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Adaptive Evolution and Trait Formation of Animals

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A special issue of Animals (ISSN 2076-2615). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: closed (31 December 2023) | Viewed by 29070

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Dr. Jun-Mo Kim

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Animal Functional Genomics and Bioinformatics Lab., Department of Animal Science and Technology, Chung-Ang University, Anseong, Gyeonggi-do, Korea
Interests: quantitative genetics; functional genomics; system biology, bioinformatics
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Donghyun Shin

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Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju 54896, Korea
Interests: animal genomics; population genomics; bioinformatics

Special Issue Information

Dear Colleagues,

In evolutionary biology and genetics, the rate at which animal genomes adapt to environmental changes and its frequency of adaption processes in molecular evolution are not fully understood yet. Therefore, the main goal of evolutionary genomics is to characterize and measure adaptation at the molecular level. Several outstanding examples have emerged from recent research in this field, due to advances in omics platforms, big data generation, and genome-wide association studies. As we all know, variations arise in the DNA sequences of animals for many reasons, leading to gene deletion or duplication. Based on alternation in DNA sequences, the processes of adaptive evolution and trait formation for existence will be initiated in animals that can alter their traits or phenotype. It is essential to adopt innovative approaches for dissecting adaptive evolution and trait formation processes in animals at the molecular level for filling the gaps between genotype and phenotype. However, applications of systems biology and bioinformatics have huge potential to decipher the molecular mechanism behind adaptation and trait formation. This Special Issue aims to address the following topics of relevance to inspire work on this topic.

Prof. Dr. Jun-Mo Kim
Prof. Dr. Donghyun Shin
Guest Editors

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Keywords

evolutionary genetics and genomics
population genetics and genomics
functional physiology
GWAS
systems biology and bioinformatics

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20 pages, 4253 KiB

Open AccessArticle

Adaptive Evolution of the Greater Horseshoe Bat AANAT: Insights into the Link between AANAT and Hibernation Rhythms

by Yanhui Zhao, Lei Wang, Sen Liu, Yingting Pu, Keping Sun, Yanhong Xiao and Jiang Feng

Animals 2024, 14(10), 1426; https://doi.org/10.3390/ani14101426 - 10 May 2024

Viewed by 989

Abstract

Arylalkylamine N-acetyltransferase (AANAT) is a crucial rate-limiting enzyme in the synthesis of melatonin. AANAT has been confirmed to be independently duplicated and inactivated in different animal taxa in order to adapt to the environment. However, the evolutionary forces associated with having a single copy of AANAT remain unclear. The greater horseshoe bat has a single copy of AANAT but exhibits different hibernation rhythms in various populations. We analyzed the adaptive evolution at the gene and protein levels of AANAT from three distinct genetic lineages in China: northeast (NE), central east (CE), and southwest (SW). The results revealed greater genetic diversity in the AANAT loci of the NE and CE lineage populations that have longer hibernation times, and there were two positive selection loci. The catalytic capacity of AANAT in the Liaoning population that underwent positive selection was significantly higher than that of the Yunnan population (p < 0.05). This difference may be related to the lower proportion of α helix and the variation in two interface residues. The adaptive evolution of AANAT was significantly correlated with climate and environment (p < 0.05). After controlling for geographical factors (latitude and altitude), the evolution of AANAT by the negative temperature factor was represented by the monthly mean temperature (r = −0.6, p < 0.05). The results identified the gene level variation, functional adaptation, and evolutionary driving factors of AANAT, provide an important foundation for further understanding the adaptive evolution of the single copy of AANAT in pteropods, and may offer evidence for adaptive hibernation rhythms in bats. Full article

(This article belongs to the Special Issue Adaptive Evolution and Trait Formation of Animals)

