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McEnany J, Good BH. Predicting the First Steps of Evolution in Randomly Assembled Communities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.15.571925. [PMID: 38168431 PMCID: PMC10760118 DOI: 10.1101/2023.12.15.571925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Microbial communities can self-assemble into highly diverse states with predictable statistical properties. However, these initial states can be disrupted by rapid evolution of the resident strains. When a new mutation arises, it competes for resources with its parent strain and with the other species in the community. This interplay between ecology and evolution is difficult to capture with existing community assembly theory. Here, we introduce a mathematical framework for predicting the first steps of evolution in large randomly assembled communities that compete for substitutable resources. We show how the fitness effects of new mutations and the probability that they coexist with their parent depends on the size of the community, the saturation of its niches, and the metabolic overlap between its members. We find that successful mutations are often able to coexist with their parent strains, even in saturated communities with low niche availability. At the same time, these invading mutants often cause extinctions of metabolically distant species. Our results suggest that even small amounts of evolution can produce distinct genetic signatures in natural microbial communities.
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Affiliation(s)
- John McEnany
- Biophysics Program, Stanford University, Stanford, CA 94305, USA
| | - Benjamin H. Good
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub – San Francisco, San Francisco, CA 94158, USA
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2
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Zhu Y, Momeni B. Revisiting the invasion paradox: Resistance-richness relationship is driven by augmentation and displacement trends. PLoS Comput Biol 2024; 20:e1012193. [PMID: 38865380 PMCID: PMC11198907 DOI: 10.1371/journal.pcbi.1012193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 06/25/2024] [Accepted: 05/24/2024] [Indexed: 06/14/2024] Open
Abstract
Host-associated resident microbiota can protect their host from pathogens-a community-level trait called colonization resistance. The effect of the diversity of the resident community in previous studies has shown contradictory results, with higher diversity either strengthening or weakening colonization resistance. To control the confounding factors that may lead to such contradictions, we use mathematical simulations with a focus on species interactions and their impact on colonization resistance. We use a mediator-explicit model that accounts for metabolite-mediated interactions to perform in silico invasion experiments. We show that the relationship between colonization resistance and species richness of the resident community is not monotonic because it depends on two underlying trends as the richness of the resident community increases: a decrease in instances of augmentation (invader species added, without driving out resident species) and an increase in instances of displacement (invader species added, driving out some of the resident species). These trends hold consistently under different parameters, regardless of the number of compounds that mediate interactions between species or the proportion of the facilitative versus inhibitory interactions among species. Our results show a positive correlation between resistance and diversity in low-richness communities and a negative correlation in high-richness communities, offering an explanation for the seemingly contradictory trend in the resistance-diversity relationship in previous reports.
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Affiliation(s)
- Yu Zhu
- Biology Department, Boston College, Chestnut Hill, Massachusetts, Unites States of America
| | - Babak Momeni
- Biology Department, Boston College, Chestnut Hill, Massachusetts, Unites States of America
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3
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Xue T, Feng T, Liang Y, Yang X, Qin F, Yu J, Janssens SB, Yu S. Radiating diversification and niche conservatism jointly shape the inverse latitudinal diversity gradient of Potentilla L. (Rosaceae). BMC PLANT BIOLOGY 2024; 24:443. [PMID: 38778263 PMCID: PMC11112792 DOI: 10.1186/s12870-024-05083-8] [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: 01/06/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024]
Abstract
BACKGROUND The latitudinal diversity gradient (LDG), characterized by an increase in species richness from the poles to the equator, is one of the most pervasive biological patterns. However, inverse LDGs, in which species richness peaks in extratropical regions, are also found in some lineages and their causes remain unclear. Here, we test the roles of evolutionary time, diversification rates, and niche conservatism in explaining the inverse LDG of Potentilla (ca. 500 species). We compiled the global distributions of ~ 90% of Potentilla species, and reconstructed a robust phylogenetic framework based on whole-plastome sequences. Next, we analyzed the divergence time, ancestral area, diversification rate, and ancestral niche to investigate the macroevolutionary history of Potentilla. RESULTS The genus originated in the Qinghai-Tibet Plateau during the late Eocene and gradually spread to other regions of the Northern Hemisphere posterior to the late Miocene. Rapid cooling after the late Pliocene promoted the radiating diversification of Potentilla. The polyploidization, as well as some cold-adaptive morphological innovations, enhanced the adaptation of Potentilla species to the cold environment. Ancestral niche reconstruction suggests that Potentilla likely originated in a relatively cool environment. The species richness peaks at approximately 45 °N, a region characterized by high diversification rates, and the environmental conditions are similar to the ancestral climate niche. Evolutionary time was not significantly correlated with species richness in the latitudinal gradient. CONCLUSIONS Our results suggest that the elevated diversification rates in middle latitude regions and the conservatism in thermal niches jointly determined the inverse LDG in Potentilla. This study highlights the importance of integrating evolutionary and ecological approaches to explain the diversity pattern of biological groups on a global scale.
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Affiliation(s)
- Tiantian Xue
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tao Feng
- Biosystematics Group, Wageningen University & Research, Droevendaalsesteeg 4, Wageningen, 6708 PB, Gelderland, the Netherlands
| | - Yunfen Liang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xudong Yang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- Department of Earth System Science, Tsinghua University, Beijing, 100084, China
| | - Fei Qin
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Jianghong Yu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- College of Forestry, Guizhou University, Guiyang, 550025, China
| | - Steven B Janssens
- Meise Botanic Garden, Nieuwelaan 38, Meise, BE-1860, Belgium.
- Department of Biology, KU Leuven, Kasteelpark Arenberg 31, Leuven, BE-3001, Belgium.
| | - Shengxiang Yu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- China National Botanical Garden, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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4
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Wang Y, Zhang Z, Kang J, Chen B, Hong W, Lv B, Wang T, Qian H. Phages in different habitats and their ability to carry antibiotic resistance genes. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:133941. [PMID: 38447371 DOI: 10.1016/j.jhazmat.2024.133941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 02/19/2024] [Accepted: 02/29/2024] [Indexed: 03/08/2024]
Abstract
As the most abundant organisms on Earth, phages play a key role in the evolution of bacterial antibiotic resistance. Although previous studies have demonstrated the molecular mechanisms of horizontal gene transfer mediated by mobile genetic elements, our understanding of the intertwined relationships between antibiotic resistance genes (ARGs) and phages is limited. In this study, we analysed 2781 metagenomic samples to reveal the composition and species interactions of phage communities in different habitats as well as their capacity to carry ARGs with health risks. The composition of phage communities varies in different habitats and mainly depends on environmental conditions. Terrestrial habitats display more complex and robust interactions between phages than aquatic and human-associated habitats, resulting in the highest biodiversity of phages. Several types of phages in certain taxa (4.95-7.67%, mainly belonging to Caudoviricetes) have the capacity to carry specific ARGs and display a high potential risk to human health, especially in human-associated habitats. Overall, our results provide insights into the assembly mechanisms of phage communities and their effects on the dissemination of antibiotic resistance.
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Affiliation(s)
- Yan Wang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Jian Kang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China; College of Ecology and Environment, Anhui Normal University, Wuhu 241002, PR China
| | - Bingfeng Chen
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Wenjie Hong
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou 310012, PR China
| | - Binghai Lv
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Tingzhang Wang
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou 310012, PR China.
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China.
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5
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David KT, Harrison MC, Opulente DA, LaBella AL, Wolters JF, Zhou X, Shen XX, Groenewald M, Pennell M, Hittinger CT, Rokas A. Saccharomycotina yeasts defy long-standing macroecological patterns. Proc Natl Acad Sci U S A 2024; 121:e2316031121. [PMID: 38412132 DOI: 10.1073/pnas.2316031121] [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: 09/14/2023] [Accepted: 01/24/2024] [Indexed: 02/29/2024] Open
Abstract
The Saccharomycotina yeasts ("yeasts" hereafter) are a fungal clade of scientific, economic, and medical significance. Yeasts are highly ecologically diverse, found across a broad range of environments in every biome and continent on earth; however, little is known about what rules govern the macroecology of yeast species and their range limits in the wild. Here, we trained machine learning models on 12,816 terrestrial occurrence records and 96 environmental variables to infer global distribution maps at ~1 km2 resolution for 186 yeast species (~15% of described species from 75% of orders) and to test environmental drivers of yeast biogeography and macroecology. We found that predicted yeast diversity hotspots occur in mixed montane forests in temperate climates. Diversity in vegetation type and topography were some of the greatest predictors of yeast species richness, suggesting that microhabitats and environmental clines are key to yeast diversity. We further found that range limits in yeasts are significantly influenced by carbon niche breadth and range overlap with other yeast species, with carbon specialists and species in high-diversity environments exhibiting reduced geographic ranges. Finally, yeasts contravene many long-standing macroecological principles, including the latitudinal diversity gradient, temperature-dependent species richness, and a positive relationship between latitude and range size (Rapoport's rule). These results unveil how the environment governs the global diversity and distribution of species in the yeast subphylum. These high-resolution models of yeast species distributions will facilitate the prediction of economically relevant and emerging pathogenic species under current and future climate scenarios.
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Affiliation(s)
- Kyle T David
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235
| | - Marie-Claire Harrison
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235
| | - Dana A Opulente
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, Department of Energy (DOE) Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726
- Department of Biology, Villanova University, Villanova, PA 19085
| | - Abigail L LaBella
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223
| | - John F Wolters
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, Department of Energy (DOE) Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726
| | - Xiaofan Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China
| | - Xing-Xing Shen
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | | | - Matt Pennell
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089
| | - Chris Todd Hittinger
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, Department of Energy (DOE) Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235
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Zhou N, Miao K, Liu C, Jia L, Hu J, Huang Y, Ji Y. Historical biogeography and evolutionary diversification of Lilium (Liliaceae): New insights from plastome phylogenomics. PLANT DIVERSITY 2024; 46:219-228. [PMID: 38807906 PMCID: PMC11128834 DOI: 10.1016/j.pld.2023.07.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 07/22/2023] [Accepted: 07/30/2023] [Indexed: 05/30/2024]
Abstract
Here, we infer the historical biogeography and evolutionary diversification of the genus Lilium. For this purpose, we used the complete plastomes of 64 currently accepted species in the genus Lilium (14 plastomes were newly sequenced) to recover the phylogenetic backbone of the genus and a time-calibrated phylogenetic framework to estimate biogeographical history scenarios and evolutionary diversification rates of Lilium. Our results suggest that ancient climatic changes and geological tectonic activities jointly shaped the distribution range and drove evolutionary radiation of Lilium, including the Middle Miocene Climate Optimum (MMCO), the late Miocene global cooling, as well as the successive uplift of the Qinghai-Tibet Plateau (QTP) and the strengthening of the monsoon climate in East Asia during the late Miocene and the Pliocene. This case study suggests that the unique geological and climatic events in the Neogene of East Asia, in particular the uplift of QTP and the enhancement of monsoonal climate, may have played an essential role in formation of uneven distribution of plant diversity in the Northern Hemisphere.
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Affiliation(s)
- Nian Zhou
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ke Miao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Changkun Liu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
| | - Linbo Jia
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Jinjin Hu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Yongjiang Huang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Yunheng Ji
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Population, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
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7
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Wacker KS, Winger BM. An Elevational Phylogeographic Diversity Gradient in Neotropical Birds Is Decoupled from Speciation Rates. Am Nat 2024; 203:362-381. [PMID: 38358813 DOI: 10.1086/728598] [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] [Indexed: 02/17/2024]
Abstract
AbstractA key question about macroevolutionary speciation rates is whether they are controlled by microevolutionary processes operating at the population level. For example, does spatial variation in population genetic differentiation underlie geographical gradients in speciation rates? Previous work suggests that speciation rates increase with elevation in Neotropical birds, but underlying population-level gradients remain unexplored. Here, we characterize elevational phylogeographic diversity between montane and lowland birds in the megadiverse Andes-Amazonian system and assess its relationship to speciation rates to evaluate the link between population-level differentiation and species-level diversification. We aggregated and georeferenced nearly 7,000 mitochondrial DNA sequences across 103 species or species complexes in the Andes and Amazonia and used these sequences to describe phylogeographic differentiation across both regions. Our results show increased levels of both discrete and continuous metrics of population structure in the Andean mountains compared with the Amazonian lowlands. However, higher levels of population differentiation do not predict higher rates of speciation in our dataset. Multiple potential factors may lead to our observed decoupling of initial population divergence and speciation rates, including the ephemerality of incipient species and the multifaceted nature of the speciation process, as well as methodological challenges associated with estimating rates of population differentiation and speciation.
