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Extended Data Fig. 2 in Skeleton of a Cretaceous mammal from Madagascar reflects long-term insularity

Extended Data Fig. 2 | Bivariate plots of body mass estimates for A. hui. a, Relationship between cranial length and body mass in 423 extant mammals, plus estimated body mass in the gondwanatherians A.hui and Vintana sertichi. b, Relationship between cranial width and body mass in 423 extant mammals, plus the estimated body mass in A. hui and V.sertichi. c, Relationship between cranial size and body mass in 423 extant mammals,plus the estimated body mass in A.hui and V.sertichi. d, Relationship between humeral length and body mass in 187 extant therian mammals,plus the estimated body mass in A.hui. e, Relationship between femoral length and body mass in 184 extant species of therian mammal,plus the estimated body mass in A.hui. f, Relationship between stylopodial diaphyseal circumference and body mass as calculated for a sample of 245 tetrapod species45 (data points shown for mammals only, n = 200),plus the estimated body mass in A.hui. Regression lines in a–e are from ordinary least squares regressions,whereas the regression line shown in f is from a phylogenetic generalized least squares regression.Measurement data,methods and references are provided in the Supplementary Information.

Fig. 2 in Skeleton of a Cretaceous mammal from Madagascar reflects long-term insularity

Fig. 2 | Cranium, lower jaw and dentition of A. hui holotype (UA 9030). a–d, Reconstructed cranium in dorsal (a), ventral (b), right lateral (c) and anterior (d) views.e–g, Reconstructed right lower jaw in lateral (e), dorsal (= occlusal) (f) and medial (g) views.h–k, Micro-computed tomography (ΜCT) digital renderings of right upper dentition,showing the postcanine teeth (h), distal incisor (i) and mesial incisor (j) in buccal views,and the postcanine teeth in occlusal view (k). l–n, ΜCT digital renderings of right lower dentition, showing the postcanine teeth (l) and incisor (m) in buccal views,and the postcanine teeth in occlusal view (n). Scale bars,2 cm (a–g; scale bar above e and f applies to a–g), 5 mm (h–n). PC,upper postcanine tooth; pc,lower postcanine tooth.

Fig. 4 in Skeleton of a Cretaceous mammal from Madagascar reflects long-term insularity

Fig. 4 | Key stages in plate tectonic history of Madagascar. a, Position of Madagascar before rifting between West Gondwana (South America and Africa) and East Gondwana (Madagascar,Seychelles,Indian subcontinent, Sri Lanka,Antarctica and Australia) at 183 Myr ago (Early Jurassic epoch). b, Separation of Indo-Madagascar from Antarctica and Australia at 124 Myr ago (mid-Early Cretaceous epoch).c, Separation of Indian subcontinent from Madagascar at 88 Myr ago (mid-Late Cretaceous epoch).d, Approximate time of deposition of Maevarano Formation at 66 Myr ago (latest Cretaceous period).Solid black lines indicate current coastlines of Madagascar and east Africa; brown represents Precambrian terranes;and yellow indicates sedimentary basins along west coast of Madagascar.The discovery site of UA 9030 is indicated by red star in d. Scale bars,500 km.Maps adapted from Earthworks (www.reeves.nl/gond.com).

Extended Data Fig. 10 in Skeleton of a Cretaceous mammal from Madagascar reflects long-term insularity

Extended Data Fig. 10 | Phylogenetic relationships of A. hui and selected mammaliaforms. Strict consensus tree of 16 equally parsimonious trees (tree length = 2,315,consistency index = 0.3015 and retention index = 0.7001) derived from analysis of 84 cynodont taxa and 530 characters,with multistate characters unordered and unweighted.Bremer values are listed next to the nodes.Adalatherium is highlighted in red.Allotheria—consisting of Cifelliodon, Euharamiyida,Gondwanatheria (including Adalatherium) and Multituberculata—is highlighted in blue.Taxon and character lists,the data matrix,limitations and assumptions,phylogenetic methods and a more detailed explanation of the results are provided in the Supplementary Information.

Extended Data Fig. 5 in Skeleton of a Cretaceous mammal from Madagascar reflects long-term insularity

Extended Data Fig. 5 | Lower jaw of A. hui holotype (UA 9030). Photographs of left dentary in left column; photographs of right dentary in right column. a, b, Lateral views.c, d, Dorsal (occlusal) views.e, f, Medial views.i, lower incisor;pc, lower postcanine tooth.

