1
|
Shridhar SV, Beghini F, Alexander M, Singh A, Juárez RM, Brito IL, Christakis NA. Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages. Cell Rep 2024; 43:114442. [PMID: 38968070 DOI: 10.1016/j.celrep.2024.114442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 04/27/2024] [Accepted: 06/19/2024] [Indexed: 07/07/2024] Open
Abstract
Despite a growing interest in the gut microbiome of non-industrialized countries, data linking deeply sequenced microbiomes from such settings to diverse host phenotypes and situational factors remain uncommon. Using metagenomic data from a community-based cohort of 1,871 people from 19 isolated villages in the Mesoamerican highlands of western Honduras, we report associations between bacterial species and human phenotypes and factors. Among them, socioeconomic factors account for 51.44% of the total associations. Meta-analysis of species-level profiles across several datasets identified several species associated with body mass index, consistent with previous findings. Furthermore, the inclusion of strain-phylogenetic information modifies the overall relationship between the gut microbiome and the phenotypes, especially for some factors like household wealth (e.g., wealthier individuals harbor different strains of Eubacterium rectale). Our analysis suggests a role that gut microbiome surveillance can play in understanding broad features of individual and public health.
Collapse
Affiliation(s)
- Shivkumar Vishnempet Shridhar
- Yale Institute for Network Science, Yale University, New Haven, CT, USA; Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Francesco Beghini
- Yale Institute for Network Science, Yale University, New Haven, CT, USA
| | - Marcus Alexander
- Yale Institute for Network Science, Yale University, New Haven, CT, USA
| | - Adarsh Singh
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | | | - Ilana L Brito
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA.
| | - Nicholas A Christakis
- Yale Institute for Network Science, Yale University, New Haven, CT, USA; Department of Biomedical Engineering, Yale University, New Haven, CT, USA; Department of Statistics and Data Science, Yale University, New Haven, CT, USA; Department of Medicine, Yale School of Medicine, New Haven, CT, USA.
| |
Collapse
|
2
|
Hofmann S, Rödder D, Andermann T, Matschiner M, Riedel J, Baniya CB, Flecks M, Yang J, Jiang K, Jianping J, Litvinchuk SN, Martin S, Masroor R, Nothnagel M, Vershinin V, Zheng Y, Jablonski D, Schmidt J, Podsiadlowski L. Exploring Paleogene Tibet's warm temperate environments through target enrichment and phylogenetic niche modelling of Himalayan spiny frogs (Paini, Dicroglossidae). Mol Ecol 2024:e17446. [PMID: 38946613 DOI: 10.1111/mec.17446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 05/25/2024] [Accepted: 06/17/2024] [Indexed: 07/02/2024]
Abstract
The Cenozoic topographic development of the Himalaya-Tibet orogen (HTO) substantially affected the paleoenvironment and biodiversity patterns of High Asia. However, concepts on the evolution and paleoenvironmental history of the HTO differ massively in timing, elevational increase and sequence of surface uplift of the different elements of the orogen. Using target enrichment of a large set of transcriptome-derived markers, ancestral range estimation and paleoclimatic niche modelling, we assess a recently proposed concept of a warm temperate paleo-Tibet in Asian spiny frogs of the tribe Paini and reconstruct their historical biogeography. That concept was previously developed in invertebrates. Because of their early evolutionary origin, low dispersal capacity, high degree of local endemism, and strict dependence on temperature and humidity, the cladogenesis of spiny frogs may echo the evolution of the HTO paleoenvironment. We show that diversification of main lineages occurred during the early to Mid-Miocene, while the evolution of alpine taxa started during the late Miocene/early Pliocene. Our distribution and niche modelling results indicate range shifts and niche stability that may explain the modern disjunct distributions of spiny frogs. They probably maintained their (sub)tropical or (warm)temperate preferences and moved out of the ancestral paleo-Tibetan area into the Himalaya as the climate shifted, as opposed to adapting in situ. Based on ancestral range estimation, we assume the existence of low-elevation, climatically suitable corridors across paleo-Tibet during the Miocene along the Kunlun, Qiangtang and/or Gangdese Shan. Our results contribute to a deeper understanding of the mechanisms and processes of faunal evolution in the HTO.
Collapse
Affiliation(s)
- Sylvia Hofmann
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn, Germany
| | - Dennis Rödder
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn, Germany
| | - Tobias Andermann
- Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | | | - Jendrian Riedel
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn, Germany
| | - Chitra B Baniya
- Central Department of Botany, Tribhuvan University, Kathmandu, Nepal
| | - Morris Flecks
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn, Germany
| | - Jianhuan Yang
- Kadoorie Conservation China, Kadoorie Farm and Botanic Garden, Hong Kong, China
| | - Ke Jiang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Jiang Jianping
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | | | - Sebastian Martin
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn, Germany
| | | | - Michael Nothnagel
- Statistical Genetics and Bioinformatics, Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Vladimir Vershinin
- Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russia
- Institute of Natural Sciences and Mathematics, Eltsyn Ural Federal University, Yekaterinburg, Russia
| | - Yuchi Zheng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Daniel Jablonski
- Department of Zoology, Comenius University in Bratislava, Bratislava, Slovakia
| | - Joachim Schmidt
- General and Systematic Zoology, Institute of Biosciences, University of Rostock, Rostock, Germany
| | - Lars Podsiadlowski
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn, Germany
| |
Collapse
|
3
|
Halali S, Brakefield PM, Brattström O. Phenotypic plasticity in tropical butterflies is linked to climatic seasonality on a macroevolutionary scale. Evolution 2024; 78:1302-1316. [PMID: 38635459 DOI: 10.1093/evolut/qpae059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 01/15/2024] [Accepted: 04/16/2024] [Indexed: 04/20/2024]
Abstract
Phenotypic plasticity can be adaptive in fluctuating environments by providing rapid environment-phenotype matching and this applies particularly in seasonal environments. African Bicyclus butterflies have repeatedly colonized seasonal savannahs from ancestral forests around the late Miocene, and many species now exhibit seasonal polyphenism. On a macroevolutionary scale, it can be expected that savannah species will exhibit higher plasticity because of experiencing stronger environmental seasonality than forest species. We quantified seasonality using environmental niche modeling and surveyed the degree of plasticity in a key wing pattern element (eyespot size) using museum specimens. We showed that species occurring in highly seasonal environments display strong plasticity, while species in less seasonal or aseasonal environments exhibit surprisingly variable degrees of plasticity, including strong to no plasticity. Furthermore, eyespot size plasticity has a moderate phylogenetic signal and the ancestral Bicyclus likely exhibited some degree of plasticity. We propose hypotheses to explain the range of plasticity patterns seen in less seasonal environments and generate testable predictions for the evolution of plasticity in Bicyclus. Our study provides one of the most compelling cases showing links between seasonality and phenotypic plasticity on a macroevolutionary scale and the potential role of plasticity in facilitating the colonization of novel environments.
