Phylogenetic congruence between Neotropical primates and plants is driven by frugivory

Seed dispersal, by entailing multiple benefits to plants and frugivores, potential drives trait evolution and species diversification. Frugivory and seed dispersal shaped the coevolution of interacting clades, with consequences to speciation and diversification evidenced for e.g., primates. Evidences for macro-coevolutionary patterns in multi-specific, plant-animal mutualisms are scarce, and the mechanisms driven them remain unexplored. We tested for phylogenetic congruences in primate-plant interactions in Neotropics and show that both primates and plants share evolutionary history. Phylogenetic congruence between Platyrrhini and Angiosperms was asymmetrically driven by the most generalist primates interacting with a wide-range of specialist Angiosperms. Consistently similar eco-evolutionary dynamics seem to be operating irrespective of local assemblages, since the signal emerged independently across three Neotropical regions. Our analysis supports the idea that macroevolutionary, coevolved patterns among interacting mutualistic partners are driven by super-generalist taxa. Trait convergence among multiple partners within multi-specific assemblages appears as a mechanism favouring these coevolved outcomes.

Download Full-text

Evolutionary history of New World monkeys revealed by molecular and fossil data

10.1101/178111 ◽

2017 ◽

Cited By ~ 1

Author(s):

Daniele Silvestro ◽

Marcelo F. Tejedor ◽

Martha L. Serrano-Serrano ◽

Oriane Loiseau ◽

Victor Rossier ◽

...

Keyword(s):

Body Mass ◽

Evolutionary History ◽

New World ◽

Evolutionary Dynamics ◽

Middle Eocene ◽

Small Body ◽

Rapid Change ◽

Molecular Evidence ◽

New World Monkeys ◽

Wide Range

AbstractNew World monkeys (parvorder Platyrrhini) are one of the most diverse groups of primates, occupying today a wide range of ecosystems in the American tropics and exhibiting large variations in ecology, morphology, and behavior. Although the relationships among the almost 200 living species are relatively well understood, we lack robust estimates of the timing of origin, the ancestral morphology, and the evolution of the distribution of the clade. Here we integrate paleontological and molecular evidence to investigate the evolutionary dynamics of extinct and extant platyrrhines. We develop an analytical framework to infer ancestral states, the evolution of body mass, and changes in latitudinal ranges through time. Our results show that extant platyrrhines originated some 5–10 million years earlier than previously assumed, likely dating back to the Middle Eocene (∼ 43 million years ago, Ma). The estimated ancestral platyrrhine was strikingly small – weighing ∼ 0.4 kg, as compared to the largest modern species over 10 kg – matching the size of their presumed Eocene North African ancestors. Small-sized callitrichines (marmosets and tamarins) retained a small body mass throughout their evolutionary history, thus challenging the hypothesis of phyletic dwarfism as an explanation to their adaptive traits. In contrast, a rapid change in body mass range took place as the three families diverged between the Late Oligocene and the Early Miocene. That period also marks a peak in diversity of fossil platyrrhines and is associated with their widest latitudinal range, expanding as far to the South as Patagonia. This geographic expansion is temporally coincident with a significant increase in platyrrhine population size inferred from genomic data, and with warm and humid climatic conditions linked to the Miocene Climatic Optimum and the lower elevation of the Andes. These results unveil the early evolution of an iconic group of monkeys and showcase the advantages of integrating fossil and molecular data for estimating evolutionary rates and trends.

Download Full-text

Out of the Qinghai-Tibetan Plateau (QTP) and rapid radiation across Eurasia for Allium section Daghestanica (Amaryllidaceae)

AoB Plants ◽

10.1093/aobpla/plab017 ◽

2021 ◽

Author(s):

Min-Jie Li ◽

Huan-Xi Yu ◽

Xian-Lin Guo ◽

Xing-Jin He

Keyword(s):

Evolutionary History ◽

Divergence Time ◽

Time Estimation ◽

Adjacent Region ◽

Rapid Radiation ◽

Divergence Time Estimation ◽

Species Diversification ◽

The Third ◽

Evolutionary Line ◽

History Of

Abstract The disjunctive distribution (Europe-Caucasus-Asia) and species diversification across Eurasia for the genus Allium sect. Daghestanica has fascinating attractions for researchers aiming to understanding the development and history of the modern Eurasia flora. However, no any studies have been carried out to address the evolutionary history of this section. Based on the nrITS and cpDNA fragments (trnL-trnF and rpl32-trnL), the evolutionary history of the third evolutionary line (EL3) of the genus Allium was reconstructed and we further elucidate the evolutionary line of sect. Daghestanica under this background. Our molecular phylogeny recovered two highly supported clades in sect. Daghestanica: the Clade I includes Caucasian-European species and Asian A. maowenense, A. xinlongense and A. carolinianum collected in Qinghai; the Clade II comprises Asian yellowish tepal species, A. chrysanthum, A. chrysocephalum, A. herderianum, A. rude and A. xichuanense. The divergence time estimation and biogeography inference indicated that Asian ancestor located in the QTP and the adjacent region could have migrated to Caucasus and Europe distributions around the Late Miocene and resulted in further divergence and speciation; Asian ancestor underwent the rapid radiation in the QTP and the adjacent region most likely due to the heterogeneous ecology of the QTP resulted from the orogeneses around 4–3 Mya. Our study provides a picture to understand the origin and species diversification across Eurasia for sect. Daghestanica.