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15 pages, 6445 KiB

Open AccessArticle

Identification, Expression and Evolutional Analysis of Two cyp19-like Genes in Amphioxus

by Yajun Wang, Jingyuan Lin, Wenjin Li, Guangdong Ji and Zhenhui Liu

Animals 2024, 14(8), 1140; https://doi.org/10.3390/ani14081140 - 9 Apr 2024

Viewed by 997

Abstract

The mechanism of sex determination and differentiation in animals remains a central focus of reproductive and developmental biology research, and the regulation of sex differentiation in amphioxus remains poorly understood. Cytochrome P450 Family 19 Subfamily A member 1 (CYP19A1) is a crucial sex differentiation gene that catalyzes the conversion of androgens into estrogens. In this study, we identified two aromatase-like genes in amphioxus: cyp19-like1 and cyp19-like2. The cyp19-like1 is more primitive and may represent the ancestral form of cyp19 in zebrafish and other vertebrates, while the cyp19-like2 is likely the result of gene duplication within amphioxus. To gain further insights into the expression level of these two aromatase-like, we examined their expression in different tissues and during different stages of gonad development. While the expression level of the two genes differs in tissues, both are highly expressed in the gonad primordium and are primarily localized to microsomal membrane systems. However, as development proceeds, their expression level decreases significantly. This study enhances our understanding of sex differentiation mechanisms in amphioxus and provides valuable insights into the formation and evolution of sex determination mechanisms in vertebrates. Full article

(This article belongs to the Special Issue Adaptive Evolution and Trait Formation of Animals)

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10 pages, 2385 KiB

Open AccessArticle

Molecular Characterization and Phylogenetic Analysis of Flightin Gene in Vespa basalis (Hymenoptera, Vespidae)

by Hasin Ullah, Xiaojuan Huang, Tong Zhou, Yan Tang, Danyang Zhu, Hongli Xu and Jiangli Tan

Animals 2024, 14(6), 978; https://doi.org/10.3390/ani14060978 - 21 Mar 2024

Viewed by 1208

Abstract

Flight is a complex physiological process requiring precise coordination of muscular contraction. A key protein in insect flight is flightin, which plays an integral role in the flight muscles. This research sought to evaluate the flight competence of the social wasp V. basalis by characterizing the molecular components involved. Our study focused on Vespa basalis, one of the most dangerous hornet species, utilizing PCR to obtain a partial cDNA sequence of the flightin protein. We then employed phylogenetic and sequence analysis to gain insights into this protein in flight-related adaptations. The cDNA has an 1189-base pair sequence including an open reading frame (453 bp) encoding 150 amino acids. Analyzing the deduced amino acid sequence using an online tool revealed a molecular weight of 18.05 kDa, an isoelectric point of 5.84, four functional site patterns, and no transmembrane topology. We constructed a phylogenetic tree of flightin based on 38 species. Our analysis indicated that V. basalis is most closely related to V. mandarinia; this alignment is consistent with their similar aggressive behavior, but their evolutionary relationship, based on mitochondrial sequences, presents a contrast. These initial findings on the flightin gene in V. basalis lay the groundwork for future functional studies to elucidate its specific role in flight adaptations and explore its potential as a target for pest management strategies. Full article

(This article belongs to the Special Issue Adaptive Evolution and Trait Formation of Animals)

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18 pages, 4586 KiB

Open AccessArticle

Whole-Genome Scanning for Selection Signatures Reveals Candidate Genes Associated with Growth and Tail Length in Sheep