Collapse
Affiliation(s)
- Sridhar Halali
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
- Department of Biology, Lund University, Lund, Sweden
| | - Paul M Brakefield
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Oskar Brattström
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
- School of Biodiversity, One Health, and Veterinary Medicine, University of Glasgow, Glasgow, United Kingdom
- African Butterfly Research Institute, Nairobi, Kenya
| |
Collapse
|
4
|
Frandsen PB, Holzenthal RW, Espeland M, Breinholt J, Thomas Thorpe JA, Simon S, Kawahara AY, Plotkin D, Hotaling S, Li Y, Nelson CR, Niehuis O, Mayer C, Podsiadlowski L, Donath A, Misof B, Moriarty Lemmon E, Lemmon A, Morse JC, Liu S, Pauls SU, Zhou X. Phylogenomics recovers multiple origins of portable case making in caddisflies (Insecta: Trichoptera), nature's underwater architects. Proc Biol Sci 2024; 291:20240514. [PMID: 38955232 DOI: 10.1098/rspb.2024.0514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 06/10/2024] [Indexed: 07/04/2024] Open
Abstract
Caddisflies (Trichoptera) are among the most diverse groups of freshwater animals with more than 16 000 described species. They play a fundamental role in freshwater ecology and environmental engineering in streams, rivers and lakes. Because of this, they are frequently used as indicator organisms in biomonitoring programmes. Despite their importance, key questions concerning the evolutionary history of caddisflies, such as the timing and origin of larval case making, remain unanswered owing to the lack of a well-resolved phylogeny. Here, we estimated a phylogenetic tree using a combination of transcriptomes and targeted enrichment data for 207 species, representing 48 of 52 extant families and 174 genera. We calibrated and dated the tree with 33 carefully selected fossils. The first caddisflies originated approximately 295 million years ago in the Permian, and major suborders began to diversify in the Triassic. Furthermore, we show that portable case making evolved in three separate lineages, and shifts in diversification occurred in concert with key evolutionary innovations beyond case making.
Collapse
Affiliation(s)
- Paul B Frandsen
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA
| | | | - Marianne Espeland
- Museum Koenig Bonn, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Bonn, Germany
| | | | | | - Sabrina Simon
- Rosenheim University of Applied Sciences, Rosenheim, Germany
| | - Akito Y Kawahara
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- Entomology and Nematology Department, University of Florida, Gainesville, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - David Plotkin
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Scott Hotaling
- Department of Watershed Sciences, Utah State University, Logan, UT, USA
| | - Yiyuan Li
- Institute of Plant Virology, Ningbo University, Ningbo, Zhejiang Province, People's Republic of China
| | - C Riley Nelson
- Department of Biology, Brigham Young University, Provo, UT, USA
| | - Oliver Niehuis
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), University of Freiburg, Freiburg, Germany
| | - Christoph Mayer
- Museum Koenig Bonn, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Bonn, Germany
| | - Lars Podsiadlowski
- Museum Koenig Bonn, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Bonn, Germany
| | - Alexander Donath
- Museum Koenig Bonn, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Bonn, Germany
| | - Bernhard Misof
- Museum Koenig Bonn, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Bonn, Germany
- Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | | | - Alan Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL, USA
| | - John C Morse
- Department of Plant & Environmental Sciences, Clemson University, Clemson, SC, USA
| | - Shanlin Liu
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, People's Republic of China
| | - Steffen U Pauls
- LOEWE Center for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany
- Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt, Germany
- Department of Insect Biotechnology, Justus-Liebig-University Gießen, Gießen, Germany
| | - Xin Zhou
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, People's Republic of China
| |
Collapse
|
5
|
Mull CG, Pennell MW, Yopak KE, Dulvy NK. Maternal investment evolves with larger body size and higher diversification rate in sharks and rays. Curr Biol 2024; 34:2773-2781.e3. [PMID: 38843829 DOI: 10.1016/j.cub.2024.05.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 12/19/2023] [Accepted: 05/10/2024] [Indexed: 06/13/2024]
Abstract
Across vertebrates, live bearing evolved at least 150 times from ancestral egg laying into diverse forms and degrees of prepartum maternal investment.1,2 A key question is how reproductive diversity arose and whether reproductive diversification underlies species diversification.3,4,5,6,7,8,9,10,11 To test this, we evaluate the most basal jawed vertebrates: the sharks, rays, and chimaeras, which have one of the greatest ranges of reproductive and ecological diversity among vertebrates.2,12 We reconstruct the sequence of reproductive mode evolution across a phylogeny of 610 chondrichthyans.13 We reveal egg laying as ancestral, with live bearing evolving at least seven times. Matrotrophy evolved at least 15 times, with evidence of one reversal. In sharks, transitions to live bearing and matrotrophy are more prevalent in larger-bodied tropical species. Further, the evolution of live bearing is associated with a near doubling of the diversification rate, but there is only a small increase associated with the appearance of matrotrophy. Although pre-copulatory sexual selection is associated with increased rates of speciation in teleosts,3 sexual size dimorphism in chondrichthyans does not appear to be related to sexual selection,14,15 and instead we find increased rates of speciation associated with the colonization of novel habitats. This highlights a potential key difference between chondrichthyans and other fishes, specifically a slower rate of evolution of reproductive isolation following speciation, suggesting different rate-limiting mechanisms for diversification between these clades.16 The chondrichthyan diversification and radiation, particularly throughout shallow tropical shelf seas and oceanic pelagic habitats, appear to be associated with the evolution of live bearing and proliferation of a wide range of maternal investment in developing offspring.
