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The influence of climate on species distribution over time and space during the late Quaternary
... We collected fossil occurrences for 21 extinct and 10 extant large mammals living in Eurasia during the last 200 ka, belonging to the orders of Artiodactyla, Carnivora, Perissodactyla and Proboscidea. We enriched the fossil mammal occurrence databases published in Raia et al. (2009) and Carotenuto et al. (2016), by adding new records and supplementing stratigraphic context and aging of the fossil layers. Radiocarbon dates were calibrated by using the 'Bchron' R package (Parnell 2016), applying the 'Intcal20' calibration curve (Reimer et al. 2020). ...
... The imprint of humans on wildlife has gone through a long history, tracing back to the Late Pleistocene, when Homo sapiens started to colonize the world biota outside its African homeland, contributing to a massive extinction crisis affecting large mammals worldwide (Rule et al. 2012, Sandom et al. 2014, Berti and Svenning 2020. The effect of H. sapiens on its mammalian preys and competitors is more apparent where species were naïve to the new super-predator, that is in the Americas and Oceania, whilst the signature of human effects is milder in Africa and Eurasia (where megafauna species and H. sapiens had been in contact much longer) and possibly superseded by the contemporary effects of intense global climate change there (Cooper et al. 2015, Carotenuto et al. 2016, Di Febbraro et al. 2017. Current, large-scale investigations on Pleistocene ecosystems and their evolution are common for North America (Tóth et al. 2019, Seersholm et al. 2020 and Oceania (Rule et al. 2012, Hocknull et al. 2020) but rare for Eurasia, despite the highquality fossil record. ...
The idea that several small, rather than a single large, habitat areas should hold the highest total species richness (the so-called SLOSS debate) brings into question the importance of habitat fragmentation to extinction risk. SLOSS studies are generally addressed over a short time scale, potentially ignoring the long-term dimension of extinction risk. Here, we provide the first long-term evaluation of the role of habitat fragmentation in species extinction, focusing on 22 large mammal species that lived in Eurasia during the last 200 000 years. By combining species distribution models and landscape pattern analysis, we compared temporal dynamics of habitat spatial structure between extinct and extant species, estimating the size, number and degree of the geographical isolation of their suitable habitat patches. Our results evidenced that extinct mammals went through considerable habitat fragmentation during the last glacial period and started to fare worse than extant species from about 50 ka. In particular , our modelling effort constrains the fragmentation of habitats into a narrow time window, from 46 to 36 ka ago, surprisingly coinciding with known extinction dates of several megafauna species. Landscape spatial structure was the second most important driver affecting megafauna extinction risk (ca 38% importance), after body mass (ca 39%) and followed by dietary preferences (ca 20%). Our results indicate a major role played by landscape fragmentation on extinction. Such evidence provides insights on what might likely happen in the future, with climate change, habitat loss and fragmentation acting as the main forces exerting their negative effects on biodiversity.
... The function combines different phylogenies into a single synthetic time-calibrated tree. Here, the source phylogenies were published in Carotenuto et al. (2016) and Castiglione et al. (2021). The data, species and climatic variables are the same as in Mondanaro et al. (2021), which is welcome since it allows comparing SDM accuracy in this study directly to the SDM results we got in that study, where the entire fossil record was used. ...
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 to sample from, we demonstrate ENphylo provides good SDM evaluation scores, with area under the curve and Sørensen Index both consistently above 0.75, True Skills Statistics above 0.4 and Boyce Index above 0.5 in most cases, when just 10 fossil occurrences are randomly drawn from their respective fossil records. ENphylo proved significantly more accurate than ENFA and the ensemble of bivariate models using Maxent, Generalized Linear Model and Random Forest algorithms. Intriguingly, we found that randomly drawing as little as 10 occurrence data points per species allows ENphylo to perform equally well as Maxent run using the entire fossil record of these same species and data.
ENphylo provides a fast and accurate solution to perform species distribution modelling with rare species, which will help predicting their distribution in the light of climate change, and to delineate how rare extinct species reacted to past climatic variation.
... In order to measure the proximity of Montopoli to other fossil localities considered in this study, we performed a bootstrapping cluster analysis (BCA) on the occurrences of all the considered fossil sites. This partitioning methodology has been found to be useful for testing the robustness of the clustering results as shown in various papers (Raia et al., 2009;Carotenuto et al., 2016;Bartolini-Lucenti et al., 2022a, b). The procedure and steps of the BCA have been detailed in Bartolini-Lucenti et al., (2022a, b). ...
The Italian paleontologist Giovanni Capellini (1833-1922), internationally renowned for his studies on cetaceans, was the first to discover one of the most important sites for European land mammals biochronology of the Pliocene and Pleistocene, Montopoli (Pisa province; Tuscany). Excavated during the second half of the nineteenth century by the Swiss paleontologist Charles Immanuel Forsyth Major (1843-1923), the fauna from Montopoli differs greatly from the older sites of Italy and Europe. The presence of taxa adapted to more open country environments, typical of arid and progressively cooler habits, contrasts with the faunas of the Early Villafranchian (generally characterized by wooded, tropical/subtropical taxa). This difference led several scholars to regard the fauna of Montopoli as the base of the Middle s. The present study aims to investigate the relationships, in terms of similarity/differences, between the faunal association of Montopoli as compared to other Pliocene and Pleistocene ones from the Old World. Toward achieving this objective we used generic-based resemblance indices and permutative clustering methods attested in literature for their discrimination power. The results of our analysis strengthen the interpretation of the pivotal importance of the faunal association of Montopoli, not only at a regional level but also within a pan-Eurasian Pliocene and Pleistocene framework.
... Bootstrapping cluster analysis is a partitioning methodology that is useful to test the robustness of the clustering results. It was used in recent studies (Raia et al., 2009;Carotenuto et al., 2016b) to statistically identify Pleistocene communities of Eurasian large mammals. This methodology starts by performing a first clustering of items by means of the unweighted pair group method with arithmetic mean algorithm (UPGMA; Sokal, 1958) to generate a reference cluster of the original data set in which the fossil localities are grouped according to their taxonomic similarity. ...
We undertake a comparative mammalian zoogeographic analysis with the aim of revealing the extent to which the Dmanisi Early Pleistocene large mammal assemblage resembles, at the genus level, African, Arabian, and Eurasian localities of similar age. The inclusion of Old World Pliocene and Pleistocene mammalian faunas provides us with insights into the provincial origins of specific mammalian taxa and permits us to assess the relative affiliation of the Dmanisi mammalian faunas to other faunas in the Old World. Our analysis also allows us to consider hypotheses about the timing and direction of zoogeographic connections between western Eurasia and Africa during the Early Pleistocene. We utilize multiple zoogeographic analytical tools as a cross-comparison of Dmanisi with 42 other Eurasian and African mammalian-bearing localities between 2.7 and 0.7 Ma. Overall, we find that Dmanisi compares most closely with a subgroup of Greek, Italian, and Spanish localities that are slightly younger than Dmanisi itself. This could suggest a progressive dispersal from East to West of the large mammal communities during the late Early Pleistocene and the first occurrence at Dmanisi, and then later in Western Europe, of some taxa such as Stephanorhinus ex gr. etruscus-hundsheimensis, Equus altidens, Bison georgicus, Soergelia minor, Megantereon whitei, Canis borjgali, Canis (Xenocyon) lycaonoides. Dmanisi's habitats included drier areas, probably of open wooded savannah and grassland and by mountainous to semiarid rocky terrain. There is evidence that Dmanisi records short intervals of increased aridity in the middle part of the succession contemporaneous with the occurrence of Homo.
... With each glacial expansion and retreat over the Quaternary, species distributions would have been substantially altered (Gibson-Reinemer et al., 2015;Waltari et al., 2007). Broadly speaking, it is thought that the geographic distributions of cool-adapted species would have expanded during glacial maxima but contracted into refugia during interglacial periods, whereas warm-adapted species would experience the opposite effect (Carotenuto et al., 2016;Ohlemüller et al., 2012). ...
Climate shifts during the Quaternary Period have driven changes in regional range dynamics for many species, influencing population structure of species and in some cases promoting speciation. Within southern Africa, the psammophine snakes Psammophis trinasalis and P. namibensis were historically considered subspecies of P. leightoni but were elevated to species rank based on ecological differences. Preliminary phylogenetic analyses suggested intraspecific, not interspecific genetic variation between these taxa, but this finding was based on very limited data and could not be confirmed. To assess the level of genetic differentiation within the P. leightoni species complex, we explored the evolutionary history of these snakes by combining phylogenetic analyses, species distribution modelling and an examination of morphology. We generated a comprehensive, multi-gene phylogeny for Psammophis that included wider geographic sampling of the three species in the complex. Using this phylogeny, Bayesian and distance-based species delimitation analyses showed intraspecific, not interspecific divergences between taxa in the complex, suggesting that they collectively represent a single taxon. Furthermore, non-metric multidimensional scaling analysis of scalation characters showed no differences between the species. Moreover, palaeo-modelling at three time periods since the last interglacial period suggest that there have been varying levels of connectivity between these taxa, which has likely facilitated gene flow between them. Given the evidence, we propose that the P. leightoni complex represents a single species and therefore formally synonymise the three species.
