scholarly journals Seed size and its rate of evolution correlate with species diversification across angiosperms

2016 ◽  
Author(s):  
J. Igea ◽  
E. F. Miller ◽  
A. S. T. Papadopulos ◽  
A. J. Tanentzap
Keyword(s):  
Seed Size ◽  
Large Scale ◽  
Seed Mass ◽  
Rate Of Change ◽  
Ecological Niches ◽  
Phenotypic Change ◽  
Diversification Rates ◽  
Angiosperm Phylogeny ◽  
Speciation Rates ◽  
Taxonomic Groups

AbstractSpecies diversity varies greatly across the different taxonomic groups that comprise the Tree of Life (ToL). This imbalance is particularly conspicuous within angiosperms, but is largely unexplained. Seed mass is one trait that may help clarify why some lineages diversify more than others because it confers adaptation to different environments, which can subsequently influence speciation and extinction. The rate at which seed mass changes across the angiosperm phylogeny may also be linked to diversification by increasing reproductive isolation and allowing access to novel ecological niches. However, the magnitude and direction of the association between seed mass and diversification has not been assessed across the angiosperm phylogeny. Here, we show that absolute seed size and the rate of change in seed size are both associated with variation in diversification rates. Based on the largest available angiosperm phylogenetic tree, we found that smaller-seeded plants had higher rates of diversification, possibly due to improved colonisation potential. The rate of phenotypic change in seed size was also strongly positively correlated with speciation rates, providing rare, large-scale evidence that rapid morphological change is associated with species divergence. Our study now reveals that variation in morphological traits and, importantly, the rate at which they evolve can contribute to explaining the extremely uneven distribution of diversity across the ToL.

scholarly journals Linking population-level and microevolutionary processes to understand speciation dynamics at the macroevolutionary scale

2021 ◽  
Author(s):  
Laura Alencar ◽  
Tiago Bosisio Quental
Keyword(s):  
Population Level ◽  
Theoretical Models ◽  
Intrinsic Properties ◽  
Diversification Rates ◽  
Apparent Inconsistency ◽  
Speciation Rates ◽  
Physical Barriers ◽  
Methodological Approaches ◽  
Taxonomic Groups ◽  
Mechanistic View

Although speciation dynamics have been described for several taxonomic groups in distinct geographic regions, most macroevolutionary studies still lack a detailed mechanistic view on how or why speciation rates change. To help partially fill this gap, we suggest that the interaction between the time taken by a species to geographically expand and the time populations take to evolve reproductive isolation should be considered when we are trying to understand macroevolutionary patterns. We introduce a simple conceptual index to guide our discussion on how demographic and microevolutionary processes might produce speciation dynamics at macroevolutionary scales. Our framework is developed under different scenarios: when speciation is mediated by geographical or resource-partitioning opportunities, and when diversity is limited or not. We also discuss how organismal intrinsic properties and different overall geographical settings can influence the tempo and mode of speciation. We argue that specific conditions observed at the micro-scale might produce a pulse in speciation rates even without a pulse in either climate or physical barriers. We also propose a hypothesis to reconcile the apparent inconsistency between speciation measured at the micro and macro scales and emphasize that diversification rates are better seen as an emergent property. We hope to bring the reader’s attention to interesting mechanisms to be further studied, to motivate the development of new theoretical models that connect micro and macroevolution, and to inspire new empirical and methodological approaches to more adequately investigate speciation dynamics either using neontological or paleontological data.

scholarly journals Estimating rates and patterns of diversification with incomplete sampling: A case study in the rosids

2019 ◽  
Author(s):  
Miao Sun ◽  
Ryan A. Folk ◽  
Matthew A. Gitzendanner ◽  
Robert P. Guralnick ◽  
Pamela S. Soltis ◽  
...  
Keyword(s):  
Large Scale ◽  
Molecular Data ◽  
Diversification Rates ◽  
Sampling Schemes ◽  
Incomplete Coverage ◽  
Speciation Rates ◽  
The Impact ◽  
Incomplete Sampling ◽  
Empirical Case Studies