Download Full-text

Multiple cellular compartments engagement in Nicotiana benthamiana-peanut stunt virus-satRNA interactions revealed by systems biology approach

Plant Cell Reports ◽

10.1007/s00299-021-02706-4 ◽

2021 ◽

Author(s):

Barbara Wrzesińska ◽

Agnieszka Zmienko ◽

Lam Dai Vu ◽

Ive De Smet ◽

Aleksandra Obrępalska-Stęplowska

Keyword(s):

Virus Infection ◽

Nicotiana Benthamiana ◽

Cellular Localization ◽

Plant Interactions ◽

Satellite Rna ◽

Functional Connections ◽

Cell Compartments ◽

Wide Range ◽

Peanut Stunt Virus ◽

Cellular Compartments

Abstract Key message PSV infection changed the abundance of host plant’s transcripts and proteins associated with various cellular compartments, including ribosomes, chloroplasts, mitochondria, the nucleus and cytosol, affecting photosynthesis, translation, transcription, and splicing. Abstract Virus infection is a process resulting in numerous molecular, cellular, and physiological changes, a wide range of which can be analyzed due to development of many high-throughput techniques. Plant RNA viruses are known to replicate in the cytoplasm; however, the roles of chloroplasts and other cellular structures in the viral replication cycle and in plant antiviral defense have been recently emphasized. Therefore, the aim of this study was to analyze the small RNAs, transcripts, proteins, and phosphoproteins affected during peanut stunt virus strain P (PSV-P)–Nicotiana benthamiana interactions with or without satellite RNA (satRNA) in the context of their cellular localization or functional connections with particular cellular compartments to elucidate the compartments most affected during pathogenesis at the early stages of infection. Moreover, the processes associated with particular cell compartments were determined. The ‘omic’ results were subjected to comparative data analyses. Transcriptomic and small RNA (sRNA)–seq data were obtained to provide new insights into PSV-P–satRNA–plant interactions, whereas previously obtained proteomic and phosphoproteomic data were used to broaden the analysis to terms associated with cellular compartments affected by virus infection. Based on the collected results, infection with PSV-P contributed to changes in the abundance of transcripts and proteins associated with various cellular compartments, including ribosomes, chloroplasts, mitochondria, the nucleus and the cytosol, and the most affected processes were photosynthesis, translation, transcription, and mRNA splicing. Furthermore, sRNA-seq and phosphoproteomic analyses indicated that kinase regulation resulted in decreases in phosphorylation levels. The kinases were associated with the membrane, cytoplasm, and nucleus components.

Download Full-text

Adaptation limits ecological diversification and promotes ecological tinkering during the competition for substitutable resources

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1807530115 ◽

2018 ◽

Vol 115 (44) ◽

pp. E10407-E10416 ◽

Cited By ~ 10

Author(s):

Benjamin H. Good ◽

Stephen Martis ◽

Oskar Hallatschek

Keyword(s):

Evolutionary Dynamics ◽

Competitive Exclusion ◽

Directional Selection ◽

Ecological Niches ◽

Ecological Diversification ◽

Effective Competition ◽

Uptake Rates ◽

Wide Range ◽

Dynamical Features ◽

Adaptation Limits

Microbial communities can evade competitive exclusion by diversifying into distinct ecological niches. This spontaneous diversification often occurs amid a backdrop of directional selection on other microbial traits, where competitive exclusion would normally apply. Yet despite their empirical relevance, little is known about how diversification and directional selection combine to determine the ecological and evolutionary dynamics within a community. To address this gap, we introduce a simple, empirically motivated model of eco-evolutionary feedback based on the competition for substitutable resources. Individuals acquire heritable mutations that alter resource uptake rates, either by shifting metabolic effort between resources or by increasing the overall growth rate. While these constitutively beneficial mutations are trivially favored to invade, we show that the accumulated fitness differences can dramatically influence the ecological structure and evolutionary dynamics that emerge within the community. Competition between ecological diversification and ongoing fitness evolution leads to a state of diversification–selection balance, in which the number of extant ecotypes can be pinned below the maximum capacity of the ecosystem, while the ecotype frequencies and genealogies are constantly in flux. Interestingly, we find that fitness differences generate emergent selection pressures to shift metabolic effort toward resources with lower effective competition, even in saturated ecosystems. We argue that similar dynamical features should emerge in a wide range of models with a mixture of directional and diversifying selection.