... Understanding the effect of past climate changes on the composition of communities and its change over time and space is one of the major aims in ecology and paleoecology (Walther et al. 2002, Ovaskainen et al. 2013, Carotenuto et al. 2016) and a key challenge for forecasting species' susceptibility to future climate changes. Whilst climate change has gone on continuously throughout Earth's history, current human-driven climate changes apparently have no parallel in recent geological history (IPCC 2018). ...
Capsule: The distribution range of the European Roller Coracias garrulus has undergone large changes over geological times, but although the species is warm-adapted, the human induced climate change is predicted to affect negatively the range of the currently large populations.
Aim: Information on species-specific vulnerability to climate change is crucial not only for designing interventions and setting conservation goals, but also to inform conservation decision-making. Our goal was to map climate suitability for the European Roller in the Western Palaearctic under current climate, and for past (last glacial maximum and mid-Holocene) and future (2050 and 2070) climate scenarios.
Methods: We used MaxEnt for species distribution modelling based on the reconstructed distribution map of the species.
Results: Our results suggest that during glacial periods Rollers persisted in small southern refugia, and then spread and colonized northern latitudes during the mid-Holocene. In the future, our models forecast a shift in climatically suitable range towards northern latitudes and an overall small range contraction (4.5–5.5%). Warmer temperatures will increase climate suitability in northern countries where the species is currently declining or became locally extinct. On the other hand, wide suitable areas under current climatic conditions are predicted to become unsuitable in the future (35–38% by 2050 and 2070, respectively), significantly impacting large populations such as those in Romania, Spain, Bulgaria and Hungary. French and Italian populations are identified to be future key populations for Roller conservation.
Conclusions: Our findings suggest that future climate changes will likely amplify the impacts of existing threats on the majority of large European Roller populations in Europe.
... Understanding the effect of past climate changes on the composition of communities and its change over time and space is one of the major aims in ecology and paleoecology (Walther et al. 2002, Ovaskainen et al. 2013, Carotenuto et al. 2016) and a key challenge for forecasting species' susceptibility to future climate changes. Whilst climate change has gone on continuously throughout Earth's history, current human-driven climate changes apparently have no parallel in recent geological history (IPCC 2018). ...
The decline of farmland and grassland biodiversity is one the major conservation concerns nowadays. The European roller is a secondary cavity nester species typically inhabiting grasslands and farmlands. It has suffered large declines both in size and range of the population since the 1960s, but this negative trend has been reversed in several countries by applying direct conservation actions. As part of this study we aimed to evaluate the current habitat suitability of the historical breeding area of the species within Hungary, to promote the recolonization and the enlargement of the breeding range in the Carpathian Basin, and to evaluate the potential significance of the Natura 2000 network in this process. We applied species distribution modelling (SDM) based on nest-box occupancy data to map potential areas for nest-box supplementation. Grasslands, broad-leaved forests and agricultural sites with significant areas of natural vegetation were found to be the most important predictors. The majority (71%) of the predicted area has no occupied nest-boxes. A significantly larger proportion of grid cells with archive data still preserve suitable land cover composition for rollers, than cells where former breeding wasn’t confirmed, and only a small proportion of former breeding area has become completely unsuitable for the species. Our results indicate large overlaps between the Natura 2000 network and the predicted area, of wich 28.3% overlaps with Special Protection Area (SPA) sites and 23.8% with Special Area of Conservation (SAC/SCI) sites. Our study highlights the importance of promoting the recolonization of the European roller in the Transdanubian region of Hungary and provides a useful tool for direct conservation planning for the species. Our results also suggest that a coordinated network of protected areas such as Natura 2000 can potentially serve as core areas in the recolonization processes.
... We calibrated SDMs for U. spelaeus using its occurrence records from the Late Pleistocene fossil large mammal database published in Carotenuto et al. (2016). We extracted 160 occurrences covering the 72-24 kya timespan. ...
Cave bears (Ursus spelaeus) are an iconic component of the European late Quaternary Ice Age megafauna. Recent demographic analyses based on cave bear mtDNA sequences and refined radiocarbon dating indicate that cave bear population size and genetic diversity started to decline some 50 kilo years ago (kya). Hence, neither the coldest phase of the last glaciation (started some 24 kya), nor the colonization of Europe by Palaeolithic hunters (started some 45 kya) coincides with the beginning of population decline. Here, we reconstructed cave bear climatic niche evolution through time. Then, we performed spatially explicit population viability analyses to assess cave bear demographics through time in response to climatic changes, human effects on bear survival and their combination. We found that climate change was responsible for a 10‐fold decrease in cave bear population size after 40 kya. However, climate change on its own could not explain U. spelaeus extinction at 24 kya. Additional negative effects consistent with human population expansion are required to explain both U. spelaeus' retreat from eastern Europe since 40 kya and its final extinction.
... Considering the pairwise correlation between the predictors, we computed the variation inflation factors using a stepwise procedure. We then sub-selected the bioclimatic variables according to a threshold value of 10 (Carotenuto et al. 2016) and included six predictors: Mean Diurnal Range (BIO2), Isothermality (BIO3), Mean Temperature of Warmest Quarter (BIO10), Precipitation of Driest Month (BIO14), Precipitation of Warmest Quarter (BIO18), and Precipitation of Coldest Quarter (BIO19). ...
Interspecific variation in the craniofacial morphology of kangaroos and wallabies is associated with diet and feeding behaviors. Yet, to how fine a taxonomic scale this relationship might exist is unknown. Using a combination of established morphometric analyses and novel finite element approaches, we test the limits of these associations by examining three closely-related pademelon taxa: the red-necked pademelon (Thylogale thetis), and two subspecies of the red-legged pademelon (Thylogale stigmatica stigmatica and Thylogale stigmatica wilcoxi). All three taxa have distinct proportions of graze (grasses) and browse (leaves, stems, and branches of trees and shrubs) in their diets. We identified clear morphological differences in the crania between all three taxa and significant influences of geography and climate on cranial shape. We found significant differences in shape and strain magnitudes along the muzzle and cheek bones of each group that are consistent with the properties of their respective diets. These results suggest that feeding ecology influences craniofacial morphology down to the subspecies scale for at least some kangaroos and wallabies, which mirrors what is known at the macroevolutionary level for these species. This lends further weight to the predictive value of cranial morphology in determining feeding ecology among the Macropodiformes and may be of use in inferring feeding ecology of less accessible species for conservation and management.
... Megafauna extinction is also linked to climatic changes (Martin & Wright, 1967;Martin & Klein, 1984;Stuart, 1991;Carotenuto et al., 2016). Sometimes, overkill by H. sapiens is described as being the primary cause of extinctions, with only a small role for climate change (Sandom et al., 2014;Bartlett et al., 2016). ...
... P R E -P R I N T V E R S I O N causa más probable de la extinción, generando un activo debate que aún continúa (Koch y Barnosky, 2006;Smith et al., 2016;Ricánková et al., 2018). Algunos científicos sostienen que antes de su extinción muchas especies de la megafauna experimentaron un declive continuado que se ha correlacionado con importantes cambios climáticos (Guthrie, 2001;Nogués-Bravo et al., 2010;Carotenuto et al., 2016;Ricánková et al., 2018), otros, proponen que una intensa caza o la alteración de los hábitats por los humanos condujeron a la extinción de estos animales (Martin, 1967;Martin y Steadman, 1999;Surovell et al., 2005Surovell et al., , 2016Gill et al., 2009;Zimov et al., 2012, Sandom et al., 2014a y, finalmente, el grupo más numeroso de autores suponen que la extinción se produjo por una combinación de ambas causas (Stuart, 2005(Stuart, , 2015Koch y Barnosky 2006;Pushkina y Raia, 2008;MacDonald et al., 2012;Markova et al., 2013;Bartlett et al., 2016). Por otra parte, se ha descrito cómo la pérdida de la megafauna determinó una cascada de efectos ecológicos que afectaron profundamente a la estructura de la vegetación y la función de los ecosistemas (Johnson, 2009;Gill, 2014;Bakker et al., 2016;Mahli et al., 2016;Smith et al., 2016), las interacciones planta-animal (Guimaraes et al., 2008), los regímenes de fuego (Rule et al., 2012), los ciclos biogeoquímicos (Doughty y Malhi, 2013) y el clima (Doughty et al., 2010;Smith et al., 2010). ...