Fig. 3 in Skeleton of a Cretaceous mammal from Madagascar reflects long-term insularity

Fig. 3 | Skeleton of A. hui holotype (UA 9030). a–g, Digitally reconstructed skeleton in left lateral view,highlighting the left scapulocoracoid in lateral view (a), thoracic vertebra 6 and lumbar vertebra 7 in anterior and dorsal views (missing parts mirrored and rendered as semi-transparent) (b), the left femur in distal and anterior views (c), the left humerus in anterior and distal views (d), the left astragalus and navicular in anterior view,and left calcaneus in medial and dorsal views (e), left hind foot in dorsal view (f), and the left tibia in lateral and anterior views (g). L,lumbar vertebra; T,thoracic vertebra.Scale bars,5 cm (main skeleton),1 cm (a–d, f, g), 5 mm (e).

Fig. 1 in Skeleton of a Cretaceous mammal from Madagascar reflects long-term insularity

Fig. 1 | Skull and postcranial skeleton of A. hui holotype (UA 9030). a, 'Top' view,as preserved.Scale bar,5 cm.b, Reconstruction in left lateral view.Left and right sides indicated as (l) and (r), respectively.

Extended Data Fig. 9 in Skeleton of a Cretaceous mammal from Madagascar reflects long-term insularity

Extended Data Fig. 9 | Pectoral and pelvic girdle elements of A. hui holotype (UA 9030). a–d, ΜCT images.a, b, Left scapulacoracoid,left and right clavicle and manubrium in 'top' (a) and 'bottom' (b) views (as preserved).c, d, Left os coxa and epipubic bone in lateral (c) and medial (d) views.

Extended Data Fig. 3 in Skeleton of a Cretaceous mammal from Madagascar reflects long-term insularity

Extended Data Fig. 3 | Cranium of A. hui holotype (UA 9030). a–e, Photographs of external surfaces of cranium in right lateral (a), left lateral (b), dorsal (c), ventral (d) and anterior (e) views.a'–e', Labelled ΜCT images of cranium in the same views as in a–e, respectively.f, Labelled ΜCT image of medial view of right side of nasal cavity.aC,alveolus for upper canine; as, alisphenoid;eo, exoccipital; fr,frontal;ID,distal upper incisor;IM,mesial upper incisor; ju, jugal; la, lacrimal;mx, maxilla; na, nasal;os/ps, orbitosphenoid/presphenoid complex;PC,upper postcanine tooth;pe, petrosal;pmx,premaxilla;pt,pterygoid;smx,septomaxilla;sq, squamosal; v,vomer.

opencc-zeroMay 2021View details →

Data from: Long-term mark-recapture and growth data for large-sized migratory brown trout (Salmo trutta) from Lake Mjøsa, Norway

This data package contains two unique publicly available time series of individual-based data originating from a 51-year mark-recapture study of a land-locked population of large-sized migratory brown trout (Salmo trutta) in Norway: the Hunder trout. In the period 1966-2015, nearly 14,000 adult Hunder trout have been captured and individually marked during their spawning migration from Lake Mjøsa to the river Gubrandsdalslågen. Almost a third of those individuals were later recaptured alive during a later spawning run and/or captured by fishermen and reported dead or alive. This has resulted in the first data series: a mark-recapture-recovery dataset spanning half a century and more than 18,000 capture records. The second data series consists of additional data on juvenile and adult growth and life-history schedules from half of the marked individuals, obtained by means of scale sample analysis. The two datasets offer a rare long-term perspective on individuals and population dynamics and provide unique opportunities to gain insights into questions surrounding management, conservation, and restoration of migratory salmonid populations and freshwater ecosystems.

opencc-zeroAug 2020View details →

Data from: Gene flow at the leading range edge - the long-term consequences of isolation in European Beech (Fagus sylvatica L. Kuhn)

