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opencc-zeroDec 2018View details →

Data from: Late Pleistocene range expansion of North American topminnows accompanied by admixture and introgression.

Aim: We used genome-scale sampling to assess the phylogeography of a group of topminnows in the Fundulus notatus species complex. Two of the species have undergone extensive range expansions resulting in broadly overlapping distributions, and sympatry within drainages has provided opportunities for hybridization and introgression. We assess the timing and pattern of range expansion in the context of late-Pleistocene-Holocene drainage events, and evaluate the evidence for introgressive hybridization between species. Location: Central and southern United States including drainages of the Gulf of Mexico Coastal Plain and portions of the Mississippi River drainage in and around the Central Highlands. Taxon: Topminnows, Genus Fundulus, subgenus Zygonectes - Fundulus notatus, Fundulus olivaceus, Fundulus euryzonus Methods: We sampled members of the F. notatus species complex throughout their respective ranges, including numerous drainage systems where species co-occur. We collected genome-wide Single Nucleotide Polymorphisms (SNPs) using the Genotype by Sequencing (GBS) method, and subjected data to population genetic analyses to infer the population histories of both species, including explicit tests for admixture and introgression. The methods employed included STRUCTURE, Principle Coordinates Analysis, TreeMix and Approximate Bayesian Computation. Results: Genetic data are presented for 749 individuals sampled from 14 F. notatus, 20 F. olivaceus, and two F. euryzonus populations. Members of the species complex differed in phylogeographic structure, with F. notatus exhibiting geographic clusters corresponding to Pleistocene coastal drainages, and F. olivaceus comparatively lacking in phylogeographic structure. Evidence for interspecific introgression varied by drainage. Main Conclusions: Populations of F. notatus and F. olivaceus exhibited contrasting patterns of lineage diversity among coastal drainages, indicating inter-specific differences in their Pleistocene southern refugia. Phylogeographic patterns in both species indicated that range expansions into the northern limits of contemporary distributions coincided with and continued subsequent to the Last Glacial Maximum. There was evidence of introgression between species in some, but not all drainages where the species co-occur, in a pattern that is correlated with previous estimates of hybridization rates.

opencc-zeroFeb 2024View details →

Late Pleistocene stickleback environmental genomes reveal the chronology of freshwater adaptation

Directly observing the chronology and tempo of adaptation in response to ecological change is rarely possible in natural ecosystems. Sedimentary aDNA (sedaDNA) has been shown to be a tractable source of genome-scale data of long-dead organisms, and to thereby potentially provide an understanding of the evolutionary histories of past populations. To date, time series of ecosystem biodiversity have been reconstructed from sedaDNA, typically using DNA metabarcoding or shotgun sequence data generated from less than one gram of sediment. Here we maximise sequence coverage by extracting DNA from ~50x more sediment per sample than the majority of previous studies, to achieve genotype resolution. From a time-series of Late Pleistocene sediments spanning from a marine to freshwater ecosystem, we compare adaptive genotypes reconstructed from the environmental genomes of threespine stickleback at key time points of this transition. We find a staggered temporal dynamic, in which freshwater alleles at known loci of large effect in marine-freshwater divergence of threespine stickleback (e.g. EDA) were already established during the brackish phase of the formation of the isolation basin. Yet marine alleles were still detected across the majority of marine-freshwater divergence associated loci, even after the complete isolation of the lake from marine ingression. Our retrospective approach to studying adaptation from environmental genomes of threespine sticklebacks at the end of the last glacial period complements contemporary experimental approaches and highlights the untapped potential for retrospective 'evolve-and-resequence' natural experiments using sedaDNA.

opencc-zeroMar 2024View details →

Data from: The latest freshwater giants: a new Peltocephalus (Pleurodira: Podocnemididae) turtle from the Late Pleistocene of the Brazilian Amazon

Overkill of large mammals is recognised as a key driver of Pleistocene megafaunal extinctions in the Americas and Australia. While this phenomenon primarily affected mega-mammals, its impact on large Quaternary reptiles has been debated. Freshwater turtles, due to the scarcity of giant forms in the Quaternary record, have been largely neglected in such discussions. Here we present a new giant podocnemidid turtle, Peltocephalus maturin sp. nov., from the Late Pleistocene Rio Madeira Formation in the Brazilian Amazon, that challenges this assumption. Morphological and phylogenetic analyses of the holotype, a massive partial lower jaw, reveal close affinities to extant Amazonian species and suggests an omnivorous diet. Body size regressions indicate Pe. maturin possibly reached about 180 cm in carapace length and is amongst the largest freshwater turtles ever found. This finding presents the latest known occurrence of giant freshwater turtles, hinting at coexistence with early human inhabitants in the Amazon.

opencc-by-4.0Nov 2018View details →

Fig. 1 in Fossil Ovibos Moschatus (Artiodactyla, Bovidae) From Buryn, With Reference To Muskox Dispersal In The Late Pleistocene Of Ukraine

