The most significant driver of adaptive radiation in the New World leaf‐nosed bats (Phyllostomidae) is their remarkably diverse feeding habits, yet there remains a notable scarcity of studies addressing the genetic underpinnings of dietary diversification in this family. In this study, we have assembled a new genome for a representative species of phyllostomid bat, the fringe‐lipped bat (Trachops cirrhosis), and integrated it with eight published phyllostomid genomes, along with an additional 10 genomes of other bat species. Comparative genomic analysis across 10 200 orthologus genes has unveiled that those genes subject to divergent selection within the Phyllostomidae clade are notably enriched in metabolism‐related pathways. Furthermore, we identified molecular signatures of divergent selection in the bitter receptor gene Tas2r1, as well as 14 genes involved in digesting key nutrients such as carbohydrates, proteins, and fats. In addition, our cell‐based functional assays conducted on Tas2r1 showed a broader spectrum of perception for bitter compounds in phyllostomids compared to nonphyllostomid bats, suggesting functional diversification of bitter taste in Phyllostomidae. Together, our genomic and functional analyses lead us to propose that divergent selection of genes associated with taste, digestion and absorption, and metabolism assumes a pivotal role in steering the extreme dietary diversification in Phyllostomidae. This study not only illuminates the genetic mechanisms underlying dietary adaptations in Phyllostomidae bats but also enhances our understanding of their extraordinary adaptive radiation.
{"title":"Genomic and functional insights into dietary diversification in New World leaf‐nosed bats (Phyllostomidae)","authors":"Yi‐Ran Xu, Ying‐Can Li, Hui‐Qiao Hu, Heng‐Wu Jiao, Hua‐Bin Zhao","doi":"10.1111/jse.13059","DOIUrl":"https://doi.org/10.1111/jse.13059","url":null,"abstract":"The most significant driver of adaptive radiation in the New World leaf‐nosed bats (Phyllostomidae) is their remarkably diverse feeding habits, yet there remains a notable scarcity of studies addressing the genetic underpinnings of dietary diversification in this family. In this study, we have assembled a new genome for a representative species of phyllostomid bat, the fringe‐lipped bat (<jats:italic>Trachops cirrhosis</jats:italic>), and integrated it with eight published phyllostomid genomes, along with an additional 10 genomes of other bat species. Comparative genomic analysis across 10 200 orthologus genes has unveiled that those genes subject to divergent selection within the Phyllostomidae clade are notably enriched in metabolism‐related pathways. Furthermore, we identified molecular signatures of divergent selection in the bitter receptor gene <jats:italic>Tas2r1</jats:italic>, as well as 14 genes involved in digesting key nutrients such as carbohydrates, proteins, and fats. In addition, our cell‐based functional assays conducted on <jats:italic>Tas2r1</jats:italic> showed a broader spectrum of perception for bitter compounds in phyllostomids compared to nonphyllostomid bats, suggesting functional diversification of bitter taste in Phyllostomidae. Together, our genomic and functional analyses lead us to propose that divergent selection of genes associated with taste, digestion and absorption, and metabolism assumes a pivotal role in steering the extreme dietary diversification in Phyllostomidae. This study not only illuminates the genetic mechanisms underlying dietary adaptations in Phyllostomidae bats but also enhances our understanding of their extraordinary adaptive radiation.","PeriodicalId":17087,"journal":{"name":"Journal of Systematics and Evolution","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140011211","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
East Asia constitutes one of the largest and most complex areas of plant diversity globally. This complexity is attributable to the geological history and climatic diversity of East Asia. However, controversy persists over the biogeographical hypotheses and different studies on this topic. The demographical complexity of temperate deciduous woody plants and heterogeneity of geological and climatic fluctuations in East Asia remain poorly understood. We aimed to assemble the chloroplast and nuclear genomes of 360 individuals from five walnut (Juglans) species in East Asia and comprehensively analyze the phylogenetic inference, genetic structure, population demographic, and selection pressure. The results showed that East Asian walnuts could be divided into two major groups, that is, section Juglans/Dioscaryon and sect. Cardiocaryon. Within sect. Cardiocaryon, the samples were categorized into the northern clade and southern clade, both of which were affected by Quaternary glaciation; however, the southern clade was affected to a lesser extent. The population expansion events observed in sect. Cardiocaryon and sect. Dioscaryon since the late Miocene indicated that Neogene climate cooling substantially affected the distribution of Tertiary relict plants in East Asia. Biogeographic analysis results showed that the uplift of the Qinghai–Tibetan Plateau (QTP) might have contributed to the divergence within sect. Dioscaryon. Our findings highlight the heterogeneity of climatic fluctuations in the northern and southern regions of East Asia during the late Neogene and Quaternary periods and suggest that the uplift of QTP could have facilitated the divergence of temperate deciduous woody plants.
