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International Journal of Molecular Evolution and Biodiversity 2024, Vol.14, No.3 http://ecoevopublisher.com/index.php/ijmeb © 2024 EcoEvoPublisher, registered at the publishing platform that is operated by Sophia Publishing Group, founded in British Columbia of Canada. All Rights Reserved. Publisher EcoEvo Publisher Editedby Editorial Team of International Journal of Molecular Evolution and Biodiversity Email: edit@ijmeb.ecoevopublisher.com Website: http://ecoevopublisher.com/index.php/ijmeb Address: 11388 Stevenston Hwy, PO Box 96016, Richmond, V7A 5J5, British Columbia Canada International Journal of Molecular Evolution and Biodiversity (ISSN 1927-6664) is an open access, peer reviewed journal published online by EcoEvoPublisher. The journal publishes all the latest and outstanding research articles, letters and reviews in all areas of molecular evolution and biodiversity, topics addressed including experimental and theoretical work of molecular evolution; the evolution of informational macromolecules and their relation to more complex levels of biological organization; investigations of molecular evolutionary patterns and processes, tests of evolutionary hypotheses that use molecular data, and studies; on all matters concerning the integrity and wellness of ecosystems and the diversity of species; as well as the study of species interactions and the role of species in structuring marine ecosystem functioning. All the articles published in International Journal of Molecular Evolution and Biodiversity are Open Access, and are distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. EcoEvoPublisher uses CrossCheck service to identify academic plagiarism through the world’s leading plagiarism prevention tool, iParadigms, and to protect the original authors’ copyrights. EcoEvoPublisher is an international Open Access publishing platform that publishes scientific journals in the field of ecology and evolution registered at the publishing platform that is operated by Sophia Publishing Group (SPG), founded in British Columbia of Canada.
International Journal of Molecular Evolution and Biodiversity (online), 2024, Vol. 14, No.3 ISSN 1927-6664 https://ecoevopublisher.com/index.php/ijmeb © 2024 EcoEvoPublisher, registered at the publishing platform that is operated by Sophia Publishing Group, founded in British Columbia of Canada. All Rights Reserved. Latest Content Calling for the Protection of Endangered Animals on International Biodiversity Day International Journal of Molecular Evolution and Biodiversity, 2024, Vol. 14, No. 3, 104 Genomic Interpretation and Phylogenetic Analysis: Exploring the Origins and Diversity of Hawaiian Mint Species Ben J.L. Zhong International Journal of Molecular Evolution and Biodiversity, 2024, Vol. 14, No. 3, 105-107 Population Genomics of Primates: Diversity, Structure, and Evolutionary Dynamics YepingHan International Journal of Molecular Evolution and Biodiversity, 2024, Vol. 14, No. 3, 108-119 Phylogenetic Insights into Cassava’s Domestication: Unraveling Genetic Origins and Evolutionary Trajectories Wenzhong Huang International Journal of Molecular Evolution and Biodiversity, 2024, Vol. 14, No. 3, 120-132 The Origin and Evolution of Endemic Birds in the Qinghai-Tibet Plateau Jingya Li, Jun Li International Journal of Molecular Evolution and Biodiversity, 2024, Vol. 14, No. 3, 133-146
International Journal of Molecular Evolution and Biodiversity 2024, Vol.14, No.3, 104 http://ecoevopublisher.com/index.php/ijmeb 104 Calling for the Protection of Endangered Animals on International Biodiversity Day Received: 19 May, 2024 Accepted: 22 May, 2024 Published: 25 May, 2024 This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: 2024, Calling for the protection of endangered animals on International Biodiversity Day, International Journal of Molecular Evolution and Biodiversity, 14(3): 104 (doi: 10.5376/ijmeb.2024.14.0012) ay 22nd is International Biodiversity Day, a special day to remind us to focus on and protect the rich diversity of life on Earth. At this important moment, we call on the international community to work together to protect wildlife, especially the ecosystems of endangered species. Biodiversity is not only a rich expression of life on Earth but also the foundation of our human survival and development. It provides clean air and water, fertile soil, abundant food resources, as well as numerous medicinal plants and industrial materials. However, with the expansion of human activities, the survival environments of many species are severely threatened, and biodiversity is decreasing at an alarming rate. Endangered species are one of the most obvious signs of the biodiversity crisis. The numbers of these species are declining sharply, and many are on the brink of extinction. The main reasons include habitat loss, overhunting, pollution, and climate change. These factors not only threaten the survival of endangered species but also disrupt the balance of entire ecosystems. In terms of protecting endangered species, the international community has made some important progress. For example, the Convention on Biological Diversity is a key legal framework for the protection of biodiversity worldwide, and many countries have also formulated and implemented various conservation laws and policies. However, laws and policies alone are not enough; actual conservation actions are key. Let’s look at some specific examples of endangered animals to more clearly understand the urgency of protecting them: Spotted Owl in British Columbia, Canada The Spotted Owl is one of the most endangered birds in Canada. Due to habitat loss and excessive logging, their numbers have drastically decreased. Currently, the conservation efforts for Spotted Owls are focused on protecting their habitats and increasing their numbers through captive breeding programs. Hainan Gibbon in Hainan Island, China The Hainan Gibbon is one of the most endangered primates in the world, with fewer than 30 individuals remaining, all living in the tropical rainforests of Hainan Island. The key to protecting them lies in protecting and restoring their