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8
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Harmáčková L, Remeš V. The Evolution of Local Co-occurrence in Birds in Relation to Latitude, Degree of Sympatry, and Range Symmetry. Am Nat 2024; 203:432-443. [PMID: 38358810 DOI: 10.1086/728687] [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] [Indexed: 02/17/2024]
Abstract
AbstractRecent speciation rates and the degree of range-wide sympatry are usually higher farther from the equator. Is there also a higher degree of secondary syntopy (coexistence in local assemblages in sympatry) at higher latitudes and, subsequently, an increase in local species richness? We studied the evolution of syntopy in passerine birds using worldwide species distribution data. We chose recently diverged species pairs from subclades not older than 5 or 7 million years, range-wide degree of sympatry not lower than 5% or 25%, and three definitions of the breeding season. We related their syntopy to latitude, the degree of sympatry (breeding range overlap), range symmetry, and the age of split. Syntopy was positively related to latitude, but it did not differ between tropical and temperate regions, instead increasing from the Southern to the Northern Hemisphere. Syntopy was also higher in species pairs with a higher degree of sympatry and more symmetric ranges, but it did not predict local species richness. Following speciation, species in the Northern Hemisphere presumably achieve positive local co-occurrence faster than elsewhere, which could facilitate their higher speciation rates. However, this does not seem to be linked to local species richness, which is probably governed by other processes.
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9
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Wang X, Xiao Y, Lv YW, He ZH, Yeh FC, Hu XS. A Community-Based Framework Integrates Interspecific Interactions into Forest Genetic Conservation. PLANTS (BASEL, SWITZERLAND) 2024; 13:435. [PMID: 38337968 PMCID: PMC10856838 DOI: 10.3390/plants13030435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 01/22/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024]
Abstract
Forest genetic conservation is typically species-specific and does not integrate interspecific interaction and community structure. It mainly focuses on the theories of population and quantitative genetics. This approach depicts the intraspecific patterns of population genetic structure derived from genetic markers and the genetic differentiation of adaptive quantitative traits in provenance trials. However, it neglects possible interspecific interaction in natural forests and overlooks natural hybridization or subspeciation. We propose that the genetic diversity of a given species in a forest community is shaped by both intraspecific population and interspecific community evolutionary processes, and expand the traditional forest genetic conservation concept under the community ecology framework. We show that a community-specific phylogeny derived from molecular markers would allow us to explore the genetic mechanisms of a tree species interacting with other resident species. It would also facilitate the exploration of a species' ecological role in forest community assembly and the taxonomic relationship of the species with other species specific to its resident forest community. Phylogenetic β-diversity would assess the similarities and differences of a tree species across communities regarding ecological function, the strength of selection pressure, and the nature and extent of its interaction with other species. Our forest genetic conservation proposal that integrates intraspecific population and interspecific community genetic variations is suitable for conserving a taxonomic species complex and maintaining its evolutionary potential in natural forests. This provides complementary information to conventional population and quantitative genetics-based conservation strategies.
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Affiliation(s)
- Xi Wang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.W.); (Y.X.); (Y.-W.L.); (Z.-H.H.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
| | - Yu Xiao
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.W.); (Y.X.); (Y.-W.L.); (Z.-H.H.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
| | - Yan-Wen Lv
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.W.); (Y.X.); (Y.-W.L.); (Z.-H.H.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
| | - Zi-Han He
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.W.); (Y.X.); (Y.-W.L.); (Z.-H.H.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
| | - Francis C. Yeh
- Department of Renewable Resources, University of Alberta, 751 General Service Building, Edmonton, AB T6G 2H1, Canada;
| | - Xin-Sheng Hu
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.W.); (Y.X.); (Y.-W.L.); (Z.-H.H.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
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10
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Tian Q, Stull GW, Kellermann J, Medan D, Nge FJ, Liu SY, Kates HR, Soltis DE, Soltis PS, Guralnick RP, Folk RA, Onstein RE, Yi TS. Rapid in situ diversification rates in Rhamnaceae explain the parallel evolution of high diversity in temperate biomes from global to local scales. THE NEW PHYTOLOGIST 2024; 241:1851-1865. [PMID: 38229185 DOI: 10.1111/nph.19504] [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: 08/27/2023] [Accepted: 11/20/2023] [Indexed: 01/18/2024]
Abstract
The macroevolutionary processes that have shaped biodiversity across the temperate realm remain poorly understood and may have resulted from evolutionary dynamics related to diversification rates, dispersal rates, and colonization times, closely coupled with Cenozoic climate change. We integrated phylogenomic, environmental ordination, and macroevolutionary analyses for the cosmopolitan angiosperm family Rhamnaceae to disentangle the evolutionary processes that have contributed to high species diversity within and across temperate biomes. Our results show independent colonization of environmentally similar but geographically separated temperate regions mainly during the Oligocene, consistent with the global expansion of temperate biomes. High global, regional, and local temperate diversity was the result of high in situ diversification rates, rather than high immigration rates or accumulation time, except for Southern China, which was colonized much earlier than the other regions. The relatively common lineage dispersals out of temperate hotspots highlight strong source-sink dynamics across the cosmopolitan distribution of Rhamnaceae. The proliferation of temperate environments since the Oligocene may have provided the ecological opportunity for rapid in situ diversification of Rhamnaceae across the temperate realm. Our study illustrates the importance of high in situ diversification rates for the establishment of modern temperate biomes and biodiversity hotspots across spatial scales.
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Affiliation(s)
- Qin Tian
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
- Key Laboratory of Plant Diversity and Specialty Crops, Chinese Academy of Sciences, Beijing, 100093, China
- Naturalis Biodiversity Center, Darwinweg 2, 2333CR, Leiden, the Netherlands
| | - Gregory W Stull
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Jürgen Kellermann
- State Herbarium of South Australia, Botanic Gardens and State Herbarium, Hackney Road, Adelaide, SA, 5000, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Diego Medan
- Cátedra de Botánica General, Facultad de Agronomía, Universidad de Buenos Aires, Ave San Martín 4453, C1417DSE, Buenos Aires, Argentina
| | - Francis J Nge
- State Herbarium of South Australia, Botanic Gardens and State Herbarium, Hackney Road, Adelaide, SA, 5000, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
- IRD - Institut de Recherche pour le Développement, Ave Agropolis BP 64501, Montpellier, 34394, France
| | - Shui-Yin Liu
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
- Key Laboratory of Plant Diversity and Specialty Crops, Chinese Academy of Sciences, Beijing, 100093, China
| | - Heather R Kates
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Robert P Guralnick
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Ryan A Folk
- Department of Biological Sciences, Mississippi State University, Mississippi, MS, 39762, USA
| | - Renske E Onstein
- Naturalis Biodiversity Center, Darwinweg 2, 2333CR, Leiden, the Netherlands
- Evolution and Adaptation, German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, Leipzig, 04103, Germany
- Leipzig University, Leipzig, 04013, Germany
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
- Key Laboratory of Plant Diversity and Specialty Crops, Chinese Academy of Sciences, Beijing, 100093, China
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11
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Shoemaker WR, Grilli J. Investigating macroecological patterns in coarse-grained microbial communities using the stochastic logistic model of growth. eLife 2024; 12:RP89650. [PMID: 38251984 PMCID: PMC10945690 DOI: 10.7554/elife.89650] [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] [Indexed: 01/23/2024] Open
Abstract
The structure and diversity of microbial communities are intrinsically hierarchical due to the shared evolutionary history of their constituents. This history is typically captured through taxonomic assignment and phylogenetic reconstruction, sources of information that are frequently used to group microbes into higher levels of organization in experimental and natural communities. Connecting community diversity to the joint ecological dynamics of the abundances of these groups is a central problem of community ecology. However, how microbial diversity depends on the scale of observation at which groups are defined has never been systematically examined. Here, we used a macroecological approach to quantitatively characterize the structure and diversity of microbial communities among disparate environments across taxonomic and phylogenetic scales. We found that measures of biodiversity at a given scale can be consistently predicted using a minimal model of ecology, the Stochastic Logistic Model of growth (SLM). This result suggests that the SLM is a more appropriate null-model for microbial biodiversity than alternatives such as the Unified Neutral Theory of Biodiversity. Extending these within-scale results, we examined the relationship between measures of biodiversity calculated at different scales (e.g. genus vs. family), an empirical pattern previously evaluated in the context of the Diversity Begets Diversity (DBD) hypothesis (Madi et al., 2020). We found that the relationship between richness estimates at different scales can be quantitatively predicted assuming independence among community members, demonstrating that the DBD can be sufficiently explained using the SLM as a null model of ecology. Contrastingly, only by including correlations between the abundances of community members (e.g. as the consequence of interactions) can we predict the relationship between estimates of diversity at different scales. The results of this study characterize novel microbial patterns across scales of organization and establish a sharp demarcation between recently proposed macroecological patterns that are not and are affected by ecological interactions.
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Affiliation(s)
- William R Shoemaker
- Quantitative Life Sciences, The Abdus Salam International Centre for Theoretical Physics (ICTP)TriesteItaly
| | - Jacopo Grilli
- Quantitative Life Sciences, The Abdus Salam International Centre for Theoretical Physics (ICTP)TriesteItaly
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12
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Tytgat B, Verleyen E, Sweetlove M, Van den Berge K, Pinseel E, Hodgson DA, Chown SL, Sabbe K, Wilmotte A, Willems A, Vyverman W. Polar lake microbiomes have distinct evolutionary histories. SCIENCE ADVANCES 2023; 9:eade7130. [PMID: 37976353 PMCID: PMC10656066 DOI: 10.1126/sciadv.ade7130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 10/19/2023] [Indexed: 11/19/2023]
Abstract
Toward the poles, life on land is increasingly dominated by microorganisms, yet the evolutionary origin of polar microbiomes remains poorly understood. Here, we use metabarcoding of Arctic, sub-Antarctic, and Antarctic lacustrine benthic microbial communities to test the hypothesis that high-latitude microbiomes are recruited from a globally dispersing species pool through environmental selection. We demonstrate that taxonomic overlap between the regions is limited within most phyla, even at higher-order taxonomic levels, with unique deep-branching phylogenetic clades being present in each region. We show that local and regional taxon richness and net diversification rate of regionally restricted taxa differ substantially between polar regions in both microeukaryotic and bacterial biota. This suggests that long-term evolutionary divergence resulting from low interhemispheric dispersal and diversification in isolation has been a prominent process shaping present-day polar lake microbiomes. Our findings illuminate the distinctive biogeography of polar lake ecosystems and underscore that conservation efforts should include their unique microbiota.