Aim: Isolation is expected to lead to negative impacts on populations due to a reduction in effective population size and gene flow, exacerbating the effects of genetic drift, which might be stronger in peripheral and fragmented populations. Fagus sylvatica (European beech) in southern Sweden presents a gradient of isolation towards the leading range edge of the species. We sought to determine the impact of long-term isolation on genetic diversity and population genetic structure within populations of this species. Location: Samples were obtained from 14 sites towards the northern edge of the native range of beech in Sweden. Taxon: Fagaceae Methods: Using historical sources, we obtained area- and distance-based measures of isolation. We measured genetic diversity and structure by using nuclear microsatellite marker data, and performed parentage analysis to estimate external pollen-mediated gene flow. We implemented a partial least squares regression to determine the effects of isolation on each of the genetic diversity estimators and the measures of external pollen-mediated gene flow. Results: Long-term isolation generally had a negative impact on genetic diversity, which is exacerbated over time, further affecting progeny and suggesting that isolated populations are subject to strong genetic drift, possibly due to the combination of founder events and persistent small population sizes. Bayesian cluster analysis revealed that isolation was also acting as a barrier to gene flow in the north-eastern distribution of beech. Main conclusions: Isolation at the leading range edge of beech in Sweden has created gradients of contemporary gene flow within the species. The long-term cumulative effects of isolation on this wind-pollinated tree species and its negative impacts on genetic diversity and gene flow, could lead to inbreeding depression and higher extinction risk where populations remain small and isolated.

opencc-zeroAug 2020View details →

Shift from short-term competition to facilitation with drought stress is due to a decrease in long-term facilitation

Disentangling short- and long-term neighbour effects, using both removal and observational methods within a single experiment, has strongly improved our understanding of the driving mechanisms of plant-plant interactions. However, there has been no attempt to assess two important underlying processes of their changes along gradients, environmental-severity (changes in target performance without neighbours) and neighbour-traits (changes in performance with neighbours) effects, the former previously shown in alpine communities to be involved in competition and the latter in facilitation. We addressed this goal in an experiment conducted in continental saline depressions (sebkhas) from the Mediterranean arid climate of central Tunisia. We quantified short- and long-term effects of dominant shrubs, transplanting three target grass species in open, nurse and removed-nurse microhabitats of two habitats of different salinity levels in height sebkhas. The design extended geographically from central Tunisia to the Libyan border, 500km southeastward. We used the Relative Interaction Index to calculate short- and long-term effects of neighbours on target species before and after the dry summer seasons and to disentangle environmental-severity from neighbour-trait effects. Short-term effects were slightly negative and long-term effects strongly positive before the dry summer season in the two habitats. Short-term effects switched to positive with increasing drought stress, due to increasing environmental severity (decrease in the response without neighbours), whereas long-term effects decreased due to decreasing environmental mitigation (decrease in the response with neighbours). Soil moisture measurements showed that both changes were due to vanishing shrub soil engineering-effects during the summer drought. We conclude that an increase in short-term facilitation with increasing drought stress through time, apparently supporting the Stress-Gradient-Hypothesis, might be due to a decrease in long-term facilitation. Our study highlights that assessing the effects of neighbours with both the removal and observational methods is crucial for understanding the driving processes of plant-plant interactions in arid systems.

opencc-zeroAug 2020View details →

Data from: Long-term ecological legacies in western Amazonia

1. Modifications of Amazonian forests by pre-Columbian peoples are thought to have left ecological legacies that have persisted to the modern day. Most Amazonian palaeoecological records do not, however, provide the required temporal resolution to document the nuanced changes of pre-Columbian disturbance or post-disturbance succession and recovery, making it difficult to detect any direct, or indirect, ecological legacies on tree species. 2. Here, we investigate the fossil pollen, phytolith, and charcoal history of Lake Kumpaka, Ecuador, during the last 2415 years in c. 3-50 year time intervals to assess ecological legacies resulting from pre-Columbian forest modification, disturbance, cultivation, and fire usage. 3. Two cycles of pre-Columbian cultivation (one including slash-and burn cultivation, the other including slash-and-mulch cultivation) were documented in the record around 2150-1430 cal. yr BP and 1250-680 cal. yr BP, with following post-disturbance succession dynamics. Modern disturbance was documented after c. 10 cal. yr BP. The modern disturbance produced a plant composition unlike those of the two past disturbances, as fire frequencies reached their peak in the 2415-year record. The disturbance periods varied in intensity and duration, while the overturn of taxa following a disturbance lasted for hundreds of years. The recovery periods following pre-Columbian disturbance shared some similar patterns of early succession, but the longer-term recovery patterns differed. 4. Synthesis. The trajectories of change after a cessation of cultivation can be anticipated to differ depending on the intensity, scale, duration, and manner of the past disturbance. In the Kumpaka record, no evidence of persistent enrichment or depletion of intentionally altered taxa (i.e. direct legacy effects) was found but indirect legacy effects, however, were documented and have persisted to the modern day. These findings highlight the strengths of using empirical data to reconstruct past change rather than relying solely on modern plant populations to infer past human management and ecological legacies, and challenge some of the current hypotheses involving the persistence of pre-Columbian legacies on modern plant populations.

