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Supplemental Data Tables (Table S1-S4) for results related to manuscript "<strong>How a <em>Homo</em> goes extinct. Climatic change and the demise of our ancestors"</strong>
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According to the island rule, small-bodied vertebrates will tend to evolve larger body size on islands, whereas the opposite happens to large-bodied species. This controversial pattern has been studied at the macroecological and... more
According to the island rule, small-bodied vertebrates will tend to evolve larger body size on islands, whereas the opposite happens to large-bodied species. This controversial pattern has been studied at the macroecological and biogeographical scales, but new developments in quantitative evolutionary genetics now allow studying the island rule from a mechanistic perspective. Here, we develop a simulation approach based on an individual-based model to model body size change on islands as a progressive adaptation to a moving optimum, determined by density-dependent population dynamics. We applied the model to evaluate body size differentiation in the pigmy extinct hominin <i>Homo floresiensis,</i> showing that dwarfing may have occurred in only about 360 generations (95% CI ranging from 150 to 675 generations). This result agrees with reports suggesting rapid dwarfing of large mammals on islands, as well as with the recent discovery that small-sized hominins lived in Flores as early as 700 kyr ago. Our simulations illustrate the power of analysing ecological and evolutionary patterns from an explicit quantitative genetics perspective.
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Tools for geometric morphometric analysis. The package includes tools of virtual anthropology to align two not articulated parts belonging to the same specimen and to build virtual cavities as endocast. In addition, we supply functions to... more
Tools for geometric morphometric analysis. The package includes tools of virtual anthropology to align two not articulated parts belonging to the same specimen and to build virtual cavities as endocast. In addition, we supply functions to import and export the coordinates of landmarks and 3D paths into 'landmarkAscii' and 'am' format files.
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Colonization of islands often activate a complex chain of adaptive events that, over a relatively short evolutionary time, may drive strong shifts in body size, a pattern known as the Island Rule. It is arguably difficult to perform a... more
Colonization of islands often activate a complex chain of adaptive events that, over a relatively short evolutionary time, may drive strong shifts in body size, a pattern known as the Island Rule. It is arguably difficult to perform a direct analysis of the natural selection forces behind such change in body size. Here, we used quantitative evolutionary genetic models, coupled with simulations and pattern-oriented modelling, to analyse the evolution of brain and body size in <i>Homo floresiensis</i>, a diminutive hominin species that appeared around 700 kya and survived up to relatively recent times (60–90 kya) on Flores Island, Indonesia. The hypothesis of neutral evolution was rejected in 97% of the simulations, and estimated selection gradients are within the range found in living natural populations. We showed that insularity may have triggered slightly different evolutionary trajectories for body and brain size, which means explaining the exceedingly small cranial volume of <i>H. floresiensis</i> requires additional selective forces acting on brain size alone. Our analyses also support previous conclusions that <i>H. floresiensis</i> may be most likely derived from an early Indonesian <i>H. erectus</i>, which is coherent with currently accepted biogeographical scenario for <i>Homo</i> expansion out of Africa.
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Tools for Geometric Morphometrics
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Calcareous nannofossil Watznaueria barnesiae is a resistant and tolerant species and previous morphometric studies have evidenced minor (Erba et al., 2010; Lubke et al.2016) or no size changes during Oceanic Anoxic Events (OAEs)... more
Calcareous nannofossil Watznaueria barnesiae is a resistant and tolerant species and previous morphometric studies have evidenced minor (Erba et al., 2010; Lubke et al.2016) or no size changes during Oceanic Anoxic Events (OAEs) (Bornemann et al. 2006; and Faucher et al. 2017b) as well as during the Cenomanian to Maastrichtian (Linnert et al. 2014). Here, we present the morphometric record from the western Tethys (Cismon core from the Belluno Basin; Piobbico core and the Monte Petrano section from Umbria-Marche Basin, Italy) across the latest Barremian- late Cenomanian which represents a relatively long-time interval (ca. 26 Myrs) marked by interludes of profound changes in the ocean and climatic conditions named (OAE 1a, 1b and 1d). Our study shows that indeed W. barnesiae experienced coccolith and central unit variations during the studied interval. Specifically, smaller coccoliths with also smaller central unit marked the early Aptian to early Albian. The middle Albian to the early Cenomanian was characterized by larger and rounded coccoliths without significant changes in the central unit dimension. Short-term size changes are detected in correspondence of OAE 1a and OAE 1b marked by W. barnesiae size decrease. Particularly, OAE 1a was characterized by the smallest and most elliptical specimens of the studied interval. During the OAE 1b W. barnesiae coccoliths were characterized by a moderate decrease in the mean size, because specimens were already smaller before the event. The morphometric data were correlated with calcareous nannofossil temperature and nutrient indices calculated on the same samples investigated for morphometry. Long-term size changes do not show a clear correspondence with temperature and nutrient variations. W. barnesiae size changes across the early Aptian to early Albian may be related to large igneous province activity. Short-term size variations during OAE 1a and OAE 1b were influenced by the combination of large CO2 emissions, temperature and fertility increase. In conclusion, although W. barnesiae is a resistant and tolerant species it shows morphometric changes both in short- and long-term, probably in response to partially different causes.
