 Climate change poses a threat to species' ability to track their niche through range shifts

 Genetic variation is necessary for adaptation and persistence under climate change
 Genomic vulnerability studies identify populations lacking necessary variation, but often ignore hybridization as a source of
adaptive variation

 Study focused on closely related species of rainbowfish (Melanotaenia spp.) across an elevational gradient in the Australian Wet
Tropics
 Estimated environmental niche models and genomic vulnerability for pure and hybrid populations
 Examined overlaps between introgressed and adaptive genomic regions

the article discusses the impact of climate change on narrow endemic rainbowfish populations, which are hybridizing with warm-
adapted generalist species. The study used genomic vulnerability assessments and historical ecological niche models to predict the
evolutionary change needed to respond to projected climate change. The findings suggest that hybrid populations are less
vulnerable to climate change due to their capacity for adaptive introgression, which accelerates adaptive shifts in response to
environmental change. Furthermore, the study suggests that hybrid populations may buffer species-level vulnerability in the short
term, either directly via introgressed adaptive alleles or through indirect effects such as increased local effective population sizes.
However, the genetic and demographic consequences of hybridization are difficult to predict and require careful consideration
when assessing whether negative effects are offset by potential gains in adaptive resilience. Finally, the study highlights the need for
conservation managers to take into account the potential role of hybrid populations in retaining unique diversity from the narrow
endemic rainbowfish lineages in the futur
The passage describes a genetic study of rainbowfish species in the Australian Wet Tropics. DNA samples were collected
from 344 individuals belonging to five species, as well as an additional outgroup species. The DNA was extracted using a modified
salting-out protocol, and double digest restriction-site-associated DNA sequencing libraries were prepared using two restriction
enzymes. The libraries were then sequenced using Illumina HiSeq2500, with individual barcodes used to multiplex samples. The raw
sequencing data were demultiplexed, trimmed, and aligned to a reference genome before duplicate reads were removed and SNPs
were called using BCFtools. The genotypes were filtered for missing data, mapping quality, HWE, and MAF before pruning to reduce
the effect of linkage disequilibrium. The average R2 was found not to change significantly after 605 bp, and SNPs <300 bp apart
were pruned resulting in 99.3% of SNP pairs separated by >100 Kbp. The study aimed to investigate the genetic diversity and
population structure of the rainbowfish species in the Australian Wet Tropics.

his is a description of the methods used in a study to assess genetic diversity and introgression between
different species of rainbowfish. The study used various statistical methods, including hierarchical F-statistics,
Wilcoxon rank sum tests, ADMIXTURE, gghybrid, NewHybrids, Treemix, Dsuite, and sliding window analysis.

To identify individuals with hybrid ancestry, ADMIXTURE was used to estimate individual ancestry proportions
assuming a K value of five ancestral species. Individuals with a Q value of >0.95 were classified as pure, while those
with both M. splendida and one other species with ancestry of >0.1 and the remaining species’ Q values <0.05 were
classified as hybrids. Hybrid indices were also estimated using the gghybrid package and visualized with triangle
plots.

Simulations were performed using NewHybrids and the Hybriddetective R package to test the power of the data for
detecting hybrids and to assign individuals to hybrid classes. Treemix was used to examine introgression between
branches of the rainbowfish phylogeny, and Dsuite was used to assess gene flow between M. splendida and the
other species and to identify introgressed loci.
The sliding window analysis was implemented with the Dinvestigate function in Dsuite, using a sliding window of 50
SNPs with a step of 10 SNPs. Windows in the top 5% of the fdM distribution were considered as candidate
introgressed loci, and overlapping candidate windows were merged using BEDtools to provide a minimum set of
candidate regions for each trio. The 13,734 SNP dataset was then mapped to the candidate introgressed regions
using BCFtools view to identify any overlap with the candidate climate-adapted SNPs.
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The passage describes the methods used to predict the vulnerability of fish species to climate change. Bioclimatic
variables were extracted from CHELSA v.1.2, and projections for 2070 under intermediate and high emissions
scenarios were obtained. Historic climate models were also downloaded from PaleoClim for three different time
periods in the Holocene. Ecological niche models were generated for each species and time period using biomod2
v.3.4.6. Occurrence data for each species were obtained from the genomic samples and Atlas of Living Australia. A
PCA was conducted on raster data to avoid collinearity among variables. Ensemble models were built using four
algorithms, and the weighted mean of probabilities ensemble models for each species were converted to binary
representation using a probability threshold of 70%. The relative range sizes for each species were estimated for each
time period.
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The passage describes a study that aims to identify climate-adapted loci for tropical Australian rainbowfish
and assess their vulnerability to future climate change. The following steps were taken in the study:
1.
GEA analysis using RDA: to detect associations between population allele frequencies and two climatic variables
(Bio05 and Bio19) using the RDA function in the vegan R package. Moran’s eigenvector maps (MEM) were estimated
using the mgQuick function from the MEMGENE R package to control for the nonlinear spatial phylogenetic
structure in the RDA. A forward selection procedure was used to identify significant MEM eigenvectors to use as
conditioning variables. The final model was tested for significance using the anova.cca function and 1,000
permutations.
2.
3.
Identification of candidate loci: the mean locus score was calculated for each of the first two RDA axes, and those
scoring greater than three standard deviations from the mean were considered candidates for hydroclimatic
selection. Overlap between the GEA and introgressed candidate loci identified were considered as potential signals of
adaptive introgression. Gene ontology terms and Kyoto Encyclopedia of Genes and Genomes pathway enrichment
analyses were explored using the STRING web server.
4.
5.
PCA analyses: to assess changes in the environment since the early Holocene and how climate is predicted to change
over the next 50 years, PCA was performed on climate data for each time period based on the retained bioclim
variables from the RDA. The population.shift function from the AlleleShift R package was used to visualize and
compare the magnitude and direction of environmental changes between periods. An additional PCA was also
performed using the retained current environmental data and plotting convex hulls surrounding the sampling sites
for each species to highlight the relative size and any overlap of the environmental niche space occupied by each
species.
6.
7.
AlleleShift modeling: to model the rate of past evolutionary change and to predict future genomic vulnerability based
on the candidate adapted loci. An initial two-step calibration was performed to build a model and predict the
relationship between allele counts and the environmental data. The predicted allele counts were used as independent
variables in a generalized additive model with observed allele frequencies as the response. Model fit was evaluated
for each population, and those for which the model performed poorly were omitted from the final analyses. Based on
the calibrated allele frequency–environment model, allele counts were predicted for the 2070 projected
environmental data, and genomic vulnerability was expressed as the difference between median values of the
observed and predicted allele frequencies among the current and projected environmental models (delta allele
frequency).
8.
9.
Linear model: constructed to examine the relationship between genomic vulnerability and the proportion of M.
splendida ancestry for each population.
10.
11.
Assessment of pure NER populations: to assess the capacity for the pure NER populations to adapt in situ assuming
no gene flow from M. splendida or the hybrid populations, the number of loci missing the adaptive allele (as
predicted by the AlleleShift model) was identified.
12.
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