{"title":"Demographical complexity within walnut species provides insights into the heterogeneity of geological and climatic fluctuations in East Asia","authors":"Fang‐Dong Geng, Meng‐Fan Lei, Nai‐Yu Zhang, Yao‐Lei Fu, Hang Ye, Meng Dang, Xue‐Dong Zhang, Miao‐Qing Liu, Meng‐Di Li, Zhan‐Lin Liu, Peng Zhao","doi":"10.1111/jse.13061","DOIUrl":"https://doi.org/10.1111/jse.13061","url":null,"abstract":"East Asia constitutes one of the largest and most complex areas of plant diversity globally. This complexity is attributable to the geological history and climatic diversity of East Asia. However, controversy persists over the biogeographical hypotheses and different studies on this topic. The demographical complexity of temperate deciduous woody plants and heterogeneity of geological and climatic fluctuations in East Asia remain poorly understood. We aimed to assemble the chloroplast and nuclear genomes of 360 individuals from five walnut (<jats:italic>Juglans</jats:italic>) species in East Asia and comprehensively analyze the phylogenetic inference, genetic structure, population demographic, and selection pressure. The results showed that East Asian walnuts could be divided into two major groups, that is, section <jats:italic>Juglans</jats:italic>/<jats:italic>Dioscaryon</jats:italic> and sect. <jats:italic>Cardiocaryon</jats:italic>. Within sect. <jats:italic>Cardiocaryon</jats:italic>, the samples were categorized into the northern clade and southern clade, both of which were affected by Quaternary glaciation; however, the southern clade was affected to a lesser extent. The population expansion events observed in sect. <jats:italic>Cardiocaryon</jats:italic> and sect. <jats:italic>Dioscaryon</jats:italic> since the late Miocene indicated that Neogene climate cooling substantially affected the distribution of Tertiary relict plants in East Asia. Biogeographic analysis results showed that the uplift of the Qinghai–Tibetan Plateau (QTP) might have contributed to the divergence within sect. <jats:italic>Dioscaryon</jats:italic>. Our findings highlight the heterogeneity of climatic fluctuations in the northern and southern regions of East Asia during the late Neogene and Quaternary periods and suggest that the uplift of QTP could have facilitated the divergence of temperate deciduous woody plants.","PeriodicalId":17087,"journal":{"name":"Journal of Systematics and Evolution","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140011448","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The Sui people living in Guizhou province have a unique ethnic culture and population history due to their long‐time isolation from other populations. To investigate the genetic structure of Sui populations in different regions of Guizhou, we genotyped 89 individuals from four Sui populations using genome‐wide single nucleotide polymorphisms arrays. We analyzed the data using principal component analysis, ADMIXTURE analysis, f‐statistics, qpWave/qpAdm, TreeMix analysis, fineSTRUCTURE, and GLOBETROTTER. We found that Sui populations in Guizhou were genetically homogeneous and had a close genetic affinity with Tai‐Kadai‐speaking populations, Hmong‐Mien‐speaking Hmong, and some ancient populations from southern China. The Sui populations could be modeled as an admixture of 33.5%–37.9% of Yellow River Basin farmer‐related ancestry and 62.1%–66.5% of Southeast Asian‐related ancestry, indicating that the southward expansion of northern East Asian‐related ancestry influenced the formation of the Tai‐Kadai‐speaking Sui people. Future publications of more ancient genomics in southern China could effectively provide further insight into the demographic history and population structure of the Sui people.