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Affiliation(s)
- Bjorn Tytgat
- Laboratory of Protistology and Aquatic Ecology, Ghent University, Gent, Belgium
| | - Elie Verleyen
- Laboratory of Protistology and Aquatic Ecology, Ghent University, Gent, Belgium
| | - Maxime Sweetlove
- Laboratory of Protistology and Aquatic Ecology, Ghent University, Gent, Belgium
| | - Koen Van den Berge
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Gent, Belgium
| | - Eveline Pinseel
- Laboratory of Protistology and Aquatic Ecology, Ghent University, Gent, Belgium
- Meise Botanic Garden, Meise, Belgium
| | - Dominic A. Hodgson
- British Antarctic Survey, Natural Environment Research Council, Cambridge, UK
- Department of Geography, Durham University, Durham, UK
| | - Steven L. Chown
- Securing Antarctica’s Environmental Future, School of Biological Sciences, Monash University, Melbourne, VIC, Australia
| | - Koen Sabbe
- Laboratory of Protistology and Aquatic Ecology, Ghent University, Gent, Belgium
| | - Annick Wilmotte
- InBio-Centre for Protein Engineering, University of Liège, Liège, Belgium
| | - Anne Willems
- Laboratory of Microbiology, Ghent University, Gent, Belgium
| | | | - Wim Vyverman
- Laboratory of Protistology and Aquatic Ecology, Ghent University, Gent, Belgium
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13
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Scott JE. The macroevolutionary dynamics of activity pattern in mammals: Primates in context. J Hum Evol 2023; 184:103436. [PMID: 37741141 DOI: 10.1016/j.jhevol.2023.103436] [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: 03/02/2023] [Revised: 08/30/2023] [Accepted: 08/30/2023] [Indexed: 09/25/2023]
Abstract
Activity pattern has played a prominent role in discussions of primate evolutionary history. Most primates are either diurnal or nocturnal, but a small number are active both diurnally and nocturnally. This pattern-cathemerality-also occurs at low frequency across mammals. Using a large sample of mammalian species, this study evaluates two macroevolutionary hypotheses proposed to explain why cathemerality is less common than diurnality and nocturnality: 1) that cathemeral lineages have higher extinction probabilities (differential diversification) and 2) that transitions out of cathemerality are more frequent, making it a less persistent state (differential state persistence). Rates of speciation, extinction, and transition between character states were estimated using hidden-rates models applied to a phylogenetic tree containing 3013 mammals classified by activity pattern. The models failed to detect consistent differences in diversification dynamics among activity patterns, but there is strong support for differential state persistence. Transition rates out of cathemerality tend to be much higher than transition rates out of nocturnality. Transition rates out of diurnality are similar to those for cathemerality in most clades, with two important exceptions: diurnality is unusually persistent in anthropoid primates and sciurid rodents. These two groups combine very low rates of transition out of diurnality with high speciation rates. This combination has no parallels among cathemeral lineages, explaining why diurnality has become more common than cathemerality in mammals. Similarly, the combination of rates found in anthropoids is sufficient to explain the low relative frequency of cathemerality in primates, making it unnecessary to appeal to high extinction probabilities in cathemeral lineages in this clade. These findings support the hypothesis that the distribution of activity patterns across mammals has been influenced primarily by differential state persistence, whereas the effect of differential diversification appears to have been more idiosyncratic.
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Affiliation(s)
- Jeremiah E Scott
- Department of Medical Anatomical Sciences, College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA.
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14
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Henao-Diaz LF, Pennell M. The Major Features of Macroevolution. Syst Biol 2023; 72:1188-1198. [PMID: 37248967 DOI: 10.1093/sysbio/syad032] [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: 12/23/2021] [Revised: 05/02/2023] [Accepted: 05/29/2023] [Indexed: 05/31/2023] Open
Abstract
Evolutionary dynamics operating across deep time leave footprints in the shapes of phylogenetic trees. For the last several decades, researchers have used increasingly large and robust phylogenies to study the evolutionary history of individual clades and to investigate the causes of the glaring disparities in diversity among groups. Whereas typically not the focal point of individual clade-level studies, many researchers have remarked on recurrent patterns that have been observed across many different groups and at many different time scales. Whereas previous studies have documented various such regularities in topology and branch length distributions, they have typically focused on a single pattern and used a disparate collection (oftentimes, of quite variable reliability) of trees to assess it. Here we take advantage of modern megaphylogenies and unify previous disparate observations about the shapes embedded in the Tree of Life to create a catalog of the "major features of macroevolution." By characterizing such a large swath of subtrees in a consistent way, we hope to provide a set of phenomena that process-based macroevolutionary models of diversification ought to seek to explain.
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Affiliation(s)
- L Francisco Henao-Diaz
- Department of Ecology and Evolution, University of Chicago, Chicago, USA
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | - Matt Pennell
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, USA
- Department of Biological Sciences, University of Southern California, Los Angeles, USA
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15
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Bakry SM, Aboul Naser AF, El Negoumy SIM, Kassem MES, Meselhy MR, Abdel-Sattar E. Comparative LC-MS/MS-based molecular networking, DNA fingerprinting, and in vitro anti-Helicobacter pylori activity of three Egyptian Ficus cultivars. J Pharm Biomed Anal 2023; 235:115620. [PMID: 37557066 DOI: 10.1016/j.jpba.2023.115620] [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: 04/28/2023] [Revised: 07/30/2023] [Accepted: 07/30/2023] [Indexed: 08/11/2023]
Abstract
Ficus species (Moraceae) have been used for nutrition and traditional medicine, and plants from this family are phytochemically abundant and serve as a potential source of natural products. As a result of the inherent complexity of the plant metabolomes and the fact that these Ficus species chemical space has not yet been fully decoded, it is still difficult to characterize their phytochemistry. Therefore, this study, we suggest the use of the molecular networking to elucidate the chemical classes existing in leaves of three Ficus species (F. deltoidei Jack, F. drupacea Thunb and F. sycomorus L.) and highlight the importance of molecular networking in examining their chemotaxonomy . By using computational tools, 90 metabolites were annotated , including phenolic acids, flavonoids, furanocoumarins, fatty acids and terpenoids. Phenolic acids were detected as the main class present in the three studied species. Flavonoids-C-glycosides, flavonoids-O-glycosides and isoflavonoids were mainly present in F. drupacea and F. sycomorus, while furanocoumarins were proposed in F. sycomorus. Vomifoliol-based sesquiterpenes were proposed in F. deltoidei. The chemotaxonomic differentiation agreed with the DNA fingerprinting using SCOT and ISSR markers. F. deltoidei, in particular, had a divergent chemical fingerprint as well as a different genotype. Chemotype differentiation using chemical fingerprints, in conjunction with the proposed genetic markers, creates an effective identification tool for the quality control of the raw materials and products derived from those three Ficus species. As well, F. drupacea exploited the most potent inhibition of H. pylori with MIC of 7.81 µg/ mL compared with clarithromycin. Overall, molecular networking provides a promising approach for the exploration of the chemical space of plant metabolomes and the elucidation of chemotaxonomy.
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Affiliation(s)
- Sherien M Bakry
- Phytochemistry and Plant Systematics Department, National Research Centre (NRC), 33 El Bohouth St., Dokki, 12622 Giza, Egypt
| | - Asmaa F Aboul Naser
- Therapeutic Chemistry Department, National Research Centre (NRC), 33 El Bohouth St., Dokki, 12622 Giza, Egypt
| | - Sabry I M El Negoumy
- Phytochemistry and Plant Systematics Department, National Research Centre (NRC), 33 El Bohouth St., Dokki, 12622 Giza, Egypt
| | - Mona E S Kassem
- Phytochemistry and Plant Systematics Department, National Research Centre (NRC), 33 El Bohouth St., Dokki, 12622 Giza, Egypt
| | - Meselhy R Meselhy
- Pharmacognosy Department, Faculty of Pharmacy, Cairo University, 11562 Cairo, Egypt
| | - Essam Abdel-Sattar
- Pharmacognosy Department, Faculty of Pharmacy, Cairo University, 11562 Cairo, Egypt.
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16
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González-Caro S, Tello JS, Myers JA, Feeley K, Blundo C, Calderón-Loor M, Carilla J, Cayola L, Cuesta F, Farfán W, Fuentes AF, Garcia-Cabrera K, Grau R, Idarraga Á, Loza MI, Malhi Y, Malizia A, Malizia L, Osinaga-Acosta O, Pinto E, Salinas N, Silman M, Terán-Valdéz A, Duque Á. Historical Assembly of Andean Tree Communities. PLANTS (BASEL, SWITZERLAND) 2023; 12:3546. [PMID: 37896011 PMCID: PMC10610186 DOI: 10.3390/plants12203546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 08/28/2023] [Accepted: 09/13/2023] [Indexed: 10/29/2023]
Abstract
Patterns of species diversity have been associated with changes in climate across latitude and elevation. However, the ecological and evolutionary mechanisms underlying these relationships are still actively debated. Here, we present a complementary view of the well-known tropical niche conservatism (TNC) hypothesis, termed the multiple zones of origin (MZO) hypothesis, to explore mechanisms underlying latitudinal and elevational gradients of phylogenetic diversity in tree communities. The TNC hypothesis posits that most lineages originate in warmer, wetter, and less seasonal environments in the tropics and rarely colonize colder, drier, and more seasonal environments outside of the tropical lowlands, leading to higher phylogenetic diversity at lower latitudes and elevations. In contrast, the MZO hypothesis posits that lineages also originate in temperate environments and readily colonize similar environments in the tropical highlands, leading to lower phylogenetic diversity at lower latitudes and elevations. We tested these phylogenetic predictions using a combination of computer simulations and empirical analyses of tree communities in 245 forest plots located in six countries across the tropical and subtropical Andes. We estimated the phylogenetic diversity for each plot and regressed it against elevation and latitude. Our simulated and empirical results provide strong support for the MZO hypothesis. Phylogenetic diversity among co-occurring tree species increased with both latitude and elevation, suggesting an important influence on the historical dispersal of lineages with temperate origins into the tropical highlands. The mixing of different floras was likely favored by the formation of climatically suitable corridors for plant migration due to the Andean uplift. Accounting for the evolutionary history of plant communities helps to advance our knowledge of the drivers of tree community assembly along complex climatic gradients, and thus their likely responses to modern anthropogenic climate change.
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Affiliation(s)
- Sebastián González-Caro
- Departamento de Ciencias Forestales, Universidad Nacional de Colombia sede Medellín, Medellín 1027, Colombia
| | - J. Sebastián Tello
- Center for Conservation and Sustainable Development, Missouri Botanical Garden, Saint Louis, MO 63110, USA; (J.S.T.)
| | - Jonathan A. Myers
- Department of Biology, Washington University in Saint Louis, Saint Louis, MO 63112, USA;
| | - Kenneth Feeley
- Biology Department, University of Miami, Coral Gables, FL 33146, USA;
| | - Cecilia Blundo
- Instituto de Ecología Regional (IER), Universidad Nacional de Tucumán (UNT)—Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Tucumán 4107, Argentina; (C.B.); (J.C.)
| | - Marco Calderón-Loor
- Grupo de Investigación en Biodiversidad, Medio Ambiente y Salud–BIOMAS–Universidad de Las Américas (UDLA), Quito 170124, Ecuador
- Albo Climate, Ehad Ha’am, 9, Tel Aviv, 65251, Israel
| | - Julieta Carilla
- Instituto de Ecología Regional (IER), Universidad Nacional de Tucumán (UNT)—Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Tucumán 4107, Argentina; (C.B.); (J.C.)
| | - Leslie Cayola
- Herbario Nacional de Bolivia (LPB), La Paz 10077, Bolivia
- Missouri Botanical Garden, St. Louis, MO 63110, USA
| | - Francisco Cuesta
- Grupo de Investigación en Biodiversidad, Medio Ambiente y Salud–BIOMAS–Universidad de Las Américas (UDLA), Quito 170124, Ecuador
| | - William Farfán
- Center for Conservation and Sustainable Development, Missouri Botanical Garden, Saint Louis, MO 63110, USA; (J.S.T.)
- Department of Biology, Washington University in Saint Louis, Saint Louis, MO 63112, USA;
- Living Earth Collaborative, Washington University in Saint Louis, St. Louis, MO 63112, USA
| | - Alfredo F. Fuentes
- Herbario Nacional de Bolivia (LPB), La Paz 10077, Bolivia
- Missouri Botanical Garden, St. Louis, MO 63110, USA
| | - Karina Garcia-Cabrera
- Escuela Profesional de Biología, Universidad Nacional de San Antonio Abad del Cusco, Cusco 08003, Peru
| | - Ricardo Grau
- Instituto de Ecología Regional (IER), Universidad Nacional de Tucumán (UNT)—Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Tucumán 4107, Argentina; (C.B.); (J.C.)
| | - Álvaro Idarraga
- Fundación Jardín Botánico de Medellín, Medellín 050010, Colombia
| | - M. Isabel Loza
- Center for Conservation and Sustainable Development, Missouri Botanical Garden, Saint Louis, MO 63110, USA; (J.S.T.)
