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opencc-zeroDec 2012View details →

Data from: Timing of morphological and ecological innovations in the cyanobacteria – a key to understanding the rise in atmospheric oxygen

When cyanobacteria originated and diversified, and what their ancient traits were, remain critical unresolved problems. Here, we used a phylogenomic approach to construct a well-resolved 'core' cyanobacterial tree. The branching positions of four lineages (Thermosynechococcus elongatus, Synechococcus elongatus, Synechococcus PCC 7335 and Acaryochloris marina) were problematic, probably due to long branch attraction artifacts. A consensus genomic tree was used to study trait evolution using ancestral state reconstruction (ASR). The early cyanobacteria were probably unicellular, freshwater, had small cell diameters, and lacked the traits to form thick microbial mats. Relaxed molecular clock analyses suggested that early cyanobacterial lineages were restricted to freshwater ecosystems until at least 2.4 Ga, before diversifying into coastal brackish and marine environments. The resultant increases in niche space and nutrient availability, and consequent sedimentation of organic carbon into the deep oceans, would have generated large pulses of oxygen into the biosphere, possibly explaining why oxygen rose so rapidly. Rapid atmospheric oxidation could have destroyed the methane-driven greenhouse with simultaneous drawdown in pCO(2), precipitating 'Snowball Earth' conditions. The traits associated with the formation of thick, laminated microbial mats (large cell diameters, filamentous growth, sheaths, motility and nitrogen fixation) were not seen until after diversification of the LPP, SPM and PNT clades, after 2.32 Ga. The appearance of these traits overlaps with a global carbon isotopic excursion between 2.2 and 2.1 Ga. Thus, a massive re-ordering of biogeochemical cycles caused by the appearance of complex laminated microbial communities in marine environments may have caused this excursion. Finally, we show that ASR may provide an explanation for why cyanobacterial microfossils have not been observed until after 2.0 Ga, and make suggestions for how future paleobiological searches for early cyanobacteria might proceed. In summary, key evolutionary events in the microbial world may have triggered some of the key geologic upheavals on the Paleoproterozoic Earth.

opencc-zeroSep 2019View details →

Data from: Ecological constraints coupled with deep-time habitat dynamics predict the latitudinal diversity gradient in reef fishes

We develop a spatially explicit model of diversification based on paleohabitat to explore the predictions of four major hypotheses potentially explaining the latitudinal diversity gradient (LDG), namely, the 'time-area', 'tropical niche conservatism', 'ecological limits' and 'evolutionary speed' hypotheses. We compare simulation outputs to observed diversity gradients in the global reef fish fauna. Our simulations show that these hypotheses are non-mutually exclusive and that their relative influence depends on the time scale considered. Indeed, simulations suggest that reef habitat dynamics produced the LDG during deep geological time, while ecological constraints shaped the modern LDG, with a strong influence of the reduction in the latitudinal extent of tropical reefs during the Neogene. Overall, this study illustrates how mechanistic models in ecology and evolution can provide a temporal and spatial understanding of the role of speciation, extinction and dispersal in generating contemporary biodiversity patterns.

opencc-zeroDec 2011View details →

Data from: A question of time: the land snail Murella muralis (Gastropoda: Pulmonata) reveals constrains to past ecological speciation

The lively debate about speciation currently focuses on the relative importance of factors driving population differentiation. While many studies are increasingly producing results on the importance of selection, little is known about the interaction between drift and selection. Moreover there is still little knowledge on the spatial-temporal scales at which speciation occurs, i.e. arrangement of habitat patches, abruptness of habitat transitions, climate and habitat changes interacting with selective forces. To investigate these questions, we quantified variation on a fine geographical scale analysing morphological (shell) and genetic datasets coupled with environmental data in the land snail Murella muralis, endemic to the Mediterranean island of Sicily. Analysis of a fragment of the mitochondrial DNA Cytochrome Oxidase I gene (COI) and eight nuclear microsatellite loci showed that genetic variation is highly structured at a very fine spatial scale by local palaeogeographical events and historical population dynamics. Molecular clock estimates, calibrated here specifically for Tyrrhenian land snails, provided a framework of palaeogeographical events responsible for the observed geographical variations and migration routes. Finally, we showed for the first time well documented lines of evidences of selection in the past, which explains divergence of land snail shell shapes. We suggest that time and palaeogeographical history acted as constraints in the progress along the ecological speciation continuum. Our study shows that testing for correlation among palaeogeography, morphology and genetic data on a fine geographical scale provides information fundamental for a detailed understanding of ecological speciation processes.

opencc-zeroDec 2016View details →

Data from: Ecological opportunity alters the timing and shape of adaptive radiation

