierarchical spatial scales: cave, hydrographic basin, and karstic massif. Both epigean and hypogean species were taken in account. Two data sets were used in computing copepod species richness: 1. samples collected continuously during one year (dripping water) and seven months (pools) from five caves, and 2. samples collected from pools in twelve additional caves (data gathered from literature). Differences in copepod species richness among caves and hydrographic basins suggest that local environmental features are important in determining local species richness trends

FIGURE 6 in 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

FIGURE 6. Fossil material of Amiracarus pliocennatus Miko, n. gen., n. sp. Upper row—original photographs of Oana Moldovan, published here to allow matching with individuals as reported in Moldovan et al. (2011): A—holotype from Trhlovca Cave, Slovenia (reported in Moldovan et al. (2011) as Miracarus sp. on Fig. 3A, Fig. 5 and Tab 2 (both in Pliocene sections), B–C—paratypes from Račiška pečina Cave in Slovenia (individuals reported in Moldovan et al. (2011) Miracarus sp. on Fig. 5 and Tab 2 in Pleistocene sections; individual under B was later lost so the more recent photographs are not available). Bars indicating 100 µm. Middle row—Amiracarus pliocennatus Miko, n. gen., n. sp., holotype (same individual as sub A): D—dorsal view, E—ventral view, F—lateral view. Bars indicating 50 µm. Lower row—A. pliocennatus Miko, n. gen., n. sp., paratype (same individual as sub C): G—dorsal view, H—ventral view, I— lateral view. Bars indicating 50 µm.Published as part of <i>Miko, Ladislav, Mourek, Jan, Meleg, Ioana N. & Moldovan, Oana T., 2013, 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, pp. 557-578 in Zootaxa 3670 (4)</i> on page 572, DOI: 10.11646/zootaxa.3670.4.8, <a href="http://zenodo.org/record/10098155">http://zenodo.org/record/10098155</a&gt

FIGURE 8. Amiracarus pliocennatus Miko, n. gen., n in 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

FIGURE 8. Amiracarus pliocennatus Miko, n. gen., n. sp., details of holotype and paratype (individuals under A and C from Plate 1). A—lamellar cuspis of holotype in detail, B—lamellar cuspis of paratype in detail, D—sensillus of holotype, E—sensillus of paratype, C—detail of rostrum, paratype, F—lateral view of prodorsum of holotype, G— lateral view of prodorsum, paratype. Abbreviations: bo—bothridium, ctu1—cuspis of tutorial carina 1, ctu3—cuspis of tutorial carina 3, cus—cuspis of lamella, inc—rostral incision, ku—carina ku on pedotectum I, lam—lamella, pd1— pedotectum I, pt—pteromorph, ss—sensillus, tu1—tutorial carina 1, tu2—tutorial carina 2, tu3—tutorial carina 3. Rest represents names of setae or setal insertions and lyrifissures.Published as part of <i>Miko, Ladislav, Mourek, Jan, Meleg, Ioana N. & Moldovan, Oana T., 2013, 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, pp. 557-578 in Zootaxa 3670 (4)</i> on page 574, DOI: 10.11646/zootaxa.3670.4.8, <a href="http://zenodo.org/record/10098155">http://zenodo.org/record/10098155</a&gt

FIGURE 2 in 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

FIGURE 2. Amiracarus senensis (Bernini 1975) n. comb. (fossil individual from sediments of cave Ponicova, Romania). A—dorsal view; B—ventral view; C—lateral view; D—detail of tutorium; E—sensilus. Legs missing, only trochanters III and IV remained preserved. Bar indicating 100 µm (A, B, C). Abbreviation: ao—anal opening, cgl— circumgastric line, cpl—circumpedal line, dis—discidium, go—genital opening, lam—lamella, mt– mentotectum, pd1— pedotectum I, pd2—pedotectum II, pt—pteromorph, R—acetabular protrusion of leg III, sl—notogastral lateromedial furrow, ss—sensillus, trIV—trochanter IV, tu—tutorium, tu1—tutorial carina 1, tu2—tutorial carina 2, tu3—tutorial carina 3. Rest represents names of setae or setal insertions and lyrifissures.Published as part of <i>Miko, Ladislav, Mourek, Jan, Meleg, Ioana N. & Moldovan, Oana T., 2013, 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, pp. 557-578 in Zootaxa 3670 (4)</i> on page 563, DOI: 10.11646/zootaxa.3670.4.8, <a href="http://zenodo.org/record/10098155">http://zenodo.org/record/10098155</a&gt

FIGURE 1. Miracarus hurkai Kunst, 1959 in 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

FIGURE 1. Miracarus hurkai Kunst, 1959 (holotype). A—dorsal view (without legs); B—ventral view (legs only partly depicted); C—dorsolateral view of prodorsum (notogaster and ventral structures only partly sketched); D—detailed view of sensillus. Bar indicating 100 µm (A, B, C). Abbreviations: an—anal plate, cgl—circumgastric line, cpl—circumpedal line, dis—discidium, g—genital plate, lam—lamella, mt—mentotectum, pd1—pedotectum I, pd2—pedotectum II, pt— pteromorph, R—acetabular protrusion of leg III, ro—rostrum, sl—notogastral lateromedial furrow, ss—sensillus, TrIII— trochanter III, Tr IV—trochanter IV, tsII—trochanteral seta II, tu—tutorium, tu1—tutorial carina 1, tu2—tutorial carina 2, tu3—tutorial carina 3. Rest represents names of setae or setal insertions and lyrifissures.Published as part of <i>Miko, Ladislav, Mourek, Jan, Meleg, Ioana N. & Moldovan, Oana T., 2013, 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, pp. 557-578 in Zootaxa 3670 (4)</i> on page 560, DOI: 10.11646/zootaxa.3670.4.8, <a href="http://zenodo.org/record/10098155">http://zenodo.org/record/10098155</a&gt

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

Miko, Ladislav, Mourek, Jan, Meleg, Ioana N., Moldovan, Oana T. (2013): 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. Zootaxa 3670 (4): 557-578, DOI: 10.11646/zootaxa.3670.4.