habitats and strengthening law enforcement to prevent illegal hunting and habitat destruction. Andean Bear in the High Altitude Wetlands of the Andes Mountains, South America The Andean Bear, also known as the Spectacled Bear, is the only bear species in South America, primarily living in the high-altitude wetlands and forests of the Andes Mountains. Due to habitat loss and human activity interference, their numbers are rapidly decreasing. Conservation measures include establishing protected areas and reducing human activities’ impact on their habitats. African Elephant in Serengeti National Park, Africa The African Elephant is one of the largest land animals on Earth, but due to the ivory trade and habitat loss, they face serious survival threats. Protecting African elephants requires the international community to jointly combat illegal ivory trade and protect their natural habitats. Great Barrier Reef Turtle in Australia The Great Barrier Reef Turtle faces multiple threats such as habitat destruction, climate change, and pollution. Protecting these turtles is key to protecting the marine environment, reducing pollution, and taking measures to address climate change. On this International Biodiversity Day, we have a unique opportunity to make our voices heard. By advocating for comprehensive and immediate implementation of plans, we can challenge the status quo and prioritize ecological health over industrial interests. Our goal must be to establish a future that prioritizes ecosystem health, endangered species, and our right to a sustainable future. Collective action can amplify our impact. It is our shared responsibility to protect the land and water. By demanding strong legal protections for biodiversity, we fulfill this responsibility and work towards a sustainable future. We urge our readers and the scientific community to join us in this important effort. Let us not only celebrate biodiversity with words but also ensure the preservation for future generations through meaningful actions. M The Editorial Open Access
International Journal of Molecular Evolution and Biodiversity 2024, Vol.14, No.3, 105-107 http://ecoevopublisher.com/index.php/ijmeb 105 Scientific Commentary Open Access Genomic Interpretation and Phylogenetic Analysis: Exploring the Origins and Diversity of Hawaiian Mint Species Ben J.L. Zhong Hainan Institute of Tropical Agricultural Resources, Sanya, 572024, Hainan, China Corresponding author: zhongjianli8888@gmail.com International Journal of Molecular Evolution and Biodiversity, 2024, Vol.14, No.3 doi: 10.5376/ijmeb.2024.14.0013 Received: 19 Apr., 2024 Accepted: 21 May, 2024 Published: 27 May, 2024 Copyright © 2024 Zhong, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Zhong B.J.L., 2024, Genomic interpretation and phylogenetic analysis: exploring the origins and diversity of Hawaiian mint species, International Journal of Molecular Evolution and Biodiversity, 14(3): 105-107 (doi: 10.5376/ijmeb.2024.14.0013) Published on April 10, 2024, by the Department of Biological Sciences at the State University of New York at Buffalo, the School of Biological Sciences at Nanyang Technological University, Singapore, and the Faculty of Biological and Environmental Sciences at the University of Helsinki, Finland, the research findings were published in the journal Nature Communications. Crystal M. Tomlin is the lead author, with Victor A. Albert and Charlotte Lindqvist as corresponding authors. The article is titled “Allopolyploid origin and diversification of the Hawaiian endemic mints”. The study was funded by the School of Biological Sciences at Nanyang Technological University, the National Science Foundation (2139311; 2030871), and the Research Council of Norway (154145). The research produced a chromosome-level reference genome for a representative species, ‘Stenogyne calaminthoides’, and resequenced its 45 close relatives. The study found that these plants evolved through multiple polyploidization events, including an allopolyploid event directly related to North American ancestors, leading to the radiation and diversification of this group in the Hawaiian Islands. 1 Interpretation of Experimental Data Detailed genomic information about Stenogyne calaminthoides and its related species also revealed their complex interactions and diversification strategies during evolution. Figure 1 describes the assembly and structural evolution of the Stenogyne calaminthoides genome in detail. Part (a) displays a physical photograph of the species, providing a visual reference for species morphology. Part (b)’s Hi-C contact map, marked with blue-framed chromosomes, shows the interactions and spatial structure between chromosomes, providing key information for understanding the three-dimensional structure of the genome. Part (c) reveals the distribution of genes and various types of repetitive sequences (such as Copia, Helitron, Gypsy) in the genome, displaying density per 1 Mb area and highlighting homologous regions with different colors, enhancing our understanding of genomic complexity. Part (d) compares the S. calaminthoides genome with grape chromosomes through a fractional deviation plot, showing conservation and variation in genome evolution. Part (e)’s phylogenetic tree discusses the history of polyploidy events within the genus Stenogyne, including unique whole-genome duplication events, which are crucial for understanding their adaptive evolution. Figure 2 depicts the phylogenetic relationships and genetic admixture among Hawaiian mint species and their related groups through two types of phylogenetic trees. The tree on the left is based on a dataset of single nucleotide polymorphisms (SNPs) and analyzed using a maximum likelihood approach, while the tree on the right is based on the coalescent analysis of single-copy nuclear genes, each highlighting the evolutionary relationships and gene flow among species. The figure also includes an ADMIXTURE analysis, which reveals the gene flow and diversity of genetic backgrounds among species, with each color representing different ancestral populations, thus illustrating the complex dynamics of genetic mixing and species formation.