Collapse
Affiliation(s)
- Christopher G Mull
- Earth to Ocean Research Group, Department of Biological Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada; Integrated Fisheries Lab, Department of Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada.
| | - Matthew W Pennell
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90007, USA
| | - Kara E Yopak
- Department of Biology and Marine Biology and UNCW Center for Marine Science, University of North Carolina Wilmington, Wilmington, NC 28403, USA
| | - Nicholas K Dulvy
- Earth to Ocean Research Group, Department of Biological Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| |
Collapse
|
6
|
Kramer EM, Enelamah J, Fang H, Tayjasanant PA. Karyotype depends on sperm head morphology in some amniote groups. Front Genet 2024; 15:1396530. [PMID: 38903758 PMCID: PMC11186999 DOI: 10.3389/fgene.2024.1396530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 05/15/2024] [Indexed: 06/22/2024] Open
Abstract
The karyotype of an organism is the set of gross features that characterize the way the genome is packaged into separate chromosomes. It has been known for decades that different taxonomic groups often have distinct karyotypic features, but whether selective forces act to maintain these differences over evolutionary timescales is an open question. In this paper we analyze a database of karyotype features and sperm head morphology in 103 mammal species with spatulate sperm heads and 90 sauropsid species (birds and non-avian reptiles) with vermiform heads. We find that mammal species with a larger head area have more chromosomes, while sauropsid species with longer heads have a wider range of chromosome lengths. These results remain significant after controlling for genome size, so sperm head morphology is the relevant variable. This suggest that post-copulatory sexual selection, by acting on sperm head shape, can influence genome architecture.
Collapse
Affiliation(s)
- Eric M. Kramer
- Department of Physics, Bard College at Simon’s Rock, Great Barrington, MA, United States
- Department of Biology, Bard College at Simon’s Rock, Great Barrington, MA, United States
| | - Joshua Enelamah
- Department of Physics, Bard College at Simon’s Rock, Great Barrington, MA, United States
| | - Hao Fang
- Department of Physics, Bard College at Simon’s Rock, Great Barrington, MA, United States
| | - P. A. Tayjasanant
- Department of Physics, Bard College at Simon’s Rock, Great Barrington, MA, United States
| |
Collapse
|
7
|
Wold ES, Aiello B, Harris M, Bin Sikandar U, Lynch J, Gravish N, Sponberg S. Moth resonant mechanics are tuned to wingbeat frequency and energetic demands. Proc Biol Sci 2024; 291:20240317. [PMID: 38920055 DOI: 10.1098/rspb.2024.0317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 05/15/2024] [Indexed: 06/27/2024] Open
Abstract
An insect's wingbeat frequency is a critical determinant of its flight performance and varies by multiple orders of magnitude across Insecta. Despite potential energetic benefits for an insect that matches its wingbeat frequency to its resonant frequency, recent work has shown that moths may operate off their resonant peak. We hypothesized that across species, wingbeat frequency scales with resonance frequency to maintain favourable energetics, but with an offset in species that use frequency modulation as a means of flight control. The moth superfamily Bombycoidea is ideal for testing this hypothesis because their wingbeat frequencies vary across species by an order of magnitude, despite similar morphology and actuation. We used materials testing, high-speed videography and a model of resonant aerodynamics to determine how components of an insect's flight apparatus (stiffness, wing inertia, muscle strain and aerodynamics) vary with wingbeat frequency. We find that the resonant frequency of a moth correlates with wingbeat frequency, but resonance curve shape (described by the Weis-Fogh number) and peak location vary within the clade in a way that corresponds to frequency-dependent biomechanical demands. Our results demonstrate that a suite of adaptations in muscle, exoskeleton and wing drive variation in resonant mechanics, reflecting potential constraints on matching wingbeat and resonant frequencies.
Collapse
Affiliation(s)
- Ethan S Wold
- School of Biological Sciences, Georgia Institute of Technology , Atlanta, GA 30332, USA
| | - Brett Aiello
- School of Natural and Health Sciences, Seton Hill University , Greensburg, PA 15601, USA
| | - Manon Harris
- School of Physics, Georgia Institute of Technology , Atlanta, GA 30332, USA
| | - Usama Bin Sikandar
- School of Electrical and Computer Engineering, Georgia Institute of Technology , Atlanta, GA 30332, USA
| | - James Lynch
- Mechanical and Aerospace Engineering, University of California San Diego , San Diego, CA 92161, USA
| | - Nick Gravish
- Mechanical and Aerospace Engineering, University of California San Diego , San Diego, CA 92161, USA
| | - Simon Sponberg
- School of Biological Sciences, Georgia Institute of Technology , Atlanta, GA 30332, USA
- School of Physics, Georgia Institute of Technology , Atlanta, GA 30332, USA
| |
Collapse
|
8
|
Stephens RE, Gallagher RV, Méndez M, Sauquet H. Zygomorphic flowers last longer: the evolution of floral symmetry and floral longevity. Biol Lett 2024; 20:20240082. [PMID: 38889773 DOI: 10.1098/rsbl.2024.0082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 05/07/2024] [Indexed: 06/20/2024] Open
Abstract
Floral longevity, the length of time a flower remains open and functional, is a phylogenetically conserved trait that balances floral costs against the rate at which flowers are pollinated. Floral symmetry has long been considered a key trait in floral evolution. Although zygomorphic (bilaterally symmetric) flowers typically receive fewer floral visitors than actinomorphic (radially symmetric) flowers, it is yet to be determined whether this could be associated with longer floral longevity. Using newly collected field data combined with data from the literature on 1452 species in 168 families, we assess whether floral longevity covaries with floral symmetry in a phylogenetic framework. We find that zygomorphic flowers last on average 1.1 days longer than actinomorphic flowers, a 26.5% increase in longevity, with considerable variation across both groups. Our results provide a basis to discuss the ecological and evolutionary costs of zygomorphy for plants. Despite these costs, zygomorphy has evolved numerous times throughout angiosperm history, and we discuss which rewards may outweigh the costs of slower pollination in zygomorphic flowers.
