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opencc-by-4.0Jun 2022View details →

Protostars and Planets VII -- Figures and Table for "The Origin and Evolution of Multiple Star Systems"

Figures 1-9 and Table 1 for "The Origin and Evolution of Multiple Star Systems" chapter to appear in Protostars and Planet VII.

opencc-by-4.0Jul 2023View details →

Data set for the article "Synchronous replication initiation of multiple origins"

This data set contains the data of the submitted article "Synchronous replication initiation of multiple origins". The data was generated using simulations in python that are linked below. Experiments indicate that E. coli initiates DNA replication at multiple origins synchronously in fast growth conditions. We study by mathematical modelling under what conditions replication is initiated synchronously.

opencc-by-4.0Feb 2020View details →

FIGURE 2 in Dating the origin and diversiFIcation of Pan-Chelidae (Testudines, Pleurodira) under multiple molecular clock approaches

FIGURE 2 Opening of Tasman Sea; Pal., Paleocene; P, Pliocene; Pe, Pelomedusa; Pel, Pelusios; Pelt, Peltocephalus; (cont.) Ph, Phrynops; Pl, Platemys; Ple, Pleurodira; Po, Podocnemis; Ps, Pseudemydura; Q, Quaternary; R, Rheodytes; Rh, Rhinemys. *, constrained nodes based on the TE MP topology; †, extinct taxa; ↑, origin of total groups Pan-Chelidae and Pan-Pelomedusioides. Downloaded from Brill.com10/07/2022 07:36:56PM via free access

opencc-by-4.0Feb 2020View details →

FIGURE 3 in Dating the origin and diversiFIcation of Pan-Chelidae (Testudines, Pleurodira) under multiple molecular clock approaches

FIGURE 3 Comparison of the three dating analyses performed in this study (simplified trees). Node number as in table 2. Abbreviations of analyses as in table 1. Abbreviations of geological events as in fig. 2. Abbrevia- tions of genera as in figs. 1 and 2. * constrained nodes based on the MP topologies; ↑, origin of total groups Pan-Chelidae and Pan- Pelomedusioides.

opencc-by-4.0Feb 2020View details →

FIGURE 4 in Dating the origin and diversiFIcation of Pan-Chelidae (Testudines, Pleurodira) under multiple molecular clock approaches

FIGURE 4 Comparison of dates produced by the three analyses of this study and four previous molecular clock studies. Abbreviations: Dea (2011), Dornburg et al. (2011); Jea (2013), Joyce et al. (2013); Pea (2017), Pereira et al. (2017); TS-M TD, This study morphological tip-dating; TS- ND, This study node-dating; TS-TE TD, This study total-evidence tip- dating; R&DF (2016), Rodrigues & Diniz-Filho (2016). Node numbers as in table 2.

opencc-by-4.0Aug 2020View details →

Going underwater! Multiple origins and functional morphology of piercing-sucking feeding and tracheal system adaptations in water scavenger beetle larvae (Coleoptera: Hydrophiloidea)

Supplementary videos: Video S1. Typical feeding behavior of chewing larvae. Tropisternus latus Brullé, 1837 first-instar larva. Note that feeding occurs above water surface. Video S2. Alternative chewing feeding strategy of moluscivorous larvae. Hydrophilus (Dibolocelus) palpalis Brullé, 1837 second-instar larva feeding. Video S3. Piercing-sucking feeding behavior of Hemiosus dejeanii (Solier, 1849) third-instar larva. Note that feeding occurs under water surface. Video S4. Piercing-sucking feeding behavior of Oocyclus magnifica Hebauer & Wang, 1998. Note that feeding occurs inside water film.

opencc-zeroSep 2020View details →

The origins of coca: museum genomics reveals multiple independent domestications from progenitor Erythroxylum gracilipes

Coca is the natural source of cocaine as well as a sacred and medicinal plant farmed by South American Amerindians and mestizos. The coca crop comprises four closely related varieties classified into two species (Amazonian and Huánuco varieties within Erythroxylum coca Lam., and Colombian and Trujillo varieties within E. novogranatense (D.Morris) Hieron.) but our understanding of their wild progenitor(s) and origins remains rudimentary. In this study we use genomic data from natural history collections to estimate the geographic origins and genetic diversity of this economically and culturally important crop in the context of its wild relatives. Our phylogeographic analyses clearly demonstrate the four varieties of coca comprise two or three exclusive groups nested within the diverse lineages of the widespread, wild species E. gracilipes; establishing a new and robust hypothesis of domestication wherein coca originated two or three times from this wild progenitor. The Colombian and Trujillo coca varieties are descended from a single, ancient domestication event in northwestern South America. Huánuco coca was domesticated more recently, possibly in southeastern Peru. Amazonian coca either shares a common domesticated ancestor with Huánuco coca, or it was the product of a third and most recent independent domestication event in the western Amazon basin. This chronology of coca domestication reveals different Holocene peoples in South America were able to independently transform the same natural resource to serve their needs; in this case, a workaday stimulant.