{"title":"Genetic formation of Sui populations in southwest China","authors":"Ming‐Xia Xie, Xing‐Yue Hu, Qi‐Yang Wang, Zheng Ren, Yu‐Bo Liu, Mei‐Qing Yang, Xiao‐Ye Jin, Xiao‐Min Yang, Rui Wang, Chuan‐Chao Wang, Jiang Huang","doi":"10.1111/jse.13056","DOIUrl":"https://doi.org/10.1111/jse.13056","url":null,"abstract":"The Sui people living in Guizhou province have a unique ethnic culture and population history due to their long‐time isolation from other populations. To investigate the genetic structure of Sui populations in different regions of Guizhou, we genotyped 89 individuals from four Sui populations using genome‐wide single nucleotide polymorphisms arrays. We analyzed the data using principal component analysis, ADMIXTURE analysis, <jats:italic>f</jats:italic>‐statistics, <jats:italic>qpWave/qpAdm</jats:italic>, TreeMix analysis, fineSTRUCTURE, and GLOBETROTTER. We found that Sui populations in Guizhou were genetically homogeneous and had a close genetic affinity with Tai‐Kadai‐speaking populations, Hmong‐Mien‐speaking Hmong, and some ancient populations from southern China. The Sui populations could be modeled as an admixture of 33.5%–37.9% of Yellow River Basin farmer‐related ancestry and 62.1%–66.5% of Southeast Asian‐related ancestry, indicating that the southward expansion of northern East Asian‐related ancestry influenced the formation of the Tai‐Kadai‐speaking Sui people. Future publications of more ancient genomics in southern China could effectively provide further insight into the demographic history and population structure of the Sui people.","PeriodicalId":17087,"journal":{"name":"Journal of Systematics and Evolution","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140011450","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yang Yue, Da-Hu Zou, Shi-Lin Tian, Heng-Wu Jiao, Hua-Bin Zhao
Dietary specialization stands as a major factor in the study of adaptive evolution and the field of conservation biology among animals. Although bats show unparalleled dietary diversification among mammals, specialized carnivory remains relatively rare within this group. Consequently, our comprehension of the genetic and conservation aspects associated with this specific dietary niche in bats has largely remained uncharted. To investigate molecular adaptations and conservation genetics in carnivorous bats, we produced a new draft genome assembly for the carnivorous bat Vampyrum spectrum. Furthermore, we utilized this genome alongside another distantly related carnivorous bat Megaderma lyra, to conduct genome-wide comparative analyses with other bat species. Our findings unveil that genes linked to lipid metabolism exhibit signatures of positive selection and convergent molecular adaptation in the two divergent lineages of carnivorous bats. Intriguingly, we have uncovered that the evolution of dietary specialization in carnivorous bats is accompanied by molecular adaptations acting on genes in the peroxisome proliferator-activated receptors pathways, which are crucial in regulating plasma lipid metabolism and sustaining lipid homeostasis. Additionally, our genomic analyses also reveal low genetic diversity in both carnivorous bat species. This pattern is attributed to their continuously declining population sizes and low levels of heterozygosity, signaling their vulnerability and emphasizing the pressing need for conservation efforts. These genomic discoveries advance our understanding of genetic underpinnings of carnivory in bats and underscore substantial conservation concerns associated with carnivorous bat species.
{"title":"Comparative genomics reveals convergent adaptations in lipid metabolism and low genetic diversity in carnivorous bats","authors":"Yang Yue, Da-Hu Zou, Shi-Lin Tian, Heng-Wu Jiao, Hua-Bin Zhao","doi":"10.1111/jse.13060","DOIUrl":"https://doi.org/10.1111/jse.13060","url":null,"abstract":"Dietary specialization stands as a major factor in the study of adaptive evolution and the field of conservation biology among animals. Although bats show unparalleled dietary diversification among mammals, specialized carnivory remains relatively rare within this group. Consequently, our comprehension of the genetic and conservation aspects associated with this specific dietary niche in bats has largely remained uncharted. To investigate molecular adaptations and conservation genetics in carnivorous bats, we produced a new draft genome assembly for the carnivorous bat <i>Vampyrum spectrum</i>. Furthermore, we utilized this genome alongside another distantly related carnivorous bat <i>Megaderma lyra</i>, to conduct genome-wide comparative analyses with other bat species. Our findings unveil that genes linked to lipid metabolism exhibit signatures of positive selection and convergent molecular adaptation in the two divergent lineages of carnivorous bats. Intriguingly, we have uncovered that the evolution of dietary specialization in carnivorous bats is accompanied by molecular adaptations acting on genes in the peroxisome proliferator-activated receptors pathways, which are crucial in regulating plasma lipid metabolism and sustaining lipid homeostasis. Additionally, our genomic analyses also reveal low genetic diversity in both carnivorous bat species. This pattern is attributed to their continuously declining population sizes and low levels of heterozygosity, signaling their vulnerability and emphasizing the pressing need for conservation efforts. These genomic discoveries advance our understanding of genetic underpinnings of carnivory in bats and underscore substantial conservation concerns associated with carnivorous bat species.","PeriodicalId":17087,"journal":{"name":"Journal of Systematics and Evolution","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139987759","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Roser Vilatersana, Juan Antonio Calleja, Sonia Herrando‐Moraira, Núria Garcia‐Jacas, Alfonso Susanna
