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opencc-zeroMay 2020View details →

Data from: The evolutionary origins of natural pedagogy: Rhesus monkeys show sustained attention following nonsocial cues versus social communicative signals

The natural pedagogy hypothesis proposes that human infants preferentially attend to communicative signals from others, facilitating rapid cultural learning. In this view, sensitivity to such signals are a uniquely human adaptation and as such nonhuman animals should not produce or utilize these communicative signals. We test these evolutionary predictions by examining sensitivity to communicative cues in 206 rhesus monkeys (Macaca mulatta) using an expectancy looking time task modeled on prior work with infants. Monkeys observed a human actor who either made eye contact and vocalized to the monkey (social cue), or waved a fruit in front of her face and produced a tapping sound (nonsocial cue). The actor then either looked at an object (referential look) or looked towards empty space (look away). We found that, unlike human infants in analogous situations, rhesus monkeys looked longer at events following nonsocial cues, regardless of the demonstrator's subsequent looking behavior. Moreover, younger and older monkeys showed similar patterns of responses across development. These results provide support for the natural pedagogy hypothesis, while also highlighting evolutionary changes in human sensitivity to communicative signals.

opencc-zeroNov 2019View details →

Data from: Analysis of evolutionary relationships provides new clues to the origins of weedy rice

Weedy rice (Oryza sativa f. spontanea) is considered to be a pest in modern rice production systems because it competes for resources, has poor yield characteristics, and subsequently has a negative effect on rice grain yield. The evolutionary relationships among weedy rice, landrace rice, improved rice cultivars, and wild rice are largely unknown. In this study, we conducted a population genetic analysis based on neutral markers and gene haplotypes in 524 rice accessions and a comparative transcriptomic analysis using 15 representative samples. The results showed that weedy rice populations have the highest level of genetic diversity (He=0.8386), and can be divided into two groups (japonica-type and indica-type). The japonica-type weedy rice accessions from HLJ, JL, LN, and NX provinces clustered with the landraces grown in these same provinces. The indica-types from JS province also clustered with the indica-type landraces from JS province. Comparative transcriptome analysis of weedy rice populations, improved rice populations. and landrace rice from HLJ, JL and LN provinces showed that the weedy rice still clustered with the landrace rice, and that the improved rice lines comprise a single population. Thirty-two differentially expressed genes were shared by the improved rice and landrace rice groups as well as between the improved rice and weedy rice groups. Using GO analysis, we identified 19 shared GO terms in the improved rice and landrace rice groups as well as between the improved rice and weedy rice groups. Our results suggest that weedy rice populations in China have diverse origins, and comparative transcriptome analysis of different types of rice from HLJ, JL, and LN suggests that improved rice populations have become a medium or end point in the evolution of weedy rice, which provides a new perspective for the study of weedy rice origins and lays a solid foundation for rice breeding.

opencc-zeroSep 2019View details →

Data from: The molecular phylogenetics of Trachymyrmex ants and their fungal cultivars provide insights into the origin and co-evolutionary history of 'higher-attine' ant agriculture

The fungus‐growing ants and their fungal cultivars constitute a classic example of a mutualism that has led to complex coevolutionary dynamics spanning c. 55–65 Ma. Of the five agricultural systems practised by fungus‐growing ants, higher‐attine agriculture, of which leaf‐cutter agriculture is a derived subset, remains poorly understood despite its relevance to ecosystem function and human agriculture across the Neotropics and parts of North America. Among the ants practising higher‐attine agriculture, the genus Trachymyrmex Forel, as currently defined, shares most‐recent common ancestors with both the leaf‐cutter ants and the higher‐attine genera Sericomyrmex Mayr and Xerolitor Sosa‐Calvo et al. Although previous molecular‐phylogenetic studies have suggested that Trachymyrmex is a paraphyletic grade, until now insufficient taxon sampling has prevented a full investigation of the evolutionary history of this group and limited the possibility of resolving its taxonomy. Here we describe the results of phylogenetic analyses of 38 Trachymyrmex species, including 27 of the 49 described species and at least 11 new species, using four nuclear markers, as well as phylogenetic analyses of the fungi cultivated by 23 species of Trachymyrmex using two markers. We generated new genetic data for 112 ants (402 new gene sequences) and 95 fungi (153 new gene sequences). Our results corroborate previous findings that Trachymyrmex, as currently defined, is paraphyletic. We propose recognizing two new genera, Mycetomoellerius gen.n. and Paratrachymyrmex gen.n., and restricting the continued use of Trachymyrmex to the clade of nine largely North American species that contains the type species [Trachymyrmex septentrionalis (McCook)] and that is the sister group of the leaf‐cutting ants. Our fungal cultivar phylogeny generally corroborates previously observed broad patterns of ant–fungus association, but it also reveals further violations of those patterns. Higher‐attine fungi are divided into two groups: (i) the single species Leucoagaricus gongylophorus (Möller); and (ii) its sister clade, consisting of multiple species, recently referred to as Leucoagaricus Singer 'clade B'. Our phylogeny indicates that, although most non‐leaf‐cutting higher‐attine ants typically cultivate species in clade B, some species cultivate L. gongylophorus, whereas still others cultivate fungi typically associated with lower‐attine agriculture. This indicates that the attine agricultural systems, which are currently defined by associations between ants and fungi, are not entirely congruent with ant and fungal phylogenies. They may, however, be correlated with as yet poorly understood biological traits of the ants and/or of their microbiomes.

