tidysdm: Leveraging the flexibility of tidymodels for species distribution modelling in R DOI Creative Commons
Michela Leonardi, Margherita Colucci, Andrea Vittorio Pozzi

et al.

Methods in Ecology and Evolution, Journal Year: 2024, Volume and Issue: 15(10), P. 1789 - 1795

Published: Sept. 9, 2024

Abstract In species distribution modelling (SDM), it is common practice to explore multiple machine learning (ML) algorithms and combine their results into ensembles. R, many implementations of different ML are available but, as they were mostly developed independently, often use inconsistent syntax data structures. For this reason, repeating an analysis with combining can be challenging. Specialised SDM packages solve problem by providing a simpler, unified interface wrapping the original functions tackle each specific requirement. However, creating maintaining such interfaces time‐consuming, approach, user cannot easily integrate other methods that may become available. Here, we present tidysdm , R package solves taking advantage tidymodels universe. provide standardised grammar, structures interfaces, well‐documented infrastructure new metrics. The wide adoption means most metrics already integrated, add additional ones. Moreover, because broad statistical approaches tend implemented quickly, making them integrated existing pipelines analyses. takes universe flexible fully customisable pipeline fit SDM. It includes SDM‐specific metrics, facilitate spatial within . Additionally, first software natively allows performed using from periods, expanding availability for scholars working in palaeontology, archaeology, palaeobiology, palaeoecology disciplines focussing on past.

Language: Английский

Worldwide Late Pleistocene and Early Holocene population declines in extant megafauna are associated with Homo sapiens expansion rather than climate change DOI Creative Commons
Juraj Bergman, Rasmus Østergaard Pedersen, Erick J. Lundgren

et al.

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Nov. 24, 2023

The worldwide extinction of megafauna during the Late Pleistocene and Early Holocene is evident from fossil record, with dominant theories suggesting a climate, human or combined impact cause. Consequently, two disparate scenarios are possible for surviving this time period - they could have declined due to similar pressures, increased in population size reductions competition other biotic pressures. We therefore infer histories 139 extant species using genomic data which reveal declines 91% throughout Quaternary period, larger experiencing strongest decreases. Declines become ubiquitous 32-76 kya across all landmasses, pattern better explained by Homo sapiens expansion than changes climate. estimate that, consequence, total abundance, biomass, energy turnover decreased 92-95% over past 50,000 years, implying major human-driven ecosystem restructuring at global scale.

Language: Английский

Citations

43
The Persian plateau served as hub for Homo sapiens after the main out of Africa dispersal DOI Creative Commons
Leonardo Vallini, Carlo Zampieri,

Mohamed Javad Shoaee

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: March 25, 2024

Abstract A combination of evidence, based on genetic, fossil and archaeological findings, indicates that Homo sapiens spread out Africa between ~70-60 thousand years ago (kya). However, it appears once outside Africa, human populations did not expand across all Eurasia until ~45 kya. The geographic whereabouts these early settlers in the timeframe to 45 kya has been difficult reconcile. Here we combine genetic evidence palaeoecological models infer location acted as Hub for our species during phases colonisation Eurasia. Leveraging available genomic show from Persian Plateau carry an ancestry component closely matches population settled Africa. With paleoclimatic data date, built ecological showing was suitable occupation could sustain a larger compared other West Asian regions, strengthening this claim.

Language: Английский

Citations

16
The Neanderthal niche space of Western Eurasia 145 ka to 30 ka ago DOI Creative Commons
Peter Yaworsky, Emil Schou Nielsen, Trine Kellberg Nielsen

et al.

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: April 2, 2024

Abstract Neanderthals occupied Western Eurasia between 350 ka and 40 ago, during the climatically volatile Pleistocene. A key issue is to what extent Neanderthal populations expanded into areas of conditions facilitated such range expansions. The generally based on distribution material, but land-altering nature glacial periods has erased much already sparse material evidence Neanderthals, particularly in northern latitudes. To overcome this obstacle species models can estimate past distributions however, most implementations are constrained spatially temporally may be artificially truncating niche space. Using dated contexts from sites across Eurasia, millennial-scale paleoclimate reconstructions, a spatiotemporal model, we infer fundamental climatic space occupation. We find that (a.) despite long timeframe, occupy relatively narrow space, (b.) estimated projected potential suggests larger geographic than record suggests, (c.) there was general decline size 145 ago onward, possibly contributing their extinction.