Understanding the richness and diversification processes in the Mediterranean basin requires both knowledge of the current environmental complexity and paleogeographic and paleoclimate events and information from studies that introduce the temporal dimension. The Carthamus–Carduncellus complex (Cardueae, Compositae) constitutes a good case study to investigate the biogeographic history of this region because it evolved throughout the basin. We performed molecular dating, ancestral area estimation, and diversification analyses based on previous phylogenetic studies of a nearly complete taxon sampling of the complex. The main aims were to determine the role of tectonic and climatic events in the disjunction of the complex and the expansion route of the two main lineages, Carduncellus s.l. and Carthamus. Our results suggest that the main lineages in the complex originated during the Miocene. Later, all main paleogeographic and paleoclimatic events during the Neogene and Pleistocene in the Mediterranean basin had an important imprint on the evolutionary history of the complex. The Messinian Salinity Crisis facilitated the dispersion of the genus Carduncellus from North Africa to the Iberian Peninsula and the split of the genera Phonus and Femeniasia from the Carduncellus lineage. The onset of the Mediterranean climate in the Pliocene together with some orogenic processes could be the main causes of the diversification of the genus Carduncellus. In contrast, Pleistocene glaciations played a key role in the species diversification of Carthamus. In addition, we emphasize the problems derived from secondary dating and the existing differences between two previous dating analyses of the tribe Cardueae.
{"title":"Untangling the origin and diversification of the Carthamus–Carduncellus complex (Cardueae, Compositae) in the Mediterranean basin","authors":"Roser Vilatersana, Juan Antonio Calleja, Sonia Herrando‐Moraira, Núria Garcia‐Jacas, Alfonso Susanna","doi":"10.1111/jse.13057","DOIUrl":"https://doi.org/10.1111/jse.13057","url":null,"abstract":"Understanding the richness and diversification processes in the Mediterranean basin requires both knowledge of the current environmental complexity and paleogeographic and paleoclimate events and information from studies that introduce the temporal dimension. The <jats:italic>Carthamus–Carduncellus</jats:italic> complex (Cardueae, Compositae) constitutes a good case study to investigate the biogeographic history of this region because it evolved throughout the basin. We performed molecular dating, ancestral area estimation, and diversification analyses based on previous phylogenetic studies of a nearly complete taxon sampling of the complex. The main aims were to determine the role of tectonic and climatic events in the disjunction of the complex and the expansion route of the two main lineages, <jats:italic>Carduncellus</jats:italic> s.l. and <jats:italic>Carthamus</jats:italic>. Our results suggest that the main lineages in the complex originated during the Miocene. Later, all main paleogeographic and paleoclimatic events during the Neogene and Pleistocene in the Mediterranean basin had an important imprint on the evolutionary history of the complex. The Messinian Salinity Crisis facilitated the dispersion of the genus <jats:italic>Carduncellus</jats:italic> from North Africa to the Iberian Peninsula and the split of the genera <jats:italic>Phonus</jats:italic> and <jats:italic>Femeniasia</jats:italic> from the <jats:italic>Carduncellus</jats:italic> lineage. The onset of the Mediterranean climate in the Pliocene together with some orogenic processes could be the main causes of the diversification of the genus <jats:italic>Carduncellus</jats:italic>. In contrast, Pleistocene glaciations played a key role in the species diversification of <jats:italic>Carthamus</jats:italic>. In addition, we emphasize the problems derived from secondary dating and the existing differences between two previous dating analyses of the tribe Cardueae.","PeriodicalId":17087,"journal":{"name":"Journal of Systematics and Evolution","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139949720","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pterocarya (Juglandaceae) is disjunctly distributed in East Asia and the Caucasus region today, but its fossils are widely distributed in the Northern Hemisphere. We first inferred phylogeny with time estimation of Pterocarya under node‐dating (ND) based on plastomes of all eight extant species and tip‐dating (TD) based on plastomes and 69 morphological characters of 19 extant and extinct species, respectively. We compared the biogeographical reconstructions on the timetrees from ND and TD, respectively, and then compiled 83 fossil records and 599 current occurrences for predicting the potential distributions for the past and the future. The most recent comment ancestor of Pterocarya is inferred in East Asia at 40.46 Ma (95% highest posterior density [HPD]: 28.04–54.86) under TD and 26.81 Ma (95% HPD: 23.03–33.12) under ND. The current distribution was attributed to one dispersal and one vicariant event without fossils, but as many as six dispersal, six vicariant, and 11 local extinction events when considering fossils. Pterocarya migrated between East Asia and North America via the Bering Land Bridge during the early Oligocene and the early Miocene periods. With the closure of Turgai Strait, Pterocarya dispersed between East Asia and Europe through the Miocene. The potential distribution analyses indicated that Pterocarya preferred warm temperate regions across the Northern Hemisphere since the Oligocene, but the drastic temperature decline caused its extinction in high latitudes. Except for Pterocarya fraxinifolia and Pterocarya stenoptera, suitable habitats for this genus are predicted to contract by 2070 due to climate change.