opencc-zeroNov 2023View details →

Ancient mitochondrial genomes unveil the origins and evolutionary history of New Zealand's enigmatic takahe and moho

Many avian species endemic to Aotearoa New Zealand were driven to extinction or reduced to relict populations following successive waves of human arrival, due to hunting, habitat destruction, and the introduction of mammalian predators. Among the affected species were the large flightless South Island takahe (Porphyrio hochstetteri) and the moho (North Island takahe; P. mantelli), with the latter rendered extinct and the former reduced to a single relictual population. Little is known about the evolutionary history of these species prior to their decline and/or extinction. Here we sequenced mitochondrial genomes from takahe and moho subfossils (12 takahe and four moho) and retrieved comparable sequence data from takahemuseum skins (n = 5) and contemporary individuals (n = 17) to examine the phylogeny and recent evolutionary history of these species. Our analyses suggest that prehistoric takahepopulations lacked deep phylogeographic structure, in contrast to moho, which exhibited significant spatial genetic structure, albeit based on limited sample sizes (n = 4). Temporal genetic comparisons show that takahe have lost much of their mitochondrial genetic diversity, likely due to a sudden demographic decline soon after human arrival (~750 years ago). Time-calibrated phylogenetic analyses strongly support a sister-species relationship between takahe and moho, suggesting these flightless taxa diverged around 1.5 million years ago, following a single colonisation of New Zealand by a flighted Porphyrio ancestor approximately four million year ago. This study highlights the utility of palaeogenetic approaches for informing the conservation and systematic understanding of endangered species whose ranges have been severely restricted by anthropogenic impacts.

opencc-zeroMar 2024View details →

A diadectid skin impression and its implications for the evolutionary origin

Corneous skin appendages are common and diverse in crown-group amniotes but are also present in some modern amphibians. This raises the still unresolved question of whether the ability to form corneous skin appendages is an apomorphy of a common ancestor of amphibians and amniotes or evolved independently in both groups. So far, there is no palaeontological contribution to the issue due to the lack of keratin soft tissue preservation in Palaeozoic anamniotes. New data is provided by a recently discovered ichnofossil specimen from the early Permian of Poland that shows monospecific tetrapod footprints associated with a partial scaly body impression. The traces can be unambiguously attributed to diadectids and are interpreted as the globally first evidence of horned scales in tetrapods close to the origin of amniotes. Taking hitherto little-noticed scaly skin impressions of lepospondyl stem amniotes from the early Permian of Germany into account, the possibility has to be considered that the evolutionary origin of epidermal scales deeply roots among anamniotes.

opencc-zeroMar 2022View details →

Supporting trees and alignments for the publication: Cryptic and abundant marine viruses at the evolutionary origins of Earth's RNA virome