opencc-zeroJan 2021View details →

Phylogeographic and demographic modelling analyses of the multiple origins of the rheophytic goldenrod Solidago yokusaiana

Understanding adaptation mechanisms is important in evolutionary biology. Parallel adaptation provides good opportunities to investigate adaptive evolution. To confirm parallel adaptation, it is effective to examine whether the phenotypic similarity has one or multiple origins and to use demographic modelling to consider the gene flow between ecotypes. Solidago yokusaiana is a rheophyte endemic to the Japanese Archipelago that diverged from Solidago virgaurea. This study examined the parallel origins of S. yokusaiana by distinguishing between multiple and single origins and subsequent gene flow. The haplotypes of non-coding chloroplast DNA and genotypes at 14 nuclear simple sequence repeat (nSSR) loci and single nucleotide polymorphisms (SNPs) revealed by double-digest restriction-associated DNA sequencing (ddRADseq) were used for phylogeographic analysis; the SNPs were also used to model population demographics. Some chloroplast haplotypes were common to S. yokusaiana and its ancestor S. virgaurea. Also, the population genetic structures revealed by nSSR and SNPs did not correspond to the taxonomic species. The demographic modelling supported the multiple origins of S. yokusaiana in at least four districts and rejected a single origin with ongoing gene flow between the two species, implying that S. yokusaiana independently and repeatedly adapted to frequently flooding riversides.

opencc-zeroOct 2022View details →

Data from: Multiple origins of lipid-based structural colors contribute to a gradient of fruit colors in Viburnum (Adoxaceae)

Structural color is poorly known in plants relative to animals. In fruits, only a handful of cases have been described, including in Viburnum tinus where the blue color results from a disordered multilayered reflector made of lipid droplets. Here, we examine the broader evolutionary context of fruit structural color across the genus Viburnum. We obtained fresh and herbarium fruit material from 30 Viburnum species spanning the phylogeny and used transmission electron microscopy, optical simulations, and ancestral state reconstruction to (1) identify the presence/absence of photonic structures in each species, (2) understand the mechanism producing structural color in newly identified species, (3) relate the development of cell wall structure to reflectance in V. dentatum, and (4) describe the evolution of cell-wall architecture across Viburnum. We identify at least two (possibly three) origins of blue fruit color in Viburnum, both of which produce large photonic structures made of lipid droplets embedded in the cell wall and which reflect blue light. Examining species that may exhibit structural color in combination with anthocyanin and carotenoid pigments, rather than focusing on the most extreme examples, will yield further insights into the diversity, ecology and evolution of fruit color.

opencc-by-4.0Aug 2017View details →

Multiple origin of the Phaenonotum beetles in the Greater Antilles (Coleoptera: Hydrophilidae): phylogeny, biogeography and systematics

The systematics and the phylogenetic position of the Caribbean representatives of Phaenonotum Sharp (Coleoptera: Hydrophilidae) are investigated in order to understand the composition of the Caribbean fauna and its origin. Phylogenetic analysis based on mitochondrial and nuclear genes has revealed the Caribbean species to be situated in three deeply nested clades, inferring multiple colonization of Caribbean islands from the continent. Time-tree analysis and BioGeoBEARS analyses of ancestral ranges estimated the oldest clade, consisting of wingless single-island endemics of Cuba (P. delgadoi), Jamaica (P. ondreji sp. nov.) and Hispaniola (P. laterale sp. nov.), to have diverged ca. 46.6 Ma from the South American ancestor and subsequently colonizing the Caribbean most likely via the GAARlandia land bridge connecting South America with Greater Antilles. The remaining three Caribbean species, including the Puerto Rican endemic, P. borinquenum sp. nov., are of more recent (Miocene to Pliocene) origin and colonized the Greater Antilles by over-water dispersal. All the Caribbean species are illustrated and diagnosed and three new species are described. The genus Phaenonotum, excluding P. caribense Archangelsky, is confirmed as a monophylum. We demonstrate that species-level taxonomy of Phaenonotum is difficult to solve by morphology alone, and ideally requires the combination of morphology and molecular markers.