Collapse
Affiliation(s)
- R E Stephens
- School of Natural Sciences, Macquarie University , Ryde, New South Wales, Australia
- National Herbarium of NSW, Botanic Gardens of Sydney , Mount Annan, New South Wales, Australia
| | - R V Gallagher
- School of Natural Sciences, Macquarie University , Ryde, New South Wales, Australia
- Hawkesbury Institute for the Environment, Western Sydney University , Richmond, New South Wales, Australia
| | - M Méndez
- Area of Biodiversity and Conservation, Universidad Rey Juan Carlos , Madrid, Spain
| | - H Sauquet
- National Herbarium of NSW, Botanic Gardens of Sydney , Mount Annan, New South Wales, Australia
- Evolution & Ecology Research Centre, University of New South Wales , Sydney, New South Wales, Australia
| |
Collapse
|
9
|
Nzei JM, Martínez-Médez N, Mwanzia VM, Kurauka JK, Wang QF, Li ZZ, Chen JM. Climatic niche evolution and niche conservatism of Nymphaea species in Africa, South America, and Australia. BMC PLANT BIOLOGY 2024; 24:476. [PMID: 38816799 PMCID: PMC11137912 DOI: 10.1186/s12870-024-05141-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Accepted: 05/13/2024] [Indexed: 06/01/2024]
Abstract
BACKGROUND Interest in the evolution of climatic niches, particularly in understanding the potential adaptive responses of species under climate change, has increased both theoretically and within macroecological studies. These studies have provided valuable insights into how climatic traits of species influence their niche evolution. In this study, we aim to investigate whether niche conservatism plays a role in the species diversification of Nymphaea, a group of aquatic plants with a cosmopolitan distribution that is facing severe habitat loss. We will use climatic models and phylogenetic data for 23 species to reconstruct Nymphaea's niche evolution, measure niche overlap, and assess disparity through time while testing for evolutionary models. RESULTS There was a lot of overlap in niches both within and between groups, especially for species that can be found in many places. The breadth and peaks of the niche profile varied depending on the bioclimatic variables, which suggested that the species evolved differently to cope with changes in climate. The analysis also showed that evolutionary changes happened across the phylogeny, with weak to moderate signals. The morphological disparity index (MDI) values indicated that there were disparities within subclades over time but not between or among them. Niche reconstruction and evolution analysis revealed both convergent and divergent evolution among various variables. For example, N. immutabilis, N. atrans, N. violancea, and N. nouchali evolved towards intermediate temperatures for bio2 and bio3 (isothermity) while moving towards extreme temperatures for bio8 and bio9 (wettest and driest average quarterly temperatures). CONCLUSION Our study will improve our understanding of how changes in climatic niches are potentially driving the evolution of Nymphaea. It has significant scientific implications for the limits, assemblages, evolution, and diversification of species. This information is crucial for the ongoing efforts of conservation and management, particularly considering the inevitable effects of climate change.
Collapse
Affiliation(s)
- John M Nzei
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Norberto Martínez-Médez
- Departamento de Zoología, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Ciudad de México, México
| | - Virginia M Mwanzia
- School of Agriculture Technical Studies and Natural Sciences, Lukenya University, P.O Box 90-90128, Mtito Andei, Kenya
| | - Joseph K Kurauka
- School of Agriculture and Environmental Sciences, Kenyatta University, P.O. Box 43844-00100, Nairobi, Kenya
| | - Qing-Feng Wang
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Zhi-Zhong Li
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
| | - Jin-Ming Chen
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
| |
Collapse
|
10
|
Lu X, Dai Z, Xue J, Li W, Ni P, Xu J, Zhou C, Zhang W. Discovery of novel RNA viruses through analysis of fungi-associated next-generation sequencing data. BMC Genomics 2024; 25:517. [PMID: 38797853 PMCID: PMC11129472 DOI: 10.1186/s12864-024-10432-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 05/20/2024] [Indexed: 05/29/2024] Open
Abstract
BACKGROUND Like all other species, fungi are susceptible to infection by viruses. The diversity of fungal viruses has been rapidly expanding in recent years due to the availability of advanced sequencing technologies. However, compared to other virome studies, the research on fungi-associated viruses remains limited. RESULTS In this study, we downloaded and analyzed over 200 public datasets from approximately 40 different Bioprojects to explore potential fungal-associated viral dark matter. A total of 12 novel viral sequences were identified, all of which are RNA viruses, with lengths ranging from 1,769 to 9,516 nucleotides. The amino acid sequence identity of all these viruses with any known virus is below 70%. Through phylogenetic analysis, these RNA viruses were classified into different orders or families, such as Mitoviridae, Benyviridae, Botourmiaviridae, Deltaflexiviridae, Mymonaviridae, Bunyavirales, and Partitiviridae. It is possible that these sequences represent new taxa at the level of family, genus, or species. Furthermore, a co-evolution analysis indicated that the evolutionary history of these viruses within their groups is largely driven by cross-species transmission events. CONCLUSIONS These findings are of significant importance for understanding the diversity, evolution, and relationships between genome structure and function of fungal viruses. However, further investigation is needed to study their interactions.
Collapse
Affiliation(s)
- Xiang Lu
- Institute of Critical Care Medicine, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, 212002, China
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Ziyuan Dai
- Department of Clinical Laboratory, Affiliated Hospital 6 of Nantong University, Yancheng Third People's Hospital, Yancheng, Jiangsu, China
| | - Jiaxin Xue
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Wang Li
- Clinical Laboratory Center, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, 225300, China
| | - Ping Ni
- Clinical Laboratory Center, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, 225300, China
| | - Juan Xu
- Clinical Laboratory Center, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, 225300, China.
| | - Chenglin Zhou
- Clinical Laboratory Center, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, 225300, China.
| | - Wen Zhang
- Institute of Critical Care Medicine, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, 212002, China.
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, China.
- Clinical Laboratory Center, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, 225300, China.
| |
Collapse
|
11
|
Suissa JS, Li FW, Moreau CS. Convergent evolution of fern nectaries facilitated independent recruitment of ant-bodyguards from flowering plants. Nat Commun 2024; 15:4392. [PMID: 38789437 PMCID: PMC11126701 DOI: 10.1038/s41467-024-48646-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
Plant-herbivore interactions reciprocally influence species' evolutionary trajectories. These interactions have led to many physical and chemical defenses across the plant kingdom. Some plants have even evolved indirect defense strategies to outsource their protection to ant bodyguards by bribing them with a sugary reward (nectar). Identifying the evolutionary processes underpinning these indirect defenses provide insight into the evolution of plant-animal interactions. Using a cross-kingdom, phylogenetic approach, we examined the convergent evolution of ant-guarding nectaries across ferns and flowering plants. Here, we discover that nectaries originated in ferns and flowering plants concurrently during the Cretaceous, coinciding with the rise of plant associations in ants. While nectaries in flowering plants evolved steadily through time, ferns showed a pronounced lag of nearly 100 My between their origin and subsequent diversification in the Cenozoic. Importantly, we find that as ferns transitioned from the forest floor into the canopy, they secondarily recruited ant bodyguards from existing ant-angiosperm relationships.