<div class="page"> <div class="layoutArea"> <div class="column"> Whereas DNA viruses are known to be abundant, diverse, and commonly key ecosystem players, RNA viruses are relatively understudied outside disease settings. Here, we analyzed ≈28 terabases of Global Ocean RNA sequences to expand Earth's RNA virus catalogues and their taxonomy, investigate their evolutionary origins, and assess their marine biogeography from pole to pole. Using new approaches to optimize discovery and classification, we identified RNA viruses that necessitate substantive revisions of taxonomy (doubling phyla and adding >50% new classes) and evolutionary understanding. "Species"-rank abundance determination revealed that viruses of new phyla "Taraviricota", a missing link in early RNA virus evolution, and "Arctiviricota" are widespread and dominant in the oceans. These efforts provide foundational knowledge critical to integrating RNA viruses into ecological and epidemiological models. </div> </div> </div>

opencc-by-4.0Dec 2018View details →

Fig. 6 in The origin and diversification of the Entorrhizales: deep evolutionary roots but recent speciation with a phylogenetic and phenotypic split between associates of the Cyperaceae and Juncaceae

Fig. 6 Spores of Entorrhiza fuirenae (holotype) seen by light microscopy. Scale bar = 10 μm

opencc-by-4.0Mar 2019View details →

Extreme isolation of WN3/O3 stars and implications for their evolutionary origin as the elusive stripped binaries

MESA inlists associated with <a href="https://ui.adsabs.harvard.edu/#abs/2018MNRAS.475..772S/abstract">Smith et al. (2018)</a>. MESA version 8118. Publication DOI: <a href="https://doi.org/10.1093/mnras/stx3181">10.1093/mnras/stx3181</a>

opencc-by-4.0Aug 2024View details →

Shared evolutionary origin and clade-specific signatures of symbiosis in lifestyle distinctive fungi

Data repository established for the appendix dataset documented in Scarlet M. Au’s MPhil in Biological Science (Plant Sciences) thesis, submitted to the University of Cambridge, UK.  Appendix A. List of 182 species from the Mucoromycota subphylum Appendix B. List of 535 BUSCO single copy genes identified for single copy phylogenies.  1) Appendix B-1 contains BUSCO genes mostly annotated relative to the Rhizophagus irregularis DAOM_181602_v1.0. For genes that were missing, annotations were drawn from the Lyc-1 and the Thamnidium elegans genomes.  2) Appendix B-2 contains BUSCO genes annotated relative to the Rhizophagus irregularis DAOM_181602_v1.0 genome.  3) Appendix B-3 contains BUSCO genes annotated relative to the Lyc-1 genome. 4) Appendix B-4 contains BUSCO genes annotated relative to the Thamnidium elegans genome.  Appendix C. Hierarchical clustering by orthogroup absence/presence and abundance.  1) Full hierarchical clustering by row (species) and columns (orthogroups) for binary matrix.  2) Full hierarchical clustering by row (species) and columns (orthogroups) for normalised matrix.  3) Full hierarchical clustering by row (species) only for binary matrix.  4) Full hierarchical clustering by row (species only) for normalised matrix. Appendix D. 36 out of 72 orthogroups shared between MFRE and AM fungal genomes contain known functional annotations.

FIGURE 8 in The marine-associated lifestyle of ameronothroid mites (Acari, Oribatida) and its evolutionary origin: a review

FIGURE 8: Algal habitat as substrate and food resource: A – Intertidal alga Bostrychia sp. growing on mangrove root (El Limón, Dominican Republic). B – Enlarged view of Bostrychia sp. showing Alismobates inexpectatus individuals foraging on alga and depositing fecal pellets.

FIGURE 7 in The marine-associated lifestyle of ameronothroid mites (Acari, Oribatida) and its evolutionary origin: a review

FIGURE 7: Examples of distinct sexual dimorphism littoral ameronothroid mites (see text for explanation): A – Alaskozetes antarcticus (modified after Wallwork 1962); B – Fortuynia atlantica (modified after Krisper and Schuster 2008); C – Fortuynia dimorpha (modified after Pfingstl 2015a).

FIGURE 6 in The marine-associated lifestyle of ameronothroid mites (Acari, Oribatida) and its evolutionary origin: a review

FIGURE 6: Photographs illustrating characteristic behaviors intertidal Fortuynia atlantica: A – Adult specimens aggregating in a small depression of substrate; B – Three adults and larva rafting on water surface – "floating behavior" (white rings on mites are reflections of ring-light illuminator).