Download Full-text

A test statistic to quantify treelikeness in phylogenetics

10.1101/2021.02.16.431544 ◽

2021 ◽

Author(s):

Caitlin Cherryh ◽

Bui Quang Minh ◽

Rob Lanfear

Keyword(s):

Evolutionary History ◽

Incomplete Lineage Sorting ◽

Phylogenetic Analyses ◽

Phylogenetic Network ◽

Parametric Bootstrap ◽

Lineage Sorting ◽

Test Statistic ◽

Sequence Alignments ◽

Wide Range ◽

History Of

AbstractMost phylogenetic analyses assume that the evolutionary history of an alignment (either that of a single locus, or of multiple concatenated loci) can be described by a single bifurcating tree, the so-called the treelikeness assumption. Treelikeness can be violated by biological events such as recombination, introgression, or incomplete lineage sorting, and by systematic errors in phylogenetic analyses. The incorrect assumption of treelikeness may then mislead phylogenetic inferences. To quantify and test for treelikeness in alignments, we develop a test statistic which we call the tree proportion. This statistic quantifies the proportion of the edge weights in a phylogenetic network that are represented in a bifurcating phylogenetic tree of the same alignment. We extend this statistic to a statistical test of treelikeness using a parametric bootstrap. We use extensive simulations to compare tree proportion to a range of related approaches. We show that tree proportion successfully identifies non-treelikeness in a wide range of simulation scenarios, and discuss its strengths and weaknesses compared to other approaches. The power of the tree-proportion test to reject non-treelike alignments can be lower than some other approaches, but these approaches tend to be limited in their scope and/or the ease with which they can be interpreted. Our recommendation is to test treelikeness of sequence alignments with both tree proportion and mosaic methods such as 3Seq. The scripts necessary to replicate this study are available at https://github.com/caitlinch/treelikeness

Download Full-text

Unbiased estimation of linkage disequilibrium from unphased data

10.1101/557488 ◽

2019 ◽

Cited By ~ 2

Author(s):

Aaron P. Ragsdale ◽

Simon Gravel

Keyword(s):

Linkage Disequilibrium ◽

Population Size ◽

Evolutionary History ◽

Unbiased Estimation ◽

Sequencing Data ◽

Unbiased Estimators ◽

Population Size Estimates ◽

Wide Range ◽

The Common ◽

Size Estimates

AbstractLinkage disequilibrium is used to infer evolutionary history and to identify regions under selection or associated with a given trait. In each case, we require accurate estimates of linkage disequilibrium from sequencing data. Unphased data presents a challenge because the co-occurrence of alleles at different loci is ambiguous. Commonly used estimators for the common statistics r2 and D2 exhibit large and variable upward biases that complicate interpretation and comparison across cohorts. Here, we show how to find unbiased estimators for a wide range of two-locus statistics, including D2, for both single and multiple randomly mating populations. These provide accurate estimates over three orders of magnitude in LD. We also use these estimators to construct an estimator for r2 that is less biased than commonly used estimators, but nevertheless argue for using rather than r2 for population size estimates.

Download Full-text

Defaunation precipitates the extinction of evolutionarily distinct interactions in the Anthropocene

Science Advances ◽

10.1126/sciadv.aav6699 ◽

2019 ◽

Vol 5 (6) ◽

pp. eaav6699 ◽

Cited By ~ 7

Author(s):

Carine Emer ◽

Mauro Galetti ◽

Marco A. Pizo ◽

Pedro Jordano ◽

Miguel Verdú

Keyword(s):

Seed Dispersal ◽

Evolutionary History ◽

Bird Species ◽

Forest Fragments ◽

Ecological Interactions ◽

Rescue Effect ◽

History Of ◽

Local Extinctions ◽

Functional Features ◽

Avian Seed Dispersal

Species on Earth are interconnected with each other through ecological interactions. Defaunation can erode those connections, yet we lack evolutionary predictions about the consequences of losing interactions in human-modified ecosystems. We quantified the fate of the evolutionary history of avian–seed dispersal interactions across tropical forest fragments by combining the evolutionary distinctness of the pairwise-partner species, a proxy to their unique functional features. Both large-seeded plant and large-bodied bird species showed the highest evolutionary distinctness. We estimate a loss of 3.5 to 4.7 × 104 million years of cumulative evolutionary history of interactions due to defaunation. Bird-driven local extinctions mainly erode the most evolutionarily distinct interactions. However, the persistence of less evolutionarily distinct bird species in defaunated areas exerts a phylogenetic rescue effect through seed dispersal of evolutionarily distinct plant species.