- Herbario Nacional de Bolivia (LPB), La Paz 10077, Bolivia
- Living Earth Collaborative, Washington University in Saint Louis, St. Louis, MO 63112, USA
| | - Yadvinder Malhi
- Environmental Change Institute, School of Geography and the Environment, University of Oxford, Oxford OX14BH, UK;
| | - Agustina Malizia
- Instituto de Ecología Regional (IER), Universidad Nacional de Tucumán (UNT)—Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Tucumán 4107, Argentina; (C.B.); (J.C.)
| | - Lucio Malizia
- Facultad de Ciencias Agrarias, Universidad Nacional de Jujuy, Jujuy 4600, Argentina;
| | - Oriana Osinaga-Acosta
- Instituto de Ecología Regional (IER), Universidad Nacional de Tucumán (UNT)—Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Tucumán 4107, Argentina; (C.B.); (J.C.)
| | - Esteban Pinto
- Grupo de Investigación en Biodiversidad, Medio Ambiente y Salud–BIOMAS–Universidad de Las Américas (UDLA), Quito 170124, Ecuador
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Norma Salinas
- Institute for Nature Earth and Energy, Pontifical Catholic University of Peru, 15088, Peru
| | - Miles Silman
- Center for Energy, Environment and Sustainability, Winston-Salem, NC 27106, USA
| | - Andrea Terán-Valdéz
- Centro Jambatú de Investigación y Conservación de Anfibios Quito Ecuador, Quito 170131, Ecuador
| | - Álvaro Duque
- Departamento de Ciencias Forestales, Universidad Nacional de Colombia sede Medellín, Medellín 1027, Colombia
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17
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Cerezer FO, Dambros CS, Coelho MTP, Cassemiro FAS, Barreto E, Albert JS, Wüest RO, Graham CH. Accelerated body size evolution in upland environments is correlated with recent speciation in South American freshwater fishes. Nat Commun 2023; 14:6070. [PMID: 37770447 PMCID: PMC10539357 DOI: 10.1038/s41467-023-41812-7] [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: 02/01/2023] [Accepted: 09/15/2023] [Indexed: 09/30/2023] Open
Abstract
Speciation rates vary greatly among taxa and regions and are shaped by both biotic and abiotic factors. However, the relative importance and interactions of these factors are not well understood. Here we investigate the potential drivers of speciation rates in South American freshwater fishes, the most diverse continental vertebrate fauna, by examining the roles of multiple biotic and abiotic factors. We integrate a dataset on species geographic distribution, phylogenetic, morphological, climatic, and habitat data. We find that Late Neogene-Quaternary speciation events are strongly associated with body-size evolution, particularly in lineages with small body sizes that inhabit higher elevations near the continental periphery. Conversely, the effects of temperature, area, and diversity-dependence, often thought to facilitate speciation, are negligible. By evaluating multiple factors simultaneously, we demonstrate that habitat characteristics associated with elevation, as well as body size evolution, correlate with rapid speciation in South American freshwater fishes. Our study emphasizes the importance of integrative approaches that consider the interplay of biotic and abiotic factors in generating macroecological patterns of species diversity.
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Affiliation(s)
- Felipe O Cerezer
- Swiss Federal Research Institute for Forest, Snow, and Landscape (WSL), Birmensdorf, Switzerland.
- Programa de Pós-Graduação em Biodiversidade Animal, Departamento de Ecologia e Evolução, Universidade Federal de Santa Maria, Santa Maria, Brazil.
| | - Cristian S Dambros
- Programa de Pós-Graduação em Biodiversidade Animal, Departamento de Ecologia e Evolução, Universidade Federal de Santa Maria, Santa Maria, Brazil
| | - Marco T P Coelho
- Swiss Federal Research Institute for Forest, Snow, and Landscape (WSL), Birmensdorf, Switzerland
| | - Fernanda A S Cassemiro
- Programa de Pós-Graduação em Ecologia e Evolução, Universidade Federal de Goiás, Goiânia, Brazil
| | - Elisa Barreto
- Swiss Federal Research Institute for Forest, Snow, and Landscape (WSL), Birmensdorf, Switzerland
| | - James S Albert
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA, USA
| | - Rafael O Wüest
- Swiss Federal Research Institute for Forest, Snow, and Landscape (WSL), Birmensdorf, Switzerland
| | - Catherine H Graham
- Swiss Federal Research Institute for Forest, Snow, and Landscape (WSL), Birmensdorf, Switzerland
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18
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García-Andrade AB, Tedesco PA, Carvajal-Quintero JD, Arango A, Villalobos F. Same process, different patterns: pervasive effect of evolutionary time on species richness in freshwater fishes. Proc Biol Sci 2023; 290:20231066. [PMID: 37700646 PMCID: PMC10498035 DOI: 10.1098/rspb.2023.1066] [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: 05/12/2023] [Accepted: 08/18/2023] [Indexed: 09/14/2023] Open
Abstract
Tropical lands harbour the highest number of species, resulting in the ubiquitous latitudinal diversity gradient (LDG). However, exceptions to this pattern have been observed in some taxa, explained by the interaction between the evolutionary histories and environmental factors that constrain species' physiological and ecological requirements. Here, we applied a deconstruction approach to map the detailed species richness patterns of Actinopterygian freshwater fishes at the class and order levels and to disentangle their drivers using geographical ranges and a phylogeny, comprising 77% (12 557) of all described species. We jointly evaluated seven evolutionary and ecological hypotheses posited to explain the LDG: diversification rate, time for speciation, species-area relationship, environmental heterogeneity, energy, temperature seasonality and past temperature stability. We found distinct diversity gradients across orders, including expected, bimodal and inverse LDGs. Despite these differences, the positive effect of evolutionary time explained patterns for all orders, where species-rich regions are inhabited by older species compared to species-poor regions. Overall, the LDG of each order has been shaped by a unique combination of factors, highlighting the importance of performing a joint evaluation of evolutionary, historical and ecological factors at different taxonomic levels to reach a comprehensive understanding on the causes driving global species richness patterns.
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Affiliation(s)
- Ana Berenice García-Andrade
- Laboratorio de Macroecología Evolutiva, Red de Biología Evolutiva, Instituto de Ecología, A.C. Carretera antigua a Coatepec 351, El Haya, 91070 Xalapa, Veracruz, México
| | - Pablo A. Tedesco
- UMR 5174 EDB—Evolution & Diversité Biologique, Institut de Recherche pour le Développement, Université Paul Sabatier - Bat. 4R1, 118 route de Narbonne, 31062 Toulouse cedex 4, France
| | - Juan D. Carvajal-Quintero
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, D-04103 Leipzig, Germany
| | - Axel Arango
- Laboratorio de Macroecología Evolutiva, Red de Biología Evolutiva, Instituto de Ecología, A.C. Carretera antigua a Coatepec 351, El Haya, 91070 Xalapa, Veracruz, México
| | - Fabricio Villalobos
- Laboratorio de Macroecología Evolutiva, Red de Biología Evolutiva, Instituto de Ecología, A.C. Carretera antigua a Coatepec 351, El Haya, 91070 Xalapa, Veracruz, México
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19
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Smyčka J, Toszogyova A, Storch D. The relationship between geographic range size and rates of species diversification. Nat Commun 2023; 14:5559. [PMID: 37689787 PMCID: PMC10492861 DOI: 10.1038/s41467-023-41225-6] [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: 08/29/2022] [Accepted: 08/24/2023] [Indexed: 09/11/2023] Open
Abstract
Range size is a universal characteristic of every biological species, and is often assumed to affect diversification rate. There are strong theoretical arguments that large-ranged species should have higher rates of diversification. On the other hand, the observation that small-ranged species are often phylogenetically clustered might indicate high diversification of small-ranged species. This discrepancy between theory and the data may be caused by the fact that typical methods of data analysis do not account for range size changes during speciation. Here we use a cladogenetic state-dependent diversification model applied to mammals to show that range size changes during speciation are ubiquitous and small-ranged species indeed diversify generally slower, as theoretically expected. However, both range size and diversification are strongly influenced by idiosyncratic and spatially localized events, such as colonization of an archipelago or a mountain system, which often override the general pattern of range size evolution.
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Affiliation(s)
- Jan Smyčka
- Center for Theoretical Study, Charles University and the Academy of Sciences of the Czech Republic, CZ-11000, Prague, Czech Republic.
| | - Anna Toszogyova
- Center for Theoretical Study, Charles University and the Academy of Sciences of the Czech Republic, CZ-11000, Prague, Czech Republic
| | - David Storch
- Center for Theoretical Study, Charles University and the Academy of Sciences of the Czech Republic, CZ-11000, Prague, Czech Republic
- Department of Ecology, Faculty of Science, Charles University, CZ-12844, Prague, Czech Republic
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20
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Lawrence ER, Pedersen EJ, Fraser DJ. Macrogenetics reveals multifaceted influences of environmental variation on vertebrate population genetic diversity across the Americas. Mol Ecol 2023; 32:4557-4569. [PMID: 37365672 DOI: 10.1111/mec.17059] [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: 12/17/2021] [Revised: 06/02/2023] [Accepted: 06/15/2023] [Indexed: 06/28/2023]
Abstract
The broad scale distribution of population-specific genetic diversity (GDP ) across taxa remains understudied relative to species diversity gradients, despite its relevance for systematic conservation planning. We used nuclear DNA data collected from 3678 vertebrate populations across the Americas to assess the role of environmental and spatial variables in structuring the distribution of GDP , a key component of adaptive potential in the face of environmental change. We specifically assessed non-linear trends for a metric of GDP, expected heterozygosity (HE ), and found more evidence for spatial hotspots and cold spots in HE rather than a strict pattern with latitude. We also detected inconsistent relationships between HE and environmental variables, where only 11 of 30 environmental comparisons among taxa groups were statistically significant at the .05 level, and the shape of significant trends differed substantially across vertebrate groups. Only one of six taxonomic groups, freshwater fishes, consistently showed significant relationships between HE and most (four of five) environmental variables. The remaining groups had statistically significant relationships for either two (amphibians, reptiles), one (birds, mammals), or no variables (anadromous fishes). Our study highlights gaps in the theoretical foundation upon which macrogenetic predictions have been made thus far in the literature, as well as the nuances for assessing broad patterns in GDP among vertebrate groups. Overall, our results suggest a disconnect between patterns of species and genetic diversity, and underscores that large-scale factors affecting genetic diversity may not be the same factors as those shaping taxonomic diversity. Thus, careful spatial and taxonomic-specific considerations are needed for applying macrogenetics to conservation planning.
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Affiliation(s)
| | - Eric J Pedersen
- Department of Biology, Concordia University, Montreal, Quebec, Canada
- Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - Dylan J Fraser
- Department of Biology, Concordia University, Montreal, Quebec, Canada
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21
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Boulila S, Peters SE, Müller RD, Haq BU, Hara N. Earth's interior dynamics drive marine fossil diversity cycles of tens of millions of years. Proc Natl Acad Sci U S A 2023; 120:e2221149120. [PMID: 37428908 PMCID: PMC10629558 DOI: 10.1073/pnas.2221149120] [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: 12/13/2022] [Accepted: 05/24/2023] [Indexed: 07/12/2023] Open
Abstract
The fossil record reveals that biotic diversity has fluctuated quasi-cyclically through geological time. However, the causal mechanisms of biotic diversity cycles remain unexplained. Here, we highlight a common, correlatable 36 ± 1 Myr (million years) cycle in the diversity of marine genera as well as in tectonic, sea-level, and macrostratigraphic data over the past 250 Myr of Earth history. The prominence of the 36 ± 1 Myr cycle in tectonic data favors a common-cause mechanism, wherein geological forcing mechanisms drive patterns in both biological diversity and the preserved rock record. In particular, our results suggest that a 36 ± 1 Myr tectono-eustatically driven sea-level cycle may originate from the interaction between the convecting mantle and subducting slabs, thereby pacing mantle-lithospheric deep-water recycling. The 36 ± 1 Myr tectono-eustatic driver of biodiversity is likely related to cyclic continental inundations, with expanding and contracting ecological niches on shelves and in epeiric seas.