FIGURE 9 in The marine-associated lifestyle of ameronothroid mites (Acari, Oribatida) and its evolutionary origin: a review

FIGURE 9: Simplified schemes illustrating two different evolutionary theories explaining origin of marine-associated Ameronothroidea: A – Monophyletic origin of Ameronothroidea implying single land-to-sea transition event (e.g. supported by Schulte and Weigmann 1977); B – Polyphyletic Ameronothroidea and three independent invasions marine littoral (e.g. supported by Proche¸s 2001). T = last terrestrial ancestor, invading littoral environment. (Schemes are not to be seen as phylogenetic trees, length of lines does not correspond with time or number of evolutionary changes).

FIGURE 3 in The marine-associated lifestyle of ameronothroid mites (Acari, Oribatida) and its evolutionary origin: a review

FIGURE 3: Types of tarsal claws present in intertidal oribatid mites. Upper row – different kinds of elongated sickle-shaped claws, lower row – claws with additional teeth: A – Ameronothrus sp.; B – Fortuynia smiti; C – Selenoribatidae gen. nov.; D – Carinozetes bermudensis (one proximoventral tooth); E – Selenoribates arotroventer (two proximoventral teeth); F – Selenoribates satanicus (one proximoventral and one proximodorsal tooth).

FIGURE 2 in The marine-associated lifestyle of ameronothroid mites (Acari, Oribatida) and its evolutionary origin: a review

FIGURE 2: SEM-micrographs – juxtaposition of typical intertidal and typical terrestrial oribatid mites, showing no obvious differences (excepting tarsal claws much more prominent in intertidal species): A – Alismobates inexpectatus, inhabitant of rocky intertidal shores (Western Atlantic); B – Scutovertex ianus, found in moss (Central Europe).

FIGURE 1 in The marine-associated lifestyle of ameronothroid mites (Acari, Oribatida) and its evolutionary origin: a review

FIGURE 1: Global distribution of marine-associated ameronothroid mite families. Ameronothridae – blue circles; relictual terrestrial Ameronothridae – black circles; Selenoribatidae – orange circles; Fortuyniidae – red squares; Podacaridae – violet squares. Arrowheads pointing to occurrences of taxa specifically discussed in the text. 1 – Alaskozetes coriaceus; 2 – Ameronothrus bilineatus; 3 – Aquanothrus; 4 – Chudalupia meridionalis.

FIGURE 4 in The marine-associated lifestyle of ameronothroid mites (Acari, Oribatida) and its evolutionary origin: a review

FIGURE 4: Photographs of flooded fortuyniid specimens from Bonaire Isl. Retained air can be seen as silvery shimmer on body surfaces.

FIGURE 5 in The marine-associated lifestyle of ameronothroid mites (Acari, Oribatida) and its evolutionary origin: a review

FIGURE 5: SEM-micrograph of Fortuynia maledivensis, lateral view, demonstrating the configuration of Van der Hammen's organ. Arrows point to each lateral cuticular channel of this organ; Ss – sensillus, la – lateral anterior notogastral seta, I–III – legs.

opencc-zeroFeb 2023View details →

Data for: Ecological and evolutionary origin of Costus flammulus (Costaceae): A new species from the montane cloud forests of the volcanic cordilleras in northern Costa Rica

Costus flammulus is a new herbaceous species endemic to montane cloud forests of the volcanic cordilleras in northern Costa Rica. Costus flammulus has been mistaken for C. wilsonii, but phylogenetic evidence demonstrates that it is closely related to the widespread lowland species C. pulverulentus. Here, we used an integrated framework of species concepts to evaluate whether C. flammulus and C. pulverulentus are distinct species. First, we re-evaluate prior phylogenetic analyses to assess whether C. flammulus bifurcated from or budded off from within C. pulverulentus and whether C. flammulus is monophyletic. We then compare phenotypic traits to determine which diagnostic vegetative and inflorescence traits can be used to identify species in herbarium specimens and examine whether floral traits may confer floral isolation. We compare pollinator assemblages to examine whether pollinator specificity may contribute to reproductive isolation. Finally, we model species distributions and climatic niche overlap to assess ecogeographic isolation. We found that C. flammulus is a monophyletic species phenotypically, ecologically, and geographically distinct from C. pulverulentus and may have speciated as a peripheral isolate at the high elevation range edge of C. pulverulentus. Several lines of evidence, such as C. pulverulentus paraphyly, range size asymmetry, and C. flammulus' nested distribution and vegetative traits, suggest that C. flammulus budded off from a C. pulverulentus‐like progenitor species, evolving to tolerate a colder and more seasonal montane environment.