Geographic And Taxonomic Occurrence R‐based Scrubbing (gatoRs): An R package and workflow for processing biodiversity data

Applications in Plant Sciences, Journal Year: 2024, Volume and Issue: 12(2)

Published: March 1, 2024

Abstract Premise Digitized biodiversity data offer extensive information; however, obtaining and processing can be daunting. Complexities arise during cleaning, such as identifying removing problematic records. To address these issues, we created the R package Geographic And Taxonomic Occurrence R‐based Scrubbing (gatoRs). Methods Results The gatoRs workflow includes functions that streamline downloading records from Global Biodiversity Information Facility (GBIF) Integrated Biocollections (iDigBio). We also to clean downloaded specimen Unlike previous packages, accounts for differences in download structure between GBIF iDigBio allows user control via interactive cleaning steps. Conclusions Our pipeline enables scientific community process efficiently is accessible coding novice. anticipate will useful both established beginning users. Furthermore, expect our facilitate introduction of biodiversity‐related concepts into classroom use herbarium specimens.

Language: Английский

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The Ecological Risks and Invasive Potential of Introduced Ornamental Plants in China

Plants, Journal Year: 2025, Volume and Issue: 14(9), P. 1361 - 1361

Published: April 30, 2025

The import of ornamental plants has become a major source alien invasive in China, posing threats to local ecosystems. However, research on their potential and management strategies remains limited. This study evaluated the invasion risks nine representative introduced (including naturalized species) China (IOPCs). Using ecospat perform climatic niche comparisons, we found significant unfilling expansion (>50%) most plants, indicating strong invasiveness. Species distribution models (SDMs) were applied predict current future distributions these IOPCs under four shared socioeconomic pathways (SSPs: SSP1-2.6, SSP2-4.5, SSP3-7.0, SSP5-8.5) across time periods (2021–2040, 2041–2060, 2061–2080, 2081–2100). SDM results showed that high-risk areas are concentrated southern China. Under climate change, moderate- zones projected shift northward, with total increasing significantly, namely moderate-risk by 106.10% 64.35%, particularly border regions Jiangxi, Fujian, Zhejiang. We recommend establishing restricted introduction lists for non-native enhancing monitoring regions, implementing early eradication measures. quantified providing scientific basis effective control strategies.

Language: Английский

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RAD‐seq data provide new insights into biogeography, diversity anomaly, and species delimitation in eastern Asian–North American disjunct clade Benthamidia of Cornus (Cornaceae)

Journal of Systematics and Evolution, Journal Year: 2023, Volume and Issue: 62(1), P. 1 - 19

Published: Dec. 13, 2023

Abstract The big‐bracted dogwood clade Benthamidia of Cornus is a typical example the well‐known eastern Asia (EA) and North America (NA) floristic disjunction, with greater species diversity in EA than NA. lineage provides an opportunity to explore factors contributing plant unevenness between NA test hypotheses on origin disjunct distribution from phylogenetic perspective. We generated RAD‐seq data, conducted phylogenomic biogeographic analyses for sampling all (9) subspecies (10) currently recognized floras. also assessed delineation calculated evaluate Finally, we examined variation diversification rates ecological niches phylogeny potential causes underlying observed pattern. Our results revealed relationships congruent previous studies suggested trans‐Beringian ancestral mid‐Oligocene, dispersal Mexico United States mid‐Miocene, early SW China. confirmed rate clade. Species delimitation analysis 17 , including subspecies. By integrating molecular data morphology, proposed retain without changing their ranks. increased as intrinsic factor explaining region driven mainly by isolation partially niche divergence.