Divergent evolution of mutation rates and biases in the long-term evolution experiment with Escherichia coli

Abstract All organisms encode enzymes that replicate, maintain, pack, recombine, and repair their genetic material. For this reason, mutation rates and biases also evolve by mutation, variation, and natural selection. By examining metagenomic time series of the Lenski long-term evolution experiment (LTEE) with Escherichia coli (Good, et al. 2017), we find that local mutation rate variation has evolved during the LTEE. Each LTEE population has evolved idiosyncratic differences in their rates of point mutations, indels, and mobile element insertions, due to the fixation of various hypermutator and antimutator alleles. One LTEE population, called Ara+3, shows a strong, symmetric wave pattern in its density of point mutations, radiating from the origin of replication. This pattern is largely missing from the other LTEE populations, most of which evolved missense, indel, or structural mutations in topA, fis, and dusB— loci that all affect DNA topology. The distribution of mutations in those genes over time suggests epistasis and historical contingency in the evolution of DNA topology, which may have in turn affected local mutation rates. Overall, the replicate populations of the LTEE have largely diverged in their mutation rates and biases, even though they have adapted to identical abiotic conditions.

Data from: Influence of climate change and post-delisting management on long-term population viability of the conservation-reliant Kirtland's warbler

Rapid global climate change is resulting in novel abiotic and biotic conditions and interactions. Identifying management strategies that maximize probability of long-term persistence requires an understanding of the vulnerability of species to environmental changes. We sought to quantify the vulnerability of Kirtland's Warbler (Setophaga kirtlandii), a rare Neotropical migratory songbird that breeds almost exclusively in the Lower Peninsula of Michigan and winters in the Bahamian Archipelago, to projected environmental changes on the breeding and wintering grounds. We developed a population-level simulation model that incorporates the influence of annual environmental conditions on the breeding and wintering grounds, and parameterized the model using empirical relationships. We simulated independent and additive effects of reduced breeding grounds habitat quantity and quality, and wintering grounds habitat quality, on population viability. Our results indicated the Kirtland's Warbler population is stable under current environmental and management conditions. Reduced breeding grounds habitat quantity resulted in reductions of the stable population size, but did not cause extinction under the scenarios we examined. In contrast, projected large reductions in wintering grounds precipitation caused the population to decline, with risk of extinction magnified when breeding habitat quantity or quality also decreased. Our study indicates that probability of long-term persistence for Kirtland's Warbler will depend on climate change impacts to wintering grounds habitat quality, and contributes to the growing literature documenting the importance of considering the full annual cycle for understanding population dynamics of migratory species.

The response of carbon assimilation and storage to long-term drought in tropical trees is dependent on light availability

1) Whether tropical trees acclimate to long-term drought stress remains unclear. This uncertainty is amplified if drought stress is accompanied by changes in other drivers such as the increases in canopy light exposure that might be induced by tree mortality or other disturbances. 2) Photosynthetic capacity, leaf respiration, non-structural carbohydrate (NSC) storage and stomatal conductance were measured on 162 trees at the world's longest running (15 yr) tropical forest drought experiment. We test whether surviving trees have altered strategies for carbon storage and carbon use in the drier and elevated light conditions present following drought-related tree mortality. 3) Relative to control trees, the surviving trees experiencing the drought treatment showed functional responses including: i) moderately reduced photosynthetic capacity; ii) increased total leaf NSC; and iii) a switch from starch to soluble sugars as the main store of branch NSC. This contrasts with earlier findings at this experiment of no change in photosynthetic capacity or NSC storage. The changes detected here only occurred in the subset of drought-stressed trees with canopies exposed to high radiation and were absent in trees with less-exposed canopies, and also in the community average. In contrast to previous results acquired through less intensive species sampling from this experiment, we also observe no species-average drought-induced change in leaf respiration. 4) Our results suggest that long-term responses to drought stress are strongly influenced by a tree's full-canopy light environment and therefore that disturbance-induced changes in stand density and dynamics are likely to substantially impact tropical forest responses to climate change. We also demonstrate that, while challenging, intensive sampling is essential in tropical forests to avoid sampling biases caused by limited taxonomic coverage.