International Journal of Molecular Evolution and Biodiversity 2024, Vol.14, No.3, 105-107 http://ecoevopublisher.com/index.php/ijmeb 106 Figure 1 Assembly and structural evolution of the Stenogyne calaminthoides genome Figure 2 Phylogenetic relationships and admixture among Hawaiian mints and relatives 2 Insight into Research Findings The research conducted an in-depth exploration of the origins and evolutionary history of Hawaiian mints through genome size prediction, chromosome assembly quality assessment, repetitive sequence analysis, and phylogenetic analysis. The study indicates that geographical isolation and genetic drift in small populations played a major role in species formation, while local mixed mating may have also played a significant role in early lineage diversity. 3 Evaluation of the Research This research utilized high-quality genomic data and advanced analytical methods, providing valuable insights into the formation of island biodiversity. However, direct evidence for specific adaptive traits and niche differentiation remains insufficient, areas that future research could further explore.
International Journal of Molecular Evolution and Biodiversity 2024, Vol.14, No.3, 105-107 http://ecoevopublisher.com/index.php/ijmeb 107 4 Concluding Remarks The study demonstrates that Hawaiian mint species have adapted to the unique ecological environment of the Hawaiian Islands through a series of complex evolutionary processes, including allopolyploidy and interspecies hybridization. These processes provide a genomic basis for species ecological adaptation and morphological diversity. 5 Access the Full Text Tomlin C.M., Rajaraman S., Sebesta J.T., et al., Allopolyploid origin and diversification of the Hawaiian endemic mints, Nat Commun 15, 3109 (2024). https://doi.org/10.1038/s41467-024-47247-y. 6 Acknowledgements Thanks to the open access policy of Nature Communications, which allows readers to freely share this valuable research. Thanks to Victor A. Albert and Charlotte Lindqvist (corresponding authors) and their research team for providing a great case study for the community of species origin and genome researchers. I apologize if my review’s perspective on the research data and findings differs from the authors' intentions. Disclaimer/Publisher’s Note: The statements, opinions, and data contained in all publications are solely those of the individual authors and contributors and do not represent the views of the publishing house and/or its editors. The publisher and/or its editors disclaim all responsibility for any harm or damage to persons or property that may result from the application of ideas, methods, instructions, or products discussed in the content. Publisher remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
International Journal of Molecular Evolution and Biodiversity 2024, Vol.14, No.3, 108-119 http://ecoevopublisher.com/index.php/ijmeb 108 Review Article Open Access Population Genomics of Primates: Diversity, Structure, and Evolutionary Dynamics YepingHan Institute of Life Sciences, Jiyang Colloge of Zhejiang A&F University, Zhuji, 311800, Zhejiang, China Corresponding author: liviayphan@gmail.com International Journal of Molecular Evolution and Biodiversity, 2024, Vol.14, No.3 doi: 10.5376/ijmeb.2024.14.0014 Received: 21 Apr., 2024 Accepted: 23 May, 2024 Published: 30 May, 2024 Copyright © 2024 Han, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Han Y.P., 2024, Population genomics of primates: diversity, structure, and evolutionary dynamics, International Journal of Molecular Evolution and Biodiversity, 14(3): 108-119 (doi: 10.5376/ijmeb.2024.14.0014) Abstract This study synthesizes current research to provide a comprehensive understanding of genetic diversity, population structure, and evolutionary dynamics within and between primate species. Advances in genomic technologies, such as high-throughput sequencing and comparative genomics, have unveiled significant genetic variation across various primate species, including endangered ones like the black and white ruffed lemur and Coquerel’s sifaka. Despite their endangered status, these species exhibit high levels of genetic diversity, underscoring the importance of genomic data in conservation efforts. Key findings from phylogenomic studies emphasize the need to consider ancestral population variation when interpreting sequence divergence and evolutionary histories. Genomic data have illuminated long-term evolutionary processes and population dynamics that are otherwise difficult to observe, providing critical insights into gene regulatory evolution and phenotypic diversity across primates. Unique insights from case studies, particularly on African great apes, highlight complex demographic histories, including ancient admixture events, and significant genetic differentiation among populations. These studies underscore the intricate interplay between gene flow, selection, and genetic drift in shaping primate genomes. This study highlights the crucial role of population genomics in elucidating the evolutionary mechanisms driving primate diversity and adaptation, offering valuable perspectives for both evolutionary biology and conservation strategies. Keywords Primates; Genetic diversity; Population structure; Evolutionary dynamics; Conservation genomics 1 Introduction Population genomics is a field of study that focuses on understanding the genetic composition of populations and how it changes over time due to various evolutionary forces such as mutation, selection, recombination, and genetic drift. This field is significant in evolutionary biology as it provides insights into the mechanisms driving genetic diversity and adaptation within and between species (Peter et al., 2016). Historically, advancements in genomic technologies, such as high-throughput DNA sequencing, have revolutionized our ability to analyze genetic variation at a genome-wide scale, enabling more precise estimates of genetic diversity and evolutionary dynamics (Osada, 2015). The integration of phylogenetics and population genetics, known as phylogenomics, has further enhanced our understanding of evolutionary histories and the functional elements within genomes (Siepel, 2009). Primates hold a unique position in evolutionary biology due to their close genetic relationship to humans. Studying primate genomics is crucial for understanding human evolution, as it allows researchers to identify genetic differences and similarities that have shaped the phenotypic traits of humans and their closest relatives (Stone and Verrelli, 2006). Primates also exhibit a rich diversity in morphology, behavior, and ecological adaptations, making them an ideal group for studying the impact of genomic diversity on biological processes (Kuderna et al., 2023). Furthermore, many primate species are threatened with extinction due to anthropogenic effects, highlighting the importance of conservation genomics to inform population management and preserve biodiversity (Orkin et al., 2020).