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Research Interests: Quaternary and Mammal
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To investigate the role of vegetation and ecosystem diversity on hominin adaptation and migration, we identify past human habitat preferences over time using a transient 3-million-year earth system-biome model simulation and an extensive... more
To investigate the role of vegetation and ecosystem diversity on hominin adaptation and migration, we identify past human habitat preferences over time using a transient 3-million-year earth system-biome model simulation and an extensive hominin fossil and archaeological database. Our analysis shows that early African hominins predominantly lived in open environments such as grassland and dry shrubland. Migrating into Eurasia, hominins adapted to a broader range of biomes over time. By linking the location and age of hominin sites with corresponding simulated regional biomes, we also find that our ancestors actively selected for spatially diverse environments. The quantitative results lead to a new diversity hypothesis: Homo species, in particular Homo sapiens , were specially equipped to adapt to landscape mosaics.
Research Interests: Geography, Human Evolution, Science, Ecology, Multidisciplinary, and 5 moreHabitat, Homo Sapiens, Grassland, Shrubland, and Biome
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Species distribution models (SDMs) are a useful mean to understand how environmental variation influences species geographical distribution. SDMs are implemented by several different algorithms. Unfortunately, these algorithms... more
Species distribution models (SDMs) are a useful mean to understand how environmental variation influences species geographical distribution. SDMs are implemented by several different algorithms. Unfortunately, these algorithms consistently lose accuracy exactly when they are needed the most, that is with rare species, originating the so‐called rare‐species modelling paradox. Although approaches exist to tackle this problem, most notably by performing and then averaging a number of bivariate models, they are usually computationally intensive and were never shown to apply successfully to the rarest species (i.e. with less than 20 geographical occurrences). Here, we present a new algorithm, ENphylo, embedded in the readily‐available R package RRdtn, which couples Environmental Niche Factor Analysis (ENFA) and phylogenetic imputation to model the distribution of rare species. Using the fossil record of 31 species of large mammals that lived during the late Pleistocene as the source data...
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There is solid recognition that phylogenetic effects must be acknowledged to appreciate climatic niche variability among species clades properly. Yet, most currently available methods either work at the intra‐specific level (hence they... more
There is solid recognition that phylogenetic effects must be acknowledged to appreciate climatic niche variability among species clades properly. Yet, most currently available methods either work at the intra‐specific level (hence they ignore phylogeny) or rely on the Brownian motion model of evolution to estimate phylogenetic effects on climatic niche variation. The Brownian motion model may be inappropriate to describe niche evolution in several cases, and even a significant phylogenetic signal in climatic variables does not indicate that the effect of shared ancestry was relevant to niche evolution. We introduce a new phylogenetic comparative method which describes significant changes in the width and position of the climatic niche at the inter‐specific (clade) level, while making no a priori assumption about how niche evolution took place. We devised the R function phylo.niche.shift to estimate whether the climatic niches of individual clades in the tree are either wider or narr...
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Large brains are a defining feature of primates, as is a clear allometric trend between body mass and brain size. However, important questions on the macroevolution of brain shape in primates remain unanswered. Here we address two: (i),... more
Large brains are a defining feature of primates, as is a clear allometric trend between body mass and brain size. However, important questions on the macroevolution of brain shape in primates remain unanswered. Here we address two: (i), does the relationship between the brain size and its shape follow allometric trends and (ii), is this relationship consistent over evolutionary time? We employ three-dimensional geometric morphometrics and phylogenetic comparative methods to answer these questions, based on a large sample representing 151 species and most primate families. We found two distinct trends regarding the relationship between brain shape and brain size. Hominoidea and Cercopithecinae showed significant evolutionary allometry, whereas no allometric trends were discernible for Strepsirrhini, Colobinae or Platyrrhini. Furthermore, we found that in the taxa characterized by significant allometry, brain shape evolution accelerated, whereas for taxa in which such allometry was ab...