Fig. 1. Localities with fossil muskox remains on the territory of Ukraine.

opencc-by-4.0Jan 2018View details →

Fig. 1 in Late Pleistocene Birds from Binagada (Azerbaijan) in Collection of the National Museum of Natural History (Kyiv, Ukraine)

Fig. 1. Map of Azerbaijan showing the location of the Binagada asphalt lake.

opencc-by-4.0Apr 2022View details →

Dental microwear and mesowear raw data for European and East Asian Late Pleistocene hyenas Crocuta spelaea and C. ultima ussurica

Raw microwear data related to the paper "Comparison of paleodiet and niches of European and East Asian Late Pleistocene hyenas Crocuta spelaea and C. ultima ussurica based on the study of tooth microwear"

opencc-zeroAug 2022View details →

Data from: Cranial remains of Ramsayia magna from the Late Pleistocene of Australia and the evolution of gigantism in wombats (Vombatidae; Marsupialia)

Giant wombats (defined here as body mass ≥ 70 kg) are found in the genera Phascolonus, Ramsayia, and perhaps also Sedophascolomys. Of these, Ramsayia is the currently the most poorly known, having been described from fragmentary mandibular and cranial fragments. Here, we report the most complete cranial remains attributable to the genus, identified as the species R. magna. The remains provide new important insights into the anatomy of the species and the evolutionary adaptations to gigantism in Vombatidae. We record parietal sinuses in a vombatid for the first time, an adaptation to increased skull size relative to the braincase. The presence of a prominent premaxillary spine may indicate the species possessed a large, fleshy nose. Both of features are convergent on other large-bodied, non-vombatid extinct megaherbivores of Australia such as Diprotodon optatum. We use the cranial remains to examine the phylogenetic relationships of the giant wombats to other vombatids. Phylogenetic analysis using maximum parsimony and Bayesian inference indicates that Phascolomys, Ramsayia, and Sedophascolomys form a clade, suggesting a single origin of gigantism within Vombatidae. This origin may have been related to the exploitation of poor-quality foods by these taxa, and preceded the extreme specialisations observed in the incisor and cranial anatomy of the giant wombats. U-series and combined U-series and Electron Spin Resonance (ESR) dating methods were applied to one fossil tooth. All sources of uncertainty considered, age calculations systematically correlate the fossil remains to Marine Isotope Stage 5, and an age of approximately 80,000 years can be proposed for this specimen. With only a single well dated occurrence for this taxon, it is currently impossible to determine when and why R. magna became extinct.

FIGURE 7 in Late Pleistocene insects from the Dubrovino site at Ob River (West Siberia, Russia) and their paleoenvironmental significance

FIGURE 7. Late Pleistocene and modern ranges of Otiorhynchus janovskii Korotyaev, 1990.

FIGURE 6 in Late Pleistocene insects from the Dubrovino site at Ob River (West Siberia, Russia) and their paleoenvironmental significance

FIGURE 6. Late Pleistocene and modern ranges of Stephanocleonus isochromus Suvorov, 1912.

FIGURE 5 in Late Pleistocene insects from the Dubrovino site at Ob River (West Siberia, Russia) and their paleoenvironmental significance

FIGURE 5. Late Pleistocene and modern ranges of Stephanocleonus favens Faust, 1884.

FIGURE 2 in Late Pleistocene insects from the Dubrovino site at Ob River (West Siberia, Russia) and their paleoenvironmental significance

FIGURE 2. Stratigraphic diagram of the Dubrovino section on the Ob River.

opencc-zeroJun 2024View details →

Data from: Osteology of Crocodylus palaeindicus from the late Miocene–Pleistocene of South Asia and the phylogenetic relationships of crocodyloids

Fossil crocodylian remains have been documented from India and other parts of South Asia since the mid-19th century, but specimens attributed to several extinct and extant species of Crocodylus have largely been neglected in modern taxonomic treatments. Here, we present a detailed anatomical description of the extinct species Crocodylus palaeindicus, which we restrict to the Late Miocene to early Middle Pleistocene of India. Using an autapomorphy-based approach to species-level identification, we regard Crocodylus sivalensis as a junior synonym of C. palaeindicus, and provide taxonomic reidentifications of all specimens previously referred to these two species. We present a new diagnosis for C. palaeindicus that facilitates its distinction from the extant mugger crocodile, C. palustris, which does not unequivocally appear in the fossil record prior to the Pleistocene. The lack of clear spatiotemporal overlap, coupled with the otherwise lengthy ghost lineage implied by their sister taxon relationship in our phylogenetic analyses, provides tentative support that the extant species is either the descendant of C. palaeindicus, or originated via budding cladogenesis. An expanded phylogenetic analysis recovers the Late Miocene African C. checchiai and Pliocene South American C. falconensis as species within the Neotropical Crocodylus clade, supporting an African origin for this radiation. We also recover Kinyang, from the early–middle Miocene of Kenya, as a crocodyline, rather than an osteolaemine as originally described, and it is potentially the stratigraphically earliest known member of the Crocodylus lineage. Other notable results from our phylogenetic analyses suggest that crocodyloids might not have been present in North America prior to the late Neogene arrival of Crocodylus, with Albertosuchus knudsenii, Prodiplocynodon langi, and 'Crocodylus' affinis all recovered outside of Crocodyloidea. Furthermore, we demonstrate that an alligatoroid placement for the recently erected latest Cretaceous–Paleogene East Asian clade Orientalosuchina is highly labile, with relationships at the 'base' of Crocodylia unstable.