International Journal of Molecular Evolution and Biodiversity 2024, Vol.14, No.3, 108-119 http://ecoevopublisher.com/index.php/ijmeb 109 This study is to summarize the current knowledge on primate population genomics, focusing on the diversity, population structure, and evolutionary dynamics of primate species. By synthesizing findings from recent genomic studies, this study will provide a comprehensive overview of the genetic variation within and between primate populations and the evolutionary forces shaping this diversity. Additionally, this study will explore the implications of these findings for understanding human evolution and for the conservation of primate species, and identify future research directions and challenges in the field of primate population genomics, emphasizing the need for continued advancements in genomic technologies and analytical methods. 2 Genetic Diversity in Primates 2.1 Intraspecific genetic variation Genetic diversity within primate species varies significantly, influenced by factors such as population size, habitat fragmentation, and evolutionary history. For instance, rhesus macaques (Macaca mulatta) exhibit a high level of nucleotide diversity, approximately 2.5 times greater than that observed in humans. This diversity includes over 43.7 million single-nucleotide variants, which have implications for both functional and non-functional genomic regions (Xue et al., 2016). Prado-Martinez et al. (2013) found that chimpanzees, particularly the common chimpanzee, display significant genetic diversity, with distinct genetic populations identified within the species. For example, the Nigeria-Cameroon/western and central/eastern populations of common chimpanzees are genetically distinct, highlighting the complex population history and gene flow within this species. In macaques, whole-genome sequencing has revealed extensive genetic variation, including numerous variants that affect protein sequences and gene regulation, underscoring the species’ utility as a model for human disease studies (Xue et al., 2016). Similarly, studies on lemurs have shown that even critically endangered species like the black and white ruffed lemur and Coquerel’s sifaka maintain high levels of genetic diversity, suggesting that conservation efforts can be effective if timely (Perry et al., 2012). 2.2 Interspecific genetic variation Comparative genomic studies have provided insights into the genetic differences between various primate species. For instance, humans and chimpanzees, despite sharing 98.7% of their genomic DNA, exhibit significant differences in gene expression patterns, particularly in the brain, which may underlie the distinct cognitive and behavioral traits observed between the species (Enard et al., 2002). Additionally, the genetic diversity observed in great apes, including gorillas and orangutans, has been linked to their population history and varying levels of inbreeding, which affect their susceptibility to diseases and overall genetic health. Great apes, such as chimpanzees and gorillas, show extensive genetic variation, with evidence of gene flow and distinct population structures within species. In contrast, New World monkeys and Old World monkeys exhibit different patterns of genetic diversity and evolutionary pressures. For example, the genetic diversity in rhesus macaques, an Old World monkey, is shaped by a large and fluctuating population size, which has led to higher levels of nucleotide diversity compared to humans (Xue et al., 2016). These differences highlight the varied evolutionary trajectories and selective pressures experienced by different primate lineages. 2.3 Factors influencing genetic diversity Mutation, recombination, and genetic drift are fundamental forces shaping genetic diversity in primates. Mutations introduce new genetic variants, while recombination shuffles these variants, creating new combinations of alleles. Genetic drift, particularly in small populations, can lead to significant changes in allele frequencies over time. For example, the high level of genetic polymorphism observed in the common ancestor of the African ape clade (Homo-Pan-Gorilla) suggests that genetic drift played a significant role in shaping the genetic landscape of these species. Population size, habitat fragmentation, and gene flow are critical factors influencing genetic diversity. Large populations tend to maintain higher levels of genetic diversity due to a greater number of breeding individuals and reduced effects of genetic drift. Conversely, habitat fragmentation can isolate populations, reducing gene flow and
International Journal of Molecular Evolution and Biodiversity 2024, Vol.14, No.3, 108-119 http://ecoevopublisher.com/index.php/ijmeb 110 increasing the risk of inbreeding. For instance, the extensive inbreeding observed in eastern gorillas is likely a consequence of habitat fragmentation and reduced population sizes. Gene flow, on the other hand, can introduce new genetic variants into a population, enhancing genetic diversity and adaptive potential. The genetic distinctiveness of chimpanzee populations, for example, is partly due to historical gene flow events that have shaped their current genetic structure. 3 Population Structure in Primates 3.1 Geographical patterns of genetic structure Geographical patterns of genetic structure in primates are influenced by various factors, including historical migrations, environmental barriers, and social behaviors. Studies have shown that genetic diversity and differentiation can vary significantly across different geographic regions. For instance, In gorillas, nucleotide diversity studies have shown that western lowland gorillas possess the highest levels of genetic diversity among African apes, which is about twice that of humans (Yu et al., 2004). This high diversity is indicative of substantial historical population sizes and migrations. In baboons, genome sequencing of six species has revealed multiple episodes of admixture and introgression, highlighting the complex evolutionary history and geographic structuring within the genus Papio (Figure 1) (Rogers et al., 2019). Figure 1 Papio baboon species (Adopted from Rogers et al., 2019) Image caption: (A) The appearance and current distribution of each baboon species, and the locations of three well-documented active hybrid zones are also shown. x1: hybrid zone between P. hamadryas and P. anubis (Phillips-Conroy et al., 1991; Bergman et al., 2008); x2: hybrid zone between P. cynocephalus and P. anubis (Tung et al., 2008; Charpentier et al., 2012); x3: hybrid zone between P. kindae and P. ursinus (Jolly et al., 2011); Drawings of each species by S. Nash. (B) Distinguishing features of Papio species (Adopted from Rogers et al., 2019) 3.2 Social structure and genetic differentiation Social organization plays a crucial role in shaping the genetic structure of primate populations. In species where males are the dispersing sex, such as baboons, social structure and behavior can predict molecular genetic measures of relatedness and reproductive success. For example, in Guinea baboons, female-biased gene flow has been observed, contrasting with the male-biased dispersal seen in other baboon species. This unique social system results in a lack of genetic-geographic structuring and higher genetic variation within demes (Kopp et al., 2013). 3.3 Historical demography Reconstructing the historical demography of primates involves analyzing genetic data to infer past population sizes and migration events. For instance, studies on baboons have utilized ancient DNA to demonstrate long-term population continuity in southern Africa, providing insights into the demographic history of the species (Mathieson et al., 2020). Similarly, nucleotide diversity analyses in gorillas have been used to estimate long-term effective population sizes, shedding light on their historical population dynamics (Yu et al., 2004).