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calculate.niche.overlap <strong>Description</strong> The function allows to reproduce all of the results presented in the manuscript "Modelling Homo extinction. Climatic change and the demise of our ancestors" with... more
calculate.niche.overlap <strong>Description</strong> The function allows to reproduce all of the results presented in the manuscript "Modelling Homo extinction. Climatic change and the demise of our ancestors" with the exception of CENFA, that is implemented in the companion function "calculate.vulnerability". In particular, the user can select one of six <em>Homo</em> species and perform the following analyses: i) calculation of niche overlap between each bin climatic niche (BCN) and the evolutionary climatic niche (ECN); ii) leave-one-out procedure to evaluate whether niche overlap during the last bin shows a trend; and iii) calculation of multivariate distance between the barycentres of BCNs and ECN. Importantly, the function starts by <strong>downloading</strong> species occurrences as geopagkage files, as well as a number of ancillary R codes/functions embedded within a single .R file which are necessary to run the function properly, in a user-defined target directory (to be set in the target.dir argument). As the function runs, the following subfolders will be created within the target directory: "<em>HOMO_OCCURRENCE DATA</em>" (where geopackage files will be placed), and "<em>Niche_overlap</em>". Within the "<em>Niche_overlap</em>" folder, an additional subdirectory named as the <em>Homo </em>species the user chose to analyze will be automatically created. In such subdirectory, all the results generated by the function are stored. The function run ends by exporting three graphs (as .TIFF files) showing boxplots with BCNs vs ECN niche overlap ("SchoenersD_boxplot.tif"), multivariate distance between the barycentres of BCNs and ECN ("Bary.dist_boxplot.tif") and PCA plots ("Niche.pca.plot.tif"; see main manuscript for further details). calculate.vulnerability <strong>Description</strong> The function calculates the <em>Homo </em>species vulnerability to climatic changes occurred between the penultimate and the last bin. For <em>H. neanderthalensis</em> and <em>H</em>.<em> sapiens</em>, the function calculates [...]
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This study investigates the effect of climate changes (during the Ice Ages) on the evolution of Plio-Pleistocene large land mammal communities of the Italian peninsula. We recognized paleocommunities by using both the classic,... more
This study investigates the effect of climate changes (during the Ice Ages) on the evolution of Plio-Pleistocene large land mammal communities of the Italian peninsula. We recognized paleocommunities by using both the classic, biochronologic approach and with a special type of cluster analysis able to recognize a statistically discrete number of paleocommunities. These approaches ensure the potential for including rare species, dilute taphonomic biases, and give stronger emphasis on the conjoint occurrence of species. Irrespective of the way we partitioned the fossil record, our results are consistent with the prediction that climate changes affected Turnover Rates (TRs). We found out that only cold shifts in climate were effective in influencing communities' turnover. Phylogenetic and ecologic inheritance from Pliocene (warmer) climate probably made large mammal communities by far more sensitive to cold than to warm shifts in global temperature.Eventually, we discuss various potential flaws affecting studies on TRs. Those flaws depend on the phylogenetic, geographic and body-size level of investigation. The existence of these restrictions makes studies on turnover hardly comparable with each other.
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When, where, and how often hominin interbreeding happened is largely unknown. We study the potential for Neanderthal-Denisovan admixture using species distribution models that integrate extensive fossil, archaeological, and genetic data... more
When, where, and how often hominin interbreeding happened is largely unknown. We study the potential for Neanderthal-Denisovan admixture using species distribution models that integrate extensive fossil, archaeological, and genetic data with transient coupled general circulation model simulations of global climate and biomes. Our Pleistocene hindcast of past hominins’ habitat suitability reveals pronounced climate-driven zonal shifts in the main overlap region of Denisovans and Neanderthals in central Eurasia. These shifts, which influenced the timing and intensity of potential interbreeding events, can be attributed to the response of climate and vegetation to past variations in atmospheric carbon dioxide and Northern Hemisphere ice-sheet volume. Therefore, glacial-interglacial climate swings likely played an important role in favoring gene flow between archaic humans.