{"title":"Biogeographic history of Pterocarya (Juglandaceae) inferred from phylogenomic and fossil data","authors":"Hua Yan, Peng Zhou, Wei Wang, Jian‐Fei Ye, Shao‐Lin Tan, Chun‐Ce Guo, Wen‐Gen Zhang, Zi‐Wei Zhu, Yi‐Zhen Liu, Xiao‐Guo Xiang","doi":"10.1111/jse.13055","DOIUrl":"https://doi.org/10.1111/jse.13055","url":null,"abstract":"<jats:italic>Pterocarya</jats:italic> (Juglandaceae) is disjunctly distributed in East Asia and the Caucasus region today, but its fossils are widely distributed in the Northern Hemisphere. We first inferred phylogeny with time estimation of <jats:italic>Pterocarya</jats:italic> under node‐dating (ND) based on plastomes of all eight extant species and tip‐dating (TD) based on plastomes and 69 morphological characters of 19 extant and extinct species, respectively. We compared the biogeographical reconstructions on the timetrees from ND and TD, respectively, and then compiled 83 fossil records and 599 current occurrences for predicting the potential distributions for the past and the future. The most recent comment ancestor of <jats:italic>Pterocarya</jats:italic> is inferred in East Asia at 40.46 Ma (95% highest posterior density [HPD]: 28.04–54.86) under TD and 26.81 Ma (95% HPD: 23.03–33.12) under ND. The current distribution was attributed to one dispersal and one vicariant event without fossils, but as many as six dispersal, six vicariant, and 11 local extinction events when considering fossils. <jats:italic>Pterocarya</jats:italic> migrated between East Asia and North America via the Bering Land Bridge during the early Oligocene and the early Miocene periods. With the closure of Turgai Strait, <jats:italic>Pterocarya</jats:italic> dispersed between East Asia and Europe through the Miocene. The potential distribution analyses indicated that <jats:italic>Pterocarya</jats:italic> preferred warm temperate regions across the Northern Hemisphere since the Oligocene, but the drastic temperature decline caused its extinction in high latitudes. Except for <jats:italic>Pterocarya fraxinifolia</jats:italic> and <jats:italic>Pterocarya stenoptera</jats:italic>, suitable habitats for this genus are predicted to contract by 2070 due to climate change.","PeriodicalId":17087,"journal":{"name":"Journal of Systematics and Evolution","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139949625","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Luísa Azevedo, Daniela Cristina Zappi, Daniela Melo Garcia de Oliveira, Leila Meyer, Eimear Nic Lughadha, Rosie Clegg, Leonardo Dias Meireles, Pablo Hendrigo Alves de Melo, R. Toby Pennington, Danilo M. Neves
The geodiversity of rocky ecosystems includes diverse plant communities with specific names, but their continental‐scale floristic identity and the knowledge on the role of macroclimate remain patchy. Here, we assessed the identity of plant communities in eastern Brazil across multiple types of rocky landscapes and evaluated the relative importance of climatic variables in constraining floristic differentiation. We provided lists of diagnostic species and an assessment of the conservation status of the identified floristic groups. We compiled a data set of 151 sites (4498 species) from rocky ecosystems, including campos rupestres, campos de altitude, granitic‐gneiss lowland inselbergs, and limestone outcrops. We used unsupervised clustering analysis followed by ANOSIM to assess floristic groups among sites. We performed a random forest variable selection to test whether the identified floristic groups occupy distinct climatic spaces. Six groups (lithobiomes) segregated floristically according to lithology and climate. Alongside campos de altitude and limestone outcrops, inselbergs were divided according to the biome in which they occur (Atlantic Forest or Caatinga), and campos rupestres were largely segregated according to their lithological matrix (ironstone or quartzitic). Plant communities of Caatinga inselbergs were more similar to limestone outcrops, while Atlantic Forest inselbergs communities resembled campos de altitude. The composition of plant communities on outcrops seems to be largely constrained by lithology, but climatic factors are also meaningful for sites with similar lithology. The current network of protected areas does not cover these unique ecosystems and their floristic heterogeneity, with Caatinga inselbergs and limestone outcrops being the least protected.