Language: Английский

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An updated phylogeny, biogeography, and PhyloCode‐based classification of Cornaceae based on three sets of genomic data

American Journal of Botany, Journal Year: 2022, Volume and Issue: 110(2)

Published: Dec. 8, 2022

A major goal of systematic biology is to uncover the evolutionary history organisms and translate that knowledge into stable classification systems. Here, we integrate three sets genome-wide data resolve phylogenetic relationships in Cornaceae (containing only Cornus s.l.), reconstruct biogeographic clade, provide a revised using PhyloCode stabilize names for this taxonomically controversial group.We conducted analyses 312 single-copy nuclear genes 70 plastid from Angiosperms353 Hyb-Seq, plus numerous loci RAD-Seq. We integrated fossils morphological produced dated phylogeny biogeographical analysis.A well-resolved, strongly supported, comprehensive was obtained. Biogeographic support an origin rapid diversification four morphologically distinct clades Northern Hemisphere (with eastern Asian ancestor) during late Cretaceous. Dispersal Africa Asia likely occurred along Tethys Seaway Paleogene, whereas dispersal South America Neogene. Diversification within northern hemisphere involved repeated independent colonization new areas Paleogene Neogene Bering Land Bridge, North Atlantic Seaway. Thirteen supported were named following rules PhyloCode.Our study provides example integrating genomic produce robust, explicit species includes fossil taxa, which updated scheme names.

Language: Английский

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Evolutionary origins of the eastern North American–Mesoamerican floristic disjunction: Current status and future prospects

American Journal of Botany, Journal Year: 2023, Volume and Issue: 110(3)

Published: Feb. 16, 2023

Biogeographic disjunction patterns, where multiple taxa are shared between isolated geographic areas, represent excellent systems for investigating the historical assembly of modern biotas and fundamental biological processes such as speciation, diversification, niche evolution, evolutionary responses to climate change. Studies on plant genera disjunct across northern hemisphere, particularly eastern North America (ENA) Asia (EAS), have yielded tremendous insight geologic history rich temperate floras. However, one most prevalent patterns involving ENA forests has been largely overlooked: that cloud Mesoamerica (MAM), with examples including Acer saccharum, Liquidambar styraciflua, Cercis canadensis, Fagus grandifolia, Epifagus virginiana. Despite remarkable nature this pattern, which recognized over 75 years, there few recent efforts empirically examine its ecological origins. Here I synthesize previous systematic, paleobotanical, phylogenetic, phylogeographic studies establish what is known about pattern provide a roadmap future research. argue evolution fossil record Mexican flora more broadly, represents key missing piece in broader puzzle hemisphere biogeography. also suggest ENA-MAM an system examining questions how traits life strategies mediate change predicting broadleaf will respond ongoing climatic pressures Anthropocene.

Language: Английский

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Niche unfilling dominates the naturalization of species from intercontinentally disjunct genera

Global Ecology and Biogeography, Journal Year: 2023, Volume and Issue: 32(11), P. 1977 - 1990

Published: Aug. 28, 2023

Abstract Aim Quantifying niche shifts of non‐native species and their interactions with natives is vital in evaluating invasion risk yet remains difficult. Climate filtering competition native congeners are two important processes impacting changes yielding contradictory predictions for the coexistence species. Closely related representing Eastern Asia (EA)–Eastern North America (ENA) floristic disjunction provide a powerful unexplored system assessing relative roles these processes. Here, we tested three change scenarios (unfilling, expansion stable) using EA naturalized ENA. We aim to answer: (1) which scenario observed species? (2) how has overlap between ENA changed after naturalization? Location EA. Time Period Present. Major Taxa Studied Angiosperms. Methods Niches were estimated both occurrences generated by ecological models. Niche measured Schoener's D. Contributions unfilling on niches evaluated hierarchical partitioning linear regressions. further pairwise phylogenetic distances among association overlap. Results Unfilling‐dominated postintroduction exhibited lower compared range populations These results remain when considering time since introduction potential physical dispersal limitations interpreted projecting suitable space However, limitation may contribute degree unfilling. Main Conclusions Using intercontinental disjunct as study system, found that naturalization shaped jointly climate congeners, providing valuable insights underlying global exchanges.

