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opencc-zeroJun 2020View details →

Data from: Homogenisation of carnivorous mammal ensembles caused by global range reductions of large-bodied hypercarnivores during the late Quaternary

Carnivorous mammals play crucial roles in ecosystems by influencing prey densities and behaviour, and recycling carrion. Yet, the influence of carnivores on global ecosystems has been affected by extinctions and range contractions throughout the Late Pleistocene and Holocene (~130 000 years ago to the current). Large-bodied mammals were particularly affected, but how dietary strategies influenced species' susceptibility to geographic range reductions remains unknown. We investigated 1) the importance of dietary strategies in explaining range reductions of carnivorous mammals (≥5% vertebrate meat consumption), and 2) differences in functional diversity of continental carnivore ensembles by comparing current, known ranges to current, expected ranges under a present-natural counterfactual scenario. The present-natural counterfactual estimates current mammal ranges had modern humans not expanded out of Africa during the Late Pleistocene and were not a main driver of extinctions and range contractions, alongside changing climates. Ranges of large-bodied hypercarnivorous mammals are currently smaller than expected, compared to smaller-bodied carnivorous mammals that consume less vertebrate meat. This resulted in consistent differences in continental functional diversity, whereby current ensembles of carnivorous mammals have undergone homogenisation through structural shifts towards smaller-bodied insectivorous and herbivorous species. The magnitude of ensemble structural shift varied among continents, with Australia experiencing the greatest difference. Weighting functional diversity by species' geographic range sizes caused a three-fold greater shift in ensemble centroids than when using presence-absence alone. Conservation efforts should acknowledge current reductions in the potential geographic ranges of large-bodied hypercarnivores and aim to restore functional roles in carnivore ensembles, where possible, across continents.

opencc-zeroJul 2020View details →

Data from: Late Quaternary environmental and human impacts on the mitochondrial DNA diversity of four commensal rodents in Myanmar

We addressed the spatiotemporal characteristics of four commensal rodent species occurring in Myanmar in comparison with other areas of the Indo-Malayan region. We examined sequence variations of the mitochondrial cytochrome bgene (Cytb) in the Pacific rat (Rattus exulans), roof rat(Rattus rattuscomplex, RrC), lesser bandicoot rat (Bandicota bengalensis), and house mouse(Mus musculus) using the recently developed time-dependent evolutionary rates of mtDNA. The Cytbsequences of RrC from Myanmar were shown to belong to RrC Lineage II, and their level of genetic diversity was relatively high compared to those of the other three species. RrC was found to have experienced bottleneck and rapid expansion events at least twice in the late Pleistocene period in Myanmar and a nearby region. Accordingly, paleoclimatic environmental fluctuations were shown to be an important factor affecting rodents in the subtropics of the Indo-Malayan region. Our results show that human activities during the last 10,000 years of the Holocene period affected the population dynamics of the rodent species examined, including introducing them to Myanmar from neighboring countries. Further study of these four commensal rodents in other geographic areas of the Indo-Malayan region would allow us to better understand the factors that drove their evolution and their ecological trends.

opencc-zeroSep 2020View details →

Data from: Community assembly and climate mismatch in Late-Quaternary eastern North American pollen assemblages

Plant community response to climate change ranges from synchronous tracking to strong mismatch. Explaining this variation in climate change response is critical for accurate global change modeling. Here we quantify how closely assemblages track changes in climate (match/mismatch) and how broadly climate niches are spread within assemblages (narrow/broad ecological tolerance, or 'filtering') using data for the last 21 ka for 531 eastern North American fossil pollen assemblages. Although climate matching has been strong over the last 21 millennia, mismatch increased in 30% of assemblages during the rapid climate shifts between 14.5 to 10 ka BP. Assemblage matching rebounded towards the present day in 10-20% of assemblages. Climate-assemblage mismatch was greater in tree-dominated and high-latitude assemblages, consistent with persisting populations, slower dispersal rates, and glacial retreat. In contrast, climate matching was greater for assemblages comprising taxa with higher median seed mass. Over half of the assemblages were climatically filtered at any given time, with peak filtering occurring at 8.5 ka BP for nearly 80% of assemblages. Thus, vegetation assemblages have highly variable rates of climate mismatch and filtering over millennial scales. These climate responses can be partially predicted by species' traits and life histories. These findings help constrain predictions for plant community response to contemporary climate change.

opencc-zeroOct 2020View details →

Data for Body mass-related changes in mammal community assembly patterns during the late Quaternary of North America