{"title":"On the rocks: Biogeography and floristic identity of rocky ecosystems in eastern South America","authors":"Luísa Azevedo, Daniela Cristina Zappi, Daniela Melo Garcia de Oliveira, Leila Meyer, Eimear Nic Lughadha, Rosie Clegg, Leonardo Dias Meireles, Pablo Hendrigo Alves de Melo, R. Toby Pennington, Danilo M. Neves","doi":"10.1111/jse.13052","DOIUrl":"https://doi.org/10.1111/jse.13052","url":null,"abstract":"The geodiversity of rocky ecosystems includes diverse plant communities with specific names, but their continental‐scale floristic identity and the knowledge on the role of macroclimate remain patchy. Here, we assessed the identity of plant communities in eastern Brazil across multiple types of rocky landscapes and evaluated the relative importance of climatic variables in constraining floristic differentiation. We provided lists of diagnostic species and an assessment of the conservation status of the identified floristic groups. We compiled a data set of 151 sites (4498 species) from rocky ecosystems, including <jats:italic>campos rupestres, campos de altitude</jats:italic>, granitic‐gneiss lowland inselbergs, and limestone outcrops. We used unsupervised clustering analysis followed by ANOSIM to assess floristic groups among sites. We performed a random forest variable selection to test whether the identified floristic groups occupy distinct climatic spaces. Six groups (lithobiomes) segregated floristically according to lithology and climate. Alongside <jats:italic>campos de altitude</jats:italic> and limestone outcrops, inselbergs were divided according to the biome in which they occur (Atlantic Forest or Caatinga), and <jats:italic>campos rupestres</jats:italic> were largely segregated according to their lithological matrix (ironstone or quartzitic). Plant communities of Caatinga inselbergs were more similar to limestone outcrops, while Atlantic Forest inselbergs communities resembled <jats:italic>campos de altitude</jats:italic>. The composition of plant communities on outcrops seems to be largely constrained by lithology, but climatic factors are also meaningful for sites with similar lithology. The current network of protected areas does not cover these unique ecosystems and their floristic heterogeneity, with Caatinga inselbergs and limestone outcrops being the least protected.","PeriodicalId":17087,"journal":{"name":"Journal of Systematics and Evolution","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139949718","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jay Edneil C. Olivar, Frank Hauenschild, Hannah J. Atkins, Gemma L.C. Bramley, Alexandra N. Muellner‐Riehl
The general dynamic model (GDM) of oceanic island biogeography views oceanic islands predominantly as sinks rather than sources of dispersing lineages. To test this, we conducted a biogeographic analysis of a highly successful insular plant taxon, Cyrtandra, and inferred the directionality of dispersal and founder events throughout the four biogeographical units of the Indo‐Australian Archipelago (IAA), namely Sunda, Wallacea, Philippines, and Sahul. Sunda was recovered as the major source area, followed by Wallacea, a system of oceanic islands. The relatively high number of events originating from Wallacea is attributed to its central location in the IAA and its complex geological history selecting for increased dispersibility. We also tested if diversification dynamics in Cyrtandra follow predictions of adaptive radiation, which is the dominant process as per the GDM. Diversification dynamics of dispersing lineages of Cyrtandra in the Southeast Asian grade showed early bursts followed by a plateau, which is consistent with adaptive radiation. We did not detect signals of diversity‐dependent diversification, and this is attributed to Southeast Asian cyrtandras occupying various niche spaces, evident by their wide morphological range in habit and floral characters. The Pacific clade, which arrived at the immaturity phase of the Pacific Islands, showed diversification dynamics predicted by the island immaturity speciation pulse model (IISP), wherein rates increase exponentially, and their morphological range is controlled by the least action effect favoring woodiness and fleshy fruits. Our study provides a first step toward a framework for investigating diversification dynamics as predicted by the GDM in highly successful insular taxa.