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Affiliation(s)
- Slah Boulila
- Sorbonne Université, CNRS, Institut des Sciences de la Terre Paris, ParisF-75005, France
- Astronomie et Systèmes Dynamiques/Institut de Mécanique Céleste et de Calcul des Ephémérides, CNRS-UMR8028, Observatoire de Paris, Paris Sciences & Lettres University, Sorbonne Université, Paris75014, France
| | - Shanan E. Peters
- Department of Geoscience, University of Madison, Madison, WI53706
| | - R. Dietmar Müller
- EarthByte Group, School of Geosciences, University of Sydney, Sydney, NSW2006, Australia
| | - Bilal U. Haq
- Sorbonne Université, CNRS, Institut des Sciences de la Terre Paris, ParisF-75005, France
- Smithsonian Institution, Washington,DC20024
| | - Nathan Hara
- Département d’astronomie, Université de Genève, Genève1290, Switzerland
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22
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Quintero I, Landis MJ, Jetz W, Morlon H. The build-up of the present-day tropical diversity of tetrapods. Proc Natl Acad Sci U S A 2023; 120:e2220672120. [PMID: 37159475 PMCID: PMC10194011 DOI: 10.1073/pnas.2220672120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 04/04/2023] [Indexed: 05/11/2023] Open
Abstract
The extraordinary number of species in the tropics when compared to the extra-tropics is probably the most prominent and consistent pattern in biogeography, suggesting that overarching processes regulate this diversity gradient. A major challenge to characterizing which processes are at play relies on quantifying how the frequency and determinants of tropical and extra-tropical speciation, extinction, and dispersal events shaped evolutionary radiations. We address this question by developing and applying spatiotemporal phylogenetic and paleontological models of diversification for tetrapod species incorporating paleoenvironmental variation. Our phylogenetic model results show that area, energy, or species richness did not uniformly affect speciation rates across tetrapods and dispute expectations of a latitudinal gradient in speciation rates. Instead, both neontological and fossil evidence coincide in underscoring the role of extra-tropical extinctions and the outflow of tropical species in shaping biodiversity. These diversification dynamics accurately predict present-day levels of species richness across latitudes and uncover temporal idiosyncrasies but spatial generality across the major tetrapod radiations.
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Affiliation(s)
- Ignacio Quintero
- Institut de Biologie de l’ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université Paris Science & Lettres, Paris75005, France
| | - Michael J. Landis
- Landis Lab, Department of Biology, Washington University in St. Louis, St. Louis, MO63130
| | - Walter Jetz
- Jetz Lab, Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT06511
- Center for Biodiversity and Global Change, Yale University, New Haven, CT06511
| | - Hélène Morlon
- Institut de Biologie de l’ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université Paris Science & Lettres, Paris75005, France
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23
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Freedman AH, Harrigan RJ, Zhen Y, Hamilton AM, Smith TB. Evidence for ecotone speciation across an African rainforest-savanna gradient. Mol Ecol 2023; 32:2287-2300. [PMID: 36718952 DOI: 10.1111/mec.16867] [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: 06/03/2022] [Revised: 11/07/2022] [Accepted: 01/16/2023] [Indexed: 02/01/2023]
Abstract
Accelerating climate change and habitat loss make it imperative that plans to conserve biodiversity consider species' ability to adapt to changing environments. However, in biomes where biodiversity is highest, the evolutionary mechanisms responsible for generating adaptative variation and, ultimately, new species are frequently poorly understood. African rainforests represent one such biome, as decadal debates continue concerning the mechanisms generating African rainforest biodiversity. These debates hinge on the relative importance of geographic isolation versus divergent natural selection across environmental gradients. Hindering progress is a lack of robust tests of these competing hypotheses. Because African rainforests are severely at-risk due to climate change and other anthropogenic activities, addressing this long-standing debate is critical for making informed conservation decisions. We use demographic inference and allele frequency-environment relationships to investigate mechanisms of diversification in an African rainforest skink, Trachylepis affinis, a species inhabiting the gradient between rainforest and rainforest-savanna mosaic (ecotone). We provide compelling evidence of ecotone speciation, in which gene flow has all but ceased between rainforest and ecotone populations, at a level consistent with infrequent hybridization between sister species. Parallel patterns of genomic, morphological, and physiological divergence across this environmental gradient and pronounced allele frequency-environment correlation indicate speciation is mostly probably driven by ecological divergence, supporting a central role for divergent natural selection. Our results provide strong evidence for the importance of ecological gradients in African rainforest speciation and inform conservation strategies that preserve the processes that produce and maintain biodiversity.
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Affiliation(s)
- Adam H Freedman
- Faculty of Arts and Sciences Informatics Group, Harvard University, Cambridge, Massachusetts, USA
| | - Ryan J Harrigan
- Centre for Tropical Research and Institute of the Environment and Sustainability, University of California, Los Angeles, California, USA
| | - Ying Zhen
- Centre for Tropical Research and Institute of the Environment and Sustainability, University of California, Los Angeles, California, USA
- School of Life Sciences, Westlake University, Hangzhou, China
| | - Alison M Hamilton
- Department of Biological Sciences, University of Massachusetts-Lowell, Lowell, Massachusetts, USA
| | - Thomas B Smith
- Centre for Tropical Research and Institute of the Environment and Sustainability, University of California, Los Angeles, California, USA
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA
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24
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Shipley BR, McGuire JL. Disentangling the drivers of continental mammalian endemism. GLOBAL CHANGE BIOLOGY 2023; 29:2421-2435. [PMID: 36749035 DOI: 10.1111/gcb.16628] [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: 10/21/2022] [Revised: 02/03/2023] [Accepted: 02/04/2023] [Indexed: 05/28/2023]
Abstract
Endemic species and species with small ranges are ecologically and evolutionarily distinct and are vulnerable to extinction. Determining which abiotic and biotic factors structure patterns of endemism on continents can advance our understanding of global biogeographic processes, but spatial patterns of mammalian endemism have not yet been effectively predicted and reconstructed. Using novel null model techniques, we reconstruct trends in mammalian endemism and describe the isolated and combined effects of physiographic, ecological, and evolutionary factors on endemism. We calculated weighted endemism for global continental ecoregions and compared the spatial distribution of endemism to niche-based, geographic null models of endemism. These null models distribute species randomly across continents, simulating their range sizes from their degree of climatic specialization. They isolate the effects of physiography (topography and climate) and species richness on endemism. We then ran linear and structural models to determine how topography and historical climate stability influence endemism. The highest rates of mammalian endemism were found in topographically rough, climatically stable ecoregions with many species. The null model that isolated physiography did not closely approximate the observed distribution of endemism (r2 = .09), whereas the null model that incorporated both physiography and species richness did (r2 = .59). The linear models demonstrate that topography and climatic stability both influenced endemism values, but that average climatic niche breadth was not highly correlated with endemism. Climate stability and topography both influence weighted endemism in mammals, but the spatial distribution of mammalian endemism is driven by a combination of physiography and species richness. Despite its relationship to individual range size, average climate niche breadth has only a weak influence on endemism. The results highlight the importance of historical biogeographic processes (e.g. centers of speciation) and geography in driving endemism patterns, and disentangle the mechanisms structuring species ranges worldwide.
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Affiliation(s)
- Benjamin R Shipley
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Jenny L McGuire
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, Georgia, USA
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25
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Barreto E, Lim MCW, Rojas D, Dávalos LM, Wüest RO, Machac A, Graham CH. Morphology and niche evolution influence hummingbird speciation rates. Proc Biol Sci 2023; 290:20221793. [PMID: 37072043 PMCID: PMC10113027 DOI: 10.1098/rspb.2022.1793] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 03/21/2023] [Indexed: 04/20/2023] Open
Abstract
How traits affect speciation is a long-standing question in evolution. We investigate whether speciation rates are affected by the traits themselves or by the rates of their evolution, in hummingbirds, a clade with great variation in speciation rates, morphology and ecological niches. Further, we test two opposing hypotheses, postulating that speciation rates are promoted by trait conservatism or, alternatively, by trait divergence. To address these questions, we analyse morphological (body mass and bill length) and niche traits (temperature and precipitation position and breadth, and mid-elevation), using a variety of methods to estimate speciation rates and correlate them with traits and their evolutionary rates. When it comes to the traits, we find faster speciation in smaller hummingbirds with shorter bills, living at higher elevations and experiencing greater temperature ranges. As for the trait evolutionary rates, we find that speciation increases with rates of divergence in the niche traits, but not in the morphological traits. Together, these results reveal the interplay of mechanisms through which different traits and their evolutionary rates (conservatism or divergence) influence the origination of hummingbird diversity.
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Affiliation(s)
- Elisa Barreto
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
- Departamento de Ecologia, Universidade Federal de Goiás, Campus Samambaia, Goiânia, Goiás, Brazil
| | - Marisa C. W. Lim
- Department of Ecology and Evolution, Stony Brook University, 650 Life Sciences Building, Stony Brook, NY 11794, USA
| | - Danny Rojas
- Department of Natural Sciences and Mathematics, Pontificia Universidad Javeriana Cali, Cl. 18 #118-250, Cali, Valle del Cauca, Colombia
| | - Liliana M. Dávalos
- Department of Ecology and Evolution, Stony Brook University, 650 Life Sciences Building, Stony Brook, NY 11794, USA
- Consortium for Inter-Disciplinary Environmental Research, Stony Brook University, 129 Dana Hall, Stony Brook, NY 11794, USA
| | - Rafael O. Wüest
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
| | - Antonin Machac
- Villum Center for Global Mountain Biodiversity and Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
- Center for Theoretical Study, Charles University and the Czech Academy of Science, Jilska 1, 11000 Prague, Czechia
- Department of Ecology, Charles University, Vinicna 7, 12844 Prague, Czechia
| | - Catherine H. Graham
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
- Department of Ecology and Evolution, Stony Brook University, 650 Life Sciences Building, Stony Brook, NY 11794, USA
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26
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Moritz MA, Batllori E, Bolker BM. The role of fire in terrestrial vertebrate richness patterns. Ecol Lett 2023; 26:563-574. [PMID: 36773965 DOI: 10.1111/ele.14177] [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: 07/19/2022] [Revised: 12/13/2022] [Accepted: 12/14/2022] [Indexed: 02/13/2023]
Abstract
Productivity is strongly associated with terrestrial species richness patterns, although the mechanisms underpinning such patterns have long been debated. Despite considerable consumption of primary productivity by fire, its influence on global diversity has received relatively little study. Here we examine the sensitivity of terrestrial vertebrate biodiversity (amphibians, birds and mammals) to fire, while accounting for other drivers. We analyse global data on terrestrial vertebrate richness, net primary productivity, fire occurrence (fraction of productivity consumed) and additional influences unrelated to productivity (i.e., historical phylogenetic and area effects) on species richness. For birds, fire is associated with higher diversity, rivalling the effects of productivity on richness, and for mammals, fire's positive association with diversity is even stronger than productivity; for amphibians, in contrast, there are few clear associations. Our findings suggest an underappreciated role for fire in the generation of animal species richness and the conservation of global biodiversity.
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Affiliation(s)
- Max A Moritz
- University of California Cooperative Extension, Oakland, California, USA
- Bren School of Environmental Science & Management, University of California, Santa Barbara, California, USA
| | - Enric Batllori
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain
| | - Benjamin M Bolker
- Departments of Mathematics & Statistics and Biology, McMaster University, Hamilton, Ontario, Canada
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27
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Chen Y, Rasool MA, Hussain S, Meng S, Yao Y, Wang X, Liu Y. Bird community structure is driven by urbanization level, blue-green infrastructure configuration and precision farming in Taizhou, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 859:160096. [PMID: 36372169 DOI: 10.1016/j.scitotenv.2022.160096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 10/24/2022] [Accepted: 11/05/2022] [Indexed: 06/16/2023]
Abstract
Land use/land cover (LULC) changes and high urbanization rates are the main drivers of avian habitat loss in developing countries. However, few studies have examined the effects of urbanization intensity on avian diversity distribution and its importance in guiding eco-friendly urban planning. We surveyed bird distribution (n = 67 species) in different seasons using local ecological knowledge (LEK) and transect line methods in Jiangyan District from July 2018 to May 2019. One-way analysis of variance (ANOVA) was used to assess the effects of urbanization levels on birds relative density and richness during spring-summer (breeding season) and autumn-winter seasons (non-breeding season). Generalized linear models (GLM) were identified for the landscape composition and configuration that drive relative density and richness in native bird communities. Using redundancy analysis (RDA), we identified the landscape composition and configuration factors affecting bird foraging and roosting at urbanization levels. The results showed high dependency of waders and granivores on paddy fields and dry arable land respectively during the breeding season. During non-breeding season, wetland abundance, land cover, connectivity and total area of BGI were important habitat factors in attracting birds. Moreover, the landscape composition and configuration factors of BGI: wetlands as well as farmland habitats, are the main environmental cues that influence bird foraging. Therefore, to increase habitat suitability over landscape matrix, we propose creation of multiple waterbodies and green corridors of variable types and sizes on natural patches to improve the connectivity of ecological network. We also recommend land management interventions in farmland ecosystems, which could contribute to natural habitat restoration and improve bird biodiversity in urban areas.