by Taotao Li, Meilin Jin, Huihua Wang, Wentao Zhang, Zehu Yuan and Caihong Wei

Animals 2024, 14(5), 687; https://doi.org/10.3390/ani14050687 - 22 Feb 2024

Cited by 2 | Viewed by 1835

Abstract

Compared to Chinese indigenous sheep, Western sheep have rapid growth rate, larger physique, and higher meat yield. These excellent Western sheep were introduced into China for crossbreeding to expedite the enhancement of production performance and mutton quality in local breeds. Here, we investigated population genetic structure and genome-wide selection signatures among the Chinese indigenous sheep and the introduced sheep based on whole-genome resequencing data. The PCA, N-J tree and ADMIXTURE results showed significant genetic difference between Chinese indigenous sheep and introduced sheep. The nucleotide diversity (π) and linkage disequilibrium (LD) decay results indicated that the genomic diversity of introduced breeds were lower. Then, F_st & π ratio, XP-EHH, and de-correlated composite of multiple signals (DCMS) methods were used to detect the selection signals. The results showed that we identified important candidate genes related to growth rate and body size in the introduced breeds. Selected genes with stronger selection signatures are associated with growth rate (CRADD), embryonic development (BVES, LIN28B, and WNT11), body size (HMGA2, MSRB3, and PTCH1), muscle development and fat metabolism (MSTN, PDE3A, LGALS12, GGPS1, and SAR1B), wool color (ASIP), and hair development (KRT71, KRT74, and IRF2BP2). Thus, these genes have the potential to serve as candidate genes for enhancing the growth traits of Chinese indigenous sheep. We also identified tail-length trait-related candidate genes (HOXB13, LIN28A, PAX3, and VEGFA) in Chinese long-tailed breeds. Among these genes, HOXB13 is the main candidate gene for sheep tail length phenotype. LIN28A, PAX3, and VEGFA are related to embryonic development and angiogenesis, so these genes may be candidate genes for sheep tail type traits. This study will serve as a foundation for further genetic improvement of Chinese indigenous sheep and as a reference for studies related to growth and development of sheep. Full article

(This article belongs to the Special Issue Adaptive Evolution and Trait Formation of Animals)

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9 pages, 1585 KiB

Open AccessCommunication

Genome-Wide Selection Signal Analysis to Investigate Wide Genomic Heredity Divergence between Eurasian Wild Boar and Domestic Pig

by Xinming Wu, Haoyuan Zhang, Haoyuan Long, Dongjie Zhang, Xiuqin Yang, Di Liu and Guangxin E

Animals 2023, 13(13), 2158; https://doi.org/10.3390/ani13132158 - 30 Jun 2023

Viewed by 2021

Abstract

As important livestock species, pigs provide essential meat resources for humans, so understanding the genetic evolution behind their domestic history could help with the genetic improvement of domestic pigs. This study aimed to investigate the evolution of convergence and divergence under selection in European and Asian domestic pigs by using public genome-wide data. A total of 164 and 108 candidate genes (CDGs) were obtained from the Asian group (wild boar vs. domestic pig) and the European group (wild boar vs. domestic pig), respectively, by taking the top 5% of intersected windows of a pairwise fixation index (FST) and a cross population extended haplotype homozygosity test (XPEHH). GO and KEGG annotated results indicated that most CDGs were related to reproduction and immunity in the Asian group. Conversely, rich CDGs were enriched in muscle development and digestion in the European group. Eight CDGs were subjected to parallel selection of Eurasian domestic pigs from local wild boars during domestication. These CDGs were mainly involved in olfactory transduction, metabolic pathways, and progesterone-mediated oocyte maturation. Moreover, 36 and 18 haplotypes of INPP5B and TRAK2 were identified in this study, respectively. In brief, this study did not only improve the understanding of the genetic evolution of domestication in pigs, but also provides valuable CDGs for future breeding and genetic improvement of pigs. Full article

(This article belongs to the Special Issue Adaptive Evolution and Trait Formation of Animals)

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17 pages, 22768 KiB

Open AccessArticle

Comparative Analyses Reveal the Genetic Mechanism of Ambergris Production in the Sperm Whale Based on the Chromosome-Level Genome

by Chuang Zhou, Kexin Peng, Yi Liu, Rusong Zhang, Xiaofeng Zheng, Bisong Yue, Chao Du and Yongjie Wu

Animals 2023, 13(3), 361; https://doi.org/10.3390/ani13030361 - 20 Jan 2023

Cited by 1 | Viewed by 3022

Abstract

Sperm whales are a marine mammal famous for the aromatic substance, the ambergris, produced from its colon. Little is known about the biological processes of ambergris production, and this study aims to investigate the genetic mechanism of ambergris production in the sperm whale based on its chromosome-level genome. Comparative genomics analyses found 1207 expanded gene families and 321 positive selected genes (PSGs) in the sperm whale, and functional enrichment analyses suggested revelatory pathways and terms related to the metabolism of steroids, terpenoids, and aldosterone, as well as microbiota interaction and immune network in the intestine. Furthermore, two sperm-whale-specific missense mutations (Tyr393His and Leu567Val) were detected in the PSG LIPE, which has been reported to play vital roles in lipid and cholesterol metabolism. In total, 46 CYP genes and 22 HSD genes were annotated, and then mapped to sperm whale chromosomes. Furthermore, phylogenetic analysis of CYP genes in six mammals found that CYP2E1, CYP51A and CYP8 subfamilies exhibited relative expansion in the sperm whale. Our results could help understand the genetic mechanism of ambergris production, and further reveal the convergent evolution pattern among animals that produce similar odorants. Full article