Collapse
Affiliation(s)
- Jacob S Suissa
- Department of Ecology and Evolutionary Biology, University of Tennessee Knoxville, Knoxville, TN, USA.
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, USA
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Corrie S Moreau
- Department of Ecology and Evolutionary Biology Cornell University, Ithaca, NY, USA
- Department of Entomology, Cornell University, Ithaca, NY, USA
| |
Collapse
|
12
|
Zavala B, Dineen L, Fisher KJ, Opulente DA, Harrison MC, Wolters JF, Shen XX, Zhou X, Groenewald M, Hittinger CT, Rokas A, LaBella AL. Genomic factors shaping codon usage across the Saccharomycotina subphylum. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.23.595506. [PMID: 38826271 PMCID: PMC11142207 DOI: 10.1101/2024.05.23.595506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Codon usage bias, or the unequal use of synonymous codons, is observed across genes, genomes, and between species. The biased use of synonymous codons has been implicated in many cellular functions, such as translation dynamics and transcript stability, but can also be shaped by neutral forces. The Saccharomycotina, the fungal subphylum containing the yeasts Saccharomyces cerevisiae and Candida albicans , has been a model system for studying codon usage. We characterized codon usage across 1,154 strains from 1,051 species to gain insight into the biases, molecular mechanisms, evolution, and genomic features contributing to codon usage patterns across the subphylum. We found evidence of a general preference for A/T-ending codons and correlations between codon usage bias, GC content, and tRNA-ome size. Codon usage bias is also distinct between the 12 orders within the subphylum to such a degree that yeasts can be classified into orders with an accuracy greater than 90% using a machine learning algorithm trained on codon usage. We also characterized the degree to which codon usage bias is impacted by translational selection. Interestingly, the degree of translational selection was influenced by a combination of genome features and assembly metrics that included the number of coding sequences, BUSCO count, and genome length. Our analysis also revealed an extreme bias in codon usage in the Saccharomycodales associated with a lack of predicted arginine tRNAs. The order contains 24 species, and 23 are computationally predicted to lack tRNAs that decode CGN codons, leaving only the AGN codons to encode arginine. Analysis of Saccharomycodales gene expression, tRNA sequences, and codon evolution suggests that extreme avoidance of the CGN codons is associated with a decline in arginine tRNA function. Codon usage bias within the Saccharomycotina is generally consistent with previous investigations in fungi, which show a role for both genomic features and GC bias in shaping codon usage. However, we find cases of extreme codon usage preference and avoidance along yeast lineages, suggesting additional forces may be shaping the evolution of specific codons.
Collapse
|
13
|
Jiang H, Wang Y, Zhang G, Jia A, Wei Z, Wang Y. Identification and Evolutionary Analysis of the Widely Distributed CAP Superfamily in Spider Venom. Toxins (Basel) 2024; 16:240. [PMID: 38922134 PMCID: PMC11209345 DOI: 10.3390/toxins16060240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 05/18/2024] [Accepted: 05/22/2024] [Indexed: 06/27/2024] Open
Abstract
Venom plays a crucial role in the defense and predation of venomous animals. Spiders (Araneae) are among the most successful predators and have a fascinating venom composition. Their venom mainly contains disulfide-rich peptides and large proteins. Here, we analyzed spider venom protein families, utilizing transcriptomic and genomic data, and highlighted their similarities and differences. We show that spiders have specific combinations of toxins for better predation and defense, typically comprising a core toxin expressed alongside several auxiliary toxins. Among them, the CAP superfamily is widely distributed and highly expressed in web-building Araneoidea spiders. Our analysis of evolutionary relationships revealed four subfamilies (subA-subD) of the CAP superfamily that differ in structure and potential functions. CAP proteins are composed of a conserved CAP domain and diverse C-terminal domains. CAP subC shares similar domains with the snake ion channel regulator svCRISP proteins, while CAP subD possesses a sequence similar to that of insect venom allergen 5 (Ag5). Furthermore, we show that gene duplication and selective expression lead to increased expression of CAP subD, making it a core member of the CAP superfamily. This study sheds light on the functional diversity of CAP subfamilies and their evolutionary history, which has important implications for fully understanding the composition of spider venom proteins and the core toxin components of web-building spiders.
Collapse
Affiliation(s)
- Hongcen Jiang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400715, China; (H.J.)
| | - Yiru Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400715, China; (H.J.)
| | - Guoqing Zhang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400715, China; (H.J.)
| | - Anqiang Jia
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400715, China; (H.J.)
- Yazhouwan National Laboratory, Sanya 572024, China
| | - Zhaoyuan Wei
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400715, China; (H.J.)
| | - Yi Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400715, China; (H.J.)
| |
Collapse
|
14
|
Puginier C, Libourel C, Otte J, Skaloud P, Haon M, Grisel S, Petersen M, Berrin JG, Delaux PM, Dal Grande F, Keller J. Phylogenomics reveals the evolutionary origins of lichenization in chlorophyte algae. Nat Commun 2024; 15:4452. [PMID: 38789482 PMCID: PMC11126685 DOI: 10.1038/s41467-024-48787-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
Mutualistic symbioses have contributed to major transitions in the evolution of life. Here, we investigate the evolutionary history and the molecular innovations at the origin of lichens, which are a symbiosis established between fungi and green algae or cyanobacteria. We de novo sequence the genomes or transcriptomes of 12 lichen algal symbiont (LAS) and closely related non-symbiotic algae (NSA) to improve the genomic coverage of Chlorophyte algae. We then perform ancestral state reconstruction and comparative phylogenomics. We identify at least three independent gains of the ability to engage in the lichen symbiosis, one in Trebouxiophyceae and two in Ulvophyceae, confirming the convergent evolution of the lichen symbioses. A carbohydrate-active enzyme from the glycoside hydrolase 8 (GH8) family was identified as a top candidate for the molecular-mechanism underlying lichen symbiosis in Trebouxiophyceae. This GH8 was acquired in lichenizing Trebouxiophyceae by horizontal gene transfer, concomitantly with the ability to associate with lichens fungal symbionts (LFS) and is able to degrade polysaccharides found in the cell wall of LFS. These findings indicate that a combination of gene family expansion and horizontal gene transfer provided the basis for lichenization to evolve in chlorophyte algae.