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Affiliation(s)
- Yixue Chen
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, Hohai University, Nanjing 210098, China
| | | | - Sarfraz Hussain
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, Hohai University, Nanjing 210098, China
| | - Shuang Meng
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, Hohai University, Nanjing 210098, China
| | - Yipeng Yao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, Hohai University, Nanjing 210098, China
| | - Xue Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, Hohai University, Nanjing 210098, China
| | - Yuhong Liu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China.
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28
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Shi W, Song W, Chen Z, Cai H, Gong Q, Liu J, Shi C, Wang S. Comparative chloroplast genome analyses of diverse Phoebe (Lauraceae) species endemic to China provide insight into their phylogeographical origin. PeerJ 2023; 11:e14573. [PMID: 36755871 PMCID: PMC9901306 DOI: 10.7717/peerj.14573] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 11/28/2022] [Indexed: 02/05/2023] Open
Abstract
The genus Phoebe (Lauraceae) includes about 90 evergreen tree species that are an ideal source of timber. Habitat destruction and deforestation have resulted in most of them being endemic to China. The accurate identification of endangered Phoebe species in China is necessary for their conservation. Chloroplast genome sequences can play an important role in species identification. In this study, comparative chloroplast genome analyses were conducted on diverse Phoebe species that are primarily distributed in China. Despite the conserved nature of chloroplast genomes, we detected some highly divergent intergenic regions (petA-psbE, ndhF-rpl32, and psbM-trnD-GUC) as well as three highly divergent genes (rbcL, ycf1, and ycf2) that have potential applications in phylogenetics and evolutionary analysis. The phylogenetic analysis indicated that various Phoebe species in China were divided into three clades. The complete chloroplast genome was better suited for phylogenetic analysis of Phoebe species. In addition, based on the phylogeographical analysis of Phoebe species in China, we inferred that the Phoebe species in China first originated in Yunnan and then spread to other southern areas of the Yangtze River. The results of this research will add to existing case studies on the phylogenetic analysis of Phoebe species and have the potential to contribute to the conservation of Phoebe species that are in danger of extinction.
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Affiliation(s)
- Wenbo Shi
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Weicai Song
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Zimeng Chen
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Haohong Cai
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Qin Gong
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Jin Liu
- Yunnan Institute of Tropical Crops, Xishuangbanna, China
| | - Chao Shi
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China,Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, China
| | - Shuo Wang
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
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29
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Brodie JF, Mannion PD. The hierarchy of factors predicting the latitudinal diversity gradient. Trends Ecol Evol 2023; 38:15-23. [PMID: 36089412 DOI: 10.1016/j.tree.2022.07.013] [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: 11/24/2020] [Revised: 07/26/2022] [Accepted: 07/29/2022] [Indexed: 12/24/2022]
Abstract
The numerous explanations for why Earth's biodiversity is concentrated at low latitudes fail to explain variation in the strength and even direction of the gradient through deep time. Consequently, we do not know if today's gradient is representative of what might be expected on other planets or is merely an idiosyncrasy of Earth's history. We propose a hierarchy of factors driving the latitudinal distribution of diversity: (i) over geologically long time spans, diversity is largely predicted by climate; (ii) when climatic gradients are shallow, diversity tracks habitat area; and (iii) historical contingencies linked to niche conservatism have geologically short-term, transient influence at most. Thus, latitudinal diversity gradients, although variable in strength and direction, are largely predictable on our planet and possibly others.
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Affiliation(s)
- Jedediah F Brodie
- Division of Biological Sciences & Wildlife Biology Program, University of Montana, Missoula, MT 59812, USA; Institute of Biodiversity and Environmental Conservation, Universiti Malaysia Sarawak, 94 300 Kota Samarahan, Malaysia.
| | - Philip D Mannion
- Department of Earth Sciences, University College London, Gower Street, London, WC1E 6BT, UK
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30
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Princepe D, de Aguiar MAM, Plotkin JB. Mito-nuclear selection induces a trade-off between species ecological dominance and evolutionary lifespan. Nat Ecol Evol 2022; 6:1992-2002. [PMID: 36216905 DOI: 10.1038/s41559-022-01901-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 09/02/2022] [Indexed: 12/15/2022]
Abstract
Mitochondrial and nuclear genomes must be co-adapted to ensure proper cellular respiration and energy production. Mito-nuclear incompatibility reduces individual fitness and induces hybrid infertility, which can drive reproductive barriers and speciation. Here, we develop a birth-death model for evolution in spatially extended populations under selection for mito-nuclear co-adaptation. Mating is constrained by physical and genetic proximity, and offspring inherit nuclear genomes from both parents, with recombination. The model predicts macroscopic patterns including a community's species diversity, species abundance distribution, speciation and extinction rates, as well as intraspecific and interspecific genetic variation. We explore how these long-term outcomes depend upon the parameters of reproduction: individual fitness governed by mito-nuclear compatibility, constraints on mating compatibility and ecological carrying capacity. We find that strong selection for mito-nuclear compatibility reduces the equilibrium number of species after a radiation, increasing species' abundances and simultaneously increasing both speciation and extinction rates. The negative correlation between species diversity and diversification rates in our model agrees with the broad empirical pattern of lower diversity and higher speciation/extinction rates in temperate regions, compared to the tropics. We conclude that these empirical patterns may be caused in part by latitudinal variation in metabolic demands and corresponding variation in selection for mito-nuclear function.
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Affiliation(s)
- Débora Princepe
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Campinas, Brazil.
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.
| | - Marcus A M de Aguiar
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Campinas, Brazil
| | - Joshua B Plotkin
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
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31
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Potential distribution of threatened maples in China under climate change: Implications for conservation. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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32
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Ge D, Qu Y, Deng T, Thuiller W, Fišer C, Ericson PGP, Guo B, de la Sancha NU, von der Heyden S, Hou Z, Li J, Abramov A, Vogler AP, Jønsson KA, Mittermeier R. New progress in exploring the mechanisms underlying extraordinarily high biodiversity in global hotspots and their implications for conservation. DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Affiliation(s)
- Deyan Ge
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology, Chinese Academy of Sciences Beijing China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology, Chinese Academy of Sciences Beijing China
| | - Tao Deng
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of Botany, Chinese Academy of Sciences Kunming China
| | - Wilfried Thuiller
- Univ. Grenoble Alpes Univ. Savoie Mont Blanc, CNRS, LECA Laboratoire d'Ecologie Alpine Grenoble France
| | - Cene Fišer
- Biotechnical Faculty University of Ljubljana Ljubljana Slovenia
| | - Per G. P. Ericson
- Department of Bioinformatics and Genetics Swedish Museum of Natural History Stockholm Sweden
| | - Baocheng Guo
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology, Chinese Academy of Sciences Beijing China
| | - Noé U. de la Sancha
- Department of Biological Sciences Chicago State University Illinois Chicago USA
| | - Sophie von der Heyden
- Evolutionary Genomics Group Department of Botany and Zoology Stellenbosch University Matieland South Africa
| | - Zhonge Hou
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology, Chinese Academy of Sciences Beijing China
| | - Jiatang Li
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province Chengdu Institute of Biology, Chinese Academy of Sciences Chengdu, Sichuan China
| | - Alexei Abramov
- Zoological Institute Russian Academy of Sciences Saint Petersburg Russia
| | | | - Knud A. Jønsson
- Natural History Museum of Denmark University of Copenhagen Copenhagen East Denmark
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33
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Carruthers M, Edgley DE, Saxon AD, Gabagambi NP, Shechonge A, Miska EA, Durbin R, Bridle JR, Turner GF, Genner MJ. Ecological Speciation Promoted by Divergent Regulation of Functional Genes Within African Cichlid Fishes. Mol Biol Evol 2022; 39:msac251. [PMID: 36376993 PMCID: PMC10101686 DOI: 10.1093/molbev/msac251] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Rapid ecological speciation along depth gradients has taken place repeatedly in freshwater fishes, yet molecular mechanisms facilitating such diversification are typically unclear. In Lake Masoko, an African crater lake, the cichlid Astatotilapia calliptera has diverged into shallow-littoral and deep-benthic ecomorphs with strikingly different jaw structures within the last 1,000 years. Using genome-wide transcriptome data, we explore two major regulatory transcriptional mechanisms, expression and splicing-QTL variants, and examine their contributions to differential gene expression underpinning functional phenotypes. We identified 7,550 genes with significant differential expression between ecomorphs, of which 5.4% were regulated by cis-regulatory expression QTLs, and 9.2% were regulated by cis-regulatory splicing QTLs. We also found strong signals of divergent selection on differentially expressed genes associated with craniofacial development. These results suggest that large-scale transcriptome modification plays an important role during early-stage speciation. We conclude that regulatory variants are important targets of selection driving ecologically relevant divergence in gene expression during adaptive diversification.
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Affiliation(s)
- Madeleine Carruthers
- School of Biological Sciences, University of Bristol,
Bristol BS8 1TQ, United
Kingdom
| | - Duncan E Edgley
- School of Biological Sciences, University of Bristol,
Bristol BS8 1TQ, United
Kingdom
| | - Andrew D Saxon
- School of Biological Sciences, University of Bristol,
Bristol BS8 1TQ, United
Kingdom
| | - Nestory P Gabagambi
- Tanzanian Fisheries Research Institute, Kyela Research
Centre, P.O. Box 98, Kyela, Mbeya, Tanzania
| | - Asilatu Shechonge
- Tanzanian Fisheries Research Institute, Dar es Salaam Research
Centre, P.O. Box 9750, Dar es Salaam, Tanzania
| | - Eric A Miska
- Wellcome/CRUK Gurdon Institute, University of Cambridge,
Cambridge CB2 1QN, United
Kingdom
- Department of Genetics, University of Cambridge,
Cambridge CB2 3EH, United
Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus,
Cambridge CB10 1SA, United Kingdom
| | - Richard Durbin
- Department of Genetics, University of Cambridge,
Cambridge CB2 3EH, United
Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus,
Cambridge CB10 1SA, United Kingdom
| | - Jon R Bridle
- School of Biological Sciences, University of Bristol,
Bristol BS8 1TQ, United
Kingdom
| | - George F Turner
- School of Natural Sciences, Bangor University,
Bangor, Wales LL57 2UW, United
Kingdom
| | - Martin J Genner
- School of Biological Sciences, University of Bristol,
Bristol BS8 1TQ, United
Kingdom
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34
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Scott JE. Variation in macroevolutionary dynamics among extant primates. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2022; 179:405-416. [PMCID: PMC9826261 DOI: 10.1002/ajpa.24622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 08/05/2022] [Accepted: 09/03/2022] [Indexed: 09/25/2023]
Abstract
Objectives This study examines how speciation and extinction rates vary across primates, with a focus on the recent macroevolutionary dynamics that have shaped extant primate biodiversity. Materials and methods Lineage‐specific macroevolutionary rates were estimated for each tip in a tree containing 307 species using a hidden‐state likelihood model. Differences in tip rates among major clades were evaluated using phylogenetic ANOVA. Differences among diurnal, nocturnal, and cathemeral lineages were also evaluated, based on previous work indicating that activity pattern influences primate diversification. Results Rate variation in extant primates is low within clades and high between clades. As in previous studies, cercopithecoids stand out in having high net diversification rates, driven by high speciation rates and very low extinction rates. Platyrrhines combine high speciation and high extinction rates, giving them high rates of lineage turnover. Strepsirrhines and tarsiids have low rates of speciation, extinction, turnover, and net diversification. Hominoids are intermediate between platyrrhines and the strepsirrhine‐tarsiid group, and there is evidence for differentiation between hominids and hylobatids. Diurnal lineages have significantly higher speciation rates than nocturnal lineages. Conclusions Recent anthropoid macroevolution has been characterized by marked variation in diversification dynamics among clades. Strepsirrhines and tarsiids are more uniform, despite divergent evolutionary and biogeographic histories. Higher speciation rates in diurnal lineages may be driven by greater ecological opportunity or reliance on visual signals for mate recognition. However, the differences among anthropoids indicate that factors other than activity pattern (e.g., clade competition, historical contingency) have had a more influential role in shaping recent primate diversification.