Language: Английский

Citations

12
The ROCEEH Out of Africa Database (ROAD): A large-scale research database serves as an indispensable tool for human evolutionary studies DOI Creative Commons
Andrew W. Kandel, Christian Sommer, Zara Kanaeva

et al.

PLoS ONE, Journal Year: 2023, Volume and Issue: 18(8), P. e0289513 - e0289513

Published: Aug. 1, 2023

Large scale databases are critical for helping scientists decipher long-term patterns in human evolution. This paper describes the conception and development of such a research database illustrates how big data can be harnessed to formulate new ideas about past. The Role Culture Early Expansions Humans (ROCEEH) is transdisciplinary center whose aim study origins culture multifaceted aspects expansions across Africa Eurasia over last three million years. To support its research, ROCEEH team developed an online tool named Out Database (ROAD) implemented web-based applications. ROAD integrates geographical as well archaeological, paleoanthropological, paleontological paleobotanical content within robust chronological framework. In fact, unique feature ability dynamically link scientific both spatially temporally, thereby allowing reuse ways that were not originally conceived. stem from published sources spanning 150 years, including those generated by team. Descriptions these rely on standardized vocabulary profit explanations each table attribute. By synthesizing legacy data, facilitates heritage novel ways. queries yield structured information variety interoperable formats. visualizing maps, users explore this vast dataset develop their own theories. downloading conduct further quantitative analyses, example with Geographic Information Systems, modeling programs artificial intelligence. paper, we demonstrate innovative nature show it helps studying evolution access datasets different fields, connecting social natural sciences. Because permits “old” ways, now indispensable researchers paleogeography.

Language: Английский

Citations

18
Current sika deer effective population size is near to reaching its historically highest level in the Japanese archipelago by release from hunting rather than climate change and top predator extinction DOI
Hayato Iijima, Junco Nagata, Ayako Izuno

et al.

The Holocene, Journal Year: 2023, Volume and Issue: 33(6), P. 718 - 727

Published: March 9, 2023

Deer species were repeatedly overexploited and protected for their meat fur they had strong impacts on ecosystems human society by damaging crops planted trees, altering vegetation, deer vehicle collision, increasing ticks that vector zoonosis. To accomplish appropriate population management, the historical demography its main driver need to be clarified. In this study, we estimated of effective size ( Ne) sika Cervus nippon Temminck) in Hokkaido Hyogo Prefectures Japanese archipelago. We Ne >100 generations from present (2020) folded single nucleotide polymorphisms (SNP) frequency spectra and, within 100 present, linkage disequilibrium between SNP. Hokkaido, drastically increased around 3.0 ky BP decreased 100–150 years ago with assumption generation length as 4 or 9 years. The a 10th before recent bottleneck. Hyogo, 80 1 100–250 ago. 100th After these bottlenecks, both regions recovered current has nearly reaches highest level last BP. Literature survey paleoclimate indicates decrease increase archipelago may caused variations hunting activity humans rather than climate change top predator extinction.

Language: Английский

Citations

17
Ecology and demography of early Homo sapiens : a synthesis of archaeological and climatic data from eastern Africa DOI Creative Commons
Lucy Timbrell

Azania Archaeological Research in Africa, Journal Year: 2024, Volume and Issue: 59(1), P. 76 - 110

Published: Jan. 2, 2024

Eastern Africa maintains a key position in debates surrounding the emergence of Homo sapiens across Africa. Extensive research region has revealed rich fossil record association with 'generic' but variable Middle Stone Age (MSA) material culture, providing an important laboratory for testing hypotheses about behavioural evolution our species. For example, multiple archaeological studies eastern African MSA note link between distribution and density sites, diversity environmental conditions, ecology demography often cited as drivers cultural evolution. This article formulates new using theoretical models complex fitness landscapes reviews climatic records Middle-late Pleistocene light these ideas. It proposes that evidence from implicates much refugial zone within Africa, consistently suitable conditions survival were characterised by high changing biodiversity, facilitating population growth interconnectivity well culture diversification. Interactions different evolutionary processes likely resulted mosaic observed including appearance 'specific' innovations against backdrop more elements.