The uneven distribution of diversity is a conspicuous phenomenon across the tree of life. Ecological opportunity is a prominent catalyst of adaptive radiation and therefore may alter patterns of diversification. We evaluated the distribution of shifts in diversification rates across the cichlid phylogeny and the distribution of major clades across phylogenetic space. We also tested if ecological opportunity influenced these patterns. Colonization-associated ecological opportunity altered the tempo and mode of diversification during the adaptive radiation of cichlid fishes. Clades that arose following colonization events diversified faster than other clades. Speciation rate shifts were non-randomly distributed across the phylogeny such that they were disproportionally concentrated around nodes that corresponded with colonization events (i.e., of continents, river basins, or lakes). Young clades tend to expand faster than older clades; however, colonization-associated ecological opportunity accentuated this pattern. There was an interaction between clade age and ecological opportunity that explained the trajectory of clades through phylogenetic space over time. Our results indicate that ecological opportunities afforded by continental- and ecosystem-scale colonization events explain the dramatic speciation rate heterogeneity and phylogenetic imbalance that arose during the evolutionary history of cichlid fishes.

opencc-zeroDec 2015View details →

Data from: Genomic data detect corresponding signatures of population size change on an ecological time scale in two salamander species

Understanding the demography of species over recent history (e.g., < 100 years) is critical in studies of ecology and evolution, but records of population history are rarely available. Surveying genetic variation is a potential alternative to census-based estimates of population size, and can yield insight into the demography of a population. However, to assess the performance of genetic methods it is important to compare their estimates of population history to known demography. Here, we leveraged the exceptional resources from a wetland with 37 years of amphibian mark-recapture data to study the utility of genetically-based demographic inference on salamander species with documented population declines (Ambystoma talpoideum) and expansions (A. opacum); patterns that have been shown to be correlated with changes in wetland hydroperiod. We generated ddRAD data from two temporally sampled populations of A. opacum (1993, 2013) and A. talpoideum (1984, 2011) and used coalescent-based demographic inference to compare alternate evolutionary models. For both species, demographic model inference supported population size changes that corroborated mark-recapture data. Parameter estimation in A. talpoideum was robust to our variations in analytical approach, while estimates for A. opacum were highly inconsistent, tempering our confidence in detecting a demographic trend in this species. Overall, our robust results in A. talpoideum suggest that genome-based demographic inference has utility on an ecological scale, but researchers should also be cognizant that these methods may not work in all systems and evolutionary scenarios. Demographic inference may be an important tool for population monitoring and conservation management planning.

opencc-zeroDec 2017View details →

Data from: Phylogeny, ecology and deep time: 2D outline analysis of anuran skulls from the Early Cretaceous to Recent

Anurans have a long fossil record, spanning from the Early Jurassic to Recent. However, specimens are often severely flattened, limiting their inclusion in quantitative analyses of morphological evolution. We perform a two-dimensional morphometric analysis of anuran skull outlines, incorporating 42 Early Cretaceous to Miocene species, as well as 93 extant species in 32 families. Outlines were traced in tpsDig2 and analysed with elliptical Fourier analysis. Fourier coefficients were used in MANOVAs, phylogenetic MANOVAs (as significant phylogenetic signal was found) and disparity analyses across multiple ecological and life history groupings. The Neotropical realm showed higher disparity than the Australian, Palearctic and Oriental realms (p = 0.007, 0.013, 0.038, respectively), suggesting concordance of disparity and diversity. Developmental strategy had a weak effect on skull shape (R2 = 0.02, p = 0.039), and disparity was similar in metamorphosing and direct developing frogs. Ecological niche was a significant discriminator of skull shape (F = 1.43, p = 0.004), but not after phylogenetic correction. Evolutionary allometry had a small but significant influence on the cranial outlines of the combined extant and fossil dataset (R2 = 0.05, p = 0.004). Finally, morphospace occupation appears to have changed over time (F = 1.59, p = 5 × 10-10). However, as with ecological signal, this shift appears to be largely driven by phylogeny and was not significant after phylogenetic correction (R2 = 0.26, p = 0.22). This study thus suggests that frog skull evolution is shaped more by phylogenetic constraints than by ecology.

opencc-zeroMay 2019View details →

Supplementary material 1 from: Cerrato C, Rocchia E, Brunetti M, Bionda R, Bassano B, Provenzale A, Bonelli S, Viterbi R (2019) Butterfly distribution along altitudinal gradients: temporal changes over a short time period. In: Mazzocchi MG, Capotondi L, Freppaz M, Lugliè A, Campanaro A (Eds) Italian Long-Term Ecological Research for understanding ecosystem diversity and functioning. Case studies from aquatic, terrestrial and transitional domains. Nature Conservation 34: 91-118. https://doi.org/10.3897/natureconservation.34.30728

Supplementary data

FIGURE 4 in Feeding in marine mammals: An integration of evolution and ecology through time

FIGURE 4. Anatomical features associated with filter feeding in crabeater seal (Lobodon carcinophaga skull, public domain image), and gray whale (Eschrichtius robustus skull, authors' work).