Mega-herbivores (body mass greater than 1000 kg) help structuring the plant landscape through consumption, breakage and uprooting of numerous woody plants, tending to transform wooded areas into grass, shrub and forest mosaics. These mosaics contribute to maintain a high biodiversity, since they enable the persistence of plants and animals of dense forests and treeless steppes, which alternated in the European landscapes following the glacial cycles of the Pleistocene. The disappearance of the mega-herbivores from the Iberian Peninsula at the end of the Pleistocene probably caused a cascade of ecological effects that remains unknown. We also do not know if the causes of their disappearance were natural or anthropogenic, and consequently it is not know if the plant landscapes that developed later, in the Holocene, have a natural or anthropogenic origin.The aim of this review is to explore in the scientific literature the hypothesis that the transformation of the natural landscape by humans began after their arrival in Europe through the intensive hunting of large herbivores, until their disappearance or extreme reduction. Consequently, the forest recovery of the end of the Pleistocene and beginning of the Holocene might have taken place without the containment that these animals would have exerted on woody vegetation in the previous interglacials. As a result, dense forests would spread over large territories reducing pastures and herbivores of open spaces, which were the sustenance of Homo sapiens in the Pleistocene. This limitation would force humans to change their diet to survive and, in a relatively short period of time, to adopt a new way of life-style based on livestock and agriculture.The results of the review do not allow us to support or reject the hypothesis raised, or even any of the most relevant issues arising from it. Some fundamental grounds of this hypothesis are currently debated, and are giving rise to contrasting interpretations.The most relevant ecological aspects found after the literature review are discussed, some ideas are proposed for their interpretation, and the limitations of the paleo-ecological information available in the literature to answer general questions such as those posed here, are emphasized.
... Associating traits with responses in the correlated response model allows explaining differences in the estimated model coefficients among trait groups (Hui and Poisot, 2016). We fitted our JSDM using a Poisson distribution of errors including two latent variables (Carotenuto et al., 2016;D'Amen et al., 2017;Inoue et al., 2017). Moreover, we accounted for potential non-independence of sampling sites by including plot ID as a random effect (i.e., random 'site' effect; Hui and Poisot, 2016). ...
Deadwood and microhabitats play a fundamental role in many forest ecosystem processes. Deadwood provides the substrate for a multitude of wood-dependent organisms, as well as a variety of microhabitats. Deadwood is a key factor in maintaining the ecosystem functionality and increasing the overall forest biodiversity. In Mediterranean forests, the relationship between stand-structure attributes and species-diversity indicators is still poorly investigated. In this study, we hypothesized that the abundance of saproxylic species was influenced by (i) the composition and amount of deadwood, and (ii) the heterogeneity in types and density of microhabitats. The investigation was carried out in a broadleaved mixed forest located in Central Apennine (Italy), in which silvicultural interventions were interrupted for several decades. The experimental area extends on approximately 240 ha; structural traits, deadwood and microhabitats were sampled on 50 plots of 530 m 2. Saproxylic beetles were collected using window flight traps and emergence traps on decaying deadwood. We applied joint species distribution models (JSDM) to quantify the relationship between forest attributes and the abundance of sa-proxylic species, explicitly including their functional traits (e.g., trophic level). Results demonstrated that mi-crohabitats, living biomass, basal area and coarse woody debris had a significant effect of saproxylic beetles belonging to different trophic categories. Considering the conservation status, only the stand basal area significantly affected the abundance of Near Threatened (NT) saproxylic beetles. This study highlighted the importance of integrating multiple biodiversity indicators to find sustainable solutions for conservation purposes, unlike many studies on conservation-oriented management strategies, more frequently focused on independent forest biodiversity indicators.
... We applied Bayesian co-occurrence analysis to evaluate how far the co-occurrence pattern of the breeding sites of the two species may be explained by similar environmental requirements rather than by other factors, namely biotic interactions. To explore this pattern, we used joint SDMs (Pollock et al., 2014;Hui et al., 2015;Carotenuto et al., 2016;Di Febbraro et al., 2017). This method prescribes modelling species cooccurrence using multivariate probit regression models (Agresti, 2007), parameterized by a latent variable formulation. ...
The peregrine falcon has shown an increasing tendency to replace the lanner falcon at its breeding sites in the Mediterranean area. This has been suggested as the main cause of the reduction in the distribution of the lanner observed in central Italy. We focused on these two falcon species to disentangle the relative contribution of habitat filtering and biotic interactions on the co-occurrence of their breeding sites. We hypothesized that the replacement of lanner breeding sites with peregrine falcon breeding sites is due to competitive exclusion rather than to environmental factors, and predicted how land-use change might affect falcon species distributions and biotic interactions. To test our hypothesis, we proposed a modelling framework including niche overlap tests, Bayesian co-occurrence analysis and species distribution models (SDMs). A significant niche similarity emerged between the breeding sites used exclusively by peregrine or lanner falcons, and those used by both species. Bayesian co-occurrence analysis showed that biotic interactions significantly explained the negative co-occurrence between the two falcon species. SDMs predicted that land-use change would reduce suitable breeding habitats exclusive of each species as well as those suitable for both falcons. Results of niche overlap and co-occurrence analysis provided strong support for the hypothesis of competitive interaction for breeding sites between peregrine and lanner falcons in central Italy. The out-competed lanner falcon would be displaced from optimal habitats by the peregrine and forced to exploit suboptimal habitats to minimize competition. While competition with the peregrine may represent a threat for the lanner in the short term, habitat loss due to land-use change will pose a more severe threat for the long-term persistence of lanner falcon in central Italy.
... To construct this database, we started from the late Pleistocene fossil large mammal database published in Carotenuto et al. (2016). Whereas, for humans, we considered a temporal interval between 40 and 10 ka, for the megafauna, we extended the data back to 72 ka, which is the limit of the palaeoclimatic data. ...
... Th is conceptual approach is in line with the tendency to bridge gaps between evolutionary history and community ecology to gain a better understanding on biogeographical patterns of species richness (Hawkins et al. 2005, Cadotte et al. 2010. Recent studies in Quaternary science are starting to jointly apply SDMs and phylogenetic comparative methods to better understand the infl uence of climate changes in the assemblage of mammalian communities over space and time (Carotenuto et al. 2016). We explicitly explore the hypothesis that species richness is an accumulative result of historical processes. ...
Quaternary climate changes have contributed to shape the biogeographic distribution of extant species. The combination of climatic niche conservatism and glacial-interglacial cycles forced many species to retract their range limits for surviving under the advance of Pleistocene ice-sheets. Refugia offered geographical opportunities for species to retreat, persist and, later on, begin recolonization processes under favourable environmental conditions. Here we explore the hypothesis that refugia have been not only crucial for the survival of multiple species but also acted as speciation centres for Western Palaearctic mammals. We define ‘recurrent massive refugia’ as those geographical regions that have historically accumulated the highest levels of co-occurring species for several Quaternary cycles. Our assemblage-level analyses identify the existence of refugia within the Iberian Peninsula and the Atlantic French margin that were recurrently selected by most mammals. The topographic heterogeneity, climatic stability and microhabitat availability of these refugial areas may have offered suitable habitat conditions for multiple species during different climatic events over time. Using a Bayesian analysis of macroevolutionary mixtures we detected that the higher level of divergence and accumulative evolutionary changes in mammals of the Western Palaearctic are found in refugia. The continuous retractions and expansions of species’ ranges during the Pleistocene promoted temporal changes in the composition and richness of communities in this biogeographic region. The reorganization of ecological composition driven by cyclical climatic events may have favoured the emergence of biotic interactions and ecological responses conducive to novel selective pressures. Our findings suggest, first, that multiple climatic changes in the form of glacial-interglacial transitions during the Quaternary have left a detectable imprint on the observed geographical patterns of species richness in mammalian faunas of the Western Palaearctic, and second, highlight the importance of refugia for the preservation of species (‘museums’) and as centers of speciation and endemism (‘cradles’) as well. This article is protected by copyright. All rights reserved.
Understanding the processes that underlie the current distribution of genetic diversity in endangered species is a goal of modern conservation biology. Specifically, the role of colonization and dispersal events throughout a species’ evolutionary history often remains elusive. The loggerhead sea turtle (Caretta caretta) faces multiple conservation challenges due to its migratory nature and philopatric behaviour. Here, using 4207 mtDNA sequences, we analysed the colonisation patterns and distribution of genetic diversity within a major ocean basin (the Atlantic), a regional rookery (Cabo Verde Archipelago) and a local island (Island of Boa Vista, Cabo Verde). Data analysis using hypothesis-driven population genetic models suggests the colonization of the Atlantic has occurred in two distinct waves, each corresponding to a major mtDNA lineage. We propose the oldest lineage entered the basin via the isthmus of Panama and sequentially established aggregations in Brazil, Cabo Verde and in the area of USA and Mexico. The second lineage entered the Atlantic via the Cape of Good Hope, establishing colonies in the Mediterranean Sea, and from then on, re-colonized the already existing rookeries of the Atlantic. At the Cabo Verde level, we reveal an asymmetric gene flow maintaining links across island-specific nesting groups, despite significant genetic structure. This structure stems from female philopatric behaviours, which could further be detected by weak but significant differentiation amongst beaches separated by only a few kilometres on the island of Boa Vista. Exploring biogeographic processes at diverse geographic scales improves our understanding of the complex evolutionary history of highly migratory philopatric species. Unveiling the past facilitates the design of conservation programmes targeting the right management scale to maintain a species’ evolutionary potential.