Language: Английский

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Foliar endophyte diversity in Eastern Asian-Eastern North American disjunct tree species – influences of host identity, environment, phylogeny, and geographic isolation

Frontiers in Plant Science, Journal Year: 2023, Volume and Issue: 14

Published: Dec. 13, 2023

Introduction The well-known eastern Asian (EA) and North American (ENA) floristic disjunction provides a unique system for biogeographic evolutionary studies. Despite considerable interest in the disjunction, few studies have investigated patterns their underlying drivers of allopatric divergence sister species or lineages isolated two areas. Endophyte diversity assembly disjunct taxa, as an ecological trait, may played important role processes evolution, but no examined endophytes these lineages. Here we compared foliar endophytic fungi bacteria-archaea (FEF FEB) 17 EA-ENA clade pairs from genera representing conifers 10 orders five major groups angiosperms 23 Cornus EA America. Methods Metagenomic sequencing fungal ITS bacterial-archaeal 16S rDNA was used to capture communities. Alpha beta bacteria were at multiple scales dimensions gain insights into relative roles historical geographic isolation, host identity, phylogeny, environment samples different sites shaping patterns. Results We found that varied greatly among plant individuals within between same sampling site, three sites, little variation region-of-origin all (EA vs ENA) counterparts genera. Various numbers indicator differing abundance identified each genus species. An overall significant correlation endophyte community dissimilarity phylogenetic distance plants detected not . However, correlations diversities taxonomic distances observed. Discussion Our results suggest identity (sampling sites), likely minor isolation pattern lead hypothesis taxa ENA differ FEF FEB when growing native habitats due differences local environments, which potentially drive functional features

Language: Английский

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Niche similarity accompanying COI genetic differentiations in asexual and sexual Corbicula lineages within East and Southeast Asia

Hydrobiologia, Journal Year: 2024, Volume and Issue: 851(18), P. 4521 - 4534

Published: June 20, 2024

Language: Английский

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Different resource partitioning explains plant species richness patterns in tropical alpine ecosystems

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: June 27, 2024

Abstract Species co-existence based on resource partitioning modulates biodiversity patterns across latitudes and altitudes. Resource can occur via specialisation or separation in the geographic range niche. Here, we compare two tropical alpine ecosystems with similar climates to test for climatic niche strategies explaining species richness difference. We species-rich ecosystem South American Andes more species-poor one eastern African mountains. combine phylogenomic data three locally diversified plant lineages each region occurrence records estimate metrics (size overlap). found that Andean have overall larger niches than species, thus smaller indicating is not explanation higher Andes. Instead, overlapping ranges, tend show less overlap effective separation. Taken together, propose different degrees of geographically hence, a pattern partitioning, explain differences between ecosystems.

Language: Английский

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Ecological and Evolutionary Factors Contribute to the Uneven Diversification of Firs in the Northern Hemisphere

Journal of Biogeography, Journal Year: 2024, Volume and Issue: 52(2), P. 505 - 519

Published: Nov. 22, 2024

ABSTRACT Aim The Northern Hemisphere harbours the greatest diversity of temperate plants on Earth, with East Asia having highest species richness compared North America and Europe. When how this uneven diversification pattern emerged remains unclear. Here, we use a conifer genus that forms extensive forests in to explore fundamental question ecology evolution: what processes underlie biodiversity through time space? Location Hemisphere. Taxon Abies . Methods To reconstruct well‐supported framework for estimating rate, performed phylogenetic analyses using concatenation coalescent methods based 58 fir taxa 56 nuclear single‐copy genes. Niche evolution was explored occurrence data environmental factors l1ou model. Multiple regression carried out identify correlations between variables at global regional scales, evaluate preference, potentially explain evolutionary history firs. Results We identified as speciation rate. Two clade‐specific niche shifts corresponding distribution firs were detected, one Himalaya‐Hengduan Mountains ( c. 12.2 Ma) other Mexican highlands 14.3 Ma), but none Euro‐Mediterranean region. Fir increased cool temperatures both globally regionally. Seasonal precipitation showed significant positive correlation scale Soil trends moderate highlands. Main Conclusions Our results indicate modern prefer climates seasonal rainfall. Asian experienced Himalayan orogeny Middle Miocene. Novel heterogeneous habitats due changes topography establishment monsoon climate, accompanied by shift, can account high Asia. A similar process is found highland In contrast, cold–dry continental climate since late Paleogene lack rainfall relatively stable region are main limiting diversification. study rejects ‘clade age’ hypothesis supports shift related rate triggered heterogeneity underlies

Language: Английский

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