skip to main content

Attention:

The NSF Public Access Repository (NSF-PAR) system and access will be unavailable from 11:00 PM ET on Thursday, October 10 until 2:00 AM ET on Friday, October 11 due to maintenance. We apologize for the inconvenience.


Title: An integrative genomic and phenomic analysis to investigate the nature of plant species in Escallonia (Escalloniaceae)
Abstract

What we mean by species and whether they have any biological reality has been debated since the early days of evolutionary biology. Some biologists even suggest that plant species are created by taxonomists as a subjective, artificial division of nature. However, the nature of plant species has been rarely tested critically with data while ignoring taxonomy. We integrate phenomic and genomic data collected across hundreds of individuals at a continental scale to investigate this question inEscallonia(Escalloniaceae), a group of plants which includes 40 taxonomic species (the species proposed by taxonomists). We first show that taxonomic species may be questionable as they match poorly to patterns of phenotypic and genetic variation displayed by individuals collected in nature. We then use explicit statistical methods for species delimitation designed for phenotypic and genomic data, and show that plant species do exist inEscalloniaas an objective, discrete property of nature independent of taxonomy. We show that such species correspond poorly to current taxonomic species ($$< 20\%$$<20%) and that phenomic and genomic data seldom delimit congruent entities ($$< 20\%$$<20%). These discrepancies suggest that evolutionary forces additional to gene flow can maintain the cohesion of species. We propose that phenomic and genomic data analyzed on an equal footing build a broader perspective on the nature of plant species by helping delineate different ‘types of species’. Our results caution studies which take the accuracy of taxonomic species for granted and challenge the notion of plant species without empirical evidence. Note: A version of the complete manuscript in Spanish is available in the Supplemental Materials.

 
more » « less
Award ID(s):
1939128
NSF-PAR ID:
10383785
Author(s) / Creator(s):
; ; ;
Publisher / Repository:
Nature Publishing Group
Date Published:
Journal Name:
Scientific Reports
Volume:
11
Issue:
1
ISSN:
2045-2322
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Abstract

    Given a compact doubling metric measure spaceXthat supports a 2-Poincaré inequality, we construct a Dirichlet form on$$N^{1,2}(X)$$N1,2(X)that is comparable to the upper gradient energy form on$$N^{1,2}(X)$$N1,2(X). Our approach is based on the approximation ofXby a family of graphs that is doubling and supports a 2-Poincaré inequality (see [20]). We construct a bilinear form on$$N^{1,2}(X)$$N1,2(X)using the Dirichlet form on the graph. We show that the$$\Gamma $$Γ-limit$$\mathcal {E}$$Eof this family of bilinear forms (by taking a subsequence) exists and that$$\mathcal {E}$$Eis a Dirichlet form onX. Properties of$$\mathcal {E}$$Eare established. Moreover, we prove that$$\mathcal {E}$$Ehas the property of matching boundary values on a domain$$\Omega \subseteq X$$ΩX. This construction makes it possible to approximate harmonic functions (with respect to the Dirichlet form$$\mathcal {E}$$E) on a domain inXwith a prescribed Lipschitz boundary data via a numerical scheme dictated by the approximating Dirichlet forms, which are discrete objects.

     
    more » « less
  2. Abstract

    We propose a new measurement of the ratio of positron-proton to electron-proton elastic scattering at DESY. The purpose is to determine the contributions beyond single-photon exchange, which are essential for the Quantum Electrodynamic (QED) description of the most fundamental process in hadronic physics. By utilizing a 20 cm long liquid hydrogen target in conjunction with the extracted beam from the DESY synchrotron, we can achieve an average luminosity of$$2.12\times 10^{35}$$2.12×1035 cm$$^{-2}\cdot $$-2·s$$^{-1}$$-1 ($$\approx 200$$200times the luminosity achieved by OLYMPUS). The proposed two-photon exchange experiment (TPEX) entails a commissioning run at a beam energy of 2 GeV, followed by measurements at 3 GeV, thereby providing new data up to$$Q^2=4.6$$Q2=4.6 (GeV/c)$$^2$$2(twice the range of current measurements). We present and discuss the proposed experimental setup, run plan, and expectations.

