scholarly journals The evolution of fungal substrate specificity in a widespread group of crustose lichens

2018 ◽  
Vol 285 (1889) ◽  
pp. 20180640 ◽  
Author(s):  
Philipp Resl ◽  
Fernando Fernández-Mendoza ◽  
Helmut Mayrhofer ◽  
Toby Spribille
Keyword(s):  
Substrate Specificity ◽  
Phylogenetic Signal ◽  
Niche Conservatism ◽  
Substrate Type ◽  
Evolutionary Trajectory ◽  
Diversification Rates ◽  
Lichen Symbiosis ◽  
Substrate Specialization ◽  
Crustose Lichens

Lichens exhibit varying degrees of specialization with regard to the surfaces they colonize, ranging from substrate generalists to strict substrate specialists. Though long recognized, the causes and consequences of substrate specialization are poorly known. Using a phylogeny of a 150–200 Mya clade of lichen fungi, we asked whether substrate niche is phylogenetically conserved, which substrates are ancestral, whether specialists arise from generalists or vice versa and how specialization affects speciation/extinction processes. We found strong phylogenetic signal for niche conservatism. Specialists evolved into generalists and back again, but transitions from generalism to specialism were more common than the reverse. Our models suggest that for this group of fungi, ‘escape’ from specialization for soil, rock and bark occurred, but specialization for wood foreclosed evolution away from that substrate type. In parallel, speciation models showed positive diversification rates for soil and rock dwellers but not other specialists. Patterns in the studied group suggest that fungal substrate specificity is a key determinant of evolutionary trajectory for the entire lichen symbiosis.

Niche conservatism predominates in adaptive radiation: comparing the diversification of Hawaiian arthropods using ecological niche modelling

2019 ◽  
Vol 127 (2) ◽  
pp. 479-492 ◽  
Author(s):  
Anna E Hiller ◽  
Michelle S Koo ◽  
Kari R Goodman ◽  
Kerry L Shaw ◽  
Patrick M O’Grady ◽  
...  
Keyword(s):  
Adaptive Radiation ◽  
Phylogenetic Signal ◽  
Niche Overlap ◽  
Oceanic Islands ◽  
Niche Conservatism ◽  
Environmental Niche ◽  
Niche Modelling ◽  
Closely Related Species ◽  
Species Comparisons

Abstract The role of the environmental niche in fostering ecological divergence during adaptive radiation remains enigmatic. In this study, we examine the interplay between environmental niche divergence and conservatism in the context of adaptive radiation on oceanic islands, by characterizing the niche breadth of four Hawaiian arthropod radiations: Tetragnatha spiders (Tetragnathidae Latreille, 1804), Laupala crickets (Gryllidae Otte, 1994), a clade of Drosophila flies (Drosophilidae Fallén, 1823) and Nesosydne planthoppers (Delphacidae Kirkaldy, 1907). We assembled occurrence datasets for the four lineages, modelled their distributions and quantified niche overlap. All four groups occupy the islands in distinct ways, highlighting the contrasting axes of diversification for different lineages. Laupala and Nesosydne have opposite environmental niche extents (broad and narrow, respectively), whereas Tetragnatha and Drosophila share relatively intermediate tolerances. Temperature constrains the distributions of all four radiations. Tests of phylogenetic signal suggest that, for Tetragnatha and Drosophila, closely related species exhibit similar environmental niches; thus, diversification is associated with niche conservatism. Sister species comparisons also show that populations often retain similar environmental tolerances, although exceptions do occur. Results imply that diversification does not occur through ecological speciation; instead, adaptive radiation occurs largely within a single environment.

scholarly journals Climatic niche evolution in the viviparousSceloporus torquatusgroup (Squamata: Phrynosomatidae)

PeerJ ◽  
2019 ◽  
Vol 6 ◽  
pp. e6192 ◽  
Author(s):  
Norberto Martínez-Méndez ◽  
Omar Mejía ◽  
Jorge Ortega ◽  
Fausto Méndez-de la Cruz
Keyword(s):  
Phylogenetic Signal ◽  
Principal Component ◽  
Niche Differentiation ◽  
Cold Climate ◽  
Niche Conservatism ◽  
Niche Evolution ◽  
Climatic Niche ◽  
Precipitation Seasonality ◽  
Bioclimatic Variables ◽  
Dry Conditions