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&lt;p&gt;&lt;strong&gt;It has previously been suggested that climate shifts during the last 2 million years played an important role in the evolution of our genus &lt;em&gt;Homo&lt;/em&gt;. However,... more
&lt;p&gt;&lt;strong&gt;It has previously been suggested that climate shifts during the last 2 million years played an important role in the evolution of our genus &lt;em&gt;Homo&lt;/em&gt;. However, quantifying this linkage has remained challenging. Here we use an unprecedented transient Pleistocene Coupled General Circulation model simulation in combination with an extensive compilation of fossil and archaeological records, to study the spatio-temporal habitat suitability of five hominin species over the past 2 million years. We show that astronomically-forced changes in temperature, rainfall and terrestrial net primary production had a major impact on their observed distributions. During the early Pleistocene hominins primarily settled in environments with weak orbital-scale climate variability. This behaviour changed drastically after the mid-Pleistocene-transition when archaic humans became global wanderers who adapted to a wide range of spatial climatic gradients, which increased &amp;#160;the likelihood for habitat overlap and cladogenic transitions.&amp;#160;Our robust numerical simulations of climate-induced habitat changes provide a novel framework to test hypotheses on our human origin. &lt;/strong&gt;&lt;/p&gt;
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It has long been believed that climate shifts during the last 2 million years had a pivotal role in the evolution of our genus Homo1–3. However, given the limited number of representative palaeo-climate datasets from regions of... more
It has long been believed that climate shifts during the last 2 million years had a pivotal role in the evolution of our genus Homo1–3. However, given the limited number of representative palaeo-climate datasets from regions of anthropological interest, it has remained challenging to quantify this linkage. Here, we use an unprecedented transient Pleistocene coupled general circulation model simulation in combination with an extensive compilation of fossil and archaeological records to study the spatiotemporal habitat suitability for five hominin species over the past 2 million years. We show that astronomically forced changes in temperature, rainfall and terrestrial net primary production had a major impact on the observed distributions of these species. During the Early Pleistocene, hominins settled primarily in environments with weak orbital-scale climate variability. This behaviour changed substantially after the mid-Pleistocene transition, when archaic humans became global wande...
Research Interests: Climate Change, Ecology, Medicine, Multidisciplinary, Pleistocene, and 3 moreNature, Habitat, and Homo Sapiens
Research Interests: Ichnology and Vertebrate
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&amp;amp;lt;p&amp;amp;gt;There are many interdisciplinary theories as to how climate variability impacted hominin migration, and subsequently human evolution. One such hypothesis concerns so-called &amp;amp;amp;#8220;green... more
&amp;amp;lt;p&amp;amp;gt;There are many interdisciplinary theories as to how climate variability impacted hominin migration, and subsequently human evolution. One such hypothesis concerns so-called &amp;amp;amp;#8220;green corridors,&amp;amp;amp;#8221; in which climate and biome variability periodically opened vegetated corridors between habitable areas. The periodic opening of these corridors may have acted as a pump through uninhabitable barrier regions, allowing for more wide-spread dispersal. We present results from a climate-forced agent-based model that furthers the green corridor hypothesis to include the effect of stochastic resonance in penetrating barrier regions. In other words, while it intuitively makes sense that hominins would explore and disperse as green corridors opened up, the potential for green corridors to act as a dispersal pump likely depended on having the right amount of stochasticity (randomness) in hominin movement to resonate with orbitally-paced climate signals, effectively penetrating these corridors and dispersing into other regions. We integrate data from a 2-million-year CESM model, from the BIOME4 vegetation model, and from archaeological archives to create a map of habitat suitability based on a species-specific climate envelope. This habitat suitability forces the agent-based hominin migration model, in which agents seek more habitable areas and the added randomness in that agent movement is varied. While our conclusions are largely independent of species, we show results from a &amp;amp;lt;em&amp;amp;gt;Homo erectus&amp;amp;lt;/em&amp;amp;gt; migration simulation. In my presentation I will discuss how stochastic hominin movement, the opening up of green corridors, and climate variability affected hominin dispersal throughout the Plio-Pleistocene.&amp;amp;lt;/p&amp;amp;gt;
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Sampling details. (XLSX 54 kb)
1Dipartimento di Biologia Ambientale, Sapienza Università di Roma, Rome (Italy) 2PalaeoHub, Department of Archaeology, University of York, York (United Kingdom) 3Dipartimento di Scienze Cardiovascolari, Respiratorie, Nefrologiche,... more