International Journal of Molecular Evolution and Biodiversity 2024, Vol.14, No.3, 108-119 http://ecoevopublisher.com/index.php/ijmeb 111 We can also apply similar methods to reconstruct the population history of other primate species. For example, analyzing mitochondrial and nuclear DNA sequences can reveal past population sizes, migration patterns, and the impact of historical events on genetic diversity. These insights are crucial for understanding the evolutionary dynamics and conservation needs of these primates. 4 Evolutionary Dynamics of Primates 4.1 Natural selection Natural selection plays a crucial role in shaping the genetic architecture of primate populations. The detection of selection signatures in primate genomes involves identifying regions where genetic variation is influenced by selective pressures. Various methods have been developed to detect these signatures, including long-range haplotype methods and machine learning approaches, which can identify selective sweeps and other patterns indicative of selection (Hohenlohe et al., 2010; Liu et al., 2013; Kumar et al., 2022). For instance, the use of genome-wide scans has revealed widespread genomic signatures of natural selection in hominid evolution, highlighting the reduction in neutral sequence diversity near conserved features due to selection (McVicker et al., 2009). Additionally, balancing selection, which maintains genetic diversity within populations, has been increasingly recognized as a significant driver of diversity, with sophisticated methods now available to detect its signatures (Bitarello et al., 2023). Adaptations to various environmental pressures, including diet and disease resistance, are evident in primate genomes. For example, genes associated with lactase persistence, skin pigmentation, and sickle cell anemia have been identified as targets of positive selection in human populations, reflecting adaptations to dietary changes and disease resistance (Rochus et al., 2018). Comparative genomics has also uncovered a role for positive Darwinian selection in genes involved in immune response, sensory perception, and reproduction, which are critical for survival and adaptation to environmental challenges (Ellegren, 2008). These findings underscore the importance of natural selection in driving the evolutionary dynamics of primates. 4.2 Genetic drift and bottlenecks Genetic drift and demographic fluctuations, such as population bottlenecks, significantly impact genetic diversity in primate populations. Bottlenecks, which occur when populations experience a drastic reduction in size, can lead to a loss of genetic variation and an increase in inbreeding. This effect is particularly pronounced in island primates and endangered species, where limited population sizes exacerbate the impact of genetic drift (Siepel, 2009). The study of demographic history through genome sequencing has provided insights into how these fluctuations shape genetic diversity and influence evolutionary trajectories (Ellegren, 2008). Island primates, such as those found in Madagascar, often experience severe genetic bottlenecks due to their isolated habitats and small population sizes. These bottlenecks can lead to reduced genetic diversity and increased vulnerability to environmental changes and diseases. Similarly, endangered primate species, such as certain great apes, face significant genetic challenges due to habitat loss and human activities. Understanding the genetic consequences of these bottlenecks is crucial for conservation efforts and for maintaining the evolutionary potential of these species (Ellegren, 2008; Siepel, 2009). 4.3 Gene flow and hybridization Gene flow, the transfer of genetic material between populations, plays a vital role in shaping genetic diversity in primates. It can introduce new genetic variants into populations, enhancing genetic diversity and potentially facilitating adaptation to changing environments. Gene flow can also counteract the effects of genetic drift and inbreeding, maintaining genetic health in small populations (Ellegren, 2008; Siepel, 2009). Hybrid zones, where different primate species or subspecies interbreed, provide valuable insights into the role of gene flow in evolution. For example, hybrid zones in macaques have been studied to understand how gene flow influences genetic diversity and adaptation. Similarly, introgression, the incorporation of genetic material from one species into the gene pool of another through hybridization, has been observed in baboons. These examples highlight the complex interplay between gene flow and hybridization in shaping the evolutionary dynamics of primates (Ellegren, 2008; Siepel, 2009).