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Affiliation(s)
- Jeremiah E. Scott
- Department of Medical Anatomical Sciences, College of Osteopathic Medicine of the PacificWestern University of Health SciencesPomonaCaliforniaUSA
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35
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Dagilis AJ, Peede D, Coughlan JM, Jofre GI, D'Agostino ERR, Mavengere H, Tate AD, Matute DR. A need for standardized reporting of introgression: Insights from studies across eukaryotes. Evol Lett 2022; 6:344-357. [PMID: 36254258 PMCID: PMC9554761 DOI: 10.1002/evl3.294] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/04/2022] [Accepted: 06/12/2022] [Indexed: 01/04/2023] Open
Abstract
With the rise of affordable next-generation sequencing technology, introgression-or the exchange of genetic materials between taxa-has become widely perceived to be a ubiquitous phenomenon in nature. Although this claim is supported by several keystone studies, no thorough assessment of the frequency of introgression across eukaryotes in nature has been performed to date. In this manuscript, we aim to address this knowledge gap by examining patterns of introgression across eukaryotes. We collated a single statistic, Patterson's D, which can be used as a test for introgression across 123 studies to further assess how taxonomic group, divergence time, and sequencing technology influence reports of introgression. Overall, introgression has mostly been measured in plants and vertebrates, with less attention given to the rest of the Eukaryotes. We find that the most frequently used metrics to detect introgression are difficult to compare across studies and even more so across biological systems due to differences in study effort, reporting standards, and methodology. Nonetheless, our analyses reveal several intriguing patterns, including the observation that differences in sequencing technologies may bias values of Patterson's D and that introgression may differ throughout the course of the speciation process. Together, these results suggest the need for a unified approach to quantifying introgression in natural communities and highlight important areas of future research that can be better assessed once this unified approach is met.
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Affiliation(s)
| | - David Peede
- Biology DepartmentUniversity of North CarolinaChapel HillNCUSA
- Department of Ecology, Evolution, and Organismal BiologyBrown UniversityProvidenceRIUSA
- Center for Computational Molecular BiologyBrown UniversityProvidenceRIUSA
| | - Jenn M. Coughlan
- Biology DepartmentUniversity of North CarolinaChapel HillNCUSA
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCTUSA
| | - Gaston I. Jofre
- Biology DepartmentUniversity of North CarolinaChapel HillNCUSA
| | - Emmanuel R. R. D'Agostino
- Biology DepartmentUniversity of North CarolinaChapel HillNCUSA
- Department of Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNJUSA
| | - Heidi Mavengere
- Biology DepartmentUniversity of North CarolinaChapel HillNCUSA
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36
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Crouch NMA, Jablonski D. Is species richness mediated by functional and genetic divergence? A global analysis in birds. Funct Ecol 2022; 37:125-138. [PMID: 37064506 PMCID: PMC10086807 DOI: 10.1111/1365-2435.14153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 06/10/2022] [Indexed: 11/28/2022]
Abstract
Unravelling why species richness shows such dramatic spatial variation is an ongoing challenge. Common to many theories is that increasing species richness (e.g. with latitude) requires a compensatory trade-off on an axis of species' ecology. Spatial variation in species richness may also affect genetic diversity if large numbers of coexisting, related species result in smaller population sizes.Here, we test whether increasing species richness results in differential occupation of morphospace by the constituent species, or decreases species' genetic diversity. We test for two potential mechanisms of morphological accommodation: denser packing in ecomorphological space, and expansion of the space. We then test whether species differ in their nucleotide diversity depending on allopatry or sympatry with relatives, indicative of potential genetic consequences of coexistence that would reduce genetic diversity in sympatry. We ask these questions in a spatially explicit framework, using a global database of avian functional trait measurements in combination with >120,000 sequences downloaded from GenBank.We find that higher species richness within families is not systematically correlated with either packing in morphological space or overdispersion but, at the Class level, we find a general positive relationship between packing and species richness, but that points sampled in the tropics have comparatively greater packing than temperate ones relative to their species richness. We find limited evidence that geographical co-occurrence with closely related species or tropical distributions decreases nucleotide diversity of nuclear genes; however, this requires further analysis.Our results suggest that avian families can accumulate species regionally with minimal tradeoffs or cost, implying that external biotic factors do not limit species richness. Read the free Plain Language Summary for this article on the Journal blog.
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Affiliation(s)
- Nicholas M. A. Crouch
- Dept. of the Geophysical Sciences The University of Chicago s Chicago Illinois U.S.A
| | - David Jablonski
- Dept. of the Geophysical Sciences The University of Chicago s Chicago Illinois U.S.A
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37
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Tianpei G, Owens JR, Kong Y, Jian Y, Xiaodong G, Yanling S. The need for
IUCN
species distribution update—The case from takin (
Budorcas taxicolor
) in Southwest China. Ecol Evol 2022. [DOI: 10.1002/ece3.9222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Guan Tianpei
- Institute of Qinghai‐Tibetan Plateau Southwest Minzu University Chengdu China
| | - Jacob R. Owens
- Los Angeles Zoo and Botanical Garden Los Angeles California USA
| | - Yang Kong
- Institute of Qinghai‐Tibetan Plateau Southwest Minzu University Chengdu China
| | - Yang Jian
- Institute of Qinghai‐Tibetan Plateau Southwest Minzu University Chengdu China
| | - Gu Xiaodong
- Sichuan Station of Wildlife survey and Management Chengdu China
| | - Song Yanling
- Institute of Zoology, Chinese Academy of Sciences Beijing China
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38
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Freeman BG, Strimas-Mackey M, Miller ET. Interspecific competition limits bird species' ranges in tropical mountains. Science 2022; 377:416-420. [PMID: 35862538 DOI: 10.1126/science.abl7242] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Species' geographic ranges are limited by climate and species interactions. Climate is the prevailing explanation for why species live only within narrow elevational ranges in megadiverse biodiverse tropical mountains, but competition can also restrict species' elevational ranges. We test contrasting predictions of these hypotheses by conducting a global comparative test of birds' elevational range sizes within 31 montane regions, using more than 4.4 million citizen science records from eBird to define species' elevational ranges in each region. We find strong support that competition, not climate, is the leading driver of narrow elevational ranges. These results highlight the importance of species interactions in shaping species' ranges in tropical mountains, Earth's hottest biodiversity hotspots.
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Affiliation(s)
- Benjamin G Freeman
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.,Department of Zoology, University of British Columbia, Vancouver, BC, Canada
| | | | - Eliot T Miller
- Cornell Lab of Ornithology, Ithaca, New York, USA, 14850
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39
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Yi X, Latch EK. Systematics of the New World bats Eptesicus and Histiotus suggest trans-marine dispersal followed by Neotropical cryptic diversification. Mol Phylogenet Evol 2022; 175:107582. [PMID: 35810969 DOI: 10.1016/j.ympev.2022.107582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 05/23/2022] [Accepted: 06/15/2022] [Indexed: 01/13/2023]
Abstract
Biodiversity can be boosted by colonization of new habitats such as remote islands and separated continents. Molecular studies have suggested that recently evolved organisms probably colonized already separated continents by dispersal, either via land bridge connections or crossing the ocean. Here we test the on-land and trans-marine dispersal hypotheses by evaluating possibilities of colonization routes over the Bering land bridge and across the Atlantic Ocean in the cosmopolitan bat genus Eptesicus (Chiroptera, Vespertilionidae). Previous molecular studies have found New World Eptesicus more closely related to Histiotus, a Neotropical endemic lineage with enlarged ears, than to Old World Eptesicus. However, phylogenetic relationships within the New World group remained unresolved and their evolutionary history was unclear. Here we studied the systematics of New World Eptesicus and Histiotus using extensive taxonomic and geographic sampling, and genomic data from thousands of ultra-conserved elements (UCEs). We estimated phylogenetic trees using concatenation and multispecies coalescent. All analyses supported four major New World clades and a novel topology where E. fuscus and Histiotus are sister clades that together diverged from two sister clades of Neotropical Eptesicus. Intra-clade divergence suggested cryptic diversity that has been concealed by morphological features, especially in the Neotropics where taxonomic re-evaluations are warranted. Molecular dating estimated that Old World and New World clades diverged around 17 million years ago followed by radiation of major New World clades in the mid-Miocene, when climatic changes might have facilitated global dispersal and radiation events. Biogeographic ancestral reconstruction supported the Neotropical origin of the New World clades, suggesting a trans-Atlantic colonization route from North Africa to the northern Neotropics. We highlight that trans-marine dispersal may be more prevalent than currently acknowledged and may be an important first step to global biodiversification.
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Affiliation(s)
- Xueling Yi
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA.
| | - Emily K Latch
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
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40
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Irwin D, Schluter D. Hybridization and the Coexistence of Species. Am Nat 2022; 200:E93-E109. [DOI: 10.1086/720365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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41
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Si X, Cadotte MW, Davies TJ, Antonelli A, Ding P, Svenning JC, Faurby S. Phylogenetic and functional clustering illustrate the roles of adaptive radiation and dispersal filtering in jointly shaping late-Quaternary mammal assemblages on oceanic islands. Ecol Lett 2022; 25:1250-1262. [PMID: 35275608 DOI: 10.1111/ele.13997] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 11/29/2021] [Accepted: 02/11/2022] [Indexed: 12/15/2022]
Abstract
Islands frequently harbour unique assemblages of species, yet their ecological roles and differences are largely ignored in island biogeography studies. Here, we examine eco-evolutionary processes structuring mammal assemblages on oceanic islands worldwide, including all extant and extinct late-Quaternary mammal species. We find island mammal assemblages tend to be phylogenetically clustered (share more recent evolutionary histories), with clustering increasing with island area and isolation. We also observe that mammal assemblages often tend to be functionally clustered (share similar traits), but the strength of clustering is weak and generally independent from island area or isolation. These findings indicate the important roles of in situ speciation and dispersal filtering in shaping island mammal assemblages under pre-anthropogenic conditions, notably through adaptive radiation of a few clades (e.g. bats, with generally high dispersal abilities). Our study demonstrates that considering the functional and phylogenetic axes of diversity can better reveal the eco-evolutionary processes of island community assembly.
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Affiliation(s)
- Xingfeng Si
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China.,Institute of Eco-Chongming (IEC), Shanghai, China
| | - Marc W Cadotte
- Department of Biological Sciences, University of Toronto-Scarborough, Toronto, Ontario, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - T Jonathan Davies
- Departments of Botany, and Forest & Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alexandre Antonelli
- Department of Biological & Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.,Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden.,Royal Botanic Gardens, Richmond, Surrey, UK.,Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Ping Ding
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jens-Christian Svenning
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, Aarhus C, Denmark.,Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, Aarhus C, Denmark
| | - Søren Faurby
- Department of Biological & Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.,Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
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42
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Freeman BG, Weeks T, Schluter D, Tobias JA. The latitudinal gradient in rates of evolution for bird beaks, a species interaction trait. Ecol Lett 2022; 25:635-646. [PMID: 35199924 DOI: 10.1111/ele.13726] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/21/2020] [Accepted: 02/11/2021] [Indexed: 11/29/2022]
Abstract
Where is evolution fastest? The biotic interactions hypothesis proposes that greater species richness creates more ecological opportunity, driving faster evolution at low latitudes, whereas the 'empty niches' hypothesis proposes that ecological opportunity is greater where diversity is low, spurring faster evolution at high latitudes. We tested these contrasting predictions by analysing rates of beak evolution for a global dataset of 1141 avian sister species. Rates of beak size evolution are similar across latitudes, with some evidence that beak shape evolves faster in the temperate zone, consistent with the empty niches hypothesis. The empty niches hypothesis is further supported by a meta-analysis showing that rates of trait evolution and recent speciation are generally faster in the temperate zone, whereas rates of molecular evolution are slightly faster in the tropics. Our results suggest that drivers of evolutionary diversification are either similar across latitudes or more potent in the temperate zone, thus calling into question multiple hypotheses that invoke faster tropical evolution to explain the latitudinal diversity gradient.