Collapse
Affiliation(s)
- Camille Puginier
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, INP, Toulouse, 31320, Castanet-Tolosan, France
| | - Cyril Libourel
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, INP, Toulouse, 31320, Castanet-Tolosan, France
| | - Juergen Otte
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Pavel Skaloud
- Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ-12800, Praha 2, Czech Republic
| | - Mireille Haon
- INRAE, Aix Marseille Université, UMR1163 Biodiversité et Biotechnologie Fongiques (BBF), 13009, Marseille, France
- INRAE, Aix Marseille Université, 3PE Platform, 13009, Marseille, France
| | - Sacha Grisel
- INRAE, Aix Marseille Université, UMR1163 Biodiversité et Biotechnologie Fongiques (BBF), 13009, Marseille, France
- INRAE, Aix Marseille Université, 3PE Platform, 13009, Marseille, France
| | - Malte Petersen
- High Performance Computing & Analytics Lab, University of Bonn, Friedrich-Hirzebruch-Allee 8, 53115, Bonn, Germany
| | - Jean-Guy Berrin
- INRAE, Aix Marseille Université, UMR1163 Biodiversité et Biotechnologie Fongiques (BBF), 13009, Marseille, France
- INRAE, Aix Marseille Université, 3PE Platform, 13009, Marseille, France
| | - Pierre-Marc Delaux
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, INP, Toulouse, 31320, Castanet-Tolosan, France.
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.
- LOEWE Centre for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.
- Department of Biology, University of Padova, Padua, Italy.
| | - Jean Keller
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, INP, Toulouse, 31320, Castanet-Tolosan, France.
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, 07745, Jena, Germany.
| |
Collapse
|
15
|
Zou Y, Zhang Z, Zeng Y, Hu H, Hao Y, Huang S, Li B. Common Methods for Phylogenetic Tree Construction and Their Implementation in R. Bioengineering (Basel) 2024; 11:480. [PMID: 38790347 PMCID: PMC11117635 DOI: 10.3390/bioengineering11050480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 05/04/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
A phylogenetic tree can reflect the evolutionary relationships between species or gene families, and they play a critical role in modern biological research. In this review, we summarize common methods for constructing phylogenetic trees, including distance methods, maximum parsimony, maximum likelihood, Bayesian inference, and tree-integration methods (supermatrix and supertree). Here we discuss the advantages, shortcomings, and applications of each method and offer relevant codes to construct phylogenetic trees from molecular data using packages and algorithms in R. This review aims to provide comprehensive guidance and reference for researchers seeking to construct phylogenetic trees while also promoting further development and innovation in this field. By offering a clear and concise overview of the different methods available, we hope to enable researchers to select the most appropriate approach for their specific research questions and datasets.
Collapse
Affiliation(s)
- Yue Zou
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China; (Y.Z.); (Z.Z.); (Y.Z.); (H.H.); (Y.H.)
| | - Zixuan Zhang
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China; (Y.Z.); (Z.Z.); (Y.Z.); (H.H.); (Y.H.)
| | - Yujie Zeng
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China; (Y.Z.); (Z.Z.); (Y.Z.); (H.H.); (Y.H.)
| | - Hanyue Hu
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China; (Y.Z.); (Z.Z.); (Y.Z.); (H.H.); (Y.H.)
| | - Youjin Hao
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China; (Y.Z.); (Z.Z.); (Y.Z.); (H.H.); (Y.H.)
| | - Sheng Huang
- Animal Nutrition Institute, Chongqing Academy of Animal Science, Chongqing 402460, China
| | - Bo Li
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China; (Y.Z.); (Z.Z.); (Y.Z.); (H.H.); (Y.H.)
| |
Collapse
|
16
|
Tavera EA, Lank DB, Douglas DC, Sandercock BK, Lanctot RB, Schmidt NM, Reneerkens J, Ward DH, Bêty J, Kwon E, Lecomte N, Gratto-Trevor C, Smith PA, English WB, Saalfeld ST, Brown SC, Gates HR, Nol E, Liebezeit JR, McGuire RL, McKinnon L, Kendall S, Robards M, Boldenow M, Payer DC, Rausch J, Solovyeva DV, Stalwick JA, Gurney KEB. Why do avian responses to change in Arctic green-up vary? GLOBAL CHANGE BIOLOGY 2024; 30:e17335. [PMID: 38771086 DOI: 10.1111/gcb.17335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 03/29/2024] [Accepted: 04/17/2024] [Indexed: 05/22/2024]
Abstract
Global climate change has altered the timing of seasonal events (i.e., phenology) for a diverse range of biota. Within and among species, however, the degree to which alterations in phenology match climate variability differ substantially. To better understand factors driving these differences, we evaluated variation in timing of nesting of eight Arctic-breeding shorebird species at 18 sites over a 23-year period. We used the Normalized Difference Vegetation Index as a proxy to determine the start of spring (SOS) growing season and quantified relationships between SOS and nest initiation dates as a measure of phenological responsiveness. Among species, we tested four life history traits (migration distance, seasonal timing of breeding, female body mass, expected female reproductive effort) as species-level predictors of responsiveness. For one species (Semipalmated Sandpiper), we also evaluated whether responsiveness varied across sites. Although no species in our study completely tracked annual variation in SOS, phenological responses were strongest for Western Sandpipers, Pectoral Sandpipers, and Red Phalaropes. Migration distance was the strongest additional predictor of responsiveness, with longer-distance migrant species generally tracking variation in SOS more closely than species that migrate shorter distances. Semipalmated Sandpipers are a widely distributed species, but adjustments in timing of nesting relative to variability in SOS did not vary across sites, suggesting that different breeding populations of this species were equally responsive to climate cues despite differing migration strategies. Our results unexpectedly show that long-distance migrants are more sensitive to local environmental conditions, which may help them to adapt to ongoing changes in climate.