     
    more » « less
  3. Abstract

    We perform path-integral molecular dynamics (PIMD), ring-polymer MD (RPMD), and classical MD simulations of H$$_2$$2O and D$$_2$$2O using the q-TIP4P/F water model over a wide range of temperatures and pressures. The density$$\rho (T)$$ρ(T), isothermal compressibility$$\kappa _T(T)$$κT(T), and self-diffusion coefficientsD(T) of H$$_2$$2O and D$$_2$$2O are in excellent agreement with available experimental data; the isobaric heat capacity$$C_P(T)$$CP(T)obtained from PIMD and MD simulations agree qualitatively well with the experiments. Some of these thermodynamic properties exhibit anomalous maxima upon isobaric cooling, consistent with recent experiments and with the possibility that H$$_2$$2O and D$$_2$$2O exhibit a liquid-liquid critical point (LLCP) at low temperatures and positive pressures. The data from PIMD/MD for H$$_2$$2O and D$$_2$$2O can be fitted remarkably well using the Two-State-Equation-of-State (TSEOS). Using the TSEOS, we estimate that the LLCP for q-TIP4P/F H$$_2$$2O, from PIMD simulations, is located at$$P_c = 167 \pm 9$$Pc=167±9 MPa,$$T_c = 159 \pm 6$$Tc=159±6 K, and$$\rho _c = 1.02 \pm 0.01$$ρc=1.02±0.01 g/cm$$^3$$3. Isotope substitution effects are important; the LLCP location in q-TIP4P/F D$$_2$$2O is estimated to be$$P_c = 176 \pm 4$$Pc=176±4 MPa,$$T_c = 177 \pm 2$$Tc=177±2 K, and$$\rho _c = 1.13 \pm 0.01$$ρc=1.13±0.01 g/cm$$^3$$3. Interestingly, for the water model studied, differences in the LLCP location from PIMD and MD simulations suggest that nuclear quantum effects (i.e., atoms delocalization) play an important role in the thermodynamics of water around the LLCP (from the MD simulations of q-TIP4P/F water,$$P_c = 203 \pm 4$$Pc=203±4 MPa,$$T_c = 175 \pm 2$$Tc=175±2 K, and$$\rho _c = 1.03 \pm 0.01$$ρc=1.03±0.01 g/cm$$^3$$3). Overall, our results strongly support the LLPT scenario to explain water anomalous behavior, independently of the fundamental differences between classical MD and PIMD techniques. The reported values of$$T_c$$Tcfor D$$_2$$2O and, particularly, H$$_2$$2O suggest that improved water models are needed for the study of supercooled water.

     
    more » « less
  4. Abstract

    Recent spectacular advances by AI programs in 3D structure predictions from protein sequences have revolutionized the field in terms of accuracy and speed. The resulting “folding frenzy” has already produced predicted protein structure databases for the entire human and other organisms’ proteomes. However, rapidly ascertaining a predicted structure’s reliability based on measured properties in solution should be considered. Shape-sensitive hydrodynamic parameters such as the diffusion and sedimentation coefficients ($${D_{t(20,w)}^{0}}$$Dt(20,w)0,$${s_{{\left( {{20},w} \right)}}^{{0}} }$$s20,w0) and the intrinsic viscosity ([η]) can provide a rapid assessment of the overall structure likeliness, and SAXS would yield the structure-related pair-wise distance distribution functionp(r) vs.r. Using the extensively validated UltraScan SOlution MOdeler (US-SOMO) suite, a database was implemented calculating from AlphaFold structures the corresponding$${D_{t(20,w)}^{0}}$$Dt(20,w)0,$${s_{{\left( {{20},w} \right)}}^{{0}} }$$s20,w0, [η],p(r) vs.r, and other parameters. Circular dichroism spectra were computed using the SESCA program. Some of AlphaFold’s drawbacks were mitigated, such as generating whenever possible a protein’s mature form. Others, like the AlphaFold direct applicability to single-chain structures only, the absence of prosthetic groups, or flexibility issues, are discussed. Overall, this implementation of the US-SOMO-AF database should already aid in rapidly evaluating the consistency in solution of a relevant portion of AlphaFold predicted protein structures.

     
    more » « less
  5. Abstract

    We report on a measurement of Spin Density Matrix Elements (SDMEs) in hard exclusive$$\rho ^0$$ρ0meson muoproduction at COMPASS using 160 GeV/cpolarised$$ \mu ^{+}$$μ+and$$ \mu ^{-}$$μ-beams impinging on a liquid hydrogen target. The measurement covers the kinematic range 5.0 GeV/$$c^2$$c2$$< W<$$<W<17.0 GeV/$$c^2$$c2, 1.0 (GeV/c)$$^2$$2$$< Q^2<$$<Q2<10.0 (GeV/c)$$^2$$2and 0.01 (GeV/c)$$^2$$2$$< p_{\textrm{T}}^2<$$<pT2<0.5 (GeV/c)$$^2$$2. Here,Wdenotes the mass of the final hadronic system,$$Q^2$$Q2the virtuality of the exchanged photon, and$$p_{\textrm{T}}$$pTthe transverse momentum of the$$\rho ^0$$ρ0meson with respect to the virtual-photon direction. The measured non-zero SDMEs for the transitions of transversely polarised virtual photons to longitudinally polarised vector mesons ($$\gamma ^*_T \rightarrow V^{ }_L$$γTVL) indicate a violation ofs-channel helicity conservation. Additionally, we observe a dominant contribution of natural-parity-exchange transitions and a very small contribution of unnatural-parity-exchange transitions, which is compatible with zero within experimental uncertainties. The results provide important input for modelling Generalised Parton Distributions (GPDs). In particular, they may allow one to evaluate in a model-dependent way the role of parton helicity-flip GPDs in exclusive$$\rho ^0$$ρ0production.

     
    more » « less