Estimating fossil species' geographic range is a major goal for paleobiologists. In the deep time, this is most commonly performed by using polygon‐based methods such as the minimum convex polygon (MCP) or the Alpha‐Hull. Unfortunately, such methods provide a poor representation of the fossil species' actual range, because they are unable to take control of the severe stochastic and taphonomic biases.
Here, we introduce MInOSSE (massively interpolated occurrences for species spatial estimation), a model‐based method that combines a machine learning algorithm and geostatistical approaches to reconstruct a target fossil species' geographic ranges by relying on the distribution of other coeval species and without using environmental predictors.
We tested MInOSSE by using many simulated fossil species' distributions, comparing its performance with MCP and Alpha‐Hull outcomes and applying it to real case studies.
In all simulations, MInOSSE outperformed the competing methods. Interestingly, the superior performance of MInOSSE becomes more apparent when the fossil record of the target species is scarce, that is, when appropriate range reconstruction is most problematic with polygon‐based methods.
MInOSSE is a powerful tool for researchers interested in studying geographic range evolution, effects of range size on extinction risk, as well as biodiversity dynamics and macroecological patterns in the deep time.
Paleozoologists have long used taxa represented by ancient faunal remains to reconstruct paleoenvironments. Those ancient environments were the selective contexts in which hominin biological and cultural evolution took place. Knowing about those particularistic selective environments and how organisms responded to them is increasingly seen as critically important to identifying both how biota will respond to future (to some degree anthropogenically driven) environmental change, and biological conservation and management applications that will ensure sustainability of ecological resources and services. Reconstructing paleoenvironments requires knowledge of species’ ecological tolerances, geographic ranges, habitats, environments, and niches. It also requires assumptions that extant species had the same ecological tolerances in the past as they do today and that changes in taxonomic composition or abundances reflect environmental change rather than sampling or taphonomic factors. Greater knowledge of ecological processes as well as increased analytical sophistication in paleozoology is providing increasingly rigorous and detailed insights to paleoenvironments.
Species co-occur with different sets of other species across their geographical distribution,which can be either closely or distantly related. Such co-occurrence patterns and their phylogenetic structure within individual species ranges represent what we call the species phylogenetic fields (PFs). These PFs allow investigation of the role of historical processes—speciation, extinction and dispersal—in shaping species co-occurrence patterns, in both extinct and extant species. Here, we investigate PFs of large mammalian species during the last 3 Myr, and how these correlate with trends in diversification rates. Using the fossil record, we evaluate species’ distributional and co-occurrence patterns along with their phylogenetic structure. We apply a novel Bayesian framework on fossil occurrences to estimate diversification rates through time. Our findings highlight the effect of evolutionary processes and past climatic changes on species’ distributions and co-occurrences. From the Late Pliocene to the Recent, mammal species seem to have responded in an individualistic manner to climate changes and diversification dynamics, co-occurring with different sets of species from different lineages across their geographical ranges. These findings stress the difficulty of forecasting potential effects of future climate changes on biodiversity. © 2016 The Author(s) Published by the Royal Society. All rights reserved.
Large herbivores and carnivores (the megafauna) have been in a state of decline and extinction since the Late Pleistocene, both on land and more recently in the oceans. Much has been written on the timing and causes of these declines, but only recently has scientific attention focused on the consequences of these declines for ecosystem function. Here, we review progress in our understanding of how megafauna affect ecosystem physical and trophic structure, species composition, biogeochemistry, and climate, drawing on special features of PNAS and Ecography that have been published as a result of an international workshop on this topic held in Oxford in 2014. Insights emerging from this work have consequences for our understanding of changes in biosphere function since the Late Pleistocene and of the functioning of contemporary ecosystems, as well as offering a rationale and framework for scientifically informed restoration of megafaunal function where possible and appropriate.
Significance
Coincident with the human colonization of the Western Hemisphere, dozens of genera of Pleistocene megafauna were lost to extinction. Following Martin, we argue that declines in the record of radiocarbon dates of extinct genera may be used as an independent means of detecting the first presence of humans in the New World. Our results, based on analyses of radiocarbon dates from Eastern Beringia, the contiguous United States, and South America, suggest north to south, time, and space transgressive declines in megafaunal populations as predicted by the overkill hypothesis. This finding is difficult to reconcile with other extinction hypotheses. However, it remains to be determined whether these findings will hold with larger samples of radiocarbon dates from all regions.
Debate over the late Quaternary megafaunal extinctions has focussed on whether human colonisation or climatic changes were more important drivers of extinction, with few extinctions being unambiguously attributable to either. Most analyses have been geographically or taxonomically restricted and the few quantitative global analyses have been limited by coarse temporal resolution or overly simplified climate reconstructions or proxies. We present a global analysis of the causes of these extinctions which uses high-resolution climate reconstructions and explicitly investigates the sensitivity of our results to uncertainty in the palaeological record. Our results show that human colonisation was the dominant driver of megafaunal extinction across the world but that climatic factors were also important. We identify the geographic regions where future research is likely to have the most impact, with our models reliably predicting extinctions across most of the world, with the notable exception of mainland Asia where we fail to explain the apparently low rate of extinction found in in the fossil record. Our results are highly robust to uncertainties in the palaeological record, and our main conclusions are unlikely to change qualitatively following minor improvements or changes in the dates of extinctions and human colonisation.This article is protected by copyright. All rights reserved.
Body mass has important physiological and ecological implications. The high degree of variability in herbivore mammals' body mass is linked to differences in their gut anatomy, which, in turn, has important effects on their feeding habits. We aimed to untangle the effects of Cope's and Bergmann's rule on the evolution of body size in even-toed hoofed mammals (Artiodactyla, Mammalia). By using variation partitioning techniques and direct sister species comparisons, we estimated the potential effects of latitude, time and phylogeny on body size variation in Cenozoic Artiodactyls. We tested whether species tend to be larger when living at higher latitudes as compared to their phylogenetically closest relative, whether closely-related species living in sympatry tend to diverge more in body size, and whether recent species tend to be larger than their older relatives. Our results showed that both latitudinal and temporal trends in Artiodactyla body size are evident throughout the Cenozoic, and became particularly intense during the coldest part of it. Artiodactyls tend to be larger than their close relatives when living at higher latitudes, in keeping with Bergmann's rule. Yet, this relationship is weakened by the strong tendency for sister species to diverge in body size when living nearby. We also found a clear tendency for late Artiodactyl species to be larger, and live for shorter, than their ancestors.
Thus, there is strong evidence that the evolution of body size in even-toed hoofed mammals was influenced by climatic changes, and by an overall tendency to grow larger, mostly in coincidence with the vegetation shift from forested to grassland biomes which characterized the second half (Neogene) of the Cenozoic. Although Cope's and Bergmann's rule in mammals are often portrayed as having climate change as a common explanation, our data suggest they are mechanistically separate phenomena.
We study a mechanistic mathematical model of extinction and coexistence in a
generic hunter-prey ecosystem. The model represents typical scenarios of human
invasion and environmental change, characteristic of the late Pleistocene,
concomitant with the extinction of fauna in many regions of the world. As a
first approach we focus on a small trophic web of three species, including two
herbivores in asymmetric competition, in order to characterize the generic
behaviors. Specifically, we use a stochastic dynamical system, allowing the
study of the role of fluctuations and spatial correlations. We show that the
presence of hunters drives the superior herbivore to extinction even in
habitats that would allow coexistence, and even when the pressure of hunting is
lower than on the inferior one. The role of system size and fluctuating
populations is addressed, showing an ecological meltdown in small systems in
the presence of humans. The time to extinction as a function of the system
size, as calculated with the model, shows a good agreement with paleontological
data. Other findings show the intricate play of the anthropic and environmental
factors that may have caused the extinction of megafauna.
Many paleontologists have noticed the broadly similar patterns between the changes in Cenozoic mammalian diversity and taxonomic dominance and climate changes. Yet detailed studies of fossil population samples with fine-scale temporal resolution during episodes of climate change like the Eocene-Oligocene transition in the White River Group, and the late Pleistocene at Rancho La Brea tar pits, demonstrates that most fossil mammal species are static and show no significant microevolutionary response to major climate changes. This mismatch between patterns seems best explained by species sorting. As the punctuated equilibrium model demonstrated, over long time spans most fossil species are stable and do not respond to climate change. Instead, change occurs at the next hierarchical level, with species sorting adding and subtracting to the total diversity pattern revealed by coarse-scale taxon counting, apparently responding to longer-term changes in climate as revealed by proxies like the oxygen isotope record.