The cold-climate hypothesis maintains that viviparity arose as a means to prevent increased egg mortality in nests owing to low temperatures, and this hypothesis represents the primary and most strongly supported explanation for the evolution of viviparity in reptiles. In this regard, certain authors have stated that viviparous species will exhibit speciation via climatic niche conservatism, with similar climatic niches being observed in allopatric sister species. However, this prediction remains to be tested with bioclimatic variables relevant to each viviparous group. In the present study, we examined climatic niche evolution in a group of North American viviparous lizards to determine whether their diversification is linked to phylogenetic niche conservatism (PNC). We evaluated the phylogenetic signal and trait evolution of individual bioclimatic variables and principal component (PC) scores of a PC analysis, along with reconstructions of ancestral climate tolerances. The results suggest that diversification of theSceloporus torquatusgroup species is associated with both niche differentiation and PNC. Furthermore, we did not observe PNC across nearly all bioclimatic variables and in PC2 and PC3. However, in Precipitation Seasonality (Bio15), in Precipitation of Coldest Quarter (Bio19) and in PC1 (weakly associated with variability of temperature), we did observe PNC. Additionally, variation of the scores along the phylogeny and Pagel’s delta (δ) >1 of PC3 suggests a fast, recent evolution to dry conditions in the clade that sustainsS. serrifer.

scholarly journals Niche conservatism and elevated diversification shape species diversity in drylands: evidence from Zygophyllaceae

2018 ◽  
Vol 285 (1890) ◽  
pp. 20181742 ◽  
Author(s):  
Qinggang Wang ◽  
Shengdan Wu ◽  
Xiangyan Su ◽  
Linjing Zhang ◽  
Xiaoting Xu ◽  
...  
Keyword(s):  
Species Diversity ◽  
Water Availability ◽  
Woody Species ◽  
Diversification Rate ◽  
Niche Conservatism ◽  
Evolutionary Mechanisms ◽  
Diversification Rates ◽  
Diversity Patterns ◽  
Geographical Unit ◽  
Global Patterns

The integrated contributions of climate and macroevolutionary processes to global patterns of species diversity are still controversial in spite of a long history of studies. The niche conservatism hypothesis and the net diversification rate hypothesis have gained wide attention in recent literature. Many studies have tested these two hypotheses for woody species in humid forests; however, the determinants of species diversity patterns for arid-adapted plants remain largely ignored. Here, using a molecular phylogeny and the global distributions of Zygophyllaceae, a typical arid-adapted plant family, we assessed the effects of contemporary climate and net diversification rates on species diversity patterns in drylands. We found the variables representing water availability to be the best predictors for Zygophyllaceae diversity. Specifically, Zygophyllaceae species diversity significantly decreased with the increase in water availability, probably owing to phylogenetic conservatism of water-related niches. The net diversification rates of Zygophyllaceae accelerated sharply in the recent 10 Myr, coinciding roughly with the period of global aridification. The species diversity of Zygophyllaceae significantly increased with the increase in mean net diversification rates per geographical unit, especially in the Old World, supporting the net diversification rate hypothesis. Our study provides a case exploring climatic and evolutionary mechanisms of dryland species diversity patterns, and suggests that the conservatism in water-related niches and elevated net diversification rates in drylands may have jointly determined the global patterns of dryland species diversity.

scholarly journals The phylogenetic signal of diversification rates

2020 ◽  
Vol 58 (4) ◽  
pp. 1432-1436
Author(s):  
Fernanda S. Caron ◽  
Marcio R. Pie
Keyword(s):  
Phylogenetic Signal ◽  
Diversification Rates

Biogeographical patterns and processes in the genus group Scotussae (Acrididae: Melanoplinae): an integrative approach

2020 ◽  
Vol 131 (2) ◽  
pp. 417-433
Author(s):  
María Celeste Scattolini ◽  
Andrés Lira-Noriega ◽  
Viviana Andrea Confalonieri ◽  
Silvia Pietrokovsky ◽  
María Marta Cigliano
Keyword(s):  
Ecological Niche ◽  
Phylogenetic Signal ◽  
Total Evidence ◽  
Integrative Approach ◽  
Niche Conservatism ◽  
Phylogenetic Distance ◽  
Ecological Processes ◽  
Phylogenetic Niche Conservatism ◽  
Patterns And Processes