AbstractPremise of the StudyRecent advances in generating large-scale phylogenies enable broad-scale estimation of species diversification rates. These now-common approaches typically (1) are characterized by incomplete coverage without explicit sampling methodologies, and/or (2) sparse backbone representation, and usually rely on presumed phylogenetic placements to account for species without molecular data. Here we use an empirical example to examine effects of incomplete sampling on diversification estimation and provide constructive suggestions to ecologists and evolutionists based on those results.MethodsWe used a supermatrix for rosids, a large clade of angiosperms, and its well-sampled subclade Cucurbitaceae, as empirical case studies. We compared results using this large phylogeny with those based on a previously inferred, smaller supermatrix and on a synthetic tree resource with complete taxonomic coverage. Finally, we simulated random and representative taxon sampling and explored the impact of sampling on three commonly used methods, both parametric (RPANDA, BAMM) and semiparametric (DR).Key ResultsWe find the impact of sampling on diversification estimates is idiosyncratic and often strong. As compared to full empirical sampling, representative and random sampling schemes either depress or exaggerate speciation rates depending on methods and sampling schemes. No method was entirely robust to poor sampling, but BAMM was least sensitive to moderate levels of missing taxa.ConclusionsWe (1) urge caution in use of summary backbone trees containing only higher-level taxa, (2) caution against uncritical modeling of missing taxa using taxonomic data for poorly sampled trees, and (3) stress the importance of explicit sampling methodologies in macroevolutionary studies.

scholarly journals Linking population-level and microevolutionary processes to understand speciation dynamics at the macroevolutionary scale

2021 ◽  
Author(s):  
Laura Alencar ◽  
Tiago Quental
Keyword(s):  
Population Level ◽  
Theoretical Models ◽  
Intrinsic Properties ◽  
Diversification Rates ◽  
Apparent Inconsistency ◽  
Speciation Rates ◽  
Physical Barriers ◽  
Methodological Approaches ◽  
Taxonomic Groups ◽  
Mechanistic View

Although speciation dynamics have been described for several taxonomic groups in distinct geographic regions, most macroevolutionary studies still lack a detailed mechanistic view on how or why speciation rates change. To help to partially fill this gap, we suggest that the interaction between the time taken by a species to geographically expand and the time populations take to evolve reproductive isolation should be considered when we are trying to understand macroevolutionary patterns. We introduce a simple conceptual index to guide our discussion on how demographic and microevolutionary processes might produce speciation dynamics at macroevolutionary scales. Our framework is developed under different scenarios: when speciation is mediated by geographical or resource-partitioning opportunities, and when diversity is limited or not. We also discuss how organismal intrinsic properties and different overall geographical settings can influence the tempo and mode of speciation. We argue that specific conditions observed at the micro scale might produce a pulse in speciation rates even without a pulse in either climate or physical barriers. We also propose a hypothesis to reconcile the apparent inconsistency between speciation measured at the micro and macro scales, and emphasize that diversification rates are better seen as an emergent property. We hope to bring the reader’s attention to interesting mechanisms to be further studied, to motivate the development of new theoretical models that connect micro and macroevolution, and to inspire new empirical and methodological approaches to more adequately investigate speciation dynamics either using neontological or paleontological data.

scholarly journals Thermal reaction norms of key metabolic enzymes reflect divergent physiological and behavioral adaptations of closely related amphipod species

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Lena Jakob ◽  
Kseniya P. Vereshchagina ◽  
Anette Tillmann ◽  
Lorena Rivarola-Duarte ◽  
Denis V. Axenov-Gribanov ◽  
...  
Keyword(s):  
Lactate Dehydrogenase ◽  
Lake Baikal ◽  
Enzyme Activities ◽  
Large Scale ◽  
Metabolic Enzymes ◽  
Thermal Reaction ◽  
Reaction Norms ◽  
Ecological Niches ◽  
Amphipod Species ◽  
Thermal Plasticity