(This article belongs to the Special Issue Adaptive Evolution and Trait Formation of Animals)

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14 pages, 3650 KiB

Open AccessArticle

Rubbing Salt in the Wound: Molecular Evolutionary Analysis of Pain-Related Genes Reveals the Pain Adaptation of Cetaceans in Seawater

by Xiaoyue Ding, Fangfang Yu, Xiaofang He, Shixia Xu, Guang Yang and Wenhua Ren

Animals 2022, 12(24), 3571; https://doi.org/10.3390/ani12243571 - 16 Dec 2022

Cited by 2 | Viewed by 11281

Abstract

Pain, usually caused by a strong or disruptive stimulus, is an unpleasant sensation that serves as a warning to organisms. To adapt to extreme environments, some terrestrial animals have evolved to be inherently insensitive to pain. Cetaceans are known as supposedly indifferent to pain from soft tissue injury representatives of marine mammals. However, the molecular mechanisms that explain how cetaceans are adapted to pain in response to seawater environment remain unclear. Here, we performed a molecular evolutionary analysis of pain-related genes in selected representatives of cetaceans. ASIC4 gene was identified to be pseudogenized in all odontocetes (toothed whales) except from Physeter macrocephalus (sperm whales), and relaxed selection of this gene was detected in toothed whales with pseudogenized ASIC4. In addition, positive selection was detected in pain perception (i.e., ASIC3, ANO1, CCK, and SCN9A) and analgesia (i.e., ASIC3, ANO1, CCK, and SCN9A) genes among the examined cetaceans. In this study, potential convergent amino acid substitutions within predicted proteins were found among the examined cetaceans and other terrestrial mammals, inhabiting extreme environments (e.g., V441I of TRPV1 in cetaceans and naked mole rats). Moreover, specific amino acid substitutions within predicted sequences of several proteins were found in the studied representatives of cetaceans (e.g., F56L and D163A of ASIC3, E88G of GRK2, and F159L of OPRD1). Most of the substitutions were located within important functional domains of proteins, affecting their protein functions. The above evidence suggests that cetaceans might have undergone adaptive molecular evolution in pain-related genes through different evolutionary patterns to adapt to pain, resulting in greater sensitivity to pain and more effective analgesia. This study could have implications for diagnosis and treatment of human pain. Full article

(This article belongs to the Special Issue Adaptive Evolution and Trait Formation of Animals)

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13 pages, 4192 KiB

Open AccessArticle

Complete Mitochondrial Genome, Genetic Diversity and Phylogenetic Analysis of Pingpu Yellow Chicken (Gallus gallus)

by Sihua Jin, Jingjing Xia, Fumin Jia, Lijun Jiang, Xin Wang, Xuling Liu, Xing Liu and Zhaoyu Geng

Animals 2022, 12(21), 3037; https://doi.org/10.3390/ani12213037 - 4 Nov 2022

Cited by 2 | Viewed by 2346

Abstract

In this study, the complete mitochondrial genome sequence of one female Pingpu Yellow chicken (PYC) and the D-loop sequences obtained from 60 chickens were analyzed to investigate their genetic diversity and phylogeny. The total length of the PYC mitogenome is 16,785 bp and that of the complete D-loop is 1231 to 1232 bp. The mitogenome comprises 22 transfer ribonucleic acids (tRNAs), 2 ribosomal ribonucleic acids (rRNAs), 13 protein-coding genes (PCGs), and 1 non-coding control region (D-loop). Additionally, the total length of the 13 PCGs is 11,394 bp, accounting for 67.88% of the complete mitogenome sequence, and the PCGs region has 3798 codons. A majority of the PCGs have ATG as the start codon. The haplotype and nucleotide diversity of PYC were 1.00000 ± 0.00029 and 0.32678 ± 0.29756, respectively. In the D-Loop data set, we found 25 polymorphic sites, which determined 18 haplotypes and 3 major haplogroups (A–C). Therefore, PYC has a classical vertebrate mitogenome, with comparatively high nucleotide diversity and potentially three maternal lineages. The neighbor-joining (NJ) tree analysis results showed PYC grouped with the Luhua (MT555049.1) and Nandan chickens (KP269069.1), which indicates that PYC is closely related to these two breeds. Full article