Abstract A biogeographical study of the genus group Scotussae, a clade of grasshoppers endemic to the subtropical temperate region of the La Plata Basin, South America, was performed within a phylogenetic context to test whether wing reduction reflects evolutionary and ecological processes within the clade. We used an integrative biogeographical approach to determine the role of geohistorical events, geography, ecology and phylogenetic niche conservatism on the distribution and diversification processes of the group. We performed a total evidence phylogenetic analysis and tested the phylogenetic signal of ecological niche traits (niche optimum and niche breadth). We also assessed the degree to which phylogenetic distance is correlated with geographical and ecological niche traits and we used BioGeoBEARS to estimate ancestral ranges. The results provided evidence for phylogenetic niche conservatism as well as a significant association between phylogeny and both geographical and, more strongly, ecological traits. Two main clades were clearly associated with wing development, and evidence points to the evolutionary and ecological processes within these two groups being different. The Brachypterous clade shows evidence that allopatric speciation was the main source of diversification, while for the Macropterous clade sympatric speciation seems more likely.

scholarly journals Climatic niche breadths of the Atlantic Forest snakes do not increase with increasing latitude

2021 ◽  
Author(s):  
José Thales da Motta Portillo ◽  
Fausto Erritto Barbo ◽  
Ricardo J Sawaya
Keyword(s):  
Atlantic Forest ◽  
Phylogenetic Signal ◽  
Generalized Least Squares ◽  
Niche Conservatism ◽  
General View ◽  
South American ◽  
Climatic Niche ◽  
Trade Off ◽  
Phylogenetic Niche Conservatism ◽  
Temperature And Precipitation

Abstract The climatic niche is a central concept for understanding species distribution, with current and past climate interpreted as strong drivers of present and historical geographical ranges. Our aim is to understand whether Atlantic Forest snakes follow the general geographical pattern of increasing species climatic niche breadths with increasing latitude. We also tested if there is a trade-off between temperature and precipitation niche breadths of species in order to understand if species with larger breadths of one niche dimension have stronger dispersal constraints by the other due to narrower niche breadths. Niche breadths were calculated by the subtraction of maximal and minimal values of temperature and precipitation across species ranges. We implemented Phylogenetic Generalized Least Squares (PGLS) to measure the relationship between temperature and precipitation niche breadths and latitude. We also tested phylogenetic signals by Lambda statistics to analyze the degree of phylogenetic niche conservatism to both niche dimensions. Temperature niche breadths were not related to latitude. Precipitation niche breadths decreased with increasing latitude and presented a high phylogenetic signal, i.e. significant phylogenetic niche conservatism. We rejected the trade-off hypotheses of temperature and precipitation niche breadths. Our results also indicate that precipitation should be an important ecological constraint affecting the geographical distribution of snake lineages across the South American Atlantic Forest. We then provide a general view of how phylogenetic niche conservatism could impact the patterns of latitudinal variation of climatic niches across this biodiversity hotspot.

scholarly journals Consequences of the divergence of Methionine AdenosylTransferase

2020 ◽  
Author(s):  
Bhanupratap Singh Chouhan ◽  
Madhuri H. Gade ◽  
Desirae Martinez ◽  
Saacnicteh Toledo-Patino ◽  
Paola Laurino
Keyword(s):  
Substrate Specificity ◽  
Sequence Divergence ◽  
Methionine Adenosyltransferase ◽  
Evolutionary Trajectory ◽  
Ideal System ◽  
Sequence Reconstruction ◽  
Domains Of Life ◽  
Functional Consequences ◽  
High Degree ◽  
Structural Levels

AbstractMethionine adenosyltransferase (MAT), which catalyzes the biosynthesis of S-adenosylmethionine from L-methionine and ATP, is an ancient, highly conserved enzyme present in all three domains of life. Although the MAT enzymes of each domain are believed to share a common ancestor, the sequences of archaeal MATs show a high degree of divergence from the sequences of bacterial and eukaryotic MATs. However, the structural and functional consequences of this sequence divergence are not well understood. Here, we use structural bioinformatics analysis and ancestral sequence reconstruction to highlight the consequences of archaeal MAT divergence. We show that the dimer interface containing the active site, which would be expected to be well conserved across all three domains, diverged considerably between the bacterial/eukaryotic MATs and archaeal MATs. Furthermore, the characterization of reconstructed ancestral archaeal MATs showed that they probably had low substrate specificity which expanded during their evolutionary trajectory hinting towards the observation that all the modern day MAT enzymes from the three-kingdom probably originated from a common specific ancestor and then archaea MATs diverged in sequence, structure and substrate specificity. Altogether, our results show that the archaea MAT is an ideal system for studying an enzyme family which evolved to display high degrees of divergence at the sequence/structural levels and yet are capable of performing the same catalytic reactions as their orthologous counterparts.