This paper provides an overview of the contentious issue of global megafaunal extinctions in the Late Quaternary. The main proposed causes are ‘overkill’, environmental change or a combination of both. There are major objections to the other suggested causes. Extinctions were highly variable in their severity between different zoogeographical regions, with the greatest impact in North America, South America and Australia, but also substantial in northern Eurasia. Sub-Saharan Africa and Southern Asia were much less affected. For northern Eurasia, detailed chronologies show a staggered extinction pattern, in which each megafaunal species exhibits unique and complex distributional shifts, culminating in extinction for some species and survival in others. Environmental drivers were clearly very important, although the possible role of humans is not yet clear. Alaska/Yukon also has a good radiocarbon record which also suggests a staggered extinction pattern. However, the available data for the rest of North America are largely unsatisfactory. South America also boasted spectacular extinct megafauna, but again the currently available dates are insufficient to reliably discern patterns or possible causes. Australia and New Guinea also suffered major losses, but extinctions probably occurred much earlier than elsewhere, so that establishing a chronology is especially difficult. Africa and Southern Asia have the least available data. In order to make meaningful progress, it is vital to establish a large database of reliable radiocarbon dates for each region made directly on securely identified megafaunal remains. The need is for much more high quality data, not more debate based on imperfect evidence. Copyright © 2014 John Wiley & Sons, Ltd.
Deep-time perspectives in macroecology are essential with regard to understanding the impact of climate forcing on faunal communities. Using late Miocene rodent faunas (12 to 5 Ma) from two different biogeographical provinces from southwestern Europe, we asked whether the waxing and waning of faunas with dissimilar ecological affinities tracked climate in different ways. The latest middle Miocene featured a fauna dominated by dormice with forest and mixed-habitat affinities. This group declined towards the Upper Miocene. Rodent taxa with the highest values of richness at the beginning of the Upper Miocene are generalists in the southern province and specialists of forested habitats in the northern province. Finally, we identified a third, increasingly significant group of rodents linked to open landscapes towards the end of the Miocene. These three broad ecological groups showed differential responses to a complex set of interconnected circumstances, including the biogeographic structure of the study area and climatic changes throughout time.
Background: Community phylogenetics is an emerging field of research that has made
important contributions to understanding community assembly. The rapid development of this
field can be attributed to the merging of phylogenetics and community ecology research to
provide improved clarity on the processes that govern community structure and composition.
Question: What are the major challenges that impede the sound interpretation of the patterns
and processes of phylogenetic community assembly?
Methods: We use four scenarios to illustrate explicitly how the phylogenetic structure of
communities can exist in stable or transient phases, based on the different combinations
of phylogenetic relationships and phenotypic traits among co-occurring species. We discuss
these phases by implicating a two-way process in the assembly and disintegration of the given
ecological community.
Conclusions: This paper synthesizes the major concepts of community phylogenetics using
habitat filtering and competition processes to elucidate how the understanding of phylogenetic
community structure is currently hindered by the dynamics of community assembly and
disassembly.
Environmental conditions, dispersal lags, and interactions among species are major factors structuring communities through time and across space. Ecologists have emphasized the importance of biotic interactions in determining local patterns of species association. In contrast, abiotic limits, dispersal limitation, and historical factors have commonly been invoked to explain community structure patterns at larger spatiotemporal scales, such as the appearance of late Pleistocene no-analog communities or latitudinal gradients of species richness in both modern and fossil assemblages. Quantifying the relative influence of these processes on species co-occurrence patterns is not straightforward. We provide a framework for assessing causes of species associations by combining a null-model analysis of co-occurrence with additional analyses of climatic differences and spatial pattern for pairs of pollen taxa that are significantly associated across geographic space.
Recent hypotheses argue that phylogenetic relatedness should predict both the niche differences that stabilise coexistence and the average fitness differences that drive competitive dominance. These still largely untested predictions complicate Darwin's hypothesis that more closely related species less easily coexist, and challenge the use of community phylogenetic patterns to infer competition. We field parameterised models of competitor dynamics with pairs of 18 California annual plant species, and then related species' niche and fitness differences to their phylogenetic distance. Stabilising niche differences were unrelated to phylogenetic distance, while species' average fitness showed phylogenetic structure. This meant that more distant relatives had greater competitive asymmetry, which should favour the coexistence of close relatives. Nonetheless, coexistence proved unrelated to phylogeny, due in part to increasing variance in fitness differences with phylogenetic distance, a previously overlooked property of such relationships. Together, these findings question the expectation that distant relatives should more readily coexist.
The European wild ass (Equus hydruntinus) is a globally extinct Eurasian equid. This species was widespread in Europe and southwest Asia during the Late Pleistocene, but its distribution became restricted to southern Europe and adjacent geographic regions in the Holocene. Previous research on E. hydruntinus has focused predominantly on its taxonomy and Late Pleistocene distribution. However, its Holocene distribution and extinction remain poorly understood, despite the fact that the European wild ass represents one of Europe's very few globally extinct Holocene megafaunal mammal species. We summarise all available Holocene zooarchaeological spatio-temporal occurrence data for the species, and analyse patterns of its distribution and extinction using point pattern analysis (kernel density estimation and Clark Evans index) and optimal linear estimation. We demonstrate that the geographic range of E. hydruntinus became highly fragmented into discrete subpopulations during the Holocene, which were associated with separate regions of open habitat and which became progressively extinct between the Neolithic and Iron Age. These data challenge previous suggestions of the late survival of E. hydruntinus into the medieval period in Spain, and instead suggest that postglacial climate-driven vegetational changes were a primary factor responsible for extinction of the species, driving isolation of small remnant subpopulations that may have been increasingly vulnerable to human exploitation. This study contributes to a more nuanced understanding of Late Quaternary species extinctions in Eurasia, suggesting that they were temporally staggered and distinct in their respective extinction trajectories.
A primary goal of ecology is to understand the fundamental processes underlying the geographic distributions of species. Two major strands of ecology – habitat modelling and community ecology – approach this problem differently. Habitat modellers often use species distribution models ( SDM s) to quantify the relationship between species’ and their environments without considering potential biotic interactions. Community ecologists, on the other hand, tend to focus on biotic interactions and, in observational studies, use co‐occurrence patterns to identify ecological processes. Here, we describe a joint species distribution model ( JSDM ) that integrates these distinct observational approaches by incorporating species co‐occurrence data into a SDM .
JSDM s estimate distributions of multiple species simultaneously and allow decomposition of species co‐occurrence patterns into components describing shared environmental responses and residual patterns of co‐occurrence. We provide a general description of the model, a tutorial and code for fitting the model in R. We demonstrate this modelling approach using two case studies: frogs and eucalypt trees in Victoria, Australia.
Overall, shared environmental correlations were stronger than residual correlations for both frogs and eucalypts, but there were cases of strong residual correlation. Frog species generally had positive residual correlations, possibly due to the fact these species occurred in similar habitats that were not fully described by the environmental variables included in the JSDM . Eucalypt species that interbreed had similar environmental responses but had negative residual co‐occurrence. One explanation is that interbreeding species may not form stable assemblages despite having similar environmental affinities.
Environmental and residual correlations estimated from JSDM s can help indicate whether co‐occurrence is driven by shared environmental responses or other ecological or evolutionary process (e.g. biotic interactions), or if important predictor variables are missing. JSDM s take into account the fact that distributions of species might be related to each other and thus overcome a major limitation of modelling species distributions independently.
At the last deglaciation Earth's largest biome, mammoth-steppe, vanished. Without knowledge of the productivity of this ecosystem, the evolution of man and the glacial–interglacial dynamics of carbon storage in Earth's main carbon reservoirs cannot be fully understood. Analyzes of fossils 14C dates and reconstruction of mammoth steppe climatic envelope indicated that changing climate wasn't a reason for extinction of this ecosystem. We calculate, based on animal skeleton density in frozen soils of northern Siberia, that mammoth-steppe animal biomass and plant productivity, even in these coldest and driest of the planet's grasslands were close to those of an African savanna. Numerous herbivores maintained ecosystem productivity. By reducing soil moisture and permafrost temperature, accumulating carbon in soils, and increasing the regional albedo, mammoth-steppe amplified glacial–interglacial climate variations. The re-establishment of grassland ecosystems would slow permafrost thawing and reduce the current warming rate. Proposed methods can be used to estimate animal density in other ecosystems.