opencc-by-nd-4.0Mar 2010View details →

FIGURE 2 in Phylogeny Of Dermanyssoidea (Acari: Parasitiformes) Suggests Multiple Origins Of Parasitism

FIGURE 2: Phylogenetic hypothesis from Figure 1 with vertebrate parasitic lineages denoted by dashed branches and arthropod associates labeled with a star. Labels A-J are referred to in the text.

opencc-by-nd-4.0Mar 2010View details →

FIGURE 1 in Phylogeny Of Dermanyssoidea (Acari: Parasitiformes) Suggests Multiple Origins Of Parasitism

FIGURE 1: Phylogenetic hypothesis of dermanyssoids relationships. Thickened black lines represent branches supported by posterior probabilities and bootstrap values greater than 85%. Remaining branches have both statistical measures between 70-84% or in some cases one value greater than 85%, but the other lower. All branches below 70% were collapsed on the tree. Labels A-J are referred to in the text.

opencc-zeroDec 2022View details →

Data for: Convergence and contingency in the evolution of a specialized mode of life: Multiple origins and high disparity of rock-boring bivalves

Evolutionary adaptation to novel, specialized modes of life is often associated with close mapping of form to function, resulting in narrow morphological disparity. For Bivalvia, endolithy (rock-boring) has biomechanical requirements thought to diverge strongly from those of the ancestral shallow-burrowing habit in soft sediments. However, 3D morphometric data from 73 species among ~94% of extant endolithic genera and families, along with 384 non-endolithic species in those families, show that endolithy has originated at least eight times. Endolithy is evolutionarily accessible from multiple morphological starting points, evidenced by the morphologies of the oldest fossil members of families. Although some endoliths appear to converge on a limited set of shell morphologies, the total range of endolith shell morphologies among the broadest for bivalve life habits, and lacks any unifying morphological trait. Nevertheless, endolithy is a taxon-poor habit today. This limited richness evidently does not derive from damped origination or heightened extinction rates on lineages containing endoliths, and today's endoliths are not confined to low diversity biogeographic regions. Instead, endolithy may be limited by habitat availability. Both determinism (convergence among distantly related taxa) and contingency (endoliths remain close to the disparate morphologies of their source clades) underlie the occupation of endolith morphospace.

opencc-zeroFeb 2023View details →

Data from: Multiple origins of mountain biodiversity in New Zealand's largest plant radiation

Aim: How mountains accumulate species diversity remains poorly understood, particularly the relative role of in situ cladogenesis compared with colonization from lower elevations. Here, we estimated the contributions of in situ cladogenesis and colonization in generating biodiversity of a large mountain plant radiation and determined the importance of niche adaptation and divergence in these processes. We expected cladogenesis would accompany novel habitats formed by mountain uplift but colonization would become more important with time as dispersal opportunities accrue. Location: New Zealand, Southern Alps Taxon: Veronica sect. Hebe (Plantaginaceae) Methods: We estimated the most complete time-calibrated phylogeny to date for Veronica sect. Hebe to quantify rates of in situ cladogenesis and colonization of mountain habitat based on historical biogeographical models. We used environmental niche modeling to quantify species' climate niches and estimate niche disparity and divergence over time. Results: In situ cladogenesis generated more species in the mountains than colonization from lowlands. Whereas cladogenesis slowed over time, colonization increased, especially in the alpine zone. Both adaptive ecological speciation along climate niche axes and non-adaptive, vicariant speciation contributed to cladogenesis. However, climate niche disparity through time became saturated, suggesting competition for niche space was important. Colonization brought more divergent species into mountain niches. Main Conclusions: We suggest mountain diversity accumulates through three main stages: high cladogenesis after initial colonization, decreasing cladogenesis with increasing competition, and increasing colonization after niches saturate, likely promoted by niche divergence. Combining lineage and mountain uplift trajectories, these stages provide a conceptual model to understand how diversity accumulates elsewhere. Assuming these deep-time findings apply to anthropogenic conditions, alpine specialists could struggle to outcompete colonizers facilitated by climate change, especially from generalist clades. Considering novel competitive interactions alongside niche traits and biogeographical processes will be crucial for predicting the fate of alpine biodiversity in a changing world.