The late Quaternary of North America was marked by prominent ecological changes, including the end-Pleistocene megafaunal extinction, the spread of human settlements, and the rise of agriculture. Here we examine the mechanistic reasons for temporal changes in mammal species association and body size during this time period. Building upon the co-occurrence results from Lyons et al. (2016) – wherein each species pair was classified as spatially aggregated, segregated, or random – we examined body mass differences (BMD) between each species pair for each association type and time period (Late Pleistocene: 40,000 14C - 11,700 14C ybp, Holocene: 11,700 14C - 50 ybp, and Modern: 50 - 0 yrs). In the Late Pleistocene and Holocene, the BMD of both aggregated and segregated species pairs was significantly smaller than the BMD of random pairs. These results are consistent with environmental filtering and competition as important drivers of community structure in both time periods. Modern assemblages showed a breakdown between BMD and co-occurrence patterns: the average BMD of aggregated, segregated, and random species pairs did not differ from each other. Collectively, these results indicate that the late Quaternary mammalian extinctions not only eliminated many large- bodied species but were followed by a re-organization of communities that altered patterns of species coexistence and associated differences in body size.

opencc-zeroAug 2021View details →

Regionally divergent drivers of historical diversification in the late Quaternary in a widely distributed generalist species, the common pheasant Phasianus colchicus

Aim: Pleistocene climate and associated environmental changes have influenced phylogeographic patterns of many species. These not only depend on a species' life history but also vary regionally. Consequently, populations of widespread species that occur in several biomes might display different evolutionary trajectories. We aimed to identify regional drivers of diversification in the common pheasant, a widely distributed ecological generalist. Study location Asia Taxon common pheasant Phasianus colchicus Methods Using a comprehensive geographic sampling of 204 individuals from the species' entire range genotyped at seven nuclear and two mitochondrial loci, we reconstructed spatio-temporal diversification and demographic history of the common pheasant. We applied Bayesian phylogenetic inference to describe phylogeographic structure, generated a species tree, and inferred demographic history within and migration between lineages. Moreover, to establish a taxonomic framework, we conducted a species delimitation analysis. Results The common pheasant diversified during the late Pleistocene into eight distinct lineages. It originated at the edge of the Qinghai-Tibetan plateau and spread to East and Central Asia. Only the widely distributed lowland lineage of East Asia displayed recent range expansion. Greater phylogeographic structure was identified elsewhere, with lineages showing no sign of recent demographic changes. One lineage in south-central China is the result of long-term isolation within a climatically stable but topographically complex region. In lineages from arid Central Asia and China, range expansions were impeded by repeated population fragmentation during dry glacial periods and by recent aridification. Main conclusions Spatio-temporal phylogeographic frameworks of widespread taxa such as the common pheasant provide valuable opportunities to identify divergent drivers of regional diversification. Our results suggest that diversification and population histories in the eight distinct evolutionary lineages were shaped by regionally variable effects of past climate and associated environmental changes. The evolutionary history of the common pheasant is best reflected by its being split into three species.

opencc-zeroDec 2012View details →

Data from: Influence of late Quaternary climate change on present patterns of genetic variation in valley oak, Quercus lobata Née

Phylogeography and ecological niche models (ENMs) suggest that late Quaternary glacial cycles have played a prominent role in shaping present population genetic structure and diversity, but have not applied quantitative methods to dissect the relative contribution of past and present climate vs. other forces. We integrate multilocus phylogeography, climate-based ENMs and multivariate statistical approaches to infer the effects of late Quaternary climate change on contemporary genetic variation of valley oak (Quercus lobata Née). ENMs indicated that valley oak maintained a stable distribution with local migration from the last interglacial period (~120 ka) to the Last Glacial Maximum (~21 ka, LGM) to the present compared with large-scale range shifts for an eastern North American white oak (Quercus alba L.). Coast Range and Sierra Nevada foothill populations diverged in the late Pleistocene before the LGM [104 ka (28–1622)] and have occupied somewhat distinct climate niches, according to ENMs and coalescent analyses of divergence time. In accordance with neutral expectations for stable populations, nuclear microsatellite diversity positively correlated with niche stability from the LGM to present. Most strikingly, nuclear and chloroplast microsatellite variation significantly correlated with LGM climate, even after controlling for associations with geographic location and present climate using partial redundancy analyses. Variance partitioning showed that LGM climate uniquely explains a similar proportion of genetic variance as present climate (16% vs. 11–18%), and together, past and present climate explains more than geography (19%). Climate can influence local expansion–contraction dynamics, flowering phenology and thus gene flow, and/or impose selective pressures. These results highlight the lingering effect of past climate on genetic variation in species with stable distributions.