Climate change may disrupt interspecies phenological synchrony, with adverse consequences to ecosystem functioning. We present here a 40-y-long time series on 10,425 dates that were systematically collected in a single Russian locality for 97 plant, 78 bird, 10 herptile, 19 insect, and 9 fungal phenological events, as well as for 77 climatic events related to temperature, precipitation, snow, ice, and frost. We show that species are shifting their phenologies at dissimilar rates, partly because they respond to different climatic factors, which in turn are shifting at dissimilar rates. Plants have advanced their spring phenology even faster than average temperature has increased, whereas migratory birds have shown more divergent responses and shifted, on average, less than plants. Phenological events of birds and insects were mainly triggered by climate cues (variation in temperature and snow and ice cover) occurring over the course of short periods, whereas many plants, herptiles, and fungi were affected by long-term climatic averages. Year-to-year variation in plants, herptiles, and insects showed a high degree of synchrony, whereas the phenological timing of fungi did not correlate with any other taxonomic group. In many cases, species that are synchronous in their year-to-year dynamics have also shifted in congruence, suggesting that climate change may have disrupted phenological synchrony less than has been previously assumed. Our results illustrate how a multidimensional change in the physical environment has translated into a community-level change in phenology.
Glacial refugia were core areas for the survival of temperate species during unfavourable environmental conditions and were the sources of postglacial recolonizations. Unfortunately, the locations of glacial refugia of animals and plants are usually described by models, without reference to facts about real geographical ranges at that time.
Careful consideration of the faunal assemblages of archaeological sites from the Younger Palaeolithic, which are precisely dated to the Last Glacial Maximum (LGM), gives indications about the distribution of species during the LGM (23 000–16 000 bp ) and provides evidence for the locations of glacial refugia for mammalian species in Europe.
In Europe, 47 LGM sites, dating from 23 000 to 16 000 bp and containing typical temperate mammal species, have been described. The geographical range of these archaeological sites clearly shows a distribution which differs from the hypothesized traditional refuge areas of the temperate fauna. A considerable number of sites situated in the Dordogne in south‐western France and the Carpathian region contain records of red deer Cervus elaphus , roe deer Capreolus capreolus , wild boar Sus scrofa and red fox Vulpes vulpes .
The faunal composition of the majority of the evaluated Palaeolithic sites in the southern European peninsulas (with the exception of Greece), as well as France and the Carpathian region, indicates the co‐occurrence of these temperate species with cold‐adapted faunal elements such as mammoth Mammuthus primigenius and/or reindeer Rangifer tarandus .
The survival of species in Central European refugia would have significant consequences for phylogeography and would be revealed by the dominant distribution of haplotypes, originating from this region. A Carpathian refuge could also be the reason for the very early records of small mammals or mustelids from the Late‐Glacial or Interstadials before the LGM in regions like southern Germany.
Bootstrapping is a common method for assessing confidence in phylogenetic analyses. Although bootstrapping was first applied in phylogenetics to assess the repeatability of a given result, bootstrap results are commonly interpreted as a measure of the probability that a phylogenetic estimate represents the true phylogeny. Here we use computer simulations and a laboratory-generated phylogeny to test bootstrapping results of parsimony analyses, both as measures of repeatability (i.e., the probability of repeating a result given a new sample of characters) and accuracy (i.e., the probability that a result represents the true phylogeny). Our results indicate that any given bootstrap proportion provides an unbiased but highly imprecise measure of repeatability, unless the actual probability of replicating the relevant result is nearly one. The imprecision of the estimate is great enough to render the estimate virtually useless as a measure of repeatability. Under conditions thought to be typical of most phylogenetic analyses, however, bootstrap proportions in majority-rule consensus trees provide biased but highly conservative estimates of the probability of correctly inferring the corresponding clades. Specifically, under conditions of equal rates of change, symmetric phylogenies, and internodal change of less-than-or-equal-to 20% of the characters, bootstrap proportions of greater-than-or-equal-to 70% usually correspond to a probability of greater-than-or-equal-to 95% that the corresponding clade is real. However, under conditions of very high rates of internodal change (approaching randomization of the characters among taxa) or highly unequal rates of change among taxa, bootstrap proportions >50% are overestimates of accuracy.
Around 88 large vertebrate taxa disappeared from Sahul sometime during the Pleistocene, with the majority of losses (54 taxa) clearly taking place within the last 400,000 years. The largest was the 2.8-ton browsing Diprotodon optatum, whereas the ∼100- to 130-kg marsupial lion, Thylacoleo carnifex, the world's most specialized mammalian carnivore, and Varanus priscus, the largest lizard known, were formidable predators. Explanations for these extinctions have centered on climatic change or human activities. Here, we review the evidence and arguments for both. Human involvement in the disappearance of some species remains possible but unproven. Mounting evidence points to the loss of most species before the peopling of Sahul (circa 50-45 ka) and a significant role for climate change in the disappearance of the continent's megafauna.
Multiple episodes of rapid and gradual climatic changes influenced the evolution and ecology of mammalian species and communities throughout the Cenozoic. Climatic change influenced the abundance, genetic diversity, morphology, and geographic ranges of individual species. Within communities these responses interacted to catalyze immigration, speciation, and extinction. Combined they affected long-term patterns of community stability, functional turnover, biotic turnover, and diversity. Although the relative influence of climate on particular evolutionary processes is oft debated, an understanding of processes at the root of biotic change yields important insights into the complexity of mammalian response. Ultimately, all responses trace to events experienced by populations. However, many such processes emerge as patterns above the species level, where shared life history traits and evolutionary history allow us to generalize about mammalian response to climatic change. These generalizations provide the gr...
We suggest Milankovitch climate oscillations as a common cause for geographical patterns in species diversity, species' range sizes, polyploidy, and the degree of specialization and dispersability of organisms. Periodical changes in the orbit of the Earth cause climatic changes termed Milankovitch oscillations, leading to large changes in the size and location of species' geographical distributions. We name these recurrent changes "orbitally forced species' range dynamics" (ORD). The magnitude of ORD varies in space and time. ORD decreases gradual speciation (attained by gradual changes over many generations), increases range sizes and the proportions of species formed by polyploidy and other "abrupt" mechanisms, selects against specialization, and favor dispersability. Large ORD produces species prone neither to extinction nor gradual speciation. ORD increases with latitude, This produces latitudinal patterns, among them the gradient in species diversity and species' range sizes (Rapoport's rule). Differential ORD and its evolutionary consequences call for new conservation strategies on the regional to global scale.
A classic question in evolutionary biology concerns the tempo and mode of lineage evolution. Considered variously in relation to resource utilization, intrinsic constraints or hierarchic level, the question of how evolutionary change occurs in general has continued to draw the attention of the field for over a century and a half. Here we use the largest species-level phylogeny of Coenozoic fossil mammals (1031 species) ever assembled and their body size estimates, to show that body size and taxonomic diversification rates declined from the origin of placentals towards the present, and very probably correlate to each other. These findings suggest that morphological and taxic diversifications of mammals occurred hierarchically, with major shifts in body size coinciding with the birth of large clades, followed by taxonomic diversification within these newly formed clades. As the clades expanded, rates of taxonomic diversification proceeded independently of phenotypic evolution. Such a dynamic is consistent with the idea, central to the Modern Synthesis, that mammals radiated adaptively, with the filling of adaptive zones following the radiation.
Question: Does predatory pressure affect the abundance and survival of prey species in extinct communities? Data studied: Presence–absence data and body sizes of large mammals (partitioned into predators and prey) in Plio-Pleistocene Italian PaleoCommunities (PCOMs). Transformed variables: (1) Species' occupancy: number of presences/number of sites. (2) ADI: the index of disparity (ADI) reflects the relative abundance of a prey species in a PCOM. (3) Predatory pressure on a prey species: the proportion of predators in a given PCOM that are expected to feed on it. (4) Nestedness: the extent to which rare species occur only in the species-rich sites of a PCOM. Search method: For each PCOM, the effect of preservation biases on species' occupancy was assessed by a nestedness analysis. The ADI was computed for each prey species in each PCOM. Predatory pressure was calculated for each prey species. We used linear regression to test the effect of predatory pressure on ADI. Non-parametric correlation was performed to determine the effect of ADI on species survival. Results: Species prone to greater pressure appear at fewer sites than would be expected for their size alone. The relationship is limited to rare species only. Taphonomy does not explain this disparity. Abundant species survive longer than rare species. Conclusion: Predation controls abundance and local survival of rare species. In contrast, it does not affect abundant species.
The application of a new method for the analysis of the large mammal Plio-Quaternary communities of mainland Italy is presented. This method, named ''bootstrapped cluster analysis'', avoids, by mean of successive, ever more inclusive cluster analyses, the subjectivity in positioning boundaries of paleocommunities subdivisions. The results of this procedure indicate a good correspondence with previous qualitative analyses, albeit with some differences. Nevertheless, some local assemblages (e.g. Slivia) are grouped in significantly different positions than previously. The principal cause of these differences (as for unbalanced carnivores/herbivores ratio) is taphonomic bias. The bootstrapped cluster analysis approach is not affected by single species positioning as biochronological markers, grouping local assemblages upon their entire record with a statistical treatment. Moreover in this way any single paleocommunity is recognizable as an ecological/evolutionary unit.
