Range-wide neutral and adaptive genetic structure of an endemic herb from Amazonian Savannas

Abstract

Conserving genetic diversity in rare and narrowly distributed endemic species is essential to maintain their evolutionary potential and minimize extinction risk under future environmental change. In this study we assess neutral and adaptive genetic structure and genetic diversity in Brasilianthus carajensis (Melastomataceae), an endemic herb from Amazonian Savannas. Using RAD sequencing we identified a total of 9365 SNPs in 150 individuals collected across the species’ entire distribution range. Relying on assumption-free genetic clustering methods and environmental association tests we then compared neutral with adaptive genetic structure. We found three neutral and six adaptive genetic clusters, which could be considered management units (MU) and adaptive units (AU), respectively. Pairwise genetic differentiation (FST) ranged between 0.024 and 0.048, and even though effective population sizes were below 100, no significant inbreeding was found in any inferred cluster. Nearly 10 % of all analysed sequences contained loci associated with temperature and precipitation, from which only 25 sequences contained annotated proteins, with some of them being very relevant for physiological processes in plants. Our findings provide a detailed insight into genetic diversity, neutral and adaptive genetic structure in a rare endemic herb, which can help guide conservation and management actions to avoid the loss of unique genetic variation.

Combining genotype, phenotype, and environmental data to delineate site‐adjusted provenance strategies for ecological restoration

“…The snmf model implements a fast yet accurate likelihood algorithm (Frichot, Mathieu, Trouillon, Bouchard, & François, 2014), while DAPC is a robust genetic clustering method with no assumption about the underlying population genetic model (Jombart & Ahmed, 2011)⁠. Based on previous population genomic studies for other co‐occurring plant species (Carvalho et al., 2019; Lanes et al., 2018; Silva et al., 2020)⁠, we tested from 1 to 10 ancestral populations ( k ). In the case of snmf we performed 10 replicate runs for each value of k , choosing the most likely k based on minimized cross‐entropy.…”

Diversidade genética de Pilocarpus Microphyllus na Flona de Carajás – PA

“…O padrão de estruturação pode ser explicado pelo fato da espécie ser polinizada por moscas e abelhas (Meliponinae) (SILVA et al, 2000), os quais possuem como característica um curto raio de voo, pois o forrageamento ocorre principalmente a curtas distâncias (ARAÚJO et al, 2004;ROUBIK;ALUJA, 1983). Dessa maneira, é possível que P. (LANES et al, 2018;SILVA et al, 2020). Neste estudo, a endogamia foi levemente positiva em uma população de P. microphyllus, sugerindo que está ocorrendo algum nível de autopolinização (SILVA et al 2000; PIRANI; DEVECCHI, 2018) ou acasalamento entre indivíduos aparentados (TURCHETTO et al, 2016).…”

“…As bibliotecas genômicas foram sequenciadas utilizando Nextera DNA Flex Reagent (Illumina, Inc.) em um HiSeq 4000 com quatro faixas de 150 bp e a análise de genotipagem seguiu scripts personalizados (SNPsaurus, LLC), onde as reads foram cortadas utilizando a ferramenta bbduk do software BBMap (http://sourceforge.net/projects/bbmap/): bbmap/bbduk.sh in = $file out = $outfile ktrim= r k = 17 hdist = 1 mink = 8 ref =bbmap/resources/nextera.fa.gz minlen = 100 ow = t qtrim = r trimq = 10. Um arquivo FASTA com sequências de referência foi criado coletando 10 milhões de reads uniformemente das amostras e eliminando as reads com contagens inferiores a 10 ou mais de 400 e alinhadas de novo(SILVA et al, 2020). Os lócos restantes foram então alinhados entre si para identificar alelos.…”

All Populations Matter: Conservation Genomics of Australia’s Iconic Purple Wattle, Acacia purpureopetala

“…In particular, the disjunct populations that displayed exceptionally low levels of allelic variation and observed heterozygosity should be targets for genetic augmentation. Monitoring will be required to ensure that the introduced genotypes are not swamped by the local inbred populations or the opposite that local adaptive genes are lost [74]. Seed collections can be made prior to introductions to ensure local genotypes are not lost due to swamping.…”