International Journal of Molecular Evolution and Biodiversity 2024, Vol.14, No.3, 108-119 http://ecoevopublisher.com/index.php/ijmeb 112 By examining these evolutionary dynamics, we gain a deeper understanding of the processes that drive genetic diversity and adaptation in primate populations. This knowledge is essential for both evolutionary biology and conservation efforts, as it informs strategies to preserve the genetic health and evolutionary potential of primate species. 5 Genomic Tools and Approaches 5.1 High-throughput sequencing Advances in high-throughput sequencing technologies have significantly transformed the field of primate genomics, enabling comprehensive studies of genetic diversity, population structure, and evolutionary dynamics. Whole-genome sequencing (WGS) has become a cornerstone of these efforts, providing detailed insights into the genetic makeup of various primate species. For instance, the sequencing of whole genomes from non-model organisms has revealed patterns of recombination rates, adaptive evolution, and gene family expansions that are crucial for understanding evolutionary biology (Ellegren, 2014). Additionally, the decreasing cost of sequencing has made it feasible to sequence entire primate genomes at the population level, which is essential for conservation genomics (Orkin et al., 2020). Exome sequencing, which focuses on the protein-coding regions of the genome, has also been employed to uncover the molecular basis of phenotypic differences among primates. This approach has identified genes under positive selection that are involved in the conversion of epithelial cells in skin, hair, and nails to keratin, highlighting the power of targeted capture methods in comparative genomics (George et al., 2011). RNA sequencing (RNA-seq) has further expanded our understanding by revealing substantial genetic variation and gene expression differences among endangered primates, providing insights into species-specific adaptations and evolutionary forces (Perry et al., 2012). 5.2 Genomic data analysis The analysis of genomic data in population genomics involves a variety of computational tools designed to infer population structure, demographic history, and selection pressures. Population structure analysis helps in understanding the genetic differentiation among populations, while demographic inference provides insights into historical population sizes and migration patterns. For example, a comprehensive overview of current population genomics methods has highlighted more than 100 state-of-the-art tools that can handle whole-genome data, facilitating the integration of selection into historical frameworks (Bourgeois and Warren, 2021). Selection scans are another critical aspect of genomic data analysis, aiming to identify regions of the genome that have been subject to natural selection. These scans have been instrumental in uncovering genes involved in adaptation and speciation. For instance, the identification of genes under positive selection in primate exomes has provided valuable information on the evolutionary history and phenotypic diversity of these species (George et al., 2011). Additionally, the “Simple Fool’s Guide to Population Genomics via RNA-seq” offers a user-friendly protocol for analyzing high-throughput sequencing data, making these advanced techniques more accessible to population biologists (Wit et al., 2012). 5.3 Comparative genomics Comparative genomics involves the analysis of genome sequences from different species to understand their evolutionary relationships and functional genomics. Genome alignments and phylogenomic analyses are fundamental tools in this field, allowing researchers to reconstruct the evolutionary history of primates and identify conserved and divergent genomic regions. For example, genome assemblies for various primate species have provided new insights into the evolutionary origins of the human genome and the processes involved (Rogers and Gibbs, 2014). Phylogenomics, which combines phylogenetic and genomic data, has been essential in unlocking valuable information about evolutionary history and genomic function, despite challenges posed by variation in ancestral populations (Siepel, 2009).
International Journal of Molecular Evolution and Biodiversity 2024, Vol.14, No.3, 108-119 http://ecoevopublisher.com/index.php/ijmeb 113 Functional genomics approaches, such as the analysis of gene expression and regulatory elements, have further enriched our understanding of primate evolution. Comparative RNA sequencing has revealed genetic variation and gene expression differences that are consistent with positive selection, shedding light on the genetic basis of species-specific adaptations (Perry et al., 2012). Moreover, the creation of a global catalog of whole-genome diversity from 233 primate species has provided a comprehensive resource for studying the impact of genomic diversity on biological processes, evolutionary divergence, and conservation efforts (Kuderna et al., 2023). 6 Case Studies in Primate Population Genomics 6.1 Population genomics of African great apes (chimpanzees, bonobos, and gorillas) Research on the population genomics of African great apes, including chimpanzees, bonobos, and gorillas, has revealed significant insights into their genetic diversity, structure, and evolutionary dynamics. Chimpanzees and bonobos exhibit complex demographic histories with evidence of ancient admixture. For instance, de Manuel et al. found that gene flow occurred from bonobos into the ancestors of central and eastern chimpanzees between 200,000 and 550,000 years ago, contributing less than 1% to the central chimpanzee genomes (Manuel et al., 2016). Additionally, studies have shown that chimpanzees have a nucleotide diversity (pi) of 0.134%, which is higher than that of humans but lower than previously thought (Yu et al., 2003). Gorillas, on the other hand, exhibit the highest nucleotide diversity among African apes, with a (pi) value of 0.158% (Yu et al., 2004). The genetic structure of chimpanzee populations has been extensively studied, revealing three distinct populations: western, central, and eastern chimpanzees, with little evidence of gene flow between them (Becquet et al., 2007). Furthermore, Chaisson et al. (2018) systematically discovered structural changes (length>50 base pairs) through improved sequence adjacency and detected 614186 primate deletions, insertions, and reversals, each assigned to a specific primate lineage (Figure 2), providing deeper insights into their evolutionary trajectories. Figure 2 SMRT assemblies and SV analyses (Adopted from Chaisson et al., 2018) Image caption: (Top) Contiguity of the de novo assemblies. (Bottom, left to right) For each ape, SVdetection was done against the human reference genome as represented by a dot plot of an inversion). Human-specific SVs, identified by comparing ape SVs and population genotyping (0/0, homozygous reference),were compared to single-cell gene expression differences [range: low (dark blue) to high (dark red)] in primary and organoid tissues. Each heatmap row is a gene that intersects an insertion or deletion (green), duplication (cyan), or inversion (light green) (Adopted from Chaisson et al., 2018)