opencc-by-4.0Jul 2024View details →

Research compendium for "Beyond Large Shaped Tools: Technological innovations and continuities at the late Early Pleistocene assemblage of El Barranc de la Boella (Tarragona, Spain)."

Overview of contents and how to reproduce: This repository contains the codes and datasets for reproducing the results of Lombao,D., Morales, J.I., Mosquera, M., Ollé, A., Saladié, P., Vallverdú, J.  "Beyond Large Shaped Tools: Technological innovations and continuities at the late Early Pleistocene assemblage of El Barranc de la Boella (Tarragona, Spain)." Journal of Paleolithic Archaeology. DOI : 10.1007/s41982-024-00189-9 Readers can start their own analyses by using the R Markdown file and the datasets. Please, download the complete repository and reproduce the results using `Research compendium for Beyond Large Shaped Tools.Rproj.

opencc-by-4.0Dec 2012View details →

Text-fig. 2 Section in proglacial sands and gravels in the abandoned sand pit near Fukov. in Fossils In Late Cretaceous To Early Palaeocene Flint Nodules Embedded In Pleistocene Glaciofluvial Sediments Near Fukov (Děčín District, Northern Bohemia)

Text-fig. 2 Section in proglacial sands and gravels in the abandoned sand pit near Fukov.

opencc-by-4.0Dec 2012View details →

Fig. 1 in Osteometric analysis of the scapula and humerus of Rangifer tarandus and Cervus elaphus: A contribution to the discrimination of Late Pleistocene cervids

Fig. 1. Geographic location of Kiputz IX (Mutriku, Gipuzkoa).

opencc-by-4.0Dec 2012View details →

Fig. 2 in Osteometric analysis of the scapula and humerus of Rangifer tarandus and Cervus elaphus: A contribution to the discrimination of Late Pleistocene cervids

Fig. 2. Stratigraphic section and radiocarbon dates for the locality of Kiputz IX.

opencc-zeroDec 2016View details →

Data from: A late Pleistocene marine glacial refugium in the south-west of Hainan Island, China: Phylogeographical insights from the brown alga Sargassum polycystum

Aim: Hainan Island, southern China, is characterized by rich diversity and endemism of marine organisms, yet the underpinning mechanisms and processes contributing to speciation and diversification are poorly understood. Here, the brown alga Sargassum polycystum is used as a model to identify putative marine glacial refugia and explore biogeographical patterns driven by climate change in the late Pleistocene ice ages. Location: South-East Asia. Methods: Mitochondrial cox1 and cox3 and nuclear internal transcribed spacer-2 (ITS2) were obtained from 310, 325 and 313 individuals of S. polycystum (23 localities), respectively. Phylogenetic trees (maximum likelihood and Bayesian inference) and haplotype/ribotype networks were constructed to elucidate phylogeographical patterns. Analysis of molecular variance (AMOVA), neutrality tests (Tajima's D and Fu & Li's D*), current (θπ) and historical (θw) genetic diversities and extended Bayesian skyline plots (EBSP) were used to estimate historical demography. Results: The populations from the south-west of Hainan Island harboured much higher genetic diversity and unique endemism in comparison with other populations in the distribution range. Sargassum polycystum experienced relatively long-term stable population size followed by a continued period of demographic expansion in the late Pleistocene. Main conclusions: Our phylogeographical evidence revealed the existence of a previously unidentified marine refugium specific to S. polycystum in the south-west of Hainan Island, China (the Central Depression of the Yinggehai Basin), along with a possible secondary refugium around the Bali Island, Indonesia. These biogeographical findings provide important insights regarding speciation, adaptation and evolution of marine organisms in South-East Asia and the conservation of unique biodiversity under climate change.

opencc-by-4.0Jun 2021View details →

Sea-ice, primary productivity and ocean temperatures at the Antarctic marginal zone during late Pleistocene

These data in excel refer to all proxies used to reconstruct late Quaternary sea ice and productivity in in cape Adare, Ross Sea, Antarctica, for the publication in Quaternary Science Reviews, for open access