AbstractLake Baikal is inhabited by more than 300 endemic amphipod species, which are narrowly adapted to certain thermal niches due to the high interspecific competition. In contrast, the surrounding freshwater fauna is commonly represented by species with large-scale distribution and high phenotypic thermal plasticity. Here, we investigated the thermal plasticity of the energy metabolism in two closely-related endemic amphipod species from Lake Baikal (Eulimnogammarus verrucosus; stenothermal and Eulimnogammarus cyaneus; eurythermal) and the ubiquitous Holarctic amphipod Gammarus lacustris (eurythermal) by exposure to a summer warming scenario (6–23.6 °C; 0.8 °C d−1). In concert with routine metabolic rates, activities of key metabolic enzymes increased strongly with temperature up to 15 °C in E. verrucosus, whereupon they leveled off (except for lactate dehydrogenase). In contrast, exponential increases were seen in E. cyaneus and G. lacustris throughout the thermal trial (Q10-values: 1.6–3.7). Cytochrome-c-oxidase, lactate dehydrogenase, and 3-hydroxyacyl-CoA dehydrogenase activities were found to be higher in G. lacustris than in E. cyaneus, especially at the highest experimental temperature (23.6 °C). Decreasing gene expression levels revealed some thermal compensation in E. cyaneus but not in G. lacustris. In all species, shifts in enzyme activities favored glycolytic energy generation in the warmth. The congruent temperature-dependencies of enzyme activities and routine metabolism in E. verrucosus indicate a strong feedback-regulation of enzymatic activities by whole organism responses. The species-specific thermal reaction norms reflect the different ecological niches, including the spatial distribution, distinct thermal behavior such as temperature-dependent migration, movement activity, and mating season.

scholarly journals Effects of Climatic Drivers and Teleconnections on Late 20th Century Trends in Spring Freshet of Four Major Arctic-Draining Rivers

Water ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 179
Author(s):  
Roxanne Ahmed ◽  
Terry Prowse ◽  
Yonas Dibike ◽  
Barrie Bonsal
Keyword(s):  
Arctic Ocean ◽  
Large Scale ◽  
Southern Oscillation ◽  
Rate Of Change ◽  
The Arctic ◽  
Late 20Th Century ◽  
Basin Scale ◽  
The Arctic Ocean ◽  
Spring Freshet ◽  
Climatic Drivers

Spring freshet is the dominant annual discharge event in all major Arctic draining rivers with large contributions to freshwater inflow to the Arctic Ocean. Research has shown that the total freshwater influx to the Arctic Ocean has been increasing, while at the same time, the rate of change in the Arctic climate is significantly higher than in other parts of the globe. This study assesses the large-scale atmospheric and surface climatic conditions affecting the magnitude, timing and regional variability of the spring freshets by analyzing historic daily discharges from sub-basins within the four largest Arctic-draining watersheds (Mackenzie, Ob, Lena and Yenisei). Results reveal that climatic variations closely match the observed regional trends of increasing cold-season flows and earlier freshets. Flow regulation appears to suppress the effects of climatic drivers on freshet volume but does not have a significant impact on peak freshet magnitude or timing measures. Spring freshet characteristics are also influenced by El Niño-Southern Oscillation, the Pacific Decadal Oscillation, the Arctic Oscillation and the North Atlantic Oscillation, particularly in their positive phases. The majority of significant relationships are found in unregulated stations. This study provides a key insight into the climatic drivers of observed trends in freshet characteristics, whilst clarifying the effects of regulation versus climate at the sub-basin scale.

scholarly journals Equatorial ionospheric disturbance observed through a transequatorial HF propagation experiment

2006 ◽  
Vol 24 (5) ◽  
pp. 1401-1409 ◽  
Author(s):  
T. Maruyama ◽  
M. Kawamura
Keyword(s):  
Large Scale ◽  
Ionospheric Disturbance ◽  
Great Circle ◽  
Rate Of Change ◽  
Spatial Distance ◽  
Propagation Path ◽  
Multiple Signal Classification ◽  
Radio Broadcasting ◽  
Equatorial Plasma Bubbles ◽  
Propagation Experiment

Abstract. A transequatorial radio-wave propagation experiment at shortwave frequencies (HF-TEP) was done between Shepparton, Australia, and Oarai, Japan, using the radio broadcasting signals of Radio Australia. The receiving facility at Oarai was capable of direction finding based on the MUSIC (Multiple Signal Classification) algorithm. The results were plotted in azimuth-time diagrams (AT plots). During the daytime, the propagation path was close to the great circle connecting Shepparton and Oarai, thus forming a single line in the AT plots. After sunset, off-great-circle paths, or satellite traces in the AT plot, often appeared abruptly to the west and gradually returned to the great circle direction. However, there were very few signals across the great circle to the east. The off-great-circle propagation was very similar to that previously reported and was attributed to reflection by an ionospheric structure near the equator. From the rate of change in the direction, we estimated the drift velocity of the structure to range mostly from 100 to 300 m/s eastward. Multiple instances of off-great-circle propagation with a quasi-periodicity were often observed and their spatial distance in the east-west direction was within the range of large-scale traveling ionospheric disturbances (LS-TIDs). Off-great-circle propagation events were frequently observed in the equinox seasons. Because there were many morphological similarities, the events were attributed to the onset of equatorial plasma bubbles.