International Journal of Molecular Evolution and Biodiversity 2024, Vol.14, No.3, 108-119 http://ecoevopublisher.com/index.php/ijmeb 114 6.2 Genomic studies on Asian primates (orangutans) Genomic studies on Asian primates, particularly orangutans, have provided valuable insights into their population history and adaptive evolution. For example, high-quality genome assemblies of orangutans have enabled the identification of lineage-specific genetic variations and structural changes (Chaisson et al., 2018). These studies have highlighted the importance of structural variations in shaping the genetic landscape of orangutans and their adaptive evolution. Comparative analyses have also shown that orangutans possess unique genetic features that distinguish them from other great apes. These features include specific structural variants and gene expression patterns that have evolved over millions of years (Stone and Verrelli, 2006). Such findings underscore the significance of genomic studies in understanding the evolutionary dynamics and population history of Asian primates. 6.3 Population genomics of New World monkeys (capuchins, howler monkeys, and marmosets) New World monkeys, such as capuchins (genus Cebus), howler monkeys (genus Alouatta), and marmosets (genus Callithrix), have been studied to understand their genetic diversity and evolutionary dynamics. Capuchins, known for their intelligence and complex behaviors, exhibit significant genetic diversity across their range (Aristide et al., 2013). Howler monkeys, with their distinct vocalizations and folivorous diet, show genetic differentiation that corresponds with their geographic distribution. Marmosets, small and socially complex primates, provide insights into the genetic basis of social behavior and adaptation. 7 Implications for Conservation 7.1 Genetic monitoring and management The use of genomic data in conservation planning has become increasingly feasible and essential due to advancements in sequencing technologies and the decreasing cost of genomic analyses. Genomic data can provide precise estimates of effective population size, inbreeding levels, demographic history, and population structure, which are critical for conservation efforts (Steiner et al., 2013; Hohenlohe et al., 2020). For instance, genomic tools can identify genetic loci responsible for inbreeding depression or adaptation to changing environments, thereby informing strategies to manage adaptive variation and enhance the evolutionary potential of populations (Harrisson et al., 2014; Hohenlohe et al., 2020). Genomic data can be used to identify and introduce genetic diversity into small, inbred populations to reduce inbreeding depression and increase fitness. This approach has been successfully applied in various species, where the introduction of individuals from a related subspecies increased genetic diversity and improved population viability (Steiner et al., 2013). Genomic data can also help manage captive breeding programs by ensuring that genetic diversity is maintained, which is crucial for the long-term survival of species. For example, genomic analyses have been used to manage the genetic diversity of captive primate populations, ensuring that they retain the evolutionary potential to adapt to future environmental changes (Supple et al., 2018; Orkin et al., 2020). 7.2 Identifying conservation units Defining management units based on genetic data is crucial for effective conservation planning. Genomic data can reveal fine-scale population structure and historical isolation, which are often not apparent from morphological or ecological data alone (Coates et al., 2018; Supple et al., 2018). This information can be used to delineate conservation units that represent unique genetic diversity and evolutionary potential. Genomic studies have identified distinct genetic populations within endangered primate species, such as lemurs and lorisoids, which were previously considered a single management unit. For example, the black and white ruffed lemur and the Coquerel’s sifaka, despite being critically endangered, were found to harbor considerable genetic diversity, suggesting the presence of multiple conservation units within these species (Perry et al., 2012). This information is vital for developing targeted conservation strategies that preserve the genetic integrity of each unit.
International Journal of Molecular Evolution and Biodiversity 2024, Vol.14, No.3, 108-119 http://ecoevopublisher.com/index.php/ijmeb 115 7.3 Addressing challenges in conservation genomics While the potential of genomic tools in conservation is immense, there are several ethical considerations and practical challenges that need to be addressed. Ethical considerations include the potential for genomic data to be misused, the need for equitable access to genomic technologies, and the importance of involving local communities in conservation decisions (Allendorf et al., 2010; Steiner et al., 2013). It is essential to develop guidelines that ensure the ethical use of genomic data in conservation. This includes protecting the privacy of genetic information, obtaining informed consent from local communities, and ensuring that the benefits of genomic research are shared equitably (Steiner et al., 2013). Implementing genomic tools in conservation requires overcoming challenges related to computational resources, sampling constraints, and the interpretation of complex genomic data. Strategies to address these challenges include investing in capacity building, developing user-friendly computational tools, and fostering collaborations between conservation biologists, geneticists, and policymakers (Allendorf et al., 2010; Supple et al., 2018). By addressing these challenges and leveraging the power of genomic data, conservation efforts can be more precisely targeted and effective, ultimately contributing to the preservation of biodiversity and the resilience of ecosystems. 