opencc-zeroDec 2017View details →

Data from: Plant controls on Late Quaternary whole ecosystem structure and function

Plants and animals influence biomass production and nutrient cycling in terrestrial ecosystems; however their relative importance remains unclear. We assessed the extent to which mega-herbivore species controlled plant community composition and nutrient cycling, relative to other factors during and after the Late Quaternary extinction event in Britain and Ireland, when two-thirds of the region's mega-herbivore species went extinct. Warmer temperatures, plant-soil and plant-plant interactions, and reduced burning contributed to the expansion of woody plants and declining nitrogen availability in our five study ecosystems. Shrub biomass in particular was consistently one of the strongest predictors of ecosystem change, equaling or exceeding the effects of other biotic and abiotic factors. In contrast, there was relatively little evidence for mega-herbivore control on plant community composition and nitrogen availability. The ability of plants to determine the fate of terrestrial ecosystems during periods of global environmental change may therefore be greater than previously thought.

opencc-zeroDec 2013View details →

Data from: Late Quaternary deep-sea ostracode taxonomy of the eastern North Atlantic Ocean

Taxonomic revision and re-evaluation of the eastern North Atlantic deep-sea ostracodes are conducted based on late Quaternary sediments from Ocean Drilling Program (ODP) Hole 982A, Rockall Plateau, eastern North Atlantic. Twenty one genera and 51 species were examined and (re-)illustrated with high-resolution scanning electron microscopy images. Six new species are described: Polycope lunaris, Argilloecia labri, Bythoceratina nuda, Cytheropteron colesoabyssorum, Cytheropteron colesopunctatum, and Cytheropteron paramediotumidum. Excellent fossil ostracode preservation in this sediment core enabled us to provide a robust taxonomic baseline of the eastern North Atlantic deep-sea ostracodes for application to palaeoceanographical, palaeoecological, and biogeographical studies.

opencc-zeroDec 2010View details →

Data from: The influence of Late Quaternary climate-change velocity on species endemism

The effects of climate change on biodiversity should depend in part on climate displacement rate (climate-change velocity) and its interaction with species' capacity to migrate. We estimated Late Quaternary glacial-interglacial climate-change velocity by integrating macroclimatic shifts since the Last Glacial Maximum with topoclimatic gradients. Globally, areas with high velocities were associated with marked absences of small-ranged amphibians, mammals and birds. The association between endemism and velocity was weakest in the highly vagile birds and strongest in the weakly dispersing amphibians, linking dispersal ability to extinction risk due to climate change. High velocity was also associated with low endemism at regional scales, especially in wet and aseasonal regions, where conditions otherwise favor high richness. Overall, we show that low-velocity areas are essential refuges for Earth's many small-ranged species.

opencc-zeroDec 2021View details →

Data from: Reintroducing extirpated herbivores could partially reverse the late Quaternary decline of large and grazing species

Aim: Reinstating large, native herbivores is an essential component of ecological restoration efforts, as these taxa can be important drivers of ecological processes. However, many herbivore species have gone globally or regionally extinct during the last 50,000 years, leaving simplified herbivore assemblages and trophically downgraded ecosystems. Here, we discuss to what extent trophic rewilding can undo these changes by reinstating native herbivores. Location: Global Time Period: We report functional trait changes from the Late Pleistocene to the present, and estimated trait changes under future scenarios. Major Taxa Studied: Wild, large (≥10 kg), terrestrial, mammalian herbivores Methods: We use a functional trait dataset containing all late Quaternary large herbivores ≥10 kg to look at changes in the body mass and diet composition of herbivore assemblages, a proxy for species' ecological effects. First, we assess how these traits have changed from the Late Pleistocene to the present. Next, we quantify how the current body mass and diet composition would change if all extant, wild herbivores were restored to their native ranges (and if no functional replacements were used), exploring scenarios with different baselines. Results: Defaunation has primarily removed large and grazing herbivores. Reinstating extant herbivores across their native ranges would reverse these changes, especially when reinstating them to their prehistoric distributions. It would partially restore herbivore body mass and diet composition to pre-anthropogenic conditions. However, in the absence of complementary interventions (e.g. introducing functional replacements), many herbivore assemblages would remain down-sized and browser dominated, relative to pre-anthropogenic conditions. Main Conclusions: Many terrestrial herbivore assemblages - and hence ecosystems - would remain trophically downgraded, even after bringing back all extant, native herbivores. Therefore, complementary interventions would be required to achieve complete functional restoration. Nevertheless, our findings suggest that reintroducing the remaining native herbivores would diversify the herbivory and disturbances of herbivore assemblages.