scholarly journals The pitfalls of biodiversity proxies: Differences in richness patterns of birds, trees and understudied diversity across Amazonia

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Camila D. Ritter ◽  
Søren Faurby ◽  
Dominic J. Bennett ◽  
Luciano N. Naka ◽  
Hans ter Steege ◽  
...  
Keyword(s):  
Species Richness ◽  
Large Scale ◽  
Spatial Scales ◽  
Local Environment ◽  
Life Forms ◽  
Taxonomic Group ◽  
Diversity Gradients ◽  
Richness Patterns ◽  
Taxonomic Groups ◽  
Micro Organisms

AbstractMost knowledge on biodiversity derives from the study of charismatic macro-organisms, such as birds and trees. However, the diversity of micro-organisms constitutes the majority of all life forms on Earth. Here, we ask if the patterns of richness inferred for macro-organisms are similar for micro-organisms. For this, we barcoded samples of soil, litter and insects from four localities on a west-to-east transect across Amazonia. We quantified richness as Operational Taxonomic Units (OTUs) in those samples using three molecular markers. We then compared OTU richness with species richness of two relatively well-studied organism groups in Amazonia: trees and birds. We find that OTU richness shows a declining west-to-east diversity gradient that is in agreement with the species richness patterns documented here and previously for birds and trees. These results suggest that most taxonomic groups respond to the same overall diversity gradients at large spatial scales. However, our results show a different pattern of richness in relation to habitat types, suggesting that the idiosyncrasies of each taxonomic group and peculiarities of the local environment frequently override large-scale diversity gradients. Our findings caution against using the diversity distribution of one taxonomic group as an indication of patterns of richness across all groups.

scholarly journals Explaining large-scale patterns of vertebrate diversity

2015 ◽  
Vol 11 (7) ◽  
pp. 20150506 ◽  
Author(s):  
John J. Wiens
Keyword(s):  
Species Richness ◽  
Large Scale ◽  
Comparative Methods ◽  
Phylogenetic Comparative Methods ◽  
Metabolic Rates ◽  
Diversification Rates ◽  
Richness Patterns ◽  
Current Species

The major clades of vertebrates differ dramatically in their current species richness, from 2 to more than 32 000 species each, but the causes of this variation remain poorly understood. For example, a previous study noted that vertebrate clades differ in their diversification rates, but did not explain why they differ. Using a time-calibrated phylogeny and phylogenetic comparative methods, I show that most variation in diversification rates among 12 major vertebrate clades has a simple ecological explanation: predominantly terrestrial clades (i.e. birds, mammals, and lizards and snakes) have higher net diversification rates than predominantly aquatic clades (i.e. amphibians, crocodilians, turtles and all fish clades). These differences in diversification rates are then strongly related to patterns of species richness. Habitat may be more important than other potential explanations for richness patterns in vertebrates (such as climate and metabolic rates) and may also help explain patterns of species richness in many other groups of organisms.

scholarly journals Comparative genomics and pangenome-oriented studies reveal high homogeneity of the agronomically relevant enterobacterial plant pathogen Dickeya solani

2020 ◽  
Author(s):  
Agata Motyka-Pomagruk ◽  
Sabina Zoledowska ◽  
Agnieszka Emilia Misztak ◽  
Wojciech Sledz ◽  
Alessio Mengoni ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Large Scale ◽  
De Novo ◽  
Genetic Material ◽  
Soft Rot ◽  
Potato Production ◽  
Core Gene ◽  
Ecological Niches ◽  
Dickeya Solani ◽  
High Level