Download Full-text

Comparative mitochondrial phylogeography of two legless lizards (Pygopodidae) from Queensland’s fragmented woodlands

Israel Journal of Ecology and Evolution ◽

10.1163/22244662-20191081 ◽

2020 ◽

Vol 66 (3-4) ◽

pp. 142-150

Author(s):

Jessica Worthington Wilmer ◽

Andrew P. Amey ◽

Carmel McDougall ◽

Melanie Venz ◽

Stephen Peck ◽

...

Keyword(s):

Genetic Diversity ◽

Evolutionary History ◽

The West ◽

European Settlement ◽

Low Genetic Diversity ◽

Eastern Australia ◽

Wide Range ◽

History Of ◽

Open Forests ◽

Fossorial Species

Sclerophyll woodlands and open forests once covered vast areas of eastern Australia, but have been greatly fragmented and reduced in extent since European settlement. The biogeographic and evolutionary history of the biota of eastern Australia’s woodlands also remains poorly known, especially when compared to rainforests to the east, or the arid biome to the west. Here we present an analysis of patterns of mitochondrial genetic diversity in two species of Pygopodid geckos with distributions centred on the Brigalow Belt Bioregion of eastern Queensland. One moderately large and semi-arboreal species, Paradelma orientalis, shows low genetic diversity and no clear geographic structuring across its wide range. In contrast a small and semi-fossorial species, Delma torquata, consists of two moderately divergent clades, one from the ranges and upland of coastal areas of south-east Queensland, and other centred in upland areas further inland. These data point to varying histories of geneflow and refugial persistance in eastern Australia’s vast but now fragmented open woodlands. The Carnarvon Ranges of central Queensland are also highlighted as a zone of persistence for cool and/or wet-adapted taxa, however the evolutionary history and divergence of most outlying populations in these mountains remains unstudied.

Download Full-text

Microbial control of host gene regulation and the evolution of host–microbiome interactions in primates

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2019.0598 ◽

2020 ◽

Vol 375 (1808) ◽

pp. 20190598 ◽

Cited By ~ 1

Author(s):

Laura Grieneisen ◽

Amanda L. Muehlbauer ◽

Ran Blekhman

Keyword(s):

Gene Expression ◽

Gene Regulation ◽

Host Species ◽

Evolutionary Dynamics ◽

Microbial Control ◽

Host Gene ◽

Primate Species ◽

Microbiome Composition ◽

Wide Range ◽

Species Specific

Recent comparative studies have found evidence consistent with the action of natural selection on gene regulation across primate species. Other recent work has shown that the microbiome can regulate host gene expression in a wide range of relevant tissues, leading to downstream effects on immunity, metabolism and other biological systems in the host. In primates, even closely related host species can have large differences in microbiome composition. One potential consequence of these differences is that host species-specific microbial traits could lead to differences in gene expression that influence primate physiology and adaptation to local environments. Here, we will discuss and integrate recent findings from primate comparative genomics and microbiome research, and explore the notion that the microbiome can influence host evolutionary dynamics by affecting gene regulation across primate host species. This article is part of the theme issue ‘The role of the microbiome in host evolution’.

Download Full-text

On tropical mistletoes: tractable models for evolutionary ecology, ecosystem function, and phytochemistry

Botany ◽

10.1139/cjb-2016-0232 ◽

2017 ◽

Vol 95 (3) ◽

pp. 211-217 ◽

Cited By ~ 4

Author(s):

David M. Watson

Keyword(s):

Seed Dispersal ◽

Host Range ◽

Plant Communities ◽

Ecosystem Function ◽

Evolutionary Ecology ◽

Life Sciences ◽

Evolutionary Trajectory ◽

Tropical Regions ◽

Wide Range

In 2001, I synthesised published information on mistletoe–animal interactions, demonstrating the pervasive influence these hemiparasites have on community composition and proposing that mistletoes represent keystone resources. Although the review was global in scope, I noted “Tropical regions, in particular, are underrepresented in the mistletoe literature, and it is unclear if mistletoe is as important in structuring these highly diverse ecosystems as in less diverse temperate areas”. Since then, research on tropical mistletoes has burgeoned, as a growing number of researchers use these forest and woodland hemiparasites to address a wide range of ecological and evolutionary questions. In this commentary, I highlight some recent findings, revisit and refine some emergent inferences, and suggest that tropical mistletoes offer many opportunities for further research, representing tractable models to address many unanswered questions in the life sciences. As well as reinforcing the role of mistletoes as facilitators for plant communities and keystone resources for animal assemblages, research on mistletoe pollination, seed dispersal, and host-range, challenge the established views about the ecological maintenance and evolutionary trajectory of specialization.

Download Full-text