8 Future Directions and Challenges 8.1 Emerging technologies The field of primate genomics is poised to benefit significantly from emerging technologies that promise to enhance our understanding of primate diversity, structure, and evolutionary dynamics. One such technology is CRISPR, which allows for precise genome editing and has the potential to elucidate gene function and evolutionary adaptations in primates (Orkin et al., 2020). Single-cell genomics is another promising technology, enabling the study of genetic variation at the cellular level, which can provide insights into cellular heterogeneity and the development of complex traits (Housman and Gilad, 2020). Additionally, environmental DNA (eDNA) techniques offer non-invasive methods to collect genetic material from primate habitats, facilitating the study of elusive or endangered species without the need for direct sampling (Orkin et al., 2020). 8.2 Integrative approaches Combining genomics with other disciplines such as ecology, behavior, and physiology is crucial for a holistic understanding of primate evolution and adaptation. Integrative approaches can reveal how genetic variations influence phenotypic traits and how these traits interact with environmental factors. For instance, combining genomic data with ecological and behavioral studies can help identify the genetic basis of adaptive traits and their evolutionary significance (Bamba et al., 2018). Interdisciplinary research is essential for addressing complex questions about primate biology and for developing effective conservation strategies. 8.3 Addressing knowledge gaps Despite significant advancements, there remain substantial knowledge gaps in primate genomics. One major challenge is the study of rare and cryptic species, which are often difficult to sample and study due to their elusive nature and low population densities (Orkin et al., 2020). Additionally, there is a need for more comprehensive genomic data across a broader range of primate species to fully understand their evolutionary histories and genetic diversity (Perelman et al., 2011). Addressing these gaps will require innovative sampling methods, increased collaboration among researchers, and the development of new analytical tools to handle complex genomic data. 9 Concluding Remarks The systematic review of population genomics in primates has revealed significant insights into genetic diversity, population structure, and evolutionary dynamics. Comparative genomic studies have highlighted substantial genetic variation across primate species, including endangered ones, with some species like the black and white ruffed lemur and Coquerel’s sifaka showing high genetic diversity despite their endangered status. Advances in genome sequencing have provided comprehensive data on primate genome content and dynamics, offering
International Journal of Molecular Evolution and Biodiversity 2024, Vol.14, No.3, 108-119 http://ecoevopublisher.com/index.php/ijmeb 116 valuable information about evolutionary origins and processes. Phylogenomic approaches have underscored the importance of considering ancestral population variation in understanding sequence divergence and evolutionary histories. Studies have also shown that genetic methods can illuminate long-term evolutionary processes and population dynamics that are not easily observable. Furthermore, research on gene regulation has expanded to include a wider range of species, providing insights into the evolutionary processes that govern gene regulatory evolution and phenotypic diversity. Population genomics studies are crucial for understanding primate evolution and conservation. They provide a detailed view of genetic diversity and population structure, which are essential for reconstructing evolutionary histories and identifying adaptive traits. These studies also offer insights into the genetic basis of species-specific adaptations and the evolutionary forces shaping genetic variation, such as mutation, selection, recombination, and drift. Understanding these dynamics is vital for conservation efforts, as it helps identify populations with significant genetic diversity that may be more resilient to environmental changes. Additionally, population genomics can inform strategies for preserving genetic diversity and managing endangered species, ensuring their long-term survival. The field of primate population genomics is rapidly advancing, driven by new technologies and collaborative efforts. Future research should focus on expanding genomic studies to include more primate species, particularly those that are critically endangered or have limited genomic data available. High-throughput sequencing and functional genomics approaches will enhance our understanding of genotype-phenotype relationships and the evolutionary processes underlying primate diversity. Collaborative efforts across disciplines and institutions will be essential for generating comprehensive genomic data and developing effective conservation strategies. Continued research in this field will not only deepen our understanding of primate evolution but also contribute to the broader knowledge of genetic diversity and evolutionary dynamics in other species. Encouraging ongoing research and fostering international collaborations will be key to unlocking the full potential of population genomics in primates and ensuring the conservation of these remarkable species. Acknowledgments The author thanks the two anonymous peer reviewers for their thorough review of this study and for their valuable suggestions for improvement. Conflict of Interest Disclosure The authors affirm that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest. References Allendorf F., Hohenlohe P., and Luikart G., 2010, Genomics and the future of conservation genetics. Nature Reviews Genetics, 11: 697-709. https://doi.org/10.1038/nrg2844 PMid:20847747 Aristide L., Soto I., Mudry M., and Nieves M., 2013, Intra and interspecific variation in cranial morphology on the southernmost distributed Cebus (Platyrrhini, Primates) species, Journal of Mammalian Evolution, 21: 349-355. https://doi.org/10.1007/s10914-013-9249-y Bamba M., Kawaguchi Y., and Tsuchimatsu T., 2018, Plant adaptation and speciation studied by population genomic approaches, Development, 61: 12-24. https://doi.org/10.1111/dgd.12578 PMid:30474212 Becquet C., Patterson N., Stone A., Przeworski M., and Reich D., 2007, Genetic structure of chimpanzee populations, PLoS Genetics, 3. https://doi.org/10.1371/journal.pgen.0030066 PMid:17447846 PMCid:PMC1853122 Bergman T.J., Phillips-Conroy J.E., and Jolly C.J., 2008, Behavioral variation and reproductive success of male baboons (Papio anubis ×Papio hamadryas) in a hybrid social group, Am. J. Primatol, 70: 136-147. https://doi.org/10.1002/ajp.20467 PMid:17724672 Bitarello B., Brandt D., Meyer D., and Andrés A., 2023, Inferring balancing selection from genome-scale data, Genome Biology and Evolution, 15. https://doi.org/10.1093/gbe/evad032 PMid:36821771 PMCid:PMC10063222
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