Language: Английский

Citations

6
Reconstruction of warm-season temperatures in central Europe during the past 60 000 years from lacustrine branched glycerol dialkyl glycerol tetraethers (brGDGTs) DOI Creative Commons
Paul D. Zander,

Daniel Böhl,

Frank Sirocko

et al.

Climate of the past, Journal Year: 2024, Volume and Issue: 20(4), P. 841 - 864

Published: April 8, 2024

Abstract. Millennial-scale climate variations during the last glacial period, such as Dansgaard–Oeschger (DO) cycles and Heinrich events, have been extensively studied using ice core marine proxy records. However, there is a limited understanding of magnitude these temperature fluctuations in continental regions, questions remain about seasonal signal events. This study presents 60 000-year-long reconstruction based on branched glycerol dialkyl tetraethers (brGDGTs) extracted from lake sediments Eifel Volcanic Field, Germany. brGDGTs are bacterial membrane-spanning lipids that known to strong relationship with temperature, making them suitable for reconstructions. We test several calibration models modern samples taken soils multiple maar lakes. find negative bias brGDGT-based estimates associated water depth anoxic conditions can be corrected by accounting brGDGT isomer only produced conditions. The correlates model spanning same time validating approach we selected. millennial-scale variability significantly dampened record, contrast other Northern Hemisphere records, stadials, temperatures actually increase. demonstrate apparent discrepancies explained unique response paleothermometer months above freezing (TMAF). Our data support view warm-season Europe varied minimally period abrupt events were defined colder, longer winters. continuous high-resolution provides important information used inform studies paleoecological change.

Language: Английский

Citations

5
More Than Surface Finds: Nubian Levallois Core Metric Variability and Site Distribution Across Africa and Southwest Asia DOI Creative Commons
Osama Samawi, Emily Hallinan

Journal of Paleolithic Archaeology, Journal Year: 2024, Volume and Issue: 7(1)

Published: Sept. 11, 2024

Language: Английский

Citations

4
A comparative analysis of stone- and earth-wall settlement locations of the Lower Xiajiadian Culture in Aohan Banner, China DOI Creative Commons
Xuan Zhang,

Yukun Zhang,

Lifeng Tan

et al.

Archaeological and Anthropological Sciences, Journal Year: 2025, Volume and Issue: 17(1)

Published: Jan. 1, 2025

Language: Английский

Citations

0
Patrones de riqueza de especies y conservadurismo filogenético del nicho ecológico en la Zona de Transición Mexicana: evidencia y herramientas para su estudio DOI Creative Commons
Viridiana Lizardo, Adriana Ruggiero, Juan J. Morrone

et al.

Revista Mexicana de Biodiversidad, Journal Year: 2025, Volume and Issue: 96, P. e965347 - e965347

Published: Jan. 28, 2025

Los patrones de riqueza resultan la superposición geográfica los nichos ecológicos múltiples especies. El conservadurismo filogenético del nicho ecológico y dispersión son procesos esenciales para entender geográficos en Aquí actualizamos teoría ensamble biótico Zona Transición Mexicana (ZTM) incorporando al concepto ecológico. La ZTM recurre cenocrón (i.e., conjunto linajes una misma afinidad biogeográfica que comparten historia tiempo dispersión) explicar gradientes Revisamos fundamentos ecológico, postulados su relación con otras hipótesis propuestas especies, el fin comparar las predicciones se derivan ZTM. Ofrecemos guía posibilidades metodológicas evaluar aplicando método comparativo filogenético. Incluimos breve descripción técnicas software disponibles, cómo ingresar datos necesarios otros requisitos implementación, mostramos ejemplos aplicación

Citations

0