opencc-by-4.0Jan 2022View details →

LegacyPollen 1.0: A taxonomically harmonized global Late Quaternary pollen dataset of 2831 records with standardized chronologies

This repository consists of code for downloading pollen data from the Neotoma Paleoecology Database, the harmonization of pollen taxa, and the assignment of age-depth data so that datasets for customized harmonization levels can be easily established. The input data includes a harmonization table and example data, stored in machine-readable data format (.CSV).

opennotspecifiedNov 2017View details →

Distribution. Recorded as living animal from the vicinity of Lake Habbema (3225 m) and an area close to Mt Trikora, WC New Guinea. Late Quaternary subfossils reported (as Hydromys habbema) from Kelangurr Cave and from alluvial terrace of West Baliem River, at 280-2950 m,Papua Province. Tentative record of habbema from a fissure deposit at 3450 m on Mt Jaya requires confirmation. in Muridae

Distribution. Recorded as living animal from the vicinity of Lake Habbema (3225 m) and an area close to Mt Trikora, WC New Guinea. Late Quaternary subfossils reported (as Hydromys habbema) from Kelangurr Cave and from alluvial terrace of West Baliem River, at 280-2950 m,Papua Province. Tentative record of habbema from a fissure deposit at 3450 m on Mt Jaya requires confirmation.

FIGURE 4 in A new species of extinct Late Quaternary giant tortoise from Hispaniola

FIGURE 4. Plastron and carapace fragments of Chelonoidis marcanoi sp. nov. from Pedernales Province, Dominican Republic: a, d, epiplastron fragment (MNHNSD FOS 23.1056), external and internal views; b, e, epiplastron fragment (MNHNSD FOS 23.1060), external and internal views; c, h, costal fragment (NHMUK PV R 36955), internal and external views; f–g, peripheral fragment (MNHNSD FOS 23.1061), external and internal views; i–j, fragment from border of carapacial rim, including two peripherals and part of costal plate (MNHNSD FOS 23.1062), external and internal views. Scale bar=2 cm.

FIGURE 1 in A new species of extinct Late Quaternary giant tortoise from Hispaniola

FIGURE 1. Map of Hispaniola, showing geotectonic boundaries and locations of cave sites from which giant tortoise fossils have been reported. Capital cities indicated with filled stars. Key: 1, Cueva del Papayo; 2, Cueva No. 12; 3, Cueva de las Tortugas; 4, Cueva del Muerto; 5, Cueva de las Caritas; 6, Bayaguana.

FIGURE 3 in A new species of extinct Late Quaternary giant tortoise from Hispaniola

FIGURE 3. Femora of Chelonoidis marcanoi sp. nov. from Pedernales Province, Dominican Republic: a–c, MNHNSD FOS 23.1063, left femur (young individual), lateral, anterior and medial views; d–e, MNHNSD FOS 23.1055, right distal femur, anterior and lateral views. Scale bar=2 cm.

FIGURE 2 in A new species of extinct Late Quaternary giant tortoise from Hispaniola

FIGURE 2. Humeri of Chelonoidis marcanoi sp. nov. from Pedernales Province, Dominican Republic: a–b, NHMUK PV R 36954 (holotype), right humerus, anterior and medial views; c–d, MNHNSD FOS 23.1064, left proximal humerus, medial and lateral views; e–f, MNHNSD FOS 23.1058, right humerus, anterior and lateral views; g–h, MNHNSD FOS 23.1054, left humerus, anterior and medial views; i, MNHNSD FOS 23.1059, right distal humerus, anterior view; j–k, MNHNSD FOS 23.1057, left humerus (young individual), anterior and medial views. Scale bar=2 cm.

FIGURE 6 in A new species of extinct Late Quaternary giant tortoise from Hispaniola

FIGURE 6. Schematic drawing of dermal bones of chelonian carapace (left) and plastron (right), indicating approximate estimated position of described shell fragments of Chelonois marcanoi sp. nov. from Pedernales Province, Dominican Republic. Original position on either the left or right side of the carapace is uncertain for the two specimens indicated with asterisks.