Detection of genes positively selected in Cuban <i>Anolis</i> lizards that naturally inhabit hot and open areas and currently thrive in urban areas

Kanamori, Shunsuke; Cádiz, Antonio; Díaz, Luis M.; Ishii, Yuu; Nakayama, Takuro; Kawata, Masakado

doi:10.1002/ece3.7161

Cited by 8 publications

(14 citation statements)

References 56 publications

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“…Gene models for repeat masked genome assemblies of A. isolepis, A. allisoni, A. porcatus, A. allogus, A. homolechis , and A. sagrei were constructed using BRAKER v2.1.6 (Brůna et al 2021) with RNA-seq data and protein sequences of A. carolinensis obtained from Ensemble release 104. RNA-seq reads of each Anolis lizard (Akashi et al 2016; Kanamori et al 2021), available from the DDBJ Sequence Read Archive (DRA) of the DNA Data Bank of Japan (DDBJ) (Supplementary Table 1), were aligned to each genome assembly using GSNAP (Wu & Nacu 2010). Other nondefault options set when we run BRAKER were “--etpmode, --softmasking, --gff3.” BLAST search was used to identify predicted protein coding genes that did not match any protein sequence of UniProtKB/Swiss-Prot database, and Funannotate v1.8.7 (Palmer & Stajich 2020) was used to filter out such genes, predict UTR regions, and annotate gene names and Gene Ontology (GO) terms for each gene.…”

Section: Methodsmentioning

confidence: 99%

Section: Gene Annotation Ortholog Grouping and Duplicated Gene Identi...mentioning

confidence: 99%

“…Akashi et al (2018) also showed that the temperature-triggering escape behavior from heat and the activation of a molecular heat sensor, TRPA1 in A. sagrei and A. homolechis were higher than those in A. allogus . Moreover, phylogenetic analysis of several Cuban Anolis lizard’s coding sequences suggested that genes involved in stress response and cardiac function had undergone positive selection as A. allisoni and A. porcatus and A. sagrei adapted to open areas, and that these genes may be related to their current thriving in urban areas (Kanamori et al 2021). Recently, genome editing technology has also been established in A. sagrei (Rasys et al 2019).…”

Section: Introductionmentioning

confidence: 99%

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Draft genome of six Cuban Anolis lizards and insights into genetic changes during the diversification

Kanamori

Díaz²,

Cádiz

et al. 2022

Preprint

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The detection of various type of genomic variants and their accumulation processes during species diversification and adaptive radiation is important for understanding the molecular and genetic basis of evolution. Anolis lizards in the West Indies are good models for studying the mechanism of the evolution because of the repeated evolution of their morphology and the ecology. In this study, we performed de novo genome assembly of six Cuban Anolis lizards with different ecomorphs and thermal habitats (Anolis isolepis, Anolis allisoni, Anolis porcatus, Anolis allogus, Anolis homolechis, and Anolis sagrei). As a result, we obtained six novel draft genomes with relatively long and high gene completeness, with scaffold N50 ranging from 5.56–39.79 Mb, and vertebrate Benchmarking Universal Single-Copy Orthologs completeness ranging from 77.5% to 86.9%. Subsequently, we performed comparative analysis of genomic contents including those of mainland Anolis lizards to estimate genetic variations that had emerged and accumulated during the diversification of Anolis lizards. Comparing the repeat element compositions and repeat landscapes revealed differences in the accumulation process between Cuban trunk-crown and trunk-ground species, LTR accumulation observed only in A. carolinensis, and separate expansions of several families of LINE in each of Cuban trunk-ground species. The analysis of duplicated genes suggested that the proportional difference of duplicated gene number among Cuban Anolis lizards may be associated to the difference of their habitat range. Furthermore, Pairwise Sequentially Markovian Coalescent analysis proposed that the effective population sizes of each species might have been affected by Cuba’s geohistory. Hence, these six novel draft genome assemblies and detected genetic variations can be a springboard for the further genetic elucidation of the Anolis lizard’s diversification.SignificanceAnolis lizard in the West Indies is excellent model for studying the mechanisms of speciation and adaptive evolution. Still, due to a lack of genome assemblies, genetic variations and accumulation process of them involved in the diversification remain largely unexplored. In this study, we reported the novel genome assemblies of six Cuban Anolis lizards and analyzed evolution of genome contents. From comparative genomic analysis and inferences of genetic variation accumulation process, we detected species- and lineage-specific transposon accumulation processes and gene copy number evolution, considered to be associated with the adaptation to their habitats. Additionally, we estimated past effective population sizes and the results suggested its relationship to Cuba’s geohistory.