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Affiliation(s)
- Benjamin G Freeman
- Biodiversity Research Centre, University of British Columbia, Vancouver, Canada.,Department of Zoology, University of British Columbia, Vancouver, Canada
| | - Thomas Weeks
- Department of Life Sciences, Imperial College London, London, UK.,Department of Life Sciences, Natural History Museum, London, UK
| | - Dolph Schluter
- Biodiversity Research Centre, University of British Columbia, Vancouver, Canada.,Department of Zoology, University of British Columbia, Vancouver, Canada
| | - Joseph A Tobias
- Department of Life Sciences, Imperial College London, London, UK
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43
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Integrating Earth–life systems: a geogenomic approach. Trends Ecol Evol 2022; 37:371-384. [DOI: 10.1016/j.tree.2021.12.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 12/04/2021] [Accepted: 12/08/2021] [Indexed: 12/26/2022]
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44
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Singhal S, Colli GR, Grundler MR, Costa GC, Prates I, Rabosky DL. No link between population isolation and speciation rate in squamate reptiles. Proc Natl Acad Sci U S A 2022; 119:e2113388119. [PMID: 35058358 PMCID: PMC8795558 DOI: 10.1073/pnas.2113388119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 11/19/2021] [Indexed: 11/26/2022] Open
Abstract
Rates of species formation vary widely across the tree of life and contribute to massive disparities in species richness among clades. This variation can emerge from differences in metapopulation-level processes that affect the rates at which lineages diverge, persist, and evolve reproductive barriers and ecological differentiation. For example, populations that evolve reproductive barriers quickly should form new species at faster rates than populations that acquire reproductive barriers more slowly. This expectation implicitly links microevolutionary processes (the evolution of populations) and macroevolutionary patterns (the profound disparity in speciation rate across taxa). Here, leveraging extensive field sampling from the Neotropical Cerrado biome in a biogeographically controlled natural experiment, we test the role of an important microevolutionary process-the propensity for population isolation-as a control on speciation rate in lizards and snakes. By quantifying population genomic structure across a set of codistributed taxa with extensive and phylogenetically independent variation in speciation rate, we show that broad-scale patterns of species formation are decoupled from demographic and genetic processes that promote the formation of population isolates. Population isolation is likely a critical stage of speciation for many taxa, but our results suggest that interspecific variability in the propensity for isolation has little influence on speciation rates. These results suggest that other stages of speciation-including the rate at which reproductive barriers evolve and the extent to which newly formed populations persist-are likely to play a larger role than population isolation in controlling speciation rate variation in squamates.
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Affiliation(s)
- Sonal Singhal
- Department of Biology, California State University, Dominguez Hills, Carson, CA 90747;
| | - Guarino R Colli
- Departamento de Zoologia, Universidade de Brasília, Brasília, Distrito Federal 70910-900, Brazil
| | - Maggie R Grundler
- Department of Environmental Science, Policy, & Management, University of California, Berkeley, CA 94720
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720
| | - Gabriel C Costa
- Department of Biology and Environmental Sciences, Auburn University at Montgomery, Montgomery, AL 36117
| | - Ivan Prates
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109
- Museum of Zoology, University of Michigan, Ann Arbor, MI 48109
| | - Daniel L Rabosky
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109;
- Museum of Zoology, University of Michigan, Ann Arbor, MI 48109
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45
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Onditi KO, Song WY, Li XY, Chen ZZ, Li Q, He SW, Musila S, Kioko E, Jiang XL. Patterns and Predictors of Small Mammal Phylogenetic and Functional Diversity in Contrasting Elevational Gradients in Kenya. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2021.742524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Mountains of the Afrotropics are global biodiversity hotspots and centers of speciation and endemism; however, very few studies have focused on the phylogenetic and functional dimensions of Afromontane small mammals. We investigated the patterns and mechanisms of small mammal phylogenetic and functional diversity and assembly along elevational gradients in Mount Kenya, the second highest mountain in Africa, and a contrasting low mountain range, Chyulu Hills. We sampled 24 200-m interval transects in both sites; 18 in Mt. Kenya (9 each in the windward side, Chogoria, and the leeward side, Sirimon) and 6 in Chyulu. We extracted the mitochondrial Cytochrome b gene to reconstruct a time-calibrated species tree for estimating phylogenetic diversity indices [phylogenetic richness (PD), mean nearest taxon distance (PDMNTD), and nearest taxon index (PDNTI)]. A functional trait data set was compiled from the field-recorded measurements and published data sets for estimating functional diversity indices [functional richness (FD), mean nearest taxon distance (FDMNTD), and nearest taxon index (FDNTI)]. Several environmental variables representing water-energy availability, primary habitat productivity, and topographic heterogeneity were used to estimate the predictive power of abiotic conditions on diversity variances using generalized linear and generalized additive regression models. The PD and FD peaked around mid-elevations in Mt. Kenya, unimodally increased or decreased in Chogoria and Sirimon, and monotonically increased in Chyulu. The divergence and community structure indices—PDMNTD, FDMNTD, and PDNTI and FDNTI—were relatively weakly associated with elevation. Overall, the tendency of assemblages to be phylogenetically and functionally closely related than expected by chance decreased with elevation in Mt. Kenya but increased in Chyulu. Across the indices, the annual precipitation and topographic ruggedness were the strongest predictors in Mt. Kenya, evapotranspiration and temperature seasonality were the strongest predictors in Chyulu, while temperature seasonality and terrain ruggedness overlapped as the strongest predictors in Chogoria and Sirimon in addition to annual precipitation in the latter and normalized difference vegetation index in the former. The observed contrasting trends in diversity distribution and the strongest predictors between elevational gradients are integral to the sustainable management of the high faunal biodiversity in tropical Afromontane ecosystems.
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46
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Diversity of Land Snail Tribe Helicini (Gastropoda: Stylommatophora: Helicidae): Where Do We Stand after 20 Years of Sequencing Mitochondrial Markers? DIVERSITY 2021. [DOI: 10.3390/d14010024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Sequences of mitochondrial genes revolutionized the understanding of animal diversity and continue to be an important tool in biodiversity research. In the tribe Helicini, a prominent group of the western Palaearctic land snail fauna, mitochondrial data accumulating since the 2000s helped to newly delimit genera, inform species-level taxonomy and reconstruct past range dynamics. We combined the published data with own unpublished sequences and provide a detailed overview of what they revealed about the diversity of the group. The delimitation of Helix is revised by placing Helix godetiana back in the genus and new synonymies are suggested within the genera Codringtonia and Helix. The spatial distribution of intraspecific mitochondrial lineages of several species is shown for the first time. Comparisons between species reveal considerable variation in distribution patterns of intraspecific lineages, from broad postglacial distributions to regions with a fine-scale pattern of allopatric lineage replacement. To provide a baseline for further research and information for anyone re-using the data, we thoroughly discuss the gaps in the current dataset, focusing on both taxonomic and geographic coverage. Thanks to the wealth of data already amassed and the relative ease with which they can be obtained, mitochondrial sequences remain an important source of information on intraspecific diversity over large areas and taxa.
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47
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Biogeography of Long-Jawed Spiders Reveals Multiple Colonization of the Caribbean. DIVERSITY 2021. [DOI: 10.3390/d13120622] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Dispersal ability can affect levels of gene flow thereby shaping species distributions and richness patterns. The intermediate dispersal model of biogeography (IDM) predicts that in island systems, species diversity of those lineages with an intermediate dispersal potential is the highest. Here, we tested this prediction on long-jawed spiders (Tetragnatha) of the Caribbean archipelago using phylogenies from a total of 318 individuals delineated into 54 putative species. Our results support a Tetragnatha monophyly (within our sampling) but reject the monophyly of the Caribbean lineages, where we found low endemism yet high diversity. The reconstructed biogeographic history detects a potential early overwater colonization of the Caribbean, refuting an ancient vicariant origin of the Caribbean Tetragnatha as well as the GAARlandia land-bridge scenario. Instead, the results imply multiple colonization events to and from the Caribbean from the mid-Eocene to late-Miocene. Among arachnids, Tetragnatha uniquely comprises both excellently and poorly dispersing species. A direct test of the IDM would require consideration of three categories of dispersers; however, long-jawed spiders do not fit one of these three a priori definitions, but rather represent a more complex combination of attributes. A taxon such as Tetragnatha, one that readily undergoes evolutionary changes in dispersal propensity, can be referred to as a ‘dynamic disperser’.
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48
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Buitrago‐Guacaneme A, Molineri C, Cristóbal L, Dos Santos DA. The inter‐forest line could be the master key to track biocoenotic effects of climate change in a subtropical forest. Biotropica 2021. [DOI: 10.1111/btp.13026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
| | - Carlos Molineri
- Instituto de Biodiversidad Neotropical (UNT‐CONICET) Cúpulas Universitarias Tucumán Argentina
| | - Luciana Cristóbal
- Instituto de Biodiversidad Neotropical (UNT‐CONICET) Cúpulas Universitarias Tucumán Argentina
| | - Daniel Andrés Dos Santos
- Instituto de Biodiversidad Neotropical (UNT‐CONICET) Cúpulas Universitarias Tucumán Argentina
- Cátedra de Biología Animal Facultad de Ciencias Naturales Universidad Nacional de Tucumán Tucumán Argentina
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49
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Cerezer FO, Cáceres NC, Dambros CS. Effect of Productivity on Community Size Explains the Latitudinal Diversity Gradient of South American Small Mammals. Am Nat 2021; 198:E111-E121. [PMID: 34559610 DOI: 10.1086/716171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractAlthough many studies have shown that species richness increases from high to low latitudes (the latitudinal diversity gradient), the mechanisms responsible for generating and maintaining higher species richness in the tropics remain intensely debated. Here we investigate how the effects of temperature on speciation rates (kinetic effects) and the effects of productivity on community size (chemical effects) explain the latitudinal diversity gradient of South American small mammals. We implemented Bayesian models that integrate processes from the neutral and metabolic theories, comparing model predictions with empirical richness patterns. The neutral-metabolic model predicted the latitudinal richness gradient in South American small mammals. We found evidence that the effects of productivity on community size are more important for explaining differences in species richness than the effects of temperature on speciation rates. These results suggest that differences in species richness along latitudinal gradients are regulated primarily by the chemical effects of productivity on speciation-extinction dynamics.
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San Roman M, Wagner A. Diversity begets diversity during community assembly until ecological limits impose a diversity ceiling. Mol Ecol 2021; 30:5874-5887. [PMID: 34478597 PMCID: PMC9293205 DOI: 10.1111/mec.16161] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 08/17/2021] [Accepted: 08/20/2021] [Indexed: 12/20/2022]
Abstract
Microbial communities are hugely diverse, but we do not yet understand how species invasions and extinctions drive and limit their diversity. On the one hand, the ecological limits hypothesis posits that diversity is primarily limited by environmental resources. On the other hand, the diversity‐begets‐diversity hypothesis posits that such limits can be easily lifted when new ecological niches are created by biotic interactions. To find out which hypothesis better explains the assembly of microbial communities, we used metabolic modelling. We represent each microbial species by a metabolic network that harbours thousands of biochemical reactions. Together, these reactions determine which carbon and energy sources a species can use, and which metabolic by‐products—potential nutrients for other species—it can excrete in a given environment. We assemble communities by modelling thousands of species invasions in a chemostat‐like environment. We find that early during the assembly process, diversity begets diversity. By‐product excretion transforms a simple environment into one that can sustain dozens of species. During later assembly stages, the creation of new niches slows down, existing niches become filled, successful invasions become rare, and species diversity plateaus. Thus, ecological limitations dominate the late assembly process. We conclude that each hypothesis captures a different stage of the assembly process. Species interactions can raise a community's diversity ceiling dramatically, but only within limits imposed by the environment.
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Affiliation(s)
- Magdalena San Roman
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
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- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland.,The Santa Fe Institute, Santa Fe, NM, USA.,Stellenbosch Institute for Advanced Study, Wallenberg Research Centre at Stellenbosch University, Stellenbosch, South Africa
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