Collapse
Affiliation(s)
| | - David B Lank
- Simon Fraser University, Burnaby, British Columbia, Canada
| | - David C Douglas
- Alaska Science Center, U.S. Geological Survey, Anchorage, Alaska, USA
| | | | | | | | - Jeroen Reneerkens
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - David H Ward
- Alaska Science Center, U.S. Geological Survey, Anchorage, Alaska, USA
| | - Joël Bêty
- Université du Québec à Rimouski and Centre d'études nordiques, Rimouski, Quebec, Canada
| | - Eunbi Kwon
- Max Planck Institute for Biological Intelligence, Seewiesen, Germany
| | | | - Cheri Gratto-Trevor
- Science and Technology Branch, Environment and Climate Change Canada, Saskatoon, Saskatchewan, Canada
| | - Paul A Smith
- Science and Technology Branch, Environment and Climate Change Canada, Ottawa, Ontario, Canada
| | | | | | | | - H River Gates
- Manomet, Shorebird Recovery Program, Plymouth, Massachusetts, USA
- Migratory Bird Management, U.S. Fish and Wildlife Service, Anchorage, Alaska, USA
| | - Erica Nol
- Trent University, Peterborough, Ontario, Canada
| | | | | | | | - Steve Kendall
- U.S. Fish and Wildlife Service, Arctic National Wildlife Refuge, Fairbanks, Alaska, USA
| | | | | | | | - Jennie Rausch
- Canadian Wildlife Service, Environment and Climate Change Canada, Yellowknife, Northwest Territories, Canada
| | - Diana V Solovyeva
- Institute of Biological Problems of the North, Far Eastern Branch, Russian Academy of Sciences, Magadan, Russia
| | - Jordyn A Stalwick
- Science and Technology Branch, Environment and Climate Change Canada, Saskatoon, Saskatchewan, Canada
| | - Kirsty E B Gurney
- Science and Technology Branch, Environment and Climate Change Canada, Saskatoon, Saskatchewan, Canada
| |
Collapse
|
17
|
Turanov SV, Smirnov AV, Kartavtsev YP. Taxonomic position of holothurian Eupentactafraudatrix (Echinodermata, Holothuroidea). Zookeys 2024; 1197:237-248. [PMID: 38680633 PMCID: PMC11046087 DOI: 10.3897/zookeys.1197.117752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 03/14/2024] [Indexed: 05/01/2024] Open
Abstract
Samples of the holothurian Eupentactafraudatrix (Djakonov & Baranova in Djakonov, Baranova & Saveljeva, 1958) from the Sea of Japan were studied and the relationships of the genera Eupentacta and Sclerodactyla, as well as related taxa, were evaluated on the basis of phylogenetic analysis of the mitochondrial DNA COI and 16S rRNA genes. Using three methods, phylogenetic trees were constructed, and the degree of reliability of topological reconstructions was estimated by means of a nonparametric bootstrap test for the neighbor joining (NJ) and maximum likelihood (ML) techniques, as well as by a posteriori probability for Bayesian inference (BI) analysis. Genetic data confirm the validity of the assignment of Cucumariafraudatrix to the genus Eupentacta Deichmann, 1938. The study of sequences obtained from the holothurian specimens collected in Russian waters, near the city of Vladivostok, and determined by morphological characters clearly indicate that these specimens belong to the genus Eupentacta and are assigned as E.fraudatrix . The specimens from China in GenBank named as Sclerodactylamultipes and used in the present study, were likely misidentified, and after re-examination they may be assigned to the genus Eupentacta, either as E.fraudatrix or another taxon. Analyses of morphological characters of S.multipes unequivocally affirm that this species must be excluded from Sclerodactyla Ayres, 1851 and is provisionally assigned to the genus Sclerothyone Thandar, 1989 based on the external morphological characters and the body wall ossicles.
Collapse
Affiliation(s)
- Sergei V. Turanov
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Russian Academy of Sciences, Vladivostok, RussiaA.V. Zhirmunsky National Scientific Center of Marine Biology, Russian Academy of SciencesVladivostokRussia
- Far Eastern State Technical Fisheries University, Vladivostok, RussiaFar Eastern State Technical Fisheries UniversityVladivostokRussia
| | - Alexey V. Smirnov
- Zoological Institute of Russian Academy of Sciences, St. Petersburg, RussiaZoological Institute of Russian Academy of SciencesSt. PetersburgRussia
| | - Yuri Ph. Kartavtsev
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Russian Academy of Sciences, Vladivostok, RussiaA.V. Zhirmunsky National Scientific Center of Marine Biology, Russian Academy of SciencesVladivostokRussia
| |
Collapse
|
18
|
Torralba Sáez M, Hofreiter M, Straube N. Shark genome size evolution and its relationship with cellular, life-history, ecological, and diversity traits. Sci Rep 2024; 14:8909. [PMID: 38632352 PMCID: PMC11024215 DOI: 10.1038/s41598-024-59202-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 04/08/2024] [Indexed: 04/19/2024] Open
Abstract
Among vertebrates, sharks exhibit both large and heterogeneous genome sizes ranging from 2.86 to 17.05 pg. Aiming for a better understanding of the patterns and causalities of shark genome size evolution, we applied phylogenetic comparative methods to published genome-size estimates for 71 species representing the main phylogenetic lineages, life-histories and ecological traits. The sixfold range of genome size variation was strongly traceable throughout the phylogeny, with a major expansion preceding shark diversification during the late Paleozoic and an ancestral state (6.33 pg) close to the present-day average (6.72 pg). Subsequent deviations from this average occurred at higher rates in squalomorph than in galeomorph sharks and were unconnected to evolutionary changes in the karyotype architecture, which were dominated by descending disploidy events. Genome size was positively correlated with cell and nucleus sizes and negatively with metabolic rate. The metabolic constraints on increasing genome size also manifested at higher phenotypic scales, with large genomes associated with slow lifestyles and purely marine waters. Moreover, large genome sizes were also linked to non-placental reproductive modes, which may entail metabolically less demanding embryological developments. Contrary to ray-finned fishes, large genome size was associated neither with the taxonomic diversity of affected clades nor with low genetic diversity.