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Section: Methodsmentioning

confidence: 99%

Section: Gene Annotation Ortholog Grouping and Duplicated Gene Identi...mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Draft genome of six Cuban Anolis lizards and insights into genetic changes during the diversification

Kanamori

Díaz²,

Cádiz

et al. 2022

Preprint

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“…This littlestudied "trunk-ground" anole species is typically found at the edges of forest margins but also occurs in the urban environment (Rodríguez Schettino 1999, Cádiz et al 2013). Similar to Anolis sagrei (Losos 2009), a well studied sinurban (Rodríguez Schettino 1999; Kanamori et al 2021) and invasive species (Kolbe et al 2004), A. homolechis shows typical "trunk-ground" anole characteristics such as stocky shape, medium size and long hind limbs (Cádiz et al 2013). Nonetheless, to the best of our knowledge, there is no information comparing urban and forest populations of A. homolechis.…”

Section: Introductionmentioning

confidence: 99%

Differences in Sex Ratio, Tail Autotomy, Body Size and Body Condition Between Suburban and Forest Populations of the Cuban Endemic Lizard Anolis Homolechis

Vidal

Mancina

Cézilly

2022

Preprint

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Although growing evidence suggests that natural and sexual selection pressures may differ between natural and urban habitats, their consequences in terms of morphological differentiation, extent of sexual dimorphism and sex ratio remain poorly studied. Anolis lizards are an ideal model to study the phenotypic effects of urbanization, as they are well known for the existence of ecomorphs adapted to particular microhabitats. However, so far most studies of urban populations of anoles have considered invasive species and largely focused on males. Here, we compared morphological differentiation, sexual dimorphism and sex ratio between suburban and forest populations of the native A. homolechis, in Western Cuba, based on large sample size (n > 800) and a balanced nested design. Overall, both male and female individuals from surburban populations were larger and in better body condition than individuals from forest populations. In addition, evidence of caudal autotomy was more than twice more frequent in suburban populations compared to forest ones, with no sex effect. Habitat type and season of the year had additive effects on sex ratios, with a significant excess of males in surburban habitats and during the non-reproductive season. Accordingly, the extent of sexual dimorphism in size was more pronounced in suburban populations compared to forest ones. Our results suggest that the shape and direction of natural selection may differ between urban and natural populations of anoles.

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“…2021 ; Farré et al. 2021 Jul; Kanamori et al. 2021 )) and, more specifically, among aquatic mammals (e.g., ( Hammond et al.…”

Section: Introductionmentioning

confidence: 99%

Evidence of Selection in the Ectodysplasin Pathway among Endangered Aquatic Mammals

Font-Porterias

McNelis

Comas

et al. 2022

Integrative Organismal Biology

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The ectodysplasin pathway has been a target of evolution repeatedly. Genetic variation in the key genes of this pathway (EDA, EDAR, and EDARADD) results in a rich source of pleiotropic effects across ectodermally-derived structures, including teeth, hair, sweat glands, and mammary glands. In addition, a non-canonical wnt pathway has a very similar functional role, making variation in the WNT10A gene also of evolutionary significance. The adaptation of mammals to aquatic environments has occurred independently in at least four orders, whose species occupy a wide geographic range (from equatorial to polar regions) and exhibit great phenotypic variation in ectodermally-derived structures, including the presence or absence of fur and extreme lactational strategies. The role of the ectodysplasin pathway in the adaptation to aquatic environments has been never explored in mammalian species. In the present study, we analyze the genetic variation in orthologous coding sequences from EDA, EDAR, EDARADD and WNT10A genes together with ectodermally-derived phenotypic variation from 34 aquatic and non-aquatic mammalian species to assess signals of positive selection, gene-trait coevolution, and genetic convergence. Our study reveals strong evidence of positive selection in a proportion of coding sites in EDA and EDAR genes in three endangered aquatic mammals (the Hawaiian monk seal, the Yangtze finless porpoise, and the sea otter). We hypothesize functional implications potentially related to the adaptation to the low-latitude aquatic environment in the Hawaiian monk seal and the freshwater in the Yangtze finless porpoise. The signal in the sea otter is likely the result of an increased genetic drift after an intense bottleneck and reduction of genetic diversity. Besides positive selection, we have not detected robust signals of gene-trait coevolution or convergent amino acid shifts in the ectodysplasin pathway associated with shared phenotypic traits among aquatic mammals. This study provides new evidence of the evolutionary role of the ectodysplasin pathway and encourages further investigation, including functional studies, to fully resolve its relationship with mammalian aquatic adaptation.

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Detection of genes positively selected in Cuban Anolis lizards that naturally inhabit hot and open areas and currently thrive in urban areas

Cited by 8 publications

References 56 publications

Draft genome of six Cuban Anolis lizards and insights into genetic changes during the diversification

Draft genome of six Cuban Anolis lizards and insights into genetic changes during the diversification

Differences in Sex Ratio, Tail Autotomy, Body Size and Body Condition Between Suburban and Forest Populations of the Cuban Endemic Lizard Anolis Homolechis

Evidence of Selection in the Ectodysplasin Pathway among Endangered Aquatic Mammals

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