Abstract Background: Dickeya solani is an important plant pathogenic bacterium causing severe losses in European potato production. This species draws a lot of attention due to its remarkable virulence, great devastating potential and easier spread in contrast to other Dickeya spp. In view of a high need for extensive studies on economically important soft rot Pectobacteriaceae , we performed a comparative genomics analysis on D. solani strains to search for genetic foundations that would explain the differences in the observed virulence levels within the D. solani population. Results: High quality assemblies of 8 de novo sequenced D. solani genomes have been obtained. Whole-sequence comparison, ANIb, ANIm, Tetra and pangenome-oriented analyses performed on these genomes and the sequences of 14 additional strains revealed an exceptionally high level of homogeneity among the studied genetic material of D. solani strains. With the use of 22 genomes, the pangenome of D. solani , comprising 84.7% core, 7.2% accessory and 8.1% unique genes, has been almost completely determined, suggesting the presence of a nearly closed pangenome structure. Attribution of the genes included in the D. solani pangenome fractions to functional COG categories showed that higher percentages of accessory and unique pangenome parts in contrast to the core section are encountered in phage/mobile elements- and transcription- associated groups with the genome of RNS 05.1.2A strain having the most significant impact. Also, the first D. solani large-scale genome-wide phylogeny computed on concatenated core gene alignments is herein reported. Conclusions: The almost closed status of D. solani pangenome achieved in this work points to the fact that the unique gene pool of this species should no longer expand. Such a feature is characteristic of taxa whose representatives either occupy isolated ecological niches or lack efficient mechanisms for gene exchange and recombination, which seems rational concerning a strictly pathogenic species with clonal population structure. Finally, no obvious correlations between the geographical origin of D. solani strains and their phylogeny were found, which might reflect the specificity of the international seed potato market.

scholarly journals Development of specific markers for the detection of Tolypella canadensis eDNA in water samples

2021 ◽  
Vol 4 ◽  
Author(s):  
Christina Wiebe ◽  
Petra Nowak ◽  
Hendrik Schubert
Keyword(s):  
Rare Species ◽  
Environmental Samples ◽  
Large Scale ◽  
Morphological Characters ◽  
Its2 Region ◽  
Specific Marker ◽  
Specific Primers ◽  
Species Specific ◽  
Taxonomic Groups ◽  
Scale Integration

Assessing the biodiversity of an ecosystem plays a major role in ecosystem management. However, proper determination on species-level is often tricky when morphological features are scarce and especially rare species require huge sampling efforts to be detected in the aquatic realm. As an alternative to conventional methods, environmental samples can be examined via the eDNA method, allowing for large-scale integration as well as taxa resolution independent from expression of morphological characters. However, to apply this technique genetic markers that are specific to a species or at least a genus are required. Such markers until now have been successfully developed only for a few well studied taxonomic groups like, e.g., fishes and amphibians, but are still missing for others, especially plants and algae (e.g. Bista et al. 2017). This project focusses on the development of species-specific markers for the macrophytic green algae Tolypella canadensis (Characeae, Charophyta), a rare alga preferring deep water and known so far mainly from remote places. Tolypella canadensis is a circumpolar species and prefers oligotrophic lakes, where it grows in depths up to 13 m (Langangen 2002; Romanov and Kopyrina 2016). In addition, proper determination of Tolypella-species is a field of a few specialists, further complicating monitoring or even detection of this rare species. The design of the species-specific primers was based on reference nucleotide sequences of the chloroplast genes rbcL, psbC and atpB and of the ribosomal internal transcribed spacer regions ITS1 and ITS2, obtained from GenBank (Perez et al. 2017). To determine the specificity of the newly designed primers, DNA isolates obtained from T. canadensis specimens collected from the Torneträsk (Sweden, 2018) and other charophyte species were prepared in different proportions. The sensitivity of the primers was experimentally assayed by using serial dilutions of T. canadensis DNA. Additionally, a mock test comprised of a sample with the DNA of several charophyte species was conducted and finally, the markers were tested on environmental samples from the Torneträsk. Tolypella canadensis-specific primers of the ITS2 region yielded positive PCR amplifications of one single band when T. canadensis was present in a sample. Cross-amplification was not found during the mock test; other charophyte species did not yield positive amplification. The eDNA samples from the Torneträsk validated the performance of the ITS2 marker. The T. canadensis-specific marker designed in this project was proven to be sensitive and accurate. It could be recommended as a useful tool to detect the presence of T. canadensis DNA, even at low concentration and in complex samples containing other charophyte species.

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