(This article belongs to the Special Issue Adaptive Evolution and Trait Formation of Animals)

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13 pages, 3816 KiB

Open AccessArticle

Genetic Variation in Schizothorax kozlovi Nikolsky in the Upper Reaches of the Chinese Yangtze River Based on Genotyping for Simplified Genome Sequencing

by Jiayang He, Zhi He, Deying Yang, Zhijun Ma, Hongjun Chen, Qian Zhang, Faqiang Deng, Lijuan Ye, Yong Pu, Mingwang Zhang, Song Yang, Shiyong Yang and Taiming Yan

Animals 2022, 12(17), 2181; https://doi.org/10.3390/ani12172181 - 25 Aug 2022

Cited by 2 | Viewed by 2020

Abstract

Schizothorax kozlovi Nikolsky is a unique cold−water fish in the upper reaches of the Yangtze River in China and has high economic value. In our study, genetic diversity and population structure analyses were performed on seven wild populations (originating from the Jinsha River, Yalong River, and Wujiang River) in the upper reaches of the Yangtze River by genotyping by sequencing (GBS). The results indicated that a total of 303,970 single−nucleotide polymorphisms (SNPs) were identified from the seven wild populations. Lower genetic diversity was exhibited among the intrapopulations of the three tributaries, and the Wujiang River population had significant genetic differentiation when compared to the Jinsha River and Yalong River populations. Furthermore, the selected SNPs were enriched in cellular processes, environmental adaptation, signal transduction, and related metabolic processes between the Wujiang population and the other two populations. The above results indicate that the populations of S. kozlovi have different degrees of tolerance and selection pressure in response to temperature and altitude. The Wujiang intrapopulation has greater genetic diversity and differentiation than the Jinsha River and Yalong River populations, which demonstrates that the Jinsha and Yalong populations require more attention and resources for their protection. The results of this study will increase our understanding of the diversity of S. kozlovi in the upper reaches of the Yangtze River and provide a basis for the conservation and utilization of wild resources. Full article

(This article belongs to the Special Issue Adaptive Evolution and Trait Formation of Animals)

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18 pages, 385 KiB

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The Genetic Basis Underpinning Sexually Selected Traits across Different Animal Lineages: Are There Genetic Mechanisms in Common?

by Ji Hyoun Kang

Animals 2024, 14(6), 841; https://doi.org/10.3390/ani14060841 - 8 Mar 2024

Viewed by 1828

Abstract

Sexual selection involving female choice or female preference (‘inter-sexual’ selection) and/or male–male competition (‘intra-sexual’ selection) is one of the key mechanisms for evolutionary diversification and speciation. In particular, sexual selection is recently suggested to be an important mode to drive the evolution of the “novel” phenotype (i.e., “evolutionary novelty”). Despite extensive studies performed on sexually selected traits or male-specific ornaments (or weapon-like structures) with respect to their evolutionary origin, history and fitness benefits, relatively little is known about the molecular genetic mechanisms underlying their developmental process. However, with advances in genomic technologies (including whole transcriptome analysis using Next Generation Sequencing [NGS] techniques; RNA-Seq), progress has been made to unveil the genetic background underpinning diverse sexually selected traits in different animal taxa. In the present review, empirical data on the genes, genetic mechanisms, or regulatory pathways underlying various sexually selected traits were compiled to explore whether “common” genetic architectures shape the development and evolution of these traits across evolutionarily distant animal lineages. It is shown that the recruitment of the pre-existing genetic network for a new purpose (i.e., gene network “co-option”) is rather widespread in the development and evolution of sexually selected traits, indicating that particular genes or gene sets are repeatedly involved in different sexually selected traits. Information on genes or genetic mechanisms regulating the development of sexually selected traits is an essential piece to complete a whole picture of the origin and evolution of sexually selected traits. Full article

(This article belongs to the Special Issue Adaptive Evolution and Trait Formation of Animals)

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