Rainfall pulses mediate long-term plant community compositional dynamics in a semi-arid rangeland

1. Semi-arid rangelands, comprising more than 40% of the Earth's land surface, provide critical ecosystem services. Worldwide, these ecosystems are experiencing rapid degradation due to overgrazing and precipitation changes. However, how plants respond to these interacting factors remains relatively unexplored, and precisely which and how rainfall factors determine plant community dynamics in rangelands has not been well developed. 2. We used a long-term (1953‒2018) dataset from semi-arid rangeland to investigate coupled effects of grazing intensity and rainfall intensity (the total amount of precipitation) on different groups of plant cover (herbaceous, woody, and cacti plants) using linear mixed-effects models, redundancy analysis and structural equation models. We examined how rainfall intensity influenced plant cover dynamics according to pulse size (intensity over time) categories, which we analyzed at three scales: yearly, within the wet season only (June to September), and within the dry season only (October to May). 3. Plant community cover showed a humpbacked trend in the last six decades, mostly through changes in woody plants. Although both grazing intensity and rainfall presented similar humpbacked trends with plant community cover, our models demonstrated that the reduction of plant cover from the 1990s has been mainly caused by a decrease of rainfall rather than grazing intensity, particularly due to profound reductions of the intensity of relatively small rainfall pulses (e.g., 5.1 ~ 15 mm·day-1) during the dry season. Specifically, these small rainfall pulses can increase plant cover of all subgroups of woody and herbaceous species, thereby increasing plant community cover. Moreover, rainfall pulses during the wet season had negative effects on herbaceous species and positive effects on woody plants. These results suggest a phenological niche partitioning between woody plants and herbaceous in subtropical rangelands. 4. Synthesis and applications. Our results show how critical seasonal rainfall pulses are for regulating plant community compositional dynamics, which has significant implications for rangeland management and our ability to adapt and mitigate amplified climate influences in semi-arid ecosystems.

opencc-zeroOct 2020View details →

Long-term cloud forest response to climate warming revealed by insect speciation history

Montane cloud forests are areas of high endemism, and are one of the more vulnerable terrestrial ecosystems to climate change. Thus, understanding how they both contribute to the generation of biodiversity, and will respond to ongoing climate change, are important and related challenges. The widely accepted model for montane cloud forest dynamics involves upslope forcing of their range limits with global climate warming. However, limited climate data provides some support for an alternative model, where range limits are forced downslope with climate warming. Testing between these two models is challenging, due to the inherent limitations of climate and pollen records. We overcome this with an alternative source of historical information, testing between competing model predictions using genomic data and demographic analyses for a species of beetle tightly associated to an oceanic island cloud forest. Results unequivocally support the alternative model: populations that were isolated at higher elevation peaks during the Last Glacial Maximum are now in contact and hybridising at lower elevations. Our results suggest that genomic data is a rich source of information to further understand how montane cloud forest biodiversity originates, and how it is likely to be impacted by ongoing climate change.

opencc-zeroOct 2020View details →

Negative trait-based association between abundance of nitrogen fixing trees and long-term tropical forest biomass accumulation

1. Plant functional traits are thought to drive biomass production and biogeochemical cycling in tropical forests, but it remains unclear how nitrogen (N)-fixing legumes influence the functional traits of neighboring trees and forest-wide biomass dynamics. Further, the degree to which effects of N-fixers are density-dependent and may depend on stem size and spatial scale remain largely unknown. 2. Here, we examine 30-years of stem demography data for ~20,000 trees in a lowland tropical forest in Trinidad that span a wide range of functional traits thought to drive aboveground biomass (AGB) dynamics. 3. These forests show positive but decreasing long-term net AGB accumulation resulting from constant average productivity but increasing mortality of non-fixing trees over time. We find that high abundance of N-fixing trees is associated with compositional shifts in non-fixer functional traits that confer lower competitive performance and biomass accumulation. Across tree size classes, most interactions between N-fixers and non-fixers were negative, density dependent, and strongest at smaller spatial scales. 4. Synthesis. Overall, our findings suggest that local trait-based interactions between N-fixing and non-fixing trees can influence long-term carbon accumulation in tropical forests.