{"title":"Early diversification dynamics in a highly successful insular plant taxon are consistent with the general dynamic model of oceanic island biogeography","authors":"Jay Edneil C. Olivar, Frank Hauenschild, Hannah J. Atkins, Gemma L.C. Bramley, Alexandra N. Muellner‐Riehl","doi":"10.1111/jse.13049","DOIUrl":"https://doi.org/10.1111/jse.13049","url":null,"abstract":"The general dynamic model (GDM) of oceanic island biogeography views oceanic islands predominantly as sinks rather than sources of dispersing lineages. To test this, we conducted a biogeographic analysis of a highly successful insular plant taxon, <jats:italic>Cyrtandra</jats:italic>, and inferred the directionality of dispersal and founder events throughout the four biogeographical units of the Indo‐Australian Archipelago (IAA), namely Sunda, Wallacea, Philippines, and Sahul. Sunda was recovered as the major source area, followed by Wallacea, a system of oceanic islands. The relatively high number of events originating from Wallacea is attributed to its central location in the IAA and its complex geological history selecting for increased dispersibility. We also tested if diversification dynamics in <jats:italic>Cyrtandra</jats:italic> follow predictions of adaptive radiation, which is the dominant process as per the GDM. Diversification dynamics of dispersing lineages of <jats:italic>Cyrtandra</jats:italic> in the Southeast Asian grade showed early bursts followed by a plateau, which is consistent with adaptive radiation. We did not detect signals of diversity‐dependent diversification, and this is attributed to Southeast Asian cyrtandras occupying various niche spaces, evident by their wide morphological range in habit and floral characters. The Pacific clade, which arrived at the immaturity phase of the Pacific Islands, showed diversification dynamics predicted by the island immaturity speciation pulse model (IISP), wherein rates increase exponentially, and their morphological range is controlled by the least action effect favoring woodiness and fleshy fruits. Our study provides a first step toward a framework for investigating diversification dynamics as predicted by the GDM in highly successful insular taxa.","PeriodicalId":17087,"journal":{"name":"Journal of Systematics and Evolution","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139949923","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ana M. Bossa‐Castro, Matheus Colli‐Silva, José R. Pirani, Barbara A. Whitlock, Laura T. Morales Mancera, Natalia Contreras‐Ortiz, Martha L. Cepeda‐Hernández, Federica Di Palma, Martha Vives, James E. Richardson
Crop wild relatives (CWRs) of cultivated species may provide a source of genetic variation that can contribute to improving product quantity and quality. To adequately use these potential resources, it is useful to understand how CWRs are related to the cultivated species and to each other to determine how key crop traits have evolved and discover potentially usable genetic information. The chocolate industry is expanding and yet is under threat from a variety of causes, including pathogens and climate change. Theobroma cacao L. (Malvaceae), the source of chocolate, is a representative of the tribe Theobromateae that consists of four genera and c. 40 species that began to diversify over 25 million years ago. The great diversity within the tribe suggests that its representatives could exhibit advantageous agronomic traits. In this study, we present the most taxonomically comprehensive phylogeny of Theobromateae to date. DNA sequence data from WRKY genes were assembled into a matrix that included 56 morphological characters and analyzed using a Bayesian approach. The inclusion of a morphological data set increased resolution and support for some branches of the phylogenetic tree. The evolutionary trajectory of selected morphological characters was reconstructed onto the phylogeny. This phylogeny provides a framework for the study of morphological and physiological trait evolution, which can facilitate the search for agronomically relevant traits.
