DOI: 10.5061/dryad.rv15dv4fq
title: Unveiling the impacts of land use on the phylogeography of zoonotic New World Hantaviruses

description: Billions of genomic sequences are stored in public repositories (NCBI) as
 well as records of species occurrence (GBIF). By implementing analytical
 tools from different scientific disciplines, data mining on these
 databases can be a source of information to aid in the global surveillance
 of zoonotic pathogens that circulate among wildlife. We illustrate this by
 investigating the hantavirus-rodent system in the Americas, i.e. New World
 Hantaviruses (NWH). First we draw the circulation of pathogenic NWH among
 rodents; by inferring the phylogenetic links among 278 genomic samples of
 the S segment (N protein) of NWH found in 55 species of Cricetidae
 rodents. Second, machine learning was used to assess the impact of land
 use on the probability of presence of the rodent species linked with
 reservoirs of pathogenic hantaviruses. Our results show that hosts are
 widely present across the Americas. Some hosts are present in the primary
 forest and agricultural land, but not in the secondary forest; whereas
 other hosts are present in secondary forest and agricultural land. The
 diversity of host species allows Hantavirus to circulate on a wide
 spectrum of habitats, in particular rural rather than urban. We highlight
 that Public repositories of genomic data and species occurrence are very
 useful resources for monitoring potential enzootic transmission and
 spillover of zoonotic viruses in relation with the changes that humans
 produce in the Biosphere.
description: Data analysis follows 4 main steps: 
 <strong>Data Collection and Curation.</strong>
 GenBank Accesion Numbers of Hantavirus sequences were obtained from a
 BLAST query, metadata was collected, taxonomic names homogenized, and
 sequences found in wild animals were selected. 
 <strong>Genetic Sequence Alignment and Phylogenetic
 Inference</strong>. Genetic data was aligned and used to infer the
 phylogenetic relationships among the samples. 
 <strong>Phylogenetic Network analysis on the genetic links of
 Hantaviruses among hosts</strong>. Phylogenetic network was built
 from the phylogentic tree of New World Hantavirus. 
 <strong>Geographic analysis on the habitat suitability of hosts
 linked in the phylogenetic network</strong>. Habitat suitability
 within the distribution areas of each species was modeled with
 classification trees. Historical records on the species presence were used
 to assess the land use change in the time of sampling, and train a model
 to predict the presence of the species based on 12 land use variables.
 These models were used to predict the area of suitable habittat in a
 projection of land use for 2025. 
description: ## **Unveiling the Impacts of Land Use on the Phylogeography of Zoonotic
 New World Hantaviruses** Gabriel E García-Peña and André V. Rubio.
 Ecography 2024. DOI: 10.1111/ecog.06996 ##### *Supplementary Material* ##
 Description of the data and file structure Analysis presented in the main
 article was performed in R (R Core Team 2022); MAFFT (Katoh 2005) and
 JModelTest2 (Darriba et al. 2012), following 4 main steps: ##### 1. Data
 Collection and Curation. **BLAST_Nprot.csv** : Accession numbers from the
 BLAST search for Hanatavirus. With this list of accesion numbers, it is
 possible to download the genetic sequences in R, by using the function
 read.GenBank() from the library ape. Metadata of these sequences can be
 accesed with the R code presented in the file: **fetch.metadata.R** (see
 code section). ##### 2. Genetic Sequence Alignment and Phylogenetic
 Inference. **Nprot_MaxAlign.fas**: Fasta file with Multiple sequence
 alignment of the genetic sequences. Fasta file can be read in R with the
 function read.dna() from the library ape. These data can be analyzed with
 the software JModelTest2. **AIC_tree.nwk**: Phylogenetic relationships
 with topology and branch lengths infered with JModelTest2; presented in a
 newick format. The file can be read with the function read.tree() from the
 R library ape. The Figure of the tree is included in this repository
 (**phylogeny_NWH.jpeg**) ##### 3. Phylogenetic Network analysis on the
 genetic links of Hantaviruses among hosts. The phylogenetic network was
 infered from the phylogenetic trees contained in **AIC_tree.nwk**, the R
 code (**phylonet.R**), and the dataset **hosts_america_PH.csv**. ##### 4.
 Geographic analysis on the habitat suitability of hosts linked in the
 phylogenetic network. **taxa_in_network_NWH.zip**. The zip file conatins
 the results of the habitat suitability analysis performed with the R code
 ***predict_suitable_habitat.R***. These maps are in geojson files named
 after each species and capture the probability of species presence (X1)
 and absence (X0) within pixels of 0.25 ° arc inside the distribution area
 of the species. Within each location, land use variables for 2015 are
 included. These variables are proportions of the pixel covered by each
 vegetation type, including: primary forest (primf), primary non-forest
 (primnf), secondary forest (secdf), secondary non forest (secdn),
 rangeland (range), pasture (pastr), annual C4 crops (C4ann), perennial C4
 crops (C4per), C3 crops perenial (C3per) and annual (C3ann) , and nitrogen
 fixing plants (C3fix). These land use variables were used to predict X1
 and X0. Files can be viewed with a geographic information software
 including R. Occurrence data used to analyse habitat suitability can be
 accesed from the original source: GBIF data:
 ## Sharing/Access information
 Primary data used to perform the analysis can be accessed from the oﬃcial
 repositories: * GBIF data: *
 Historical land-use dataset states.nc (LUH2 v2h) covers the period
 850-2015 and projections for 2025: 
 * Distributions of rodent species from the IUCN:
 ##
 Code/Software #### Description of files within this repository: 1.
 ***fetch.metadata.R***: Code of a Web scrapper to retrieve information
 about the sequences in the NCBI repository. 2. **BLAST_Nprot.csv**: lists
 with the accession numbers obtained from the BLAST search. 3.
 **Nprot_MaxAlign.fas**: Fasta file with the nucleotide sequences analysed;
 278 genomic samples of the S segment (N protein) of NWH found in 55
 species of Cricetidae rodents. 4. **AIC_tree.nwk**: Phylogenetic tree
 infered. 5. **hosts_america_PH.csv**: List of species known to host New
 World Hantavirus. Fisrt column contains the genus name, column 2 the
 speices name, and column 3 denotes (1) whether the species is known to
 harbor a pathogen strain of Hantavirus, or not (0). 6. **phylonet.R**:
 Code describing the phylogenetic network analysis. 7.
 ***predict_suitable_habitat.R***: Code of Classification tree analysis on
 the habitat suitability of the rodent hosts. 8.
 **taxa_in_network_NWH.zip**: Maps for each species analysed with a
 prediction of habitat suitability (X1) in the distribution range of the
 species, drawn from the land use change variables (García-Peña et al.
 2021).