Temporal patterns in species occupancy and geographic range size are a major topic in evolutionary ecology research. Here we investigate these patterns in Pliocene to Recent large mammal species and genera in Western Eurasia. By using an extensively sampled fossil record including some 700 fossil localities, we found occupancy and range size trajectories over time to be predominantly peaked among both species and genera, meaning that occupancy and range size reached their maxima midway along taxon existence. These metrics are strongly correlated with each other and to body size, after phylogeny is accounted for by using two different phylogenetic topologies for both species and genera. Phylogenetic signal is strong in body size, and weaker but significant in both occupancy and range size mean values among genera, indicating that these variables are heritable. The intensity of phylogenetic signal is much weaker and often not significant at the species level. This suggests that within genera, occupancy and range size are somewhat variable. However, sister taxa inherit geographic position (the center of their geographic distribution). Taken together, the latter two results indicate that sister species occupy similar positions on the earth's surface, and that the expansion of the geographic range during the existence of a given genus is driven by range expansion of one or more of the species it includes, rather than simply being the summation of these species ranges.
Mandibular corpus shape variability was investigated in seven families of both extant and extinct mammalian carnivores using two-dimensional landmarks and geometric morphometric methods. The landmark configuration represents the position of the fourth premolar relative to the canine and the lower carnassial, plus related features of the corpus profile. Between families, the corpus manifests differences in shape and allometry. Additionally, families differ in the relationship between the angle (a carnassial trait proxy for hypo-hypercarnivory) and mandibular corpus shape. When phylogenetic relatedness is taken into account using five different phylogenies as covariates, interspecific scaling is still present but the relationship between and corpus shape is no longer significant. This suggests that the allometric relationship reflects the physical constraints of mastication, resulting in relatively increased corpus depth with higher loads. In contrast, the angle is related to corpus curvature and this relationship is phylogenetically constrained by the reduction of the molar battery in large feliforms early during the carnivore radiation. In summary, large fissiped carnivores show extensive functional convergence in mandibular corpus shape although the evolutionary routes leading to such functional convergence are different. © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society, 2008, 154, 832–845.
Between fifty and ten thousand years ago, most large mammals be-came extinct everywhere except Africa. Slow-breeding animals also were hard hit, regardless of size. This unusual extinction of large and slow-breeding animals provides some of the strongest support for a human contribution to their extinction and is consistent with vari-ous human hunting models, but it is difficult to explain by models relying solely on environmental change. It is an oversimplification, however, to say that a wave of hunting-induced extinctions swept continents immediately after first human contact. Results from re-cent studies suggest that humans precipitated extinction in many parts of the globe through combined direct (hunting) and perhaps indirect (competition, habitat alteration) impacts, but that the tim-ing and geography of extinction might have been different and the worldwide magnitude less, had not climatic change coincided with human impacts in many places.
In the future, Arctic warming and the melting of polar glaciers will be considerable, but the magnitude of both is uncertain. We used a global climate model, a dynamic ice sheet model, and paleoclimatic data to evaluate Northern Hemisphere high-latitude warming and its impact on Arctic icefields during the Last Interglaciation. Our simulated climate matches paleoclimatic observations of past warming, and the combination of physically based climate and ice-sheet modeling with icecore constraints indicate that the Greenland Ice Sheet and other circum-Arctic ice fields likely contributed 2.2 to 3.4 meters of sea-level rise during the Last Interglaciation.
Farth's climate has experienced strong changes on timescales ranging from decades to millions of years. As biodiversity has evolved under these circumstances, dependence on these climate dynamics is expected. In this review, we assess the current state of knowledge on paleoclimatic legacies in biodiversity and ecosystem patterns. Paleoclimate has had strong impacts on past biodiversity dynamics, driving range shifts and extinctions as well as diversification. We outline theory for how these dynamics may have left legacies in contemporary patterns and review the empirical evidence. We report ample evidence that Quaternary glacial interglacial climate change affects current patterns of species distributions and diversity across a broad range of organisms and regions. We also report emerging evidence for paleoclimate effects on current patterns in phylogenetic and functional diversity and ecosystem functioning and for legacies of deeper-time paleoclimate conditions. Finally, we discuss implications for Anthropocene ecology and outline an agenda to improve our understanding of paleoclimate's role in shaping contemuoran-biodiversity and ecosystems.
Earth's climate has experienced strong changes on timescales ranging from decades to millions of years. As biodiversity has evolved under these circumstances, dependence on these climate dynamics is expected. In this review, we assess the current state of knowledge on paleoclimatic legacies in biodiversity and ecosystem patterns. Paleoclimate has had strong impacts on past biodiversity dynamics, driving range shifts and extinctions as well as diversification. We outline theory for how these dynamics may have left legacies in contemporary patterns and review the empirical evidence. We report ample evidence that Quaternary glacial-interglacial climate change affects current patterns of species distributions and diversity across a broad range of organisms and regions. We also report emerging evidence for paleoclimate effects on current patterns in phylogenetic and functional diversity and ecosystem functioning and for legacies of deeper-time paleoclimate conditions. Finally, we discuss implications for Anthropocene ecology and outline an agenda to improve our understanding of paleoclimate's role in shaping contemporary biodiversity and ecosystems.
Clovis groups in Late Pleistocene North America occasionally hunted several now extinct large mammals. But whether their hunting drove 37 genera of animals to extinction has been disputed, largely for want of kill sites. Overkill proponents argue that there is more archaeological evidence than we ought to expect, that humans had the wherewithal to decimate what may have been millions of animals, and that the appearance of humans and the disappearance of the fauna is too striking to be a mere coincidence. Yet, there is less to these claims than meets the eye. Moreover, extinctions took place amid sweeping climatic and environmental changes as the Pleistocene came to an end. It has long been difficult to link those changes to mammalian extinctions, but the advent of ancient DNA, coupled with high-resolution paleoecological, radiocarbon, and archeological records, should help disentangle the relative role of changing climates and people in mammalian extinctions.
Acknowledgements Chapter 1. Introduction 2. Ocean Sediments and Ice Cores 3. Ice Age Palaeoclimates and Computer Simulations 4. Glaciation History from the Last Interglacial to the Last Glacial Maximum 5. The Melting of the Last Great Ice Sheets 6. Ice Age Periglacial Environments 7. Lakes, Bogs and Mines 8. Rivers 9. Ice Age Aeolian Activity 10. Late Quarternary Volcanic Activity 11. Crustal and Sub-Crustal Effects 12. Late Quarternary Sea Level changes 13. Milankovitch Cycles and Late Quarternary Climate Change
The turnover-pulse hypothesis (TPH) makes explicit predictions concerning the potential responses of species to climate change, which is considered to be a major cause of faunal turnover (extinction, speciation, and migration). Previous studies have tested the TPH primarily by examining temporal correlations between turnover pulses and climatic events. It is rarely possible to dissect such correlations and observe turnover as it is occurring or to predict how different lineages will respond to climate change. Thus, whether climate change drives faunal turnover in the manner predicted by the TPH remains unclear. In this study, we test the underlying mechanics of the TPH using well-dated Quaternary ungulate records from southern Africa's Cape Floristic Region (CFR). Changes in sea level, vegetation, and topographic barriers across glacial-interglacial transitions in southern Africa caused shifts in habitat size and configuration, allowing us to generate specific predictions concerning the responses of ungulates characterized by different feeding habits and habitat preferences. Examples from the CFR show how climatically forced vegetation change and allopatry can drive turnover resulting from extinction and migration. Evidence for speciation is lacking, suggesting either that climate change does not cause speciation in these circumstances or that the evolutionary outcome of turnover is contingent on the nature and rate of climate change. Migrations and extinctions are observed in the CFR fossil record over geologically short time intervals, on the order of Milankovitch-scale climate oscillations. We propose that such climate oscillations could drive a steady and moderate level of faunal turnover over 10 4 -year time scales, which would not be resolved in paleontological records spanning 10 5 years and longer. A turnover pulse, which is a marked increase in turnover relative to previous and subsequent time periods, requires additional, temporally constrained climatic forcing or other processes that could accelerate evolutionary change, perhaps mediated through biotic interactions.
Unconstrained ordination is commonly used in ecology to visualize multivariate data, in particular, to visualize the main trends between different sites in terms of their species composition or relative abundance.
Methods of unconstrained ordination currently used, such as non‐metric multidimensional scaling, are algorithm‐based techniques developed and implemented without directly accommodating the statistical properties of the data at hand. Failure to account for these key data properties can lead to misleading results.