Collapse
Affiliation(s)
- Mario Torralba Sáez
- Ichthyology Section, Bavarian State Collection of Zoology (SNSB-ZSM), 81247, Munich, Germany
- Systematic Zoology, Department Biology II, Faculty of Biology, Ludwig Maximilian University of Munich (LMU), 82152, Munich, Germany
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Nicolas Straube
- Department of Natural History, University Museum Bergen, University of Bergen (UiB), 5007, Bergen, Norway.
| |
Collapse
|
19
|
Forni D, Pozzoli U, Cagliani R, Sironi M. Dinucleotide biases in the genomes of prokaryotic and eukaryotic dsDNA viruses and their hosts. Mol Ecol 2024; 33:e17287. [PMID: 38263702 DOI: 10.1111/mec.17287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/21/2023] [Accepted: 01/15/2024] [Indexed: 01/25/2024]
Abstract
The genomes of cellular organisms display CpG and TpA dinucleotide composition biases. Such biases have been poorly investigated in dsDNA viruses. Here, we show that in dsDNA virus, bacterial, and eukaryotic genomes, the representation of TpA and CpG dinucleotides is strongly dependent on genomic G + C content. Thus, the classical observed/expected ratios do not fully capture dinucleotide biases across genomes. Because a larger portion of the variance in TpA frequency was explained by G + C content, we explored which additional factors drive the distribution of CpG dinucleotides. Using the residuals of the linear regressions as a measure of dinucleotide abundance and ancestral state reconstruction across eukaryotic and prokaryotic virus trees, we identified an important role for phylogeny in driving CpG representation. Nonetheless, phylogenetic ANOVA analyses showed that few host associations also account for significant variations. Among eukaryotic viruses, most significant differences were observed between arthropod-infecting viruses and viruses that infect vertebrates or unicellular organisms. However, an effect of viral DNA methylation status (either driven by the host or by viral-encoded methyltransferases) is also likely. Among prokaryotic viruses, cyanobacteria-infecting phages resulted to be significantly CpG-depleted, whereas phages that infect bacteria in the genera Burkolderia and Staphylococcus were CpG-rich. Comparison with bacterial genomes indicated that this effect is largely driven by the general tendency for phages to resemble the host's genomic CpG content. Notably, such tendency is stronger for temperate than for lytic phages. Our data shed light into the processes that shape virus genome composition and inform manipulation strategies for biotechnological applications.
Collapse
Affiliation(s)
- Diego Forni
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Uberto Pozzoli
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Rachele Cagliani
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Manuela Sironi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| |
Collapse
|
20
|
Xu L, Wang J, Zhang T, Xiao H, Wang H. Characterizing complete mitochondrial genome of Aquilegia amurensis and its evolutionary implications. BMC PLANT BIOLOGY 2024; 24:142. [PMID: 38413922 PMCID: PMC10900605 DOI: 10.1186/s12870-024-04844-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 02/21/2024] [Indexed: 02/29/2024]
Abstract
BACKGROUND Aquilegia is a model system for studying the evolution of adaptive radiation. However, very few studies have been conducted on the Aquilegia mitochondrial genome. Since mitochondria play a key role in plant adaptation to abiotic stress, analyzing the mitochondrial genome may provide a new perspective for understanding adaptive evolution. RESULTS The Aquilegia amurensis mitochondrial genome was characterized by a circular chromosome and two linear chromosomes, with a total length of 538,736 bp; the genes included 33 protein-coding genes, 24 transfer RNA (tRNA) genes and 3 ribosomal RNA (rRNA) genes. We subsequently conducted a phylogenetic analysis based on single nucleotide polymorphisms (SNPs) in the mitochondrial genomes of 18 Aquilegia species, which were roughly divided into two clades: the European-Asian clade and the North American clade. Moreover, the genes mttB and rpl5 were shown to be positively selected in European-Asian species, and they may help European and Asian species adapt to environmental changes. CONCLUSIONS In this study, we assembled and annotated the first mitochondrial genome of the adaptive evolution model plant Aquilegia. The subsequent analysis provided us with a basis for further molecular studies on Aquilegia mitochondrial genomes and valuable information on adaptive evolution in Aquilegia.
Collapse
Affiliation(s)
- Luyuan Xu
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, 130024, China
| | - Jinghan Wang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, 130024, China
| | - Tengjiao Zhang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, 130024, China
| | - Hongxing Xiao
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, 130024, China.
| | - Huaying Wang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, 130024, China.
| |
Collapse
|
21
|
Xavier GM, Moura RR, Vasconcellos-Neto J, Gonzaga MO. Influences of sociality and maternal size on reproductive strategies: trade-offs between offspring size and quantity in five Anelosimus species (Araneae, Theridiidae). THE SCIENCE OF NATURE - NATURWISSENSCHAFTEN 2024; 111:7. [PMID: 38315245 DOI: 10.1007/s00114-024-01895-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/27/2024] [Accepted: 01/30/2024] [Indexed: 02/07/2024]
Abstract
Individuals can experience accentuated disputes for resources when living with many conspecifics, even in situations in which cooperative behaviors assure benefits associated with an increase in the frequency of food acquisition and in diet breadth. Thus, intraspecific competition may exert a significant selective pressure on social animals. Theoretical models suggest that females of social species could improve their fitness by producing relatively large offspring, since body size can provide competitive advantages during foraging activities. As female reserves are limited, the production of large offspring would occur at the expense of their number. Using five Anelosimus (Araneae, Theridiidae) species, we assessed whether the social ones produce fewer and larger eggs than the subsocials. In addition, we tested the effect of female size on the adoption of each particular reproductive strategy. Small females could hypothetically invest in producing large offspring since they cannot produce as many offspring as large females. Our results suggested that, indeed, sociality influences reproductive strategies. Females of social species produced fewer and larger offspring than females of subsocial species. Subsociality, in turn, would benefit the production of many small spiderlings, possibly because a large number of siblings is important to maintain and expand new webs and to subdue prey during their initial instars. Our results also indicated that large females produce more eggs without necessarily reduce their sizes. We discussed how the costs and benefits of group living may influence reproductive strategies.
Collapse
Affiliation(s)
- Gabriel M Xavier
- Programa de Pós-Graduação Em Ecologia, Conservação E Biodiversidade, Instituto de Biologia, Universidade Federal de Uberlândia, Uberlândia, MG, Brazil.
- Núcleo de Extensão E Pesquisa Em Ecologia E Evolução (NEPEE), Departamento de Ciências Agrárias E Naturais, Universidade Do Estado de Minas Gerais, UEMG, R. Ver. Geraldo Moisés da Silva, S/N - Universitário, Ituiutaba, MG, CEP 38302-192, Brazil.
| | - Rafael R Moura
- Núcleo de Extensão E Pesquisa Em Ecologia E Evolução (NEPEE), Departamento de Ciências Agrárias E Naturais, Universidade Do Estado de Minas Gerais, UEMG, R. Ver. Geraldo Moisés da Silva, S/N - Universitário, Ituiutaba, MG, CEP 38302-192, Brazil
| | - João Vasconcellos-Neto
- Departamento de Biologia Animal, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Marcelo O Gonzaga
- Instituto de Biologia, Universidade Federal de Uberlândia, Uberlândia, MG, Brazil
| |
Collapse
|