FIGURE 10 in Feeding in marine mammals: An integration of evolution and ecology through time

FIGURE 10. Odontoceti stem and familial level diversity through time. The group "Delphinoidea" includes Delphinidae, Monodontidae, and Phocoenidae, as well as extinct members of this crown group of uncertain phylogenetic placement. The "river dolphins" closely related to these taxa (Inioidea and Lipotidae) are plotted separately to emphasize their diversity in the fossil record compared to the present. "Ziphioidea" includes Ziphiidae and closely related stem taxa as identified by Bianucci et al. (2016). Dashed vertical lines: black, epoch boundaries; gray, age boundaries.

FIGURE 6 in Feeding in marine mammals: An integration of evolution and ecology through time

FIGURE 6. Generic level diversity of marine mammal groups through time. Dashed vertical lines: black, epoch boundaries; gray, age boundaries. All silhouettes used in Figures 6-20 are the authors' own work.

FIGURE 9 in Feeding in marine mammals: An integration of evolution and ecology through time

FIGURE 9. Mysticeti stem and familial level diversity through time. "Cetotheriidae s.l." is a paraphyletic group including all taxa that belong to crown Mysticeti but are not grouped with any of the four living families. Dashed vertical lines: black, epoch boundaries; gray, age boundaries.

FIGURE 2 in Feeding in marine mammals: An integration of evolution and ecology through time

FIGURE 2. Anatomical features associated with biting (pierce, grip-and-tear, and crushing) feeding. 1: Crushing in sea otter (Enhydra lutris skull, from Lawlor, 1979), 2: Grip-and-tear in leopard seal (Hydruga leptonyx skull, authors' work), 3: Pierce in Southern sea lion, (Otaria byronia skull, authors' work) and in Amazon river dolphin (Inia geoffrensis skull, authors' work).

FIGURE 12 in Feeding in marine mammals: An integration of evolution and ecology through time

FIGURE 12. Hypothesized ecological replacement of desmostylians (circles) by sirenians (squares) in the North Pacific Ocean. On the top, map of the localities of Tortonian age (11 Ma) where desmostylian and sirenian were recorded. On the bottom, map of the localities of Zanclean age (5 Ma) where sirenians were recorded. Desmostylia disappear from the fossil record by the end of the Tortonian (7.2 Ma) when sirenians, particularly Hydrodamalis spp., start colonizing this region, likely feeding on the same resources. Only one occurrence per genus is reported in each locality. Locality data for each occurrence of Desmostylia and Sirenia in the Tortonian and Zanclean were downloaded from PBDB (https://paleobiodb.org) using the search parameters described in Materials and Methods and then plotted on the map.

opencc-zeroAug 2021View details →

Repeatable individual variation in migration timing in two anadromous salmonids and ecological consequences

Consistent individual differences in behaviour has been demonstrated for many animals, but there are few studies of consequences of such repeated behaviour in the wild. We tested consistency in migration timing to and from the sea among anadromous Arctic char (Salvelinus alpinus) and brown trout (Salmo trutta), using data from a study period of about 25 years, including more than 27,000 uniquely Carlin-tagged individuals that migrated to sea for feeding in the spring and returned to the river in late summer for up to 13 successive years. Consistency was found between individuals across time in timing of the seaward migration. Individuals migrating early during their first migration tended to migrate early the following years, and late migrants tended to migrate late. The same pattern was found also at ascent to freshwater. Hence, this study demonstrated that individual fish in nature can differ in behaviour related to migration timing, and that these differences can be consistent during their life time. Early migrants increased their mass more than late migrants, and had a higher specific growth rate. Early migrating Arctic char, but not brown trout, experienced a longer life after the first migration to sea than late migrants. In both species, maturity occurred earlier in individuals that migrated early. For brown trout, but not for Arctic char, fecundity was significantly correlated to the timing of smolt migration. Hence, the repeatable individual variation in migration timing seemed to have ecological and fitness consequences in terms of growth, longevity, timing of maturity, and life-time fecundity.

publicSep 2019View details →

Data from: Ecological constraints coupled with deep-time habitat dynamics predict the latitudinal diversity gradient in reef fishes

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publicSep 2013View details →

Data from: Timing of morphological and ecological innovations in the cyanobacteria – a key to understanding the rise in atmospheric oxygen

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