A model‐based approach to unconstrained ordination can address this issue, and in this study, two types of models for ordination are proposed based on finite mixture models and latent variable models. Each method is capable of handling different data types and different forms of species response to latent gradients. Further strengths of the models are demonstrated via example and simulation.
Advantages of model‐based approaches to ordination include the following: residual analysis tools for checking assumptions to ensure the fitted model is appropriate for the data; model selection tools to choose the most appropriate model for ordination; methods for formal statistical inference to draw conclusions from the ordination; and improved efficiency, that is model‐based ordination better recovers true relationships between sites, when used appropriately.
Quantitative analysis of macroecological patterns for late Pleistocene assemblages can be useful for disentangling the causes of late Quaternary extinctions (LQE). However, previous analyses have usually assumed linear relationships between macroecological traits, such as body size and range size/range shift, that may have led to erroneous interpretations. Here, we analyzed mammalian datasets to show how macroecological patterns support climate change as an important driver of the LQE, which is contrary to previous analyses that did not account for more complex relationships among traits. We employed quantile regression methods that allow a detailed and fine-tuned quantitative analysis of complex macroecological patterns revealed as polygonal relationships (i.e., constraint envelopes). We showed that these triangular-shaped envelopes that describe the macroecological relationship between body size and geographical range shift reflect nonrandom extinction processes under which the large-bodied species are more prone to extinction during events of severe habitat loss, such as glacial/interglacial transitions. Hence, we provide both a theoretical background and methodological framework to better understand how climate change induces body size-biased species sorting and shapes complex macroecological patterns.
Cited By (since 1996):18, Export Date: 26 November 2013, Source: Scopus
If we were to describe all the species on Earth and determine their distributions, we would solve the popularly termed 'Linnean' and 'Wallacean' shortfalls in biodiversity conservation. Even so, we would still be hindered by a 'Darwinian shortfall', that is, the lack of relevant phylogenetic information for most organisms. Overall, there are too few comprehensive phylogenies, large uncertainties in the estimation of divergence times, and, most critically, unknown evolutionary models linking phylogenies to relevant ecological traits and life history variation. Here, we discuss these issues and offer suggestions for further research to support evolutionary-based conservation planning.
1. Observed patterns in the fossil record reflect not just macroevolutionary dynamics, but preservation patterns. Sampling rates themselves vary not simply over time or among major taxonomic groups, but within time intervals over geography and environment, and among species within clades. Large databases of presences of taxa in fossil-bearing collections allow us to quantify variation in per-collection sampling rates among species within a clade. We do this separately not just for different time/stratigraphic intervals, but also for different geographic or ecologic units within time/stratigraphic intervals. We then re-assess per-million-year sampling rates given the distributions of per-collection sampling rates
2. We use simple distribution models (geometric and lognormal) to assess general models of per-locality sampling rate distributions given occurrences among appropriate fossiliferous localities. We break these down not simply by time period, but by general biogeographic units in order to accommodate variation over space as well as among species.
3. We apply these methods to occurrence data for Meso-Cenozoic mammals drawn from the Paleobiology Database and the New and Old Worlds fossil mammal database. We find that all models of distributed rates do vastly better than the best uniform sampling rates and that the lognormal in particular does an excellent job of summarizing sampling rates. We also show that the lognormal distributions vary fairly substantially among biogeographic units of the same age.
4. As an example of the utility of these rates, we assess the most likely divergence times for basal (Eocene–Oligocene) carnivoramorphan mammals from North America and Eurasia using both stratigraphic and morphological data. The results allow for unsampled taxa or unsampled portions of sampled lineages to be in either continent and also allow for the variation in sampling rates among species. We contrast five models using stratigraphic likelihoods in different ways to summarize how they might affect macroevolutionary inferences.
Red Queen hypotheses maintain that biotic interactions are the most important drivers of evolutionary change, whereas Court Jester hypotheses regard physical-environmental perturbations, such as climate change, as most important. Tests for the biotic effects of climate change that are conducted on too large a geographic scale can falsely reject the Court Jester because climate is so complex its manifestation is in opposite directions in different geographic areas. Consequently, faunal responses vary from place to place, and lumping of data from different climate zones averages out any local faunal responses. Likewise, tests that are conducted at inappropriate temporal scales will not be effective at distinguishing between the Red Queen and Court Jester.A test at a temporal and geographic scale that takes the above considerations into account suggests a biotic response of mammals to a climatic warming event in the northern Rocky Mountains 18.5–14.0 Ma (the late-Early Miocene climatic optimum). During the environmental perturbation, mammalian species richness possibly increased, faunal turnover was pronounced, and taxa adapted to warm, arid environments became more abundant in numbers of species and density of individuals. The data are consistent with environmental change—the Court Jester—driving evolutionary change at sub-continental spatial scales and temporal scales that exceed typical Milankovitch oscillations. The Red Queen may be active at smaller temporal and geographic scales.
Summary The use of a multidimensional extension of the minimum final prediction error (FPE) criterion which was originally developed
for the decision of the order of one-dimensional autoregressive process [1] is discussed from the standpoint of controller
design. It is shown by numerical examples that the criterion will also be useful for the decision of inclusion or exclusion
of a variable into the model. Practical utility of the procedure was verified in the real controller design process of cement
rotary kilns.
In this study we collected, in a database, faunal lists for more than 800 Eurasian fossil localities yielding large mammal remains so as to produce continental-level ecologic-evolutionary units (Eurasian Paleocommu-nities, EA PCOMs) via bootstrapped cluster analysis. EA PCOMs are meant to represent taxonomically distinct assemblages of species. EA PCOMs allow the evolution of large mammal assemblages to be traced both in time and space. This latter attribute (spatial resolution) represents the most important innovation here and contrasts with classic biochronologic schemes, from which EA PCOMs clearly depart. The merits and limitations of this innovation are discussed in detail.
Phylogenetic community structure and assembly is a burgeoning field in the discipline of community ecology. An array of statistical techniques have been developed in order to study whether or not local assemblages of species are a phylogenetically random, overdispersed, or clustered subset of the regional species pool to which they belong. Phylogenetic clustering or overdispersion depends on aspects of species evolutionary ecology, such as habitat preference, limits of similarity among closely related species, and how traits are inherited in ancestor-descendant relationships. Here I applied the first analysis of phylogenetic community structure and assembly to Plio-Pleistocene large mammal communities of western Eurasia, with the additional goal of verifying if the existing statistics are suitable to be used with fossil data. The results demonstrate that (1) the use of phylogeny in the study of community evolution is feasible with a number of diverse metrics, (2) phylogenetic distance between fossil communities provides an important addition to classic turnover metrics, and (3) the phylogenetic structure of Eurasian Ice-Age mammal communities changed significantly around 1 Ma, when these communities were filled with closely related species from both carnivore and herbivore clades.
The cave bear (Ursus spelaeus) was one of several spectacular megafaunal species that became extinct in northern Eurasia during the late Quaternary. Vast numbers of their remains have been recovered from many cave sites, almost certainly representing animals that died during winter hibernation. On the evidence of skull anatomy and low δ15N values of bone collagen, cave bears appear to have been predominantly vegetarian. The diet probably included substantial high quality herbaceous vegetation. In order to address the reasons for the extinction of the cave bear, we have constructed a chronology using only radiocarbon dates produced directly on cave bear material. The date list is largely drawn from the literature, and as far as possible the dates have been audited (screened) for reliability. We also present new dates from our own research, including results from the Urals. U. spelaeus probably disappeared from the Alps and adjacent areas – currently the only region for which there is fairly good evidence –c. 24 000 radiocarbon years BP (c. 27 800 cal. yr BP), approximately coincident with the start of Greenland Stadial 3 (c. 27 500 cal. yr BP). Climatic cooling and inferred decreased vegetational productivity were probably responsible for its disappearance from this region. We are investigating the possibility that cave bear survived significantly later elsewhere, for example in southern or eastern Europe.
Key Words community assembly and organization, phylogenetic conservatism, biogeography, species diversity, niche differentiation s Abstract As better phylogenetic hypotheses become available for many groups of organisms, studies in community ecology can be informed by knowledge of the evo-lutionary relationships among coexisting species. We note three primary approaches to integrating phylogenetic information into studies of community organization: 1. examining the phylogenetic structure of community assemblages, 2. exploring the phylogenetic basis of community niche structure, and 3. adding a community context to studies of trait evolution and biogeography. We recognize a common pattern of phy-logenetic conservatism in ecological character and highlight the challenges of using phylogenies of partial lineages. We also review phylogenetic approaches to three emer-gent properties of communities: species diversity, relative abundance distributions, and range sizes. Methodological advances in phylogenetic supertree construction, charac-ter reconstruction, null models for community assembly and character evolution, and metrics of community phylogenetic structure underlie the recent progress in these ar-eas. We highlight the potential for community ecologists to benefit from phylogenetic knowledge and suggest several avenues for future research.