scholarly journals Genomic landscape of the global oak phylogeny

2019 ◽  
Author(s):  
Andrew L. Hipp ◽  
Paul S. Manos ◽  
Marlene Hahn ◽  
Michael Avishai ◽  
Cathérine Bodénès ◽  
...  
Keyword(s):  
Restriction Site ◽  
Phylogenetic Signal ◽  
Population Divergence ◽  
List Type ◽  
Lineage Sorting ◽  
Diversification Rates ◽  
Genomic Landscape ◽  
History Of ◽  
Fossil Data ◽  
Lineage Diversification

SummaryThe tree of life is highly reticulate, with the history of population divergence buried amongst phylogenies deriving from introgression and lineage sorting. In this study, we test the hypothesis that there are regions of the oak (Quercus, Fagaceae) genome that are broadly informative about phylogeny and investigate global patterns of oak diversity.We utilize fossil data and restriction-site associated DNA sequencing (RAD-seq) for 632 individuals representing ca. 250 oak species to infer a time-calibrated phylogeny of the world’s oaks. We use reversible-jump MCMC to reconstruct shifts in lineage diversification rates, accounting for among-clade sampling biases. We then map the > 20,000 RAD-seq loci back to a recently published oak genome and investigate genomic distribution of introgression and phylogenetic support across the phylogeny.Oak lineages have diversified among geographic regions, followed by ecological divergence within regions, in the Americas and Eurasia. Roughly 60% of oak diversity traces back to four clades that experienced increases in net diversification due to climatic transitions or ecological opportunity.The support we find for the phylogeny contrasts with high genomic heterogeneity in phylogenetic signal and introgression. Oaks are phylogenomic mosaics, and their diversity may in fact depend on the gene flow that shapes the oak genome.

scholarly journals The legacy of Eastern Mediterranean mountain uplifts: rapid disparity of phylogenetic niche conservatism and divergence in mountain vipers

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Mohsen Ahmadi ◽  
Mahmoud-Reza Hemami ◽  
Mohammad Kaboli ◽  
Masoud Nazarizadeh ◽  
Mansoureh Malekian ◽  
...  
Keyword(s):  
Mediterranean Region ◽  
Ecological Niche ◽  
Eastern Mediterranean ◽  
Phylogenetic Signal ◽  
Eastern Mediterranean Region ◽  
Ecological Niches ◽  
Niche Conservatism ◽  
Niche Evolution ◽  
Biogeographic History ◽  
Temperature Seasonality

Abstract Background The orogeny of the eastern Mediterranean region has substantially affected ecological speciation patterns, particularly of mountain-dwelling species. Mountain vipers of the genus Montivipera are among the paramount examples of Mediterranean neo-endemism, with restricted ranges in the mountains of Anatolia, the Levant, Caucasus, Alborz, and Zagros. Here we explore the phylogenetic and ecological diversification of Montivipera to reconstruct its ecological niche evolution and biogeographic history. Using 177 sequences of three mitochondrial genes, a dated molecular phylogeny of mountain vipers was reconstructed. Based on 320 occurrence points within the entire range of the genus and six climatic variables, ecological niches were modelled and used to infer ancestral niche occupancy. In addition, the biogeographic history and ancestral states of the species were reconstructed across climate gradients. Results Dated phylogenetic reconstruction revealed that the ancestor of mountain vipers split into two major clades at around 12.18 Mya followed by multiple vicariance events due to rapid orogeny. Montivipera colonised coastal regions from a mountain-dwelling ancestor. We detected a highly complex ecological niche evolution of mountain vipers to temperature seasonality, a variable that also showed a strong phylogenetic signal and high contribution in niche occupation. Conclusion Raising mountain belts in the Eastern Mediterranean region and subsequent remarkable changes in temperature seasonality have led to the formation of important centres of diversification and endemism in this biodiversity hotspot. High rates of niche conservatism, low genetic diversity, and segregation of ranges into the endemic distribution negatively influenced the adaptive capacity of mountain vipers. We suggest that these species should be considered as evolutionary significant units and priority species for conservation in Mediterranean mountain ecosystems.

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