{"title":"A phylogenetic framework to study desirable traits in the wild relatives of Theobroma cacao (Malvaceae)","authors":"Ana M. Bossa‐Castro, Matheus Colli‐Silva, José R. Pirani, Barbara A. Whitlock, Laura T. Morales Mancera, Natalia Contreras‐Ortiz, Martha L. Cepeda‐Hernández, Federica Di Palma, Martha Vives, James E. Richardson","doi":"10.1111/jse.13045","DOIUrl":"https://doi.org/10.1111/jse.13045","url":null,"abstract":"Crop wild relatives (CWRs) of cultivated species may provide a source of genetic variation that can contribute to improving product quantity and quality. To adequately use these potential resources, it is useful to understand how CWRs are related to the cultivated species and to each other to determine how key crop traits have evolved and discover potentially usable genetic information. The chocolate industry is expanding and yet is under threat from a variety of causes, including pathogens and climate change. <jats:italic>Theobroma cacao</jats:italic> L. (Malvaceae), the source of chocolate, is a representative of the tribe Theobromateae that consists of four genera and <jats:italic>c</jats:italic>. 40 species that began to diversify over 25 million years ago. The great diversity within the tribe suggests that its representatives could exhibit advantageous agronomic traits. In this study, we present the most taxonomically comprehensive phylogeny of Theobromateae to date. DNA sequence data from <jats:italic>WRKY</jats:italic> genes were assembled into a matrix that included 56 morphological characters and analyzed using a Bayesian approach. The inclusion of a morphological data set increased resolution and support for some branches of the phylogenetic tree. The evolutionary trajectory of selected morphological characters was reconstructed onto the phylogeny. This phylogeny provides a framework for the study of morphological and physiological trait evolution, which can facilitate the search for agronomically relevant traits.","PeriodicalId":17087,"journal":{"name":"Journal of Systematics and Evolution","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139949623","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Alba Rodríguez-Pacheco, Victoria Formoso-Freire, M. Olalla Lorenzo-Carballa, Andrés Baselga, Carola Gómez-Rodríguez
Given the sensitivity of mountain biodiversity to human pressure, it is essential to quantify changes in montane biological communities and contrast them with expectations based on potential drivers of change. This need is particularly pressing for biological groups representing important but little-studied fractions of biodiversity, such as insects. We analyze the temporal changes (between 1998 and 2015) of leaf beetle communities in an altitudinal gradient in the Sierra de Ancares (NW Spain). Our results show temporal changes in the composition of local communities, with a tendency to assemblage thermophilization, as well as a homogenization of the spatial turnover pattern, mostly driven by an increased similarity between communities at the lower and intermediate altitudes. These temporal changes in community composition and in the spatial structure of biodiversity were associated with upward shifts of the upper altitudinal limit of warm-adapted species and with downward shifts of the lower altitudinal limit of cold-adapted species. While this upward shift is consistent with expectations of climate change effects, the observed downward shift suggests a land-use change effect. Our results point to the joint effect of multiple factors (climate and land-use change) behind temporal changes of these leaf beetle communities, which result in compositional reorganization and biotic homogenization, rather than a mere coherent displacement toward higher altitudes. More generally, we show that understanding temporal change of biodiversity requires assessing multiple community-level metrics (e.g., variation in assemblage composition and/or changes in spatial turnover) for the detection of tendencies among the species-specific signals (e.g., altitudinal range shifts).
{"title":"Thermophilization and reshuffling of montane leaf beetle communities over a two-decade period","authors":"Alba Rodríguez-Pacheco, Victoria Formoso-Freire, M. Olalla Lorenzo-Carballa, Andrés Baselga, Carola Gómez-Rodríguez","doi":"10.1111/jse.13054","DOIUrl":"https://doi.org/10.1111/jse.13054","url":null,"abstract":"Given the sensitivity of mountain biodiversity to human pressure, it is essential to quantify changes in montane biological communities and contrast them with expectations based on potential drivers of change. This need is particularly pressing for biological groups representing important but little-studied fractions of biodiversity, such as insects. We analyze the temporal changes (between 1998 and 2015) of leaf beetle communities in an altitudinal gradient in the Sierra de Ancares (NW Spain). Our results show temporal changes in the composition of local communities, with a tendency to assemblage thermophilization, as well as a homogenization of the spatial turnover pattern, mostly driven by an increased similarity between communities at the lower and intermediate altitudes. These temporal changes in community composition and in the spatial structure of biodiversity were associated with upward shifts of the upper altitudinal limit of warm-adapted species and with downward shifts of the lower altitudinal limit of cold-adapted species. While this upward shift is consistent with expectations of climate change effects, the observed downward shift suggests a land-use change effect. Our results point to the joint effect of multiple factors (climate and land-use change) behind temporal changes of these leaf beetle communities, which result in compositional reorganization and biotic homogenization, rather than a mere coherent displacement toward higher altitudes. More generally, we show that understanding temporal change of biodiversity requires assessing multiple community-level metrics (e.g., variation in assemblage composition and/or changes in spatial turnover) for the detection of tendencies among the species-specific signals (e.g., altitudinal range shifts).","PeriodicalId":17087,"journal":{"name":"Journal of Systematics and Evolution","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139752933","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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