1Dipartimento di Biologia Ambientale, Sapienza Università di Roma, Rome (Italy) 2PalaeoHub, Department of Archaeology, University of York, York (United Kingdom) 3Dipartimento di Scienze Cardiovascolari, Respiratorie, Nefrologiche, Anestesiologiche e Geriatriche, Sapienza Università di Roma, Rome (Italy) 4Catalan Institute of Human Paleoecology and Social Evolution (IPHES), Tarragona (Spain) 5Àrea de Prehistòria, Facultat de Lletres, Universitat Rovira i Virgili, Tarragona (Spain) 6Dipartimento di Scienze della Terra, dell’Ambiente e delle Risorse, Università di Napoli, Federico II, Naples (Italy) 7Dipartimento di Biologia e di Biotecnologia, Sapienza Università di Roma, Rome (Italy) 8Dipartimento di Architettura, Università degli Studi di Roma Tre, Rome (Italy) 9Sincrotrone Trieste, SYRMEP, Trieste (Italy)
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Research Interests: Morphometrics and Biology
Research Interests: Mathematics and R package
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ObjectivesThe statistical analysis of fossil remains is essential to understand the evolution of the genus Homo. Unfortunately, the human fossil record is straight away scarce and plagued with severe loss of information caused by... more
ObjectivesThe statistical analysis of fossil remains is essential to understand the evolution of the genus Homo. Unfortunately, the human fossil record is straight away scarce and plagued with severe loss of information caused by taphonomic processes. The recently developed field of Virtual Anthropology helps to ameliorate this situation by using digital techniques to restore damaged and incomplete fossils.Materials and methodsWe present the package Arothron, an R software suite meant to process and analyze digital models of skeletal elements. Arothron includes tools to digitally extract virtual cavities such as cranial endocasts, to statistically align disarticulated or broken bony elements, and to visualize local variations between surface meshes and landmark configurations.ResultsWe describe the main functionalities of Arothron and illustrate their usage through reproducible case studies. We describe a tool for segmentation of skeletal cavities by showing its application on a mal...
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Background Understanding the mechanisms promoting or constraining morphological diversification within clades is a central topic in evolutionary biology. Ecological transitions are of particular interest because of their influence upon... more
Background Understanding the mechanisms promoting or constraining morphological diversification within clades is a central topic in evolutionary biology. Ecological transitions are of particular interest because of their influence upon the selective forces and factors involved in phenotypic evolution. Here we focused on the humerus and mandibles of talpid moles to test whether the transition to the subterranean lifestyle impacted morphological disparity and phenotypic traits covariation between these two structures. Results Our results indicate non-subterranean species occupy a significantly larger portion of the talpid moles morphospace. However, there is no difference between subterranean and non-subterranean moles in terms of the strength and direction of phenotypic integration. Conclusions Our study shows that the transition to a subterranean lifestyle significantly reduced morphological variability in talpid moles. However, this reduced disparity was not accompanied by changes ...
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Research Interests: Evolutionary Biology, Zoology, Multivariate Statistics, Morphometrics, Geometric Morphometrics, and 14 moreDiversity, Principal Component Analysis, Biology, Evolution, Systematics, Medicine, Language evolution and development, Procrustes Analysis, Growth, Allometry, Splines, Shape Space, Language Evolution and Development, and Univariate Analysis
Aim A major Late Quaternary vertebrate extinction event affected mostly large‐bodied ‘megafauna’. This is well documented in both mammals and birds, but evidence of a similar trend in reptiles is scant. We assess the relationship between... more
Aim A major Late Quaternary vertebrate extinction event affected mostly large‐bodied ‘megafauna’. This is well documented in both mammals and birds, but evidence of a similar trend in reptiles is scant. We assess the relationship between body size and Late Quaternary extinction in reptiles at the global level.Location Global.Methods We compile a body size database for all 82 reptile species that are known to have gone extinct during the last 50,000 years and compare them with the sizes of 10,090 extant reptile species (97% of known extant diversity). We assess the body size distributions in the major reptile groups: crocodiles, lizards, snakes and turtles, while testing and correcting for a size bias in the fossil record. We examine geographical biases in extinction by contrasting mainland and insular reptile assemblages, and testing for biases within regions and then globally by using geographically weighted models.Results Extinct reptiles were larger than extant ones, but there wa...